RICE RESEARCH FOR ENHANCING

PRODUCTIVITY, PROFITABILITY
AND CLIMATE RESILIENCE

H Pathak
AK Nayak
M Jena
ON Singh
P Samal
SG Sharma

ICAR-National Rice Research Institute

Cuttack 753006, Odisha, India
Correct Citation
Rice Research for Enhancing Productivity, Profitability and Climate Resilience (2018)
p………..

ISBN: 81-88409-04-09

Editors
H Pathak
AK Nayak
M Jena
ON Singh
P Samal
SG Sharma

Published by
Director, ICAR-National Rice Research Institute, Cuttack 753006, Odisha, India

Design and layout

SK Sinha

May, 2018

Disclaimer
ICAR-National Rice Research Institute, Cuttack, Odisha is not liable for any loss arising due to
improper interpretation of the scientific information provided in this book.

©All Rights Reserved

ICAR-National Rice Research Institute, Cuttack, Odisha, India

Laser typeset at the ICAR-National Rice Research Institute, Cuttack 753 006, Odisha, India. Printed by the Print-Tech Offset Pvt. Ltd.,
Bhubaneswar 751 024, Odisha, India for Director, ICAR-National Rice Research Institute, Cuttack-753 006.
 Preface
Rice, the world’s most important food crop, has been grown for more than 6000
years in South Asia. Wild rice, however, grew in the Himalayas 15,000-16,000 years
back. Currently, rice is the staple food for about four billion people i.e., half of the
humankind on the planet. Rice fields cover around 160 million hectares in a wide
range of climatic conditions spanning from 44oN in North Korea to 35oS in Australia.
It is cultivated from 6 feet below sea level (such as in Kerala, India) to 2700 feet above
sea level in the Himalayas. The crop occupies a significant position in the culture and
heritage of many Asian countries. In India, particularly in the eastern states, it is a
part of almost every ritual. The crop has been referred in the Vedas, Ramayana,
Mahabharata, Buddhist and other ancient literature.
India has the world’s largest area and is the second highest producer of rice. The
crop is grown under varying climatic and soil conditions under diverse ecologies
spread over about 43 million hectares. The crop is cultivated round the year in one or
the other parts of the country. Since last two years the country has recorded the
highest rice production of about 110 million tons. It is the staple food for more than
two thirds of Indian population contributing more than 40% to the total food grain
production, thereby, occupies a pivotal role in the food and livelihood security of
people.
During the last decades, significant advancements have been made on developing
high yielding and disease-resistant rice varieties and production technologies for
different ecologies. The country, so far has released about 1200 varieties. Several
viable rice production technologies have also been developed for adoption in the
farmers’ fields. Along with increasing the productivity, emphasis has been given on
developing varieties with improved stress-tolerance and nutritional quality to ensure
nutritional security for the large section of the population depending on rice as staple
food. Currently, about 85% of rice area is covered with high-yielding varieties. India’s
rice export has also steadily increased with the current export of more than 10 million
tons annually making it the leading rice exporter.
However, in the backdrop of all these achievements, rice farmers and researchers
are facing new challenges of climate change, low water availability, poor soil health,
low nutrient use efficiency and increased emergence of insects and diseases. There is
now growing concern that non-price factors such as declining scope for further gains
from existing modern varieties, deteriorating soil and ground water supplies, and
reduced public investment in research have contributed to poor productivity growth
in recent years. The challenge is to integrate productivity and profitability improvement
of rice while enhancing the climate resilience and quality of the environment on which
production depends.
The objective of the publication ‘Rice Research for Enhancing Productivity,
Profitability and Climate Resilience’, published by ICAR-National Rice Research
Institute, Cuttack, Odisha is to review the scientific and technical literature available
on the developments in rice science and its implications on productivity, profitability
and climate resilience; provide science-backed, policy-relevant information for
improving rice farming and suggest implementable research and development
guidelines to the stakeholders.
Thirty-one chapters of the book cover the state-of the-art information in national
and international contexts on enhancing productivity, profitability and climate
resilience. The chapters capture various aspects of rice viz., (1) improvement i.e.,
conservation of genetic resources; quality seed production; genetic improvement for
enhancing resistance to biotic stresses, input use efficiency, aroma, nutrition and
grain quality, and climate resilience; harnessing heterosis; new generation rice for
breaking yield ceiling and biotechnological strategies and genomic resources for rice
improvement; (2) production i.e., enhancing productivity and resource use efficiency;
decreasing energy and water footprints; agro-ecology-based intensification; integrated
rice-based farming systems; resource conserving technologies; weed management;
efficient use of rice straw; mechanization of rice-based cropping systems and
harnessing microbial resources; (3) protection i.e., exploration of new sources of
resistance; bio-ecology of rice pest and diseases; bio-intensive approaches and
optimization of chemical pesticide-use for management of rice pest; (4) physiology
and biochemistry in relation to grain quality and nutritional improvement; multiple
abiotic stress tolerance and improvement of photosynthetic efficiency of rice; and (5)
socio-economic aspects i.e., yield gap analysis and impact assessment to aid rice
research and policies, and developing extension approaches to enhance income of
rice farmers. The chapters comprehensively present the technologies for effective
management of rice crop in favorable and unfavorable ecologies to make rice farming
profitable and sustainable. The authors have also captured the achievements of the
ICAR-National Rice Research Institute on rice research and development over the
years.
In the course of preparing the book, the authors and editors have received help
and support from different individuals. We are extremely grateful to each one of them.
The editors take this opportunity to express their gratitude to all the authors for
developing the chapters in a comprehensive and time-bound manner. We thank Dr. T.
Mohapatra, Director General, Indian Council of Agricultural Research and Secretary,
Department of Agricultural Research and Education for taking keen interest in bringing
out this publication. We are thankful to the members of the publication committee of
NRRI for their help and support and Mr. Sunil Sinha for type-setting, formatting and
developing the outline, cover page of the publication.
We hope that the publication would be useful to the researchers, teachers, policy
makers, planners, administrators, progressive farmers and students of rice sciences.

H Pathak
AK Nayak
Mayabini Jena
ON Singh
P Samal
SG Sharma

EDITORS
 Content
Chapter No. Topic Pages
1. Revitalizing Rice Production System for Enhancing ..........................
Productivity, Profitability and Climate Resilience
H Pathak, P Samal and M Shahid

1.1. Rice Genetic Resources- Its collection, conservation, .......................

maintenance and utilization
BC Patra, BC Marndi, P Sanghamitra, S Samantarai, N Umakanta and
JL Katara

1.2 Quality Seed Production and Maintenance Breeding for ...................

Enhancing Rice Yield
RK Sahu, RP Sah, P Sanghamitra, RL Verma, NKB Patil, M Jena,
AK Mukherjee, MK Bag and ON Singh

1.3 Utilization of Cultivated and Wild Gene Pools of Rice for ..................
Resistance to Biotic Stresses
MK Kar, L K Bose, M Chakraborti, M Azharudheen, S Ray, S Sarkar,
SK Dash, JN Reddy, DR Pani, M Jena, AK Mukherjee, S Lenka,
SD Mohapatra and NN Jambhulkar

1.4 Enhancing Input Use Efficiency in Direct-Seeded Rice ......................

with Classical and Molecular Breeding
A Anandan, J Meher, RP Sah, S Samantaray, C Parameswaran,
P Panneerselvam, SK Dash, P Swain, M Annamalai, Prabhu Kartikeyan,
Gaurav Kumar

1.5 Genetic Improvement of Rice for Aroma, Nutrition and ......................

Grain Quality
S Sarkar, SSC Pattanaik, K Chattopadhay, M Chakraborti,
P Sanghamitra, N Basak, A Anandan, S Samantaray,
HN Subudhi, J Meher, MK Kar, B Mandal and AK Mukherjee

1.6 Genetic Improvement of Rainfed Shallow-lowland Rice for ................

Higher Yield and Climate Resilience
SK Pradhan, M Chakraborti, K Chakraborty, L Behera,
J Meher, HN Subudhi, SK Mishra, E Pandit and JN Reddy

1.7 Genetic Improvement of Rice for Multiple Stress ...............................

Tolerance in Unfavorable Rainfed Ecology
K Chattopadhyay, JN Reddy, SK Pradhan, SSC Patnaik, BC Marndi,
P Swain, AK Nayak, A Anandan, K Chakraborty, RK Sarkar, LK Bose,
JL Katara, C Parameswaram, AK Mukherjee, SD Mohapatra,
A Poonam, SK Mishra and RR Korada

1.8 Harnessing Heterosis in Rice for Enhancing Yield and Quality ..........
RL Verma, JL Katara, RP Sah, M Azharuddin TP, S Samantaray,
S Sarkar, LK Bose, BC Patra, A Anandan, RK Sahu, AK Mukherjee,
SD Mohapatra, Somnath Roy, Amrita Banerjee and ON Singh
Chapter No. Topic Pages
1.9 New Generation Rice for Breaking Yield Ceiling .................................
SK Dash, P.Swain, L Bose, R Sah, M Chakraboty, N Umakanta,
K Chakraborty, M Azharudheen TP, S Lenka, HN Subudhi, J. Meher,
S Sarkar, A Anandan, M Kar, S Munda, SK Pradhan, L Behera and
ON Singh

1.10 Biotechnology for Rice Improvement: Achievements and .................

Challenges
S Samantaray, N Umakanta, JL Katara, C Parameswaran, RL Verma,
H Subudhi, A Kumar and S Roy

1.11 Development of Genomic Resources for Rice Improvement ..............

L Behera, C Parameswaran, A Anandan, P Sangamitra, SK Pradhan,
M Jena, N Umakanta, SK Dash, P Swain, RK Sahu, NP Mandal,
A Kumar, K Chattopdhyaya, J Meher, HN Subudhi, NN Jambhulkar
and GP Pandi

2.1 Nutrient Management for Enhancing Productivity and .....................

Nutrient Use Efficiency in Rice
AK Nayak, Sangita Mohanty Rubina Khanam, D Chatterjee, D Bhaduri,
M Shahid, R Tripathi, A Kumar, S Munda, P. Bhattacharyya,
BB Panda, U Kumar and H Pathak

2.2 Assessing energy and water footprints for increasing ......................

water productivity in rice based systems
R Tripathi, M Debnath, S Chatterjee, D Chatterjee, A Kumar,
D Bhaduri, A Poonam, PK Nayak, Md Shahid, BS Satpathy,
BB Panda and AK Nayak

2.3 Agro Ecological Intensification of Rice Based Cropping ...................

System
BB Panda, BS Satapathy, AK Nayak, R Tripathi, Md. Shahid,
S Mohanty, D Bhaduri, R Khanam and PK Nayak

2.4 Integrated Rice-based Farming Systems for Enhancing .....................

Climate Resilience and Profitability in Eastern India
Annie Poonam, Sanjoy Saha, PK Nayak, BS Sathpaty, M Shahid,
AK Nayak, R Tripathy, NN Jambhulkar, GAK Kumar, B Mondal,
PK Sahu, SC Giri, M Nedunchezhian, U Kumar and SK Lenka

2.5 Resource Conservation Technologies under Rice-based ...................

System in Eastern India
Mohammad Shahid, AK Nayak, R Tripathi, S Mohanty, D Chatterjee,
A Kumar, D Bhaduri, P Guru, S Munda, U Kumar, R Khanam,
B Mondal, P Bhattacharyya, S Saha, BB Panda and PK Nayak

2.6 Dynamics and management of Weeds in Rice ....................................

Sanjoy Saha, Sushmita Munda, BC Patra, Totan, Adak,
BS Satpathy, P Paneerselvam, P Guru, Narayan Borkar and
Sumanta Chatterjee
Chapter No. Topic Pages
Cpt2.7 Economic and Eco-friendly Use of Rice Straw
P Bhattacharyya, H Pathak, AK Nayak, P Panneerselvam,
MJ Baig, S Munda, D Bhaduri, S Satpathi, M Chakraborti,
NT Borkar and N Basak

2.8 Rice mechanization in India: Key to enhance productivity ................

and profitability
PK Guru, N Borkar, M Debnath, D Chatterjee, Sivashankari, S Saha
and BB Panda

2.9 Microbial Resources for Alleviating Abiotic and Biotic .....................

Stresses and Improving Soil Health in Rice Ecology
Upendra Kumar, P Panneerselvam, TK Dangar, A Kumar,
D Chatterjee, C Parmeswaran, SD Mohapatra, G Prasanthi,
K Chakraborty, P Swain and AK Nayak

3.1 Exploring New Sources of Resistance for Insect Pest and .................
Diseases of Rice
Mayabini Jena, PC Rath, AK Mukherjee, Raghu S, GP Pandi G,
Basana Gowda G, Prasanthi G, MK Yadav, MS Baite,
Prabhukarthikeyan SR, MK Bag, Srikant Lenka, Arvindan S,
Naveen Kumar Patil, SD Mohapatra, Annamalai M and T Adak

3.2 Bio-ecology of rice insect pests and diseases for ..............................

climate-smart rice protection
SD Mohapatra, Raghu S, Prasanthi G, MS Baite,
Prabhukarthikeyan SR, MK Yadav, Basana Gowda G,
Guru P Pandi G, A Banerjee, NB Patil, S Chatterjee, S Lenka,
K Rajsekhar Rao, AK Mukherjee, MK Bag, PC Rath and M Jena

3.3 Bio-intensive Management of Pest and Diseases of Rice ..................

AK Mukherjee, MK Bag, M Annamalai, T Adak, S Lenka,
Basanagowda G, Prasanthi G, Raghu S , M Baite,
Prabhukartikeyan SR, NB Patil, PC Rath, Guru Prasanna Pandi G,
SRR Korada, Nabaneeta Basak, U Kumar, SD Mohapatra,
S Bhagat, Amrita Banerjee, R Bhagawati and M Jena

3.4 Optimization of chemical pesticide use in rice ....................................

PC Rath, T Adak, M Jena, MK Bag, Raghu S, Annamalai M,
MS Baite, Naveenkumar B Patil, Prasanthi G, U Kumar,
P Panneerselvam, GP Pandi G, S Lenka, Basanagowda G,
SD Mohapatra, AK Mukherjee, Arvindan S, MK Yadav and
Prabhukarthikeyan SR

4.1 Improving Protein Content, Glycemic Index, Mineral .........................

Bioavailability and Antioxidant Value of Rice
Awadhesh Kumar, SG Sharma, Nabaneeta Basak, Gaurav Kumar,
Lotan K Bose and N Umakanta

4.2 Improvement of Photosynthetic Efficiency of Rice: ...........................

Towards sustainable food security under changing Climate
MJ Baig, P Swain, K Chakraborty, Awadhesh Kumar, K Ali Molla
and Gaurav Kumar
Chapter No. Topic Pages
4.3 Abiotic Stress Tolerance In Rice: Physiological .................................
Paradigm under Changing Climatic Scenario
P Swain, MJ Baig, K Chakraborty, N Basak, PK Hanjagi,
SK Pradhan, A Anandan, K Chattopadhyay, G Kumar

5.1 Innovative Extension Approaches for Increasing ..............................

Income of Rice Farmers
SK Mishra, Lipi Das, GAK Kumar, NC Rath, B Mondal,
NN Jambhulkar, P Samal, SK Pradhan, S Saha, PC Rath,
AK Mukherjee, RK Sahu, PK Guru, CV Singh, SM Prasad,
S Bhagat, S Roy, R Bhagabati and K Saikia

5.2 Quantification of yield gaps and impact assessment .........................

of rice production technologies
Biswajit Mondal, P Samal, NC Rath, GAK Kumar, SK Mishra,
Lipi Das, NN Jambhulkar, P K Guru, MK Bag, SM Prasad,
S Roy and K Saikia

6.1 Climate resilient production technologies for rainfed .........................

upland rice systems
D Maiti, NP Mandal, CV Singh, SM Prasad, S Bhagat, S Roy,
A Banerjee and BC Verma

7.1
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Revitalizing Rice-Systems for Enhancing

Productivity, Profitability and Climate Resilience

H Pathak, P Samal and M Shahid

SUMMARY
Rice (Oryza sativa L.) is the staple food for about half of the global population,
grown in 160 million ha (Mha) with 493 million tons (Mt) milled rice production. Out of
about 141 Mha of net cultivated area in India, rice occupies the maximum i.e., about 43
Mha. Over the last four decades, rice production has witnessed impressive growth
due to the development of high-yielding varieties, coupled with the adoption of
intensive input-based management practices. The task of increasing rice production
has become quite challenging, however, in recent years due to degradation in natural
resources such as soil, water and air along with shortage of labour and emerging
problem of climate change. In future, rice would have to be produced using less land,
water and labour through more efficient, environment-friendly production systems
that are more resilient to climate change and also contribute less to greenhouse gas
emission. Moreover, all of our efforts so far were production-centric. Now we need to
shift the focus to make it profit-centric. In the process of pursuing higher yield, we
neglected the environment i.e., soil, water and air, considering them to be passive and
inactive players of crop production. To increase productivity, profitability, climate
resilience and sustainability of rice production, a range of strategies i.e., technological,
infrastructural and policy need to be adopted to transform the current production-
driven rice-based cropping system to profit-driven rice-based farming system.
Agricultural research should be re-oriented with farmers’ participatory approach to
unshackle the vicious circle of poverty, reduce drudgery and fulfill the aspirations of
resource-poor, smallholder rice farmers.

1. INTRODUCTION
Rice is the staple food for about half of the world population (Table 1). Grown for
more than 6000 years, it is economically, socially, and culturally important to a large
number of people across the globe. More than 100 countries grow rice with the third
highest worldwide production of 740 million tons (Mt) of rough rice, after sugarcane
and maize. It accounts for 35-75% of the calories for more than 3 billion Asians.
Globally, it provides 27% of dietary energy, 20% of dietary protein and 3% of dietary
fat. Rice fields cover around 160 million hectares, the third largest cereal, and most
important food of majority of global poor. It is grown in a wide range of climatic
conditions spanning from 44oN latitude in North Korea to 35oS latitude in Australia. It
is cultivated from 6 ft below sea level (such as in Kerala, India) to 2700 ft above sea
level. Most of the rice in tropical countries is produced in irrigated and rainfed lowland
areas. Irrigated rice systems account for 78% of all rice production and 55% of total

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

Climate Resilience 1
Table 1. Global and national importance of rice.
Global scenario Indian scenario
a
Parameters Magnitude Per cent Magnitude Per centb
Population dependent (billion) 4 56 0.8 65
Families involved (million) 144 25 67 56
Area cultivated (Mha) 160 10 43 22
Production of milled rice (Mt) 493 20c 110 30c
-1 d
Productivity (t ha ) 2.95 80 2.56 82d
e
Providing livelihood (Million) 400 40 150 40e
Annual value (billion US$) 206 13 53 17
Fertilizer use (Mt) 25 15 6 25
Irrigation water use (km3) 880 35 200 30
Methane emission (Mt) 25 12 3.5 18
Note: Data pertain to 2015-16. a, per cent of global total; b, per cent of country total; c, of
total food production; d, of agriculture; e, of rural poor
Source: Compiled from various publications from IRRI (2016); NRRI (2016), MoA (2016)

harvested rice area, mostly concentrated in alluvial floodplains, terraces, inland valleys,
and deltas in the humid and sub-humid subtropics and humid tropics of Asia. The
crop occupies largest area in India followed by China and Indonesia, whereas China
has the highest production but, Australia has the highest productivity (Table 2).

Table 2. Area, production and yield-wise top five countries (2012-14).

Area Production Yield
Country (Mha) Country (Mt) Country (t ha-1)
India 43.67 China 137.64 Australia 6.68
China 30.67 India 105.79 Egypt 6.37
Indonesia 13.69 Indonesia 46.93 USA 5.66
Bangladesh 11.67 Bangladesh 34.27 Spain 5.14
Thailand 11.49 Vietnam 29.50 Turkey 5.11
Source: FAOSTAT (2016)

In India, rice plays a major role in diet, economy, employment, culture and history.
It is the staple food for more than 65% of Indian population contributing approximately
40% to the total food grain production, thereby, occupying a pivotal role in the food
and livelihood security of people. The country has the world’s largest area under rice
i.e., about 43 million hectare (Mha) and the second highest production i.e., about 110
Mt of milled rice at productivity of 2.56 t ha-1 (Table 1) as per 2016-17 statistics. The
crop is cultivated round the year in one or the other parts of the country. The leading
rice producing states are West Bengal, Uttar Pradesh, Punjab, Odisha, Andhra Pradesh,
Bihar and Chhattisgarh (Table 3). About 40% of the rice area in India is rainfed and
more than 70% of which is in eastern India. Out of the total rainfed area, 23% are
rainfed upland and 77% are rainfed lowland. The entire rainfed upland and 52%
rainfed lowlands are drought prone. About 17% of rainfed lowlands are flood prone.

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

2 Climate Resilience
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Table 3. Area, production and productivity of rice in different states of India (2015-
16).
State Area (000 ha) Production (000 ton) Yield (t ha-1)
Uttar Pradesh 5862 12501 2.13
West Bengal 5524 15954 2.89
Odisha 3941 5875 1.50
Chhattisgarh 3816 5789 1.51
Bihar 3232 6802 2.10
Punjab 2975 11823 3.97
Assam 2485 5125 2.06
Andhra Pradesh 2161 7489 3.47
Madhya Pradesh 2024 3547 1.75
Tamil Nadu 2000 7517 3.76
Jharkhand 1589 2882 1.81
Maharashtra 1503 2593 1.72
Haryana 1354 4145 3.06
Karnataka 1110 3021 2.72
Telangana 1046 3047 2.91
Others 2878 6298 2.19
India 43500 104408 2.40
Source: Ministry of Agriculture, Government of India.

Global demand of rice needs to increase from the current 493 Mt to about 550 Mt
in 2030 (IRRI, 2016). However, rice farming, particularly in the rainfed regions, faces
multiple risks from uncertain climate, degraded soil, water shortage and
underdeveloped markets. It has come under increasing pressure from intense
competition for land and water, a more difficult growing environment because of
climate change, higher price for energy and fertilizers, labour shortage, increasing
cost of cultivation, declining profit margin and greater demand for reduced
environmental footprint (Samal 2009; Samal 2013). The socio-economic dynamics and
food habits are also changing adding another dimension to already complex challenges
of rice cultivation. Therefore, the goal of rice research and development should be at
improving nutritional and income security of rice farmers while addressing
environmental sustainability and coping with climate change.
The chapter deals with the rice ecosystems; trends in area, production and
productivity; emerging challenges and the strategies for enhancing productivity and
profitability of rice production in India.

2. RICE ECOSYSTEMS IN INDIA

In India, rice is grown under highly diverse conditions with area stretching from
790 to 900 E longitude and 160 to 280 N latitude under varying agro-ecological zones. It
is cultivated mostly in wet season with unpredictable rainfall distribution. It is also

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

Climate Resilience 3
grown in areas, where water depth reaches 2-3 m or more. Rice culture in Kuttanad
district of Kerala is grown below the sea level, while in the state of Jammu and
Kashmir, it is grown upto an altitude of 2000 m above sea level; with temperature
range of 15-40 0C and average annual rainfall range from 30 mm in Rajasthan to more
than 2800 mm in Assam. A wide range of rainfall distribution pattern (drought,
submergence, deep water) and distinct differences in soils (coastal and inland salinity,
alkalinity, acidity), agro-climatic situations (high humidity) and seasons has resulted
in the cultivation of thousands of varieties and therefore, one can see a standing rice
crop at some parts of the country or the other in any time of the year. Rice is primarily
grown under four major ecosystems broadly classified as (i) irrigated, (ii) rainfed
lowland, (iii) rainfed upland and (iv) flood prone.
 Irrigated rice eco-system: Total area under irrigated rice in the country is about
26.0 Mha accounting for about 60% of the total area under the crop. It includes
the areas in Punjab, Haryana, Uttar Pradesh, Jammu & Kashmir, Andhra Pradesh,
Telangana, Tamil Nadu, Karnataka, Himachal Pradesh and Gujarat.
 Rainfed lowland rice ecosystem: In India, lowland rice covers an area of about
14.0 Mha, which accounts for about 32% of the total area, located mainly in
eastern India. The area is characterized by poor soil quality and frequent occurrence
of drought/flood due to erratic rains.
 Rainfed upland rice ecosystem: Total area under rainfed upland rice in the country
is about 6.0 Mha, which accounts for 13.5% of total area, located mainly in eastern
zone i.e., Assam, Bihar, Chhattisgarh, eastern Uttar Pradesh, Jharkhand, Madhya
Pradesh, Odisha, West Bengal, and North East Hill Region. The rainfed upland
ecosystem is drought prone.
 Flood-prone rice ecosystem: It occupies about 2.5 Mha in eastern states of the
country. The crop is grown in shallow (up to 30 cm), semi-deep (30-100 cm) and
deep-water (>100 cm) ecosystems in eastern Uttar Pradesh, Bihar, West Bengal,
Assam and Odisha.
Among the above ecosystems, further sub-systems are usually identified for
location-specific variations such as ‘favourable’ or ‘unfavourable’ moisture, soil type,
temperature regime, proneness to drought, submergence, both drought and
submergence; growth duration (early, medium, late maturity groups) and low light
intensity conditions.

3. ACHIEVEMENTS OF RICE RESEARCH

During the last five decades, a lot of advancements have been made on developing
high yielding and disease-resistant varieties and production technologies for different
ecosystems. The country has released about 1200 varieties including about 240
varieties released by ICAR so far for different ecologies. Most of the recent releases
are resistant to multiple diseases such as blast, sheath blight, sheath rot, false smut,
brown spot, stem rot and bacterial blight. These varieties are also tolerant to different

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

4 Climate Resilience
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

pests (gall midge, brown plant hopper, stem borer). Many varieties among them have
early maturity duration. Several viable rice production technologies have also been
developed for adoption in the farmers’ fields. Besides, the duration of maturation of
aromatic rice has been reduced from 160 days to 110 days, while the yields have
increased from less than 2.5 t ha-1 to more than 7.0 t ha-1. Shortening of the crop cycle
has not only helped in saving water and labour, but also facilitate new combinations
of crops in rotations. The hybrid rice technology contributed towards an additional
4-5 Mt to the total rice production in the country and there is a vast scope for
increased adoption of this technology by the farming community in future. Along
with increasing the productivity, emphasis has been given on improving the nutritional
quality of rice varieties and developed varieties with improved quality attributes such
as high protein (CR Dhan 310, CR Dhan 311), high zinc (DRR Dhan 45), low glycemic
index (Improved Sambha Mahsuri) in rice to provide nutritional security to the
population depending on rice as staple food. High yielding varieties of rice developed
and released by ICAR-institutes and SAUs have reached millions of farmers in different
states of the country and are cultivated under different agro-ecologies. Currently,
about 85% of rice area is covered with high-yielding varieties. Stress tolerant varieties
have also helped steady production levels making rice production systems climate-
resilient. India’s rice export has also steadily increased making it the leading rice
exporter followed by Thailand, Vietnam, USA and Pakistan. Currently, the country
exports about 10 Mt rice annually.
Production of rice has increased more than five times since 1950-51 and made
India self-reliant in rice from early 1980s (Fig. 1). The sources of growth in the past
were increase in area and yield, which has increased by 1.4 and 3.6 times, respectively
since 1950-51. Though during Green Revolution period the production growth has
accelerated, during 2000s, the growth has decelerated, threatening the national food
security. It is observed that the additional production during 2000s has decreased
over the previous decade. More precisely, additional production during 1990s over

Fig. 1. Trends in area, production and yield of rice in India.

Source: Ministry of Agriculture, Government of India (2017)

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

Climate Resilience 5
1980s was 20.3 million tons, which reduced to 9.2 tons during the 2000s, indicating
thereby that the production base is shrinking, which is a cause of concern. The
additional yield has also reduced from 387 kg ha-1 during 1990s to 200 kg ha-1 during
2000s. However, some signs of improvement were noticed during the recent period
(2010-11 to 2015-16) and the additional average yield has increased from 200 kg ha-1
during 2000s to 332 kg ha-1 during 2010-16. A major share of production increase
during the recent period is from the eastern states (Assam, Bihar, Chhattisgarh,
Jharkhand, Madhya Pradesh, Odisha, Uttar Pradesh and West Bengal). It is also
observed that the area growth has almost exhausted in rice. These observation leads
to the conclusion that the area growth in India has been exhausted and further increase
in production has to come from yield increase only.

4. PROJECTED DEMAND OF RICE

Population growth is the major driving force for increasing rice demand in India.
In addition, the low-income segment of the population will also demand more rice
with increase in income. It is estimated that about 120 and 140 Mt of rice would be
required by 2025 and 2050, respectively in India. In addition, India is exporting about
10 Mt of rice per year, which earns valuable foreign exchange for the country. There
is a growing middle-class, rice-consuming population in domestic as well as
international markets. This will increase the demand for high-quality rice creating
great opportunities for India for exporting basmati and high-quality non-basmati rice.
This increased production has to necessarily come from increased productivity rather
than increase in area under rice and that too under deteriorating soil, water and other
natural resources. Therefore, to sustain present food self-sufficiency and to meet
future demand of food and export, the production has to increase by about 1.5 Mt yr-
1
and the productivity to 3.25 t ha-1 by 2050 from the current level of 2.56 t ha-1 (2016-
17) i.e., an increase of about 30%.

5. EMERGING CHALLENGES OF RICE FARMING

Rice production is intricately linked with land and water, and this has unique and
profound implications for the environment. Hence, careful management of the natural
functioning of rice ecosystems is critically important for protecting the environment
while raising rice productivity to meet growing demand. The Green Revolution in
south Asia in the 1960s helped doubling food production with a mere expansion in
area of 10–20% and introducing seeds of high-yielding varieties, fertilizers, irrigation,
and pesticides. However, this intensification of agriculture had adverse environmental
consequences such as the deterioration of natural resources. As a result, the increase
in productivity is showing signs of slowing down/stagnating. Yield trends from long-
term continuous rice-rice experiments conducted in Bangladesh, China, India,
Indonesia, Nepal, the Philippines, and Thailand indicated that, even with the best
available cultivars and scientific management, rice yields (holding input levels

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constant) have either stagnated or declined over time since the early 1980s. The rice-
wheat cropping system of the Indo-Gangetic Plains (IGP) also showed yield stagnation/
decline in the last two decades. Earlier gains in rice output were driven by the increase
in area under modern varieties, irrigated area, fertilizer use, increased cropping intensity,
and supportive input and output price policies in irrigated areas. However, in the last
decades, there is sign of yield plateauing in major irrigated states. There is now
growing concern that other non-price factors, such as the declining scope for further
gains from existing modern varieties, deteriorating soils and ground water supplies,
and reduced public investment in research have contributed to poor performance in
recent years in irrigated areas. The challenge is to integrate productivity and
profitability improvement while conserving and enhancing the quality of the
environment on which production depends. The major environmental concerns of
modern rice farming and suggested potential remedial measures are presented below
(Pathak and Ladha 2006).
5.1. Degrading the water resource base
The productivity of water for rice is very low. Rice requires about two times as
much water as wheat or maize. In some regions, such as northwest India, water
application in rice is about 5-6 times more than that of wheat. Large water demand of
rice is expected to outstrip the available supply in the near future. The declining
availability and quality of water, increased competition from domestic and industrial
sectors, and increasing costs are already affecting the sustainability of irrigated rice
production systems in many parts of south Asia. For example, in the upper transect of
the IGP, rice cultivation resulted in a decline in water tables and water quality. A
rapidly depleting water table in many northern and southern states is also a matter of
concern for future productivity growth. Five major rice surplus states, Punjab, Haryana,
western Uttar Pradesh, Tamil Nadu, and erstwhile Andhra Pradesh, where groundwater
depletion is a major issue, account for around 42% of India’s rice production (in 2015-
16). These states contribute a significant amount to the country’s central pool, which
is critical for India’s food security and also to the functioning of India’s food
distribution program, through which poor people are provided with highly subsidized
grains. Many districts in the rice-wheat growing area of Haryana, and Punjab, show
a water table decline in the range of 3-10 m over the last two decades. The groundwater
table has fallen at about 23 cm yr-1 in the central Punjab, India. The other side of the
water problem is waterlogging in some areas. In some districts of Haryana, the water
table is rising at 0.14 to 1.0 m yr-1 and more than 0.4 Mha of land has a water table
within 3 m of the soil surface. Apart from water scarcity, the growing demand for land
from urbanization, industrialization, and for growing cash crops is likely to cause a
decline in rice area. According to the NRRI 2050 vision document, rice area may
decline by 6-7 Mha by 2050, a decline of around 15% in the next 35 years. In other
words, India will need to produce 137 million tons of rice on 37 Mha of land in 2050
compared with the current production of 105 Mt of rice on 43 Mha. Therefore, yield
will have to increase by 50% in the next three decades to keep India food secure.

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Climate Resilience 7
 The demand for fresh water is growing from other sectors of the economy like
industry, domestic and environmental use besides water for irrigation purpose to
raise crops. Among cereals, rice consumes much more water than others and it is
estimated that 2500-5000 liters of water is required to produce one kg of rice. As the
demand for water by all the sectors of the economy grows, ground water is being
depleted, water reservoirs and canals is being silted, other water ecosystems are
becoming polluted and degraded, and developing new sources of water is getting
more costly, policy makers and researchers are concerned that water will be the main
obstacle for growing enough food in the coming years.
Water application in rice production needs to be decreased by increased water-
use efficiency through reduced losses caused by seepage, percolation, and
evaporation; laser land leveling; crack plowing to reduce bypass flow; and bund
maintenance. Management options to increase the efficient use of rainwater include
crop scheduling, diversified cropping, and the construction of small ponds serving
as on-farm reservoirs for water harvesting. Various crop and water management
systems such as water-saving irrigation techniques, intermittent drying of the soil,
growing rice with reduced or no tillage either on flat land or raised beds, and shifting
away from continuously flooded (anaerobic) to partly or even completely aerobic rice
can drastically improve the efficiency of water use.
5.2. Degrading soil resource base
Concerns about sustainability are arising throughout tropical rice ecosystems
because of decreasing soil fertility as most countries move into the post-Green
Revolution era. Recent trends of yield decline/stagnation observed in long-term
experiments in south Asia were mostly due to soil-related causes such as the decline
in soil C and macro- and micro-nutrients in rice-rice and rice-wheat systems;
accumulation of phenolic compounds, Fe2+, and sulfides in the rice-rice system; and
the increase in soil salinity. Intensive use of irrigation water in rice led to a salinity
buildup. In Pakistan’s Sindh Province, large areas became saline after the introduction
of extensive irrigation. In the short term, salinity buildup leads to reduced yields,
whereas, in the long term, it can lead to abandoning of crop lands. Farmers are also
using poor-quality water for irrigation in several areas of the Indo Gangetic Plains for
rice and run the risk of further aggravating soil degradation. The soil quality of rice
systems therefore, needs to be continuously monitored.
Though farmers apply some of the macro-nutrients like N, P and K, they usually
neglect application of micronutrients. Even the N, P, K fertilizers are not applied
proportionately. In the long run, this causes an imbalance in soil and plant nutrition
resulting in yield decline. It has been reported that during 1950s, there was only one
nutrient deficiency (Nitrogen), which has increased to eight (N, Fe, P, Zn, K, S, Mn, B,
Mo) during 1990s. Moreover, the soil quality is deteriorating from the loss of organic
carbon, erosion, soil compaction, salinization, heavy metal introgression into soil
from industries and pesticides, and other anthropogenic activities.

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5.3. Burning of rice residues

Rice straws and husks are often not disposed of in an environment-friendly manner.
In a recent survey, it was noted that 60% and 82% of rice straw produced in the
northwestern states of Haryana and Punjab, respectively, is burned in the field (Pathak
et al. 2012). About 20 Mt of rice residues are burned annually in Punjab, India, alone.
The burning of rice straw is environmentally unacceptable as it leads to (1) the release
of soot particles and smoke, causing human health problems such as asthma or other
respiratory problems; (2) emission of greenhouse gases such as carbon dioxide,
methane, and nitrous oxide, causing global warming; and (3) loss of plant nutrients
such as N, P, K, and S. Almost the entire amounts of C and N, 25% of P, 50% of S, and
20% of K present in straw are lost due to burning.
One potential solution to the problem of rice straw burning would be its retention
on the soil surface. This straw mulch reduces moisture loss from soil, controls weeds,
manipulates soil temperature for better crop growth, and improves soil organic matter
content. With the development of new machines (such as the Happy Seeder), it is
now possible to sow seeds in residue-retained fields.
5.4. Climate change
Climate change effects include increase in temperature in the long-run, changes in
rainfall regimes with increasing year-to-year variability and a greater prevalence of
extreme events. Climate has changed worldwide over the last century. It is predicted
that a warming of 5°C can eliminate 20% of the coastal wetlands by the year 2080.
Apart from rice area reduction, rice yield under simulated global climatic change
scenarios have shown a decline, when temperature increase is more than 0.8°C per
decade. It is feared that a 20% decline in rice yields can occur in north-west India due
to elevated CO2 and temperature. At present, we do not have thermo-insensitive rice
varieties with comparable yield levels within the present high yielding varieties to
cope up with the situation. Besides the above, emergence of new pests with higher
degree of virulence will be there due to changing climate.
Rice production contributes to global climate change (through emissions of
methane and nitrous oxide) and in turn suffers from the consequences. An increase in
temperature has two effects on rice: decreasing spikelet fertility due to higher maximum
temperature and increasing respiration due to higher minimum temperature. The
increase in temperature, especially that of mean minimum night-time temperature, has
adverse effects on rice productivity as it reduces crop duration, increases respiration
rates, alters photosynthate partitioning to grain, affects the survival and distribution
of pest populations, hastens nutrient mineralization in soils, decreases fertilizer-use
efficiencies, and increases evapo-transpiration (Wassmann et al. 2009a; 2009b). An
increase in atmospheric carbon dioxide, on the other hand, has a fertilization effect on
rice, promoting its growth and productivity. Recent studies, however, suggested that
the effect of global warming would be largely negative for rice production because of
increased respiration and a shortened vegetative and grain-filling period. It is believed

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Climate Resilience 9
that climate change would affect the quality of crops, particularly important aromatic
crop such as basmati rice. In addition to direct effects on rice plants, climate change
and global warming might affect other organisms associated with rice and thus, alter
the occurrence and severity of rice pests. There is also a need to meet the challenge
of the increase in extreme climatic events associated with climate change, such as the
increasing severity and frequency of floods and droughts, as well as more frequent
hurricanes, and their effects on rice production.
Field measurements in several Asian countries have identified possible technical
options to mitigate methane emissions through modified water regime (mid-season
drainage, alternate flooding), modified residue management (sequestration of straw),
use of additives (phosphogypsum, nitrification inhibitors), and modified land
management (direct seeding, reduced tillage and site-specific nutrient management)
(Pathak 2015). Similarly, novel approaches of demand-driven N supply using leaf
color charts and site-specific N management minimize the pool of excessive nitrogen
in the soil and thus reduce nitrous oxide emissions. At the same time, adaptation
strategies such as (1) resilient varieties for moisture-stress environments, (2)
management systems that reduce water use, and (3) insect-pest and disease resistant
varieties should be developed to overcome the ill effects of climate change and
climatic variability.
5.5. Loss of biodiversity
The introduction of modern rice varieties and practice of monoculture have caused
a reduction in and loss of biodiversity as many traditional varieties have been
abandoned when farmers found modern varieties to be more productive and profitable.
Genetic diversity is required for the continual improvement of the rice crop, as cultivars
need to be invigorated every 5 to 15 years to better protect them against diseases and
insect pests. With the advances in biotechnology, there is a need for a diversity of
genetic material for the potential of these technologies to be fully achieved.
5.6. Increasing cost of cultivation and decreasing farmers income
The cost of cultivation has increased and profits decreased over years in majority
of the states. The cost of cultivation per ha across states varied from Rs. 37,071 to Rs.
78,968 and profits were either low or negative in many rice-growing states (Table 4).
Policy makers are now concerned, how to make rice cultivation remunerative and at
the same time supply consumers rice at affordable prices.
5.7. Increasing labour shortage
With the process of development, the non-farm sector is growing and young
people are attracted to non-farm jobs due to higher wage rates in that sector and
higher drudgery involved in agricultural operations. Therefore, growing labour
shortage is observed throughout the country during peak period of different
agricultural operations and thus, escalating agricultural wages year after year. We do
not have cost effective small size machines for different operations in rice farming.

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Table 4. State wise costs and returns of rice cultivation (2014-15).

Cost of
Cost of Gross Profit over cultivation Profit over
cultivation return C2 cost (A2+FL)** A2+FL cost
State (C2)* (Rs. ha-1) (Rs. ha-1) (Rs. ha-1) (Rs. ha-1) (Rs. ha-1)
Andhra Pradesh 78968 83972 5004 51821 32151
Assam 49887 36819 -13068 36000 819
Bihar 40097 43483 3386 26308 17175
Chhattisgarh 45775 45303 -472 30848 14455
Jharkhand 38848 43429 4582 23875 19554
Gujarat 55798 73484 17686 41447 32036
Haryana 78948 119977 41030 45717 74261
Punjab 73254 106826 33572 34041 72785
Himachal Pradesh 37071 46368 9298 26323 20045
Karnataka 68315 81571 13255 48419 33151
Kerala 71972 89927 17955 52905 37022
Madhya Pradesh 41381 37492 -3889 28415 9077
Maharashtra 68262 48758 -19505 54417 -5659
Odisha 56914 47153 -9761 42302 4851
Tamil Nadu 74077 76294 2217 55252 21042
Uttar Pradesh 58982 50417 -8565 39481 10936
Uttarakhand 45634 62115 16481 30396 31719
West Bengal 71840 58956 -12885 54259 4696
*C2, operational and fixed costs; **A2+FL, operational costs including family labour; FL,
Family labour.
Source: Ministry of Agriculture, Government of India.

6. STRATEGIES FOR ENHANCING PRODUCTIVITY AND

PROFITABILITY OF RICE PRODUCTION
Rice research should aim at tapping genetic resources and utilizing them for
breeding rice varieties with higher yield potential, better grain and nutritional quality,
enhanced input use efficiency and increased tolerance to major biotic and abiotic
stresses through conventional and innovative techniques such as marker assisted
breeding, development of transgenics, functional genomics, improvement of degree
of heterosis, and improvement of photosynthetic efficiency through C4 mechanism.
Identification of potential new donors for abiotic and biotic stresses and unravelling
the underlying tolerance mechanisms will also receive due attention. Genomics,
proteomics, metabolomics and phenomics tools will be employed for understanding
multiple abiotic/biotic stress tolerance mechanism. Redesigning rice plants for
improving photosynthesis and plant productivity under multiple abiotic stress
environments through transgenics would also be one of the approaches. Research
emphasis will be on improving water and nutrient use efficiencies with special emphasis
on conservation agriculture, climate-resilient rice and rice-based cropping and farming

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Climate Resilience 11
systems. Rice physiology and biochemistry under high CO2, ozone and temperature
would be unravelled for defining climate resilient rice cultivars. Innovative approaches
involving nano-technologies will be taken up for efficient use of fertilizers and
pesticides. Use of newer molecules for control of diseases and insect pests, including
bio-pesticides, and integrated pest management (IPM) are other areas of focus. Host-
parasite/pathogen interaction at molecular level including QTL identification to design
suitable control strategy will be the approach for resistance breeding.
Management of rice related knowledge, with due attention on extension services
and fostering linkage and collaboration with public, private, national and international
organizations are other important areas on which the institute will focus. Strategic
planning, priority setting and impact assessment of rice research in India with a
global perspective will be taken up to consolidate the gain. Capacity building of
scientists, farmers and other stakeholders will be given due importance, so as to be
globally competitive and ensure food and nutritional security of the country.
The following options are available for increasing farmers’ productivity and income
in rice-based systems.
6.1. Improving productivity and quality
6.1.1. Providing quality seed and enhancing seed replacement ratio: Seed is the
critical determinant of agricultural production on which depends the performance
and efficacy of other inputs. Quality seeds appropriate to different agro-climatic
conditions and in sufficient quantity at affordable prices are required to raise
productivity. Availability and use of quality seeds is not a onetime affair. Sustained
increase in agriculture production and productivity necessarily requires continuous
development of new and improved varieties of crops and efficient system of production
and supply of seeds to farmers. Despite a huge institutional framework for seed
production both in the public and private sector, availability of good quality seeds
continues to be a problem for the farmers. As a result, they prefer to rely on farm
saved seeds; seed replacement rate continues to remain low for most crops. As is well
known, seed replacement rate has a strong positive correlation with the productivity
and production of crops.
6.1.2. Promoting high-yielding varieties and hybrids: Due to unavailability of the
quality seeds of high yielding varieties and high seed cost of the hybrids, farmers are
unable to get those seeds and they prefer to grow their local seed materials. The yield
potential of local seeds is low and they are susceptible to many pests and diseases.
Although many government programmes are in operation for making HYV and hybrids
seeds available to the farmers, yet there is ample scope of promoting high-yielding
varieties and hybrid. Further, improved market support will encourage the farmers for
adopting high yielding varieties and hybrids.
6.1.3. Growing nutrient rich and aromatic rice: At present no support price for
farmers for high nutrient rich rice such as high protein rice CR Dhan 310 and CR Dhan
311 or any other specialty rice (aromatic non-basmati) is available. Therefore, for
popularization of the variety in suitable lands and for increasing the higher commercial

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value of these rice, initiatives from institutional and extension machinery as well as
modification in policy decision are collectively required. Higher support price for
growers and subsidy for mid-day meal rice are required to give benefits both the poor
rice-farmers and our underprivileged children in villages of India.
6.1.4. Increasing cropping intensity in rice-fallow areas: About 30% (11.7 Mha) of
the area under rice production during kharif season in India remains fallow in the
subsequent rabi due to number of biotic, abiotic and socioeconomic constraints.
Despite of ample opportunities rice fallow systems have been bypassed in the research
and developments for a numbers of constraints. Major rice fallow area (82%) is
concentrated on eastern parts of the country. States with larger area of rice-fallows
are Chhattisgarh, Madhya Pradesh, Jharkhand, Bihar, West Bengal and Orissa the
remaining 18% area lies in the states like Tamil Nadu, Karnataka and Andhra Pradesh
and there exists a large scope for expansion of area under pulse crops. Short duration
pulses are ideal candidates for their cultivation in such areas. To exploit these rice
fallow areas with pulses, location specific and economically viable technology for
better performances of pulses are required to be standardize through proper
understanding of the system ecology and constraints study.
6.2. Increasing input use efficiency
6.2.1. Crop planning: Current land use pattern for agriculture in many states are not
based on principles of comparative advantage. Crops pattern in various region are
inefficient in terms of resource use and unsustainable from natural resource use point
of view. This is resulting into serious misallocation of resources, efficiency loss,
indiscriminate use of land and water resources, and adversely affecting long term
production prospects. Due to lack of proper crop planning, problems of soil and
water degradation are aggravating. So, the need is there for proper crop planning in
the country so that it is consistent with natural endowment and resources use
efficiency.
6.2.2. Promoting water harvesting and micro-irrigation: In many farming areas,
readily available water is in short supply. Although the total annual rainfall in an area
may be enough to sustain farm needs, it is often distributed very unevenly so that
long dry periods are interspersed with periods of intense rainfall. In many cases, a
crop is unable to use a high proportion of this water, as much of it is lost through run
off or leaching. This may also cause soil erosion and loss of soil nutrients. Hence,
there is need to promoting water harvesting and micro-irrigation to achieve per drop
more crop. Further adoption of water saving technologies such as direct seeding of
rice and system of rice cultivation can save water. For surface-irrigated areas, a properly
leveled surface with the required inclination according to the irrigation method is
absolutely essential. Traditional farmers’ methods for leveling by eyesight, particularly
on larger plots, are not accurate enough and lead to extended irrigation times,
unnecessary water consumption, and inefficient water use. With laser leveling, the
unevenness of the field is reduced resulting in better water application and distribution
efficiency, and improved water productivity.

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Climate Resilience 13
6.2.3. Using soil health card and site-specific nutrient management: The soil health
card carries crop wise recommendations of nutrients/fertilizers required for farms,
making it possible for farmers to improve productivity by using appropriate inputs.
Under current management practices, nutrient use efficiency are low and farmers
often fail to apply nitrogen (N), phosphorous (P) and potash (K) in the optimal ratio
to meet the need of crops. Site Specific Nutrient Management (SSNM) provides an
approach for feeding crops with nutrients as and when needed. The SSNM eliminates
wastage of fertilizer by preventing excessive rates of fertilizer and by avoiding fertilizer
application when the crop does not require nutrient inputs.
6.2.4. Promoting farm mechanization and solar energy: Intensification of
mechanization is one of the most important factor for increasing agricultural activities
and production as well. Productivity of farms depends greatly on the availability and
judicious use of farm power. Agricultural implements and machines enable farmers to
employ the power judiciously for production purposes. Agricultural machines increase
productivity of land and labour by meeting timeliness in farm operations.
Mechanization has the advantages of proper utilization of resources, reducing drudgery
in farm operations, timely execution of various agricultural operations and best use of
the available soil moisture. Switching over from animal power to mechanical and
electrical power for enhanced power availability for various farm operations, reduce
cost of operation, and crop diversification. Promoting use of renewable energy in
farm equipment segment such as solar-powered pumps may have the immense potential
in farm operations and can create alternate source of revenue for the farmer by selling
the additional power.
6.3. Reducing crop loss
6.3.1. Adopting plant protection measures: Plant protection continues to play a
significant role in achieving targets of crop production. The major thrust areas of
plant protection are promotion of integrated pest management (IPM), ensuring
availability of safe and quality pesticides for sustaining crop production from the
ravages of pests and diseases, streamlining the quarantine measures for accelerating
the introduction of new high yielding crop varities, besides eliminating the chances
of entry of exotic pests.
6.3.2. Promoting resistant varieties and e-surveillance: The crop losses due to
pests and diseases occur despite increased pesticide use, which highlight the need
to develop sustainable approaches for pest control with less reliance on chemical
inputs. To address concerns regarding human health, environmental safety and
pesticide resistance, plant defensive traits could be exploited more widely in crop
protection strategies. Further, it is essential to have a pest monitoring system, which
will check the spread of disease pest and the crop loss.
6.3.3. Crop insurance to mitigate risks at affordable cost: Crop insurance provides
required coverage to farmers against production loss for crops. It also offers preventive
planting and repellant security. A crop insurance plan could prove a life-saver by
providing compensation. Therefore, farmers should be advised to take up insurance
plans to compensate their income during adverse years.

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6.3.4. Weather services and forecasting system: Every year crops are damaged by
pest and diseases. Due to lack of proper operational forecasting system for the
incidences of pests and diseases, it becomes difficult to adopt plant protection
measures at right time. It has been established with fair degree of accuracy that
climate/weather play major role in the incidences of pests and diseases. Thus, there is
great scope of utilizing meteorological parameters for the advance information of the
occurrences of pests and diseases and ultimately scheduling of prophylactic measures
can be taken scientifically and judiciously.
6.4. Diversification of rice areas with low productivity
6.4.1. Dairy husbandry for small farmers: Dairying is an important source of
subsidiary income to small/marginal farmers and agricultural labourers. The manure
from animals provides a good source of organic matter for improving soil fertility and
crop yields. The cow dung gas from the dung is used as fuel for domestic purposes
as also for running engines for drawing water from well. The surplus fodder and
agricultural by-products are gainfully utilized for feeding the animals. A large portion
of draught power for farm operations and transportation is supplied by bullocks.
Since agriculture is mostly seasonal, there is a possibility of finding employment
throughout the year for many persons through dairy farming. Thus, dairy also provides
employment throughout the year. The main beneficiaries of dairy programmes are
small/marginal farmers and landless labourers.
6.4.2. Promotion of intensive vegetable and fruit production: By following intensive
vegetable production, and planting fruit trees, farmers can get maximum profit from
the farm. Good planning and attention to the production and marketing practices can
help the farmers to attain high level of profit.
6.4.3. Promotion of ancillary activities like poultry, beekeeping and fisheries: Small
and marginal holdings account for about three-fourth of the total operational holdings
in the country, operating over one-fourth of the total area. Majority of small and
marginal farmers cultivate mainly low value, subsistence crops. In the absence of
adequate farm and non-farm employment opportunities, they are also forced to live
below poverty line. The situation is likely to worsen because of the growing pressure
of population on land and the limited scope of increasing additional production
through subsistence farming. Hence arises the need for commercialization and
diversification of small farms within and outside agriculture and their proper integration
with local and global markets. This is intended not only to liberate the small and
marginal farmers from the poverty trap, but also to meet the country’s growing demands
for meat, fish and eggs.
6.4.4. Strengthening organic food program: Organic food is preferred as it battles
pests and weeds in a non-toxic manner, involves less input costs for cultivation and
preserves the ecological balance while promoting biological diversity and protection
of the environment. Generally, organically grown food fetches better price in the
market.

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Climate Resilience 15
6.5. Creation of Infrastructure, market price realization and value
addition
6.5.1. Infrastructure: The availability of storage facilities is not sufficient for storage
during peak harvesting period. Similarly, the availability of number of regulated markets
is not sufficient to cater to the needs of farmers. As a result, the MSP is not effective
in eastern states. Government should review the state of procurement operations in
the six eastern states, viz. Assam, Bihar, Jharkhand, Odisha, Uttar Pradesh and West
Bengal, where the support price mechanism is not effective, on priority for taking
improvement measures.
6.5.2. Community/co-operative farming with crop-value chain: Institutional reforms
are necessary to generate collective actions through co-operative avenues to
overcome the development deadlock created due to small and uneconomical holding
sizes. This is essential not only to enhance collective bargaining power of the farmers
but also to inculcate the spirit of submerging the personal interests in collective
welfare. Earlier system of co-operative farming, emerging group approaches such as
the self help groups (SHGs) and prospects of creating farmers’ corporations need to
be explored thoroughly.
6.5.3. Using crop biomass to make products through small industry: Biomass pellets
can be sold commercially as the main fuel for industrial boilers and replace coal.
Micro-pelletization should be incentivized and its local usage promoted. There are
other small-scale industries such as cardboard manufacturing and mattress production
that can utilize crop residues. Straw can also be used for substrata for mushroom
cultivation (Pathak et al. 2012).
6.5.4. Creation of a national e-market: National farm market allows farmers and
traders to sell their produce to buyers anywhere in the country. National farm market
addresses the modern day market challenges by creating a unified market through
online trading platform, both, at state and national level and promotes uniformity,
streamlining of procedures across the integrated markets, removes information
asymmetry between buyers and sellers and promotes real time price discovery, based
on actual demand and supply, promotes transparency in auction process, and access
to a nationwide market for the farmer, with prices commensurate with quality of his
produce and online payment and availability of better quality produce and at more
reasonable prices to the consumer.
6.5.5. Agribusiness Incubation Centres to promote agri-preneurship: The Agri-
Business Incubation (ABI) program aim to promote entrepreneurs in public-private
partnership mode that maximizes the success quotient of start-up entrepreneurs by
offering them best opportunities with minimum risk. Effective communication,
coordination and cooperation among the various nodal centres, umbrella consortium
and the industry are inevitable for the successful implementation of the schemes.

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

16 Climate Resilience
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

7. CONCLUSIONS
In order to meet future rice demand, increasing production and productivity of
rice is essential. This has to be done in the face of growing shortage of land, labour
and water for rice farming. As the profit margin in rice cultivation has decreased, there
is need to not only increase in yield per se but also bring efficiency in input use in rice
production. The goal of rice research should be in developing profitable and resilient
rainfed rice farming system with a vision of enhancing productivity, profitability and
resilience for ever-green rice farming with high-quality research, partnership and
leadership in rice science. The thrust areas research should include (1) genetic
enhancement for improving productivity, quality and climate resilience of rice; (2)
ecosystem management for higher input-efficiency and lower environmental footprints;
(3) value-addition with improved quality, co-farming, processing and marketing and
(4) accelerating technology delivery, capacity building and policy formulation. The
rice-research in the past has made immense contributions in developing and
demonstrating technologies for improved rice farming. It, however, needs to be
strengthened to address the emerging challenges of low productivity and low income
of rice farmers in the face of environmental changes. A multi-disciplinary and
participatory research should be adopted to address the emerging challenges and
make rice farming more productive, profitable and climate resilient.
References
Kumar P, Joshi PK and Birthal PS (2009) Demand projections for Foodgrains in India. Agricultural
Economics Research Review 22:237-243.
Pathak H (2015) Greenhouse gas emission from Indian agriculture: Trends, drivers and mitigation
strategies. Proceeding of Indian National Science Academy 81(5): 1133-1149.
Pathak H and Ladha JK (2006) Rice: Environmental issues. Indian Farming 56(7): 46-49.
Pathak H, Bhatia A and Jain N (2012) Crop residues management with conservation agriculture:
Potential, constraints and policy needs. Indian Agricultural Research Institute, New Delhi,
vii + 32 p.
Samal P (2009) Future technological needs for rice crop in India: Socio-economic concerns. In
‘Forecasting future technological needs for rice in India’, Indian Agricultural Statistics
Research Institute, New Delhi, pp. 14-24.
Samal P (2013) Growth in production, productivity, Costs and profitability of rice in India during
1980-2010. In P Shetty, MR Hedge and M Mahadevappa (Eds.) Innovations in Rice
production, National Institute of Advanced Studies, Bangalore 12, pp. 35-51.
Tilman D, Cassman KG, Matson PA, Naylor R and Polasky S (2002) Agricultural sustainability and
intensive prodution practices. Nature 418: 671-677.
Wassmann R, Jagadish SVK, Heuer S, Ismail A, Redona E, Serraj R, Singh RK, Howell G, Pathak H,
Sumfleth K (2009) Climate change affecting rice production: The physiological and
agronomic basis for possible adaptation strategies. Advances in Agronomy 101: 59-122.
Wassmann R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, Ismail A, Serraj R, Redona E, Singh
RK, Heuer S (2009) Regional vulnerability of climate change impacts on Asian rice
production and scope for adaptation. Advances in Agronomy 102: 91-133.

Revitalizing Rice Production System for Enhancing Producitivity, Profitability and

Climate Resilience 17
 Rice Genetic Resources: Collection,
Conservation, Maintenance and Utilization

BC Patra, BC Marndi, P Sanghamitra, S Samantaray, N Umakanta

and JL Katara

SUMMARY
The increased demand for rice will have to be met from less land, less water, less
labour and fewer chemicals under changing climate. Can we meet the challenges to
rice productivity, stability and nutritional quality improvement by strategic use of the
available germplasm resources? Can India, having more than 106,000 germplasm
accessions in the National Gene Bank effectively make use of these huge resources?
Past experience suggests that germplasm still holds the key to our food and nutritional
security of future generation. It is well known that the traditional rice varieties and
their wild relatives constitute an invaluable gene pool in terms of resistance/tolerance
to biotic and abiotic stresses, which can be exploited for developing modern new
generation rice varieties having enough resilience to sustain adverse climatic changes.
All these issues have been dealt in this chapter under the ongoing Institute multi-
disciplinary research project.

1. INTRODUCTION
The plant genetic resources (PGR) constitute the basic raw material for any crop
improvement programme. It may consist of seed or vegetative propagules (tuber,
sucker, rhizome, cutting, seedling etc.) of plants, which contains the functional units
of heredity. They are generally referred to as germplasm or genetic resource material.
In fact, Sir Otto Frankel coined the word ‘Genetic Resources’. Rice (Oryza sativa L.)
is one of the most important cereal food crops for more than one-half of the world
population and provides 50–80% of daily calorie intake. Rice is grown in more than
115 countries. In India, it is cultivated under a wide range of growing conditions, such
as below sea level farming in Kuttanad in Kerala to high altitude farming in the
Himalayas. Because of its adaptation to such variable agro-ecosystems, fortunately
a rich genetic diversity and variability is encountered which helps sustain the adverse
alterations in temperature, precipitation as a result of climate change. There are varieties,
which can withstand submergence during flood and there are others which can grow
under moisture stress during drought condition and also at soil and water salinity.
Therefore, it becomes imperative to conserve them for posterity. The search for superior
genotypes regarding yielding ability, disease and pest resistance, abiotic stress
tolerance or better nutritional quality is very hard, competitive and expensive.
Evidently, there is a gap between available genetic resources and breeding activities.
However, with the advent of modern genomic tools the scope for use of vast genetic
resources has increased. Newer strategies must be designed, first for an elaborate
evaluation, and subsequently for efficient utilization of the diverse germplasm resource

Rice Genetic Resources: Collection, Conservation,

18 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

so painstakingly collected and conserved in the gene banks. Accelerated genetic

gains in rice improvement are needed to mitigate the effects of climate change and
loss of arable land, as well as to ensure a stable global food supply. The enormous
rice genetic diversity available in the gene banks will be the foundation of the genetic
improvement of the crop through unraveling the new genes and traits that will help
rice producing farmers who are facing the challenges brought about by climate change,
pests and diseases, and other unfavourable conditions.

2. ORIGIN AND EVOLUTION OF CULTIVATED RICE

Rice is cultivated as far north (53°N) on the border between Russia and China, and
as far south as central Argentina (40°S). It is grown in cool climates in the mountains
of Nepal and India, and under irrigation in the hot deserts of Iran and Egypt. It is an
upland crop in parts of Asia, Africa and Latin America. At the other environmental
extremes are floating rice, which thrive in seasonally deeply flooded areas such as
river deltas - the Mekong in Vietnam, the Irrawady in Myanmar and the Ganges-
Brahmaputra in eastern India and Bangladesh.
The centre of origin and centers of diversity of two cultivated rice species i.e.
Oryza sativa and O. glaberrima have been identified using genetic diversity, historical
and archaeological evidences and geographical distribution. It is generally agreed
that river valleys of Yangtze, Mekong Rivers could be the primary centre of origin of
Oryza sativa. The foothills of the Himalayas, Chhattisgarh, Jeypore tract of Odisha,
north eastern India, northern parts of Myanmar and Thailand, Yunnan Province of
China are some of the secondary centers of diversity for Asian cultigens. There are 22
agro-biodiversity hotspots in India, out of which five hotspots fall in eastern region
of the country, of which the Koraput region covering part of northern Eastern Ghats
is of great concern as the upland short duration drought avoiding aus types have
been originated here.
The Inner delta of Niger River and some areas around Guinean coast of the Africa
are considered to be the centre of diversity for the African cultivated species of O.
glaberrima (Chang 1976; Oka 1988). It is also assumed that the Asian annual wild
species O. nivara has given rise to the Asian cultivated species O. sativa and the
African annual wild species O. barthii to the African cultivated species O. glaberrima.
The diversity and variability within the Asian cultivated rice (O. sativa) is enormous.
Some controversy exists over when and where rice was domesticated. It is fairly safe
to say that rice was being cultivated at least 10,000 years ago and that it was
domesticated from its wild ancestor O. rufipogon (Khush 1997). Two major sub groups
of rice, indica and japonica, led rice genetic resources specialists to conclude that
there were two centers of origin. One was thought to be in the tropical regions of
South Asia where indica rice varieties dominated and the other near Central China
where japonica rice dominated (Londo et al. 2006). It has generally been recognized
that genetically the japonica (sensu stricto) is a fairly homogeneous group whereas
the indica is highly heterogeneous group (Jennings 1966).

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 19
3. WILD RICE
Genus Oryza consists of 24 species, of which two are cultivated and rests are
found wild in different parts of the world; all of them grow in the tropics only. There
are two species that are close relatives of the cultivated rice and are believed to be the
progenitor species of the cultivated ones. One of these, Oryza rufipogon, grows wild
in India, China, Southeast Asia and South Asia. The other one, known as O. barthii
(syn. O. breviligulata) grows wild in northern part of tropical Africa. These two wild
species of rice attracted the attention of Neolithic man for their grains for his
subsistence especially when he had not enough wild animals for hunting or wild
fruits to gather. In fact, some of the aborigines still continue to collect seeds of wild
rice in India, Southeast Asia and Africa. Recent study at this institute on morphological
and molecular aspect confirms the validity of two wild rice species of same AA genome
and there is distinct speciation between perennial O. rufipogon and annual O. nivara
populations (Samal et al. 2018).

4. WEEDY RICE: MYSTERY IN EVOLUTION

Weedy rice appears as hybrid swarms due to introgression of genes between wild
and cultivated species in nature. In Asian rice, it is known as Oryza spontanea whereas
in African context it is said as O. stapfii. It grows faster; produces more tillers, panicles
and biomass; makes better use of available N; shatters earlier; has better resistance to
adverse conditions; and possesses longer dormancy in soil. Because of its high
competitive ability, it becomes a serious threat to rice growers worldwide. It is also
called as red rice because of its red pericarp. One of the major constraints/bottlenecks
to attain the potential yield target of the present improved rice cultivars is considered
due to the contamination of weedy rice in the cultivated areas. Due to conspecific
form of cultivated rice makes similarity of morphological and physiological appearance
between weedy rice and cultivated rice in the field, it is very difficult to discriminate
the weedy rice phenotypically from the cultivar/variety of rice at the vegetative stages.
Therefore, chemical control measures to manage weedy rice in conventional rice
cultivars are not advisable. Some weedy rice also have inherited traits linked to wild
rice such as red pericarp, black hull, long awn, light seed weight, strong seed dormancy
and easy seed shattering which leads to loss of grain during harvesting in the field.
There is also very high level of genetic variability and plasticity found within and
among weed populations (Green et al. 2001) as the growth of weedy rice varies
considerably among different biotypes due to differences in plant height, tillering, or
leaf-producing capacity. Since, evolution of the weedy rice is not completely
understood, a preliminary study was conducted to evaluate the genetic diversity of
weedy rice lines found in the state of Odisha which includes seventy five weedy rice
collected from different locations of Odisha, India of which fifteen wild rice (six
accessions of Oryza rufipogon, nine accessions of Oryza nivara), six cultivated rice
including three each of landraces and high yielding cultivars (Ngangkham et al. 2016).
A set of SSR molecular markers from different chromosomes were used for diversity
analysis in 96 weedy rice and found to be robust enough to be used for diversity
analysis. The observed heterozygosity (Ho) in analysis was found low which might

Rice Genetic Resources: Collection, Conservation,

20 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

be due to autogamous nature of rice crop (Nachimuthu et al. 2015) and less segregation
or selection of stable progenies in the present samples. The genetic diversity was
found to be higher than the other weedy rice populations studied. The genetic similarity
coefficient of the whole 96 samples varied from 0.60 to 1 and distributed in different
clusters. This result suggests a complex and unclear evolutionary process of weedy
rice in Odisha, India. Thus, the considerable higher level of genetic diversity in weedy
rice lines of Odisha indicates a complicated type of origin of weedy rice in this region
of India which might be due to either adoption of direct seeded rice growing technique
in this region or reduced weed control practices owing to limited human labour input.
The genetic similarity coefficient of the whole 96 samples varied from 0.60 to 1 and
diversifying the whole weedy rice lines into distinct groups after their evolution.
Thus, the present investigation revealed that the origin of some of the weedy rice of
Odisha is probably through the hybridization between the wild rice and rice cultivars
cultivated in the nearby areas by the farmers.
Recent changes in farming practices and cultivation methods along with less
weed management may have promoted the re-emergence and divergence of weedy
rice. The abundant genetic diversity of weedy rice populations accompanied by the
changes of farming practices may complicate weedy rice control in future and
consequently threaten rice production. Thus, effective methodologies for weed control
and management must be developed to prevent weedy rice from extensive spreading
and infestation.

5. NERICA RICE
West Africans domesticated Oryza glaberrima about 3,500 years ago. The Asian
species O. sativa reached Africa about 450-600 years ago and slowly displaced the
native rice because of low harvest. By the 1990s, native African rice was reduced to a
few pockets on scattered farms. Then Sierra Leonean plant breeder Monty Jones and
his colleagues found a way to create a fertile hybrid between African and Asian rice.
Called “Nerica” (New Rice for Africa), it could yield a bumper harvest like its Asian
parent, but it was as tough as its African side, resistant to drought, pests and diseases.
Scientists have bred many varieties of Nerica and farmers have started growing
them. This new rice, descended from an endangered species, is helping Africa to feed
itself, yet this opportunity would have been lost if O. glaberrima had gone extinct.

6. EXPLORATION AND COLLECTION OF RICE

GERMPLASM
In the past, the scientists involved with crop improvement programme at different
research stations undertook the evaluation of germplasm and identified several donors.
They were utilized for crop improvement program and 394 varieties were recommended
for general cultivation, as pure line selections. In 1955, when Dr. N. Parthasarathy was
Director, the NRRI undertook its first planned exploration and collection mission of
rice germplasm in the erstwhile Jeypore tract (now Koraput district of Odisha). The
collection programme continued for five years (1955-59) by a team of scientists led by

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 21
Dr. S. Govindaswami and supported by a scheme sanctioned by the ICAR. This
mission was popularly known as Jeypore Botanical Survey (JBS) and was the first of
its kind, ever organized in the world to collect rice germplasm (Chang 1989). The team
explored about 27,000 km2 and collected a total of 1,745 cultivated rice and 150 wild
rice accessions (Govindaswami and Krishnamurty 1959). Recently in 2010, FAO
recognized Koraput region as one of the Globally Important Agriculture Heritage
Systems (GIAHS). Later when Dr. R.H. Richharia became Director of NRRI, he
introduced 67 varieties from Taiwan, tested them, two or three cultures were dwarf
types and one of them was identified as Taichung Native 1 (TN 1) which laid the
foundation for Green Revolution in the country. Simultaneously, a PL-480 project on
collection of rice germplasm was operative in North east during 1967-72 with Dr. M.S.
Swaminathan and Dr. S.V.S. Shastry at IARI, New Delhi and was popularly known as
Assam Rice Collection (ARC). During 1970-79, a special programme was undertaken
to collect rice germplasm from all the rice growing districts of Madhya Pradesh by Dr.
R.H. Richharia after he left NRRI in 1969. He explored 42 districts and collected a total
of 19,226 accessions which formed the Raipur Collection. A special drive for upland
paddy varieties under cultivation in Andhra Pradesh, Karnataka, Maharashtra,
Madhya Pradesh, Uttar Pradesh, Odisha and West Bengal further resulted in collection
of 1,938 cultivars. In 1975, a comprehensive exploration and collection programme
was drawn for the whole country especially for the traditional rice growing areas of
Karnataka, Maharashtra, Madhya Pradesh, Uttar Pradesh, Bihar, West Bengal and
Odisha covering 30 districts of 7 states. This programme was popularly known as
National Collection from States (NCS) and resulted in collection of 1,038 accessions.
Increased interest in herbal medicines during last few decades has necessitated
collection of rice germplasm with special emphasis on their medicinal value from
Bastar region of Chhattisgarh and Kerala for the world famous ‘njavara’ rice. During
recent evaluation, few landraces/farmers’ varieties from Assam have been found to
have high level of protein (14-15%). Traditional landraces like Bindli from Uttar Pradesh
is now reported to have high Zn (>50 ppm) in brown rice apart from having strong
aroma. Studies on the evolutionary changes in the traditional varieties grown in
particular regions have been started to find out the reasons of disappearance/extinction
of primitive varieties/landraces for the farmers’ field (Chourasia et al. 2017).

7. COLLECTION OF TRAIT SPECIFIC GERMPLASM

7.1. Medicinal rice
The documentation of indigenous traditional knowledge on the medicinal and
nutritional significance of red rice is another aspect which is gaining momentum due
to recognition of njavara rice of Kerala as one of the regions of Geographical Indication
(GI) of Goods Act 1999 under the Intellectual Property Right. This was the first time
that a rice variety of Kerala received GI Registry in 2008. Studies found that njavara
has increased level of protein and amino acid in the organically grown seeds; thus it
should be developed as baby food and a health product to save this wonder rice from
extinction. Seventy two accessions of rice germplasm were collected from Bastar
region of Chhattisgarh in which some medicinal rice namely Gudmatia, Bhejari, Danwar,
Baisur, Gathuwan were also reported.

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22 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

7.2. Saline tolerant rice

Fifty one accessions of saline tolerant rice mostly from Pokkali region of Kerala
(one of the potential regions for GI) were collected, characterized and evaluated for
better utilization.
7.3. Basmati rice
Eighty eight accessions of long slender basmati rice germplasm were collected
from eight districts of western Uttar Pradesh and six districts of Haryana state in
collaboration with NBPGR during early 1990s.
7.4. Aromatic short grained rice
Sixty seven accessions of short grained scented rice ‘Kalanamak’ germplasm
were collected from eastern Uttar Pradesh, which has been evaluated.
7.5. Boro rice
A total of 208 accessions of Boro rice germplasm were collected from Assam,
north Bihar, north Bengal and eastern Uttar Pradesh during early 2000.
7.6. Bao rice
About 126 accessions of Bao rice germplasm were collected from deep water
areas of Assam and Meghalaya, and evaluated for utilization in breeding programme.
7.7. Aman rice
A set of 69 accessions of Aman rice germplasm were collected from West Bengal.
7.8. Cold tolerant rice
A set of 116 accessions of cold tolerant rice germplasm were collected from hilly
regions of Arunachal Pradesh.
7.9. Wild and weedy rice
About 495 accessions of wild rice germplasm (O. nivara, O. rufipogon, and O.
coarctata (Syn: Porteresia coarctata) were collected in 12 exploration trips from
Odisha and West Bengal under National Agricultural Technology Project (NATP).
Apart from this about 223 accessions of weedy rice (O. sativa f. spontanea) have also
been added to the gene pool.
7.10. Specialty rice
Attempts are on to collect aromatic rice, soft rice, wine rice, glutinous or waxy rice,
colour rice (brown, green, black, red), beaten rice, pop rice, organic rice, nutritional
rice etc.

8. GERMPLASM INTRODUCTION
When the International Rice Commission (IRC) recognized NRRI as a centre for
the maintenance of world genetic stocks of rice, many varieties of south and Southeast

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 23
Asian countries were introduced to the country for their maintenance at NRRI, this
provided an opportunity to Indian scientists to test and recommend few of them for
general cultivation in the country. Since its inception in 1946 till 1977, Director, NRRI
continued to remain in charge of overall supervision of the world genetic stock for
multiplication and maintenance of the FAO designated germplasm being run at 5
countries i.e. India, Indonesia, Japan, Pakistan and USA. The world genetic stock
was comprising of japonicas, indicas, bulus and floating types. Again, when NRRI
was recognized as the main centre for the inter-racial hybridization programme between
japonicas and indicas during 1950-1964, many exotic japonica rice germplasm were
introduced into India. The participants of the southeast and south Asian countries
came with their own rice varieties for hybridization. This further provided opportunity
to Indian rice scientists to study the varieties of other countries. Some of the japonicas
when tried in temperate hilly regions were found suitable for direct introduction.
Many japonica varieties (Aikoku, Asahi, Fukoku, Gimbozu, Norin 1, Norin 6, Norin 8,
Norin 17, Norin 18, Norin 20, Rikuu 132, Taichu 65) were crossed with the popular
varieties of Odisha (T 90, T 812, T 1145, BAM 9) and the progenies were grown at the
three Rice Research Stations (Bhubaneswar, Berhampur and Jeypore) for further
selections. In all, 192 improved local varieties were selected and a total of 710 different
indica x japonica crosses were made. The F1 seeds were distributed to many countries
for further crop improvement programme. Only four varieties were released; Malinja
and Mahsuri released in Malaysia, ADT 27 in Tamil Nadu state of India and Circna in
Australia.

9. GERMPLASM CHARACTERIZATION, DOCUMENTATION

AND SEED SUPPLY
Characterization is the description of plant germplasm, which involves determining
the expression of highly heritable characters ranging from morphological or
agronomical features to seed proteins or molecular markers. It results in better insight
in the composition of the collection and the coverage of genetic diversity. Every year
new germplasm accessions are collected and conserved in Gene bank of NRRI which
is characterized for utilization in the breeding programme. So information on germplasm
also helps to facilitate the exchange of materials and information among gene banks
and help the users in experimenting with conserved germplasm.

10. STATUS OF RESEARCH

At National Rice Research Institute, all the germplasm collections including wild
and weedy rice are characterized at appropriate stages of plant growth and maturity
for agro-morphological traits based on the descriptors which include 19 qualitative
and 11 quantitative characters. These materials after characterization are harvested,
processed, packed and sent to National Gene Bank for long term storage (LTS) and
also a set of it is conserved at ICAR-NRRI under medium term storage module. The
details of germplasm characterized at NRRI during last five years are given in Table1.

Rice Genetic Resources: Collection, Conservation,

24 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Table 1. No. of germplasm characterized during last five years (2012-17).

Year No. of accessions characterized Type of germplasm
2012-13 2545 Released varieties and land races of India
2013-14 600 Landraces of India
2014-15 6406 Landraces, wild and weedy rice of India
2015-16 5800 Landraces, wild and weedy rice of India
2016-17 5800 Landraces, wild and weedy rice of India

With the aim of creating database, 14000 accessions of morphologically

characterized rice germplasm were documented (Tables 2 & 3). The data revealed that
majority of the accessions were with green basal leaf sheath, green leaf blade, well
exserted panicle, intermediate type, long fully awned, intermediate threshing, white
kernel colour, some aromatic, erect flag leaf and fast leaf senescence type (Fig. 1).

Fig. 1. Variations observed in qualitative characters of 14000 rice germplasm accessions

Table 2. Important donors identified against major diseases.

Possible donor for resistance
Diseases Landraces Improved Varieties
Blast Tetep, Tadukan, Gampai, Peta, ADT 29, ADT 25, CO 43,
(Pyricularia Sigadis, Dular, Kalamdani, Tarabali, MTU 3626, MTU 6203,
oryzae) Mugisali, Madrisali, Sollpona, MTU 7014, MTU 9992,
Rongaahu, Manoharsali, Andrewsali, WGL 26889, WGL 47969,
Gajepsali, Beganbisi 2, Rongagutia, WGL 47970, MTU 993,
Kolimekuri, Rikhojoi 2, ARC 7098, BJ-1, NLR 145, PTB 10,
AC-55 (CH-55), AC-8368 (BJ-1), NLR 36, CO 4, CO 25, CO 29,
AC-8369 (S-67), SM-6, SM-8, SM-9, CO-30, MTU 9993, Saleem,
CP-6, AC-293 (AKP-8), AC-294 Thikkana, Kotha Molagoli,
(AKP-9), AC-360 (PTB-10), Kulu-72, Pinakini, Swarna muli
AC-26904 (Tetep), Fukunishike CO-4, Dular, Vajram, Prahlad, Lacrose-
CO-29, Tadukan, Zenith, Carreon Zenith-Nira, BJ1, Karjat,
Contd.....

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 25
 Possible donor for resistance
Diseases Landraces Improved Varieties
Bacterial Dholamula, Moinasail, Kartik kolma, Pallavi, TKM 6, Sigadis,
leaf blight Japorisali, Gajepsali, Jatiosali, Pelita 1, MTU 15, MTU 16,
(Xanthomonas Kola ahu, Ahusuri, ARC 5827, ASD 5, T 1069, ARC 18562,
oryzae) AC-33523 (Tarical), AC-33557 MTU 4870, MTU 2400,
(Dulla karma), AC-33562 (Kangpui), MTU 3626, MTU 6203,
AC-3094 (TKM-6), AC-8368 (BJ)-1, MTU 7014, MTU 9992,
AC-26903 (DV-85), Chinsurah boro-II, Swarna, PLA 9180, BPT 3291,
Somera mangga, Wase Aikoku 3, Mahsuri, RNR 10786,
Malagkit, Sung son PNR 2736, RNR 4970,
RNR 10208, AS 330.
Rice Tungro Kataribhog, Latisail, Sigadis,
Virus Ambemohar, Habiganj, ARC 14766 BJ 1, PTB 18, W 1263, Gampai
(Nephotettix 15, Pankhari 203, ARC-7125,
malayanus) ARC-7149, DW-8, AC-368
(PTB-18), AC-5079
(Kataribhog), Bhagirathi,
Boitalpakhia, AC-34558
(Nalini), AC- 17933 (Kamod-
153), AC- 34650 (Usha),
AC-273 (ADT-20), AC- 297
(ASD-1), AC-304 (CO-1),
AC-315 (CO-12), AC-351
(PTB-1), AC-360 (PTB-10)
AC-3094 (TKM-6), AC-8396
(CB-1)
Helmintho Bhatta Dhan. Ch 13, Ch 45, BAM 10,
sporium oryzae AC 2550, ADT 29, CO 29.
False smut Sugandha, Sabari, Karna, Deepa, Sona, Udaya, CO 9, IR 62, MNP 85,
(Ustilaginoidea ARC 5378, AC-26570 (ADT-33), BR 16, IR 24, IR 29.
virens) AC- 40119 (PTB-23), AC-40124
(PTB-26), AC- 3070 (PTB-32)
Stem rot -- Basmati 370, Bara 62
(Helminthosporium
sigmoideum)
Ragged stunt -- PTB 21, PTB 33
virus
Grassy stunt Oryza nivara
virus
Sheath rot Bhatta Dhan AC- 26904 (Tetep), Ram Tulasi
(Sarocladium
oryzae)
Brown Spot Katak tara, Bhut muri, BAM 10,
SR-26B, CH-45, CO-20

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 Rice Research for Enhancing Productivity,
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Table 3. Important donors identified against major insect pests.

Donors
Insect Land races Improved Varieties
Brown Plant Dhoiya Bankoi, Sahiba, Salkathi,
Hopper (BPH) ARC-6650 (Gomiri bora), AC-34969 Leb Mue Nahng, Udaya,
(Nilaparvata (Baidya raj), AC-34993(Ghusuri), CR 1009, PTB 18, Vajram,
lugens) AC-34997(Jhupjhupa), AC-35014 Pratibha, Nandi, Chaitanya,
(Nal dhan), AC-371 (PTB-21), Krishna veni
AC-40634 (PTB-33), AC-30300
(MR-1523), AC-35184 (Dhoba
numberi), AC-35228 (Jalakanthi),
AC-35066 (Banspati), AC-35070
(Panidubi), AC-35108 (China bali),
AC-17912 (Ganga sagar), AC-20363
(Kalachudi), Tarapith, Haldi ganthi
ARC 7080, ARC 14766, NCS 91,
NCS 131, NCS 707, Milyang-55,
PTB 43, PTB 21, ARC 6248,
ARC 6605, ARC 6619, ARC 5757,
ARC 6158, ARC 6102, ARC-6650
(Gomiri bora), AC-34969(Baidya raj),
AC-34993(Ghusuri)
Gall Midge ARC 5984, ARC 10660, ARC 6605, Eswarakora, Siam 29,
(Orseolia oryzae) Leuang 152, ARC 5959, ARC 13516, OB 677, CR 94-1512-6,
ARC 14787. HR 13, HR 14, Ratnachudi, Shakti, PTB 18, W 1263,
Eswarakora, HR 12, HR 42, HR 63, Surekha, Orumundakam,
AC-35(Ningar small), AC-39 Velluthicheera, W 1263,
(CNAB white rice), AC-210(Bhadas-79), WGL 20471, WGL 47970,
AC-391(Bikiri sannam), ARC-5984 Pothana, Phalguna, RP 140,
(Suto syamara), ARC-10660, ORS 677, CR157-212,
ARC-12508(Khauji), ARC-12586 CR157-303, Kakatiya, Divya
(Vale matse), ARC-12588 (Amamma matse),
ARC-12670(Nien sah), ARC-13166 (Jaksa),
ARC-13210(Yangbelok), ARC-14915
(Maich dol), ARC-14967(Galong),
AC- 352 (PTB-2), AC- 362 (PTB-12),
AC- 371 (PTB-21), PTB-24, AC-26704
(Phalguna) and Leaung-152
White Backed ARC 5803, ARC 6064, ARC 7138, IET 6288
Plant Hopper ARC 7318, ARC 10340
(Sogatella furcifera)
Stem Borer ARC 6158, ARC 10386, ARC 10443, TKM 6, CB I, CB II,
(Chilo NCS 266, NCS 336, NCS 464, Manoharsali
suppressalis) ARC 5500, W 1263, AC-3094
(TKM-6), AC-392, AC-267 (ADT-14),
AC-8396 (CB-1), AC-344 (MTU-15),
AC-20006 (JBS-1638), Tepa-1

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 27
 Donors
Insect Land races Improved Varieties
Green Leaf ARC 6606 PTB 2, PTB 21, ADT 14,
Hopper (GLH) Vijaya, ADR 52
(Nephotettix spp.)
Leaf Folder ARC 1129, Gorsa, Darukasali, PTB 12
(Cnaphalocrocis AC-33849 (Bundei), AC-35034
medinalis) (Hari sankar), AC-33831 (Sunakathi),
AC-33832 (Surjana), Juli, AC-35338
(Saru chinamali)
Yellow Stem borer AC-33515, AC-33526, AC-33538,
AC-33563, ARC-5984, AC-30300
(MR-1523) and AC-30349 (Aganni)
Nematode AC-26594 (TKM-6), AC-40083
(MTU-17), AC-467 (Lalnakanda-41),
Hasma, Bahagia, AC-40509 (Manoharsali),
Amla, AC-17134 (Sathia), AC-22899
(Anang), AC-23652 (Kalakeri),
Kanyakaprashant

10.1. Sharing of germplasm for Rice improvement programme

Supply or distribution of rice germplasm is an important mandate of the institute
for the utilization in crop improvement programmes of the country. Germplasm are
supplied to various institutes/organizations through proper signing of Material
Transfer Agreement (MTA). Total germplasm supplied to various institutes/
organizations during last five years is detailed in Table 4.
Table 4. No. of rice germplasm accessions distributed within and outside institute.
Year Within institute Outside organizations Total
2012-13 2261 1929 4190
2013-14 1466 362 1828
2014-15 4821 458 5279
2015-16 5245 237 5482
2016-17 4937 254 5191
2017-18 3075 177 3252
Total 19544 1488 21032

10.2. Germplasm evaluation and utilization

The genetic erosion has been very fast in recent years due to rapid modernization
of the society and genetic diversity has been replaced by introduction of few high
yielding varieties. Farmers are leaving their own traditional varieties and growing the
improved cultures thereby many of the landraces have become extinct. The need for
both in situ and ex situ conservation is now felt as the paddy cultivation in the
country is largely affected by extreme natural calamities after rapid climate change,

Rice Genetic Resources: Collection, Conservation,

28 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

through an erratic monsoon. Earlier the biggest challenge was flood, but subsequently
other factors like salinity after frequent cyclones and sea water surge, temperature
rise and drought like situation in many parts of the country have put the challenge
before rice researchers to incorporate these genetic factors in the plant.
The importance of genetic resources is widely recognized. Activities in germplasm
banks demand qualified researchers in several areas of knowledge. Besides, the
conservation of genetic variability for the future, the actual utilization of available
accessions is another important goal. The main factors responsible for the low utilization
of plant genetic resources are lack of documentation and adequate description of
collections, accessions with restricted adaptability, insufficient plant breeders
particularly in developing countries and lack of systematic evaluation of the collections.
Low seed availability due to inadequate seed regeneration programs is another barrier
to their use (Dowswell et al. 1996). Furthermore, breeder-to-breeder exchange materials
are very common and constitute a reasonable alternative to extend genetic variability
in breeding programs.
Besides biotic stresses, rice crop frequently faces problems of drought, low
temperature, submergence, water-logging, salinity/alkalinity etc. These abiotic stress
situations cause drastic reduction in yield and thus varieties with in-built resistance
to such stresses are desirable. The germplasm having resistance to such stress
situations have been identified (Table 5). The All India Coordinated Rice Improvement
Project (AICRIP) was launched in the year 1965 and thereafter, more systematic
evaluation against major biotic stress situations was undertaken with multi-location
field screening followed by greenhouse evaluation.
After repeated screening of thousands of rice germplasm in simulated condition
for different abiotic stresses, some landraces were identified as tolerant to complete
submergence. They are Khoda, Khadara, Kusuma, Gangasiuli, Atiranga, Ande Karma,
Nahng tip, Kalaputia and so on. In some areas crop suffers from floods when it is
submerged under water for up to 10 days. Rice cultivars cannot survive such prolonged
submergence. Few rice cultivars have been identified which survive submergence up
to 80 cm water depth, for 10 to 12 days at early vegetative stage of the crop. Genetic
analysis of one such cultivar, FR 13A revealed that tolerance to submergence is
controlled by one major gene. Using FR 13A as a donor, improved rice cultivar, Swarna
Sub 1 has been developed and released in India which is gaining popularity among
the farmers.
Direct seeding is common in rainfed lowlands. In eastern India sometimes early
rain causes water stagnation in the field just after sowing which results in poor crop
establishment. Two cultivars namely Panikekoa, AC 1631 and T 1471 have been
identified as anaerobic seeding tolerant germplasm. The anaerobic seeding establishes
the crop under water, reduces cost of cultivation, saves crops from birds and rat
damage, reduces weed growth and thereby herbicide application accounting all these
towards organic farming. Similarly, several new donors were identified for salinity
tolerance at seedling stage and they are Pokkali, Orumundakan, Rahaspanjar, Bhaluki,
Kamini, Matchal, Ravana, Gitanjali and Talmugur apart from the most popular variety

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 29
Table 5. Important donors identified against abiotic stresses.
Donors
Stress Land races Improved Varieties
Drought Mahulata, Brahman nakhi, Zingsaingma CR 143-2-2, N 22,
tolerance (AC-9387, MNP-387, IC0593953), MTU 17, Kalakeri,
Sathchali, Nepalikalam, Kodibudama, Janaki, AS 313/11, AS 47,
NC 487, Dagaranga, Mettamolagolukulu, Aditya, Tulsi
NC 488, ARC 10372, NC 492, AS 180,
Hasakumra, Maibi, Koijapori, Bairing,
Ahu joha, ARC 10372, Noga ahu, Soraituni,
Lakhi, Pera vanga, Bodat Mayang,
Prabhabati, O. nivara (BCPW-30,
AC-100476, IC-330611) and O. nivara
(SRD 01-17 , AC-100374, IC-330470),
AC-254, AC-263, AC-304, AC-511,
AC-2298, AC-3035, AC-3111, AC-3577,
AC-9066, AC-9387, ARC-7063, AC-45
(CH-45), AC-40083 (MTU-17), W-691,
AC-467 (Lalnakanda-41), AC-35207 (Dular),
AC-37077 (Dhan gora), AC-37127 (Black gora),
AC-37291 (Kalakeri), AC-8205 (Surjamukhi),
AC-34440 (Salumpikit), AC- 34256
(Kabiraj Sal), AC- 34296 (Bombay murgi),
AC-34992 (Sal kain), AC-35021 (Kalon dani),
AC-35038 (Godhi akhi), AC-35046 (Nadi tikar),
AC-35059, (Phutki bari), AC-35060 (Bhuska),
AC- 35143 (Baihunda), AC-35452 (Karama)
Cold Tolerance AC 540, Siga, Rajai, CB 1,Dholiboro, Boro 33, IRGC 100081,
Dunghansali, Raja Sanula 10114, 10028, Barkat,
Kalinga 2, Tella Hamsa,
Satya, Gavinda
Submergence Bhundi (JRS-9, AC 42091, IC575277), --
Tolerance Atirang, Kalaputia, Kusuma, Gangasiuli,
Solpona, Sail badal, Dhola badal, Kolasali,
Boga bordhan, Rongasali, Khajara, Dhusara,
Nali Baunsagaja, FR 13A, FR 43B,
Chakia 59, CN 540, S 22, Madhukar,
AC-24682 (FR-13A), AC-35741(Telgri),
AC-35323(Chaula pakhia), AC-35675(Biesik),
AC-36107(SL276), AC-36470(Khoda),
Khadara, AC-26670(Janki), AC-40844
(Manasarovar), Sarumuli, AC-40916 ( Jalamagna),
AC-40604 (Jaladhi-1), Kanawar
Deep water Nagari bao, Kekoa bao, HBJ 1, Jalamagna, --
Jaladhi 1, Jaladhi 2
Coastal Saline/ Cherayi Pokkali (AC 39416, IC413644, SR 26B, Getu, Dasal,
Alkaline NC/03-98), Paloi (AC 42169,JRS-100), Patnai 23, Pokkali,
Rupsal (AC 42465,PSS-74), Talmugur Hamilton, CSR 10,
(AC 43228), SR-26B, AC-8532 (Pokkali), CSR 13, CSR 18, Vikas,
Pateni-2, AC-41360 (Nonabokra), AC-35255 Co 43
(Rahaspanjar), Canning 7, Ravana
Water- logging Tilakkachari, NC 496, Kalakher sail Jhingasail, Patnai 23

Rice Genetic Resources: Collection, Conservation,

30 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

SR 26B. Drought is another major abiotic stress that adversely affects the crop leading
to low productivity. While screening repeatedly over the years, few landraces have
been identified as tolerant to vegetative stress drought and they are Mahulata,
Sunamani, Naliakhura, Ranganatha Bao, Bhuta, Bibhisal, Brahman Nakhi, Salkain,
Gauranga, Karinagin and Kiaketi. Some of such unique germplasm have been registered
(Table 6) with NBPGR for special attention and utilization in rice improvement
programme across the country.
Table 6. Registration of Unique Rice Germplasm with ICAR-NBPGR.
Name of Year of Registration Important
Sl. No. germplasm registration no. trait
1. Khoda (PD -27) 2004 INGR No. 04001 Tolerance to
complete
submergence
2. T-1471(Kodiyan) 2005 INGR No.05001 Tolerance to
anaerobic
seeding
3. Khadara (PD33) 2008 INGR No.08108 Tolerance to
complete
submergence
4. Atiranga (RM5/232) 2008 INGR No.08109 Tolerance to
complete
submergence
5. Kalaputia (PCP-01) 2008 INGR No.08110 Tolerance to
complete
submergence
6. Gangasiuli(PB-265) 2008 INGR No. 08111 Tolerance to
complete
submergence
7. Kusuma (PD-75) 2008 INGR No.08113 Tolerance to
complete
submergence
8. Mahulata (PB-294) 2008 INGR No.08112 Tolerance to
vegetative
stage
drought
9. Medinapore (RM5/AK-225; 2010 INGR No. 10147 Tolerance to
IC-0258990) complete
submergence
10. Andekarma (JBS-420; IC-0256801)- 2010 INGR No.10148 Tolerance to
complete
submergence
11. Champakali (IC-0258830)- 2010 INGR No.10149 Tolerance to
complete
submergence
Contd.....

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 31
 Name of Year of Registration Important
Sl. No. germplasm registration no. trait
12. Brahman Nakhi (DPS-3) 2010 INGR No.10150 Tolerance to
vegetative
stage
drought
stress
13. Sal kaiin (PB-78;IC-0256590) 2010 INGR No.08112 Tolerance to
vegetative
stage
drought
stress
14. Bhundi (JRS-9; IC0575277; 2014 INGR 14025 Tolerance to
AC42091)- complete
submergence
and having
shoot
elongation
ability
15. Kalaketki (JRS-4; IC0575273; 2014 INGR 14026 Tolerance to
AC42087)- 20 days
complete
submergence
16. CR 143-2-2 (IC0513420) 2017 INGR 17019 Tolerance to
both
vegetative
and
reproductive
stage
drought
stress
17 Salkathi (AC-35181; PB-289) 2018 INGR17069 Resistance
to brown
plant
hopper
(BPH)

10.3. Conservation of Rice Germplasm

Due to the danger of genetic erosion, the effort of developing a cold storage
system for rice germplasm was initiated at NRRI in 1984. Meanwhile, during 1986, it
was decided to conserve all the germplasm of NRRI at the National Gene Bank. Since
then, more than 30,000 rice germplasm accessions have been deposited in the long
term storage (LTS) of NBPGR. Under the aegis of the Indo-USAID collaborative
project, a cold module was gifted to NRRI. The facility became operative in 1998 with
a controlled temperature of 4±2 oC and 33±5% RH and found to be rather dependable
and is meant for medium term storage (MTS) and the seeds are kept viable for 6-8
years. When accessions in the MTS working collection drops below 50 g after seed

Rice Genetic Resources: Collection, Conservation,

32 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

supply to indentor or if seed viability falls below 85%, then the accession is
rejuvenated. The japonica varieties are monitored more frequently than indica rice
as they have an inherently shorter storage life than indica varieties.
The seeds of each of the accessions are dried for reducing the moisture content
up to 10-12% and kept in 3-layered aluminum foil pouches for medium term storage.
The outer layer of the pouch is polyester of 12 micron; intermediate layer is aluminum
of 12 micron and the innermost layer is polythene of 250 gauges. These aluminum foil
pouches are stored in cold module at a regulated temperature of 4 ºC and 33% relative
humidity (RH).
There are about 106,000 accessions of rice germplasm conserved in NGB at -18 ºC
and with 3-4% RH. After thorough evaluation and screening thousands of germplasm
lines over the years, the NRRI has identified several donors resistant/tolerant to
different biotic and abiotic stresses as shown in Tables. Utilising these donors in the
breeding programme, the Institute has so far released 128 varieties for different rice
ecosystems. In the past, NRRI was supplying the germplasm even to the foreign
agencies, but in the context of IPR regime, the sharing of germplasm has been restricted
to the researchers within the country.
Several categories of germplasm are conserved for different purposes. They are
as follows-
a) Working collection: A collection of germplasm maintained and used by a breeder
or other scientist for their own breeding or research, without taking any specific
measures to conserve. The collection may have a short life span and the
composition of the collection may vary greatly during its lifetime.
b) Active collection: A collection maintained by a gene bank and used as the source
of seeds for active use, including distribution, characterization and regeneration.
It is usually conserved under short- or medium-term storage conditions.
c) Base collection: A collection of seed ideally prepared and held in prescribed
conditions for long-term conservation. The seed should be conserved and never
used except for
i. periodic germination tests
ii. regeneration of samples conserved in long-term storage when their viability
decreases below threshold
iii. regeneration to replace stocks in an active collection after accumulating 3-
successive generations of regeneration from active collection and
iv. as the primary point of rescue when the accession is accidentally lost from all
active collections.
d) Seed file: A small sample of original seed, set aside when a seed sample first
arrives at the gene bank, to serve as the definitive reference sample. The seed file
should be maintained under dry conditions preventing disease or pest damage,
although not necessarily alive. Other seed samples of the same accession, e.g. for
every new harvest, should be visually cross-checked with the seed file.

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 33
e) Safety back-up: Duplicate samples of the base collection, stored in a different
gene bank, preferably in a different continent. The storage conditions in the
safety back-up should be at least as good as those in the corresponding long-
term collection. The holder of the safety back-up has no rights to use or distribute
the seed in any way or to monitor seed health or viability. Additional duplication
of the base collection to the Svalbard Global Seed Vault provides definitive safety
back-up in case of large scale loss of crop diversity. Svalbard Global Seed Vault
(SGSV) commissioned at Arctic island of Svalbard near Norway in North Pole in
2008 conserves about 0.8 million germplasm. It is managed by Norway’s Department
of Agriculture and the Global Crop Diversity Trust (GCDT) under the International
Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) and
supported by Bill & Melinda Gates Foundation. Recently, India has deposited 25
accessions of pigeon pea in April, 2014 as the 59th Nation.

11. KNOWLEDGE GAPS

Though many rice germplasm are conserved in the gene bank but information on
germplasm is not complete. Germplasm without characterization and evaluation data
cannot be utilized for crop improvement programme. Hence a systematic
characterization, evaluation and documentation of important traits against each
germplasm required to be done for its better utilization by the breeder.

12. RESEARCH AND DEVELOPMENT NEEDS

i. Activities related to genetic resources are characterized by high cost and long
term return. Introduction and germplasm exchange, collection, characterization,
evaluation, documentation and conservation are essential steps that cannot be
overemphasized.
ii. A database on agro-morphological traits of all germplasm conserved in gene bank
need to be prepared.
iii. Also a National/central rice data-base can be prepared in collaboration with the
research centers working in rice along with NBPGR.
iv. Research work should be oriented towards developing a core collection for better
management and utilization of the germplasm. Work in this line has been initiated
at this institute (Jambhulkar et al. 2017).
v. Human resource development by imparting training to persons engaged in PGR
activities is required for proper maintenance and conservation of germplasm.

13. WAY FORWARD

i. Germplasm is basic to crop improvement programs for sustainable agriculture. A
road map depicting collection sites need to be prepared so that areas which are
not covered in the map will be explored and germplasm will be collected and
conserved. Future collections should also aim at trait specific collection of
germplasm.

Rice Genetic Resources: Collection, Conservation,

34 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

ii. Wild and primitive populations are the reserves of cryptic variability and hence
their capacity for adaptive response is high. Such genetic variation is as important
as prevalent varietal diversity for genetic conservation. It is, therefore, important
to collect and conserve the wild and weedy rice germplasm.
iii. It has been estimated that even 5% of rice germplasm conserved in different gene
banks have not been utilized. Our research should be oriented towards developing
a core collection which represents the diversity of entire collection and removes
duplicate accessions that will enhance the use of germplasm by identifying diverse
source of parents and also will ease in evaluating the germplasm against biotic
and abiotic stresses.
iv. Identifying trait-specific genetically diverse parents i.e., salt tolerance, cold
tolerance, drought tolerance, early/late heading, low chilling, tolerance/resistance
to particular pests/diseases, adaptability to water logged habitats, tillering capacity,
root system, leafiness, etc., apart from quality characteristics are the primary need
of the plant breeder for trait enhancement. So identification of new diverse sources
will help in better utilization of germplasm in the breeding programmes, aimed at
producing agronomically superior cultivars with broad genetic base.
v. A rice seed file depicting photograph of individual germplasm may be prepared
for identification of germplasm and avoiding misrepresentation of germplasm.
vi. Future works should aim at characterizing the gene bank materials and creating a
data base for better utilization in breeding programme. Morphological and molecular
characterization of a core/minicore and trait specific subsets will further enhance
the usefulness of the germplasm accessions.
vii. Realizing the importance of genetic diversity, Jeypore tract of Odisha, the Palakkad
area of Kerala and Apatani valley of Arunachal Pradesh should be protected as on
farm in situ conservation sites.

14. CONCLUSION
The importance of genetic resources is widely recognized. Activities related to
genetic resources like germplasm introduction, exchange, collection, characterization,
evaluation, documentation and conservation are characterized by high cost and long
term return. Until recent past, conservation of rice germplasm was synonymous with
repeated rejuvenation in the field. This process of maintenance subjected the
germplasm to a threat of losing their identity because of random and non-random
processes due to sampling. Also loss due to unforeseen natural calamity of the type
of super-cyclone and flood devastating the native germplasm cannot be ruled out so
far on farm ex situ conservation is concerned.
In this chapter we tried to throw light on origin of rice and discussed about wild,
weedy and Nerica rice. Various PGR activities like exploration, collection, conservation,
characterization, evaluation, documentation, its status at ICAR-NRRI have been
elaborately discussed. This chapter emphasizes collection of trait specific germplasm
for its utilization in the breeding programme. The development of improved varieties

Rice Genetic Resources: Collection, Conservation,

Maintenance and Utilization 35
through introduction and evaluation of germplasm in this institute are also highlighted.
Future research work in creating a core/minicore collection and creating data base for
better utilization of germplasm are emphasized.
References
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Chang TT (1989) Domestication and spread of the cultivated rice In D.R. Harris and G.C. Hillman
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Chourasia M, Patra BC, Parida M, Prasad SM, Sethy S, Sarangi DR, Mohanta RK, Katara JL and
Samantaray S (2017) Inventorising the traditional rice germplasm in Cuttack district after
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Dowswell CR, Paliwal RL and Cantrell RP (1996) Maize in the Third World. West view Press,
Boulder, USA.
Jambhulkar N, Patra BC, Reddy JN and Sarkar RK (2018) Developing mini core of rice germplasm
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Govindaswami S and Krishnamurty A (1959) Genetic variability among cultivated rice of Jeypore
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Nachimuthu VV, Muthurajan R, Duraialaguraja S, Sivakami R, Pandian BA, Ponniah G, Gunasekaran,
Swaminathan M, Suji KK and Sabariappan R (2015) Analysis of population structure and
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mapping of agronomic traits in Oryza sativa. Rice 8: 30.
Ngangkham U, Katara, JL, Parida M, Mohanty M, Parameswaran C, Kumar A, Patra BC, Singh ON
and Samantaray S (2016). Assessment of Genetic Diversity of Weedy Rice (Oryza sativa
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Oka HI (1988) Origin of cultivated rice. Elsevier Publishing Company. Amsterdam.
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Rice Genetic Resources: Collection, Conservation,

36 Maintenance and Utilization
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Quality Seed Production and Maintenance

Breeding for Enhancing Rice Yield

RK Sahu, RP Sah, P Sanghamitra, RL Verma, NKB Patil, M Jena,

AK Mukherjee, MK Bag and ON Singh

SUMMARY
Indian seed production system is a robust route to mitigate the seed requirement
of the country. The seed class involves Nucleus, Breeder, Foundation and Certified
seed with different seed quality standard at different levels to safe-guard the production
of large quantity of quality seed for sustainable agriculture. The maintenance breeding
is a mandatory step for the institute who are involved in development of variety. The
developer maintains the seed purity of released varieties by curbing the chance of
out crossing and genetic drift. The quality seed is the first and prime requisite for
grain production, which alone contribute about 30% of yield improvement. Further,
seed traits such as seed dormancy, viability, priming, foliar spray etc. are being given
importance to improve cultivars for seed traits. Thus, it is important to deliver a
healthy, improved variety seed to meet the seed requirement of the country and to
dissect the seed traits for development of cultivar to cope with changing climate.
Availability of good quality seed at the right time wherever it is needed with agreeable
price, very much plays a major role in the highest grain production of a nation. The
Indian seed delivery system which is backed by both formal and informal seed system
has a good structural network for sufficient availability of seed but, the seed
replacement rate and the varietal replacement rate are under desirable limit; majority
of seed requirement of our farmer is fulfilled by informal seed system is one of the
major factor responsible for this. Gaps in seed systems which include non-availability
of many high yielding varieties in the seed chain, non-availability of sufficient quantity
of quality seed, deterioration in seed quality, long time span for seed quality testing
and non-assurance of genetic purity of Marker Assisted Selection developed varieties.
Possible solutions for different constraints to strengthen the seed system has been
discussed in the Chapter.

1. INTRODUCTION
Seed is an enigmatic genetic capsule essential for multiplication and establishment
of species from one generation to another. It is a fertilized ovule containing the plant
embryo, a unit of reproduction of a flowering plant, which is capable of developing
into another true-to-type such plant. Rice crop is a monocot; seed propagating, either
annual or perennial; hollow internode, with tillering habit and the apex bearing the
panicle. The rice seed is caryopses, comprising of embryo and endosperm. The seed
surface contains several thin layers of differentiated tissues that enclose the embryo
and endosperm. The palea, lemmas, and rachilla constitute the hull in Indica rice but

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 37
in Japonica the hull usually includes rudimentary glumes and perhaps a portion of the
pedicel.
Pure seed is the basic and important input for healthy crops and good production.
Seed should be pure, free from other contaminants, and should fit within minimum
seed standard as recommended. For this purpose, a seed production system in India
recognizes different class of seed viz., Nucleus, Breeder, Foundation and Certified
seed with different seed quality standard to safe-guard the quality of large quantity
seeds of Indian farmers. The maintenance of high quality seed of a variety is referred
as ‘Maintenance breeding’, where a breeder is maintaining the seed purity of a released
variety when it undergoes production year after year. This involves maintaining
morphological, physical and genetic purity of a variety for a long period of time.
These efforts were highly successful in improving seed quality by curbing the chance
of out crossing and genetic drift. Further, to exploit the potential yield of a rice variety,
various biochemical, physiological, and management aspects were viewed under
seed technological research programme. Therefore, seed traits such as, seed dormancy,
viability, priming, foliar spray etc. are being given importance by the researchers to
improve the cultivars. Thus, rice seed production and molecular dissection are now
the researchable areas to meet the seed requirement of the country and development
of cultivar to cope with changing climate. This chapter emphasizes the status of seed
production in rice, seed research and way for minimizing constraints to safe-guard
national seed security. The objective of the chapter is to highlight the status of (i)
breeder seeds as indented by DAC-GoI, States Government, and other organizations
of India, (ii)status of seed research (iii) methods and procedure involved in quality
rice seed production, and (iv) constraints involved and mitigation for seed production
and research.

2. IMPORTANCE OF QUALITY SEED

Seed is the first input of agricultural production on which the performance and
efficacy of other inputs depend. Good quality of seeds can contribute upto 30%
increase in productivity (Hasanuzzaman2015). “Good seed harvests good crop”, a
good seed means a seed lot that adheres to all the parameters of minimum seed
standard; this seed is generally termed as quality seed. A good quality rice seed
should be pure, full and uniform in size, free from weeds, insect, disease and other
inert matters and more over it should be viable (>80% germination).
Timely availability of good quality seed as per the requirement plays a major role
in the higher grain production of a nation. In India, 75% small and marginal farmers are
lagging behind in agriculture due to unavailability of resources or inputs including
seed. Therefore, a strong and vibrant seed production and supply system is
indispensable for food security of the country and accelerating growth in agriculture.
Seed is the highest prioritized input in agriculture, on which agriculture sustains.
Over past 70 years, improvement in seed system was targeted to secure the seed
quality, accessibility and availability.

Quality Seed Production and Maintenance Breeding for

38 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

A conscious thought on quality seed surfaced in1886 when channelized seed

production began with the establishment of Swedish seed association. The association
was mainly involved in production and distribution of quality seeds of forage crop
varieties. Later near about 19th century, Dr. E Helve established a seed testing laboratory
in Denmark for seed testing and certification. Canadian scientist Dr. JW Robertson in
proposed the production of foundation seed in 1917. In 1919 an International Crop
Improvement Association (ICIA) was formed to overlook the development of procedure
and standards for quality seed production and seed certification. However, the
organization was later named as Association of Seed Certification Agencies (AOSCA
1969). The ICIA in 1946 defined 4 classes of seed in forage crops, which was also
adopted for other grain crops in 1968.
In India, Department of Agriculture of Uttar Pradesh state produced and distributed
150 tons of wheat seed in 1900. During that period limited seed testing facility was
available at Kanpur. Later, in 1920 Government of Uttar Pradesh emphasized the
production and distribution of quality seed and initiated project for establishment of
seed godown in every subdivisions/tehsil. Later the Royal Commission on Agriculture
reviewed the production and distribution of seed in India in 1925. In 1945 private seed
company entered the seed scenario (like Sutton’s for temperate vegetables) and in
1946 All India Seed Producer’s Association (AISPA) was formed by private seed
growers. A report of Famine Enquiry Commission (1945) and Grow-More Food Program
Committee (1952) emphasized that there was a need to multiply and distribute the
quality seeds of improved varieties. So, in 2nd Five Year Plan (1956–61) a shape for
India’s formal seed system was designed with special emphasis on production of
nucleus and breeder seeds, which were used in multiplication of further class of
seeds.

3. IMPETUS FOR QUALITY SEED PRODUCTION

The important developments relating to seed sector in the country are highlighted
below in the Table 1.
In 1966-67 the seed production programme for wheat and maize was started and
after a year (1967-68) rice crop was also included. After a huge review and
recommendation, on 2nd October 1969 Indian Seed Act has been in force in India.
Indian Seed Act, 1966 is an act to provide measures for regulating the quality of
certain seeds for sale and for matters connected therewith. Some highlights of this act
are (i) constitution of Central Seed Committee by Govt. of India to advice Central and
State Governments regarding the Act., (ii) establishment of Central Seed Laboratory,
(iii) establishment of State Seed Lab for seed quality analysis, (iv) provision of
notification of varieties by Govt. of India, (v) minimum limits of germination and
purity of seeds and compulsory label fixing, (vi) notified seed standard fixed, (vii)
identifiable as seed of the variety it claims, (viii) must have minimum prescribed purity
& germination, (ix) seed container must bear labels containing correct particulars of
the seed, (x) establishment of Seed Certification Agency, (xi) establishment of Central

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 39
Table 1. Milestones in the development of Indian seed sector.
Year Event Objective/s
1952 A standing experts committee The committee formulated a programme
on seeds was appointed by structure to strengthen the seed
Indian Council of Agricultural production & distribution system under
Research (ICAR). which Central Govt. provided financial
assistance to the states.
1956-57 State Seed Farm Project was Different states started producing
initiated foundation seeds in State Seed Farms.
1957-1965 All-India Coordinated Project This involved production of foundation
for maize, wheat, pearl millets and certified seeds.
and barley
1959 An agricultural production team, To bring uniform standards of seed
by Dr. Johnson was formed certification, seed laws and establishment
of Seed Testing Lab for each States.
Planning Commission appointed To review the various aspects of seed
a Seed Multiplication Team programmes.
1960 ICAR set up a Committee To suggest ways for developing a strong
seed production programme. The
Committee recommended for
establishment of Central & State agencies
for the production of foundation seed and
an independent seed certification agencies
to safe-guard the quality seed. The same
committee also recommended for
enactment of National Seed Act and
formation of agencies for enforcement of
seed act.
1963 ICAR constituted a committee National Seeds Corporation was
established and Indian Seed Act was
enacted in 1966
1964 A rapid varietal release systems The State Variety Release Committees
for improved variety (SVRC) was established

Seed Certification Board to advise the Govt. of India and State Govt. on all matters
relating to certification, (xii) appointment of Seed Analyst for seed analysis in State
Seed Laboratory, (xiii) appointment of Seed Inspector to collect seed samples of
notified kind being offered for sale for analysis, and (xiv) forfeiture of property (seeds)
belonging to any person convicted under this act due to contravention of the
procedures under this act.
Further, first turning point in shaping an organized seed industry was through
National Seed Project (NSP) Phase-I (1977-78) which initiated the establishment of
State Farms Corporation of India (SFCI), 4 State Seeds Development Corporations
(SSDCs) and Breeder Seed Production (BSP) units. In the Phase-II of NSP (1985)13

Quality Seed Production and Maintenance Breeding for

40 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

additional SSDCs and 19 state seed certification agencies were established for quality
seed production. After 10 years (1988-89) a New Seed Development Policy was
formulated which gave access to the private individuals with strong R&D base for
product development.
To achieve the food grain demand in future, it was felt that the Seed Replacement
Rate (SRR) of various crops needs to be enhanced. This would require a major increase
in the production of quality seeds with the involvement of both public and private
sector. To safeguard the interests of Indian farmers and agro-biodiversity conservation,
and to guard the exploitation of farmers by unscrupulous elements, the National Seed
Policy (2002), a regulatory system, was formed. Later for regulating the production,
distribution, quality of seeds for sale, import, export and to facilitate production and
supply of seeds of quality and for matters connected therewith or incidental thereto,
a seed bill (2004) was proposed. The government has proposed new amendments to
the bill in April 2010 and November 2010, accepting most of the recommendations
given by the Standing Committee. Few highlights of the Seed Bill (2004) are (i) all
varieties of seeds for sale have to be registered, (ii) the seeds are required to meet
minimum standards, (iii) transgenic varieties only be registered after clearance certificate
as per the Environment (Protection) Act, 1986, (iv) exemption of farmers from the
requirement of compulsory registration (v) farmers are allowed to sow, exchange or
sell their own seed and planting material without any formalities required by registered
seeds but, farmers cannot sell seed under a brand name, and (vi) provision for claim
of compensation in case a registered variety of seed fails to perform to expected
standards.

4. REGULATION OF SEED SYSTEM

The national seed requirement is taken care of through formal seed system (FSS)
and informal seed system (ISS). Formal seed system is characterized by large scale
production of seed of officially released varieties with strict quality assurance
mechanism. This system is well organized and systematic, usually starts with
development of different types of varieties/hybrids. The principles in the FSS are to
maintain varietal identity, purity and to produce seed of optimal physical, physiological
and sanitary quality (Reddy et al. 2007). Formal seed system is managed by Government
body (Government Institutions, State Government Farms, University farms & KVKs)
and registered seed growers (NGOs, Private Companies) whereas ISS is managed by
farmers and sometimes private seed growers.
Varietal deterioration may happen with the repeated multiplication of the same
variety year after year. This deterioration accommodates mixture of seeds, undesirable
pollination or outcrossing, occasional mutation and genetic drift. This overall affects
varietal genetic purity and crop performance. This deterioration is taken care of in the
FSS through production of Nucleus, Breeder, Foundation and certified seed; but in
ISS it is not well guarded. Therefore, it is required to create awareness among the
farmers/seed growers to produce quality seed in their field for their own use.

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 41
 It is reported that more than 85% of the total seed sown in India is produced by
farmers themselves where quality seed constituted only 12% of the total seed sown
each year (Reddy etal.2007) which is responsible for reduction in10-20% of yield.

5. CONSTRAINTS IN SEED PRODUCTION AND SEED

RESEARCH
Indian seed production and supply system involves both Government institution
and private sector including many collaborative ventures. A huge institutional
framework is working for quality seed production and its distribution. Despite a
healthier seed supply channel, continuous supply of good quality seeds remains as
a problem from the seed producer to farmers. Therefore, farmers prefer to rely on their
farm saved seeds which limits the SRR below 20% in many states. Besides, the variety
replacement rate (VRR) is another section for maintaining the higher contribution in
production through quality seed. More than 900 high-yielding varieties and hybrids
of rice have been released for commercial cultivation, but about 318 are in the active
seed production chain. The constraints involved in seed production and distribution
are; seed purchase from unreliable sources, deterioration of seed quality when
multiplied for long duration, unavailability of quality seeds, lower SRR or VRR,
unawareness for method of seed production, time consuming seed quality testing,
and sometimes non-assurance of genetic purity of MAS developed varieties. Further,
the research on improvement on seed setting, seed dormancy, seed viability, seed
and seedling vigour is very little which restrict varietal features and its adoption by
farmer.

6. DEVELOPMENTS IN SEED SYSTEM AND SEED

RESEARCH
A rationalized system for breeder seed production programme is taken up by the
Indian Council of Agricultural Research (ICAR) Institutes and State Agricultural
Universities (SAUs). However, certified/quality seed production programme is taken
care by the National Seeds Corporation Ltd. (NSC), the State Seeds Corporations, the
State Department of Agriculture, State Seed Farms, State Agricultural Universities
Farms, Krishak Bharati Cooperative Ltd. (KRIBHCO), Private Seed Farms etc. to ensure
quality seeds supply to farmers.
The Indian seed production programme passes through 3-4 generations of seed
multiplication in a phased manner. The system provides an adequate safeguard for
seed quality assurance during multiplication to maintain the purity of the variety as it
flows from the nucleus seed to the seed for farmer (Certified or TL seeds). A large
number of seed companies and producers are being engaged in seed channel. To
regularize the system and to monitor the quality seeds produced, about 15 State
Seeds Corporation, 2 National level seeds Corporations, 34 State Departments of
Agriculture, 21 Seed certification agencies, 94 Seed testing laboratories, many ICAR
Institutes and State Agricultural Universities are jointly working in the seed platform.

Quality Seed Production and Maintenance Breeding for

42 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

7. SEED MULTIPLICATION CHAIN OF INDIA

Once a variety is released and notified it can be included in seed chain. The chain
of seed production is presented below-
Farmer (Variety wise requirements)
↓
DAO (District Agriculture Officers) (Collected the data on variety demand)
↓
DDA (Deputy Director Agriculture) (Assessment of varietal demand, crop
situation demand)
↓
Director Agriculture (actual indent to be placed, new variety to be introduced)
↓
DAC (Dept. of Agriculture & Cooperation) (National Indent of seed)
↓
Breeder seed producing organization (Produce the indented quantity of breeder
seeds)
↓
SSC & Director Agriculture (lifting of breeder seeds and putting in seed chain)
↓
Seed Production Chain
↓
DAO (Organization of seed distribution)
↓
Farmer (Growers)
Responsibilities of the organization that takes up seed production (as per the
class of seed) and the certification norms is presented below in Table 2.

Table 2.Seed class and institution involved in seed production.

Class of seed Institutes/Organization/Agencies Supervision Certification
Nucleus seed Developer, breeder, parent institutes Breeder, No need,
developers responsibility of
parent institution or
developers
Breeder Seed Developer, breeder, parent institutes, Breeder, Members
registered organization developers assigned by seed
certification agencies
Foundation Central Government agencies, State Concern Members assigned
Seed Departments, Agriculture Universities, producer by seed certification
State Farms, Private seed companies, agencies
Farmers producer organization
Certified Seed Central Government agencies, State Concern Members assigned
Departments, Private seed companies, producer by seed certification
Farmers producer organization, agencies
Agriculture Universities, State Farms
TL Seed Any organization and farmers Concern No need,
producer responsibility of
producer

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 43
 The breeder seed production status of the last five years revealed that the rice
breeder seed producing organizations have produced more than the quantity of seed
demanded every year (Table3).
Table 3. Trends in indent and production of breeder seed of rice (Chauhan et al.2017).
Year Indent (q) Production (q)
2012-13 5267 11455
2013-14 4837 10586
2014-15 4286 7757
2015-16 5026 5449
2016-17 5119 8765
More than 300 varieties are under seed chain but, few varieties had highest indent
among them. The year wise top five varieties of last five years were presented below
(Table 4). Among these varieties Swarna, Cottondora Sannalu, IR-64, Mahamaya and
Vijetha were released long years back and Sahabhagidhan, Swarna Sub-1 and Naveen
were released recently. The old varieties are still under demand, which may be due to
its higher adaptability, buffering capacity, consistent performance and also higher
tolerance to stresses.
Table 4. Top five varieties indented for breeder seeds in last 5 years.
S. No. Variety 2012-13 2013-14 2014-15 2015-16 2016-17
1. Swarna (MTU 7029),    
2. Cottondora Sannalu (MTU 1010)     
3. IR-64   
4. Mahamaya 
5. Vijetha (MTU 1001)    
6. Sahabhagidhan    
7. Swarna Sub-1   
8. Naveen (CR-749-20-2) 
Contribution of top most 5 varieties to 27.01 30.9 34.8 28.6 31.2
total indent (%)

From 2010 to
2015 about 355.18
lakh quintal quality
rice seed was
supplied, which
was an average of
71.03 lakh quintal
per year. The year
wise production
chart is presented Fig. 1. Distribution of certified/ quality seeds of paddy
(Anonymous 2016).
in Fig. 1.

Quality Seed Production and Maintenance Breeding for

44 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

The Government of India periodically assesses the requirement and availability

of seeds through State Governments and seed producing agencies in the bi-annual
zonal seed review meetings and the national kharif and rabi meet. The DAC&FW
facilitates the seed producing agencies to ensure the requirement of seeds to the
maximum extent possible.

8. MOLECULAR RESEARCH IN SEED AND RELATED

TRAITS
The important traits included under seed traits are seed dormancy, anaerobic
germination, seed shattering, seed longevity, seed viability, seed weight and seed
vigor. Phenotypic characterization on these traits has been reported for lot of
genotypes. However, molecular studies on these traits are very scanty. Few QTLs
and genes were identified for seed traits.
Seed dormancy is the failure in germination of mature and viable seeds under
favourable condition. Generally the cultivated species are having no or short period
of dormancy than the non-cultivated ones. The phenomena may be seen in either
way i.e. weak dormancy promotes a uniform germination, whereas high dormancy
prevents pre-harvest sprouting but inhibits germination and reduce seed quality.
Thus, moderate dormancy levels (15-20 days) would be desirable. The dormancy
lasts for few days to more than a month. This trait is controlled by both environmental
as well as genetic factors inhabit in both maternal and embryonic tissues. Seed
dormancy is genetically controlled by the genotypes of both the mother plant and the
embryo. The maternal plant form tissues surrounding the embryo, such as the seed
coat (testa) which creates barriers to radicle growth on imbibition. This “coat-imposed”
dormancy depends on the anatomy of the seed. In rice, qSD7–1, a clustered QTL
(qSD7–1/qPC7) was delimited to the pleiotropic Rc locus and found to control seed
dormancy by regulating ABA biosynthetic pathway in rice. Moreover Sdr4, a global
regulator of seed maturation was cloned in rice and was positively regulated by
OsVP1 (Sugimoto et al 2010). The QTL mapped in the 12 chromosomes of rice except
chromosome 10 included clusters QTL such as qSD7/qPC7, qSD1–2/qPH1 and qSD7–
2/qPH7 (Ye et al. 2013).Further, soil flooding is one of the abiotic constraints in the
rainfed lowland areas. Starchy seeds were shown to be especially tolerant of
anaerobiosis because they are able to maintain a high energy metabolism under
oxygen deficiency when compared with fatty seeds. The calcineurin-interacting protein
kinase (CIPK15) gene was reported that signals pathway that regulates RAmy3D,
which affects the expression of coleoptiles in anoxic conditions and anaerobic
germination of rice. The first natural variant of QTL qAG-9-2 that enhances anaerobic
germination was reported and fine-mapped to OsTPP7, which is a gene encoding a
trehalose-6-phosphate phosphatase (Kretzschmar et al. 2015). Two major QTLs for
anaerobic germination viz., AG1 and AG2 were identified (Angaji et al. 2010).
Researchers has also identified candidate proteins/genes for improving seed vigour
in rice plants such as OsHSP18.2 (Kaur et al. 2015); OsALDH7, ACCase, PI3K (Liu et
al. 2012); OsLOX (Wang et al. 2008). Only these few traits have been studied at

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 45
molecular level and much closed gene were reported for seed related traits till date,
which creates a huge gap in seed research.

9. PROCESS AND PROGRESS AT ICAR-NRRI ON SEED

PRODUCTION AND RESEARCH
ICAR-NRRI is producing a large quantity of Breeder seed and Truthfully Labeled
(TL) seed as per the indent of Department of Agriculture and Cooperation (DAC),
Government of India, State Governments, other organizations and requirement of
farmers. The institute is one of the volunteer centers for rice breeder seed production
under ICAR. The AICRP-NSP (Crops) under ICAR-Indian Institute of Seed Science
(IISS), Mau, Uttar Pradesh (the coordinating center) looks after the indent / allotment
of seed production decided by DAC, Government of India and also facilitates
monitoring of the seed production plots. The information from indent of the seed to
the production and final lifting or sale is being documented in the form of BSP-I, BSP-
II, BSP-III, BSP-IV and BSP-V. The BSP-I depicts the variety-wise requirement of
Breeder Seed as per the Indent of Department of Agriculture Cooperation & Family
Welfare compilation, BSP-II elaborates the variety-wise area of production and time
of monitoring of Breeder Seed production plots, BSP-III includes State Monitoring
Report for certification, BSP IV reports on quantity of Breeder Seed Produced (Actual
Seed Production during rabi and kharif season) and BSP-V elucidates the lifting and
non-lifting status of Breeder seed by indenter (center wise).
Breeder seed plots of the institute is monitored by a Central team constituted by
ICAR-IISS, Mau to inspect the crop condition and field level purity; and also by a
state level monitoring team for seed certification. The state level monitoring team
includes breeder from NRRI, representatives of Odisha State Seed and Organic Product
Certification Agency (OSSOPCA), State Agricultural University, Odisha State Seed
Corporation (OSSC) and National Seed Corporation (NSC). The production of breeder
seed is again reviewed by ICAR-DAC in the annual breeder seed review meeting.
Being a leading research institute of rice, ICAR-NRRI is supplying high quality
breeder seeds to governments and other agencies to produce highest quality
Foundation and Certified seeds for the country. During last 5 years the institute has
produced about 3383.34 q breeder seed against the indent of 3333.50 q (Table 5).
Besides nucleus and breeder seeds, ICAR-NRRI has also been producing TL
seed under Participatory Seed Production (PSP) programme where TL seed is produced
in the farmer’s field with inputs of the farmers and technical know-how and supervision
of the NRRI scientists. This programme was initiated 5 years back and more than
3400 q seed of mega varieties viz. Swarna Sub-1, Pooja, Naveen and Sarala was
produced.
The institute is also imparting training on quality seed production, management
and storage, where farmers, state government officials, representative of various
NGO’s and seed producers were successfully trained during these last years.
Seed research was also a priority area along with seed production at our institute.
The ICAR-NRRI has characterized the released varieties of the institute for days to

Quality Seed Production and Maintenance Breeding for

46 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Table 5. Breeder seed indent and production of rice at NRRI during 2012-13 to
2016-17.
DAC No. of Production
Year Indent varieties (q) Mega indented varieties
2012-13 571 25 651.35 Swarna Sub 1, Pooja, Shatabdi, Naveen, Sarala
2013-14 481 49 483.12 Swarna Sub1, Pooja, Naveen, Shatabdi, Sarala
2014-15 622 44 607.27 Swarna Sub 1, Pooja, Naveen, Shatabdi, CR 1014
2015-16 747 62 768.70 Swarna sub 1, Naveen, Varshadhan, CR Dhan 601,
CR Dhan 501
2016-17 912.5 43 872.90 Swarna Sub 1, Naveen, CR Dhan 500, Shatabdi,
Varshadhan,
Total 3333.5 3383.34

seed dormancy and duration of viability which was depicted in NRRI Annual Report
2016-17. The seedling vigour of rice has direct relevance with antioxidant and amylose
content in seed of pigmented rice. The pigmented rice are rich in genes for seed traits
and are good source for identification of donor. The seed and seedling vigour are
important traits especially for aerobic condition (Kumar et al. 2016). The molecular
study for the seed traits has been initiated to find out the relevant markers to start
breeding for seed traits and development of essentially derived varieties.

10. SEED MULTIPLICATION SYSTEM OF INDIA

Once a variety is released, it is the responsibility of the parent Institute to safe-
guard the seed quality of that particular variety and to make available the indented
quantity of Breeder seed of the variety in the seed chain. Maintenance breeding and
production of Nucleus seed safe-guards the quality of the variety at Institute level
and this Nucleus seed is used as basic seed for production of Breeder seed which
cares for the quality of the National seed chain.
Indian seed system is a robust and full proof one that strictly adheres to three
generation system (Breeder seed→Foundation seed→Certified seed); but in exigencies
four or five generation model is followed where foundation seed stage II or certified
seed stage II is produced.
The nucleus seed plots are planted in paired rows, each paired row contains
plants from one single selected panicle. All around the plots 8 rows border line of the
same variety (from bulk breeder seed) is transplanted. If any off-type plants are
observed in any of the panicle progeny row, then that particular paired row is totally
discarded/rogued-out. If any off-type plant with different grain type is marked
(obviously observed after flowering) then the panicle progeny rows where the off-
type is observed and the adjacent progeny rows (at both sides) are discarded to
restrict chance pollination involving the off-type plant. After thorough roguing,
sufficient true-to-type panicles (at least 500) are selected based on the morphological
identity, uniformity and genetic purity to maintain nucleus seed for next generation.

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 47
The border row is supposed to restrict the foreign pollen flow and is not considered
as seed. The panicle progeny rows are harvested and threshed separately; passes
through table-top examination and later bulked as nucleus seed. This Nucleus seed is
used for production of Breeder Seed.
Breeder seed (BS) is the progeny of nucleus seed, where, after every 6-8 rows of
planting a skip row is allowed to facilitate intercultural operations and proper roguing.
Here also 8 row borders all around the plot is maintained which is not considered as
seed during harvest. Off-type plants if observed are simply rogued out. The crop is
monitored by Central and State monitoring team. The genetic purity of breeder seed
should be maintained at 100 percent. Breeder seed tag is golden yellow in colour and
size is 12x6 cm.
Foundation seed is the progeny of breeder seed, called foundation seed stage I;
and when foundation seed is the progeny of foundation seed, it is called foundation
seed stage II. The foundation seed stage I is used for the production of foundation
seed stage II. The minimum seed standard for Foundation seed stage I and stage II
are same. Production of Foundation seed stage II is undertaken only when it is
expressed by the seed certifying agencies that breeder seed is in short supply and
stage II foundation seed has to be produced to meet the seed demand. Foundation
seed is monitored by the state certifying agency. The genetic purity of foundation
seed should be maintained at 99.5 percent. Foundation seed tag is white in colour and
size is 15x7.5 cm.
Certified seed is the progeny of foundation seed I or II. But, certified seed can also
be the progeny of certified seed provided this reproduction does not exceed three
generations beyond foundation seed stage I. Certified seed produced from foundation
seed is called certified seed stage I, while Certified seed produced from certified seed
is called certified seed stage II. Certified seed is monitored by the state certifying
agency and its genetic purity is 99%. Certified seed tag is blue in colour and size
is15x7.5cm.
One additional class of seed is produced and marketed in India, known as
Truthfully labeled seed (TL Seed) where certification is not required but, minimum
seed standard must be fulfilled. It is applicable to both notified varieties and variety
developed by any person or agency. Seed inspectors are the persons who can guard
the quality of seed which is on sale. So the quality of marketed TL seed can be
inspected by them if doubt on quality arises; and if it fails the quality test, the sale of
that seed can be stopped. The tag colour of TL seed is opel green and size is 15x10 cm.

11. KNOWLEDGE GAPS

 Non-availability of many high yielding varieties in seed chain: A large number of
high yielding varieties (HYVs) suitable for different agro-climatic situations are
released in India. But, many high yielding varieties are not under seed chain may
be due to lack of popularization. Therefore, it is required to include these HYVs
under front line demonstration (FLD) programmes for popularization among the

Quality Seed Production and Maintenance Breeding for

48 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

farmers; and information regarding these varieties need to be communicated to all

the officials working under seed production and marketing for there further
popularization.
 Insufficient quantity of quality seed: Available quality seed of improved rice
varieties and hybrids is many times inadequate due to climatic disturbance,
improper technology, wrong handling etc. and is considered as one of the major
constraints for higher productivity. This problem may be due to the fact that (i)
presently, high volume-low quality seeds are available with the farmers and low
volume-high quality seeds are mostly available with the public sector, (ii) non-
lifting of produced breeder seed by Government Institutions and private agencies,
which hamper the production of sufficient quantity foundation and certified seed.
These problems can be sorted out by (a) engagement of more officials for
monitoring of quality seed production, (b) involvement of more volunteer agencies
such as village-based/community based seed banks to take up the Foundation
and Certified seed production programme and (c) designing a policy framework
for advance payment of indented quantity of seeds to limit the problem of non-
lifting.
 Seed quality deterioration: Seed is a biologically living entity, whose quality
deteriorates if the minimum standard for seed production and storage steps are
not followed. Varietal deterioration occurs due to repeated multiplication of the
same varieties year after year probably due to undesirable pollination or out-
crossing, occasional mutation and genetic drift. The formal seed system guards
against the deterioration of seed quality through production of Nucleus, Breeder,
Foundation and Certified seed, the quality of which is well monitored. But due to
non-availability of this quality seed, large number of farmers depend on their
farm-saved seeds or TL seeds from the market where quality parameters are not
well-guarded. So these seeds used by the farmers show presence of seed of other
varieties, mixtures, impurities and less germination percentage that affects the
total grain production. This seed quality deterioration can be checked through; (i)
Awareness generation among seed growers and farmers regarding quality seed
and (ii) Imparting training on Quality Seed production technology to the seed
growers and farmers.
 Long time span for seed quality testing: Grow-out-test (GOT) is a procedure to
test the genetic purity of the seed. It involves assessing the several morphological
characteristics in different developmental stages which takes a long time span,
almost the entire cropping season. Furthermore, GOT is a simple way to analyze
the genetic purity based on the basis of visual detection which can be easily
affected by growing conditions. To make it more exact and to reduce the time
span, DNA based testing will be a proven alternative for GOT.
 Non assurance of genetic purity of MAS developed varieties: The present era of
molecular breeding has now accelerating gene introgression in existing varieties
resulting in release of varieties like Improved Tapaswini, Improved Lalat, Swarna-
Sub1 etc., which are now under seed chain. Most of these MAS developed varieties

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 49
 are quite similar with parents except the introgressed genes. Here, selection of
true to type plants of varieties developed through MAS (where no distinct
phenotypical difference) can only be possible through molecular level detection
or though DNA fingerprinting. This molecular marker based genetic purity testing
(MGPT) at nucleus seed level will provide 100% purity and high level of seed
purity on subsequent class of seed.
 Awareness and training: Intermediaries seed producers involved in production
and distribution of seeds have a large contribution in supply of paddy seeds to
the farmers. The question arises whether all these seeds are quality seeds? The
report says, unawareness in many producers regarding quality seed production
procedure leads to poor quality control. Intensive training to trainers and seed
producers about seed production, quality management and purity testing will
help in increasing the high volume quality seed.
 Seed technology research: Characterization of released varieties for seed traits
like seed viability duration or longevity and seed dormancy is poorly documented.
These information are always needed by the producers and farmers for better
seed multiplication, proper time of harvesting and safe storage. There are various
theories reported for genetic basis and physiological basis of seed related traits.
But, utilization of these information is very poor. A strong platform for seed research
can be a base to utilize the existing information and dissecting the molecular,
proteomics and metabolomics basis on expression of seed related traits. The
advancement of new molecular technology will explore different seed traits which
will lead to seed trait specific breeding to improve the cultivar performance such
as improvement of cultivar for capacity to germinate under anaerobic condition,
no seed shattering, prolonged seed longevity, intermediate seed dormancy, high
seed viability, appropriate seed dimension, higher seed weight, seed pigmentation
if necessary, improve seed coat permeability etc. Introgressions of these traits are
mostly relevant for high seed vigor, seed storage and optimum plant stand in field.

12. WAY FORWARD

Indian seed delivery system for farmers has a good structural network for sufficient
availability of seed. But, the SRR and VRR are still under desirable limit. Many points
have been discussed in this chapter related to production, management and research
options for safe guarding the seed quality and to speed up the process of deliveries.
QTLs have been identified but for seed traits, only few candidate and functional
genes are known till date. The emphasis and initiatives now need to be made for (i)
designing policy framework for timely lifting of seed, (ii) involvement of more officials
for proper monitoring to produce quality seed, (iii) authorization to national level
institute for issuing certification for seed production plot; this will be helpful to cover
more seed plot area for certification, (iv) mapping and development of marker for
introgression of seed traits, (v) involvement of molecular tools for rapid purity testing
procedure,(vi) advanced level capacity building of stake holders involved in seed

Quality Seed Production and Maintenance Breeding for

50 Enhancing Rice Yield
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

chain, (vii)creation of buffer stock of seed in form of seed bank at village level, and
establishing seed hubs,(viii)development of a local seed system as an alternative to
formal system (like 4S4R model developed by ICAR-NRRI, Cuttack).Once these points
are taken care of, the quality seed production and distribution system will smoothen
and the Country will achieve higher rice grain production.
References
FAO (2017) Food and Agriculture Organization of the United Nations, Rome, Italy, 20(1), April
2017.
Annual Report (2016-17) Department of Agriculture Cooperation and Farmers Welfare, Ministry
of Agriculture and Farmers welfare, Government of India, Krishi Bhawan, New Delhi.
Hasanuzzaman M (2015) Concept note. http://hasanuzzaman.weebly.com/uploads/9/3/4/0/9340
25/seed quality.
Chauhan JS, Prasad Rajendra S, Pal Satinder and Choudhury PR (2017) Seed systems and Supply
chain of rice in India. Journal of Rice Research 10(1): 9-16.
Reddy Ch Ravinder, Tonapi VA, Bezkorowajnyj PG, Navi SS and Seetharama N (2007) Seed system
innovations in the semi-arid tropics of Andhra Pradesh, International Livestock Research
Institute (ILRI), ICRISAT, Patancheru, Andhra Pradesh, India, 224.
Anonymous2016. Agricultural Statistics at a Glance (2015) Directorate of Economics & Statistics.
Department of Agriculture, Cooperation and Farmers Welfare, Ministry of Agriculture &
Farmers Welfare, Government of India, New Delhi, 479.
Sugimoto Kazuhiko, Yoshinobu Takeuchi, Kaworu Ebana, Akio Miyao, Hirohiko Hirochika, Naho
Hara, Kanako Ishiyama, Masatomo Kobayashi, Yoshinori Ban, Tsukaho Hattori, Masahiro
Yano (2010) Molecular cloning of Sdr4, a regulator involved in seed dormancy and
domestication of rice. Proceedings of the National Academy of Sciences USA107 (13):
5792–5797.
Ye H, Beighley DH, Feng J, Gu XY (2013)Genetic and physiological characterization of two
clusters of quantitative trait loci associated with seed dormancy and plant height in rice.
G3 (Bethesda) 3:323–31.
Kretzschmar T, Pelayo MAF, Trijatmiko KR, Gabunada LFM, Alam R, Jimenez R, Mendioro MS,
Slamet-Loedin IH, Sreenivasulu N, Bailey-Serres J, Ismail AM, Mackill DJ, Septiningsih
EM (2015) A trehalose-6-phosphate phosphatase enhances anaerobic germination
tolerance in rice. Nature Plants: 15124.
Angaji SA, Septiningsih EM, Mackill DJ and Ismail AM (2010) QTLs associated with tolerance of
anaerobic conditions during germination in rice (Oryza sativa L.). Euphytica 172:159 -
168.
Kaur H, Petla BP, Kamble NU, Singh A, Rao V, Salvi P, et al. (2015) Differentially expressed seed
aging responsive heat shock protein OsHSP18.2 implicates in seed vigor, longevity and
improves germination and seedling establishment under abiotic stress. Frontiers in Plant
Science 6:71.
Kumar R, Kumawat N, Kumar S, Kumar R, Kumar M, Sah RP, Kumar U and A Kumar (2016) Direct
Seeded Rice: Research Strategies and Opportunities for Water and Weed Management.
Oryza 53(4): 354-365.
Liu J, Zhou J, and Xing D (2012) Phosphatidylinositol 3-kinase plays a vital role in regulation of
rice seed vigor via altering NADPH oxidase activity. PLoS ONE 7:e33817.
Wang R, Shen WB, Liu L, Jiang L, Zhai H and Wan J (2008) Prokaryotic expression, purification
and characterization of a novel rice seed lipoxygenase gene OsLOX1. Rice Science 15:88–
94.

Quality Seed Production and Maintenance Breeding for

Enhancing Rice Yield 51
 Utilization of Cultivated and Wild Gene Pools of
Rice for Resistance to Biotic Stresses

MK Kar, L K Bose, M Chakraborti, M Azharudheen, S Ray,

S Sarkar, SK Dash, JN Reddy, DR Pani, M Jena, AK Mukherjee,
S Lenka, SD Mohapatra and NN Jambhulkar

SUMMARY
Productivity of rice is often adversely affected by several biotic stresses. The
major biotic stresses such as blast, bacterial blight, sheath blight, brown planthopper
and yellow stem borer play crucial roles in reducing the productivity and quality of
rice. Among the various control measures available for mitigating biotic stresses,
host plant resistance is most effective, economic and eco-friendly. Wild and cultivated
gene pools of rice are important sources for many resistance genes/QTLs, which are
successfully utilized in resistance breeding programme. In this chapter, a
comprehensive assessment of the use of wild and cultivated gene pools of rice for
imparting resistance to major biotic stresses has been presented.

1. INTRODUCTION
Like all other crop plants, rice (Oryza sativa) also suffers from several biotic and
abiotic stresses that seriously affect its production. A wide range of pathogens,
insects, nematodes and other pests attack the rice plant in different parts of the world.
Magnitude and the type of damage caused by pests vary in different regions. Among
them, diseases like blast, bacterial blight (BB) and sheath blight (ShB) and insects like
brown planthopper (BPH) and yellow stem borer (YSB) are of major concern in India
as well as many other parts of the world. Despite the availability of several control
measures for mitigating pest damage in crop plants, developing cultivars tolerant to
major insect-pests and diseases prevalent in an area is the easiest, most economic
and most eco-friendly measure available to the farmers. At the same time, the system
is highly dynamic in its nature due to continuous co-evolution of genes conferring
resistance or susceptibility in hosts and their corresponding gene for virulence in
pests. Genes conferring resistance are distributed across primary, secondary and
tertiary gene pool of the crop. Judicious use of these genes and genetic resources to
minimize losses caused by pests remains an important challenge for rice researchers
worldwide.
In India, systematic research efforts to impart host plant resistance in rice is
undergoing from more than 70 years. The biotic stress breeding programme at the
National Rice Research Institute, Cuttack, Odisha has evolved over time depending
on the dynamic pest profile of the crop and advances in the technologies available.
The institute was established in 1946 in the backdrop of the Bengal famine caused
due to Helminthosporium leaf spot. Hence during the first two decades, the emphasis

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52 Resistance to Biotic Stresses
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

was mainly given to developing brown spot resistant genotypes. Eventually, breeding
for tolerance against blast and yellow stem borer (YSB) was also taken up. With the
introduction of high yielding semi-dwarf varieties like TN 1 during early 60’s, bacterial
blight became a severe threat to rice production. The 70’s and 80’s saw the major
focus being directed towards breeding for bacterial blight tolerance. With the outbreak
of brown planthopper in the late 1970’s, breeding for BPH tolerance has also taken a
centre stage. Sheath blight, though very severe even during 1960’s in countries like
the Philippines, was not a stress capable of causing economic damage to the rice
industry in India until recently. But the severe incidence of sheath blight is being
reported of late especially in the most productive parts of the country like Punjab and
even in many regions of Orissa where intensive farming is practiced to raise the crop.
The global and national efforts towards understanding the mechanism of resistance
and developing cultivars with biotic stress tolerance against the five major rice pests,
viz., blast, bacterial blight, sheath blight, brown planthopper and yellow stem borer
have been reviewed in this chapter, with major emphasis being given to the work
carried out at ICAR-NRRI, Cuttack.

2. RICE BLAST (MAGNAPORTHE ORYZAE) RESISTANCE

Rice blast disease caused by Magnaporthe oryzae is one of the most destructive
disease causing huge losses to rice yield and thereby posing a great threat to world
food security. Use of blast resistant cultivars is the most effective, economic and
environmentally sustainable way of managing this pathogen. Till today more than
100 blast resistance genes have been identified (Table 1). Of these, 45% are from
japonica cultivars, 51% from indica cultivars and the rest 4% are from wild species of
rice. Blast resistance genes and their genetic location in different rice cultivars have
been reviewed by Sharma et al. (2012). Recently, Liang et al. (2016) reported that pi
66(t) is one of the three recessive genes controlling rice blast, and is the first major
gene for resistance to be mapped on chromosome 3. Li et al. (2017) identified a new
gene from a rice variety Digu which is effective against broad spectrum of M. oryzae
races. An exhaustive list of the reported blast resistance genes with their corresponding
sources and their chromosomal locations have been mentioned in Table1.
Blast disease was first reported in India in 1913 and the first devastating epidemic
due to rice blast was reported in 1919 in Tanjore delta. Since then several works were
carried out in various parts of the country. An important gene for blast resistance, Pi-
kh was identified from indica variety Tetep at ICAR-National Research Centre for
Plant Biotechnology, New Delhi. They further characterized, fine mapped, cloned and
functionally validated the resistance gene. The corresponding virulent gene, AvrPi54
in the pathogen was also successfully cloned by the team, which contributed
significantly in the detailed understanding of host-pathogen interaction (Ray et al.
2016).
Hittalmani et al. (2000) used closely linked RFLPs and polymerase chain reaction
(PCR)-based markers to put three blast resistance genes Pi1, Piz-5 and Pita into a

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 53
Table 1. Blast resistance genes reported in rice.
Sl. No. Gene name Location (Chr No) Sources of resistance
1 Mpiz 11 Zenith
2 Pb1 11 Modan
3 PBR 11 St- No 1
4 Pi(t) 4 P167
5 Pi1 11 LAC23
6 Pi10 5 Tongil
7 Pi11 8 Zhai-Ya-Quing8
8 Pi12 12 K80-R-Hang, Jiao-Zhan, Moroberekan
9 Pi13(t) 6 O. minuta (W), Kasalath (I),Maowangu
10 Pi14(t) 2 Maowangu
11 Pi15 9 GA25
12 Pi15(t) 12 Moroberekan
13 Pi16(t) 2 Aus373
14 Pi17 7 DJ123
15 Pi18(t) 11 Suweon365
16 Pi19(t) 12 Aichi Asahi
17 Pi20 12 IR24
18 pi21 4 Owarihatamochi
19 Pi22(t) 6 Suweon365
20 Pi23 5 Suweon365
21 Pi24(t) 1 Azucena
22 Pi25 6 Gumei 2
23 Pi25(t) 2 IR6
24 Pi26 6 Gumei 2
25 Pi26(t) 5 Azucena
26 Pi27 1 Q14
27 Pi27(t) 6 IR64
28 Pi28(t) 10 IR64
29 Pi29(t) 8 IR64
30 Pi3(t) 6 Pai-kan-tao
31 Pi30(t) 11 IR64
32 Pi31(t) 12 IR64
33 Pi32(t) 12 IR64
34 Pi33 8 IR64
35 Pi34 11 Chubu32
36 Pi35(t) 1 Hokkai 188
37 Pi36 8 Q61
38 Pi37 1 St- No 1
39 Pi38 11 Tadukan
40 Pi39(t) 4,12 Chubu 111, Q15
Contd....

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Sl. No. Gene name Location (Chr No) Sources of resistance

41 Pi40(t) 6 O. australiensis
42 Pi41 12 93-11
43 Pi42(t) 12 DHR9
44 Pi44 11 Moroberekan
45 Pi47 11 Xiangzi 3150
46 Pi48 12 Xiangzi 3150
47 Pi5(t) 9 Moroberekan
48 Pi6(t) 12 Apura
49 Pi62(t) 12 Yashiro-mochi
50 Pi67 Tsuyuake
51 Pi8 6 Kasalath
52 Pi9 6 O. minuta
53 Pia 11 Aichi Asahi
54 Pib 2 Tohoku IL9
55 Pib2 11 Lemont
56 PiCO39(t) 11 CO39
57 Pid(t)1 2 Digu
58 Pid2 6 Digu
59 Pif 11 Chugoku 31-1
60 Pig(t) 2 Guangchangzhan
61 PiGD1 8 Sanhuangzhan 2
62 PiGD-2 10 Sanhuangzhan 2
63 PiGD3 12 Sanhuangzhan 2
64 Pigm(t) 6 Gumei4
65 Pii 9 Ishikari Shiroke, Fujisaa5
66 Pii1 6 Fujisaka 5
67 Pii2 9 Ishikari Shiroke
68 Piis1 11 ImochiShirazu
69 Piis2 - ImochiShirazu
70 Piis3 - ImochiShirazu
71 Pik 11 Kusabue
72 Pikg 11 GA20
73 Pikh (Pi54) 11 Tetep
74 Pikm 11 Tsuyuake
75 Pikp 11 HR22
76 Piks 11 Shin 2
77 Pikur1 4 Kuroka
78 Pikur2 11 Kuroka
79 Pilm2 11 Lemont
80 Pir2-3(t) 2 IR64
81 Pirf2-1(t) 2 O. rufipogon

Contd....

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 55
Sl. No. Gene name Location (Chr No) Sources of resistance
82 Pise 11 Sensho
83 Pise2 - Sensho
84 Pise3 - Sensho
85 Pish 1 Shin 2
86 Pish 11 Nipponbare
87 Pit 1 Tjahaja
88 Pita 12 Tadukan
89 Pita2 12 Shimokita
90 Pitp(t) 1 Tetep
91 Pitq1 6 Teqing
92 Pitq2 2 Teqing
93 Pitq3 3 Teqing
94 Pitq4 4 Teqing
95 Pi-tq5 2 Teqing
96 Pitq6 12 Teqing
97 Piy1(t) 2 Yanxian No 1
98 Piy2(t) 2 Yanxian No 1
99 Piz 6 Zenith (J), Fukunishiki,Toride 1, Tadukan
100 Pizh 8 Zhai-Ya-Quing8
101 Pi157 12 Moroberekan
102 Pi-jnw1 11 Jiangnanwan
Adapted and updated from Sharma et al. (2012)

susceptible cultivar CO39. It was reported that plants carrying two or three gene
combinations showed enhanced resistance as compared to Piz-5 alone. Singh et al.
(2011) improved the parental lines of rice hybrid Pusa RH 10 by introgressing the
blast resistant gene Pi 54 into them. The group has also developed and released a
blast-resistant basmati variety, Pusa Basmati 1637 through transfer of Pi9 using marker-
assisted selection. Introgression of blast resistance genes Pi1, Pi2 and Pi33 into rice
variety ADT43 was carried out at Tamil Nadu Agricultural University, Coimbatore.
At The National Rice Research Institute, Yadav et al. (2017) attempted to find out
the status of twelve major blast resistance genes and their diversity among eighty
released rice varieties of the institute (National Rice Research Institute, Cuttack).
Linked molecular markers for genes Pib, Piz, Piz-t, Pik, Pik-p, PikmPik-h, Pita/Pita-
2, Pi2, Pi9, Pi1 and Pi5 were used in the study. Among the 80 varieties used, 19 were
resistant, 21 were moderately resistant and 40 were susceptible to the disease. The
blast resistance genes in the different varieties varied from 4 to 12 and the frequencies
of the resistance genes ranged from 0 to100%.
Marker assisted backcross breeding strategy was applied for pyramiding blast
resistance genes (Pi2 and Pi9), into Vandana and Kalinga III through the crosses
(Kalinga III/C101A51 (Pi-2(t))//KalingaIII/O. minute der. WHD IS 75-127(Pi-9(t))
and Vandana/C101A51//Vandana /O. minute der. WHD IS 75-127). Many lines in the

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background of Vandana and Kalinga III were developed. Among the promising lines,
CR 2619-2, CR 2619-5, CR 2619-6, CR 2619-7, CR 2619-8 and CR 2619-9 are in the
background of Vandana while CR 2620-1, CR 2620-2, CR 2620-3 and CR 2620-4 are in
Kalinga III background. The promising lines were tested in Disease Screening Nursery
(DSN) under AICRIP for multi-location trials.
2.1. Bacterial blight (Xanthomonas oryzae pv. oryzae) resistance
Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae (Xoo), is a
devastating disease in the rice-growing countries of Asia. Infection at maximum tillering
stage results in blighting of leaves, which eventually causes significant yield losses
in severely infected fields ranging from 20 to 30%, but this, can reach as high as 80%.
Development of cultivars carrying major resistance (R) genes have been the most
effective and economic strategy to control BB disease. To date, at least 38 BB resistance
genes conferring host resistance against various strains of Xoo have been identified
(Table 2). All of these genes follow a Mendelian pattern of inheritance and express
resistance to a diverse group of Xoo pathogens. Several of these genes have already
been incorporated into rice cultivars, which are now widely cultivated in many countries.
BB resistance gene Xa4 is one of the most widely exploited resistance genes and it
confers durable resistance in many commercial rice cultivars. Two genes Xa 33(t) and
Xa 38 were identified from Oryza nivara. A new mutant named ‘XM14’ obtained from
IR24, which was found to be resistant to all Japanese Xoo races. The gene identified
in XM14 was designated as xa42.
In IRRI, IR24 NILs (IRBB lines) containing Xa4, xa5, xa13 and Xa21genes and
their combinations were developed which were extensively used in the breeding
programmes of many countries including India. Indian scientists from the National
Agricultural Research and Education System used these IRBB lines for transfer of BB
resistance genes in many popular high yielding varieties. The gene combinations
chosen by breeders, however, remained confined to xa13 and Xa21 or xa5, xa13 and
Xa21. However, Ellur et al. (2016) incorporated Xa38 in the basmati background of
PB1121 and found that it provides resistance to an additional race of the pathogen
when compared with its NIL pyramided with xa13+Xa21.
The Xa21 gene was identified at NRRI in the wild species Oryza longistaminata,
which was highly effective against BB races in South and Southeastern Asia. The
gene was later mapped and cloned at IRRI and is being extensively utilized by breeders
across the globe. Varietal improvement programme was initiated to improve the BB
resistance in popular high yielding varieties as recurrent parents and BB resistance
genotypes viz., Ajaya (xa5), IRBB 8 (xa8) and IRBB 60 (xa5, xa13 and Xa21) as
donors through backcross breeding coupled with artificial screening.
Resistance genes (xa5, xa13 and Xa21; either singly or in different combinations)
pyramided lines were developed through marker assisted backcross breeding in the
genetic background of Swarna and IR64 under the Asian Rice Biotechnology Network
(Reddy et. al. 1997). The promising pyramided lines identified through DSN of AICRIP
in different locations across the country were recommended for registration for their

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 57
Table 2. List of BB resistance genes reported in rice.
Xa gene Resistance to Xoo race Donor cultivar Chr.
Xa1 Japanese race -I Kogyoku, IRBB 1 4
Xa2 Japanese race -II IRBB2 4
Xa3/Xa26 Chinese, Philippine, and Wase Aikoku 3, Minghui 63, IRBB3 11
Japanese races
Xa4 Philippine race-I TKM6, IRBB4 11
xa5 Philippine races-I, II, III IRBB5 5
Xa6 Philippine race-I Zenith 11
Xa7 Philippine races DZ78 6
xa8 Philippine races P1231128 7
xa9 Philippine races Khao Lay Nhay and Sateng 11
Xa10 Philippine and Japanese races Cas 209 11
Xa11 Japanese races IB, II, IIIA, V IRS 3
Xa12 Indonesian race-V Kogyoku, Java14 4
xa13 Philippine race 6 BJ1, IRBB13 8
Xa14 Philippine race 5 TN1 4
xa15 Japanese races M41 Mutant -
Xa16 Japanese races Tetep -
Xa17 Japanese races Asominori -
Xa18 Burmese races IR24, Miayang 23, Toyonishiki -
xa19 Japanese races XM5 (Mutant of IR24) -
xa20 Japanese races XM6 (Mutant of IR24) -
Xa21 Philippine and Japanese races O. longistaminata, IRBB21 11
Xa22 Chinese races Zhachanglong 11
Xa23 Indonesian races O. rufipogon (CBB23) 11
xa24(t) Philippine and Chinese races DV86 2
Xa25 Chinese and Philippine races Minghui 63, HX-3 (Somoclonal 12
mutant of Minghui 63)
xa26(t) Philippine races Nep Bha Bong -
Xa27 Chinese strains and Philippine O. minuta, IRGC 101141, IRBB27 6
race 2 to 6
xa28 (t) Philippine race 2 Lota sail -
Xa29(t) Chinese races O. officinalis (B5) 1
Xa30 (t) Indonesian races O.rufipogon (Y235) 11
Xa31(t) Chinese races Zhachanglong 4
Xa32(t) Philippine races O. australiensis (introgression 11
line C4064)
xa33(t) Thai races Ba7 O. nivara 6
Xa33(t)
Xa34 (t) Thai races BG1222 1
Xa35(t) Philippine races O. minuta (Acc. No.101133) 11
Xa36(t) Philippine races C4059 11
Xa38 Indian Punjab races O. nivara IRGC81825 4
Xa39 Chinese and Philippine races FF329 11
Xa40(t) Korean BB races IR65482-7-216-1-2 11
xa41(t) Various Xoo strains Rice germplasm -
xa42 Japanese Xoo races XM14, a mutant of IR24 3
Adapted and updated from Kou and Wang (2013).

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use as potential donors in future breeding programmes (DRR Annual Progress Report
2003; 2005). Two lines CRMAS 2231-37 (IET 20668) and CRMAS 2231-48 (IET 20669)
in the background of IR 64 were found promising for BB endemic areas of Uttarakhand
and Andhra Pradesh and Uttarakhand and Haryana, respectively while one line
CRMAS 2232-85 (ET 20672) in the background of Swarna was recommended for the
endemic areas of Gujrat and Maharashtra. Pradhan et al. (2015) introgressed three BB
resistance genes (xa5, xa13 and Xa21) by marker-assisted backcrossing, in the
background of the popular, but highly BB susceptible deepwater variety, Jalmagna.
The pyramided lines showed a high level of BB resistance and significant yield
advantage over Jalmagna under conditions of BB infection. Lines carrying two BB
gene combinations (Xa21+xa13 and Xa21+xa5) were also developed in the background
of Jalmagna (Pradhan et al. 2016). The pyramided lines showed increased resistance
to BB isolates prevalent in the region. The parental line improvement for BB resistance
has been successfully undertaken at NRRI in case of popular rice hybrid Rajalaxmi,
by introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) through Marker-
assisted backcross (MAB) breeding (Dash et al. 2016).
Varietal improvement program at NRRI for BB resistance resulted in the release of
Improved Lalat [CRMAS 2621-7-1 (IET 21066)], Improved Tapaswini [CRMAS 2622-
7-6 (IET 21070)] and CR Dhan 800 in the genetic background of popular rice varieties
Lalat, Tapaswini and Swarna, respectively. Improved Lalat and Improved Tapaswini
carry four genes (Xa4, xa5, xa13 and Xa21) while CR Dhan 800 has three resistance
genes Xa21, xa13 and xa5. All have been effective for growing in the “bacterial
blight” endemic areas of Odisha.

3. SHEATH BLIGHT (RHIZOCTONIA SOLANI KUHN)

TOLERANCE/RESISTANCE
Sheath blight of rice, caused by the fungus, Rhizoctonia solani Kuhn, is becoming
a major threat to rice production worldwide. Though first reported as early as in 1910,
sheath blight became a prominent disease only after the introduction of high yielding
semi-dwarf varieties in the 1960’s. The intensive cropping involving cultivation of a
single variety over a large area and the high use of nitrogenous fertilizer led to a
dramatic increase in the incidence of sheath blight in major rice-growing countries of
the world as well as India. Almost all the prominent varieties grown in the country are
highly susceptible to the disease. Development of genotypes tolerant to the disease
is considered as the most sustainable, eco-friendly and economic way to combat the
disease.
Breeding for sheath blight (ShB) tolerance in rice poses many unique challenges
compared to other pests and diseases. Being caused by a necrotrophic fungus, ShB
tolerance is a quantitative trait governed by polygenes. Lack of a well-standardized
screening protocol compounded with the influence of environment and various plant
morphological features on trait expression make identification of truly resistant lines
a daunting task. Genotypes with moderate disease resistance have been reported in
the past, but a strong ShB resistant source is yet to be identified from both the
cultivated and wild gene pool of rice.

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 59
 From the moderate resistance sources identified, more than hundred QTLs (Table
3) have been reported for ShB tolerance in rice, but most of them have minor effects
and are correlated with various plant morphological features, especially plant height
and heading date. Even for the major ShB QTLs having plant morphology-independent
effect, the expression is highly affected by the genetic background, limiting the
usefulness of the QTLs in practical plant breeding. The breeding potential of few ShB
QTLs viz., qSB9-2TQ, qSB-11LE and qSB-9 TQ have been tested in different genetic
backgrounds and their effect on sheath blight tolerance was validated. Two of these
QTLs, qSB-11LE and qSB-9 TQ were fine mapped.
There are only limited reports of utilization of identified ShB QTLs in practical
plant breeding, with only limited resistance genotypes viz., Teqing, Tetep, Lemont
and Jasmine 85 being regularly used as donors of ShB tolerance. Pinson et al. (2008)
have improved the ShB tolerance of the popular American rice genotype Lemont by
introgressing ShB tolerance QTLs from TeQing. Three TeQing-into-Lemont backcross
introgression lines (TILs) containing eight ShB QTLs and having significantly less
sheath blight susceptibility compared to the recurrent parent were released in the
USA in 2007. Wang et al. (2012) have developed TeQing-into-Lemont backcross
introgression lines (TILs) of QTLs qSB9-2 and qSB12-1 and found that resistant
alleles of the QTLs from TeQing significantly improved ShB tolerance of the TILs.
Chen et al. (2014) have transferred the QTLs qSB-7 and qSB-9 from Teqing into the
genetic background of commercial japonica varieties by MAS. The two QTLs were
also pyramided in the background of the japonica variety WLJ1. There was a significant
reduction in SB incidence and yield loss in the introgressed lines and pyramiding of
two QTLs were found to be more effective rather than using single QTL. Zuo et al.
(2014) have shown that pyramiding of QTLs for ShB tolerance and tiller angle, qSB-
9TQ and TAC1TQ, had significantly increased disease tolerance in the near-isogenic
lines (NILs) carrying them. Both the QTLs have improved the ShB tolerance of the
NILs but qSB-9TQ was more effective than TAC1TQ. The NILs having both the QTLs
had more tolerance to sheath blight compared to the NILs having any one of them.
In India, ShB tolerance breeding relies mainly on the genotype Tetep, which is a
multiple biotic stress tolerant indica genotype from Vietnam. In studies conducted at
Indian Agricultural Research Institute (IARI), one major ShB QTL qSBR11-1 from
Tetep was functionally characterized and the candidate gene, a novel chitinase gene
(LOC_Os11g47510), for sheath blight tolerance was identified in the QTL region. The
QTL qSBR11-1 was introgressed into the background of ‘Improved Pusa Basmati 1’
by marker-assisted backcrossing (MAB). In another study, the sheath blight tolerance
of the line Pusa 6B, the Basmati quality maintainer line of the popular superfine
aromatic rice hybrid Pusa RH10, was enhanced by introgressing three ShB resistance
QTLs (qSBR11-1, qSBR11-2 and qSBR7-1) from Tetep by MAB.
The resistance reaction of a genotype may vary depending on the strain of the
pathogen used. Screening experiments conducted at the National Rice Research
Institute (NRRI) using the local strains of the pathogen has shown that international
check genotypes for ShB tolerance like Jasmine 85 and TeQing are susceptible to the

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Table 3. List of reported QTLs for sheath blight tolerance.

Mapping
Chr. No. QTL Resistant parent Susceptible parent population
5 qShb5.1 RP 2068-18-3-5 TN1 RIL
7 qshb7.3 ARC10531 BPT-5204 BC1F2
9 qshb9.2 ARC10531 BPT-5204 BC1F2
9 qShB9-2 Jasmine 85 Lemont RIL
9 qSBR-9 Jarjan Koshihikari BC2F3 (BIL)
1 qSBR1-1 Tetep HP2216 RIL
qSBR1-1 Tetep HP2216 RIL
7 qSBR7-1 Tetep HP2216 RIL
qSBR7-1 Tetep HP2216 RIL
8 qSBR8-1 Tetep HP2216 RIL
11 qSBR11-1 Tetep HP2216 RIL
11 qSBR11-2 Tetep HP2216 RIL
11 qSBR11-3 Tetep HP2216 RIL
11 qSB-11LE Lemont Yangdao NIL
1 - Pecos Rosemont F2
9 qShB9-2 Jasmine 85 Lemont RIL
9 qSB-9Tq Lemont Teqing CSSLs
8 Qsh8a Teqing Lemont RIL
8 Qsh8b Teqing Lemont RIL
9 Rsb-2(t) A Mutant Shuhui 881 -
1 qSB-1 Lemont Teqing RIL
3 qSB-9 Lemont Teqing RIL
5 qSB-3 WSS2 Hinohikari BC1F1
2 Rsb1 4011 XZX19 F2
11 qSBR-2 Jingxi 17 Zhaiyeqing 8 DH
2 QSbr2a Lemont Teqing NIL
3 QSbr3 Lemont Teqing NIL
2 qSB-2 Jasmine 85 Lemont F2
3 qSB-3 Jasmine 85 Lemont F2
7 qSB-7 Jasmine 85 Lemont F2
9 qSB-9-1 Jasmine 85 Lemont F2
9 qSB-9-2 Jasmine 85 Lemont F2
11 qSB-11 Jasmine 85 Lemont F2
1 QRh1 Jasmine 85 Lemont RIL
9 Qsbr3a Teqing Lemont F4 Bulk
Qsbr9a Teqing Lemont F4 Bulk
Adapted and updated from Srinivasachary et al. (2011).

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local strains. Only two genotypes, Tetep and CR 1014, a variety released from ICAR-
NRRI, showed consistent moderate resistant phenotype for sheath blight.
Conventional breeding has been less effective for the development of ShB tolerant
genotypes because of the polygenic nature of the trait. In the segregating generations
of the crosses made at ICAR-NRRI, using CR 1014 as the donor for ShB tolerance,
selection of superior recombinants has been difficult since ShB tolerance has tight
linkage with plant height. A novel ShB QTL on chromosome 1 was identified from an
F2:3 population derived from the cross Swarna Sub1 x CR 1014, which need to be fine
mapped and its effects in different genetic backgrounds need to be validated.

4. BROWN PLANTHOPPER (NILAPARVATA LUGENS

STÅL) RESISTANCE
Brown planthopper (BPH) (Nilaparvata lugens Stål) is one of the most destructive
insect-pests of rice. Besides affecting the rice crop directly, it also serves as a vector
that transmits rice grassy stunt virus and ragged stunt virus. The host resistance of
rice against BPH was first reported in the variety Mudgo and the first BPH resistance
gene (BPH 1) was identified from the same in 1967. After that 31 more genes have
been discovered (Table 4) besides several QTLs from the gene pool of cultivated and
wild rice (Deen et al. 2017). They are mapped to five of the 12 chromosomes (3, 4, 6, 11,
and 12) of rice (Cheng et al. 2013). Among those, only 17 genes (BPH1, BPH2, BPH6,
BPH9, BPH12, BPH14, BPH15, BPH17, BPH18, BPH19, BPH25, BPH26, BPH27,
BPH28, BPH29, BPH30 and BPH32) have been fine-mapped and seven of them
(BPH14, BPH17, BPH18, BPH26, BPH29, BPH9 and BPH32) have been cloned and
characterized (Jena et al. 2017). Among the cloned genes BPH 9 and BPH 26 turned
out to be the same gene (LOC_Os12g37280), and the locus IDs for BPH 17 and BPH
18 have not been yet assigned. However, almost all the identified resistance genes
are biotype/ population specific and do not provide strong resistance to other BPH
biotypes/populations. Hence, search for broad-spectrum resistance should continue
besides taking efforts for pyramiding multiple combinations of genes and
understanding the detailed molecular mechanisms involved therein.
A series of BPH tolerant varieties (e.g. IR26, IR36, IR50 and IR72) have been
developed and released from the IRRI since the 1970s, by transferring BPH resistance
genes in the background of elite susceptible cultivars. However, the improved cultivars
carrying single resistance gene lose effectiveness due to the evolution of new biotypes
and this has become a serious threat to its management in Asia. Pyramiding of BPH
resistance genes/QTLs may provide a sustainable means for developing durable
resistance against frequently evolving new biotypes. Several studies have been
reported for pyramiding of insect resistance genes. The most elaborate work was
carried out by Jena et al. (2017) in which the resistance levels of bph genes were
studied by introgressing them into the genetic background of the variety IR 24. The
group has developed 25 NILs with 9 single R genes and 16 multiple R genes
combinations. The insect resistance of the NILs, in terms of the level of antibiosis
was assessed. It was found that NILs pyramided with multiple bph genes were having

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Table 4. BPH resistance genes and their source germplasm.

S. No. Resistance gene Source
1 Bph1 Mudgo, CO22 (IT 000588), TKM6, Milyang30, Milyang34
(IT 006216), Nampungbyeo, Chilseongbyeo, Andabyeo,
Kanto PL4 (IT173362), Cheongcheongbyeo, Changsongbyeo,
Baekunchalbyeo, IR26 (IT001886), IR28 (IT001892), IR29
(IT001893), IR30 (IT001899), Hangangchalbyeo,
Yeongpungbyeo, Namyeongbyeo, Gayabyeo, Samgangbyeo,
Namcheonbyeo, MTU15, IR26, IR28, IR29, IR30, IR34,
IR44, IR45, IR46, IR64 and MGL2
2 bph2 ASD7, ASD9, IR 1154-243, Norin-PL4, Hwacheongbyeo,
PTB18, PTB33, H105, Palasithari 601, H5, IR32, IR36, IR38,
IR40, IR42, IR48, IR50, IR52, IR54, IR65
3 Bph3 Rathu Heenati, PTB19, Gangala, Horana Mawee,
Muthumanikam, Kuruhondarawala, Mudu, Kiriyal, PTB33,
IR56, IR58, IR60, IR62, IR68, IR70, IR72, IR74
4 bph4 Babawee, Gambada Samba, Hotel Samba, Kahata Samba,
Thirissa, Sulai, VellaiIllankali, Heenhoranamawee,
KuluKuruwee, Lekam Samba, Senawee and IR66
5 bph5 ARC10550
6 Bph6 Swarnalata, O. officinalis (acc.00896)
7 Bph7 T12
8 bph8 Chin Saba, Col. 5 Thailand and Col. 11 Thailand
9 Bph9 Pokkali, Balamee and Kaharamana
10 Bph10 O. australiensis and IR65482-4-136-2-2
11 bph11 O. officinalis, DV85 and IR 54751-2-44-15-24-3
12 Bph12 O. officinalis, O. latifolia, B14 and IR54751-2-34-10-6-2
13 Bph13 O. eichingeri, O. officinalis (acc.00896), acc105159 and
IR54745-2-21-12-17-6
14 Bph14 O. officinalis, RI35 and B5
15 Bph15 O. officinalis and B5
16 Bph17 Rathu Heenati
17 Bph18 O. australiensis and IR65482-7-216-1-2
18 bph19 AS20-1
19 Bph20 O. minuta (acc. 101141), IR71033-121-15 and ADR 52
20 bph21 ADR52, O. minuta (acc. 101141) and IR71033-121-15
21 Bph22 IR 75870-5-8-5-B-2-B and IR 75870-5-8-5-B-1-B
22 Bph23 IR 71033-121-15
23 bph24 IR 73678-6-9-B
24 Bph25(t) ADR52
25 Bph26(t) ADR52
26 Bph27 GX2183
27 Bph28(t) DV85
28 Bph29 RBPH54 (introgression from O rufipogon)
29 Bph31 CR2711-76
30 Bph32 PTB33
Adapted and updated from Ali and Chowdhury (2014).

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more level of antibiosis compared to NILs with single bph gene. The study throws
significant inroads into the concept of R gene deployment in which different bph
gene/gene combinations can be used in different geographical areas depending on
the biotype prevalent in the region.
Deen et al. (2017) reported the occurrence of multiple loci instead of a single
recessive gene (reported earlier) conferring resistance to the insect in case of bph5.
They identified five QTLs qBphDs6, qBphNp1, qBphNp12, qBphDw3 and qBphDw8
associated with BPH (biotype 4) resistance in ARC10550. The two major QTLs
qBphDs6 for damage score and qBphDw8 for days to wilt were important for further
investigation and use in the breeding programme. Pyramiding of BPH resistance
genes, Bph1 and Bph2, has been successfully achieved by marker-assisted breeding
(Sharma et al. 2004).
At ICAR-NRRI, several landraces showing a very high degree of resistance were
used for breeding varieties resistant to BPH. The breeding lines CR 3005-77-2 (Samba
Mahsuri/Salkathi), CR 3006-8-2 (Pusa 44/Salkathi), CR 3005-230-5 (SambaMahsuri/
Salkathi), CR 2711-76 (Tapaswini/Dhobanumberi) were found to be promising in
planthopper screening trials of AICRIP, 2011 and 2012. Molecular mapping of resistance
genes/QTLs from these two landraces- Salkathi and Dhobanumberi is underway. Two
QTLs designated as qBph4.3 and qBph4.4 were identified from Salkathi landrace
among which QBph4.3 is novel (Mohanty et al., 2017). Transfer of these two QTLs
into two popular susceptible varieties Naveen and Pooja are in progress. Recently,
Prahlada et al. (2017) at IRRI identified a single dominant gene, BPH31 on the long
arm of chromosome 3 in CR2711-76.

5. YELLOW STEM BORER (SCIRPOPHAGA

INCERTULAS) TOLERANCE/RESISTANCE IN RICE
Yellow stem borer is a major threat to rice production in tropical and subtropical
rice-growing areas. Lack of availability of an effective source of resistance to this
insect in primary gene pool poses a challenge in the study and improvement of this
trait. The complex inheritance pattern and screening methodologies for resistance
create further complications. In absence of any significant report of studies related to
YSB resistance in literature, the works carried out at ICAR-NRRI and other institutes
of India are discussed. Unlike the four other biotic stresses mentioned above,
comprehensive molecular studies for identification of genes and QTLs conferring
resistance to YSB are not available. Most of the studies are confined to classical
genetic studies.
Efforts to introgress YSB tolerance in the elite genetic background started
immediately after the establishment of the institute. Screening studies conducted
during 1950’s at ICAR-NRRI resulted in the identification of YSB tolerant genotypes
viz., TKM6, Slo-12, CB-1, MTU 15, Tepa-1, ADT-14 and JBS 1638. Among these,

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TKM6 was extensively used in the resistance breeding programme at the institute.
Three YSB tolerant varieties were released from ICAR-NRRI using TKM6 as the
donor. The varieties are, Ratna (TKM6 x IR 8) which is highly tolerant to YSB especially
at the vegetative stage, Saket 4 (sister selection of Ratna) and CR138-928 (Jaya x
TKM6). Other popular YSB tolerant varieties released from ICAR-NRRI include Vijaya
(T90 x IR8), Supriya (IR8//GEB24/T(N)1), Dharitri (Pankaj x Jagannath) and Panidhan
(CR151-79 x CR1014). Mutation breeding was also attempted to develop YSB tolerant
lines; a mutant line of Tainan3 was released in 1980 as the variety Indira (CR MUT
587-4) which possess a fair degree of YSB tolerance in addition to tolerance to blast
and BB. Besides NRRI, two more varieties, Sasyasree and Vikas with a moderate level
of resistance to YSB were released in India using TKM6 as the donor source. YSB
resistance was mapped by RAPD markers from a cross of Co43 x W1263. Though the
high yielding rice varieties enlisted above are moderately resistant to YSB, no rice
variety truly resistant to YSB has yet been developed.
Since gene(s) for resistance to YSB has not been found in the primary gene pool
of rice efforts were made to incorporate alien genes from wild species belonging to
the secondary gene pool, which are reservoirs of such traits. Wild rice germplasm has
been screened against YSB. O. brachyantha, O. officinalis, O. ridleyi and O. coarctata
were found to be resistant/tolerant against the pest. Subsequently, backcross
population of O. sativa cv. Savitri/O. brachyantha was developed to transfer YSB
resistance to the cultivated rice (Behura et al. 2011). The cytogenetic analysis of the
chromosomal variants lead to the development of monosomic alien addition lines
(MAALs). Of the 8 MAALs screened, MAAL 11 was found to be moderately resistant
to YSB.

6. STATUS OF UTILIZATION OF WILD GENE POOL FOR

BIOTIC STRESS TOLERANCE
The genus Oryza comprises of several wild species besides the two cultivated
species Oryza sativa (Asian rice) and Oryza glaberrima (African rice) (Table 5).
These wild relatives of cultivated rice are found to be grown naturally in different
ecologies around the world. The term species complex is used “for a group of species
where distinct taxonomic keys are lacking and the categorization to species or
subspecies level is rather arbitrary” (Vaughan 2005). Four major species complexes of
Oryza were identified which were designated as O. sativa complex (contains AA
genome), O. officinalis complex (comprises diploid and allotetraploid species of BB,
CC, DD or EE genomes), O. granulata complex (GG genome) and O. ridleyi complex
(allotetraploids of HH and JJ or KK genome). There is also a prominent outgroup
consisting of a lone species O. brachyantha (FF genome). These wild relatives are
considered as virtually untapped reservoir of agronomically important genes especially
for genes conferring resistance to biotic and abiotic stresses.

Utilization of Cultivated and Wild Gene Pools of Rice for

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Table 5. Different species of genus Oryza and their useful traits for biotic stress
tolerance.
Oryza species Chr. No. Genome Origin Useful traits
O. sativa complex
O. rufipogon 24 AA Tropical Asia Rresistance to BB and
tolerance to tungro
O. nivara 24 AA Tropical Asia Resistance to grassy
stunt virus and BB
O. longistaminata 24 AA Africa Resistance to BB
O. barthii 24 AA Africa -
O. meridionalis 24 AA Tropical Australia -
O. glumaepatula 24 AA South and Central -
America
O. officinalis complex
O. punctata 24, 48 BB, BBCC Africa Resistance to BPH
O. minuta 48 BBCC Philippines and Resistance to sheath
Papua New Guinea blight, blast, BB, BPH
O. malampuzhaensis 48 BBCC Southern India Resistance to BB
O. officinalis 24 CC Tropical Asia Resistance to BPH,
WBPH and GLH
O. rhizomatis 24 CC Sri Lanka -
O. eichingeri 24 CC South Asia and Resistance to BPH,
East Africa WBPH and GLH
O. latifolia 48 CCDD South America Resistance to BPH
O. alta 48 CCDD South America Resistance to stem borer
O. grandiglumis 48 CCDD South America -
O. australiensis 24 EE Tropical Australia Resistance to BPH and
blast
O. granulata complex
O. granulata 24 GG Southeast Asia -
O. meyeriana 24 GG Southeast Asia -
O. ridleyi complex
O. longiglumis 48 HHJJ Indonesia Resistance to blast and
BB
O. ridleyi 48 HHJJ South Asia Resistance to blast, BB
and stemborer
O. schlechteri 24 HHKK Papua New Guinea -
O. coarctata 48 HHKK India -
Outgroup
O. brachyantha 24 FF Africa Resistance to yellow
stem borer

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7. MAPPING OF GENES/ QTLS FROM WILD RICE AND

THEIR UTILIZATION
The rice breeders have mostly preferred hybridization among the members of
cultivated gene pool like indica-indica, japonica-japonica, indica-japonica, indica-
tropical japonica in their regular breeding programmes. Utilization of wild species
remained limited although in several cases, genetic variability for target agronomic
traits were lacking in the primary gene pool. The wild species of rice have been
utilized as a valuable source of genes for tolerance to various biotic (Table 6) and
abiotic stresses. Several major genes for resistance to brown planthopper (BPH),
white backed plant hopper (WBPH), gall midge, bacterial blight (BB), sheath rot and
leaf/neck blast have been identified from them. Several alien introgressed lines
developed using wild Oryza as the donor has been released in different countries
(Brar and Singh 2011).
The transfer of wild genes in cultivated rice depends on multiple factors like the
inheritance pattern of the trait (quantitative/qualitative or monogenic/oligogenic/
polygenic), phylogenetic relationship of cultivated and wild species and the presence
of reproductive barriers. Several pre- and post-fertilization barriers create difficulty in
hybridization of wild and cultivated rice. The transfer of desired genes or QTLs from
wild rice is difficult as the wild species are associated with several weedy traits like
grain shattering, low grain yield/quality and unwanted plant types. Along with
advancements in plant tissue culture techniques especially embryo rescue and
protoplast fusion, wild species are increasingly being used in gene transfer.
Cytogenetic techniques along with the availability of cross-transferrable markers
derived from genome sequencing projects have created further opportunities for
precise transfer of genomic regions from wild species.
Among several species of O. sativa complex, wild introgression lines for biotic
stress tolerance have been developed mostly for resistance to bacterial blight. Three
important genes for BB resistance have been mapped from the members of this species
complex namely Xa30 (t) from O. nivara, Xa23 from O. rufipogon and Xa21 from O.
longistaminata. These genes have further been utilized worldwide for rice breeding.
Ten distinct species are found in O. officinalis complex which are either diploid or
allotetraploid. The basic genomic groups are BB, CC, DD or EE. Two C- genome
species have mostly been used, namely O. offcinalis and O. eichingeri. Many of the
introgression lines derived from O. officinalis complex confers resistance to BPH
besides genes for resistance to WBPH, BLB and sheath rot. In Vietnam, four O.
officinalis derived BPH resistance lines have been released as varieties (Brar and
Singh, 2011).O. eichingeri have also been used for transfer of BPH resistance genes
to cultivated rice. Although interspecific hybrids were derived between O. sativa and
tetraploid wild species O. minuta, O. punctata and O. malampuzhaensis; development
of advanced introgression lines was only possible with O. minuta for transferring
resistance against BPH, BLB and blast. Among the three species with CCDD genome
O. latifolia, O. grandiglumis and O. alta, the third one is yet to be utilized in rice
breeding. However, introgression lines were derived from the rest two species. BPH,

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 67
Table 6. List of genes/ QTLs identified from wild rice for biotic stress resistance.
Wild species Trait Genes/QTL
O. rufipogon BB Xa23
O. nivara BB Xa30(t)
O. longistaminata BB Xa21
O. officinalis BPH Bph6, Bph11, Bph13(t), Bph15
BB Xa29
O. eichingeri BPH Bph13
O. minuta BPH Bph20(t) and Bph21(t)
BB Xa29
Blast Pi9(t).
O. latifolia BPH Bph12
O. australiensis BPH Bph10, Bph18
Leaf and neck blast Pi40(t)

WBPH and BLB resistant lines have been developed by transfer of genes from O.
latifolia. From backcross progeny lines of O. sativa × O. grandiglumis, although no
genes for stress tolerance were transferred, QTLs for yield contributing traits have
been mapped successfully. O. australiensis (EE) derived introgression with resistance
to BPH and leaf blast have been developed. Several important genes like Bph10,
Bph18 and Pi40 (t) have been tagged from these lines.
Introgression line development from O. ridleyi and O. granulata complex, as well
as O. brachyantha for biotic stress tolerance especially for the stresses considered in
this book chapter, is still lacking. However, MAAL lines with tolerance to many of
these stresses have been successfully developed by several researchers.

8. KNOWLEDGE GAPS AND RESEARCH NEEDS

Except for sheath blight and YSB, for all the pathogens and insects discussed
here, several major genes conferring resistance have been identified, fine mapped
and few of them have been cloned (Fig. 1). Many of them are also in use by the
breeders for developing disease resistant cultivars. Despite the reasonably good
amount of knowledge generated and genomic resources developed, breeders still
find difficulty in their judicious utilization in marker-assisted selection. Out of so
many genes known for disease resistance, lack of highly reproducible functional
markers for most of them creates troubles in their appropriate utilization. There is a
need for mega-scale allele mining among the large pool of susceptible and resistant
cultivars. Such a search should go beyond the cultivated species and must include
multiple accessions of wild species. Rather than targeting only one SNP, most
appropriate haplotypes must be identified after precise phenotyping.
Despite being the storehouse for genes of resistance to various biotic stresses,
utilization of genes and alleles from wild species is still very limited. Precise transfer of
genes from wild species avoiding linkage drag is quite difficult till now for most of the

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breeders. Lack of availability of

genomic resources especially
genome-wide markers for wild
species creates a major
bottleneck for this. However
with the availability of genome
sequences for more number of
wild species (genome
sequence is now available for
eight wild and two cultivated
species of Oryza) such
bottlenecks are expected to be
removed very soon.
For many biotic stresses,
despite sincere efforts, it has
not become possible till date
to assign resistance function
to a single gene. However,
QTLs with various level of
Fig. 1. Chromosomal location of cloned biotic stress
tolerance or resistance have
resistance genes in rice
been mapped. Although many
of these QTLs are genotype specific, some major QTLs were found to work across
populations. Precise mapping of those QTLs and their subsequent utilization in large
scale is expected in near future.
With large numbers of genes or QTLs being mapped, the question arises about
identifying the appropriate combinations of genes or QTLs for pyramiding in a single
background. Different genes or QTLs conferring resistance to same stress have
different mechanisms of actions. Identifying their appropriate combinations which
will confer maximum and durable resistance without any adverse effect on plant
growth and development is need of the hour. All the discovered genes or QTLs may
be pyramided in various combinations and tested across different growing
environments. Some efforts in this direction have already been initiated (Jena et al.
2017) which needs to be strengthened further.
All the research on resistance to biotic stresses will fail if there is any gap in
phenotyping methods. With increasing needs for mega-scale phenotyping for biotic
stress resistance, development of an easy yet effective protocol to clearly distinguish
the escapes from true resistance is the need of the time.

9. WAY FORWARD
The primary requirement for breeding tolerance to biotic stresses is availability of
precise phenotyping standards which will work across locations and can clearly
distinguish resistance from escapes. Whenever such phenotyping standards are

Utilization of Cultivated and Wild Gene Pools of Rice for

Resistance to Biotic Stresses 69
available, the phenotyping for those biotic stresses should be carried out in large
scale utilizing the network mode of AICRP or international trials of IRRI. This will help
in keeping track of evolution of new pathogens or insect biotypes and search for their
corresponding resistance source. The effective resistant QTLs or genes identified
though biparental mapping approaches should be supplemented with genome wide
association mapping to identify genes/QTLs which will work across populations.
After discovery of any gene or QTL, its optimum pyramiding combinations should be
worked out with reported genes or QTLs. Till date the major target of scientists
working on host plant resistance remains limited to search for R-genes in host genomes.
With advancements in genome sequencing, the scope for utilization of genome
sequences of both pest and host for understanding mechanism of resistance as well
as breakdown of resistance have increased. For identification of functional markers,
identification of superior functional haplotypes of resistance genes from both wild
and cultivated species is highly required. Prediction of R-genes from genomes of wild
species through bioinformatics approaches and their validation will also be useful. It
is important to note that stable and durable resistance genes present in wild rice are
yet to be exploited in large scale. There is urgent need for inclusion of more numbers
of wild species in breeding programmes of rice through pre-breeding and marker
assisted selection for their judicious utilization in resistance breeding of rice.
References
Ali MP, Chowdhury TR (2014) Tagging and mapping of genes and QTLs of Nilaparvata lugens
resistance in rice. Euphytica 195(1):1-30.

Behura N, Sen P and Kar MK (2011) Introgression of yellow stem borer (Scirpophaga incertulus)
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72 Resistance to Biotic Stresses
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Enhancing Input Use Efficiency in Direct-

Seeded Rice with Classical and Molecular
Breeding

A Anandan, J Meher, RP Sah, S Samantaray, C Parameswaran,

P Panneerselvam, SK Dash, P Swain, P Kartikeyan, M Annamalai
and G Kumar

SUMMARY
The dwindling freshwater resource and rising cost of rice cultivation have lead to
the debate of ways to enhance net return from rice cultivation for ever increasing
food demand for growing population. A resource use efficient system of rice cultivation
with water use efficient varieties is very much needed to improve the water productivity
in agriculture. Dry direct-seeded/aerobic rice system is a strategy that ensures water
use efficiency in rice crop to cope with the looming problem of water scarcity. To
achieve high yield, a suitable variety for this condition needs to have tolerance for
moisture stress, input use efficiency, weed competitiveness, and location-specific
pest and disease resistance. Recent developments in the field of dry direct seeded/
aerobic rice, yield component and nutrient use efficient QTLs and breeding strategies
are discussed in this chapter to improve grain yield.

1. INTRODUCTION
Puddled transplanted rice (TPR) system with stagnant water irrigation system is
reported to increase the productivity more than other systems of cultivation, wherein
restrained weed growth, trouble-free seedling establishment and increased nutrient
availability (e.g. iron, zinc, and phosphorus) are advantages of the TPR. However, the
hefty sum of water, more input, energy and time are required for TPR and these factors
make rice cultivation more expensive and less profitable. Thus, improving the crop
productivity and economic security to farmers with an alternate system of rice
production is very much necessary. Therefore, shifting of rice cultivation from TPR to
dry direct-seeded rice (DSR) is necessary to make income from rice cultivation
sustainable. Additionally, water has become a precious commodity in the era of modern
agriculture, but groundwater tables are started falling, and wells are going dry. Even
though, the green revolution met the food demand for our country, there is a demand
to extract water for irrigation has also started simultaneously. Further, millions of
farmers started to drill deeper irrigation bore wells to expand their harvests and resulting
in running down of groundwater table and wells in 20 countries, including three
countries that together produce half the world’s grain viz., India, China, and the
United States (Somanathan 2010). Consequently, the increase in production of cereal
grain came from irrigated land that has 40 percent share. But this inflated production
from irrigated land will burst when the aquifer gets depleted. Therefore, the decline in

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

Molecular Breeding 73
the supply of irrigation water is of great concern. In India, three fifths of grain harvest
come from irrigated land (Dick and Rosegrant 2009), where over-pumping of water for
irrigation is predominant. The states such as Punjab and Haryana witnessed falling
water table and green revolution achieved in India was based on water mining. In
Punjab, the number of tube wells has been increased from 1.9 lakhs in 1970 to 14 lakhs
in 2010, indicates that India’s food production is water based and may burst (Garg
and Hassan 2007) any time.
The rural-urban competition for water resource is gradually intensifying in India
and was evident that water needs of Chennai depend on popular tank-truck industry.
This stiff competition for water in urban areas of India does not favours the farmers,
as producing 1 kg of rice requires ~3,500 L of water. The greatest impact on water
consumption for urban needs is likely to continue well into the middle of the twenty-
first century (FAO 2006). Consequently, in a point, water scarcity would translate into
food scarcity. Thus, to reduce the level of water dependency and to improve the
water productivity in rice cultivation, water use efficient rice genotypes are one of the
viable options. Aerobic rice is one such extensive water-saving technology for rice
cultivation/production compared to other production methods. Aerobic rice systems
use less water than conventional flooded rice, by using suitable rice varieties capable
of responding well to reduced water inputs in non-puddled and non-saturated soils
(Atlin et al. 2006). Additionally, continuous standing water in paddy field favours
more nitrogen leaching loss than either in field capacity (aerobic) or alternate wetting
and drying. Moreover, application of recommended and/or excessive fertilizer is not
fully utilized by the plant. The unutilized portion escapes into environment through
runoff, leaching, ammonia volatilization, and N2O into atmosphere and water systems
(Zhu and Chen 2002). On the other hand, around 80–90% of applied P is also not
easily available to plant and transforms into other forms and eventually lost into the
water body causing eutrophication (Schindler et al. 2016). This detrimental impact
needs to be addressed by increasing the Nutrient Use Efficiency (NUE) of rice in
concert with other management practices. It is therefore critical that strategies for
genetic improvement of NUE needs to be undertaken for cultivating rice with less
water and higher NUE to maximize biomass and yield. Reducing the cost of inputs
would be one of the prime solutions to increase farm income in rice cultivation.
Additionally, the genetic potential of yield could be achieved through proper nutrient
and weed management. This chapter addresses the major avenues for increasing the
productivity and profitability of farmers by increasing the NUE under DSR, where
labor workforce shortage is highly prevalent in eastern India.

2. PROBLEMS OF CONVENTIONAL PUDDLED

TRANSPLANTED RICE
The anticipated climate change, shortage of water and natural resources and
shortage of man power are likely to be major researchable issues in future. Under
such circumstances, direct-seeded rice system can mitigate the adverse situation for
rice cultivation and minimizes the negative impacts of TPR by reducing the labor

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

74 Molecular Breeding
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

requirement and, increasing water and NUE. In Asia, the practice of dry seeding is
popular and extensively adopted in rainfed lowlands, uplands, and flood-prone areas
with an area of 26% in south Asia and 28% in India. Globally, 23% of rice is direct
seeded, as wet seeding is being the common practice and predominantly practiced in
irrigated areas of Australia, Brazil, Chile, Cuba, France, Italy, Japan, Korea, Malaysia,
the Philippines, Thailand, Russia, Sri Lanka, Vietnam, and in some parts of Iran, due to
shortage of skilled labour, high labour cost and availability of mechanised system
(Mahender et al. 2015). Thus, DSR system of cultivation should be encouraged, as
agricultural labor workforce is reducing relative to the total workforce in India. It is
reported that ~30 million agricultural labor workforces in India was reduced as compared
to 2004-05 (FICCI report). The states of Uttar Pradesh (28%), Odisha (14%), Bihar
(12%) and West Bengal (12%) contributed on an average of 16.5% reduction in
agricultural workforce in India.
DSR system showed substantial water saving. Trials conducted in Haryana by
adopting zero or reduced till system resulted in good grain yield comparable with TPR
under less water with more water productivity and greater net profit. Moreover, it
increases net return, efficiency in water and fertilizer use (Anandan et al. 2015). The
varieties released during and after green revolution has ability to utilize less than 50%
of applied fertilizer. These varieties combined with intensive agricultural practices,
effects environment through methane emission and eutrophication of water bodies.
Therefore, DSR, helps farmers to earn more carbon credits than TPR by mitigating
methane emission and provides higher economic returns, saves water and reduces
labour requirement. However, no specific varieties possessing all suitable traits of
DSR have been developed with nutrient and water use efficiency. Varieties that are
necessary for DSR should possess good mechanical strength in the coleoptiles to
make easy emergence of the seedlings under crust conditions, weed competitiveness
with early seedling vigour, efficient root system to tap soil moisture and nutrients
(Fig. 1 and 2), early maturing, photoperiod-insensitive with better drought tolerance
and yield stability. Specifically, improving NUE is very much needed in our rice-wheat
cropping system in India. Moreover, the consumption of N fertilizer has been increased
from 0.06 Mt in 1950-1951 to 10.8 Mt in 2000-01 and P fertilizer has steeply increased
from 0.01 Mt to 1.8 Mt in the last 50 years (FAI 2000-2007). Correspondingly, N and P
fertilizer contributed around 64% and 78%, respectively in Indian agriculture (Pathak
et al. 2010). Further, Pathak et al. (2010) highlighted that states like Tamil Nadu, Gujarat,
Haryana, Punjab and West Bengal showed 50% N use efficiency and less than 50% N
use efficiency was observed in the states like Bihar, Odisha and Uttar Pradesh. Also,
Odisha and Bihar showed minimum P balance (Pathak et al. 2010). Thus, there is a
need to increase the N use efficiency and PUE of rice in eastern India to reduce the
cost of cultivation in sustainable way and increase the per capita food availability.
Developing rice cultivars with improved NUE becomes a prerequisite in protecting
the environment by reducing the rate of nutrient loss into the ecosystems. It also
reduces input cost and improves rice yield in a sustainable manner, while maintaining
soil and groundwater quality. Nutrient use efficient varieties can also be raised in
marginal lands where nutrient availability is limited. Therefore, the present breeding
program should be prioritized to develop rice varieties with high grain yield under

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

Molecular Breeding 75
 low-nutrient conditions (Vinod and
Heuer 2012). Significant genotypic
differences in nitrogen (Singh et al.
1998) and phosphorus (Wissuwa and
Ae 2001) use efficiency exist in rice
with several mechanisms and morpho-
physiological traits to sustain their
growth. Among the several rice
accessions, it is observed that
Fig.1. Variability in rice root system.
landraces are being superior in nutrient
uptake. It is reported that P
concentration varied from 0.6 to 12.9
mg P plant”1 (Wissuwa and Ae 2001).
Therefore, the variability exists in the
form of morpho-physiological traits
related tolerance to P deficiency could
effectively be exploited through
systematic breeding program to
develop cultivars with high NUE and
water use efficiency (Ali et al. 2012).
In order to increase the NUE, traits
involved in nutrient absorption,
transport, utilization and mobilization
should be identified and in
combination with best management
practices it could provide sustainable
Fig. 2. Direct seeded rice genotypes should rice cultivation. On the other hand, role
possess good numbers of lateral and deep of microorganisms in enhancing the
roots for absorbing nutrient and water in availability of N and P needs to be
symbiotic association with AMF and bacteria
recognized. Several reports have
efficiently from soil.
proved that inoculations of the
microbial consortium have been shown
to enhance NUE particularly phosphorus, nitrogen, and carbon in many crop plants.
Rice differs from most of the crops, since it is typically cultivated in flooded soil,
resulting in aerobic and anaerobic zones within the rice rhizosphere, and preferred by
specific physiological groups of microorganisms i.e. aerobic, anaerobic, or facultative
(Brune et al. 2000). Hence, it is essential to understand the soil microbes and plant
interaction for better input resource management for sustainable rice cultivation.
Also, presence of variability in microbial association with plants (Hardoim et al. 2011)
provides the possibility of breeding cultivars for specific microbial community
(Mahender et al. 2017) to gain NUE. The objectives of this chapter are i) to review the
water and nutrient (N and P) use efficiency scenario in rice cultivation of India, and ii)
to understand how to improve water and NUE in rice through classical and molecular
breeding approaches.

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76 Molecular Breeding
 Rice Research for Enhancing Productivity,
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3. DRY DIRECT SEEDED/AEROBIC RICE ON WATER USE

EFFICIENCY
Dry direct seeded rice refers to a cultivation system in which rice is dry direct
seeded in well-tilled levelled fields with the uniform slope under unpuddled conditions.
When the crop is cultivated with no standing water throughout the season under a
well-aerated condition at field capacity is termed as aerobic rice, occasional water
stagnation may occur under rainfed low land condition. Thus, the high proportion of
water savings associated with this method compared with conventional rice growing
practices has made this method increasingly popular in irrigated areas, where the
problem of water shortage occurs (Kumar and Ladha 2011). The affinity of the rice
crop with water is universally known. Rice cultivation in puddled fields is well known,
technologies such as dry/aerobic and wet direct seeding and alternate wetting and
drying (AWD) could be aviable option to produce rice in both irrigated and rainfed
rice ecosystems. Aerobic rice is one such extensive water-saving technology for rice,
reducing labor requirements, mitigating greenhouse gas emissions, and adapting to
climatic risks; and the yield can be compared with that of transplanted rice if the crop
is properly managed (Kumar and Ladha 2011).
In Brazil and northern China, aerobic rice is grown commercially in 140,000 ha. In
China, temperate aerobic rice cultivars under supplementary irrigation exhibited grain
yield of 6 t/ha (Bouman et al. 2005). These varieties need 60% less water than that
required for lowland rice and their total water productivity was 1.6-1.9 times higher
(Guang-hui et al. 2008). In temperate zone country like the United States, lowland rice
varieties were tested under aerobic condition and observed 20-30% yield reduction in
high yielding cultivars (7-8 t/ha). The decline in yield under aerobic was due to the
reduction in panicles per meter square, spikelets per meter square, poor grain filling,
and harvest index. Comparatively, flooded rice had 20% more panicles per meter
square, 15% more spikelets per meter square and 13% higher grain filling than aerobic
rice (Visperas et al. 2002). Under scanty water supply of 450-650 mm, 4-6 t/ha of grain
yield was observed in much drier soil condition against 1300-1500 mm of water used
in lowland situation. Other than the merit of efficient use of water, aerobic rice
demonstrated better nitrogen use efficiency (George et al. 2001).
The rice that is being grown extensively in the upland ecosystem (direct seeding),
showed wide genetic variation for aerobic adaptation in rice germplasms. Several
quantitative trait loci (QTL) for grain yield have been reported for both favorable
irrigated and unfavorable upland ecology (Venuprasad et al. 2009). However, very
few reports have reported the genomic regions responsible for increased aerobic
adaptation of rice. Few encouraging reports are available regarding grain yield QTLs
found under aerobic condition from International Rice Research Institute (IRRI),
Philippines. Venuprasad et al. (2012) reported two closely linked rice microsatellite
(RM) markers RM510 and RM19367 located on chromosome 6 were found to be
associated with grain yield under aerobic soil conditions, consistently in three genetic
backgrounds. The QTL linked to this marker, qDTY6.1, was mapped to a 2.2 cM
region between RM19367 and RM3805 at a peak LOD score of 32 in the Apo/2*Swarna

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

Molecular Breeding 77
population. The effect of qDTY6.1 was tested in a total of 20 hydrological environments
over a period of five seasons and in five populations in the three genetic backgrounds
(Apo/2*Swarna, Apo/IR72, and Vandana/IR72). In the Apo/2*Swarna population,
qDTY6.1 had a large effect on grain yield under favorable aerobic (R2 d” 66%) and
irrigated lowland (R2 d” 39%) conditions but not under drought stress. Further, they
conclude that qDTY6.1 is a large-effect QTL for rice grain yield under aerobic
environment and could potentially be used in the molecular breeding of rice for the
aerobic environment. So far, no variety has been developed that possesses traits
specifically needed to produce high yield under aerobic conditions, particularly for
rainfed systems that may be prone to low fertility (Sandhu et al. 2015). Kato et al.
(2009) suggested that aerobic rice varieties should possess large numbers of spikelets
and sufficient adaptation to aerobic conditions will consistently achieve yields
comparable to the potential yield of flooded rice.
Sandhu et al. (2015) identified several promising QTLs that showed large and
consistent effects from two mapping populations derived from crosses of Aus276, a
drought tolerant aus variety, with MTU1010 and IR64, high-yielding indica mega-
varieties. They have reported that QTLs qGY1.1, qGY6.1, and qGY10.1 were found
to be effective in both populations under multiple conditions. On the other hand,
several of the QTLs identified for grain yield in their study (qGY1.1, qGY6.1, qGY8.1,
qGY9.1, and qGY10.1) were found to be previously reported and consistent across
different mapping populations, under different drought severities.
In 2012, Ye et al. (2012) have identified two major QTLs qHTSF1.1 (R2 = 12.6%)
and qHTSF4.1 (R2 = 17.6%), were detected on chromosome 1 and 4, respectively, in
BC1F1 and F2 progeny generated from the cross IR64 x N22. Later in 2015, Ye et al.
through fine-mapping validated the effect of qHTSF4.1 with PCR-based SNP markers.
They found that the sequence in the QTL region is highly conserved and large
numbers of genes in the same gene family were observed to be clustered in the
region. The QTL qHTSF4.1 consistently increased spikelet fertility in all of the
backcross populations (BC2F2, BC3F2, BC3F3, and BC5F2) and this was confirmed
again in 24 rice varieties. Most of the rice varieties with this QTL showed a certain
degree of increase in spikelet fertility. In a BC5F2 population with the clean background
of IR64, QTL qHTSF4.1 increased spikelet fertility by about 15%. Therefore, it could
be an important source for enhancing spikelet fertility in rice at the flowering stage.
PCR-based SNP markers developed from their study would be useful for QTL
introgression and for pyramiding with other agronomically important QTLs/genes
through marker-assisted selection.
Several research institutes/universities across India started developing rice
varieties that consume less water for rice cultivation with more water use efficiency.
ICAR-NRRI, too involved in aerobic rice research and developed 9 aerobic (water use
efficient) rice varieties and released through Central Sub-Committee on Seed Standards,
Notification and Release (CVRC) and State Variety Release Committee (SVRC). Three
aerobic rice varieties Anagha (ARB 6), MAS 26 and MAS 946-1 were released from

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

78 Molecular Breeding
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

the University of Agricultural Sciences (UAS), GKVK, Bangalore for the state of
Karnataka. Performance of these varieties was found to be well under aerobic with fair
degree of drought tolerance. These genotypes need to be irrigated at the intervals of
5 to 7 days and irrigation can be skipped in the event of rainfall. The grain yield
potential of these lines was 7.0 t/ha in station trials at UAS, Bangalore, while in
farmers’ field it recorded with an average yield from 3.0 to 5.0 t/ha (Shashidhar 2012).
Efforts have been taken to identify QTLs responsible for grain yield under aerobic/
dry direct seeded rice in India. However, limited reports are available in relation to
QTLs. Recently, Sandhu et al. (2013) have mapped 35 QTLs associated with 14 traits
on chromosomes 1, 2, 5, 6, 8, 9, and 11 in MAS ARB25 x Pusa Basmati 1460 and 14
QTLs associated with 9 traits were mapped on chromosomes 1, 2, 8, 9, 10, 11, and 12
in HKR47 × MAS26 from CCS Haryana Agricultural University, Hisar. The QTLs,
qGY8.1 (R2 value of 34.0%) and qGY2.1 (R2 value of 22.8%) of MAS ARB25 × Pusa
Basmati 1460 population and QTL qGY2.2 (R2 value of 43.2%) of HKR47 × MAS26
population were found promising for grain yield under aerobic condition. Among the
three yield QTLs, qGY8.1 showed an increased stable effect over two different years
and combined over two years with 26.6% yield improvement. Further, the authors
highlighted the QTL hotspot region at 25.1cM segment between RM589 and RM314
on chromosome 6 affects different root (RV, RT, and FRW) and shoot (FSW and DSW)
traits under aerobic conditions of two mapping populations (MAS ARB25 x Pusa
Basmati 1460 and HKR47 × MAS26). This region is found to be co-localized with
qDTY6.1 region reported by Venuprasad et al. (2011). It was found to be associated
with grain yield in the aerobic environment, in total of 20 hydrological environments
over a period of five seasons and in five populations in three genetic backgrounds
using bulk-segregant analysis (Venuprasad et al. 2011).

4. NUTRIENT USE EFFICIENCY

Nitrogen is an imperative element for improving higher grain yield, root development
for uptake of water and other nutrient elements from the soil, regulation of flowering
time, and grain quality. Several QTLs have been identified for N use efficiency in rice.
In a mapping population of Nipponbare and Kasalath, 6-7 QTLs have been identified
for glutamine synthase and NADH glutamate synthetase involved in nitrogen uptake
pathway (Obara et al. 2001). Similarly, qNUEP-6, pneu9 and QTL for low N tolerance
have been reported in rice (Zhou et al. 2017). Over expression of one of the nitrate
transporter gene OsNRT3.2b has been reported to increase the yield of rice.
Interestingly, a heterotrimeric G protein was identified to regulate N use efficiency in
rice (Sun et al. 2014). This gene was previously identified as dense and erect panicle
1 (DEP1) and reported to alter the panicle architecture. In addition, natural variation
of DEP1 locus was shown to increase the yield of rice (Huang et al. 2009). Thus, this
gene could be used for simultaneously increasing the yield and NUE of rice. The
genetic loci associated with N use efficiency were mapped in ASD16 x Basmati 370
population (Senthilvel et al. 2004). In another report, seven QTLs were identified for
nitrogen use in the mapping population of IR64 x Azucena (Senthilvel et al. 2008).

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

Molecular Breeding 79
 Next to nitrogen, phosphorus is considered as one of the major nutrient for rice
and essential for better root development (Bovillet al. 2013). The available form of
phosphorus in the soil is limited due to its fixation nature in the soil. Several reports
have suggested the possibility of improving the genetic potential of rice towards
efficient utilization of phosphorus. The major QTL for low phosphorus tolerance
‘phosphorus uptake 1’ (Pup1) was identified in the aus genotype Kasalath and the
causal gene (PSTOL1) was found to be a protein kinase (Gamuyao et al. 2012). It
increases the root biomass of rice crop under low P condition. On the other hand,
OsPHO1 gene was identified to play an important role in transfer of P from roots to
shoots (Secco et al. 2010). Several phosphorus transporter genes have been identified
to play an important role in P uptake and remobilization in rice. The expression studies
of phosphorus transporter genes have identified PT2 and PT6 gene as high affinity
phosphorus transporter gene in rice and PT8 as gene responsible to transport of P
from source to sink organs in rice (Li et al. 2015). Till date, several QTLs have been
reported for phosphorus use efficiency (PUE) in rice. Further, Mahender et al. (2017)
has done a comprehensive review on QTLs and recent advances on PUE. They
reported that to date around 133 P associated QTLs of morpho-physiological traits
were available and found to be distributed on all 12 chromosomes and the majority of
them were localized on chromosome 1, 2 and 12. A high density SNP mapping of RIL
population has identified 26 QTLs for eight PUE traits (Wang et al. 2014). Apart from
PUE traits, genetic variation of root traits has been studied to understand the P
uptake and low P tolerance in rice (Vejchasarn et al. 2016). Recently, Mehra et al.
(2017) characterized purple acid phosphatase (PAP21b) gene from Dular genotype
that confers low phosphorus tolerance through enhancing the availability of P present
in organic sources in the soil. On the other hand, Yugandhar et al. (2017) screened six
N22 mutants in three conditions, normal, low P and AWD and estimated the genetic
diversity. They found that Pup1 gene-specific marker, K-1 was associated with tiller
number under low P conditions.
Phosphorus use efficiency can also be improved by mycorrhization of the rice
plant with Arbuscular Mycorrhizal Fungi (AMF) that causes significant mobilization
of insoluble P in substrate and plant uptake. Arbuscular mycorrhizal fungi inoculated
rice through direct or indirect mechanism facilitates uptake of P from poorly soluble P
(Panneerselvam et al. 2016a; 2016b), Zn, Cu etc. (Harley and Smith 1983; Wellings et
al. 1991). The AMF colonization in roots helps the plants to uptake fixed soil P by
rhizosphere modification through multiple mechanisms, by secretion of organic acids,
phosphatase enzyme and metabolites like siderophores (Shenoy and Kalagudi 2005;
Panneerselvam and Saritha 2017). The mycorrhizal plant also could absorb P from
poorly soluble P source like aluminum phosphates, iron and rock phosphate (Shenoy
and Kalagudi 2005). Reports suggests that AMF association in plants also causes
changes in pH and root exudation profile (Li et al. 2001; Sowarnalisha et al. 2017),
which may alter the rhizosphere microbial community and in turn, enhances P
solubilization mechanism. However, it was observed that the plant growth performance
and nutrient uptake will vary from species to species; hence there is a need for
selection of suitable/efficient AMF for better plant growth and development (Bagyaraj
et al. 1989).

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5. RESEARCH ON DIRECT SEEDED RICE AT ICAR-

NATIONAL RICE RESEARCH INSTITUTE
The aerobic rice breeding at ICAR-NRRI was initiated with the support of the
Asian Development Bank (ADB) by hybridizing high yielding irrigated rice varieties
with drought tolerant lines, aerobic rice germplasm and other exotic donors from
International Rice Research Institute (IRRI), Philippines. Under this project, large
variability of genotypes for the aerobic condition was generated and promising
genotypes were selected by adopting the pedigree breeding method. On the other
hand, several segregating populations and fixed lines were introduced from IRRI,
Philippines, to select superior lines under Cuttack condition. In 2012, a promising
variety Apo was identified from AICRIP Varietal Improvement Programme. Apo is one
of the popular aerobic variety of Philippines was found suitable in Odisha, and it was
released as CR Dhan 200 (CR 2624-IR55423-01; IET 21214) by the Odisha State Sub-
Committee on Crop Standards, Notification, and Release of Varieties. At NRRI,
promising aerobic lines nominations were started in 2007 to the national AICRIP trials
for evaluation of materials at various target locations in different states of the country.
Subsequently, nine aerobic varieties were released through CVRC and SVRC (Table 1).
Table 1. Rice varieties released from ICAR-NRRI for dry direct/aerobic condition.
Duration Grain yield
S.No. Variety Parentage (days) (t/ha)
1 CR Dhan 200 (Pyari) CR 2624-IR 55423-01 115-120 4.0
2 CR Dhan 201 IRRI 76569-259-1-2-1/ 110-115 3.8
CT 6510-24-1-2
3 CR Dhan 202 IRRI 148/IR 78877-208-B-1-1 110 3.7
4 CR Dhan 203 (Sachala) IR78877-208-B-1-1/ IRRI 132 110-115 4.0
5 CR Dhan 205 N22/Swarna 105-110 4.2
6 CR Dhan 206 Brahmannaki/ NDR 9930077 105-110 4.2
7 CR Dhan 207 (Srimati) IR71700-247-1-1-2/ 110 -115 4.5
IR57514-PMI 5-B-1-2
8 CR Dhan 209 (Priya) IR72022-46-2-3-3-2/IRRI 105 110 -115 4.5

Upland rice is known to have significant uptake ability of P under deficient

condition. Therefore, 70 upland rice genotypes and wild species (O.nivara and O.
rufipogon) were screened under P deficient soil (6 ppm) with two tolerant checks
(Kasalath and Dular) and one susceptible check (IR 36). Among them, eight upland
genotypes and four wild species exhibited superiority over the positive checks. They
were genotyped to assess the presence of Pup1 allele. Genotypes AC100062, AC100117,
Dular, Sekri, Brown gora and AC 100117 had similar amplification pattern with Kasalath
(NRRI annual report 2014-15). Similarly, Elssa Pandit et al. (2016) genotyped 96 upland
cultivars and landraces for better P-uptake. Among them, 46 possessed the Pup1
locus that accounts for 47.92% of the total genotypes considered. The genotypes
N22, Dinoroda, Bowde, Bamawpyan, Tepiboro, Karni, Lalsankari, Surjamukhi,
Hazaridhan and Kalinga III were positive for two closest flanking and two gene
specific Pup1 markers

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Molecular Breeding 81
6. KNOWLEDGE GAPS
Direct seeded rice is a viable alternative to TPR and suitable for targeted areas
suffering from water availability and labor scarcity. Further, DSR/aerobic rice is found
most suitable for rainfed lowland areas where insufficient precipitation occurs, delta
regions where there is no availability of water in-time or delay in water release from
reservoir (Anandan et al. 2015), limited water during early stage of crop growth but
later crop faces flood, pumping from deep bore well and favorable upland has access
to supplementary irrigation (Bouman 2001) are the most suitable location to adapt
DSR/aerobic rice. Accordingly, Chhattisgarh, parts of Bihar, Jharkhand, Karnataka,
Odisha, Tamil Nadu, and eastern Uttar Pradesh are the projected areas, where there is
an uneven distribution of rainfall and frequent occurrence of soil moisture limitation.
Further, the maintenance of physical soil structure in DSR helps to have timely sowing
of succeeding crop.
The success of DSR system depends on availability of suitable variety and crop
management practices. However, non-availability of suitable breeding program and
limited knowledge on the genetics of donors are the major drawback of this system to
achieve adaptable and maximum yield potential under DSR. The ICAR-NRRI, Cuttack
has released several rice varieties (Table 1) suitable for DSR/aerobic condition and
the grain yield of those genotypes yield 4.5t/ha (Anandan et al. 2015) under continuous
aerobic condition. To improve the grain yield further, several traits adaptable for DSR
need to be addressed.
The phenotypic traits directly relevant to DSR genotypes should have the
increased ability to germinate from deeper soil depth with longer coleoptile and
mesocotyl length and uniform germination ability to have uniform plant population
with early seedling vigour (Anandan et al. 2016a; 2016b). As weed has the major
impact on DSR, uniform plant population with uniform height facilitates timely
intercultural operation to manage weeds. Increased numbers of nodal roots, root
length density, lateral root length and branching with more root hairs for proper
nutrient uptake under dry conditions are necessary traits for DSR (Fig. 2) (Kumar et
al. 2017). Anaerobic germination is another important trait that improves crop
establishment in uneven field or flash flood after rain. Roots of DSR variety should
have sufficient plasticity to function under both aerobic and water logging condition.
During early stage of crop establishment, the seedling should possess early vigour
with good canopy cover to smoother the weed growth. The later stage of crop should
have low specific leaf area, high chlorophyll, medium plant height (110-120 cm), early
flowering, slim and sturdy culm, 250-300 panicles per meter square, more number of
filled grains per meter square, retaining panicle height within the canopy level, erect
boot leaf and high harvest index (Fig. 2). Deep rooting plants would be more
advantageous, as they could mine water from deeper layer (Fig. 1). On the other hand,
switching over the rice crop from flooded condition to aerobic/dry rice, soil can
reduce the indigenous supply of P, Fe (Fan et al. 2012) and Zn. Continues cultivation
of rice over the years under dry condition, would result in soil sickness. Moreover,
soil Fe fertilization increased concentration in shoot and dry weight at tillering, but

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failed to increase the same during physiological maturity (Fan et al. 2012). Therefore,
the traits starting from germination to maturity needs to be addressed to achieve yield
on par with TPR.

7. RESEARCH AND DEVELOPMENT NEEDS

Under the growing water scarcity in Indian agriculture scenario, rice cultivation is
gradually progressing from continuous flooded TPR system to partial or complete
aerobic condition. Therefore, a new plant system that differs from regular transplanted
rice has to be developed for this condition (Fig. 2). The varieties needed for DSR
should have wider adaptation to suit the aerobic rice ecosystem with maximum water
use efficiency, along with less yield penalty.
7.1. Breeding for yield component traits
Grain yield is the collective phenotypic expression of yield component traits
whereas, adaptability is due to buffering capacity of genotypes for which many minor
genes are in additive response. Thus, the accrual of favourable genes, those expressing
at critical stage of rice plant under DSR/aerobic condition has to be combined.
7.2. Seedling vigour and its associated traits for early establishment
Early and uniform crop establishment is necessity for DSR. High seedling vigour,
improved field emergence, weed competitiveness, tolerance against anaerobic
condition and reduced moisture stress during germination (Mahender et al. 2015),
enhanced foliar growth to combat weeds at the vegetative stage (Dingkuhn et al.
1991), seedling dry weight, rapid shoot growth, shoot dry weight, mesocotyl and
coleoptile length (Fujino et al. 2008; Trachsel et al. 2010), germination rate, germination
index, amylase activity, root activity and chlorophyll content (Diwan et al. 2013; Dang
et al. 2014; Sandhu et al. 2015) are significantly contributes to early establishment in
direct seeded rice. Additionally, these traits would facilitate to overcome limited
moisture condition and/or submergence during monsoon time. Therefore, genetic
improvements in rice breeding program for direct seeded condition should focus on
improving those traits to make rice suitable for DSR. In recent years, several QTLs
were identified for early establishment of rice seedling and they were elaborated well
by Mahender et al. (2015) and Kumar et al. (2017). QTLs for traits related to early
seedling vigour such as shoot length, germination rate and root dry weight in 28 days
old seedling (Haritha et al. 2017; Anandan et al. 2016a; Mahender et al. 2015) and
qEMM1.1 for early uniform emergence were identified form direct seeded condition
(Dixit et al. 2015). Successful introgression of these QTLs would provide an
opportunity to the early establishment and increases the plant population, thereby
smothers the weed growth. Early seedling vigour cultivars are reported to be a low-
cost, durable and decrease the detrimental effect of herbicide on the environment
(Anandan et al. 2016a).

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Molecular Breeding 83
7.3. Understanding the traits for vegetative and reproductive phases
The photosynthates accumulated during vegetative stage from available biomass
of aerial and underground portion determines the final output of the crop. Therefore,
moderate tillering of 10–12 numbers and enhanced assimilate export from leaves to
stems during the late vegetative and reproductive phases are important to achieve
higher grain yield by grain filling (Dingkuhn et al. 1991). Ghosh et al. (2012) from the
ICAR-NRRI, Cuttack has observed that 17% yield decline under aerobic system occur
due to inhibition in the structural development of roots as increase in the concentration
of hydrogen peroxide (24.6%) and proline (20%) and a lower concentration of total
soluble protein (20%). Therefore, the QTLs identified under DSR would be more
appropriate to utilize in rice breeding for DSR than the QTLs identified form TPR
condition. Introgression of such QTLs would definitely be beneficial and improves
better adaptation to DSR condition with high yield potential. Successful introgression
of such QTLs provides an opportunity to study their performance and interaction
between them. Sandhu et al. (2015) identified QTLs for nodal root (qNR4.1 and qNR5.1)
and root hair density (qRHD1.1 and RHD5.1) under direct seeded condition. Similarly,
Dixit et al. (2015) reported QTLs qLDG3.1 and qLDG4.1 for lodging tolerance. Several
grain yield QTLs were identified (qGY1.1, qGY2.1, qGY2.2, qGY8.1 and qGY10.1) by
Sandhu et al. (2013; 2015) under aerobic condition. Therefore, the breeding program
for DSR should aim to increase the yield and adaptability by introgressing such QTLs
for the benefit of farmers in the target areas struggling for water and labor.
7.4. Breeding for biotic stresses
Rice cultivation under aerobic favors blast (Magnaporthe grisea), bacterial leaf
blight (BB) (Xanthomonas oryzae pv. oryzae) and brown spot (Helminthosporium
oryzae). Therefore, rice varieties of aerobic should have durable resistance genes for
blast and BB. This could also help to reduce resources to be incurred and environmental
pollution. Brown spot often occurs in poorly managed and deficient soils under
inadequate soil moisture. Therefore, balanced dose of nitrogenous fertilizer needs to
be maintained with sufficient soil moisture to avoid the incidence of blast and brown
spot. Stem borer and leaf folder are the major concern of aerobic rice. Cultivation of
resistance varieties and summer ploughing are recommended to reduce pest incidence
in aerobic. The menace of root-knot nematode Meloidogyne graminicola is increasing
under aerobic and causes severe damage to rice plants. Therefore, raising resistance
varieties are recommended to avoid yield reduction.
7.5. Breeding for nutrient use efficiency
Saturation level increases the availability of nutrients P and Fe. There are reports
on soil sickness, which appears after few years of aerobic rice cultivation. Moisture at
field capacity in aerobic condition may reduce the nutrient availability. Therefore,
detailed study must be taken to understand the nutrient dynamics of major and
micronutrient and their bioavailability. Pal et al. (2007) observed the differential
responses of rice cultivars to applied Fe. In an experiment to test rice genotypes
under aerobic condition for Fe, two lines (CT 6510-24-1-2 and IR 71525-19-1-1)

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84 Molecular Breeding
 Rice Research for Enhancing Productivity,
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performed better compared to the varieties IR 36 and IR 64 suitable for TPR. These
deferential responses sound that inherent ability of the genotype plays important
role in Fe absorption. Sandhu et al. (2015) has reported QTLs qN5.1, qP5.2, qFe5.2 for
nodal root and root hair density, that plays major role in higher nutrient uptake (Al,
Fe, and P), under DSR. QTLs for higher nutrient uptake, higher nutrient concentration
and root hair density were also found to be co-localized in the same region. Enhancing
root growth with root hair density enhances P uptake (Mahender et al. 2017). Fine
mapping of Pup1 region lead to the identification of P starvation tolerance 1 (PSTOL1)
gene encoding a PSI protein kinase. Under P deficient condition, PSTOL1 enhances
the early root elongation and improves the grain yield (Gamuyao et al. 2012). Recently
Mehra et al. (2017) characterized purple acid phosphatase (PAP21b) gene from Dular
that enhances the uptake of P present in organic form in the soil. Thus, stacking of
PSTOL1, PAP21b, and QTLs of nodal root and root hair density into elite varieties by
marker-assisted selection would definitely improve nutrient concentration in plants
under aerobic condition. Stacking up of nutrient uptake genes/QTLs may result in
improved performance by complementary effects will reduce the cost incurred by
resource-poor farmers.
7.6. Molecular understanding and their role of microbes to improve
nutrient use efficiency
The genomics and transcriptomics studies revealed that a successful AMF root
colonization is controlled by the genotype of plants. The HAR1 gene i.e.
Hypernodulation and Aberrant Root Formation1 are reported to control number of
root nodules in legumes and the same gene also plays a role in the regulation of AMF
symbiosis (Solaiman et al. 2000), but the mode of action of this gene is still not
understood. The genetic requirements for rhizobial and AMF association in plants
overlap in a common symbiosis pathway (CSP), which leads to successful root nodule
and AMF symbiosis (Tirichine et al. 2006). The CSP plays an important role in
accommodating root nodule and AMF symbionts, by which plant cells vigorously
decompose their cell wall structures to facilitate microbial colonization (Parniske,
2000). The effects of the Oryza sativa calcium/calmodulin-dependent protein kinase
(OsCCaMK) indicated that a strong expression of OsCCaMK was detected in rice
roots, where mycorrhizal colonization is expected to occur (Parniske 2009). The other
study revealed that OsCCaMK gene expression has the positive correlation with the
diversity of root-associated bacteria and the growth of rice plants (Ikeda et al. 2011).
The above information indicates that studying the plant associated gene and its
expression related to the specific microbial association is very important to develop
rice varieties, which have affinity towards the specific group of microbes to improve
the NUE in rice (Fig. 2).

8. WAY FORWARD
The modern plant breeding has moved from classical breeding to precision
breeding by adapting powerful indirect selection technique of employing molecular

Enhancing Input Use Efficiency in Direct-Seeded Rice with Classical and

Molecular Breeding 85
marker technology. During the last two decades, the modern plant breeding is
progressing in faster pace; more number of popular rice varieties of favorable land to
marginal land with assured yield is developed by researchers in India. Several genes
were identified and characterized for their functions related to yield, nutrient deficiency
tolerance, biotic and abiotic stresses. Therefore, designing of a plant variety with
desired traits becomes possible for any specific ecosystem. However, more efforts
are needed to identify new genes responsible for nutrient deficiency tolerance and
water use efficiency. On the other hand, further understanding is required to know
the genes involved for regulating the differences in use efficiency and tolerance
mechanism. This would maximize their role in crop improvement program for resource
use efficiency. Developing next-generation rice suitable for the direct seeded system
is very much necessary to tackle increased food demand under the limited labor, land,
water, and nutrient during this changing climate period. The molecular approaches
along with best crop management could significantly increase the productivity in
aerobic rice cultivation.
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 Genetic Improvement of Rice for Aroma,
Nutrition and Grain Quality

S Sarkar, SSC Pattanaik, K Chattopadhyay, M Chakraborti,

P Sanghamitra, N Basak, A Anandan, S Samantaray, HN Subudhi,
J Meher, MK Kar, B Mandal and AK Mukherjee

SUMMARY
Rice is the staple food for more than half of the world population satisfying the
variable quality preferences of consumers across the globe. Therefore, there is no
universal quality for rice. Besides, quantitative nature of their inheritance, effect of
environment in their expression, destructive methods of estimation and high error
rates in analysis, complicates breeding for quality traits. Moreover, the known traits
are often unable to explain the end use quality variations. Non destructive trait
descriptors that explain quality variations therefore need to be identified. These
parameters can then be used to formulate regression models to predict end-use quality.
Large number of QTLs and genes controlling quality has been reported. However,
their functionality across genotypes needs validation for their effective utilization in
breeding programmes. An in-depth understanding of the underlying mechanisms
controlling grain quality will enable breeders to precisely connect the missing links
with greater efficiency. The present chapter will attempt to provide an overview of the
scientific and technological advances in rice grain quality research, with special
emphasis to genetic studies and breeding efforts in India and abroad.

1. INTRODUCTION
Quality in rice refers to its physical and physico-chemical properties before and
after cooking. Physical properties include the physical appearance of grain, its size,
shape, color, uniformity in overall appearance, luster etc. Specific density of grain,
hulling and milling recovery, head rice recovery etc. represents Millers’ qualities.
Physicochemical properties include the biochemical characters of the grain especially
amylose, amylopectin, soluble starch, resistant starch, protein and micronutrient
content besides gel consistency, gelatinization temperature, pasting properties, water
uptake, volume expansion ratio, amylographic properties, etc. A new dimension to
rice quality has been added in the form of its sensory qualities which include taste,
flavor, uniformity of particles & mouth feel after chewing of the cooked whole grain
etc. The sensory qualities are highly subjective in nature and vary widely from person
to person. Among all other sensory qualities, aroma needs special mention due to its
high market demand. Basmati rice is one such example where the premium cooking
and eating quality along with pleasant aroma created a multi-billion dollar export
industry to India. However, preference for aroma is highly location specific. Besides
basmati there are other categories of aromatic rice, which fetch better prices in the

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market. Looking into the wide acceptability of rice as staple, in cuisines and in desserts,
the quality of this miracle grain can be divided under four broad categories namely its
physical appearance, milling properties, cooking & eating characteristics and nutritional
& nutraceutical quality. Nutritional quality includes grain protein, vitamins and
micronutrient content while nutraceutical properties deal with the healing compounds.
Individually each component plays significant role in maintaining good health.
Quality preferences in rice are highly variable. Different countries have different
requirements for quality. Even within countries, an array of preferences can be
observed. Therefore specific quality profiles need to be developed through extensive
survey among consumers, millers and farmers in the target region of breeding. A
preliminary survey on quality preferences of urban populations of eastern and southern
India have been undertaken by Social scientists at IRRI. They concluded that medium
slender grain type is preferred over long slender among both the populations. Aroma
was priority for 37% respondents of eastern India. The preference for aroma was
lower among the respondents of South India. However, a huge variation in grain type
preference was observed among different cities of Eastern India revealing highly
variable consumer preference for quality traits in this region. Appearance of rice
grain, its cooking and eating qualities are highly significant in deciding the market
value of produce. No rice is consumed if its cooking and eating quality does not
match the preference of consumers. Besides the cooking quality of whole grain, rice
processing quality i.e. ability of rice to be processed to different end products like
puffed rice, popped rice, flattened rice etc., is gaining attention among millers and
consumers. All these dimensions of rice quality should be understood well before
initiating breeding efforts to improve it.
Due to quantitative nature of inheritance, quality traits in rice are highly influenced
by environment. The existence of multiple genes and epistatic interactions among
them complicates their breeding procedure. The situation is further complicated by
the variable reports on genetic basis of quality traits in different populations and
destructive nature of phenotyping for these traits. However, with the advancements
in laboratory methods and instrumentation, more techniques for precise phenotyping
are becoming available. Current advancements in the science of plant genomics will
help the breeders to relate the phenotypes with specific genes or genomic regions
which are expected to transform the breeding outlook for quality improvement in near
future.
In the present chapter, we therefore have attempted to depict the shift of focus on
rice quality in the time frame of last seventy years. How the research dimensions
changed with respect to quality making it integral criteria in rice genetic improvement
in today’s world? Multidimensional aspects of rice grain quality have been discussed
especially with respect to their genetic and molecular mechanisms. The underlying
genes for various quality traits, their interactions and the resources available for
precise breeding for these traits have been discussed in details, besides the significant
achievements of classical breeding approaches. In Fig. 1, an overview of all the
components of rice quality and their importance in varietal improvement has been
presented graphically.

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 Fig.1. Graphical representation of the chapter

2. STATUS OF RESEARCH IN RICE QUALITY

Several studies have been undertaken to understand the genetic basis of quality,
and ways to improve it through established principles of genetics. Before moving
into the detailed discussion on genetic improvement of quality traits, it is very essential
to remember that genetic studies on any trait can be undertaken accurately only when
precise methods of trait phenotyping do exist. Since grain quality traits are mostly
controlled by biochemical components present in the grain, knowledge of biochemistry
is very essential for understanding the variation in quality traits. Recognizing the
importance of biochemistry in the study of quality traits, initial studies focused on
investigating the physico-chemical basis of different quality traits and formulation of
methods to quantify them. Work of Juliano at IRRI, Philippines and Bhattacharya at
CFTRI, Mysore, India needs special mention. These two researchers contributed
immensely to the understanding of physicochemical basis of rice quality during the
early days of 1960’s and 70’s and throughout. Geneticists have utilized these
advancements in that phenotyping for quality traits in classical genetic analyse as
well as detailed molecular studies. Significant amount of information is now available
to breeders for quality improvement with higher precision.
2.1. Phenotyping for quality
Among the various grain quality factors, aroma is one of the most easily
recognizable sensory qualities which have been strongly selected by cultivators
over generations. Chewing test has long been used for selection of aroma with the
subsequent development of KOH test followed by development of more sophisticated

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and sensitive instruments like gas chromatography mass spectrometry (GCMS) to

precisely measure aroma and detect the volatile compounds responsible for it. Despite
of the unavailability of standard measures for the sensory attributes including aroma,
taste and flavor of cooked rice; the traits have been selected by the farmers over
generations which is well revealed by their presence in local varieties and landraces.
There are several parameters to estimate the cooking and eating quality of rice.
Amylose content, gel consistency, gelatinization temperature and pasting properties
are objective parameters deciding the cooking and eating quality and have long been
being recognized and worked uponby researchers. Sensory qualities like aroma, flavor
and mouth feel are subjective parameters and are more recently recognized as important
in deciding the market value of the produce. The traits have been preserved by
farmers in form of landraces and local varieties at small scales for their own consumption.
Sensory qualities largely depend on human perception and are therefore very complex
to measure. Hence, the support of social scientists, psychologists and neurologists
is also envisaged in formulating methods for precise measurement of these traits.
Research efforts have been undertaken for identification of component traits which
together decide the ultimate consumers’ preference. The component traits are then
subjected to scoring by trained panelists. However, such studies were realized to be
loaded with human errors, as perception varies with health, environment, social and
psychological status of the scorer. In order to overcome the variable human errors in
those studies, instruments such as the texture analyzer, colorimeter, luster analyzer,
taste meter, electronic tongue and electric nose have been designed to imitate human
perception. Multiple regression equations based on the original data from human
perceived scores and instrument perception were developed to provide indirect
methods of measuring the sensory traits. The science of trait identification for better
explanation of sensory qualities is in its nascent stage of evolution and needs further
refinements. Methods to measure the nutritional quality of rice grain viz. protein, iron,
zinc and other micronutrients evolved later with the advancements in instrumentation
during twentieth century. Grain protein content is measured by the basic method of
Kjeldahl while micro-nutrients are estimated by their basic property of emitting a
particular wavelength of light when moved back to their ground state after ionization.
Nondestructive methods of trait estimation have been formulated utilizing the principle
of spectrophotometry and calibrating the same using multiple regression equations.
Milling qualities are comparatively easy to measure as they are highly correlated
with the physical attributes of grain and are very important for the acceptance of
variety in the market. Chalkiness has been found to significantly affect the milling
qualities by disturbing the packing of starch granules in the grain. In the chalky area,
the starch granules are loosely bound reducing its strength to endure the processing
during hulling and milling. The grain breaks in the chalky area reducing the head rice
recovery. Studies under Scanning electron microscope could correlate the orientation
of starch molecules with chalkiness and milling recoveries. Table 1 represents the
quality traits and tests available for their estimation.

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Table 1.Quality traits and their methods of evaluation.
Trait Method
Length, breadth, width, etc Vernier Callipers, Digital Annadarpan Image Analyzer
Moisture Moisture meter
Cooking quality Laboratory based methods viz. Alkali spreading value,
KOH test
Pasting properties Rheovisco analyzer (RVA)
Protein content Kjeldhal method, Near Infra Red Spectrophotometer
Antioxidants Spectrophotometry, HPLC
Micronutrient content Atomic Absorption spectrophotometer (AAS),XRF
Appearance Gloss meter, “Mido” meter, “Hunter Lab” Colorimeter
Aroma KOH test, GC, GCMS, Electronic nose
Taste HPLC, Enzyme kit, Taste sensor, Taste analyzer,
Electronic tongue
Texture Texturometer, Texture analyzer, Tensipresser

2.2. Major biochemical components of rice quality

For a comprehensive understanding of quality aspects of rice grains, it is very
important to know about their biochemical bases. The major constituent of rice
endosperm is starch which comprises about 90% of the total dry weight of polished
grains. This is followed by protein, fats, fibers, vitamins and micronutrients. Comprising
the bulk of the grain, starch quantity and quality play leading role in deciding almost
all quality traits. Amylose and amylopectin together constitute the starch molecule
and their relative abundance decides the starch quality. Amylose is long chained
polysaccharide with less branching while amylopectin is highly branched. Higher
content of amylose makes the rice fluffier, dry and non-sticky with better grain
separation after cooking. However, beyond a certain limit (when amylose is >25%) it
makes the rice hard when kept for longer time after cooking. On the other hand, lower
values of amylose (<15%) or its absence makes the rice sticky and glutinous (waxy
rice). However, deviations to this correlation do exist. These deviations have been
explained on the basis of amylose-amylopectin ratio or degree of branching of these
two chains. Besides cooking quality, starch is vital in deciding the eating and product
processing quality in rice. Nature of binding of starch molecules during grain filling
decides the overall appearance of raw grain.
The second major component of rice endosperm is protein (vary from 5–12% of
grain weight) which is the lowest among cereals. However rice protein is best in
digestibility among cereal protein due to the higher content of (~80%) glutelins. Rice
protein is also most balanced among cereal proteins due to higher content of lysine
and tryptophan, the limiting essential amino acids in cereals. In addition to the
traditional quality features, the focus of developing rice as nutricereal has gained
momentum in last two decades. Considering rice as staple food for billions, this shift
in focus from food security to nutritional security bears great significance. Fats are
important in the bran layer of rice as they are abundant there and are used to extract

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high quality γ-oryzionol (rice bran oil) containing ω-3- fatty acids. Due to the low
smoking point of rice bran oil it is mixed with other vegetable oils to improve its
cooking quality. Fibres are important as roughage and decide the glyciemic index of
rice. However, higher content of fibres, reduces palatability.
Half of the world’s population is suffering from one or more vitamin and/or mineral
deficiency. Vitamin A, iron and zinc seem to be most prominent limiting components
among them. Hence, varieties rich in micronutrients and vitamins will be the only
sustainable solution to the problem of hidden hunger. In general vitamin-A is absent
in rice grains and micronutrients like iron and zinc are present in lower concentrations.
Antioxidants are another important class of nutri-compounds that protect the cells
from harmful effects of free radicals and reactive oxygen species released during
various metabolic pathways of cells. Pigmented rice is rich in such compounds. The
main phenolic compounds in pigmented rice are anthocyanins which are the major
active components for antioxidation. Moreover, this rice is also rich in Vitamin B and
E. Beside all these features, it also needs special mention that hundreds of end products
are developed from rice in India and throughout the world. Each of these end products
have their specific quality requirements.
2.3. Genetic studies on quality traits
Following the advent of standard methods to measure different quality traits,
studies on exploring their genetic basis were undertaken. Most of the quality traits
were perceived as quantitative, except for aroma and grain pigmentation which were
perceived as present-absent type and were studied in form of discrete ratios.
Segregation ratio of aroma varied among different studies. However, the studies
could unanimously conclude that aroma gene is recessive in nature which was later
tagged by Ahn et al. (1992) as the fgr gene on long arm of chromosome 8. Bradbury et
al. (2005) cloned the gene and characterized it further. In aromatic genotypes, a deletion
in exon 7 of the gene coding for betaine aldehyde dehydrogenase (BADH2) generates
a premature stop codon which results into loss of function of the gene (Shi et al. 2008)
leading to accumulation of 2- Acetyl-1- Pyrroline (2AP). This is the main volatile
compound (out of nearly hundred reported volatiles) imparting aroma to rice grain.
Despite of being the most elaborately studied trait among all other quality traits, the
quest for aroma is still on. The search for new variants of aroma gene, other minor
genes and elucidation of its pathway are going on. The major focus of aromatic rice
breeding in India was development of basmati rice varieties in which role of ICAR-
IARI, New Delhi; CCSHAU, Hissar; PAU, Ludhiana and GBPUAT, Pantnagar were
very crucial. However comparatively lesser focus was given in case of non-basmati
aromatic rice both for basic and applied research. In a compendium prepared by the
Indian Agricultural Research Institute (IARI) and APEDA, varieties such as
Kalanamak, Tilak Chandan and Jeerabati (Uttar Pradesh), Kalajeera (Orissa), Katrani
(Bihar), Ambemohar (Maharashtra), Gobindbhog and Badshahbhog (West Bengal),
Dubraj, Badshahbhog and Jawaphool (Chhattisgarh) and Kalajoha (Assam) have
been identified which could be harnessed and developed for their export potential.
Many traditional aromatic rice genotypes viz. Bindli, Dubraj, Durgabhog, Makarkanda,

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Badshabhog, etc. were reported to surpass basmati in one or more characteristics like
aroma, texture, elongation on cooking and taste etc. and they mostly possess small to
medium grain. Kalanamak and Dubraj were reported to command a premium price in
the market. Breeding efforts for developing high yielding modern varieties of aromatic
non-basmati rice have been quite limited when compared with intensive efforts for
basmati. Mostly pureline selection and mutation approaches have been followed.
However the semi-dwarf version of the Kalanamak landrace developed by researchers
at IARI, New Delhi needs special mention. Chakraborty et al. (2016) explored the
possible existence of any locus other than BADH2 controlling aroma among 84
landraces of indica rice using functional marker (8-bp deletion) for badh2 gene.
Nearly 80 percent of the landraces carried the well-known BADH2 deletion. However,
eleven aromatic genotypes including wild ancestors lacked that particular functional
allele. This indicated the existence of an alternate gene or allele controlling aroma in
rice. Singh et al. (2010) however, have also established the role of BADH1 gene and its
haplotypes with aroma in rice.
Like aroma, anthocyanin pigmentation in rice grain was also studied as a qualitative
trait due to presence or absence type of phenotypes. Unlike aroma, this trait shows
dominant gene control and two complementarily acting genes, Rc and Rd control the
pericarp pigmentation. The Rd locus codes for dihydro flavonol reductase (DFR)
enzyme and the Rc gene codes for Basic Helix-Loop-Helix (HLH) Protein. The Rc
locus has been cloned and its three allelic variants have been well characterized. Its
null allele (rc) with 14-bp deletion creates frame shift mutation and a premature stop
codon leading to white pericarp phenotype (Brooks et al. 2008). Several pigmented
rice genotypes have been identified and characterized in India, including the Chakhao
rice of Manipur, Kalbahat rice of Maharashtra, Njavara of Kerala, etc. Njavara is well
known for its medicinal significance in Ayurvedic medicines. However, the identified
pigmented genotypes are low yielding and susceptible to lodging. Breeding
interventions to improve their plant type and yield shall be highly beneficial in their
popularization.
The quality traits other than aroma and grain pigmentation have been studied
considering them as quantitative traits. Gene action studies on these quality traits
lead to variable conclusions by different researchers. Advent of molecular markers
has opened a new era of QTL and gene discoveries. More than 600 QTLs have been
reported for different quality traits like chalkiness, cooking and eating quality, grain
dimensions, pasting properties, grain protein content, iron and zinc (http://
www.gramene.org). Table 2 summarizes the identified loci information of major quality
traits and availability of their corresponding functional markers.
Detection of such large number of QTLs poses a great challenge for the plant
breeder to efficiently and intelligently use this information for the genetic improvement
of the traits. However, a comprehensive analysis suggests that the QTLs and genes
involved in amylose biosynthesis pathway play a significant role in deciding the
physical attributes (head rice recovery, chalkiness and grain dimensions) of grain
along with its cooking and eating quality. Waxy (Wx) locus was first identified as the

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Table 2: Genes and functional markers for quality traits in rice.

Trait Gene FM Availability
Aroma/Fragrance Badh2 Available
Amylose content (AC) Wx Available
Grain size GS3 Available
Gelatinizationtemperature SSIIa Available
Iron (Fe) OsYSL1, OsMTP1,OsFER1,OsFER2 Yet to be developed
Zinc (Zn) OsARD2, OsIRT1OsNAS1, OsNAS2
Fe and Zn OsNASgene family
OsNAS3, OsNRAMP1,Heavy metal
iontransport, APRT
Source: Adapted from Lau et al. (2015)

major locus controlling majority of the variation in amylose content in grain which in
turn was known as the sole major factor affecting the cooking and eating quality of
rice. The Wx locus codes for an enzyme Granule Bound Starch Synthase I (GBSS I)
and has a minor effect in controlling gel consistency, but has no effect on gelatinization
temperature. Alternate splicing of the Wx transcript leads to several allelic variations
altering the degrees of amylose content in grain. The locus Alk is the major locus in
controlling Gelatinization temperature and codes for the enzyme Soluble Starch
Synthase IIa (Umemoto et al. 2005). Wx, SSIIa, SBE3 (Starch Branching Enzyme3),
PUL (Pullulanase) have been reported to affect the different aspects of the pasting
properties in rice. Existence of cross talks and pleiotropy among the loci has also
been reported. Cloning and characterization of several genes controlling grain
appearance traits led to better understanding of their regulation and can therefore be
utilized more efficiently in breeding programs.Chalkiness in the endosperm was
attributed to the loose binding of the starch. However, among many QTLs reported
for chalkiness only Chalk5 was isolated and characterized well (Li et al. 2014).
Interestingly, some of the QTL clusters controlling grain dimensions (grain size and
grain width) are reported to have pleiotropic effect with chalkiness.
Besides the above mentioned QTLs related to starch component of rice grains, a
large number of QTLs have also been reported for the nutritional components like
content of protein, iron, zinc etc. in grains. Expression of these traits is highly affected
by growing environment and cultural practices followed to grow the crop. This makes
their detection very difficult. Earlier, tight negative linkage was reported to exist
between yield and grain protein content (GPC). In rice, many QTLs along with
associated markers have been identified covering all 12 chromosomes for GPC among
which chromosomes 1, 2 and 7 harbor most of the QTLs. The QTL qPC1 present on
long arm of chromosome 1 control GPC through its regulation of synthesis and
accumulation of glutelins, prolamins, globulins, albumins and starch. It encodes a
putative amino acid transporter (OsAAP6) and control GPC without affecting growth
and grain yield suggesting that GPC and nutritional quality could be improved without
reduction in grain yield (Peng et al. 2014). Several QTLs have been reported for higher

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concentration of iron and zinc in rice grains some of which have been listed in Table
2. However, all these studies need support of bioavailability data for the micronutrients.
In the last decade, Indian researchers have given major attention for improving the
nutritional quality of rice grains with major emphasis on increasing grain protein, iron
and zinc concentrations. Researchers from ICAR-IIRR, Hyderabad reported that wild
relatives of rice such as O. nivara, O. rufipogon, O.barthii, and O. longistminata,
and African cultivated rice O. glaberrima have higher level of Zn. The QTLs for Zn
content were detected in Ch 3, 7 and 12 by using RIL population derived from Madhukar
x Swarna. They also developed high grain zinc containing rice variety DRR Dhan 45
through conventional breeding. It is the first rice variety with high zinc content to be
notified at national level with an average zinc content of 22.6 ppm in polished rice.
Significant progress has been achieved in development of transgenic lines
especially in terms of nutritional quality in rice. However, their large scale application
in form of cultivars is yet to be established. The biggest success in this regard was
achieved in the development of beta-carotene rich golden rice which was developed
by transformation of genes from daffodil and a soil bacterium Erwinia into rice and
expressing them in the grain. The concentration of beta carotene was further improved
by transforming the phytoene synthase gene from maize (Paine et al. 2005). Scientists
from IARI, New Delhi have transferred the genes for golden rice traits in popular
Indian rice varieties through backcross breeding strategy. In order to improve the
iron content in grain, ferritin gene has been transferred from soybean into rice. Efforts
have been made to reduce the phytic acid content which is a major anti-nutritional
factor in rice grain. It declines the bioavailability of iron in body by chelating the same
at low pH in the stomach. Simultaneously transgenics have been developed to improve
the micronutrient content in grain to combat the problem of hidden hunger. Table 3
compiles the successful transformation events undertaken to improve the nutritional
quality of rice grain. However, there is need to thoroughly analyze the stability of the
events and their utility in trait transfer into high yielding genetic back grounds through
breeding interventions.

Table 3. Genes used for transformation of rice to improve vitamin and mineral
content.
S. No Nutrient Genes used
1 Vit A Nppsy1, EucrtI,
β-carotene content Daffodil Phytoene Synthase and Erwinia Phytoenedesaturase
2 Fe Osnas2, , Afphytase, and Osnas1, Osnas3, OsYSL2, Ferritin
genes: SoyferH1, PyFerritin, rgMT, Gm ferritin,
3 Zn Osnas2, Gm ferritin, AfphytaseandOsnas1
5 Fe and Zn Nicotianamine synthase (NAS) genes [OsNAS1, OsNAS2, and
OsNAS3, OsNAS3-D1, HvNAS1, AtNAS1 and HvNAS1],
HvNAAT,HvNAAT-A, HvNAAT –B, Osfer2, SoyFerH1,
SoyFerH2, Pvferritin, OsIRO2, OsYSL2, OsYSL15, HvNAS1,
Afphytase,
23 Zn, Cu, and Ni OsNAS3
Source: Adapted from Mahender et al. (2016)

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Due to increased incidences of diabetes in world population, development of rice

genotypes with low glycemic index is receiving global attention. However the research
in this particular area is still in nascent stage and remained limited to development of
effective protocols and evaluation of limited set of germplasm. Any significant
breakthrough in terms of detection of genes/QTLs for this trait is still not achieved.
Although systematic breeding efforts for developing low glycemic index rice is in its
nascent stage in India, through screening of existing varieties, some varieties like
Swarna (low GI reported by IRRI), Improved SambhaMahsuri (ICAR-IIRR, Hyderabad)
and Madhuraj-55 (IGKV, Raipur) have been identified as low-GI-rice.
Besides all the traits discussed here, the ‘Komal-Saul’ (soft rice) of Assam with
soak-and-eat property needs special mention. However, the unique property of this
rice is highly location specific and expressed in just a few districts of north eastern
India. Assam Agriculture University, Jorhat has released a few varieties of Komal-
Dhan namely Aghonibora, Bhogalibora, etc. However, the underlying biochemical
and molecular mechanism of this unique property is yet to be deciphered.
Indian rice breeding programmes are traditionally directed towards yield
improvement. Targeted improvement for grain quality was carried out only in few
cases. With a few exceptions, only advanced generations of high yielding materials
are evaluated in nationwide trials for grain quality under All India Coordinated Rice
Improvement Project (AICRIP). However, the huge amount of data generated from
these studies have created a very useful database for the rice researchers in the
country especially for study of Genotype x Environment interaction for grain quality
along estimating the heritability, genetic gains and selection of genotypes for
generating mapping population.
Many of the reported QTLs for different quality traits are either population specific,
or control a minor portion of variation, or their expression is highly dependent on
environment. As a result such QTLs become difficult for use by breeders. Sometimes
the QTL region is so large that it becomes difficult to transfer the region intact.
Therefore studies shall be carried out to identify and customize the QTLs and more
preferably the gene combinations that can be effectively utilized under target specific
breeding programs. These QTLs and gene combinations will largely vary depending
on the target environment and market, and therefore needs validation through multi
environmental trials.
2.4. Rice quality research at NRRI
The Institute was established in the backdrop of ‘The great Bengal famine’ of
1942 caused due to huge yield loss by Helminthosporium, as a mitigation strategy to
avoid such disasters further. Since its inception, the institution is incurred with the
responsibility to feed millions of hungry bellies of an infant nation. Therefore the
main focus from the beginning was to enhance yield. Indica-japonica hybridization
program of FAO as well as trials of other introductions provided a very strong initial
support for generation of valuable variations and development of high yielding
promising genotypes. Rice cytology and genetic analysis of important traits

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contributed significantly in our present understanding of Rice science. Concern for
rice quality along with yield got attention of visionary researchers even in days of
immense pressure to feed the nation.
Breeding for fine grain began in 1953. Crosses were made to improve the grain
characters of otherwise high yielding, highly adapted early maturing, coarse and red
kernelled variety Ptb10 using pedigree method of breeding. In 1961, cultures of X-
ray irradiated Ptb10 were received which segregated for kernel color and were
subjected to further testing. Several mutation breeding programs have been undertaken
to improve grain quality of otherwise popular varieties like TN1, Taichung65, and
CR2001. Neelabati was identified as a high yielding fine grained genotype recommended
for cultivation in coastal/saline areas. Investigations on cooking quality of genotypes
using the KOH test were initiated during 1963-64 and genotypes with superior cooking
qualities were identified. As soon as a quick and reliable method to estimate the
cooking quality was adapted, inheritance study was undertaken by crossing of
contrasting genotypes. The inheritance study revealed that there are 2-3 genes that
control cooking quality in rice and the trait can be subjected to genetic improvement.
The study also indicated the possible role of minor genes for small modifications in
trait expression. However varietal development program specifically focusing on the
cooking and eating quality have not been undertaken yet.
Head Rice Recovery (HRR) percentage after hulling was also investigated during
1960s which ranged from 23.8 to 74.5%. Nature and texture of endosperm along with
shape and size of grain were reported to influence HRR. Presence of abdominal white
was found not to affect HRR. Highest recovery percentage (79.2) was reported in
Changsan variety from Manipur. HRR percentage of japonica rice was not significantly
different from that of indica types. Thorough study on the effect of time of harvesting
after flowering, moisture content during harvesting on head rice recovery after milling
was undertaken. It was observed that some genotypes like GEB24, T141, T90, etc.
were more resistant to breakage when harvested within 30 days after flowering.
However, ill filled kernels are a problem associated with early harvesting. The study
could recommend that field harvesting after 30-40 DAF at 20-23% grain moisture level
and shade drying to 11-13% moisture, gives highest hulling recovery by reducing the
development of sun cracks in the kernels during field drying.
Inheritance of red kernel colour was studied during 1960s in segregating generation
of a cross between GEB24 and Ptb10. PtB10 being well recognized for its superior
grain type. Association with other traits was studied and their linkages established.
Sanghamitra et al. (2017) reported low amylose content in purple rice genotypes,
Chakhao, Mamihunger and Manipuri Black. Lower yield along with the low grain
amylose content in these genotypes needs improvement through breeding.
Significantly higher antioxidation property in the grains of these genotypes has been
recognized. Higher heritability of the trait suggested greater scope for genetic
improvement of anthocyanin and antioxidant content in pigmented rice.
ICAR-NRRI took important initiatives for genetic improvement of short grained
aromatic rice. The aromatic landrace collections of the institute were characterized

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 Rice Research for Enhancing Productivity,
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based on phenotypic descriptors and molecular markers (Roy et al. 2014 & 2016).
Study of variation in nuclear and chloroplast DNA sequences also provided a greater
insight into the population structure and origin of aromatic landraces (Roy et al.
2016). Integration of participatory plant breeding with marker assisted pureline selection
helped in better genetic gain from selection in three landraces Kalajeera, Machhakanta,
and Haladichudi (Roy et al. 2017). Several superior pureline varieties like NuaKalajeera,
NuaDhusara and NuaChinikamini were developed and released (Patnaik et al. 2014).
Marker assisted pedigree selection helped to develop high yielding aromatic genotype
(CR Sugandh Dhan-907) by crossing Pusa 44 and Dubraj (Patnaik et al. 2015). CR
Sugandh Dhan-907 was similar to Dubraj landrace in terms of its grain quality. Besides
aromatic short grain varieties, long slender grained genotypes with aroma (Poornabhog
and Geetanjali) have been developed through mutation of basmati genotypes and
released. The Geetanjali variety is popular among the farmers and has been used for
establishment of rice value chain in Odisha.

Fig.2. Field photograph of two aromatic rice varieties developed at ICAR-

NRRI along with their respective grain type.

Protein in rice has ever been a major concern of rice researchers in past as well as
in present due to its lowest grain protein content among cereals. Positive correlation
of bran and aleurone layers with protein and thiamine content was identified and high
protein genotypes were found to have a cellular patch in spermoderm (CRRI Annual
Reports, 1949-50 and 1950-51). Studies on variation in protein content and aleurone
layer thickness were undertaken in 450 representative genotypes of japonica, indica
and javanica rice. Existence of positive correlation between aleurone layer thickness

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101
and percent protein content in rice kernels was reported. Protein content in rice
kernels varied from 6.1% to 10.1% while the aleurone layer thickness varied from 11.2ì
to 75.0μ. Moreover, protein content in japonica rice was found to be higher than in
white kernelled indica types. Inheritance of protein content was studied by the Rice
Technology Section established during 1963 and they recorded frequency of occurrence
of high protein genotypes among different duration classes of rice varieties in
temperate and tropical zones. Due to 4-5% milling, a loss of 11-12% protein as compared
to brown rice was recorded during 1966. Studies on inheritance of protein content
suggested the role of polygenes in trait expression. Appearance of transgressive
segregants in F2 suggested the possibility to breed true for higher protein than in
parents. Near infrared spectroscopy (NIR) was therefore calibrated and validated for
large scale and high throughput phenotyping of GPC (Bagchi et al. 2015). Breeding
for high protein rice was initiated involving two landraces from Assam. High protein
trait was transferred to high yielding backgrounds of Naveen and Swarna through
backcross breeding to release the first high protein variety in Naveen background as
CR Dhan 310 (released by CVRC for Odisha, Uttar Pradesh and Madhya Pradesh)
with 10.3% GPC in 2016. Another variety CR Dhan 311 has been released by State
variety Release Committee of Odisha in the name of ‘Mukul’ with GPC of 10.1% and
Zn content of 20 ppm. By using a backcross derived mapping population, a consistent
QTL (qGPC1.1) over the seasons have also been identified (DARE/ICAR Annual
Report 2015-16 and 2016-17 and NRRI Annual Report 2014-15).

Fig.3. Field photograph of two high protein rice genotypes developed at

ICAR-NRRI

3. KNOWLEDGE GAPS
Amylose is known to be the major biochemical factor influencing majority
of endosperm traits in rice. However sufficient variation for physico-chemical
properties has been observed among genotypes having same amylose content.
Later, amylopectin and protein content were also designated to play role in
deciding physico-chemical characteristics of grain. However, all these factors
taken together, more often fail to predict the physico-chemical quality of the
grain. Therefore there is need to discover some new factors that play significant
role in deciding different aspects of grain quality along with those identified
earlier.

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Knowledge regarding biochemical and physiological mechanisms of development

of superior grain quality needs to be generated for all quality traits. In case of aroma,
the gene and the biochemical factors are well characterized. However; the biochemical
pathway producing aroma is still not well understood. Similarly, knowledge regarding
the mechanism of higher accumulation of grain nitrogen in high protein rice is still to
be deciphered.
Quality traits are highly affected by environment but very few studies have been
undertaken on the effect of environmental factors on different quality traits. Moreover,
the quantification of the environmental component on different quality traits is required
to formulate mathematical equations to predict the trait expression in any environment
more accurately.
Regarding the grain protein content, the mechanism of higher accumulation of
grain protein along with the genes/QTLs having greater effect on the trait need to be
identified. Molecular and physiological basis of micronutrient accumulation in grain
requires further understanding. Stable sources of low phytic acid and high anti-
oxidant content in rice need to be identified so that the problem of mal-nutrition can
be overcome in more economic way. Researchers also need to give more emphasis to
the non-conventional quality traits especially low Glycemic Index, Soak and Eat
property, product making quality etc. as demand for the varieties carrying such
properties are expected to increase further in coming years.

4. RESEARCH AND DEVELOPMENT NEEDS

 There is need to develop methods to precisely quantify the quality traits in a small
sample volume without destroying it.
 There is need for intervention of engineers to design instruments for precise
estimation of quality traits with more automation and thereby reducing variable
human errors.
 More information on surrogate traits for different aspects of quality like grain
type, cooking and eating quality, nutritional value etc. needs to be generated.
 Information on differential expression of quality traits under variable environments
need to be generated to identify the environments for best expression of different
quality traits. The information will support the breeders to evaluate and select
genotypes for their breeding program in these environments.
 More QTLs related to quality working across genotypes and environments should
be identified, characterized and cloned. Functional markers for such QTLs shall
be highly beneficial for the breeders to undertake marker assisted breeding of
quality traits.
 There is need to develop quality preference map for the country depending on
quality preferences under different rice ecologies of different regions. This will
support breeders to decide upon the quality traits to target in their respective

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 breeding programs.A global database needs to be developed that integrates the
phenotyping data, genetic information and marker based genotyping data against
all genotypes being studied. Such database shall be easy to handle so that the
breeders can select the parents based on the available information.

5. WAY FORWARD
Since quality traits are highly influenced by environment (season/location/year),
multi environment testing shall be an integral part of any quality breeding program.
Quality evaluation data should always be supported with the GPS, agro-meteorological
and soil quality data to improve the precision in quality breeding and provide a
readymade information to the breeders to decide upon ‘when and where’ to select.
Moreover, integrating the participatory approach of selection during the later stages
of breeding program will facilitate in accelerated popularization of the developed
varieties after release.
Popular landraces known for different quality traits shall be improved through
appropriate breeding strategies to remove their critical limiting features for which
farmers are compelled to stop their cultivation. Wild species may also be evaluated
for their quality traits which may serve as useful donors for specific quality features.
An elite population comprising of large number of fixed and intermating breeding
lines with different permutations and combinations of quality QTLs/ genes shall be
developed in elite backgrounds. This will serve the need of elite genotypes for
breeding in variable ecologies and provide a wide genetic base to avoid bottlenecks.
Discovery of new functional markers for QTLs and genes controlling quality in
rice are very important so that the costly and destructive sampling methods for
quality analysis may be avoided. However, exhaustive genotyping using the available
marker information along with multi-location phenotyping must be undertaken among
the genotypes selected for gene discovery. This will prevent unnecessary duplication
of research (jumping into same QTLs/ genes) and provide strong support for
identification of new genetic factors. Moreover, these studies shall not remain limited
to demarcating the QTL region, but should also further characterize, clone and validate
the genomic regions for their effective utilization in breeding programs. A global
database for the genotypic and phenotypic data will be useful for selection of parents
for breeding. Near isogenic lines (NILs) may be developed for these regions to study
the effects of predicted genes individually and in combinations. Those single gene
NILs and pyramided NILs will be very helpful to refine our understanding about the
biochemical basis of quality. Rice quality breeding therefore, has a long way to go.
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Bagchi TB, Sharma S and Chattopadhyay K (2016) Development of NIRS models to predict
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Bradbury LM, Fitzgerald TL, Henry RJ, Jin Q and Waters DL (2005) The gene for fragrance in
rice. Plant Biotechnology Journal, 3(3): 363-70.
Brooks SA, Yan W, Jackson AK and Deren CW (2008) A natural mutation in rc reverts white-rice-
pericarp to red and results in a new, dominant, wild-type allele: Rc-g. Theoretical and
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Profitability and Climate Resilience

Genetic Improvement of Rainfed Shallow-

lowland Rice for Higher Yield and Climate
Resilience

SK Pradhan, M Chakraborti, K Chakraborty, L Behera, J Meher,

HN Subudhi, SK Mishra, E Pandit and JN Reddy

SUMMARY
In India, 16 million ha area is under rainfed lowland rice cultivation. The rainfed
shallow lowland is characterized by water accumulation of 0-50 cm and faces frequent
drought and flash floods. Rice crop faces several challenges when grown under
shallow lowland ecology. Simultaneous incorporation of drought and submergence
tolerance besides imparting lodging resistance, anaerobic germination ability, seed
dormancy and tolerance to major biotic and abiotic stresses becomes very crucial for
developing rice varieties for shallow lowlands. Well-characterized genes and QTLs
are available for majority of traits to be deployed in suitable combinations for resilient
breeding. Updated information on genetic improvement of shallow lowland rice for
attaining higher productivity has been discussed in this chapter.

1. INTRODUCTION
In India, rice is grown in 43 Mha, and approximately 50% of these areas are under
rainfed ecology with low productivity due to various abiotic and biotic stresses. The
severity of biotic and abiotic stresses is changing frequently due to the effects of
climate change. The rainfed lowland ecologies cover around 16 Mha of which 92%
are located in the eastern region of the country. Depending upon the water depth and
duration of water logging in the lowland ecology during growth period of rice, it has
been classified into rainfed shallow lowland, semi-deep, deep and very deep water or
floating type ecosystem. The rainfed shallow lowland is characterized by water
accumulation of 0-50 cm that face frequent drought and flash flood. As these areas
are not suitable for growing most of the other economically important crops,
developing high yielding climate resilient varieties of rice under those difficult ecologies
becomes very important. In future, production of rice needs to be increased from
lesser land area. In fact with the increasing scarcity of water for rice cultivation, the
future thrust for growing rice must focus with such ecologies.
Rice crop faces several challenges when grown under shallow lowland ecology.
Many rice growers under rainfed shallow lowlands adopt direct seeding of rice. These
direct seeded fields usually not properly leveled before seed sowing. After sowing
the plots get severe rain water accumulation frequently and resulting in heavy seedling
mortality and hence low yield. Presence of stagnant water for more than 10 days
period is very common in most areas under this ecology. Although by its name, the

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Higher Yield and Climate Resilience 107
ecology seems to possess sufficient amount of water and stagnant water seems to
create problems, occasional drought spells are also observed. As the crop is grown
almost completely under rainfed conditions, scope for supplementary irrigation is
very much limited. Besides, the genotypes suitable for shallow lowland ecologies
have longer maturity duration (140 days or more) and comparatively higher plant
heights. In the eastern part of the country where these varieties are grown, frequent
incidences of untimely rainfall and storms during grain maturity lead to heavy crop
loss caused by lodging and pre-harvest germination of seeds. Biotic stresses like
stem borer, brown plant hopper, gall midge, leaf folder, bacterial blight, bacterial sheath
blight and false smut are significantly affecting rice grain yield. Simulation studies
have clearly shown that, in future the distribution pattern of rains or associated wind
is expected to show more erratic behavior (Turner and Annamalai, 2012). Moreover,
disposal of paddy straw biomass is now-a-days become a burning issue and
environmental concern. Keeping the context of the country in terms of utilization of
straw, it will also be necessary to develop lodging resistant cultivars without
compromising feed quality and biodegradability. Thus, there is an urgent need of
region specific climate smart breeding in mega rice varieties with stacking of various
stress tolerance genes through multipronged approaches. Hence, simultaneous
incorporation of drought and submergence tolerance besides imparting lodging
resistance, anaerobic germination ability, seed dormancy and tolerance to major biotic
and abiotic stresses becomes very crucial for developing future rice varieties for
shallow lowlands.
Fortunately rice researchers have already discovered many such useful genes
and QTLs. A major QTL Sub1 is very useful for conferring submergence tolerance for
12 days. Many yield QTLs have been reported which works well under drought
stress. Pyramiding of these QTLs is expected to increase grain yield in rice under
drought stress. Though no host plant resistance genes are identified for stem borer,
but more than 30 resistance genes/QTLs are reported for brown plant hopper host
plant resistance. Till date, 42 resistant genes have been reported for controlling bacterial
blight disease in rice. Many yield enhancing QTLs have already been cloned in rice.
Two genes controlling anaerobic germination are already known. Now it will be
interesting to see how these QTLs or genes will behave when they are all taken
together in a single background.
The impact of the Green Revolution has sidelined the eastern Indian rainfed shallow
lowlands. Sizeable rice areas of eastern India are under shallow lowlands with low
production. We have to feed the burgeoning population in near future. The irrigated
ecology has shown symptoms of yield plateauing. Thus, this traditionally neglected
ecosystem has got tremendous potential to increase the yield level and total production
as a whole.
Keeping these factors in mind, this chapter deals with the up-to-date information
on genetic improvement of shallow lowlands rice for attaining higher productivity.
Prominent genetic approaches for obtaining higher productivity against various abiotic
and biotic stresses in this ecology namely submergence, drought, anaerobic

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germination, brown plant hopper, gall midge, leaf folder, bacterial leaf blight, bacterial
sheath blight, false smut, lodging resistance, dormancy, yield etc. are discussed here.

2. STATUS OF RESEARCH
Submergence and drought are two major abiotic stresses in rainfed rice cultivation.
Rice plants tolerant to complete submergence usually exhibit very limited elongation
during submergence and often show tolerance to complete flooding, a strategy known
as quiescence. The mechanistic understanding of molecular regulation of true
submergence tolerance/ quiescence in rice has been advanced through functional
characterization of key genes responsible for acclimatization to submergence stress
in rice (Xu et al. 2006). Limited number of rice genotypes possess inherent mechanism
to tolerate a deep transient flash flood through economization of energy reserves
(quiescence strategy) (Fukao and Xiong 2013). Quantitative trait locus (QTL) analysis
and map-based cloning revealed that the SUBMERGENCE1 (SUB1) locus, encoding
a variable cluster of two or three tandem-repeated group VII of ETHYLENE
RESPONSIVE FACTOR (ERF-VII), regulate the quiescence response (Xu et al. 2006).
Most of the reported rice accessions found to contain SUB1B and SUB1C genes at
the SUB1 locus, whereas SUB1A was reported to contribute ~70% of submergence
tolerance to some indica and aus rice varieties. The major QTL, Sub1A has been fine
mapped on chromosome 9 in the submergence tolerant cultivar FR13A (Xu et al.
2000). Researchers at International Rice Research Institute (IRRI), Philippines used
back crossing involving a double haploid derived from three tolerant parents (FR13A,
IR49830-7-1-2-2 and IR67819F2-AC-61) and a japonica rice KDML105. They were
able to develop new Jasmine rice carrying QTL for submergence tolerance retaining
the quality traits of KDML105. Under considerable stagnation of water, no other
cereals besides rice can survive and produce. This unique ability in rice is attributed
to its ability to elongate rapidly with onset of water stagnation. Under both the
situations ethylene responsive factor genes control the elongation but in opposite
direction i.e. quiescence and elongation (expansion) (Hattori et al. 2009). Snorkel 1
(SK1) and Snorkel 2 (SK2) allow rice to elongate fast whereas Submergence1A-1
(Sub1A-1) allows rice to squeeze elongation for adaptation to water stagnation and
flash floods conditions, respectively. Both SK genes and Sub1A encode ethylene-
responsive factor, a specific group of transcription factor related to gibberellin
biosynthesis or signal transduction. Several mega rice varieties, which were
submergence sensitive were being converted to submergence tolerant types through
introgression of Sub1A-1 genes through marker-assisted backcrossing and released
for commercial cultivation in different submergence prone areas of Asia and Africa.
Drought is a major yield limiting factor in rainfed lowlands. Progress in drought
breeding is very slow. The recent scenario in climate change indicates more
unpredictable drought intensity in the eastern region of the country directing us for
developing drought-resilient varieties. Fukai and Cooper (2001) have summarized the
complexity of drought tolerance and emphasized strategies that influence yield under
drought stress. The use of grain yield under drought stress is a selection criterion

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which is useful for developing high-yielding rice cultivars for rainfed rice-growing
areas. Several major quantitative trait loci (QTLs) showing effects under drought
need to be pyramided together to develop drought-tolerant versions of popular
drought-susceptible varieties. Three QTLs namely qDTY1.1, qDTY2.1 and qDTY3.1
are showing yield improvement under drought stress (Dixit et al. 2014). The QTL,
qDTY1.1, shows a consistent effect on grain yield under lowland drought. Two large-
effect QTLs influencing grain yield (qDTY2.1 and qDTY3.1) show R2 values of 16.3%
and 30.7%, respectively, under lowland drought. Another QTL, qDTY12.1 shows
consistent additive effects of 45% under drought, is mapped within the physical
interval of 2.7MB between two microsatellite markers RM28048-RM28166 (Dixit et al.
2014). A large effect QTL (qDTY3.2) shows positive effect on yield under drought
stress which co-localizes with Hd9, a locus which is related to days to flowering.
Dro1 is negatively regulated by auxin and is involved in cell elongation in the root
tip that causes asymmetric root growth and downward bending of the root in response
to gravity. Higher expression of Dro1 increases the root growth angle, whereby roots
grow in a more downward direction. Introducing Dro1 into a shallow-rooting rice
cultivar by backcrossing enabled the resulting line to avoid drought by increasing
deep rooting, which maintained high yield performance under drought conditions
relative to the recipient cultivar. Root growth angle (RGA) is an important trait that
influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (Dro1),
which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference
in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar
Kinandang Patong (Uga et al. 2013). Natural variation in RGA in rice cultivars carrying
functional Dro1 alleles may be controlled by a few major QTLs and by several additional
minor QTLs (Kitomi et al. 2015).
Rice is usually grown as direct seeded crop in the rainfed shallow lowlands of
eastern India, which frequently coincides with heavy rainfall in a poorly leveled and
with poorly drainage field resulting in poor plant stand. Submergence just after sowing
imposes stress by creating hypoxic condition (3% Oxygen) during germination as
well as during vegetative stage. Interestingly, mode of overcoming hypoxic stress by
rice plants seems to be different during germination and vegetative stages. The genes
and QTLs reported for vegetative stage submergence tolerance are of no use to
tolerate germination stage submergence and vice-versa. Being adapted to aquatic
ecology, rice has developed the unique mechanism to germinate and extend its
coleoptile under water even in complete absence of oxygen - a phenomenon termed
as anaerobic germination (AG). In general, rice coleoptile under water has been found
to elongate about 1 mm h-1 to reach the atmosphere by rapid elongation of basal cells
(up to 200 ìm in 12 h) immediately after emerging from embryo (Narsai et al. 2015).
However, anaerobic germination potential (AGP) varies greatly among different rice
genotypes, which ultimately provide an edge to a few genotypes to perform better
under oxygen deficient conditions over others.
Anaerobic respiration usually yields much less energy as compared to the aerobic
mode of respiration. Here, the energy requirement is largely fulfilled by glycolysis
followed by alcoholic fermentation. Transcriptome analysis data also revealed up-

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regulation of genes related to starch and glucose metabolism, glycolysis and

fermentation during germination under anaerobic condition/submergence (Narsai et
al. 2017). Starch degrading enzymes like α-amylase, aldolaseand sucrose synthase
are up regulated in germination stage oxygen deficiency (GSOD) tolerant cultivars
greatly compared to susceptible cultivars with higher RAmy 3D gene expression as
well as greater up-regulation of rice cytosolic hexokinase OsHXK7 (Kim et al., 2016).
The work of mapping QTLs imparting high anaerobic germination potential (AGP)
has been initiated and one of the identified QTL, qAG-9.2 has been fine-mapped to
OsTPP7 gene which encodes trehalose-6-phosphate phosphatase involved in starch
mobilization during germination (Kretzschmar et al. 2015). Recent studies showed
effective operation of anaerobic respiration and nitrogen metabolism in tolerant rice
genotypes led to more energy efficient metabolic system under oxygen limiting GSOD
condition resulting in better ROS handling and cellular pH maintenance (Vijayan et al.
2018).
Phosphorus is a limiting nutrient in the direct seeded rice ecology. Due to high
cost of phosphatic fertilizers, farmers are not applying required quantity of the fertilizer.
A major QTL Pup1, located on chromosome 12 exhibiting 78.8 % of the total phenotypic
variance for phosphorus uptake has been found to be associated with tolerance to P
deficiency and efficient P uptake in low phosphorus soil (Wissuwa et al. 2002).
Kasalath, a Pup1 donor variety has a 278 Kb INDEL and near isogenic lines with the
QTL exhibited an increase P uptake and also 2-to 4- fold increase in grain weight per
plant (Chin et al. 2010). Therefore, the development of P-efficient crop varieties that
can grow and yield better with low P supply is a key to improve rice production.
Studies have showed that after flowering, lodging one day earlier causes yield
loss to the tune of 2.6-2.7% per day in best japonica varieties grown at China. Through
systematic studies on lodging resistance from last 25 years; researchers from Japan
were able to demonstrate that lodging resistance can be significantly improved in rice
without any compromise on grain yield. In fact they were able to identify mechanisms
which simultaneously improve yield and lodging resistance and the genes were further
cloned and characterized (Yano et al. 2015). Typhoon causes major damage to rice
crop in Japan especially at maturity stage. Researchers were able to develop QTL-
NILs by transfer of a genomic region from an Indian landrace Kasalath in the
background of japonica cultivar Koshihikari which could survive two or more moderate
typhoons in a particular year without any reduction in yield (Ishimaru 2008). The
same research group was also able to identify another functional QTL which could
improve lodging resistance through prevention of factors which lead to culm strength
deterioration after grain lling (Kashiwagi et al. 2016). The prospect of combining high
biomass production and lodging resistance was demonstrated through development
of a long-culm rice forage cultivar named as ‘Leaf Star’ which was a low-lignin producing
lodging resistant rice cultivar suitable for feed and bioenergy production (Ookawa et
al. 2014). The important QTLs/genes responsible for lodging resistance in rice are
presented in Table 1. The possibility of effective utilization of lodging resistance in
rice while addressing the concern of yield and feed quality in Indian rice breeding
programme need to be considered.

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Table 1. List of QTLs/ genes identified to confer lodging resistance in rice.
QTL/ Gene Feature Population Reference
bsuc11 (Breaking Present in Chromosome 11. Chromosome Kashiwagi
strength upper Improves Breaking strength of Segment 2014
culm 11) upper culm through thickening Substitution Lines
of cortical bre tissues in (CSSLs) developed
internode and raising the level from ‘Koshihikari’
of holocellulose. and ‘Kasalath’
prl5 (Pushing Present in chromosome 5. CSSLs developed Kashiwagi and
resistance lower 5) Improves pushing resistance of from ‘Koshihikari’ Ishimaru 2004
lower plant parts (prl5) by and ‘Kasalath’
delaying senescence and
increasing carbohydrate
reaccumulation in stems.
lrt5 (Lodging Plants carrying this QTL CSSLs developed Ishimaru et al.
resistance in circumvent domino effect. from ‘Koshihikari’ 2008
atyphoon 5) Starch content of upper culm and ‘Kasalath’
in lrt5-NILs was 4.8 times when
compared with recurrent parents
SCM2 (Strong The gene simultaneously CSSLs derived Ookawa et al.
Culm 2) QTL/ improves section modulus of from Sasanishiki 2010
Aberrant Panicle culm along with grain number and Habataki
Organization1 per panicle.
(APO1) gene
SCM3 (Strong The gene simultaneously Backcross Inbred Yano et al.
Culm 3) QTL/ improves section modulus of Lines (BILs) of 2015
Teosinte Branched1 culm along with grain number Koshihikari and
(OsTB1) gene per panicle. NILs of Chugoku117
SCM2 + SCM3 further improves
both traits

Under shallow lowland condition, seed dormancy is a prerequisite for breeding of

cultivars as it prevents pre-harvest sprouting of seeds which in terms significantly
reduce the quality and storability of the harvest. Pre-harvest sprouting mostly happens
when humidity and temperatures increase during grain filling and maturation, which
are caused mostly by unseasonal rains. Several efforts for mapping QTLs/genes for
seed dormancy have been taken by researchers of China and Japan using indica x
japonica derivatives. Some of the significant findings have been listed in Table 2.
Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most
important disease of lowland rice in India. In some areas of Asia, it can reduce crop
yield by up to 50% (Khush et al. 1989) or even up to 80% (Singh et al. 1977). In
absence of effective chemical or other control agents against the pathogen, host
plant resistance has gained enormous importance in controlling this disease. Using
the gene pyramid approach, improved indica rice cultivars with broad spectrum
durable BB resistance have been developed by combining different genes (Pradhan

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112 Higher Yield and Climate Resilience
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Table 2. List of QTLs/ genes identified to confer seed dormancy in rice.

Genes/QTLs detected Population Reference
1. One QTL (Sdr1) for seed dormancy was BILs from Nipponbare Takeuchi et al.
identified which was very tightly linked to and Kasalath 2003
another QTL for heading date (Hd8)
2. Four major QTLs and several minor QTLs Doubled haploid from Guo et al. 2004
were detected. qSD-3 in chromosome 3 was indica x japonica
most important.
3. Three QTLs (Sdr6, Sdr9 and Sdr10) were CSSLs of Nona Bokra Marzougui et al.
detected and Koshihikari 2012
4. Four putative QTLs detected. qSD-6.1 BIL of Nipponbare x Sasaki et al.
most effective among those. Kasalath 2013
5. Eight additive effect QTLs for seed RILs of japonica x Wang et al. 2014
dormancy detected. Best combination for indica
pyramiding also suggested.
6. Several QTLs were mapped at 4, 5 and 6 RILs of japonica x Cheng et al.
weeks after heading in the same population indica 2014
7. Sixteen and 38 loci significantly associated Association mapping Magwa et al.
with dormancy in freshly harvested seeds in global accessions 2016
and after ripened seeds were detected. There of rice
were three common QTLs among them.
8. Six major additive effect QTLs (qSD3-2, Single Segment Zhou et al. 2017
qSD4-1, qSD7-1, qSD7-2, qSD7-3 and Substitution Line of
qSD11-2) with contributions of more than one indica rice with
or equal to 30 percent. Validated over seven several donors
cropping seasons
9. Ten SNPs were identified which Resequencing of Lee et al. 2017
significantly affect Pre Harvest Sprouting multiple accessions.
and the alleles were validated using
regression based model.

et al. 2015; 2016). A three-gene combination appeared to be the most effective; with
Xa21 contributing the largest component of resistance. Gall midge insect is an internal
feeder of rice plant and it reduces rice yield severely. Till date, 11 gall midge resistant
genes have been identified.
As overall grain yield of rice from a crop field is a very complex trait for direct
improvement; efforts have been taken worldwide for utilizing the genes and QTLs for
its component traits.Gn1a, a major QTL, has been cloned and characterized for grain
number per panicle. The functional analysis shows that Gn1a encoded cytokinin
oxidase/dehydrogenase (Ashikari et al. 2005). Ideal plant architecture1 (IPA1) changes
rice plant architecture and enhances rice grain yield. This IPA1 encodes OsSPL14
(Jiao et al. 2010). The genes/QTLs associated with the yield enhancing traits are
presented in Table 3.

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Table 3. Useful genes/QTLs for pyramiding of yield component traits for increasing
yield potential in rice.
Yield
Genes/ Chromosome Donor line/
QTLs Traits location variety Gene function Reference
1. Gn1a Grain number 1 Habataki Cytokinin Ashikari et al.
Oxidase/ 2005
Dehydrogenase2
2. SPL16 Panicle 8 ST12 Squamosa Wang et al.
branching Promoter binding 2012
protein like-14
3. SCM2 Culm diameter 6 Habataki F-box containing Ookawa et al.
protein 2010
4. Ghd7 Delayed heading 7 Minghui63 CCT domain Xue et al.
date and increased protein 2008
plant height and
yield
5. GS5 Grain length 5 Zonhhua11 Serine carboxy Li et al. 2011
peptidase
6. GW5 Grain weight 5 Nipponbare Unknown protein Weng et al.
2008
7. TGW6 Test grain weight 6 Kasalath IAA glucose Ishimaru et al.
hydrolase 2013
8. DEP1 Erect panicle, 9 Shenung265 Phosphatidy- Huang et al.
high grain number lethanol-amine 2009
binding protein
9. SPIKE1 Grain number/ 4 IR68522-10 Polar auxin Fujita et al.
panicle -2-2 protein 2013
10.GW2 Grain weight 2 Oochikara Ring-type E3 Song et al.
ligase protein 2007
phosphatase
11.GS3 Grain length 3 Minghui63 Trans membrane Fan et al.
protein 2006

FR13A, a selection from landrace ‘Dhalaputia’ is a widely used submergence

tolerance donor line in submergence breeding programme. This line is the source
material for submergence tolerance QTL, Sub1. The variety Swarna in which Sub1
has been introduced through marker-assisted breeding has become very popular in
rainfed lowland ecologies in the country. This was the first ever submergence tolerant
variety released in the country (Neeraja et al., 2007). Swarna-Sub1 was released by
SVRC, Odisha and SVRC, Uttar Pradesh and notified by Dept. Of Agriculture and
Cooperation, Ministry of Agriculture, Govt. of India. Many pyramiding works on
bacterial blight has also been performed in the country in various superior
backgrounds (Pradhan et al. 2015; 2016). Till date 11 gall midge resistance genes have

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114 Higher Yield and Climate Resilience
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been identified (Dutta et al. 2014). Researchers of ICAR-Indian Institute of Rice

Research developed drought tolerant variety DRR Dhan 42 through pyramiding of
qDTY1.1, qDTY2.1 and qDTY3.1 in IR64 background. The donor germplassm line
N22, CR143-2-2, Bala, Lalnakanda, Dagad Deshi, Moroberekan, Aus 276, Vandana,
Apo and IR55419-04 are commonly used donors for drought tolerance breeding
programme in the country.
The rice breeders in India have mostly depended upon dwarfing genes for
improving lodging resistance coupled with phenotypic selection for stronger culm.
The general perception remained that selection of high culm strength may have
negative impact on yield besides its low acceptability among farmers due to reduced
feed quality of straw. There is no significant research report about genetic studies on
lodging resistance of rice from India in last 20 years especially for waterlogged
ecologies. Only very recently a report for mapping QTLs associated with lodging
resistance in dry direct-seeded rice have been published by researchers from IRRI,
India hub (Yadav et al. 2017). Rathi et al. (2011) mapped two QTLs for seed dormancy
and one for duration of seed dormancy in a smaller F2population derived from two
indica genotypes.
The submergence tolerance property of FR13A was first reported by NRRI and
shared with other institutes, which was subsequently mapped as Sub1 and used in
rice breeding. The ICAR-NRRI has developed pyramided lines with Xa21, xa13 and
xa5 resistance genes in the backgrounds of Swarna, Jalmagna, IR 64, Lalat and
Tapaswini. The Institute also collaborated with IRRI for release of Swarna-Sub1 through
SVRC, Odisha. Under ‘QTL to variety’ project, the Institute has stacked three abiotic
stress tolerance genes viz., Sub1+ qDTY1.1+qDTY2.1 in the background of Swarna
variety. Also, under IRRI-NRRI collaborative project, Swarna variety containing Sub1,
qDTY1.1, qDTY2.1 and qDTY3.1 QTLs have been released for submergence and
drought affected areas of Andhra Pradesh, Telangana, Odisha, Uttar Pradesh and
West Bengal states of the country. A bacterial blight resistance genes pyramided line
of Swarna has been released as CR Dhan 800 by SVRC, Odisha. Efforts are made to
improve the popular lowland varieties like Gayatri, Sarala, Varshadha, Pooja and
Pratikshya with submergence tolerance by incorporating “Sub1” gene through marker-
assisted backcross breeding. Presently, the improved lines of these varieties are in
the advanced stages of testing. Closely linked markers have been identified for gall
midge resistance gene Gm4 and QTL for BPH resistance (Mohanty et al. 2017) which
can be used for pyramiding with other genes reported nationally and internationally.
The Institute has released several varieties namely Pooja, Sarala, CR Dhan 500, CR
Dhan 401, Gayatri, Savitri, Dharitri, Swarna-Sub1, CR Dhan 800, CR Dhan 801, CR
Dhan 505, CR Dhan 506 and CR Dhan 508 for cultivation under shallow lowland
ecosystem (Table 4).

Genetic Improvement of Rainfed Shallow-lowland Rice for

Higher Yield and Climate Resilience 115
Table 4. Rice varieties developed by the institute for shallow lowland ecosystem.
Potential
Year of Maturity yield Grain Special Recommended
Variety name release duration (t ha-1) type* feature** States
1. Anamika 1979 145 4.5 LB - Tamil Nadu
2. Ramakrishna 1980 130 4.0 MS BLB, GM, Odisha
tolerant to water
logging, iron
toxicity
3. Samalei 1980 150 4.5 LS GM, BL Odisha
4. Savitri 1982 155 5.5 SB BL, BB, MR Andhra
Pradesh,
Odisha,Tamil
Nadhu
5. Dharitri 1988 150 5.0 SB BI, BB, SB, GM Odisha
6. Padmini 1988 145 4.0 ShS BB Odisha
7. Moti 1988 145 5.0 LS BL, RTV, GLH Odisha
8. CR 1002 1992 145 4.5-5.0 SB ShB,GLH West Bengal,
Odisha, Bihar
9. Seema 1992 150 4.5-5.0 MS Blast, BPH, GM, Odisha
tolerant to water
logging
10. Pooja 2000 150 5.0 MS BL Odisha,
Madhya
Pradesh, West
Bengal
11. Ketekijoha 2005 145 3.5 MS BB, ShB, SB, GM Odisha
12. Nua Kalajeera 2008 145-150 3.0 SB YSB, BI, Sh.R, Odisha
Black husk
13. Nua Dhusara 2008 145-150 3.0 SM NB, ShR, RTV, Odisha
GM
14. Swarna- Sub1 2009 143 7.0 MS Tolerant to Odisha,
complete Uttar Pradesh
submergence
for two weeks
15. Reeta 2010 150 7.5 MS BL, NB, BS, Odisha,
ShB, ShR, SB, West Bengal,
LF Tamil Nadhu,
Andhra Pradesh
16. Nua Chinikamini 2010 145-150 3.5 SB RTV, SB, RGM, Odisha
NB, Sh.R
17. CR Dhan 500 2011 160 7.2 MS MR to LB, NB, Odisha,Uttar
GM, SB, LF Pradesh
18. Sumit 2012 145-150 7.5 LB LB,SB,LF Odisha
19. Poorna Bhog 2012 140-145 5.2 LS NB, GM, ShR, SB Odisha
20. Jalamani 2012 160 4.9 MS MR-LF, GLH, LB, Odisha
NB, BS, G, SB

Contd....

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116 Higher Yield and Climate Resilience
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Potential
Year of Maturity yield Grain Special Recommended
Variety name release duration (t ha-1) type* feature** States
21. Jayantidhan 2012 160 5.3 MS MR-LB, NB, ShB, Odisha
ShR, RTV, GM,
SB, LF, RT, WM
22. CR Dhan 407 2014 150 5.8 LB MR to leaf blast, Odisha,
neck blast West Bengal
23. CR Dhan 505 2014 162 7.1 MS Submergence Odisha, Assam
tolerance
24. CR Dhan 408 2014 165 7.5 LB MR-LB, NB, BB, Odisha
(Chakaakhi) Sh.R, SB, LF,
WBPH
25. CR Dhan 508 2016 160 8.5 LB MR-NB, BS, ShR, Odisha, Assam
SBR, LF, WM West Bengal
26. Pradhandhan 2016 160 7.8 LS MR-LB, NB, ShR, Odisha
(CR Dhan 409) SBR, LF
27. CR Dhan 507 2016 165 6.8 MB MR-NB, BS, ShR, Odisha
ShB, SBR, WM,
LF
28. CR Dhan 910 2016 140-145 5.6 MS MR-BL,NBl, ShR, Odisha
RTV, SB, LF,
WBPH
29. CR Dhan 909 2017 140 6.5 MS Tolerant to LB, Uttar Pradesh,
NB, Sh.R, RTD Bihar, Assam,
Maharashtra
30. CR Dhan 801 2017 140 7.8 MS For submergence Uttar Pradesh,
and drought prone Bihar, Odisha,
areas West Bengal
Note: *SB-Short bold; LS-long slender; MS-Medium slender; MB-Medium bold; LB-Long bold**Bl-
blast; BB-Bacterial blight;BPH-brown plant hopper; BS-brown spot; GB-gundhi bug; GM-gall midge;
GLH-green leaf hopper; LF-leaf folder; RTV-rice tungro virus; SB-stem borer; Sh.B-Sheath blight;
Sh.R-Sheath rot; WBPH-white backed plant hopper; YSB-yellow stem borer; HS-Helmenthosporium

3. WAY FORWARD
Research need to be carried out to reduce the yield limiting factors of the rainfed
lowland ecology. Efforts to increase yield potential of the shallow lowland rice may
further be expedited to get a quantum jump in yield from a vast neglected area of
eastern India. As the rainfed areas of the country are highly affected by climate
change effects, the high yielding varieties of the ecology need to be stacked with
stress tolerance gene(s)/QTLs for making them climate smart. Effects of the QTLs/
gene(s) need to be segregated out first and then combination effects need to be
studied so that proper pyramiding as well as stacking combinations can be identified.
Study on development of host plant resistance for the emerging diseases and insect
pests need to be taken up in an environment friendly manner. Translocation of elements
like heavy metals from soil to grains and straw need to be in a safer level. Genetic
enhancement of the materials for toxic and other problematic soils need more attention

Genetic Improvement of Rainfed Shallow-lowland Rice for

Higher Yield and Climate Resilience 117
in future. Trait combinations in superior background should lead to development of
high and sustainable performing varieties with higher benefits to the producers.
Thus, in popular varieties, multiple tolerance genes for submergence, anerobic
germination, yield QTLs under drought, bacterial blight resistance genes, gall midge
resistance genes, seed dormancy and yield enhancing QTLs need to be stacked to
make them highly resilient to the climate change.
In future, production of rice needs to be increased from lesser land area. For this
purpose there is effort towards increasing per plant yield though higher grain number
per panicle and grain weight. This will definitely increase the weight of upper part of
the rice plant and thereby increasing the chance of lodging with current plant types
of indica rice. The problem is further coupled by increasing climatic vagaries like
erratic rainfall, increase in extreme weather events and uncharacteristic wind flow
especially in eastern and southern coasts of the country. Lodging related losses in
semi dwarf varieties still remains to the extent of 35% and at some specific locations
even >85% where traditional cultivars are grown. There is a need for systematic
studies for improving lodging resistance of rice in our country. More so, understanding
the mechanism and devising strategies for improvement of lodging resistance to
indica rice would be important to breed future rice with high biomass coupled with
higher harvest index. Further it will be necessary to save rice in climate vulnerable
regions where incidences of sudden heavy rain or wind during maturity of crop cause
severe production losses.
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Genetic Improvement of Rice for Multiple Stress
Tolerance in Unfavorable Rainfed Ecology

K Chattopadhyay, JN Reddy, SK Pradhan, SSC Patnaik, BC Marndi,

P Swain, AK Nayak, A Anandan, K Chakraborty, RK Sarkar, LK
Bose, JL Katara, C Parameswaram, AK Mukherjee, SD Mohapatra,
A Poonam, SK Mishra and RR Korada

SUMMARY
Due to various abiotic stresses very low productivity of rice is noted from
unfavourable rainfed lowland ecology, which accounts 18% of total rice growing
area. Gradual change in climatic scenario including monsoon results in various abiotic
stresses in this ecology frequently at various stages of crop growth in isolation or in
combination. Coastal saline ecology is affected by salinity and excess water stresses.
Varieties developed for this ecology through conventional and marker-assisted
breeding are not significantly tolerant for either salinity or multiple abiotic stresses
such as salinity and water logging at reproductive stage. Similarly for semi-deep and
deep water ecology also requires biotic stress tolerance and tolerance to water logging
and prolonged submergence. Anaerobic germination ability is also requisite in high
yielding background for direct sowing in unfavourable lowland ecology. Validation
of QTLs including those identified by National Rice Research Institute (NRRI), Cuttack
for salt tolerance at reproductive stage is one of current research priorities.
Conventional breeding for multiple stress (salinity and excess water) tolerance is
being complemented by the efforts at NRRI, Cuttack to identify multiple stress tolerance
QTLs and introgression in high yielding background suitable for coastal ecology.
Research priorities for sustainable rice production in semi-deep and deep water ecology
include identification of QTLs for anaerobic germination ability and prolonged
submergence tolerance and pyramiding them along with genes for water logging and
biotic stress tolerance. Improvement of productivity and sustainability of this ecology
through our research efforts would definitely elevate the country’s overall rice
productivity and ensure social and economic security of people who depend on this
ecology for their livelihood.

1. INTRODUCTION
Rainfed ecology can be divided under rainfed upland, favourable lowland and
unfavourable lowland with flood prone and salinity affected areas. The low productivity
of this ecology is mainly due to various abiotic stresses, which are found alone or in
combination in the various crop growth stages. Therefore, enhancement of abiotic
stresses tolerance can only able to improve the production, productivity and overall
profitability of the system. Rice is sensitive to salinity at both seedling and
reproductive stages. Although rice is sensitive to salt stress, it is a preferred crop in
salt-affected coastal areas. Rice can withstand water-logging, and standing water

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helps in diluting and leaching salts from surface soil (Ismail et al. 2008). Therefore,
despite their low yields, many landraces are still preferred by farmers in coastal areas.
The degree of salt tolerance varies widely in these landraces, and the variability
offers an opportunity for varietal improvement for salt tolerance. On the backdrop of
lack of significant improvement of salinity tolerance in rice through traditional breeding,
marker assisted breeding using major QTL (Saltol) for seedling stage salt tolerance
was initiated in India and worldwide. Some of the introgressed high yielding varieties
were showing better survivability but that could not guarantee high yield when salt
stress occurs at flowering stage. Mitigation of the salt stress effects on rice growth
and yield has been tried through both management practices and introduction of
tolerant varieties in the affected areas; but use of fresh water supply and other
management practices alone in salt-affected areas has generally proven to be
uneconomical and not feasible to implement on a large scale. Thus, genetic
improvement of salt tolerance in rice is the most feasible and promising strategy to
provide stable food production in such a stress-prone environment. In coastal areas
rise in temperature, erratic rainfall along with penetration of salty water due to sea-
level rise can change the micro environment in multifaceted manners (Wassmann et
al. 2009). Multiple abiotic stresses are reality in coastal plains. Addressing multiple
abiotic stress tolerance, as well as the consequences of one stress followed by another
could develop knowledge related to adaptation of rice crop under variable climatic
conditions.
Apart from coastal ecosystem, unfavourable rainfed ecosystem facing problem of
prolonged submergence and water stagnation due to flood. Therefore, development
of rice varieties with flood tolerance is prime requirement. Sub1 gene has been identified,
cloned and characterized from FR13A, an indica rice variety, which gives 14 days
(two weeks) tolerance to submergence and it has also been transferred to number of
rice varieties through marker assisted introgression. But due to climate change, lowland
ecology is facing problems of prolonged submergence, which is often more than 15
days. Therefore, cultivar for such situation is urgently required for sustainable
production. On the other hand, early direct sowing in semi-deep water logged situation
before onset of monsoon is generally practiced. Moreover, sowing seeds in standing
water is an effective means of weed control and direct seeded rice in rainfed ecology
is getting popularity due to reduced cultivation cost. Therefore, anaerobic germination
ability in rainfed unfavorable ecology in high yielding cultivars is highly needed.
This chapter describes the research problems related to the coastal saline,
waterlogging and deep water ecosystems in the backdrop of changing climatic
condition and various basic, strategic and applied research carried out at international,
national and NRRI level. This also deals with the future strategies and way forward
on these issues.

2. PROBLEMS OF UNFAVOURABLE RAINFED ECOLOGY

Traditional approaches for introducing improved rice varieties to farmers have
demonstrated significant impact in favourable ecosystems. But limited success was
achieved in unfavourable ecosystems, affected by various abiotic stresses such as

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Unfavorable Rainfed Ecology 121
salinity, submergence, water logging and even drought in some cases. Through
traditional breeding many varieties with high yield potential such as CR Dhan 403, CR
Dhan 405, Panvel 3, Bhutnath, etc. have been developed for coastal saline areas. But
none of them is tolerant to high salinity stress (>6 dS m-1), especially at flowering
stage. The major reasons are relatively more complexity and genotype x environment
interaction, indicators of physiological traits and well accepted screening protocol
for salinity tolerance at flowering stage. Therefore, robust QTLs and markers are also
unavailable for marker assisted selection for this trait. Due to lack of physiological
traits controlling salinity tolerance at flowering stage and simplicity in screening
protocol, any major QTL is yet to be identified and used in marker assisted selection
for incorporating tolerance at reproductive stage.
Coastal saline areas are normally mono-cropped with rice grown during the Kharif
season. Agricultural productivity is low and unstable due to the frequent occurrence
of abiotic stresses. During our widespread survey and demonstrations of climate
resilient rice varieties in coastal region we felt that salinity and stagnant flooding in
combination affecting the rice production in greater extent (Chattopadhyay et al.
2016). Due to this reason still farmers grow local land races tolerant to both salinity
and stagnant flooding. Flooding with saline water is a common problem. Intrusion of
sea water displaces millions of people from coastal plains and causes the direct threat
of the economic security of the poor and marginal people reside along the coastal
belts (Wassmann et al. 2009). Development of rice tolerant to multiple abiotic stresses
especially salinity and stagnant flooding could improve the productivity and
sustainability of the coastal ecosystem.
Deep and semi-deep waterlogged area is another unfavorable lowland ecosystem.
Problems associated with this ecosystem are as follows.
 Several rainfed rice areas are at risk of flooding, a stress that decreases yield
substantially (Ismail et al. 2013). Poor crop establishment due to deep submergence
and water logging at the early stage of the crop growth is predominant. Prolonged
submergence/waterlogging suppresses tillering and increases mortality. Water
logging and poor drainage also leads to accumulation of toxic substance causing
problems such as iron toxicity and sulphide injury.
 Incidence of pests such as stem borer, gall midge, cutworm, GLH and leaf folder
and diseases such as bacterial blight, sheath blight sheath rot, tungro and false
smut along with abiotic stresses are also frequent in deep and semi-deep water
logged areas.
 Submergence tolerance (Sub1) has been incorporated in many high yielding
varieties adapted to rainfed lowland ecology (Singh et al. 2016). However, additional
genes are needed for imparting flood tolerance for 21 days (3 weeks) or more
because of regular flooding in India and south-east Asia due to climate change.
Better genotypes with submergence tolerance at early and late vegetative stages
for more than 21 days are not available.

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 Direct seeding is a traditional system of sowing under rainfed ecosystem and it’s
getting popular in irrigated areas, as the decrease in labor source and increase in
labor charges. This system of sowing helps in reducing cultivation charges, a
week of crop duration and maintains the physical soil structure for successive
cropping. The stagnation of water in unleveled fields after irrigation or copious
rainfall immediately after sowing leads to poor germination. Poor establishment
and uneven growth pattern due to the difference in germination affects timely
intercultural operation (weed/fertilizer, etc), that leads to poor yield. Flash flooding
during sowing to harvesting is the state of problem widespread across the south
to Eastern states of the country (Anandan et al. 2012). The activity of α-amylase
determines the germination under water enhancing stress tolerance. No popular
high yielding rice varieties possess this mechanism to germinate under anoxia.
Traditional landraces have genes for this trait, but they are tall lodging type with
red pericarp and susceptible to diseases and very poor phenotypic performance.

3. STATUS OF RESEARCH
During initial exposure to salinity, plants experience water stress, which in turn
reduces shoot growth. As time of exposure to salinity is prolonged, plants experience
ionic stress, which leads to leaf tip drying, premature senescence of leaves and
mortality of plants. As salt stress is cumulative, injury symptoms increase with time.
So, restricting the movements of toxic ions such as Na+ or Cl- to growing meristematic
tissues and young photosysnthetic organs are vital for survival. The procedure of
screening rice genotypes for salt tolerance at seedling stage has been well established
and validated through number of experiments. But due to long growing period of rice
plants and complexity in measuring tolerance level, no protocol has been found ideal
for high throughput screening till date. A salt tolerant (at seedling stage) cultivar,
Pokkali has Na+ exclusion mechanism and thereby maintains low Na+: K+ ratio in
shoot and new leaf. The Saltol QTL in rice was identified by employing a RIL
population between the tolerant landrace Pokkali and the highly sensitive IR 29.
Among more than 100 identified QTLs, this is the major QTL for seedling stage salt
tolerance contributing 43% of variation for seedling shoot Na+- K+ ratio. A plasma
membrane transporter that regulates partitioning of Na+ between roots and shoots,
OsHKT1;5 was identified as one of the causative gene located inside the Saltol-QTL,
which was fined mapped and cloned (Ren et al. 2005). Salinity tolerance in most of the
Indica genotypes is generally correlated with low Na+ ions in shoot and OsHKT1;5 is
found more active in those tolerant genotypes. But some wild rice accessions of O.
glaberrima could exclude Na+ from shoots using a mechanism independent of
OsHKT1;5 (Platten et al. 2013). Introgression lines derived from O. rufipogon × O.
sativa cross revealed 15 QTLs for salinity tolerance, 13 of them derived from the
tolerant O. rufipogon parent (Tian et al. 2011). A genotype with seedling stage salinity
tolerance may not be tolerant at reproductive stage as well. For salt tolerance at
reproductive stage, 16 QTLs for pollen fertility, Na+ concentration, Na-K ratio in flag
leaf in chromosome 1, 7, 8, 10 (Hossain et al. 2015) were identified. But none of them
was validated.

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 123
 Rice is unique compared to any other cereals to adapt with water stagnation.
Sub1 is the major QTL associated with submergence tolerance in rice. The locus was
mapped to chromosome 9, and is composed of a cluster of ethylene response factors
(ERF) genes located in tandem, named SUB1A, SUB1B and SUB1C. The tolerant
SUB1A-1 allele is derived from the aus subgroup of indica rice (Xu et al. 2006).
Niroula et al. (2012) tested 109 accessions of cultivated and wild relatives, including
12 species, for submergence tolerance, and found O. rufipogon and O. nivara tolerant
accessions that carry the SUB1A-1 allele, showing that SUB1 locus architecture
determines submergence tolerance in these species, as in O. sativa. Rice plants adapt
to very deep water stagnation (> 1 m deep) through greater elongation of stems by
the action of the gene ‘Snorkel’ 1 and 2 (Hattori et al. 2009). On the other hand, five
putative QTLs of qAG-1-2, qAG-3-1, qAG-7-2, qAG-9-1 and qAG-9-2 elucidating 17.9
to 33.5% of the PV from KhaoHlan On has been reported by Angaji et al. (2010) for
anaerobic germination. Later six QTLs on chromosomes 2, 5, 6 and 7 from the landrace
Ma-Zhan Red was identified by Septiningsih et al. (2013).
Traditionally cultivated local rice varieties in coastal area have tolerance to salinity
and submergence but are low yielding. Some of the widely used varieties are: Vikas,
Korgut, Sathi, Pichaneelu, Kuthiru, Kalundai samba, Bhurarata, Kalarata, Karekagga,
Pokkali, Chettivirippu, Bhaluki, Rupsal, Nona Bokra, Kamini, Talmugur, Patnai, Getu,
etc. These diverse traditional rice varieties are precious genetic resources that provide
ecological balance and their conservation is crucial for future food security. Using
these germplasm, many high yielding varieties such as CST1-7, Bhutnath, Panvel-3,
CSR36, etc. have been developed. Sub1 gene is attempted to transfer into popular
lowland rice varieties such as Bahadur, Ranjit, Varshadhan and Savitri. Similarly, Saltol-
QTL for salt tolerance at seedling stage is being transferred into varieties, namely,
ADT 45, Savitri, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52 (Singh et al. 2016).
CSR 27 (Pandit et al. 2010) was identified as tolerant variety for salt tolerance at
flowering stage. Number of QTLs for salt tolerance at flowering stage were identified,
but none of them were found reproducible. Due to population specificity and limited
scope of using diverse tolerant germplasm in bi-parental mapping, genome wide
association mapping exploiting large scale single nucleotide polymorphism have been
practiced to capture natural variations in loci and allelic variations in candidate genes
for complex abiotic stresses such as salinity. Using custom-designed array based on
6000 SNPs, Kumar et al. (2015) identified 20 loci associated with Na-K homeostasis.
They found Saltol as the major salt tolerance QTL not only for seedling stage, but
also for reproductive stage in relation to Na+-K+ ratio in leaves. New QTLs were also
found on chromosomes 4, 6 and 7.
At NRRI, considerable research has been carried out on many aspects of crop
improvement for unfavourable rainfed ecology.
3.1. Diversity of Saltol- QTL region and detection of Saltol introgression
lines
Landraces from Sundarban region were found diverse in respect of salt tolerance.
Salt tolerant cultivars from this area such as Kamini, Talmugur, etc. had allelic difference

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Profitability and Climate Resilience

from the widely used Saltol- introgression

line, FL 478 in the Saltol - QTL region. From
IR64/FL478 cross, eight F8 tolerant and
moderately tolerant lines at seedling stage
(at EC= 12 dSm-1) along with their parents
(FL 478 and IR 64) were subjected to
analysis for validation of the microsatellite
markers in the Saltol QTL region. Four
primers (RM10694, RM8094, AP3206,
RM493) in Saltol region were found
Fig. 1. High yielding salinity tolerant line polymorphic between FL 478 and IR64.
(IET 23400) from the cross Annapurna/ FL478 specific marker alleles for different
FL 478 carrying Saltol QTL.
loci situated from 11 Mb to 12.4 Mb region
in chromosome 1 was found in all the lines tested in homozygous condition. These
tolerant and moderately tolerant lines sharing a common segment from the donor FL
478 might carry the Saltol QTL in this region. Thirty seven tolerant and moderately-
tolerant (SES= 3-5) F7 lines (with 3-5 t ha-1 yielding ability (Fig. 1) under coastal saline
situation at dry season) derived from the Annapurna × FL478 cross. These lines are
sharing a common segment from the donor FL 478 might carry the Saltol QTL (Fig. 2)
either in homozygous or heterozygous condition (Chattopadhyay et al. 2014).

Fig. 2. Graphical genotyping of salt tolerant lines derived from Annapurna/

FL 478 carrying Saltol region in chromosome 1.

3.2. Parental combination for improvement of salt tolerance

Unlike Pokkali, Rahspunjar was efficient in maintaining higher level of K+ despite
high Na+ influx in shoot and located distant from Pokkali in 3-D plot on SSR data.
Morpho-physiological difference and the highest allelic difference between SR 26B
and Pokkali in the Saltol QTL region was supported by non-significant association
between Saltol marker RM 10745, RM 3412 with tolerance phenotype. Swarna Sub1
× Rahspunjar and Savitri × SR 26B produced more transgression segregants for
tolerance and were found ideal combination (Chattopadhyay et al. 2015).

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 125
3.3. Standardization of protocol, identification of donors and
understanding the reproductive stage salinity tolerance in rice
Chattopadhyay et al. (2017a) standardized a protocol where setup was established
with a piezometer placed in a perforated pot for continuous monitoring of soil EC and
pH. Further, fertilized soil was partially substituted by gravels for stabilization and
maintaining the uniformity of soil EC in pots without hindering its buffering capacity.
The protocol having modified medium (soil:stone 4:1) at 8 dSm-1 salinity level was
validated using seven different genotypes having differential salt sensitivity. Based
on this new medium, important selection traits such as high stability index for plant
yield, harvest index and number of grains/panicle and also high K+ concentration and
low Na+-K+ ratio in flag leaf at grain filling stage were validated and employed in the
evaluation of a mapping population. The method was found remarkably efficient for
easy maintenance of desired level of soil salinity for identification of genotypes
tolerant to salinity at reproductive stage and evaluation of mapping population.
We have also identified tolerant germplasm with QTL linked markers for salt
tolerance at flowering stage using 8 dS m-1 NaCl water (Chattopadhyay et al. 2013).
Donors for reproductive stage tolerance viz. AC41585, AC39394 (Chattopadhyay et
al. 2013), were validated with this method. Results showed that visual scoring of
stress symptom and/or SPAD reading may not correspond to the stress effect. Better
phenotyping technique such as chlorophyll fluorescence imaging can show clear cut
differences between salt treated and untreated rice plants at reproductive stage. Gene
expression analysis revealed that salt tolerant Pokkali (AC 415858) genotype showed
better K+-retention and Na+-exclusion strategies coupled with maintenance of better
membrane potential (both plasma membrane and vacuolar) by induction of ATPases
and PPases activities in flag leaf (NRRI Annual report 2016-17).
Many QTLs have been identified for salt tolerance at seedling and reproductive
stages. But none of them could be validated, fine mapped and cloned for using in salt
tolerance breeding programme (Chattopadhyay et al. 2013). At NRRI, 180 backcross
derived lines (BC3F3:5) from salt tolerant donor AC41585 and recurrent parent IR 64
were subjected to phenotype in saline (EC= 8 dS m-1) and non-saline environments in
2014 and 2015. Normal distribution with small skewness values was found for all
these significant yield attributing traits. Polymorphic 121 SSR, hyper variable-SSR
and gene based primers were used and data were analysed via inclusive composite
in-terval mapping and two dimensional scaling using QTL IciMapping v4.0.6. Map
covered a genetic distance of 1235.53 cM. Two main effect additive QTLs for DEG-S
on chromosome 2 and 4 and five additive QTLs for stress susceptibility index for
sterility (SSI-STE) on chromosome 2, 3, 4 and 11 with 17-42% phenotypic variance
were found common under salinity stress over the years. A main effect QTL with
pleiotropic effect for SSI-STE and DEG-S in 11-15 cM region on chromosome 2 was
found in marker interval HvSSR02-50 - RM13263 in 2015. Single marker analysis revealed
that over the years two markers RM17016 at 64.84cM position on chromosome 1 and

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126 Unfavorable Rainfed Ecology
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HvSSR06-63 at 77.41 cM position on chromosome 6 were associated with STE-S.

Functional genes (Os01g38980.1, Os06g45940.1, Os02g31910.1, Os02g33490.1) located
inside or just adjacent (3 cM) to QTLs detected through composite interval mapping
and single marker analysis. Functional validation is required for detection of their
possible role in salt tolerance at flowering stage (Chattopadhyay et al. 2017b).

3.4. Rice varieties for coastal saline areas

Lunishree, the first high yielding variety for coastal saline area was developed by
NRRI, Cuttack. In recent years (for the last six years) high yielding varieties such as
Luna Sampad, Luna Suvarna and Luna Barial has been developed by ICAR-NRRI for
wet season and Luna Sankhi (Fig. 3) has been developed by ICAR-NRRI in collaboration
with IRRI, Philippines for dry season cultivation in coastal saline areas. CR Dhan 402
(Luna Sampad, IET 19470) and CR Dhan 403 (Luna Suvarna, IET 18697) were developed
at the National Rice Research Institute (CRRI), Cuttack and released by the Odisha
State Sub-Committee on Crop Standards (State Varietal Release Committee) in 2010.
They were found promising in testing under the All India Coordinated Rice
Improvement Programme (AICRIP), participatory varietal selection (PVS) and other
on-farm trials conducted in rainfed coastal saline areas of Odisha. The average grain
yield of Luna Suvarna recorded over
the four years of testing in
Jagatsinghpur, Kendrapara and Puri
districts of Odisha was 4.6 t ha-1. It had
shown an average 17% yield
superiority over the national check CST
7-1 in the All India Coordinated trial.
The variety was also found promising
in Gosaba, Basanti and Sandeshkhali
blocks in the Sundarban area of West
Fig. 3. Field view of Luna Sankhi (CR Dhan Bengal. Luna Sampad also out yielded
405) developed for coastal saline areas in dry CST 7-1, the national check and
season in Odisha. Lunishree in all India Coordinated trial.
It is well accepted by farmers of
Basudevpur of Bhadrak, Marshaghai of Kendrapara and Puri districts of Odisha with
average yield with 3.6 to 4.2 t ha-1. Another rice variety, Luna Barial (CR Dhan 406, IET
19472), developed at the NRRI, Cuttack was released by the Odisha State Sub-
Committee on Crop Standards in 2012. This variety was ranked first (3908 kg/ha) in
eastern zone in the All India Coordinated trial. Under multilocation trials, it has shown
yield superiority with 3.7-4.5 t ha-1 over national and local checks in Ganjam, Cuttack,
Balasore and Khurda districts of Odisha. All the three varieties can be grown along
the coastal belt of eastern India with medium salinity stress (EC 5-7 dS m-1). The
parentage and important features of these varieties are listed in Table 1.

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 127
Table 1. High yielding rice varieties released by NRRI, Cuttack for semi-deep water
logged, deep water and coastal saline ecologies.
Released
Year of by CVRC/ Duration Reaction to biotic
Sl No Variety Ecology Parentage release SVRC (PS) and abiotic stresses
1 Utkalprabha Medium/ Waikyaku/ 1983 Odisha 155 MR or field
Semi-deep CR 1014 tolerance to major
pest and diseases
2 CR 1014 Medium/ T 90/Urang 1988 Odisha 160 MR to Sh. B. MR
Semi-deep Urangan or field tolerance to
all pest and diseases
3 Gayatri Medium/ Pankaj/ 1988 Odisha, 160 MR to Sh. B. MR or
Semi-deep Jagannath West field tolerance to all
Bengal, pest and diseases
Bihar
4 Kalashree Medium CR 151-79/ 1988 Odisha 160 Tolerant to Blast
deep CR 1014 and GM
5 Panidhan Medium/ CR 151-79/ 1988 Odisha 180 Tolerant to Blast
Semi-deep CR 1014 and GM
6 Tulasi Medium/ CR 151-79/ 1988 Odisha 170 Field tolerance to
Semi-deep CR 1014 major pests and
diseases
7 Sarala Medium/ CR 151/ 2000 Odisha 150 Intermediate, non-
Semi-deep CR 1014 lodging, Photosensi-
tive
8 Durga Medium/ Pankaj/ 2000 Odisha 155 Resistant to RTD
Semi-deep CR 1014 and suitable for late
planting
9 Varshadhan Medium/ IR 31432- 2006 Odisha 160 Non lodging and
Semi-deep 8-3-2/IR suitable for water
31406-3-3- logging situation
3-1//IR
26940-3-
3-3-1
10 Hanseswari Medium/ Pure line 2008 Odisha 150 MR- Blast, Sh B,
(CR Dhan 70) Semi-deep selection in Tol-False Smut,
composite RTV
cross
11 CR Dhan 501 Medium/ Savitri/ 2010 UP, Assam 152 R- Neck blast
Semi-deep Padmini
12 CR Dhan 500 Deep Ravana / 2011 Odisha, UP 160 MR to leaf blast,
water Mahsuri neck blast, brown
spot, gall midge
biotype 1&5, stem
borer dead heart and
white-ear head
damageand leaf
folder attack
Contd....

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Released
Year of by CVRC/ Duration Reaction to biotic
Sl No Variety Ecology Parentage release SVRC (PS) and abiotic stresses
13 Jayanti Deep Samson 2012 Odisha 160 MR- leaf blast, neck
(CR Dhan water Polo/ blast, sheath bight,
502) Jalanidhi sheath rot, rice
tungro virus and gall
midge biotype1 R-
stem borer , leaf
folder, rice thrips,
and whorl maggot.
14 Jalamani Deep Panikekoa/ 2012 Odisha 160 MR- leaf folder,
(CR Dhan water Ambika green leaf hopper,
503) leaf blast, neck
blast, brown spot,
gall midge, dead
heartand stem borer
15 CR Dhan 505 Deep CRLC 899/ 2014Odisha and Assam162 MR-blast, neck
water Ac.38606 blast, sheath rot,
sheath blight and
rice tungro virus,
stem borer, leaf
folder, whorl
maggot,
submergence
tolerance,
elongation ability
16 CR Dhan 506 Semideep CRLC 899/ 2017 Assam, 165 -
Warda2 Andhra
Pradesh &
Karnataka
17 Prasant Semideep Gayatri/ 2016 Odisha 160-165 MR-NBL, BS, ShB,
(CR Dhan Sudhir// ShR,SB, LF
507) Varshadhan
18 CR Dhan 508 Deep CRLC 899/ 2017 Odisha, 187 MR-sheath blight,
water Warda2 West brown spot and
Bengal, sheath rot
Assam
19 Lunishree Coastal Nonasail 1992 Odisha/ 145 Tolerant to coastal
saline Gamma CVRC salinity
Irradiated
Mutant
20 Luna Sampad Coastal Mahsuri / 2010 Odisha 140 Tolerant to coastal
(CR Dhan 402) saline Chakrakanda salinity
21 Luna Suvarna Coastal Mahsuri / 2010 Odisha 150 Tolerant to coastal
(CR Dhan 403) saline Ormundakan salinity
22 Luna Barial Coastal Jaya / 2012 Odisha 155 Tolerant to coastal
(CR Dhan 406) saline Lunishree salinity
23 Luna Sankhi Coastal IR31142-14- 2012 Odisha 120 Tolerant to coastal
(CR Dhan 405) saline 1-1-3-2/ salinity
(dry IR71350
season)

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 129
3.5. Enhancing excess water tolerance and biotic stress tolerance for
unfavourable rainfed lowland ecology
By screening of thousands of traditional landraces at ICAR-NRRI, several tolerant
sources form different genetic background was identified and several rice varieties
suitable for deep and semi-deep water ecosystem have been developed. Varshadhan
(Fig. 4), Sarala, Gayatri, CR Dhan 500 and CR Dhan 505 are popular among them (Table
1). Molecular marker integrated backcross breeding program has been employed to
transfer three major BB resistance genes (Xa21, xa13 and xa5) into Jalmagna variety.
The three major BB resistance genes pyramided lines exhibited high level of resistance
and provided durable resistance under deep water situation (Pradhan et al. 2015). The
ICAR-NRRI, Cuttack identified a genotype, AC 20431B, which gives submergence
tolerance up to 21 days. A mapping population was developed by crossing of Swarna-
Sub1 and AC 20431B for mapping and identification of novel genes responsible for
submergence tolerance other than Sub1 gene. An attempt was also made for
identification of linked marker(s) for 21 days submergence tolerance. The well
characterized Sub1 gene gives submergence tolerance for 14 days (2 weeks). Therefore,
Swarna-Sub1 was used as one of
the parent with AC 20431B (donor
parent) for mapping and
identification of 21 days
submergence tolerance genes
other than Sub1. A set of 568 F2
plants were submerged for 21
days. Based on selective
genotyping results, a marker
RM27322, located on chromosome
11 was found to be linked with 21 Fig. 4. Popular rice variety, Varshadhan in water
days submergence tolerance. This logged condition at Sandeshkhali-1 block of
marker will be further validated by Sundarban.
genotyping of fixed population
(NRRI Annual Report 2017).
3.6. A transcriptomic study to understand the combined effect of
waterlogging and salinity stress in rice
In coastal-saline belts rice often faces combined stresses of waterlogging and
salinity during different phases of growth. To assess the physiological and metabolic
changes in rice associated with waterlogging and salinity stresses, a transcriptome
profiling was performed in two waterlogging tolerant rice genotypes, Varshadhan
(salinity susceptible) and Rahspunjor (salinity tolerant). Transcriptome analysis in
leaf sheath at reproductive stage revealed that in response to waterlogging stress a
total of 1489 and 1028 genes were differentially expressed in Varshadhan and
Rahspunjor, respectively. Interestingly, combined stress of waterlogging and salinity
(WS) resulted in fewer numbers of differentially expressed genes (748 and 840 in
Varshadhan and Rahspunjor, respectively) in both the genotypes. Although both the

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studied genotypes were tolerant to waterlogging stress, but the transcriptome data
primarily indicated existence of differential tolerance mechanisms in them. Varshadhan
showed up-regulation of hormonal biosynthesis pathway genes (ethylene and
gibberellic acid) and triggers NADPH oxidase activity pointing towards ethylene
dependent aerenchyma formation, while Rahspunjor showed up-regulation of genes
related plant growth (SPL 8, SPL 16 etc.) as stress induced response. The combined
stress (WS) showed up-regulation of Ca2+-dependent signalling (Ca2+-ATPase, CAX
etc.) in both the genotypes, but the induction was more pronounced in Rahspunjor.
Changes in the expression level of key K+-transporters (up-regulation of HAK5 and
down-regulation of AKT1) emphasized better K+-retention ability in Rahspunjor under
salinity stress contributing towards its salt-tolerant behaviour as compared to
Varshadhan (Chakraborty et al. 2017).
3.7. Breeding for multiple abiotic stress tolerance for coastal ecology
Few elite breeding lines with salt and waterlogging tolerance were performing well
in multilocational testing (Fig. 5).
 Salt tolerant lines, CR 2459-23-1-1-S-B1-2B-1 (Gayatri/Rahspunjar) (IET 25101)
and CR 2839-1-S-10-B2-B-43-3B-1 (Swarna/ FL 496) (IET 25078) were also performed
well in waterlogged situation
with estimated grain yield of 4
t/ha. These lines were also
promoted to AVT-1 in CSTVT
trial.
 Salinity tolerant lines with
Waterlogging tolerance were
identified 2016-17
 CR 2851-S-1-B-4-1-1-1-1
(Gayatri/SR 26B)- 160 days
MS yield- 4403 kg ha-1 Fig. 5. IET 25078 (CR 2839-1-S-10-B2-B-43-3B-
 CR 2850-S-2B-12-1-1-2-1-1 1) performed well in salinity and stagnant
flooding affected Basanti block of Sundarban,
(Gayatri/FL 496) 160 days-
West Bengal in 2017.
MS- 4616 kg ha-1

3.8. Researches on agronomic practices for coastal ecosystem

On-farm trials were conducted in the Ersama block of Jagatsinghpur district (Odisha)
using rice varieties were selected nutrient management practices were evaluated and
the most promising options were validated in participatory farmer-managed trials
during 2004-2007 at six to eight locations. In the shallow lowlands, the findings suggest
that under both the shallow and intermediate lowlands, Sesbania for the wet season
and Azolla biofertilizer for the dry season are promising organic nutrient sources that
can improve soil quality and contribute to enhancing and sustaining crop productivity

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 131
in coastal areas. Among different integrated nutrient management practices, Sesbania
green manuring (GM) for intermediate lowlands (0-50 cm water depth), Sesbania GM
+ prilled urea (PU) and Sesbania GM + Azolla for shallow lowlands (0-30 cm water
depth) in the wet season, and Azolla + PU in the dry season were found to be
promising (Singh et al. 2009).
Poor crop stand and low fertilizer inputs are the important causes of poor and
unstable rice yields in coastal saline ecosystem with multiple stresses. Appropriate
crop establishment and nutrient management technology options were validated
through farmers’ participatory on-farm trials. Use of robust aged (50-day old) seedlings
raised with nursery fertilization and closer planting (15x10 cm) in the wet season, and
early planting (January 1st fortnight) in the dry season significantly improved the crop
survivability and yield. However, substantial yield improvements (91% in wet and
75% in dry season) could be achieved by combining salt-tolerant varieties with
improved crop management (Saha et al. 2008).
Studies on water management for dry season rice indicated that marginally-saline
(EC 2.4-3.1 dS m-1) water could be used safely for two weeks during the vegetative
stage under high salinity condition. Providing fresh water irrigation 2 days after
disappearance of standing water during the vegetative stage produced as much yield
as continuous ponding. These approaches would help in substantial saving of precious
fresh water and expanding the cropping area, leading to enhanced land and water
productivity. For non-rice crops, the highest yields of sunflower and groundnut were
obtained with 4 cm irrigation at 15 day intervals.

4. KNOWLEDGE GAPS
The following questions are to be addressed in the future research programme for
improvement of abiotic stress tolerance in unfavourable rainfed ecology.
 What is the robust QTL for salt tolerance at reproductive stage in rice?
 Is it possible to identify multiple stress tolerance QTLs in rice?
 Can we incorporate both salinity and waterlogging tolerance to a high yielding
background in coastal ecology through traditional and marker-assisted breeding?
 What is the robust QTL for anaerobic germination ability required for direct sowing
in lowland rainfed ecology?
 Can we utilize source for improvement of tolerance for prolonged submergence
for more than 2 weeks?
 Can we combine biotic stress tolerance (Bacterial blight and Stem borer) with
abiotic stress tolerance in unfavourable rainfed system?

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5. RESEARCH AND DEVELOPMENT NEEDS AND

RESEARCH PRIORITIES
5.1. Breeding for desirable plant characters of rice for water logged and deep water
ecologies
 Medium/semi-deep water logged lowlands: Desirable plant characters for this
ecology include 115-130 cm plant height, stiff culm, erect leaves, low to moderate
tillering ability, high N-use efficiency at low N level, early seedling vigour, drought
tolerance at seedling stage, prolonged submergence (beyond 15 days) tolerance
with less elongation and without culm elongation, photoperiod-sensitive, thermo-
insensitive, heavy panicle weight type and strong seed dormancy.
 Deep water ecology: Desirable plant characters for this ecology include 130-160
cm plant height, stiff culm, erect leaves, low tillering ability, high N- use efficiency
at low N level, early seedling vigour, drought tolerance at seedling stage,
submergence tolerance with leaf sheath and culm elongation, photoperiod-
sensitive, thermo-insensitive, heavy panicle weight type, strong seed dormancy
and kneeing ability.
5.2. Breeding scheme for water logging condition
 For multiple abiotic stress tolerance breeding for areas where submergence at
early stage of crop growth was followed by the stagnant flooding at the later
stage was frequently occurred, F2-F3 breeding lines are screened for submergence
followed by screening for pest-diseases and evaluation for stagnant flooding
tolerance. The tolerant check for screening for submergence tolerant is Swarna
Sub1 and for stagnant water are IRRI 154 and Khoda.
5.3. Breeding for desirable plant architecture for coastal saline ecology
 Coastal salinity at wet season: Desirable plant characters for this ecology include
120-130 cm plant height, more than 145 days duration, stiff culm, erect leaves,
moderate tillering ability, heavy panicle weight, early vigour, salinity tolerant at
seedling and reproductive stages, submergence and/ or water logging tolerance
with minimum elongation, photoperiod sensitive and strong seed dormancy.
 Coastal salinity at dry season: Desirable plant characters for this ecology include
100-110 cm plant height, 100-110 days duration, stiff culm, erect leaves, moderate
to high tillering ability, early vigour, tolerant to salinity at both seedling and
reproductive stages.
5.4. Breeding scheme for coastal saline condition
Wet season in eastern coastal area is affected not only by salinity but also by
submergence at vegetative stage and water logging at different crop growth stages.
Standardization of multiple stress tolerance breeding strategy and management
practices to be given priority. The suitable breeding scheme for multiple abiotic stress
tolerance in coastal saline areas in wet season is presented below with a schematic
diagram (Fig. 6).

Genetic Improvement of Rice for Multiple Stress Tolerance in

Unfavorable Rainfed Ecology 133
 Fig. 6. Breeding scheme for multiple abiotic stress tolerance in
coastal saline areas in wet season

5.5. Use of wide genetic base in rice improvement

 Evaluation of wild accession can open up the possibility of getting better tolerance
for abiotic (salinity and water logging) and biotic stress (stem borer, BB, etc.)
required in unfavourable rainfed lowland ecology. Effort is needed to utilize these
tolerance sources in developing agronomically superior elite rice lines. Introduction
of wider genetic base in pre-breeding lines and identification of new QTLs
associated with multiple abiotic stresses would help in developing more robust
varieties for this unfavourable ecology.
5.6. Molecular breeding approaches for improvement of rice for
unfavourable lowland ecology
 Saltol-QTL explained 46% variation for Na+-K+ homeostasis leading to salt
tolerance at seedling stage. QTLs other than Saltol to be identified and pyramided
in tolerant lines along with Saltol QTL.
 Lot of scope for identification of better donors, their physiology and gene
expression study in relation to salt tolerance at flowering stage. QTLs for
reproductive stage salt tolerance are to be validated.
 Pyramiding of genes/QTLs for tolerant to submergence (Sub1), salinity (Saltol)
and water logging in popular rice varieties of coastal saline areas are required.
 Pyramiding of genes/QTLs for anaerobic germination ability, tolerance to excess
water submergence during germination and vegetative stages for getting successful
crop at direct seeded rainfed lowland areas.
 Promising QTLs can be introgressed into popular rice varieties through MAB
approach to improve their performance under flash flooded condition. If

Genetic Improvement of Rice for Multiple Stress Tolerance in

134 Unfavorable Rainfed Ecology
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pyramiding of different tolerant mechanism together into a single background

would be beneficial to get tolerance under different microclimatic condition.

6. WAY FORWARD
The climate resilient varieties for rainfed unfavourable ecosystem should have
multiple stress tolerance. The orientation of research is in that direction. Identification
of new sources of multiple abiotic stress tolerance and development of mapping
populations (Swarna/Rahspunjar, Savitri/AC39416a) for identification of QTL for
multiple abiotic stress tolerance (salinity and waterlogging) is in progress. The salinity
and waterlogging tolerant germplasm from cultivated and wild (O. rufipogon and O.
nivara) rice collection are also being used for development of elite pre-breeding lines
(BC2F2). On the other hand, research is focused on the identification of the robust
QTLs other than Sub1 for excess water tolerance at various stages of crop growth
and pyramiding them along with genes of important biotic stress tolerance. The use
of community participatory approaches in the design, validation and dissemination
of technologies is required to address problems of rice cultivation in unfavourable
ecology. It is also required to anticipate and address constraints to the widespread
adoption of new salt and water logging tolerant varieties and evaluate additional
crops adapted to unfavourable ecology. Further studies will be carried out in the
ICAR-NRRI-Regional Coastal Rice Research Station, Naira on the effects of soil salinity
changes in the coastal districts on spatial and temporal scale and their consequences
of production on the economics of high yielding and salt tolerant genotypes of rice.
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Genetic Improvement of Rice for Multiple Stress Tolerance in

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 Harnessing Heterosis in Rice for Enhancing
Yield and Quality

RL Verma, JL Katara, RP Sah, M Azharuddin TP, S Samantaray,

S Sarkar, BC Patra, A Anandan, RK Sahu, AK Mukherjee,
SD Mohapatra, S Roy, A Banerjee and ON Singh

SUMMARY
Heterosis is a solitary means of exploiting hybrid vigour in crop plants. Given its
yield advantage and economic importance several hybrids in rice have been
commercialized in more than 40 countries, which creates a huge seed industry world-
wide. India has made commendable progress and commercialized 97 three-lines indica
hybrids for different ecology and duration (115-150 days) which accounted 6.8% of
total rice area in the country. Besides, several indigenous CMS lines developed in
diversified genetic and cytoplasmic background are being utilized in hybrid rice
breeding. NRRI has been pioneering to start with the technology, has developed
three popular rice hybrids viz. Ajay, Rajalaxmi and CR Dhan 701 for irrigated-shallow
lowland ecosystem. Biotechnological intervention has supplemented immensely in
excavating desirable genomic regions and their deployment for further genetic
enhancement and sustainability in rice hybrids. Besides, hybrid seed production
creates additional job opportunity (100-105 more-man days) and comparatively more
net income (70% more than production cost) than HYVs. Hence, this technology has
great scope for further enhancement in per se rice productivity and livelihood of the
nation.

1. INTRODUCTION
Heterosis is the superiority of F1 offspring over either parent, a solitary means of
exploiting hybrid vigour in crop plants. This phenomenon has benefited agriculture
and fascinated geneticists for over 100 years for development of superior cultivar in
many crops. Suitable allelic combination and manipulation has made yield advantage
in hybrid than HYVs. It covers large acreage for many crops including rice and has
fundamentally affected agricultural practices and the seed industry in the world.
Heterosis had been exploited in various practical ways for centuries before Darwin
provided an early scientific description of heterosis in maize. In rice, heterosis was
first reported by Jonse (1926 AD). However, owing to its self-pollinating nature (0.3 -
3.0% out-crossing), heterosis could be realized during middle of second half of the
twentieth century after identification and development of CMS source. Subsequently,
the China, under the leadership of Yuan Long Ping, started work on the development
of hybrid rice with a vision to make it possible to be commercial. He identified a
natural male sterile mutant plant in indica rice and pollen abortive genotypes in the
natural population of wild rice (Oryza rufipogon; 1970 Li), which later served as
donor of male sterile source (male sterile cytoplasm) for CMS development. In 1973,

Harnessing Heterosis in Rice for Enhancing Yield and Quality

138
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

through recurrent back-cross breeding several promising indica wild abortive CMS
viz. Erjiunan1A, Zhenshan 97A and V20A CMS-WA and good restorers viz., Taiyin1,
IR4 and IR1 were developed. Later during 1974, first indica rice hybrid Nanyou 2 was
released for cultivation in China. Afterward, relatively more heterotic hybrid rice
breeding approaches like two-line system (1987 AD) and super hybrids (1996 AD)
were adopted which supplemented substantially toward Chinese food security and
livelihood.
In India, systematic research on hybrid rice was initiated in 1989 when Indian
Council of Agricultural Research (ICAR) launched a special goal oriented and time
bound project ‘Promotion of Research and Development Efforts on Hybrids in Selected
Crops’ for rice at 12 network centres. After four years of meticulous research (1989-
93), first hybrid rice was released in Andhra Pradesh in 1993-94 and India became the
second country after China to develop and commercialized hybrid rice. So far, 97 rice
hybrids (33 from public organization and 64 from private sector) were developed,
suitable for different ecology and duration ranging from 115-150 days, covering 3.0
mha which accounted 6.8% of total rice area in India.
Hybrid rice technology is impressive as it enhances farm productivity of 15-25%
more than HYVs. Given its yield advantage and economic importance, several hybrids
in rice have been commercialized in more than 40 countries, which creates a huge seed
industry world-wide. Moreover, this venture also has great service opportunity, creates
additional employment for 100-105-man days/hectare in seed production. However, it
has some limitations in generation of hybrids, seed production and marginal heterosis.
Success of hybrid depends on their parental combination, adaptability and allelic
interactions, hence, faces several problems like unstable male sterility, non-abundancy
in cytoplasmic diversity, inherited CMS load, low seed producibility in seed parent,
poor grain and eating
quality, lack of responsive
parents for biotic and
abiotic stresses, hybrid
sterility, marginal heterosis
in indica hybrids etc. This
chapter deals with
information on (i) status of
hybrid rice research (ii)
breeding system and
methods involved in hybrid
rice development and
production (iii) trait specific
parental line improvement
(iv) molecular dissection of
genes and QTLs for
parental line improvement
Fig. 1. A schematic representation of hybrid rice and (v) economic
technology (seed production, trait improvement, yield opportunity (Fig. 1).
evaluation etc.).

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2. BREEDING COMPONENT AND SYSTEM IN HYBRID
RICE DEVELOPMENT
Rice is a strict self-pollinated crop; commercial exploitation of heterosis requires
some parental specificity which could excludes manual emasculation. The invention
of naturally occurred male sterility (MS) in rice thus played substantial role in realization
of heterosis in rice. Following are the genetic tools as mentioned in various heads are
required for development and commercialization of hybrid in rice:
2.1. Male sterile system
The male sterility (MS) in plants is the condition where male reproductive organ,
anthers lose their ability to dehisce and produce viable pollen and thus encourage
allo-gamous nature of reproduction. This is crucial breeding tools to harness heterosis
that exclude additional efforts of emasculation which is cumbersome process. In
plants male sterility is conditioned either by mitochondrial or nucleus genome or in
associations. The male sterility in plant was first observed by Joseph Gottlieb Kolreuter
in 1763 and later it was reported in > 610 plant species. In rice, it was reported by
Sampath and Mohanthy (1954) at ICAR-NRRI (formerly CRRI), Cuttack by studying
the differences in male fertility in reciprocal crosses of indica/japonica rice lines. The
male sterility in plant is found to be determined by several biological as well as
environmental factors. In rice, it is conditioned either by cytoplasmic genes in
association with nuclear genes (CMS) or nuclear genes alone (GMS) which cause
abnormal development in sporogenous tissue (either sporophytic or gametophytic
tissue). The sporophytic male sterility is governed by genetic constitutions of
sporogenous tissues like tapetal and meiocytes which creates improper nourishing
to developing microspores and cause pollen abortion, whereas in gametophytic male
sterility, microspore and pollen development get affected. Sporophytic male sterility
is quite useful in hybrid rice breeding as it gets fertile in heterozygous state and
encourages complete fertility in resulting hybrids. To date several types of male
sterile system viz. cytoplasmic male sterile (CMS), environment sensitive male sterile
(GMS) viz. thermo-sensitive genetic male sterility (TGMS), photo-sensitive genetic
male sterility (PGMS) and reverse photo-sensitive genetic male sterility (rPGMS) etc.
have been identified and substantially being utilized in hybrid development (Table 1).
2.2. Diversity in male sterile system and their mechanism
Cytoplasmic male sterility is a maternally inherited trait caused by improper
communication between cytoplasmic and nuclear genome (Chen 2014). Gene(s)/genic
block (s) conditioned cytoplasmic male sterility are chimeric construct, evolved due
to rearrangement of the mitochondrial genome (Fig. 2). In rice, several types of
cytoplasmic male sterility have been identified and characterized, having diversified
mechanism in MS expression. Wild abortive (WA-CMS), a sporophytic MS system
widely utilized in hybrid development. It is found to be caused by a constitutive
mitochondrial gene WA352c located down stream of rpl5 (comprised four
mitochondrial genomic segments, orf284, orf224, orf288 and cs4-cs6) and encodes a

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 Table 1. Cytoplasmic diversity in rice CMS.
CMS group Associated ORF Protein Cytoplasm source Representative CMS-line
1. Cytoplasmic male sterile line
a. BT-CMS and their lineage
BT-CMS (G) B-atp6-orf79 Membrane protein Chinsurah Boro II/Taichong 65 Liming A, Xu 9201A
LD-CMS (G) UK UK Lead Rice (Burmese indica variety) x Fujisaka 5 Fujisaka 5A
(japonica variety)
Dian1-CMS (G) UK UK Yunnan high altitude landrace rice (indica) cytoplasm Yongjing2A, Ning67A
HL-CMS (G) atp6-orfH79 Membrane protein Red-awned wild rice (Oryza rufipogon) cytoplasm Yuetai A, Luohong 3A4
b. WA-CMS and their lineage
WA-CMS (S) rpl5-WA352 Membrane protein Wild abortive rice (Oryza rufipogon) cytoplasm Zhenshan97 A,
V20AIR58025A,
CRMS31A etc.
Kalinga-I-CMS (S) UK UK Kalinga-I (indica) cytoplasm CRMS 32A
D-CMS (S) UK UK Indica rice Dissi D52/37 D-Shan A, D62A
DA-CMS (S) UK UK Dwarf abortive rice (Oryza rufipogon) cytoplasm Xieqingzao A
GA-CMS (S) UK UK Gambiaca (indica) cytoplasm Gang 46A
ID-CMS (S) UK UK Indonesia paddy rice (indica) cytoplasm II 32A, You1A
K-CMS (S) UK UK K52(japonica) cytoplasm K-17A
CMS-RT102 (S) rpl5-orf352 Membrane protein Oryza rufipogon, W1125 RT102A
CMS-RT98A (G) orf113-atp4-cox3 Membrane protein Oryza rufipogon Griff, W1109 RT98A

Harnessing Heterosis in Rice for Enhancing Yield and Quality

LX-CMS UK UK Luihui rice (indica) cytoplasm Yue 4A
Maxie-CMS UK UK MS mutant of Maweizhan (indica) with Maxie A
Xieqingzao (indica)
NX-CMS UK UK Selected from F2 male sterile plants in the progeny Neixiang 2A, Neixiang5A
of Wanhui 88 (indica) x Neihui 92–4 (indica) nucleus

Contd....

141
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 CMS group Associated ORF Protein Cytoplasm source Representative CMS-line

142
Y-CMS UK UK Yegong (indica landrace) cytoplasm Y Huanong A
CW-CMS (G) orf307 Mitochondrial Oryza rufipogon Griff. IR24A, IR64A
protein
2. Environment sensitive genetic male sterility (EGMS)
PGMS pms3 Noncoding RNA Nongken 58S, PGMS mutant of japonica 7001S, N5088S
cultivar Nongken 58
P/TGMS p/tms12-1 noncoding RNA Photoperiod and temperature sensitive genic male Pei’ai 64S
sterile (P/TGMS) derived from Nongken 58S
TGMS tms5, RNase ZS1 Nuclease enzyme Spontaneous TGMS mutants of Annong S-1 Guangzhan 63S5, Xinan S
(loss in function) and Zhu 1S
rPGMS csa OsMST8 MYB transcript Carbon starved anther (csa) mutant of japonica 9522S
regulator cultivar 9522
Note: ‘S’ stand for sporophytic male sterility and ‘G’ stand to gametophytic male sterility.

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Fig. 2. Schematic presentation of rice CMS types. Where, WA stand for

wild abortive, BT is for boro type, HL for Honglian, LD for lead rice, CW
for Chinese wild rice, RT102A and RT98A, respectively.

352-residue putative protein with three transmembrane segments. The WA352c inhibits
nuclear-encoded mitochondrial protein COX11 (essential for the assembly of
cytochrome c oxidase, TCA) and triggered premature tapetal programmed cell death
and pollen abortion (Tang et al. 2017). In contrast, BT-CMS is a gametophytic MS
reported in the Indian rice variety, Chinsurah Boro-II in which pollen development get
arrested at the tri-nucleate stage. The mitochondrial chimeric (dicistronic) gene B-
atp6-orf79 encodes a transmembrane protein, cytotoxic peptide ORF79 (Wang 2006)
which accumulates preferentially in the microspore, was found to be responsible for
male sterility. The orf79 reside downstream to the atp6 and interact with P61 and
mitochondrial complex III and impair the activity of this complex which lead to
dysfunctional energy metabolism and elevate oxidative stress and thus causing
sterility. However, in HL-CMS, which is also a gametophytic MS system, pollen
development gets arrested at di-nucleate stage. A chimeric aberrant transcript of the
mitochondrial gene atp6-orfH79 located downstream of atp6 is confirmed as candidate
gene of this MS. Transcript of orfH79 gene preferentially accumulates in mitochondria
which impairs mitochondrial function through its interaction with P61, a subunit of
electron transport chain (ETC) complex III (Wang et al. 2013) and leads male sterility.
Male sterility in CW-CMS is conditioned by mitochondrial orf307 which expressed
preferentially in anther tissue, indicating the presence of anther-specific mitochondrial
retrograde regulation of nuclear gene expression. It is a gametophytic MS in which
pollen grain appears normal but lacks the ability to germinate.
2.3. Genetic male sterility
Genetic male sterility (GMS) in rice is conditioned by recessive nuclear genes and
showing normal Mendelian inheritance. Owing to difficulties in their maintenance
(occurrence of only 50% sterility in F1), GMS could not be part of rice hybrid breeding

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programme. Some GMS lines has shown threshold nature in MS expression where
male sterility occurs in specific environmental regime (high temperature and long day
length); hence called environment sensitive genetic male sterile (EGMS). The GMS
line shows male sterility at elevated temperature i.e. >30 0C is called temperature
sensitive male sterility (TGMS) whereas male sterility in long day length i.e. >13.5 hrs
is called photoperiod-sensitive genetic male sterility (PGMS). The male sterility in
EGMS line is found to be revert into male fertile in favourable temperature (<30 0C)
and day length (<12.5 hrs) which provide its unique opportunity to be utilized in
hybrid rice breeding programme. Some lines, such as Pei’ai 64S, are male sterile under
both long day and high temperature conditions and are referred to as P/TGMS lines.
The majority (>95%) of the EGMS lines utilized in hybrid rice production were derived
from three independent progenitors i.e. PGMS line Nongken 58S (NK58S), TGMS
lines Annong S-1 and Zhu1S. Many lines derived from NK58S were P/TGMS or even
TGMS (e.g., Guangzhan 63S), but the underlying mechanism leading to such dramatic
changes has yet to be revealed. Recently, a novel type of EGMS (csa-carban starved
anther mutant) in rice called rPGMS (reverse PGMS), shows normal male fertility
under long day conditions (>13.5 hrs) and male sterile under short day conditions
(<12.5 hrs) is identified. This is found to be suitable for seed production of two-line
hybrids in tropics and subtropics (Zhang et al. 2013).
2.4. Transgenic cytoplasmic male sterility
The genetically engineered male sterile line M2BS in rice is developed by
transformation of indica rice maintainer M2B with partial-length HcPDIL5-2a (Hibiscus
cannabinus protein disulfide isomerase-like) genetic construct. Male fertility in this
CMS is reported to be arrested due to tapetum degeneration which leads pollen
abortion. Hereditary analysis indicated that the male sterility of M2BS was a maternally
inherited inability could be affirmed as a type of cytoplasmic male sterile (CMS).
Besides, by combining cysteine-protease gene (BnCysP1) of Brassica napus with
rice anther-specific P12 promoter (promoter region of Os12bglu38 gene), a transgenic
MS system was successfully created which is restored by transgenic rice plants
carrying BnCysP1Si silencing system (Rao et al. 2018). Zhou and co-workers (2016)
developed 11 “transgene clean” TGMS lines by editing most widely utilized TGMS
gene tms5 through CRISPR/Cas9.
2.5. Genetics of fertility restorer gene
Cytoplasmic male sterility in rice is found to be restored by nuclear genome i.e.
mono or oligo nuclear loci called restorer gene. In rice a total of ten Rf genes (Rf1a,
Rf1b, Rf2, Rf3, Rf4, Rf5, Rf6 and Rf17, Rf98 and Rf102) have been identified, of those
seven (Rf1a, Rf1b, Rf2, Rf4, Rf5, rf17 and Rf98) are characterized. All Rf genes are
found to be dominant in nature (except rf17, restore fertility in CW-CMS) which can
restore male fertility in heterozygous state. Restorer genes are very specific to male
sterile genome in the mechanism of fertility restoration. Genes Rf1a and Rf1b (Chr.-10)
encodes pentatricopeptide-repeat (PPR) containing proteins, have functional affinity
of fertility restoration in BT-CMS; RF1A promotes endo-nucleolytic cleavage of the

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atp6–orf79 mRNA and RF1B promotes degradation of atp6–orf79 mRNA (Wang et

al. 2006) and revert the male sterility into fertility. Whereas, HL-CMS is restored either
by Rf5 or Rf6 gene, these genes can produce 50% normal pollen grains in F1 plants
individually, however both genes in complementation could restore more than 80%
spikelets fertility in hybrids. The Rf5 encodes a PPR family protein PPR791 which
makes a restoration of fertility complex (RFC) with glycine rich protein GRP162 and
bind to the atp6-orfH79 transcripts. The RFC cleave the aberrant transcript of atp6-
orfH79 at 1169 nucleotides position (Hu et al. 2012). The Rf6 gene encodes a novel
PPR family protein (duplicate PPR motif 3-5) which in association with hexokinase
(osHXK6) targets mitochondria and process defective transcript of atp6-orfH79 at
1238 nucleotide position. Thus, PPR protein family cause editing of aberrant transcript,
inhibit their translation and at the end fertility restoration (Huang et al. 2015). Besides,
male fertility in WA-CMS is found to be counteracted by Rf3 and Rf4 genes (chrom.
-1 and 10, respectively). The gene Rf3 and Rf4 encodes a pentatricopeptide protein
(PPR) where RF4 cleave the abnormal WA352 transcript and RF3 supress translation
of WA352 into polypeptide and helps in restoring fertility in WA-CMS. Fertility in LD-
CMS is reported to be restored by either Rf1 or Rf2. The Rf2 gene encodes a
mitochondrial glycine-rich protein; replacement of isoleucine by threonine at amino
acid 78 of the RF2 protein causes functional loss of the rf2 allele. Moreover, CW-
CMS is restored by a single recessive nuclear gene, rf17 which is a retrograde-
regulated male sterility (rms) gene (Toriyama et al. 2016) (Table 2).
2.6. System of hybrid rice breeding
Commercial hybrid seed production in rice where natural out-crossing (ranged
only 0.3-3.0 %) is very low, is a cumbersome and expansive task. To be practical and
readily adoptable, it requires some specific parental requirements and agro-management
practices. Invention of male sterile lines thus provided unique opportunity to start
with the technology in rice. Based on mechanism of male sterility, threshold nature in
male sterility expression and number of parental lines used, three type of hybrid seed
production system namely three- line system (involving three parents, A, B and R),
two-line system (two parents, A and R) and one-line system (apomictic based) exist.
Among them, CGMS based three lines system is more suitable, hence widely utilized
(>90% of world’s hybrids developed utilizing this) in hybrid rice varietal development
and seed production.
2.6.1. Three-line system (involving three parents, A, B and R): Three-line hybrid
system involves three parents such as male sterile line (A-line, cytoplasmic Male
sterile), B-line (maintainer) and R (restorer) lines and two steps in seed production i.e.
CMS multiplication and hybrid seed production under strict isolation (spatial or
temporal or physical barrier). Male sterile line (A-line), because of their eliminated
manual emasculation needs, served as seed parent and facilitates large scale seed
production. A suitable CMS line to be utilized as seed parent should have complete
and stable male sterility, substantial seed producibility, wide compatibility and good
combining ability with minimum CMS load. The wealthy panicle and narrow semi
erect leaf configuration in seed parent has additional impact, assure more seed

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 Table 2. Restorer genes in rice plants.

146
S. No. Rf genes Locality Marker CMS system Restorer line Causative gene Encoded product Reference
1 Rf1a, Rf1b Chr-10 InDel-Rf1a CMS-BT BTR, IR24, PPR8-1, PPR791, PPR Tao et al. 2013
MTC10R; Rf1A, Rf1B
C 9083
2 Rf2 Chr-2 CAPS42-1 CMS-LD Kasalath, LOC_Os02g Gly. Rich protein Itabashi et al.
Minghui 63 17380.1 2011
3 Rf3 Chr-1 DRRM-Rf3-10 CMS-WA Swarna, - PPR Katara et al. 2017
PUSA 33,
4 Rf4 Chr-10 RM6100 CMS-WA IR 24, Pusa 33, PPR782a PPR Katara et al. 2017
CRL 22R
5 Rf5(t) Chr-10 RM3150 CMS-HL Milyang 23 PPR791 PPR Liu, 2004
6 Rf6 Chr-10 & 8 RM5373 CMS-HL - - - Liu, 2004
7 rf17 Chr-4 AT10.5-1, CMS-CW CWR PPR2 RNA interference- Fujii et al. 2005
SNP 7–16
8 Rf98 Chr.-10 UK CMS-RT98A RT98C PPR762 PPR Igarashi et al.
2016
9 Rf102 Chr.-12 UN CMS-RT102A RT102C, UK UK Okazaki, 2013
K102-Oryza
rufipogon. T

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production. In Indian perspective where, hybrid seed production is major dilemma,

generally keen to Rabi season, hence, CMS lines should have substantial cold tolerance
at seedling stage and heat at flowering stage.
The maintainer (B-line) on the other hand is an isogenic to the CMS line (differs
only for fertility/sterility) in their genetic constitution, able to produce functional
pollen and maintain the sterility in male sterile line/seed parent. The maintainer line
can maintain 100% male sterility in seed parent thus utilized to perpetuate CMS with
their inherent male sterile ability.
In contrast, restorer line can restore male fertility in F1s produced on male sterile
parent, thus utilized as pollen parent in hybrid seed production. A good restorer
should have substantial genetic distance with seed parent which is prerequisite and
major determinant of the extent of heterosis in hybrids (more genetic distance more
heterosis and vice -versa). Restorer is the major contributor of heterosis in three-line
hybrids, hence, should have good combining, strong fertility restoration ability
(dominant Rf gene(s) responsible for fertility restoration in CMS). Besides, restorer
line with ideal in plant type, acceptable grain quality parameters, substantial source-
sink balance, heavy pollen load and broad spectrum of resistance/tolerance against
multiple biotic/abiotic stresses is imperative in maximization of genetic gain in hybrids.
2.6.2. Two-line system (involve two parent A and R): Two-line system is a simple and
more efficient hybrid breeding system in rice, involves only two parents i.e. A and R
line in seed production. This is a threshold of genetic male sterility (EGMS) based
hybrid rice breeding system where male sterility is conditioned in specific
environmental regimes such as long photoperiod (>13.5 hrs day length) and at elevated
temperature (>30 0C). In this system male sterile parents are to be maintained by
selfing under favourable conditions (below critical sterility point i.e. <30 0C temperature
and at below CSP of photoperiod length, <12.5 hrs.).
Two-line hybrid seed production system is easy and effective alternative to CMS,
has specific advantages as requires only one step for seed production. In this system
any good combiner genotype irrespective of their fertility restoration ability can be
utilized as pollen parent. EGMS system is normal, does not exert any ill effect on the
growth and development of carrier plant, thus exploit comparatively higher extent of
heterosis (up to 5-10%) in F1 than the CGMS based three-line hybrids. The EGMS
traits are governed by major genes, thus easily transferable to any genetic background
which helps in reducing potential genetic vulnerability among the hybrids. Because
of its eliminating needs for restorer genes in the male parents, this is ideal for developing
inter-subspecific (indica/ japonica) hybrids.
2.6.3. One-line system (apomictic based): In this system, seeds of rice hybrid once
generated need not to be further produced in hybrid seed production plot. This
system is solely based on apomixes phenomenon (embryo developed apart from
mixing of sexual gametes/fertilization) where embryo developed without fertilization.
In this system hybrid seeds once generated will be maintained through apomixes in
their original heterozygous form. This system is yet to be explored in rice, in future it
is anticipated to be realized in commercial use.

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3. PROGRESS IN HYBRID RICE RESEARCH AND
DEVELOPMENT
3.1. International status
Hybrid technology is one of the greatest innovations in the modern era, contributed
greatly in yield enhancement in several important crops. Over the decades of rigorous
research Chinese could develop parental lines i.e. cytoplasmic male-sterile line,
maintainer line and restorer line which assisted in the realization of heterosis exploitation
in rice. Subsequently, hybrid seed production system was refined and world’s first
hybrid rice was released for commercial cultivation during 1974 AD. The first generation
wild abortive CMS line i.e. Zhenshan 97A was widely utilized and several elite hybrid
rice varieties were commercialized. Besides, several CMS with altered genetic
mechanism of male sterility expression were also identified and characterized.
At beginning, low seed producibility with WA-CMS was a concern for its
commercialization. However, with the keen interest of agronomist, management
practices for hybrid seed production were sustainably rationalized. The Chinese
government has supported this venture in pilot mode and established large and
effective hybrid rice seed businesses in the late 1970s at all levels. Besides, intensive
mechanization of hybrid seed production helped in modification of planting ratio (2R:
A as 6–8 rows to 40–80 rows) and reducing the cost of production. Therefore, China
could achieve seed yield by 2.7–3.0 t/ha on large scale in hybrid rice seed production
which is further enhanced to 3400 Kg/ha and maximize their acreage.
Over past three decades hybrid rice varieties have been substantial for national
food security in the China which accounted for approximately 57% of the total 30-
million-hectare rice planting area. The Ministry of Agriculture, China has launched
project on super hybrid rice development during 1996 which resulted altogether 73
super hybrids (52 three-line hybrids and 21 two-line hybrids) for commercial
cultivation. Super hybrid P64S/E32 released recently has recorded new height of
yield potential of 17.1 t/ha with some striking characteristics (Yuan et al. 2017).
Beside China, this technology has also been introduced and promoted by more
than 40 countries around the world. At beginning, IRRI helped technically and supplied
prerequisite parental materials. Later, most of the countries could establish their own
hybrid rice breeding programme and developed several heterotic hybrids. India was
the second country after china that adopted this technology in 1989 and made
substantial progress. At present, hybrid rice covers around 3.0 mha in India that has
6.8% of total rice area. Vietnam was the next to adopt this technology in 1992, harnessing
yield of 6.3–6.8 t/ha from 0.7 mha, which covers around 10% of their rice area. In
Philippines it was introduced in 1993. Several popular hybrids like Magat, Mestizo,
Mestizo 2, Mestizo 3, Bigante, Magilla, SL8H, Rizalina 28 etc. were developed and
commercialized. Hybrid seed production in Philippines has been handled by ‘seed
growers’ cooperatives, who is to produce around 60-70% of them. In Bangladesh
several rice hybrids were introduced and commercialized from China, India and
Philippines. They are almost self-sufficient in hybrid seed production, producing

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around 8000 tons to cover about 800,000 ha. In order, Indonesia also has substantial
hybrid rice area, developed several good rice hybrids like Hipa7, Hipa 8, Hipa9, Hipa10,
Hipa11, Hipa12 SBU, Hipa13, Hipa14 SBU, Hipa Jatim1, Hipa Jatim2 and Hipa Jatim3
were extensively commercialized, having yield superiority of 0.7-1.5 tons/ha over the
lowland inbred varieties.
United States of America has adopted this technology during 2000, has developed
and commercialized several two-line and three-line hybrids. Most of the hybrid rice
cultivars in USA employed Clearfield (CL) technology offering selective control of
weedy red rice. Rice hybrids viz. Clearfield XL729, Clearfield XL745, Clearfield XP756
(a late maturing) and Clearfield XP4534 (new plant type) has shown yield advantage
ranging from 16-39% over inbred cultivars are being commercialized by RiceTec.
3.2. National status
In India, systematic hybrid rice research was initiated in 1989.The first hybrid rice
was released in Andhra Pradesh during 1993-94 and India became the second country
after China to commercialize hybrid rice. India has made substantial progress and
developed total 97 (indica/indica) rice hybrids having 15-20% yield superiority with
115-150 days duration for various rice ecosystems. Recently, Savannah Private Limited
from India has made another landmark by developing 2 two-line rice hybrids viz.
SAVA-124 and SAVA-134 for commercial cultivation. In addition, more than 100 CMS
in diversified genetic and cytoplasmic background have been developed and utilized.
Amongst, the promising CMS lines CRMS 31A, CRMS 32A, CRMS 8A, PMS10A,
PMS 17A, APMS 6A, DR8A, PUSA 5A, PUSA6A, RTN 12A etc. are substantially
being utilized in development of rice hybrids in India and abroad. Notably, medium
duration seedling stage cold tolerant CMS, CRMS 32A, developed at NRRI under
Kalinga-I cytoplasm is more suitable for development of hybrids for boro ecosystem.
Two popular hybrid rice varieties namely Rajalaxmi and KRH 4 were developed using
CRMS 32A as one among the parent.
Initially, this programme was technically supported from the International Rice
Research Institute (IRRI), Philippines and Food and Agriculture Organization (FAO),
Rome; and financially supported from United Nations Development Programme
(UNDP), Mahyco Research Foundation, World Bank funded National Agricultural
Technology Project (NATP) and IRRI/ADB projects on hybrid rice. Scaling up and
popularization of hybrid rice in India was further taken over by union government
through various national schemes like RKVY, BGREI etc. To further invigorate the
hybrid rice research and development, ICAR has launched a 5-year consortium research
platform project ‘ICAR - Consortium Research Platform on Hybrid Crops Hybrid
Technology for Higher Productivity in Selected Field and Horticultural Crops, at nine
research centres. Indo-ASEAN group has also started funding for genetic
diversification of parental lines and development of inter-subspecific hybrids in India
and member’s countries.
Hybrids released in India having unambiguous specificity like specific to
ecosystem, tolerant to several abiotic/ biotic stresses and consumer preferences
(Table 3). These hybrid varieties can be utilized to up scale the hybrid rice cultivation
and productivity enhancement per se in the respective area.

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Table 3. Rice hybrids tolerant to various stresses
S. No. Stress Promising hybrids
1 Rain-fed upland DRRH-2, Pant Sankar Dhan-1, Pant Sankar Dhan-3,
KJTRH-4
2 Salinity DRRH-28, Pant Sankar Dhan-3, KRH-2, HRI-148, JRH-8,
PHB-71, Rajalaxmi
3 Alkalinity Suruchi, PHB-71, JKRH-2000, CRHR-5, DRRH-2,
DRRH-44, Rajalaxmi
4 Boro/Summer season Rajalaxmi, CRHR-4, CRHR-32, NPH 924-1, PA 6444,
Sahyadri, KRH 2
5 BB resistant BS 6444G, Arize Prima, Rajalaxmi, Ajay, CR Dhan 701,
PRH 10 etc.

Hybrids like CRHR 105, CRHR 106, 25P25, 27P31 are suitable for high temperature
regime which has more deleterious effect on seed development in hybrids. The hybrid
varieties, US 382, Indam 200-17, US 312, DRRH3, JKRH 401 having high N use efficiency
thus found suitable for cultivation in N deficient soil. Besides, hybrids PNPH 24, RH
1531, Arize Tej are under mid-early maturity group which can sustain substantially
under drought situations. The problems of coastal and shallow lowland ecosystem
sharing around 32% of total rice area can be addressed by adopting long duration
hybrids like CRHR 32, Arize Dhani, CRHR 34, CRHR 102 and Sahyadri 5 (Table 4).

Table 4. Hybrids suitable for specific condition

Aerobic condition PSD 3, PSD 1, Rajalaxmi, Ajay, ADTRH 1, PRH 122, DRRH 44,
HRI 126, JKRH 3333, KRH 2,
Early duration CRHR 105, CRHR 106, 25P25, 27P31 (heat tolerant), US 382,
Indam 200-17, US 312‘, DRRH3, JKRH 401high N use efficient;
PNPH 24 & RH 1531, Arize Tej-mid early-drought tolerant;
DRRH2, KJTRH-4 (upland)
Long duration CRHR 32, CRHR 34, CRHR 100, Sahyadri 5,
SRI TNRH CO-4, KRH 4
Idly making VNR 2355+
MS grains CRHR 32, DRRH 3, 27P63, 25P25, Suruchi
Aromatic PRH 122 (mild aroma), PRH 10

3.3. ICAR-National Rice Research Institute’s contribution

The ICAR-National Rice Research Institute, Cuttack has been pioneer to start
with the technology in late of 7th decade of last century, quite before the beginning of
their project mode programme in 1989 by ICAR. In the beginning, ICAR-NRRI has
acquired all the prerequisite materials (CMS lines viz. V 20A, Yar Ai Zhao A, Wu10A,
MS 577A, Pankhari 203A, V 41A, Er-Jiu nan A, respective maintainers, 9 other
maintainers and thirteen restorers) from the IRRI (NRRI annual report 1981-82).
Systematic hybrid rice breeding was initiated in interdisciplinary mode with objectives
to develop desirable parental lines viz., cytoplasmic genetic male sterile (CGMS)

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lines, maintainers and restorers for development of rice hybrids for irrigated and
shallow submergence. The farmers in the rain fed shallow lowland ecosystem would
be extremely benefited if the hybrid rice technology can be extended to this ecosystem,
which need hybrids of Swarna duration. Keeping in views, ICAR-NRRI has developed
three rice hybrids viz. Ajay, Rajalaxmi and CR Dhan 701 for this fragile ecosystem.
Among them CR Dhan 701 is the country’s first long duration hybrid, substitute for
popular variety Swarna. Besides, NRRI has developed several promising CMS lines
which have stable male sterility (WA, Kalinga-I and O. perennis etc. cytoplasmic
background), maintainers and effective restorers. More than 45 CMS lines in diverse
genetic and cytoplasmic background have been developed amongst, Sarasa A, Pusa
33A (WA), Annada A (WA), Kiran A (WA), Deepa A (WA), Manipuri A (WA), Moti A
(WA), Krishna A (O. perennis), Krishna A (Kalinga I), Mirai (Kalinga I), Padmini A, PS
92A and Sahabhagidhan A etc. are more prominent to be utilized in hybrid development.
The medium duration CMS, CRMS 31A (WA) and CRMS 32A (Kalinga-I) are
significantly utilized for hybrid development at NRRI and elsewhere in the country.
The CRMS 24A and CRMS 40A, developed under the nucleus background of Moti
and Padmini are found suitable for late duration hybrid breeding. Moreover, short
duration CMS, CRMS 8A, CRMS 51A and CRMS 52A and CRMS 53A having drought
tolerance are also being used for development of hybrids for drought prone ecosystem.
The latest release CR Dhan 701 (CRHR32) found suitable for irrigated-shallow
lowland of Bihar, Gujarat and Odisha having MS grain type with an average yield
capacity of 7.5 t/ha. This hybrid shows substantial tolerant to low light intensity, thus
having great scope in eastern Indian states where low light limits the potential
expression of hybrids/varieties during wet season. Moreover, hybrid Rajalaxmi (125-
130 days) was developed utilizing native CMS line CRMS 32A, released by SVRC
2006/CVRC 2010 for irrigated-shallow lowland of Odisha and boro ecosystem of
Odisha and Assam as it has seedling stage cold tolerance. Ajay is a medium duration
with long slender grain type hybrid, released for cultivation in irrigated-shallow lowland
of Odisha. As these hybrids are adaptable for eastern Indian climatic condition with
assured remuneration, 12 private seed agencies over five states have commercialized
them.
To make this technology more sustainable and amenable to farmers, trait
development strategy among the parental lines becomes mandatory. The parents of
ICAR-NRRI bred hybrids Ajay, Rajalaxmi and CR Dhan 701 has been improved for
bacterial blight, the most devastating disease of rice (Das et al. 2016). The submergence
and salinity are the major abiotic stresses occur frequently in rain-fed shallow lowland
area and causes substantial yield loss in rice. Hence, to cope up with the problems,
and make hybrid rice more sustainable during these adversity, ICAR-NRRI has
successfully stacked submergence and salinity tolerant QTLs in the seed parents
CRMS 31A and CRMS 32A. To enhance the seed producibility in seed parents,
introgression of stigma exsertion trait from O. longistaminata into CRMS 31A and
CRMS 32A, are under progress. To excavate the genetic region responding heterosis
in rice, transcriptomic analysis of hybrids Rajalaxmi and Ajay are completed and
interpreted. Availability of restorers for WA-CMS lines is very stumpy in nature, only

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15% of total rice genotypes having the ability to restore complete fertility in WA-
CMS based hybrid rice (Katara et al. 2017). Hence, good combiner genotypes having
partial fertility restorers Mahalaxmi and Gayatri were improved by introgressing fertility
restorer gene(s) Rf3 & Rf4 through MABB approach. Further, to make clear cut identity
and ensure pure seed of parents/hybrids to the stack-holder, 12 signature markers
that unambiguously distinguish 32 rice hybrids were developed, which can be utilized
for DNA fingerprinting and genetic purity testing of hybrids.

4. POTENTIAL APPLICATION OF OMICS APPROACHES IN

HYBRID RICE BREEDING
Recent advancement in molecular biology has offered tremendous opportunities
to the breeder and breeding per se in enhancement in their efficacy and speed up the
varietal development process. It has diverse application like mapping, tagging,
amplification-based cloning, gene pyramiding, marker assisted selection (MAS/
MARS), fingerprinting applications including varietal identification, ensuring seed
purity, phylogeny and evolution studies, diversity analysis and elimination of
germplasm duplication. The progress in research related to application of DNA marker
technology in hybrid rice improvement may be valuable in following way.
4.1. DNA fingerprinting and genetic purity testing
Varietal identity of hybrids and parents is imperative to assure the ownership (IPR
issue) and pure seeds to the stakeholders. The genetic purity testing of hybrid seed
is done by conducting Grow-Out-Test (GOT) which is time taking (needs one full
growing season), tedious and very expensive. Molecular markers in this context
found to be a suitable alternative, provide an unbiased means of identifying crop
varieties. Amongst, available DNA-based markers, sequence tagged microsatellite
(STMS) which are co-dominant in nature, are widely used for speedy genetic purity
assessment of the hybrids and parental lines (Behera et al. 2012; Verma et al. 2017).
Besides, ICAR-NRRI has developed another set of nine signature markers which can
distinguish parents CRMS 31A, CRMS 32A; and hybrids Ajay, Rajalaxmi and CR
Dhan 701, unambiguously.
4.2. Trait improvement in parental lines and hybrids
Hybrid rice has been one of the innovation that led the quantum jump in rice
productivity last century. However, the challenge of meeting the increasing demand
for rice and making hybrid more sustainable under impeding climatic changes, trait
development in parental lines for ideal plant type with substantial yield, grain quality,
and resistance/tolerance to multiple biotic and abiotic stresses is necessary. In this
context, conventional breeding is more cumbersome, time taking and less précised.
The advancement in molecular breeding techniques makes it convenient to improve
the parents and hybrids for desirable traits with great precision. Marker assisted
selection/MABB has provided strong utensils for indirect selection/trace the trait of
interest at any plant growth stage. The bacterial blight and blast are the two-major

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destructive diseases affecting rice plant at different growth stage and caused
substantial yield loss. Resistant genes for BB diseases has been deployed successfully
in popular hybrids Rajalaxmi, Ajay (Das et al. 2016), BS 6444G, PRH 10, (Basavaraj et al.
2009), Shanyou 63, Guangzhan 63-4S (Zhang et al. 2006, Huang et al. 2012); seed
parent of CR Dhan 701, restorers Minghui 63 and Mianhui 725 (Das et al. 2016, Chen
et al. 2014), Zhonghui 8006 and Zhonghui 218 (Cao et al. 2005) etc. The popular CMS
line Rongfeng A (Fu et al. 2012), Pusa 6A female parent of popular basmati hybrid
PRH 10 (Singh et al. 2015), RGD-7S and RGD-8S (Liu et al. 2008) were successfully
stacked with blast and BB resistant gene(s). Besides, CRMS 31A and CRMS 32A
were deployed with submergence and salinity tolerance QTLs (NRRI newsletter 2015).
Grain and eating quality in hybrids is concerns which are addressed by stacking
QTLs/genes for quality traits in parents. Zhenshan 97A seed parent of several hybrids
in China has been stacked with QTLs of AC, GC and GT (Zhou et al. 2003); Efforts
were made towards quality improvement of both the parental lines of popular indica
hybrids viz. Xieyou57, using marker assisted selection for Wx locus (Ni et al. 2011).
Yield enhancing QTLs yld1.1 and yld2.1. from O. rufipogon to restorer ‘Ce64’ (Duan
et al. 2013) are successfully stacked. Hybrid sterility in inter-subspecific (indica/
japonica) hybrids is reported to be effectively adressed by utilizing genome editing
tool ‘CRISPR/Cas9’ (Shen et al. 2017).
4.3. Screening of Rf genes in parents
Limited availability of fertility restorer system in rice makes three-line system very
selective and less heterotic. Rice genotypes have fertility restorer ability can only be
utilized as pollen parent in three-line hybrid breeding. Identification of genetically
compatible, well combining restorers is tedious process, involve laborious test cross
generation and evaluation steps. However, prior information on fertility restorer genes
in the pollen parent excludes test cross steps thus make it convenient for saving time
of hybrid development. Plenty of co-segregating molecular markers (tightly linked or
functional markers) for fertility restorer gene(s) having functional specificity to diverse
CMS systems are available (Table 3). The genic/functional markers, RM6100 and
DRRM Rf3-10 of restorer gene(s) Rf4 and Rf3 respectively are widely utilized for
screening the fertility restoration efficacy of unknown pollen parents for WA and
lineage CMS well in advance (Katara et al. 2017).
4.4. Screening of parental lines for wide compatibility genes
Hybrid sterility is common nuisance menacing breeder to exploiting heterosis in
inter-subspecific (5-10% more heterosis) hybrids. Generally, indica x japonica hybrids
are sterile due to lack of wide compatibility (WC) between parents. It is reported that
hybrid sterility in inter-subspecific crosses is mainly affected by the genes at Sb, Sc,
Sd and Se (Guo et al. 2016) loci causes male sterility in F1 and the gene at S5 locus
cause female sterility in F1. Presence of these genic region in at least one parent
ensure complete fertility in resulting hybrids. These gene(s) can be assessed in advance
by utilizing co-segregating markers (S5-InDel, functional marker to S5n (Priyadarshi et

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al. 2017) and G02-14827 (genic marker) PSM8, PSM12 and PSM180 (linked SSR);
IND19 and ID5 (indel markers) to Sb, Sc, Sd and Se, loci). Thus, it helps breeder in
selection of WC positive parent in more predictable way which circumvents laborious
test-cross and their evaluations steps.
4.5. Prediction of heterosis
Genetic distance and level of genetic gain/breeding value in parents are major
determinant of extent of heterosis in resulting hybrid. Molecular markers help in
assess the genetic diversity among parents and breeding values in progenies (through
genomic selection, high density SNP genotyping) with great convenient. There are
abundant STMS, SNP markers are available which can be utilized for assessment of
genetic diversity/genetic distance between parents and genomic selection in progenies
easily (Soni et al. 2017). Hence, this is helpful in the selection of diverse parents with
maximum breeding values in turn higher heterosis or genetic gain in hybrids.
4.6. Determination of heterotic group and heterosis pattern
The extent of genetic variation and selection strategies are key to the success of
heterosis breeding. Accurate assessment and assignment of parental lines into
heterotic groups ‘group of genotypes (related or unrelated) having similar combing
ability and heterosis response when crossed with the genotypes of other diverse
group’ are fundamental prerequisite. Usually it is evaluated by combining ability
analysis of parents and hybrids in multi-environment trials. However, advances in
molecular marker technology have made it possible to combine information on parental
pedigree and field trials with molecular marker data to detect and establish heterotic
groups. Several heterotic group has been developed and utilized for three-line and
two-line hybrid development in rice (Lu and Xu 2010).
4.7. Excavating QTLs/gene(s) responses heterosis
Omics techniques reported to have great potential in excavation of QTLs/gene(s)
responses heterosis in rice. By utilizing genomics tools many QTLs/genes for several
important traits has been mapped, validated and deployed in trait development in
rice. The transcriptomics, an emerging technique helps in genome-scale comparisons
of the transcripts of different individuals within the same species/population. It helps
in understanding the level of variation for gene expression, as measured by transcript
abundance that exists within plant species and between hybrids and their parents.
This is useful for identification of transcript and gene per se involves in heterotic
expression. Moreover, epigenetics, a post translational biochemical regulation of
gene is found to be playing substantial role in trait expression. Individuals of the
same species can have epigenetic variation in addition to genome and transcriptome
content variation. A potential role for epigenetic regulation in heterosis has been
proposed. It is possible for epigenetic variation to affect heterosis by creating stable
epialleles that would behave similarly to the genomic or transcriptomic differences.
Alternatively, hybrids may exhibit unique epigenomic states that lead to heterosis.

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5. MAJOR CHALLENGES AND POTENTIAL RESEARCH

OPPORTUNITIES
5.1. Major Challenges
Despite of being remunerative and varietal abundancy, HR technology could not
make substantial dent in the rice farming system outside China. The following are the
inherited void led poor acceptability and acreage expansion of hybrids:
5.1.1. Lack of cytoplasmic diversity in countries outside China: Outside of the
China, WA-CMS or their lineage are commonly utilized as seed parent in more than
90% rice hybrids. Several alternative MS cytoplasmic sources such as BT-CMS, HL-
CMS, CW-CMS are identified in China, but hybrid breeding programme of the other
countries relied only on WA-CMS which has several inherited abnormalities. These
narrowed genetics of sterile cytoplasm limits the extent heterosis exploitation and
make hybrids vulnerable to many biotic and abiotic stresses.
5.1.2. Marginal heterosis in intra-subspecific hybrids: Two-lines and inter-
subspecific (indica/japonica) hybrids are comparatively more heterotic (5-10%) than
three-lines indica hybrids. But owing to several inevitable difficulties in seed
production of two-line hybrids and poor grain and eating quality in inter-subspecific
hybrids, both could not be exploited in the countries like India who has vast climatic
and food affection diversity. We are utilizing three-lines indica hybrids which is
comparatively less heterotic hybrid breeding system giving low yields. Hence, focused
and intensive research is proposed to make above said hitches be addressed in
future.
5.1.3. Poor grain and eating quality: In hybrids, consumable parts are F2 grains,
segregating for various quality traits hence very poor in quality limits its acceptability
among stakeholders. Therefore, make hybrids more sustainable and popular, quality
traits in hybrids needs to be addressed urgently in the country like India where
people have vast category of food fondness. Hence, a strong breeding strategy for
quality concern in hybrids is needs to be devised and implemented.
5.1.4. Subtle information on QTLs/gene(s) responding heterosis: Although heterosis,
or hybrid vigour, is widely exploited in agriculture, but despite extensive investigation,
complete description of its molecular underpinnings has remained elusive. It appears
that there is not a single, simple explanation for heterosis. Instead, it is likely that
heterosis arises in crosses between genetically distinct individuals because of a
diversity of mechanisms. Hence, mining factors responding heterosis in rice will have
substantial role in development and exploiting heterosis in most precise way.
5.1.5. Inter-subspecific hybrid sterility: Hybrid sterility is key nuisance in inter-sub-
specific hybrids, limiting development and commercialization of more heterotic Indica/
japonica hybrid in rice. The sterility in hybrids (inter-subspecific) generally occurs
due to non-functional pollens as well as sterility in female reproductive organs. It is
reported that mutant of S-i alleles at Sb, Sc, Sd and Se loci produce sterile pollens; and
mutants of S5 locus causes sterility in female gamete. Hence, trait development for
wide compatibility in either parent has great opportunity in addressing the hybrid
sterility in rice.

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5.2. Potential research opportunity
5.2.1. Exploitation of inter-specific heterosis: Inter-subspecific (indica/japonica)
hybrids as discussed in earlier section are more heterotic than intra-subspecific
hybrids. However, owing to hybrid sterility and poor grain quality, this genetic pool
remains untapped. Grain quality of inter-subspecific hybrids proposed to be improved
by utilizing parental combinations having good combining ability but similar in quality
parameters, might reduce the concern of segregation for quality traits. Hybrid sterility
problem in inter-subspecific hybrids can be adressed by stacking indica allele (S-i) at
Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in to japonica genetic
background (Guo et al. 2016) or by silencing the S-i and S5 mutant loci through
genome editing tools (Shen et al. 2017).
5.2.2. Utilization of Iso-cytoplasmic restorers: In three-lines hybrid system, cytoplasm
of CMS exerts various unwanted effect (called CMS penalty) and reduces the complete
heterosis expression (up to 5-10%) in CGMS hybrids. Iso-cytoplasmic restorer is
fertile transgressive segregant of CGMS hybrid, having same cytoplasm as of CMS.
In combination with iso-cyto-CMS, it can normalize the fatal cyto-nuclear conflicts,
hence enhances the heterosis to substantial extent. In rice, several iso-cytoplasmic
restorers has been developed and utilized in hybrid rice research (Kumar et al. 2017).
5.2.3. Out-crossing enhancement in seed parent: Low seed producibility (1.5-2.5 t/
ha) in the CMS remains a concern, restricts seed abundancy and area expansion in
India. Trait development in seed parent for out-crossing traits like stigma exertion,
complete panicle exertion is important, needs to be addressed strategically. Recently,
a CMS line, IR-79156A possessing more than 50% out-crossing, developed by IRRI
showed seed producibility of 3.5 t/ha.
5.2.4. Ideotype hybrid breeding: To maximize genetic gain in rice, breeding of ideal
plant type was started long back in Japan and subsequently adopted by China.
Through morphological improvement and adopting inter-subspecific (indica/japonica)
hybrid strategies, substantial progress in ideotype hybrid breeding ‘super hybrid’
have been achieved. China, indeed has made considerable progress and released
more than 100 high yielding super hybrids (Yuan et al. 2017). Hence, inclusion of
inter-subspecific quality type inbreds ‘super rice’ in hybrid development will have
substantial impact in attaining quantum genetic gains in hybrids.

6. ECONOMIC IMPORTANCE
Inspite of being more cumbersome and high input intense practice, hybrid rice
seed production is a profitable venture. It creates additional job opportunity (requires
100-105 more-man days) and provides more net income (around Rs. 75,000/ha net
income, 70% more than the unit production cost) as compared to seed production of
HYV (Rs. 13,000/ha, only 18% more than production cost) (Table 5). The market price
of hybrid seed is Rs. 250-270 per kg. The farmers producing the hybrid seed get only
Rs. 80-90 per kg. In case of low production (<5 quintal/acre) farmers get minimum Rs.
45,000 as compensation from seed production agencies.

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Table 5. Cost analysis of hybrid rice seed

Cost/income (in Rs.)
Item Quantity/Number (per hectare) Hybrid seed HYV
Seed cost Male 5 kg @ Rs. 50/kg 250 2,000
Female 15 kg @ Rs.400/kg 3,000 Nil
Labour cost 250/145 @ Rs. 200/labour/day 50,000 29,000
FYM and fertilizer cost N:P:K (100:50:50) (based on market price) 5,400 5,400
Irrigation 18-20 Irrigation (weekly) @Rs.1500/ha/ 30,000
30,000
Gibberellic acid 2,000 Nil
Others 15,000 10,000
Total cost 1,05,650 76,400
Average production 2.0 t/ha 4.5
Gross income *Price @ Rs. 90/kg and Rs. 20/kg 1,80,000 90,000
Net income 74,350 13,600
* Price of seed is the price given to the farmer.

7. WAY FORWARD
Under changing climatic and agriculture scenario rice hybrid is likely to face stiff
competition to sustain in future. Despite having great potential to enhance production
and productivity, it has not been adopted on large scale as was expected. This is due
to several constraints like lack of acceptability of hybrids in some regions such as
southern India, due to region specific grain quality requirement. Moderate (15–20%)
yield advantage in hybrids is not economically very attractive and there is a need to
increase the magnitude of heterosis further. Lower market price offered for the hybrid
rice produce by millers/traders is acting as a deterrent for many farmers to take up
hybrid rice cultivation. Higher seed cost is another restrain for large scale adoption
and hence there is a need to enhance the seed yield in hybrid rice seed production
plots. Efforts for creating awareness and for technology transfer were inadequate in
initial stages. Involvement of public sector seed corporations in large scale seed
production has been less than expected. Hybrids rice for aerobic/upland, boro season
and long duration hybrids for shallow lowland conditions to be developed. Most of
the constraints mentioned above are being addressed with right earnestness through
the on-going research projects and transfer of technology efforts.
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 New Generation Rice for Breaking Yield Ceiling

SK Dash, P Swain, L Bose, R Sah, M Chakraboty, N Umakanta,

K Chakraborty, MTP Azharudheen, S Lenka, HN Subudhi,
J Meher, S Sarkar, A Anandan, M Kar, S Munda, SK Pradhan,
L Behera and ON Singh

SUMMARY
A breakthrough in yield ceiling in rice is warranted in view of increasing competition
for resources. Ideotype/ New Plant Type/ New Generation Rice is one of the potential
approach based on tailoring a plant architecture with incorporation of efficient traits
for harnessing light and nutrients for optimum biomass (source) and grain yield
(sink). Initial breakthrough in yield improvement was accomplished by introduction
of dwarfing genes during sixties from japonica. Subsequently, rice improvement focus
was shifted for augmentation of stress resistance and quality in shorter growth
duration; hence efforts towards yield increment were not much rewarding. New Plant
Type approach tried to improve the productive features from tropical japonica with
heavy panicles, high grain number and shy tillers. Subsequently, Chinese super rice
further modified it with incorporation of erect, long and wide leaves with less panicle
height for increasing biomass. Recent discoveries on mapping of QTLs/genes for
yield attributing and stress tolerant traits improves the probability of fine tuning of
existing super/popular rice cultures for trait specific complementation through marker
assisted selection and transgenic means from diverse sources, including wild rice.
Similarly, manipulation of some physiological process can also help for improving
overall performance. Over and above there should be standardized management
practices for full realization of yield potential.

1. INTRODUCTION
The Green Revolution in mid sixties increased the rice production of the world
remarkably. However, a ceiling of grain yield potentiality was mostly reported in semi-
dwarf inbred indicas since release of IR 8 (Peng et al. 2008), despite of significant
achievement in yield stability, increased per day productivity and improved grain
quality (Aggarwal et al.1996). A breakthrough in productivity barrier is warranted in
view of increasing competition for water and other resources because of increased
population coupled with higher industrialization, urbanization and diversion of
agricultural land.
There are several available options, viz., Hybrid Rice, New Plant Type/New
Generation Rice (NGR) and C4 Rice. However, there is significant progress for the first
two categories only. Hybrid rice basically targets exploitation of heterosis resulting
from heterozygous F1 from two different inbreeds, whereas, NPT focuses on tailoring
a novel plant architecture with incorporation of traits supposed to be most efficient

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for harnessing light and nutrients for optimum biomass(source) and it scompetent
and productive partition in to the grain yield (sink). Commercial success has been
achieved in China and India in respect of hybrid rice utilizing three line and two line
approaches and has clearly demonstrated the potential of this technology. However,
the success of hybrids mostly depends on the potentiality of restorer lines. Therefore,
a very high yielding restorer coupled with other critical requirements are the key for
success of hybrid rice. Furthermore, a super yielding genotype would greatly help
this technology to attend new heights of grain yield.
The C3 photosynthetic pathway is less efficient than C4 pathway.The goal is to
transform the existing photosynthetic mechanism to a higher capacity one. Taking a
lesson from evolution and converting a plant from C3 to C4 would involve a
rearrangement of cellular structures within the leaves and more efficient expression of
various enzymes related to the photosynthetic process. However, all the components
for C4 photosynthesis already exist in the rice plant, but they are distributed differently
and are not as active. The current approach targets to identify the genes responsible
to install C4 photosynthesis through different approaches, including genomic and
transcriptional. However, it may take some time to have some tangible achievements.
In all these approaches the basic aim is enhancement of grain yield potential.
Evans (1993) defined the term “yield potential” as the yield of a variety when grown
in environments to which it is most adopted, with nutrients and water non-limiting
and the pests and diseases and stresses effectively controlled. Yield potential could
be increased with enhancement of morpho-physiological traits by modifying the
plant design and harnessing better genetic gain from transgressive segregants or
hybrids. The objective of this chapter is to discuss the recent developments towards
developing high yielding varieties for breaking yield ceiling, in the light of preference
of farmers and consumers, taking into account the chronological research efforts for
yield enhancement.

2. IDEOTYPE CONCEPT
The NGR discussed is basically stands on ideotype concept or approach of crop
improvement. Ideotype (ideal plant type) is defined as “a biological model, which is
expected to perform or behave in a predictable manner within defined environment
(Donald 1968). Again a Crop ideotype is defined as “An idealized plant type with a
specific combination of characteristics favourable for photosynthesis, growth and
grain production based on knowledge of plant and crop physiology and morphology”.
There are different types of ideotype conceptualized (Singh 2002) as listed:
Isolation ideotype: It is the model plant type that performs best when the plants
are space planted. In rice, it is lax, free tilleringand leafy. A spreading plant is able to
explore environment as fully as possible. It is unlikely to perform well at crop densities.
Competition ideotype: This performs well in genetically heterogeneous population,
such as, the segregating generation of crosses and performs better while competing

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with weeds. In rice it is relatively tall, leafy, free tillering plant that is able to shade its
less aggressive neighboursand, thereby, gain larger share of nutrition and water. In
annual seed crop like rice, the seed size, speed of germination and root characters
also matters.
Communal/crop ideotype: This performs best at commercial crop densities because
it is a poor competitor. It performs well when it is surrounds by plants of same form.
But it performs less when surrounds with plants of other form, e.g., competition
ideotype and isolation. In rice, a communal or crop ideotype can be able to survive in
the highly competitive situation. The concept of ‘weak competitor’ is the central
theme of this ideotype. Different set of characters have been conceptualizedin rice by
different workers.
Tsunoda (1962) correlated yield capacity and yield response to nitrogen using
different rice plant type and could discover that varieties with superior yielding ability
and higher responsiveness to nitrogenwere closer to short sturdy stems and erect,
short, narrow, thick, and dark green leaves.
The close association between certain morphological traits and yielding ability in
response to N led to the “plant type concept” as a guide for breeding improved
varieties (Yoshida 1972). In rice, ideal plant type was hypothesized as early as 1962.
This ideal plant type was designed to maximize solar radiation interception, minimize
lodging and response to inputs

3. STATUS OF RESEARCH
3.1. International works
3.1.1. Conventional rice improvement
3.1.1.1. Quantum jump in rice productivity with dwarfing gene: A major breakthrough
in yield improvement was accomplished by introduction of dwarfing genes. During
1956, dwarfing gene was in used in breeding from local landrace Ai-zi-zhan to develop
variety Guang-chang-ai, released during 1959 (Huang 2001) in China. In 1962, rice
breeders of IRRI took initiative to introduce dwarfing genes from Taiwanese varieties
such as Dee-geo-woo-gen, Taichung Native 1, and I-geo-tse to tropical tall land
races. In 1966, IR 8, the first semi-dwarf, high-yielding modern rice variety, was released
for the tropical irrigated lowlands (Khush et al. 2001). The development of IR8
increased the yield potential of the irrigated rice varietiesin tropics from 6 to 10 t ha-1
(Chandler1982). The focus in the entire rice breeding programme was to increase in
yield potential. Tropical varieties of enormous yielding capacity, viz., Jaya in India
and Bg. 90-2 in Sri Lanka were developed. In Korea, Tongil-type rice varieties were
developed in 1971 from a japanica/ indica cross (Chung and Heu1980), showed a
30% yield increment compared with japonica varieties. Morphologically, Tongil
varieties were characterized by medium-long and erect leaves, thick leaf sheaths and
culms, short plant height but relatively long panicles, open plant shape with lodging
resistance. Similarly, during 1982, indica/japonica hybridization by Japanese breeders

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for a targeted super-high-yielding rice development, resulted in several promising

super-high-yielding cultivars such as Akenohoshi and Akichikarawith heavy
paniclealong with large number of spikelet per panicle (Wang et al.1997).
The dwarf plant type was discovered to be due to ‘sd1’ gene in Dee-Geo-Woo-
Gen and others genotypes and was a landmark in development high yielding variety,
which resulted in green revolution. This resulted in remarkable change in plant
architecture,viz., dwarf height, high
tillering, sturdy stem, dark green and erect
leaves(Fig. 1). It was further coupled with
photo-insensitiveness and fertilizer
responsiveness which enhanced its
efficiency to have a productivity of 10 t ha-1
during dry season at Philippines. Further,
Traditional land High New plant
it was contributed by the diversity of
race yielding type indica and japonica. Sufficient genetic
variety distance supposedly resulted in heterosis
Fig. 1. Different ideotypes of rice and subsequent potential transgressive
segregants with accumulation of the traits
suitable for higher grain yield eliminating the necessary bottlenecks prevailing thereof.
Subsequent plant breeding efforts towards yield increment were not much
rewarding. This might be me shifting of focus towards maintenance of productivity in
prevailing biotic stress situation by augmenting disease and pest resistance, superior
grain quality, and shorter growth duration. Beachell, Khush and the IRRI team could
succeed in developing one of the highly popular variety and extensively grown, IR36,
in the 1970s. Lately, Khush and team could improve upon it with development of IR72,
with productivity potential equivalent to IR8 but have shorter growth duration and
improved resistance to a number of important rice diseases and insect pests. When
adjusted for earlier maturity, the yield potential of IR72 is 5-10% greater than IR8 on a
yield per day basis. However, stagnant yield potential of semi-dwarf indica inbreds
observed since the release of IR8 (Peng et al.2008).
3.1.1.2. New plant typeapproach: While critically analyzing the causes of yield
stagnation, physiologists hypothesized that the stagnation might be the result of the
plant architecture having high tillering and small panicles. Several unproductive tillers
along with lodging susceptibility that supposedly limit sink size limiting yield
enhancement. Furthermore, these have excessive leaf area that may cause mutual
shading and a reduction in canopy photosynthesis and sink size, especially when
grown under direct seeded conditions (Dingkuhnet al.1991).
Several approaches were there for raising yield ceiling in irrigated ecosystem, and
New Plant Type (NPT) breeding to break yield ceiling is one of the potential and
farmers’ friendly approach conceptualized by IRRI scientists (Peng et al.2008). The
objective was to further modify the present high-yielding plant type to support a
significant increase in yield potential. The basic plan was conceptualized on the basis

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of ideotype approach along with simulation modeling taking into view the framework
proposed by crop physiologists.
Simulation models could foresee the possibility of increase in yield potential to
the tune of 25% by alternation of the following physiological and morphological
traits of the earlier plant type (Dingkuhn et al. 1991):
 A plant type with lesser tillers and high leaf growth during early vegetative stage
because this stage is mainly responsible for higher tillers.
 Retarded leaf expansion and more foliar N concentration during late vegetative
and reproductive growth.
 An abrupt reduction of the vertical N concentration gradient in the leaf canopy
with a large chunk of total leaf N in the top leaves.
 Higher carbohydrate storage capacity in stems, and
 A greater reproductive sink capacity and an extended grain-filling period.
The NPT hypothesized for another quantum jump with the rationale that grain
yield is an outcome of total dry matter and harvest index (HI). Harvest index could be
strengthened by enhancing sink capacity. However, augmenting both of these could
boost the productivity. The choice for proper traits to develop an ideal plant type for
the irrigated lowland turned up from different outlooks. It emphasized combining
heavy panicle with 200-250 grains with proportionately less tiller in short statured
plants (90-100cm).The stem should be sturdy to resist lodging and leaves should be
erect, thick and deep green to support high net assimilation rate. Moreover, it should
have high HI and deep and vigorous root system.There should be sufficient field
tolerance to major disease and pest.The genotypes with enhanced yield potential
and better responsiveness to N administered, had short sturdy stem with erect, short,
narrow, thick and dark green leaves. The “Plant Type Concept” focused mostly on
modification of certain morpho-physiological traits leading to higher grain yield in
response to nitrogen as guiding principle for breeding.
New Plant Type was designed to maximize solar radiation interception, minimize
lodging and high response to inputs with a view to improve biomass and harvest
index that paves the way for high grain yield.The target was to develop a plant type
within 8-10 years with a modest yield increment up to 30-50% than the existing semi
dwarf varieties in tropical environments during the dry season (Peng et al. 2008). With
this concept, donors with large panicle, thick stem, short stature and low tillering
types, bulu or javanica (Tropical japonica) type germplasm from Indonesia, Malasyia,
Thailand, Mynamar, Laos, Vietnam and The Phillippines were selected and
hybridization was done. Large scale hybridization and selections (2000 crosses and
100,000 pedigree lines) were done. First Generation NPTs were selected with large
panicle, few unproductive tillers and lodging resistance and extensive yield trials
were conducted to assess the performances. However, the population performance
was not satisfactory and grain yield was not encouraging. Critical analysis of this
disappointing result could find that there was low biomass production due to reduction

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in tiller number m-2, less crop growth rate (CGR) along with poor translocation of
assimilates during grain filling from the biomass accumulated at pre-flowering, in
comparision to indica varieties. Similarly, other major possible causes assigned were
poor grain filling, which might be due to less biomass, lack of epical dominance,
compact panicles, limited number of large vascular bundles and early leaf senescence
(Peng et al.2008) etc. These were coupled with susceptibility to major diseases and
pests and were having poor grain quality, hence, could not be released to farmers’
field.
Although partially successful, it provided a strong foundation for further research
on yield increment utilizing tropical japonicas. The promising 1st generation NPTs
were hybridized with elite indicas in order to increase the effective tiller numbers but
reduced the panicle size. The reduced grain number with the same panicle size made
the panicle less compact, and in turn, increased the grain filling in the second
generation NPTs. Moreover, accumulation of more genome from adapted varieties
enhanced the quality of grains and disease and pest resistance.With necessary trait
specific augmentation few lines could outyield IR 72; one among them, IR72967-12-2-
3 produced10.16 t /ha, higher to indica check PSBRc52. Few of them could be released
successfully in Philippines and China (Peng 2008).
3.1.1.3. China’s Super rice: In china, in addition to the traits proposed earlier, early
vigour was proposed to have more effect on high yield with development of bushy-
type varieties (Huang 2001). These varieties are tolerant to shading and high plant
density, and were widely grown in southern China. Supplementary advantage in yield
potential was proposed by Yang et al.(1996) from a combination of improvement in
plant type and use of growth vigor. With the influence of IRRI’s NPT programme and
super high yielding hybrid rice combination , which could record a 17.1 tha-1 yield, a’
super’ hybrid rice initiative was started in 1998 by Prof. L. P. Yuan. Here, the strategy
was to combine an ideotype approach with the use of inter-sub-specific heterosis.
The ideotype was reflected in the following traits (Peng 2008):
 Tall erect leaf canopy: The primary three leave blades from the top should be erect
and long and wide (2 cm) to have a higher leaf area. Erect leave will facilitate
reception of light in both sides and avoid mutual shading. The Flag-leaf should be
long (50 cm) followed by still longer second and third leaves (55 cm each). All
three leaves should be on the top of panicle height. Leaves should remain erect
until maturity and the angles of the top three leaves should be ~ 50, 100, and 200,
respectively. The leaf should be stiff, narrow, V-shaped and thick (specific leaf
weight of 55 g m-2) to have stay green character and delayed senescence and
enhanced photosynthetic efficiency. Moreover, leaf area index of these three
leaves should be high (>6.0).
 Moderate tillering capacity: Instead of low tiller here moderate tiller number (8-10
tillers plant-1 or 270-300 m-2) has been proposed. The plant height should be semi-
dwarf with at least 100cm and the panicle height should be 60 cm from the soil
surface during maturity.

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 Large panicle: The panicle should moderately heavy with 5.0g panicle-1. With
about 300 panicles m-2, the theoretical yield potential is 15 t ha-1.
 High HI: The harvest index should be around 0.55 or nearer to that. Harvest index
of ~0.5 requires more of biomass. An increased plant height could be an option on
morphological point of view. However, a tall plant is prone to lodging, a potential
hazard for yield loss which needs avoidance.
Physiologists advocates thicker and sturdy culm,
which again decreases HI and reduces the chance
of super grain yield. In this context, this model of
longer and thicker top three leaves provides a
plausible solution for higher biomass, HI and
resistance to lodging (Fig. 2). This is again in contrast
to the IRRI’s new plant type where short and sturdy
culm was proposed.
During 1998–2005, several super rice hybrids were
commercially released matching to the model
conceptualized. However, two such varieties, viz., Xieyou
9308 and Liangyoupeijiu could be popular because of Fig. 2. Plant type of China’s
their higher yield and superior grain quality. Xieyou 9308 supper rice
was an inter-sub specific hybrid produced 11.53 t ha in-1

an on-farm demonstration experiment, with 17.5% higher productivity than hybrid

check. Similarly, high grain yield to the tune of 12.11 tha-1 was recorded by
Liangyoupeijiu (inter-subspecific hybrid) in Hunan province of China during 2000
and itoutyielded the hybrid check by 8–15% in farmers’ fields (Peng et al. 2008).The
high yield in these cases was associated with higher LAD before heading, greater
biomass accumulation before heading, larger number of grains, and more translocation
of carbohydrates from the vegetative organ to the panicle during the grain-filling
period.
3.1.1.4. Similarities of IRRI’s NPT design and China’s ‘‘super’’ hybrid: Both NPT of
IRRI and super rice plant type of China emphasized large and heavy panicles, reduced
tillering capacity, and improved lodging resistance. It was expected that harvest index
could be improved with increased sink size and few unproductive tillers. Other common
traits are erect-leaf canopy and slightly increased plant height in order to increase
biomass production. The initial strategy for the NPT at IRRI was incorporation of
genes for large panicles and sturdy stems from TJ germplasm followed by crossing
the improved TJ with elite indica varieties to produce an intermediate plant type. In
contrast, ‘‘super’’ hybrid rice (two-line or three-line), proposed an intermediate type
between indica and japonica with an indica parent in order to use inter-sub-specific
heterosis.
Plant type of ‘‘super’’ hybrid rice, panicles are kept inside the leaf canopy by
increasing the distance between panicle height and plant height. This trait was not
clearly defined in IRRI’s NPT design because an IRRI physiologist discovered the
benefit of reducing panicle height for improving canopy photosynthesis and yield

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potential only in mid-1990s.The distance between panicle height and plant height can
be increased by either reducing panicle height or increasing plant height: used in
developing ‘‘super’’ hybrid rice. However, super hybrid had more focus on the top
three leaves.
3.1.1.5. Green super rice: Rice cultivars that can produce high and stable yield with
fewer inputs (water, fertilizers and pesticides), known as green super rice (GSR).
Thus, GSR varieties are climate-smart and can help farmers protect the environment
and themselves (Li and Ali 2016).
GSR was supposedly developed by utilizing more than 250 promising rice varieties
and hybrids that are adapted basically to different stress situations, viz., drought and
low input stress with less inorganic fertilizer and no pesticide and with quick
establishment rates so that it could well compete and overcome the weeds and require
less herbicide, thus causing less harm to environment and would be sustainable.
In the past, breeders at IRRI used only three recurrent parents, IR64, Teqing, and
IR68552-55-3-2, a new plant type variety, backcrossed with 205 donor parents. However,
the GSR concept, which was conceived by the China National Rice Molecular
Breeding Network, used 46 recurrent parents. Crosses were made with 500 donors,
resulting in a bigger pool of available genes. Subsequently, screening was done in
early generations of backcross bulk populations (BC2F2) for different traits supposed
to be important under different biotic and abiotic stress situation, viz.,traits such as
drought, salinity, flooding, and phosphorus and zinc deficiency tolerance from a very
large collection of different types of rice. The promising transgressive segregants
that exceed the performance range of their parents under extreme conditions were
selected.
Rather than focusing on developing one variety for all, GSR can be custom made
to fit any target ecosystem. For example, GSR varieties can grow rapidly to compete
strongly with weeds. Because they establish themselves much faster than the weeds,
so herbicide requirement is reduced. Similarly,the project claims to have developed
drought-tolerant GSR lines in IR64 background, i.e., IR83142-B-19-B, which performs
better than Sahbhagidhan under drought and zero-input conditions (no fertilizers
and no pesticides, and only one manual weeding) (Reyes 2009).
3.1.2. Biotechnological approach
High yield is an unending theme pursued by rice researchers. Breeding for super
rice using molecular tools could effectively supplement empirical conventional
approach. Grain yield is a complex phenomenon which is contributed by three major
yield attributing traits, viz., Number of panicles per plant (NPP), Number of grains per
panicle (NGP) and Grain weight (GW). NPP is dependent on the ability of the plant to
produce tillers. NGP depends on the number of spikelet per panicle, number of primary
and secondary branches and spikelet fertility. Similarly, GW is largely determined by
grain size and seed weight. Many yield related genes/QTLs have been identified in
rice, which are being utilized to improve yield potential through molecular breeding
approach.

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3.1.2.1. Identification of QTLs/genes for grain yield: Recently, many yield-related
genes/QTLs have been identified and cloned in rice. A comprehensive list of these
gens/QTLs related to respective trait/traits is presented in Table 1. Several scientists
had reported that out of the many agronomic traits, grain weight is highly heritable
and can be improved through marker assisted selection than other yield related traits.
Among these traits, panicle and grain architecture supposed to be the maximum
contributor for grain yield. For such traits many genes were identified either from
mutant, or from homologues or identified as locus with MSU-ID. Some of the genes/
QTLs independently govern one or the other component traits of grain yield. However,
many of them also show pleiotropic gene action. The actual genetic gain in terms of
grain yield would depend on the judicious combinations of pyramiding or stacking of
these genes/QTLs in a particular genetic background.
Table 1.Genes/QTLs for rice yield traits useful for breeding super rice (adapted
from Ying et al.2014 and Hirano et al.2017).
Trait/combination Genes (identified from Genes (identified QTLs (identified as
of traits mutant) from homologues) locus with MSU-ID)
Number of panicles D27, D10, D14, D17/ - -
per plant HTD1, D3MOC1
Number of grains LOG, LP, SP1 - Gn1a, Hd1, Ghd7,
per panicle Ghd8/DTH8, EHD1,
DEP1
Number of panicles LAX1, APO2, - OsSPL14,
per plant, number DEP2, FZP PROG1.qGY2-1
of grains per panicle
Grain weight, BRD1, SRS3, PGL2, PGL1, APG TGW6, GW2, GS3,
grain size SG1SRS5 GL3.1/qGL3, GS5,
qSW5/GW5, GW8
Grain weight, GIF1, FLO2, HGW -
grain filling
Culm strength, - - APO1 (SCM2),
number of grains OsTB1 (SCM3)
per panicle

3.1.2.2.Marker-assisted selection (MAS): Marker-aided selection (MAS) has not

yet been extensively used as a part of the regular breeding programme for yield
enhancement. However, few scientists have utilized this approach for improvement
of various traits in Indica x Japonica derivatives for breaking yield ceiling. The MAS
techniques uses tightly linked molecular markers to target the gene of interest. Using
combination of conventional and molecular breeding techniques, Wang et al.(2008)
and Yao et al. (2010) successfully pyramided important genes in several varieties
including Nanjing 46, Nanjing 5055 and Nanjing 9108. The gene for dense and erect
panicle-1 (Dep1) was used to develop NILs (Nanhui 602 x DW 135) through
backcrossing. Similarly, for grain size and exterior quality of seed, pyramiding was
done in the genetic background of Huajingxian 74 by Yang et al. (2010) and Wang et
al. (2012) effectively with GS3 and GW8 genes, governing grain length. Bacterial

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blight and blast resistance genes were incorporated in two restorer lines, Zhonghui
8006 and Zhonghui 218. These lines were used for development of series of super rice
hybrids. For improvement of grain yield, the yld 1.1 (linked marker RM 5) and yld2.1
(linked marker RG 256) QTLs were reported. The MAS technique was also utilized for
transferring grain length and width using GW6 gene from Baodali (japonica variety)
into an indica recurrent parent 9311 and a japonica variety Zhonghua 11 (ZH11)
using MABB. Three improved ZH11-GW6 lines were obtained which showed more
than 30% increase in grain weight and about 7% increase in grain yield. Seed plumpness
of these three lines were improved synchronously because the three ZH11-GW6 lines
contained GIF1 (Grain Incomplete Filling 1), which is a dominant grain filling gene.
Thus, MAS will be a useful option for rapid utilization of genetic resource in super
rice breeding.
3.1.2.3. Transgenic approach for yield improvement: Conventional breeding may be
lengthy and associatedwith linkage drags/yield penalty. In this context, genetically-
modified (GM) or transgenic technology has been shown as an alternative to the
conventional breeding approach. Unlike the former, the latter provides target specific
or limited changes in genetic materials that are well defined and to be done in a short
period of time. There have been several reports of transgenic plants but limited success
for higher yield (Paul et al. 2018). In rice, Lu et al. (2015) reported that altered expression
of OsPIN5b which encoded an endoplasmic reticulum (ER)-localized protein that
participates in auxin homeostasis, transport and distribution in vivo, which results in
higher tiller number, more vigorous root system, longer panicles and thereby improving
simultaneously plant architecture as well as yield potential. Liu et al.(2015) also
developed the GM rice by over-expressing BG1gene that significantly increased
grain size by increasing sensitivities to both auxin and N-1-naphthylphthalamic acid,
an auxin transport inhibitor and hence improved rice plant productivity. Another GM
rice had been developed by Zhang et al.(2013) through overexpression of the rice
micro RNA (miRNA) OsmiR397 that resulted enlargement of grain size and more
panicle branching leading to an increase in overall grain yield of up to 25% in a field
trial. Therefore, this approach could be integrated with conventional approach for
overall rice improvement.
3.1.2.4. Doubled haploid breeding: It is an important technique for quick fixation of
homozygosity and shortening the breeding cycle in varietal improvement.This
approach, not only increases the selection efficiency but also allows early expression
of recessive genes. In conventional breeding, the early segregating generation
population involves variable attributable to both additive and non-additive genetic
effects whereas DH lines exhibit variation only of additive genetic nature including
additive x additive type of epistasis which can be easily fixed through a single cycle
of selection. The detail of this is available in Chapter 1.10 for reference.
3.1.3.Other/novel approaches
3.1.3.1.Wild ancestors of rice in yield improvement: Narrow genetic base in cultivated
rice is caused by factors such as monophyletic origin, genetic bottlenecks, and
repetitive use of elite breeding lines and is one of the major factor limiting genetic
improvement of cultivars. Therefore, it is a necessary to use the diversity arising from
wild relatives.

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 Wild species are important sources of naturally occurring diverse alleles for further
yield improvement. The exploitation of vast genetic resources available in the genus
Oryza could be potential area of research for further improvement. In the past, wild
species were often used as a source of insect and pest resistance, but were rarely
used to improve complex traits such as yield (Bose 2005). However, evidence from
advanced backcross quantitative trait locus (AB-QTL) analysis followed by molecular
mapping studies showed that phenotypically poor wild species can contribute genes
for improving yield and such loci can be mapped after introgression into elite cultivars
(Tanksley and McCouch1997). Wild rice species are more diverse than cultivated
varieties (Swamy and Sarla 2008). Among the wild accessions, genetically moderate
distant accessions are the best choice as donor parents, because they contain less
undesirable alleles than distant accessions. In rice, yield and yield-related QTLs have
been identified from three wild rice species such as O. rufipogon, O. glumaepatula
and O. grandiglumis using AB-QTL strategy. O. rufipogon, a perennial wild progenitor
of Asian cultivated rice, is used for mapping of QTLs for yield and grain quality, and
identification of other related traits under different genetic backgrounds (Xie et al.2008).
Several plant traits directly or indirectly affect rice grain yield including days to
heading and maturity, plant height, panicle length, number of panicles per plant,
spikelets per panicle, grains per panicle, seed set, grain weight, grain size and shape,
and shattering. Yield improvement can be achieved as a result of the vast allelic
diversity for these traits found in interspecific populations, especially number of
grains per panicle which has proven to have the greatest relevance for rice breeding
programs (Tian et al 2006). Modern rice varieties are developed after an extensive
selection process to improve a few targeted traits related to cultivation and end-use
quality but primarily those associated with yield components, such as resistance to
shattering, compact growth habit and improved seed germination (Tanksley and
McCouch 1997). This prolonged breeding procedure can lead to a reduction in the
genetic variability found in modern cultivated rice. Thus identifying genetic sources
for agronomically important traits from wild Oryza species and introgressing them
into cultivated rice is desirable and necessary. Although wild Oryza species are inferior
in grain yield, especially when compared to cultivated rice, transgressive segregation
from a cross between cultivated rice and a wild Oryza species, especially the ancestral
species, O. rufipogon and O. nivara, revealed the presence of favorable alleles from
the wild parent that can increase yield in the genetic background of cultivated rice
(Brar and Singh 2011) w.r.t. panicle and plant height, suggesting it may have played a
role in the domestication of rice. Studies of QTL or genes for yield and yield
components being attributed to the wild donor parents, not only belongs to ancestral
A-genome species, O. rufipogon or O. nivara, but also in the more distant tetraploid
O. minuta with a BBCC genome (Brar and Singh 2011). Observations confirm that not
only single genes and alleles are affecting yield traits but there are epistatic interactions
and epigenetic interactions, as well as environmental factors affecting many of yield
traits, resulting as transgressive variation.

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3.1.3.2. Photosynthetic efficiency and yield improvement: Improving leaf

photosynthetic efficiency (Pmax) to increase the crop yield is a quite extensively
studied area, which has tremendous potential for yield improvement. Along with Pmax,
other leaf features viz. leaf morphological and anatomical features including leaf area
and orientation, organization of mesophyll and vasculature, strongly determine overall
photosynthetic process and yield. Theoretically, it is possible to improve plant growth
(and thus productivity and final biological or economic yield) either by increasing the
amount of photosynthesis or by reducing ‘unnecessary’ respiratory costs or by
allocating more C into appropriate sinks. Over the years, researchers had associated
higher unit leaf photosynthesis with higher crop yield, but paradoxically, selection
for higher or maximum net photosynthesis rate within a given species was often not
associated with higher productivity (Austin1990). Notably, in the rice varieties released
from IRRI between 1966 and 1980, there was a decline in Pmax, stomatal conductance,
leaf protein, chlorophyll and Rubisco content, whereas the values increased in the
varieties released after 1980. It was suggested that the grain yield in IRRI varieties
released prior to 1980 was correlated with harvest index, whereas, it was correlated
with total plant biomass, in the varieties released after 1980 (Hubbart et al. 2007).
3.2. Indian works
3.2.1. Early Rice improvement: In India, early rice improvement was mainly dealing
with improvement of popular local varieties through pure line selection. Several
improved varieties were evolved, viz., T 141, T 1242, Latisail, Manoharsali, MTU 15,
CO 25. Similarly, varieties suitable for specific biotic and abiotic stress situation were
also developed. These varieties as evolved from landraces and farmers variety, hence
mostly suitable for low management condition and had the ability to tolerate stress to
some extent, but were not promising for yield enhancement. Establishment of Central
Rice Research Institute (CRRI), Cuttak in 1946 by the Govt. of India, was a turning
point in the history of rice research and provided a momentum to it. Inter-racial
hybridization programme between japonicas and indicas during 1950-54 by The Food
and Agriculture Organization of the United Nations had resulted a limited success.
Only four varieties, viz., Malinja and Mashuri in Malaysia, ADT-27 in Tamil Nadu,
India and Circna in Australia were released from more than 700 hybrid combinations
(Parthasarathy1972). However, one variety, Mashuri was used extensively in breeding
programmes as parent of present day mega varieties, viz., Swarna and Samba Mashuri.
Since lodging was a major handicap for tall indica varieties, initiative was taken for
improvement of weak stem to stiff straw genotypes with less lodging, with the help of
short statured tropical japonicas, viz., Taichung 65, Tainan 3 and Waikyo Ku.
3.2.2. Recent works at NRRI, Cuttack: Yield improvement work was initiated following
ideotype concept to break yield ceiling. In this context, New Generation Rice (NGR)
has been conceptualized with an objective of modest grain yield of 10.0t/ha under
farmers’ field condition with a favorable management condition, notwithstanding the
limitation of low light condition of eastern India.The plant type of this rice is basically
contributed by following traits.

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 Semi dwarf but with slightly raised height (Around 110cm).
 Strong culm to resist the moderate wind speed at maturity stage.
 Top three leaves should be erect with high specific leaf weight and v-shaped.
 Moderately high tillers (8-10 all effective).
 Moderately high grains (250-300).
 Moderately heavy panicle (5g or more).
 Field tolerance to major disease and pests
 Acceptable 1000 grain weight (21.0-24.0 g 1000 grain weight) and good quality
parameters.
 Ability to continue higher photosynthesis even during Grain Filling Stage (7-25
DAF).
 Maturity duration of 130-145 days for irrigated and favorable shallow lowland.
 Yield potential of 10.0 t/ha or even more under low light condition of eastern zone.
The second generations NPTs developed at IRRI were collected in the segregating
stage, and the further trait specific selection was exercised to establish fixed lines, i.e.,
NPT selections (NPTs). These NPTs performed exceptionally well, and even some of
those showed the productivity of more than 10.0 t ha-1 during dry season 2011(Table
1) (Dash et al. 2015). However, a super rice variety is still a need of the day, which
should have productivity potential of at least 20% higher than the popular mega
varieties or best check vis-à-vis resistance to abiotic and biotic stress along with
acceptable grain quality. Moreover, it should have stable yield performance in multiple
sites even in moderate low light stress. There is no such report of super rice in India
till date. Hence, with an objective of development of indigenous super rice, the NPT
lines along with standard popular indica check varieties and tropical japonica lines
were selected for study, for identification of divergent gene pools in the backdrop of
high yield under lowlight.The divergence analysis revealed that NPT selections had
clustered differently and maintains sufficient diversity with respect to tropical
japonicas, temperate japonicas, derivatives of indica/ temperate japonicas and even
specific popular indica varieties. Therefore, NPTs could be potentially exploited for
recombination breeding with these genotypes. Similarly, Garris et al. (2005) could
detect five distinct groups, corresponding to indica, aus, aromatic, temperate
japonica, and tropical japonica rice. Nuclear and chloroplast data supports a closer
evolutionary relationship between the indica and the aus and among the tropical
japonica, temperate japonica, and aromatic groups.
It was followed by study of combining ability analysis and some of the NPTs, viz.,
IR 73963-86-1-5-2-2, IR 72967-12-2-3 and IR 73907-753-2-3 were found to be excellent
general combiners, although were not toppers in grain yield category. In this context,
these were hybridized with a set of promising tropical japonica, indica and aromatic
lines with potential yield and yield attributing traits. Out of 400 fixed lines few could

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be found with traits matching to the NPT characters and increment in grain yield to
the tune of 19-55% in comparison to popular indica check variety Swarna. Culture CR
3856-44-22-2-1-11 obtained from the cross IR 73963-86-1-5-2-2 and CR 2324-1 was
found to be one of the top runner with yield potential of 11.2 tha-1 (10.8 tha-1 and 10.4
tha-1 during 2016 and 2017, respectively in farmers field) (NRRI 2017). Coming to the
traits attributing grain yield, it was found that the high grain yield was obtained due
to heavy panicles (6-8 gpanicle-1), high grain number (250-300) with good quality
(medium slender grains, 22.0g per 1000 grains), shy tillering (6-7), raised plant height
(115-120cm), long semi erect top three leaves (length 39.0 cm, 44 and 46cm for 1st, 2nd
and 3rd respectively;width 2.4cm average for all three). Again to support heavy panicles,
it has strong and thick culm (Fig.3 and 4). However, it is also associated with some
bottlenecks which need improvement for further yield increment as well as stability. It
needs reduction in height to maximum 110 cm and the culm strength has to be enhanced
further to withstand the untimely heavy wind occurs during fag end of cropping
season. The spikelet sterility also needs to be reduced from 20% to 10%. Moreover, it
should be incorporated with resistance for BLB and few others disease and pests.

Fig. 3. Field view of CR 3856-44-22-2- Fig. 4. Single plant of

1-11 at dough CR 3856-44-22-2-1-11

Similarly another variety Maudamani (CR Dhan 307) (Parentage: Dandi/Naveen /

/ Dandi) has been released for irrigated ecosystem during 2015 has shown promising
yield potential of 11.5 tha-1 (7-11.5tha-1)
under farmers field condition. It has also
heavy panicles (6-8g), high grain
number (250-300) with short bold grains
(1000grain weight: 24.6g). It is suitable
for irrigated ecology and endowed with
characters viz., moderately strong culm,
medium tillers (7-8), wide top leaves
(2.2cm) and v-shaped stiff leaves and
stay green character.
Many genotypes were with heavy
panicles (7.93 g to 15.5g, Fig.5) were Fig. 5. Variation in Heavy panicles of
NGR(7.93-15.5g) w.r.t. popular check
selected from different crosses of NGR.
varSwarna 3.12g

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However, all of them could not be translated into higher grain yield due to inferior
population performance. This may be either due to non-uniform panicle type, or may
be due to less tillers or high spikelet sterility. Again, these NGRs with heavy panicles
were found to be more prone to biotic stresses. Therefore, trait specific supplementation
along with incorporation of disease/pest resistance would make these NGRs more
stable. Classical recombination breeding and markers assisted backcrossing for specific
traits could be the options for augmentation of characters to make these high yielders
stable.
Another focus at NRRI is given to develop NPT/Super rice varieties with increased
photosynthesis and grain yield. The highest erecto-foliage leaf orientation coupled
with highest photosynthetic rate (35.2 - 49.1 μmole CO2 m -2 s-1), maximum
photosynthetic quantum yield efficiency of PS II (Fv/Fm ratio of 0.770 - 0.808) with
high performance index (2.21 - 3.84), high biomass (10-11 tha-1), high HI (0.52), high
panicle number (340) and higher grain filling percentage (>85%) are key traits
contributing for higher yield potential (6-8 tha-1) in some NPT lines. Higher LAI (5.0-
6.3), high Pmax (40-43 μmole CO2 m-2 s-1), higher biomass (13-15 t ha-1), high HI (0.42-
0.50), higher panicle no (316-400), and higher translocation efficiency with high grain
filling percentage (>80%) contributed high grain yield of more than 6.5 t ha-1 with
yield advantage of 0.5 - 1.0 t ha-1 over the checks in NGR lines IR 73895-33- 1-3- 2, IR
73907-75- 3-2-3 and IR 73896-51-2-1- 3 (NRRI 2012). Proper physiological
complementation with existing NGR would definitely help to attain new heights of
productivity.
3.2.3. Future generation rice: Indian Institute of Rice Research, Hyderabad has
conceptualized “future generation rice” for breaking yield ceiling. It started with
screening of tropical japonica and selection of promising accessions as donors.
Popular and highly adopted varieties (NDR 359, Swarna) were taken as recurrent
parent and back crossed with these accessions. In BC2F2 stage, the elite lines were
intercrossed and generation advancement was done for necessary fixation. Initial
selected lines or 1st generation plant types were having traits, viz., semi dwarf height,
heavy panicles, indica type grains but with poor grain filling. It was also having
undesirable feature, viz., early senescence and was susceptible to major disease and
pests. However, after selected intermating within and between populations there was
improvement in grain filling, stem thickness, panicle length and duration of senesces.
Some of the genotypes were having ideal traits, viz., Plant height: 110-120cm, No. of
panicles per plant: 6-10, high grain number, strong/thick culm, test weight: 20-24g, late
senescence, shy tillers but with very less unproductive tillers with a duration of 120-
145 days. These are having high biomass with 48-50% HI and very high yield
potential.These lines are under national multi location testing. Similarly, some
O.rufipogon derived lines have shown improvement in biomass as well as sink size
and could be used as prospective parents in improving yield of present day varieties
and parental lines.

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4. AGRONOMIC MANAGEMENT FOR NEXT GENERATION

RICE
Potential productivity of any variety is accomplished not only by genetic potential,
but also by optimum agronomic management. Thus, it is imperative to understand
yield responses of NPT/super rice/ NGR to various agronomic practices. As NGR has
different morpho-physiological attributes, it necessitates new management practices.
Among the practices, nutrient management, crop establishment, water management
and pest management are the key factors in realizing the potential yields. Many
experiments have been conducted to analyze the nutrient accumulations in different
rice varieties and the variation is enormous across soil, climate, location and
management. However, limited literature is available on the management of super rice.
Reports suggest that establishment methods have differential effects on nutrient
uptake, crop growth, weed occurrence, and subsequently crop yield (Singh et al.
2006).
At National Rice Research Institute, superior grain yield was reported by
application of 120 kg Nha-1 in NPT cultures than 80kgha-1. Higher N dose of 160 kgha-
1
was not found to have any positive effect on the yield. As NPT were having some
sort of shy tillering, closer spacing (15x15 cm) was found to have high yield than
normal/higher one (20x20cm or 20x15cm) (NRRI 2013-14). Similarly, multi location trials
conducted under AICRIP recorded higher average grain yield of NPT genotypes in
closer spacing (15x15 cm) w.r.t. normal (20x20cm), whereas, other check varieties
experienced yield reduction in closer spacing (IIRR 2017).
However, further research is needed to have a comprehensive and more
quantifiable package of practices for NGR.

5. KNOWLEDGE GAPS AND SOLUTION

In future, production of rice also needs to be increased from lesser land area due
to population explosion and shrinkage of resources. As there is hardly any scope of
horizontal expansion, the vertical expansion is the only way out. For this purpose,
there is continuous effort towards increasing grain yield by means of higher plant
population per unit area, higher per plant yield though higher grain number per panicle,
higher spikelet fertility and better grain weight. This will definitely increase the weight
of upper part of the plant and thereby increasing the chance of lodging in indica rice.
The problem is further coupled by increasing climatic vagaries like erratic rainfall,
increase in extreme weather events and uncharacteristic wind flow especially in eastern
and southern coasts of the country. Without improving the actual strength of culm, it
will not be possible to break the yield ceiling of rice, as our target will be to produce
the genotype of high biomass coupled with higher harvest index. Reduction of height
to semi-dwarf stature is definitely the option, but relying solely on it might be having
some limitations, which necessitates use of other important traits to reinforce it.
Fortunately, several such useful genes as well as precisely mapped QTLs are now

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available for the breeder (Table 1), which will definitely help in designed breeding of
NGRs. However, finding the suitable combinations of these genes/QTLs are highly
essential. Yield being a highly complex trait is subjected to differentiation in component
traits. However, the major challenge is avoiding the negative trade-off among those
component traits. Hirano et al. (2017) suggested the use of combination of mild alleles
of the genes for these negative trade-off combination traits rather than use of strong
alleles, which often accompany undesirable side effects on other yield components
(e.g., strong alleles for APO1 and OsTB1 although increases grain number per panicle
and culm strength of plants, significantly reduces the tiller number). However, while
pyramiding for same trait, combining even mild alleles with similar mode of function
may again show detrimental effect on phenotype. With increasing knowledge gained
on mode of molecular function of the genes, it is easier to develop plants with ideal
traits of NGR, which can break the long pending yield ceiling of indica rice.

6. CONCLUSION
The stagnation of yield of existing high yielding rice varieties call for breaking the
yield barrier for meeting food demand of ever increasing population. Grain yield is a
complex character, where many genes and QTLs have intricate interaction with several
physiological and bio-chemical processes. Therefore, a breakthrough in yield potential
requires a comprehensive research and improvement of all the aspects that affect
grain yield and the factors affecting its production in view of changing climatic scenario.
Selection for morphological characters with physiological implication may be the first
choice for crop improvement. However, it should be supplemented for molecular
breeding for higher agronomical and physiological efficiency. Improvement of harvest
index by researchers is in focus in many grain crops including rice, but as it is
approaching a ceiling, increasing its potential has to involve an increase in biomass
which has to be achieved through increasing photosynthesis. Empirical breeding for
population improvement has resulted in a high productivity of rice for last 30 years in
tropics. Modification of plant type and utilization of heterosis are two primary strategies
now being used to increase the yield potential of irrigated lowland in the tropics.
Intra-varietal cross between indica types has only limited scope of yield improvement.
However, intersub-specific hybridization between tropical japonica and indica has
a great potentiality for increment in production potential. There are several unexploited
sources including wild rice which has already shown promise and would play a great
role in future. Prospective rice improvement has to address the issues of identification
of physiological basis of morphological traits, their GxE interaction for controlling
grain yield. Genomic assisted breeding with introgression of QTLs/genes for
quantitative traits (for higher grain yield) has immense potentiality for supplementations
of characters for attaining new heights in grain yield. However, this has to be
environment specific and clear-cut management options need to be developed for
expressing its full potential for breaking yield ceiling.

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 Biotechnology for Rice Improvement:
Achievements and Challenges

S Samantaray, N Umakanta, JL Katara, C Parameswaran,

RL Verma, H Subudhi, A Kumar, Devanna BN and S Roy

SUMMARY
Biotechnological strategies such as in-vitro culture, transgenics and genome
editing (CRISPR/Cas9) provide immense opportunities for rice improvement. These
tools have been effectively utilized for development of new varieties, mapping of
QTLs, characterization and functional validation of genes, development of novel
variants etc. However, indica rice requires special emphasis for improving callusing
potential of anthers, albino-free green shoots regeneration in androgenesis, increasing
transformation efficiency and optimization of delivery methods for CRISPR/Cas9
vectors. We could increase the callusing ability of anthers in indica rice up to 30%
using combinations of media components and achieved 100% green shoot
regeneration in androgenesis. The complex traits such as heat tolerance in rice requires
multipronged approach through fine mapping, characterization of fixed alleles of heat
stress responsive genes to understand the tolerance mechanism and effective
introgression the genes through molecular approaches. Gain/loss -of-function alleles
generated through CRISPR/Cas9 in farmers preferred varieties could modify the trait
of interest and also maintain the aesthetic value of the variety. Thus, addressing
critical issues such as callusing potential in androgenesis, higher transformation and
genome editing efficiency in indica rice could assist in development of improved rice
varieties for yield, stress tolerance and quality under this demanding climate change
driven agriculture.

1. INTRODUCTION
With the expanding growth of world population and gradually deteriorating
environment, food security has become a major challenge around the world especially
in rice growing countries. Increasing rice yield has become the most important goal of
rice production on less land with limited resources. Hence, there is a sustained need
focus on development of high yielding rice varieties with tolerance to biotic and
abiotic stresses (Hasan et al. 2015). Though rice breeding efforts over the past six
decades have contributed tremendously to the genetic improvement of rice in terms
of yield and quality, traditional approaches suffer from several limitations to increase
crop yield and productivity indefinitely. Conventional rice breeding is a slow process,
typically requires 8-10 years from initiation to varietal release which also mostly
depends on environmental conditions. Alternatively, biotechnology in recent years,
has provided a powerful means to supplement traditional methods through the use of

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molecular genetics in cloning and sequencing of genes leading to the analysis of the
genome structure, evolution and expression.
The first decade of this century brought in revolution of DNA sequencing wherein
the whole genome sequence of Arabidopsis, rice, sorghum, Medicago etc. were
accomplished and made available in public domain. The genome sequences assisted
in identification of genes, pathways, and understanding of mechanism of several
developmental and stress response in plants. Additionally, identification of genome
wide molecular markers helped in mapping of several important traits in plants. This
development was quite useful in production of stress tolerant, high yielding varieties
through marker assisted introgression. Similarly, genetic transformation shows its
significance in development of agronomically important traits such as herbicide
tolerance, shelf life, insect and disease resistance etc. in a number of crops. Besides,
doubled haploid (DH) approach has significantly reduced the time required for
development of mapping population and hastens the mapping of tolerance/resistance
genes. Another latest technology known as CRISPR/Cas9 system could revolutionize
the plant biology by editing major genes for crop improvement. Thus, DH breeding,
transgenic approaches and CRISPR/Cas9 provide varied solutions to the need of
biotechnologist in their quest for rice improvement which were highlighted in this
chapter. Since the whole work on advances of these technologies particularly DHs
and transgenics cannot be covered here, it was considered summarizing some
important findings useful for rice improvement along with our own research dealings
with androgenesis in production of DHs and transgenics for high temperature
tolerance.

2. DOUBLED HAPLOID IN RICE IMPROVEMENT

To meet the challenge of food security for the increasing population amid
diminishing resources like cultivable land and irrigation water along with climate
change associated unpredictable and unseasonal weather patterns, development of
high yielding rice varieties is need of the hour. Hybrid rice is considered as a best
option to break the yield barrier with significant yield advantages over the
conventional cultivars. Though hybrid rice can out-yield conventional cultivars by
30-40% in production fields, it has not gained its popularity among the Indian farmers
due to its complicated seed production system, non-replacement of seed every season,
higher seed cost, less preferred qualities and vulnerable to abiotic and biotic stresses.
Therefore, it is required to find out an alternative way to exploit the hybrid potential
by fixing heterosis along with the associated problems, for which DHs technology
was found efficient in rapid fixation of favourable alleles for yield and related traits.
The DH breeding technique shortens the time required for breeding a new variety
from the usual ~8 years to ~5 years (Fig. 1), thus saving on time, labour and financial
resources. Conversely, DH technique could be more appropriate for developing new
varieties from photosensitive rice genotypes. Most of these advances were achieved

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in japonica cultivars which are more
amenable to anther culture than indica rice.
Significantly, a number of varieties and
improved parental lines have been
developed through androgenic
approaches, but it is only restricted to
japonica rice cultivars. However, the use
of anther culture as a routine technique
for breeding is extremely limited in indica
rice due to poor induction of androgenic
calli and subsequent plant regeneration.
To alleviate the problems associated with
the indica hybrid rice cultivation, anther
culture could be employed to develop DH
recombinants that performed almost nearer
to hybrids (Naik et al. 2016).

Fig.1. Doubled haploid vs. Conventional

3. TRANSGENIC breeding: Duration for varietal release.
APPROACH IN RICE
Climate change could drastically reduce the productivity of crops in developing
countries like India for which finding a sustainable solution is necessarily required to
address such problem. Biotechnological interventions have been successfully utilized
in stacking of several genes within a short span of time to cope with the prevailing
situations. Since the simple traits were controlled by qualitative genes, most of the
quantitative traits governed by several genes such as drought, salinity, heat were
dependent on transgenics. Even though, the transgenic approaches are highly
successful in developing tolerance, validation of transgenic plants in most cases has
been reported only in control conditions such as phytotron or green house facility.
The evaluation of transgenic in field condition is very much essential to understand
the tolerance at field level. Thus, the constraints for using biotechnological tools for
crop improvement of complex traits are significant. Though the transgenic approach
plays a significant role in crop improvement, there are limitations for the successful
gene transfer in several crops.
Genetic engineering in rice has been utilized to transfer several genes for important
traits such as yield, quality and tolerance to biotic and abiotic stress tolerance. Cry1Ac
gene tolerant to rice pests was transformed for enhancing insect tolerance in rice (Lee
et al. 2016). Moreover, ferritin was used to increase the iron content in rice endosperm
through genetic engineering (Masuda et al. 2013). The rice vacuolar Na+/H+ antiporter
gene were used to enhance the salinity tolerance in rice (Reddy et al. 2017). Over
expression of DREB genes has been shown to increase the cold tolerance in rice (Cruz
et al. 2013). Thus, transgenic approaches in rice have contributed significantly in
development of biotic/abiotic stress tolerance and quality improvement of rice.

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4. CRISPR/CAS9 TECHNOLOGY IN RICE GENOME

EDITING
Due to gradual decline in genetic variation, the cultivated crops become more
vulnerable towards abiotic and biotic stresses. Climate change and human activities
are also contributing to this factor. Besides, natural gene pool available in wild
ancestors and landraces are useful to understand important biological mechanisms.
However, useful genetic resources from the wild genetic pool have been transferred
in cultivated rice with limited achievements to improve the genetic constituent of
cultivated crops. Conventionally, induced mutation or target mutagenesis has been
adopted to create variation in the cultivated gene pool which is beneficial for genetic
improvement of cultivated crops. In the past decades, induced mutation technology
such as physical, chemical or biological (T-DNA or transposon insertion) mutagenesis
have been widely used to identify novel mutants in model plants like Arabidopsis
and rice. However, such random mutagenesis produces many undesirable mutations
and genome rearrangements and screening of large scale mutants remains tedious
and costly (McCallum et al. 2000). Therefore, there is urgent requirement for a
revolutionary robust technology of targeted mutagenesis for genetic improvement of
traits in crops. Genome editing is a new technology widely used in the studies of
functional genomics, reverse genetics, genome engineering and targeted transgene
integration by allowing of addition, deletion or alteration of genetic material at particular
locations in the genome in an efficient and precise manner. In general, it involves the
introduction of targeted DNA double-strand breaks (DSBs) using an engineered
nuclease, which can induce site-specific changes in the genomes of cellular organisms
through a sequence-specific DNA-binding domain and a non-specific DNA cleavage
domain thereby generates desired insertions, deletions or alterations.

5. STATUS OF RESEARCH
The past and current status of research highlights the usefulness of DHs,
transgenics and CRISPR/Cas9 technology in rice improvement.
5.1. Manipulation of factors in success of anther culture
The discovery of haploids in plants led to the use of DH technology in plant
breeding. Though there are different methods to generate haploids and then obtain
DHs by chromosome doubling, in vitro methods were found to be most suitable for
production of DHs. There are two in vitro methods i.e. gynogenesis and androgenesis
available for DH production from which androgenesis shows its effectiveness and
applicability in production of haploids and DHs in numerous cereals including rice.
These systems allow completely homozygous lines to be developed from heterozygous
parents in a single generation.
The first naturally occurring haploids were reported by Blakeslee et al. (1922) in
jimson weed (Datura stramonium) and thereafter natural haploids were documented
in several other species. However, the relevance of DHs came into attention only

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when Guha and Maheshwari (1964, 1966) reported a breakthrough in the production
of haploids from anther culture of Datura (Datura innoxia). Further, their research
revolutionized the use of DH technology in plant breeding worldwide. Subsequently,
this haploid discovery by anther culture provided several opportunities for application
of this technique in crop improvement programs. In rice, first report on production of
haploids through anther culture was reported by Niizeki and Oono (1968). Thereafter,
doubled haploidy approach coupled with conventional breeding led to the
development of a number of rice varieties for pest and disease resistance, high yield,
and quality grains. In China, several varieties of rice viz. Xin-Xin, Hua-Hau-Zao,
Zhong-Hua-8, Zhong-Hua-9, Zhong-Hua-10, Zhong-Hua-11, Hua Yu-1, Hua Yu-2,
Tanfong1, Nonhau5, Nonhau11, Aya and ZheKeng 66 possessing high yield, superior
quality, tolerance to abiotic stress such as cold, early maturity, resistance to disease
have been released through the use of DHs. Further, in Japan, several successful rice
varieties developed through anther culture techniques are Joiku N. 394, Hirohikari,
Hirohonami AC No.1 and Kibinohana which are tolerant to cold and are good in taste.
Similarly, two rice varieties (Patei and Moccoi) and one rice variety (Dama) were
released in Argentina and Hungary, respectively along with two rice varieties in
Republic of Korea also employing DH approach. In India, Satyakrishna (CR Dhan 10)
and Phalguni (CR Dhan 801) are the first released indica rice varieties from DH lines
(CRRI Annual Report, 2008-09, 2010-11; www.crri.nic.in). Besides, a rice variety “Parag
401” has also been bred through DH breeding. Furthermore, anther culture could
facilitate other biotechnological approaches such as gene transformation and
identification of QTLs.
Despite all the advantages DH technology offers, it has not been put to use in the
country to that extent to take maximum advantage. This is primarily due to lack of
expertise and variable response of different genotypes under in vitro culture. Though
androgenic response to japonica type has led to release of many varieties, the potential
of the anther culture technique for indica rice breeding is not fully exploited in spite of
releasing a salt tolerant indica variety through anther culture (Senadhira et al. 2002).
Early anther necrosis, poor callus proliferation and albino-1 plant regeneration are
some of the problems encountered in case of indica rice at the time of androgenesis
which require vast improvement. The genetic diversity is also a determining factor in
the success of anther culture.
Physiology of the donor plant is an important contributory factor for the success
of rice anther culture. Anthers of panicles collected from field grown plants have been
decidedly better in their anther culture response compared to anthers collected from
pot plants placed in the green house or near the field (Veeraraghavan 2007). Usually,
the distance between the collar of the flag leaf and ligule of the penultimate leaf of the
tiller serves as a reliable guide to anther maturity. Secondly, microspore stage is
considered as an important factor for androgenic response. An easily observable
morphological trait of the plant that shows good correlation with the pollen
development stage is used as a guide to identify the required stage of microspore
(Nurhasanah et al. 2015). The most suitable stage of microspore development has

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been described as the late uni-nucleate to early bi-nucleate stage as well as early to
mid uni-nucleate stage.
A wide range of chemical and physical factors influences the androgenesis in
vitro. The most widely used pre-treatment for androgenesis is the low temperature
shock for specific duration. Mishra et al. (2013) assessed the influence of cold
pretreatment at 10°C for 7-9 days on the anther culture response of Rajalaxmi (CRHR
5) and Ajay (CRHR 7) which showed a positive influence on the callus induction
frequency irrespective of the media and PGRs employed; prolonged treatment over
the optimum proved to be inhibitory for androgenesis. However, cold treatment (10
°C) for 8 days was found to be effective for callus induction and green plant regeneration
in a popular indica rice hybrid, BS6444G (Naik et al. 2017). Besides, two days pre-
incubation period at 10 °C was quite interesting for the success of androgenesis in a
long duration indica rice hybrid (Rout et al. 2016).
The most commonly used basal media for anther culture are N6, MS, B5 and
Potato-2 medium. Subsequently, several media (MSN, SK1, He2 and RZ) were
developed from the N6 media modifying the nitrogen levels and sources, carbon level
and sources, changes in vitamins and their concentrations which were found to be
encouraging for anther response in rice. N6 media was found to induce maximum
callusing in Taraoi Basmati (Grewal et al. 2006). Minj et al. (2016) could find out the
best media for androgenesis in generation of DHs from F1s of two inter-varietal crosses
in terms of callusing (N6) and shoot regeneration (½ MS) after trial with 16 different
media. However, two basal media such as N6 and MS media were found to be effective
for callusing and green shoot regeneration, respectively in indica rice hybrids (Rout
et al. 2016; Naik et al. 2017).
Considering the importance of plant growth regulators in tissue culture, the effects
of different PGRS were investigated for androgenesis. Even though, 2,4-D has proven
to be a potent auxin for callus induction from cultured anthers, however, medium with
lower 2,4-D levels was found to be more effective for the regeneration ability of callus
induced in indica rice as compared to higher 2,4-D levels in japonica rice (Naik et al.
2017). Media supplemented with NAA (0.5 mg/l), BAP (1.0 mg/l) and Kn (1.0 mg/l)
adequately supported green plant regeneration from sub-cultured callus (Rout et al.
2016). The type and the concentration of auxins seem to determine the pathway of
microspore development with 2, 4-D inducing callus formation and IAA and NAA
promoting direct embryogenesis (Ball et al. 1993). 2,4-D was effective for callus
response while the combinations of NAA, Kn, BAP showed shoot regeneration in
generation of DHs from F1s of two inter-varietal crosses (Minj et al. 2016).
The nitrogen composition supplied in the form of nitrate and/or ammonium ions in
culture media plays a significant role for androgenesis. The ratio of nitrate (NO3-) :
ammonium (NH4+) has been observed to be an important determinant for the success
of anther culture as well as for the in vitro induction of embryogenic callus in indica
rice (Grimes and Hodges 1990). Ivanova and Van Staden (2009) investigated the
elimination of total nitrogen in media resulted in limited ability of proliferation and
shoot growth but higher ability was observed in media containing NO3- as the only

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sole of nitrogen source and replacing the NH4+ to NO3- decreased the rate of
hyperhydricity. Herath et al. (2007) proved that frequency of callus induction was
improved by modification of three different media (N6, B5 and Miller) with one half
the level of NH4+ and double the level of KNO3 nitrogen.
A carbohydrate source is essential for androgenesis because of their osmotic and
nutritional effects. The superiority of maltose over sucrose as the carbon source in
rice anther culture for callusing was aptly demonstrated by Naik et al. (2017). Replacing
sucrose (146 mM) with maltose (146 mM) in the callus induction medium had a
significant positive effect on anther response in both indica and japonica types with
a greater effect on indica rice. With respect to the effect of light quality on anther
culture, the embryogenic induction of microspores is inhibited by high-intensity
white light whereas darkness or low-intensity white light are found encouraging
(Bjornstad et al. 1989). The incubation of anthers continuously in the dark has, on
occasion, been found to be essential.
Most of the in vitro morphogenic responses are genotype-dependent. In general,
indica cultivars of rice exhibit poor androgenic response as compared to the japonica
ones. Even among the indica cultivars, a considerable variation for pollen callusing
and plant regeneration has been observed (Rout et al. 2016). Highest callus responsive
cultivars often show the best regeneration frequency and also the best responsive
genotypes to callusing exhibit low regeneration ability. Therefore, selection of a single
step either callus improvement trait or shoot regeneration trait alone may not help in
establish an effective androgenic method. It is rather important to identify genotypes
carrying the two traits for overall improvement in anther culture efficiency.
5.2. Transgenics for high temperature stress
Heat stress in crops is considered as one of the major threat to crop production by
Intergovernmental Panel on Climate Change (IPCC) (Teixeira et al. 2013). Climate
modeling analysis has predicted that 16% of rice growing areas will be subjected to
five days of heat stress during reproductive stage (Jagadish et al. 2015). Heat stress
in rice affects the spikelet sterility during anthesis and affects the grain quality during
the grain filling stages. The spikelet fertility was reduced by 7% for every one degree
increase above 30 °C in one of the famous rice variety IR64 (Jagadish et al. 2007). Rice
is sensitive to heat stress during gametogenesis and flowering stages of the crop
growth. The cardinal temperature for heat stress in rice is >35 °C (Prasad et al. 2006).
In China, post heading heat stress has reduced rice yield by 1.5 to 9.7% during last
three decades (Shi et al. 2015). High temperature (>36 ºC) causes significant increase
in spikelet sterility and also affects the grain quality in rice. There were 8 QTLs
identified on different chromosome for heat stress tolerance using Nagina22 (N22) as
donor parent (Ishimaru et al. 2016). The phenotypic variance of the identified QTLs
varied from 11-25% for spikelet fertility during heat stress in rice. A high resolution
phenotyping mapping of QTL using RIL population has identified novel QTL with
effect up to 22% and also identified candidate genes within the QTL region
(Shanmugavadivel et al. 2017).

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5.3. Genome editing

Genome editing is a new technology widely used in the studies of functional
genomics, reverse genetics, genome engineering and targeted transgene integration
by allowing of addition, deletion or alteration of genetic material at specific locations
in the genome in an efficient and precise manner. In general, it involves the introduction
of targeted DNA double-strand breaks (DSBs) using an engineered nuclease, which
can induce site-specific changes in the genomes of cellular organisms through a
sequence-specific DNA-binding domain and a non-specific DNA cleavage domain
thereby generates desired insertions, deletions or alterations. Different genome
modifications/editing can be achieved depending on the two repair pathways: NHEJ;
non-homologous end joining and HR; homologous recombination. Insertion and
deletion are the common phenomena in NHEJ pathway which causes target gene
knockout/disruption or the production of truncated proteins whereas HR normally
relies on recombination with homologous sequences in an undamaged chromatid
leads to the introduction of precise alterations to the genome, which are specified by
the template (Chandrasegaran and Carroll 2016). In addition, genome editing
technologies allow genome modification without the introduction of foreign DNA
which would be helpful to edited crops that could be classified as non-GMO. Nuclease-
mediated editing of plants and agricultural animals may greatly decrease the time
required to generate new varieties of both species relative to traditional breeding
strategies.
5.4. CRISPR/Cas9 in rice genetic improvement
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR
associated protein-9 nuclease) is a powerful and revolutionary technology for targeted
mutagenesis in molecular biology research and genetic improvement of traits in diverse
organisms including important crops (Ma et al. 2016). Unlike the protein-guided DNA
cleavage of ZFNs and TALENs, CRISPR/Cas9 depends on small RNA for sequence-
specific cleavage in genome sequence. The system is derived from bacterial innate
immune system, the type II CRISPR/Cas system of Streptococcus pyogenes (Jinek et
al. 2012). In bacteria, single nuclease Cas9 process the foreign sequences into small
segments by cleavage and introduce them into the regularly interspaced palindromic
repeats called CRISPR array and serve as templates for CRISPR RNA (crRNA). This
crRNA then hybridizes with a trans-activating RNA (tracrRNA) and form a dual complex
and guide Cas9 protein to detect and cleave the foreign DNA. In the present system,
the dual complex of crRNA:tracrRNA, is modified into a single RNA chimera; this is
called sgRNA (single guideRNA) which recognizes 20 or 24 nt sequences matching
to target sites in the upstream of protospacer adjacent motif (PAM) (Jinek et al. 2012).
This CRISPR/Cas9 construct targets specific DNA sequence with 20–24 nucleotides
which is unique in most genomes, cleave and repair thereby inducing deletion or
insertion mutation. It is particularly useful for those traits controlled by negative
regulatory genes which can be improved simply by knockout or weakening of the
gene expression. CRISPR/Cas9 system has been successfully used as an efficient
tool for genome editing in a variety of crops (Ma et al. 2016). Identification of potential

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known genes for yield improvement along with tolerance/resistant toward abiotic
and biotic stress is pre-requisites for development of superior rice lines. The CRISPR/
Cas9 system enables precise targeting and cleavage causing random mutagenesis at
the specific predetermined sequence/locus within a large genome. CRISPR/Cas9
technology has already shown its potentiality to rapidly and precisely edit specific
plant genes of interest to achieve the desired outcomes.
The most common application of the targeted editing system in genetic
improvement is to knock out completely the functions of target genes, usually by
editing site(s) in the coding sequences (CDS) to produce null-allele mutants. The
CRISPR/Cas9 based genome editing system has many applications for functional
studies of plant genes. It has also provided a robust tool for genetic improvement of
important traits such as yield, plant architecture, abiotic and biotic stress etc. For
instance, Xie et al. (2017a; 2017b) adopted CRISPR/Cas9 system to edit SaF+ or SaM+
and OgTPR1 genes at the hybrid sterility loci, Sa and S1 in rice for overcoming hybrid
sterility in inter-subspecific and inter-specific hybrid rice breeding. This technology
has been further utilized in studying the hybrid male sterility locus Sc in rice by
reducing the tandem-repeated gene copy number in indica rice allele Sc-I to improve
male fertility in japonica-indica hybrids (Shen et al. 2017). Shimatani et al. (2017)
recently developed a fusion of CRISPR/Cas9 and activation-induced cytidine
deaminase (Target-AID) system for point mutagenesis and successfully demonstrated
editing in acetolactate synthase (ALS) enzyme that confers herbicide resistance in
rice. Zhang et al. (2017) used CRISPR/Cas9 technology to validate the molecular
function of OsFIGNL1 responsible for the male sterility in rice. In another study,
knocking-out of Broad-Spectrum Resistance 1 (BSR1) using CRISPR/Cas9 system
which encodes arice receptor-like cytoplasmic kinase showed highly susceptible to
fungal pathogens (Kanda et al. 2017). Qiu et al. (2017) also cloned and characterized
the gene heat-sensitive albino1 (hsa1) responsible for chloroplast development under
heat stress in rice and deletion mutation in this gene induced by CRISPR/Cas9 system
which was found to be heat sensitive. Nieves-Cordones et al. (2017) observed that
inactivation of the (cesium) Cs+-permeable K+ transporter OsHAK1 with the CRISPR/
Cas9 system dramatically reduced Cs+ uptake in rice. Sun et al. (2017) demonstrated
the feasibility of creating high-amylose rice through CRISPR/Cas9-mediated editing
of SBEIIb gene.
5.5. Doubled haploids production and application
National Rice Research Institute (NRRI), Cuttack initiated the work in 1997 on DH
technique to overcome the constraints associated with the indica rice hybrids: 1)
expensive seed depriving the Indian marginal farmers to utilize the seed year after
year 2) unpredictable environmental condition and a synchronised flowering.
Considerable progress of NRRI has been made as evidenced by release of two DHs
as new varieties named Satyakrishna and Phalguniin in 2008 and 2010, respectively.
In the year 2013, another attempt was made to standardize androgenic protocols in
two more indica rice hybrids i.e., CRHR32 (an elite long duration rice hybrid developed
at NRRI, Cuttack) and BS6444G (a popular rice hybrid, Bayer Seed Pvt. Ltd.) for

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generation of DHs (Rout et al. 2016; Naik

et al. 2017) (Fig. 2). Further, anther culture
was used for development of mapping
population from Savitri (a high yielding
indica rice variety) x Pokkali (a salt
tolerant indica rice genotype) for
identification of salt tolerant QTL/gene.
However, the production of albinos (60-
100%) in all the cultures proved to be
detrimental for optimization of
androgenic response. Therefore, NRRI
Fig. 2. Androgenesis in development of DHs attempted to develop a protocol for
via callus culture from a rice hybrid, suppression of albinism which is also a
BS6444G (A) Mid uninucleate stage of frustrating feature in whole world. This
microspore, (B) Calli induction from pollens led to standardization of 100% albino free
of anthers, (C) Initiation of green shoot buds
shoot regeneration method in indica rice;
from calli, (D) Green shoot regeneration (E)
Well developed green shoots, (F) Rooting in patent filed 1355/KOL/2015 entitled
microshoots, (G) Anther derived plants “Method for albino free shoot
grown in net house, (H) Ploidy assessment regeneration in rice through anther
of anther derived plants, (I) DHs in Field culture”. Subsequently, the improved
protocol could generate 150, 200, 117, 73
and 30 DHs from CRHR32, BS6444G, Savitri x Pokkali, B x B and R x R respectively;
surprisingly, no haploids were observed in BS6444G. Further, six promising DH lines
each derived from CRHR32 and BS6444G showed at par yield with parent hybrid
along with acceptable grain quality. Two promising DH lines of BS6444G showing at
par yield over donor were found to be aromatic confirmed by PCR and sequencing of
badh2. Moreover, four DH lines derived from rice hybrid, CRHR32, were found
containing high protein (11.59 - 12.11%) in brown rice. Furthermore, iso-cytorestorer
lines were developed through test cross of the 13 DHs (BS6444G) carrying positive
Rf4 genes with the CMS, with an average of 500-600 grains per panicle.
A systematic study with 117 DHs derived from F1s of Savitri (popular HY rice
variety) and Pokkali (salinity tolerant) could identify 4 candidate genes such as
LOC_Os01g09550 (no apical meristem protein), LOC_Os01g09560 (mitochondrial
processing peptidase subunit alpha), LOC_Os12g06560 (putative protein) and
LOC_Os12g06570 (cyclic nucleotide-gated ion channel) for salinity tolerance at
germination stage. In 2015, an efficient androgenic protocol was developed for another
popular quality indica rice hybrid, 27P63 (M/S Pioneer, Hyderabad) and generated
315 green plants. After proper examination of ploidy status based on morphology, 246
plants were found to be diploids from which SSR markers identified a single
heterozygote plant; this was also confirmed in the A1 generation. Then 245 DHs were
advanced for further selection in identification of superior lines. A total of 170 DHs
were selected to be promising based on agronomic traits in both the seasons, 2016-17
(A3 generation). Subsequently, application of the developed androgenic protocol
could generate DHs from F1s of Chakhao x IR20 which are being evaluated in field.

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5.6. Field screening of genotypes for heat tolerance
Staggered sowing based screening for thermotolerance were performed for seven
hundred genotypes and three genotypes (AC39843, AC39834 and AC39969) were
found highly tolerant to heat stress with SES score 1 with more than 80% spikelet
fertility; these genotypes showed at par /better yield than the check, Annapurna and
N22. Besides, genotypes showing moderate degree of tolerance such as AC39975,
AC11069, AC10925 and AC39935 were identified which showed 75% spikelet fertility
under summer condition. Rice SNP seek database was used to identify the single
nucleotide polymorphism present in the five rice OsHsfA2s (A2a, A2b, A2c, A2d, and
A2d). The screening of filtered SNPs for these Hsfs identified on an average 11 SNPs
for the five HsfA2 genes. Among them, HsfA2b was found to be highly conserved in
rice with only two SNPs and HsfA2c showed maximum number of SNPs i.e. 16. But
most of the SNPs were present in UTR or upstream or downstream region of these
genes with only 1 or 2 SNPs resulted in non-synonymous substitution in the coding
sequences of the rice HsfA2s. The position of non-synonymous substitution among
the rice varieties were analyzed for comparison of divergence analysis between HsfA2
of different plants and the variation in rice. It showed, two non-synonymous
substitution amino acids identified through divergence studies also showed
divergence in different varieties of rice, i.e. arginine to isoleucine substitution in
HsfA2d and arginine to histidine substitution in HsfA2e. The allele frequency of all
the non-synonymous substitution were analyzed through SNP seek database to find
out fixation of any alleles in any specific types of rice; it showed the frequency of all
the non-synonymous substitution in OsHsfA2s was similar in all types of rice in
comparison with reference allele except for the aspartate to glutamate substitution in
HsfA2a. The non-reference allele frequency of this substitution were about 99.49% in
aus type rice lines and 94.44% in aromatic collections of rice whereas in all other types
of rice, the reference allele were found in higher frequency or at least equal frequency
with non-reference allele, denoting there was no pattern involved for other non-
synonymous substitutions. Interestingly, all the dicots HsfsA2 has glutamate as
invariant at the respective position of the HsfA2. CRISPR/Cas9 work has been initiated
at NRRI, and construct for editing of yield related genes was ready for transfer to
some popular rice varieties.

6. KNOWLEDGE GAPS
 The recalcitrant nature of indica rice requires optimization of anther culture method
which is very much important to achieve the potential yield of androgenesis
technology in indica rice lines. Even though, attempt were made by Rout et al.
(2016) and Naik et al. (2017) in these issues, additional novel attempts for media
manipulation has to be addressed to increase the callusing potential or somatic
embryogenesis.
 The identification of genomic regions that contribute to promising yield in rice
from heterotic F1 hybrids has to be addressed by analyzing the genetic structure

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of DHs. Recent studies with Arabidopsis and maize (Wang et al. 2015) suggest
that heterosis could be fixed by carefully combining genomic regions from the
parents that contribute to better performance.
 The genes and pathways involved during pollen development in rice and
characterization of heat stress responsive genes during anthesis and pollination
would significantly increase the spikelet fertility during heat stress in rice.
Additionally, strategies for robust phenotyping need to be developed for screening
of large sets of accessions for heat stress tolerance.
 The efficiency of genetic transformation is very low in indica rice for which efficient
transformation system in rice needs to be developed for successful generation of
several transgenic rice plants.
 Though CRISPR/Cas9 is considered as the highly useful tool for genome editing,
single base pair editing for altering one specific amino acids of a protein is very
difficult for which genome editing for single base pair alterations needs to be
standardized.

7. WAY FORWARD
There is a need to develop a novel media composition including plant growth
regulators and histoneacetylase inhibitors to increase the callusing potential of the
anthers from indica rice. Simultaneously, direct somatic embryogenesis from
microspores needs to be focused as this method is considered as cost effective
among all the pathways in tissue culture. Moreover, the mechanism of spontaneous
chromosome doubling in androgenesis requires immediate attention. Additionally,
the conceptual understanding of superior yield of DHs is still not clear. Thus, the
scientific basis of superior yield of DHs needs to be comprehensively studied through
generation of large number of DHs (~200 DHs from each hybrid). Further, high
throughput genotyping and validation of identified genomic loci/superior alleles has
to be evaluated in several genetic backgrounds and also through transgenic
approaches. On the other hand, a highly robust genotype independent genetic
transformation system for mega rice varieties has to be developed through combination
of several factors in indica rice. Though the variability explained through mapping
studies on heat stress tolerance is less than 30%, comprehensive phenotyping
strategies necessitate to be employed for the identification of the complete genetic
variation in tolerant cultivars. Simultaneously, heterologous expression of heat stress
responsive genes requires to be worked out for enhancing the field tolerance to heat
stress in rice. The field evaluation of rice transgenic lines should be promoted in
institutes to understand the effect of transgenic rice in field condition. Specifically,
the economic impact of cultivation of transgenic crops needs to be studied thoroughly
to assess the potential of transgenic rice cultivation. Furthermore, it is required to
standardize an efficient delivery system (Agrobacterium, biolistics, protoplast transfer)
for CRISPR/Cas9 constructs to improve the efficiency of genetic modifications.

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Profitability and Climate Resilience

Development of Genomic Resources for Rice

Improvement

L Behera, C Parameswaran, A Anandan, P Sanghamitra,

SK Pradhan, M Jena, N Umakanta, SK Dash, P Swain, RK Sahu,
A Kumar, K Chattopdhyaya, J Meher, HN Subudhi, GP Pandi and
Devenna

1. INTRODUCTION
Rice has rich genetic diversity in the form of thousands of landraces, elite breeding
lines, high yielding varieties and 21 wild species. These differ tremendously in the
levels of grain yield, quality of grains, input use efficiency, and tolerance to biotic and
abiotic stresses with immense variation. Hence, rice consist of a rich source of
naturally occurring alleles for the improvement of several traits including yield. The
yield levels of rice varieties are greatly influenced by the environmental conditions
and field management practices. There are remarkable interactions between genotypes
and environments in such a way that varieties are adapted to specific environmental
conditions. It is increasingly being recognized that exploitation of gene pools of rice
germplasm is the fastest and acceptable approach to achieve the twin goals of high
productivity and adaptability (Gur and Zamir 2004; Kovach and McCouch 2008).
Development of high yielding varieties is possible by accumulation of beneficial and
superior alleles from germplasm. More than 120,000 accessions of rice germplasm
comprising traditional varieties, landraces, genetic stocks, breeding lines and wild
relatives are preserved in gene banks at different places of India and other countries.
Therefore, it is important to identify genes/QTLs for yield, quality traits, low input
use efficiency, tolerance to biotic and abiotic stresses, etc from rice germplasm, and to
introgress these into high yielding popular rice varieties through marker-assited
selection (MAS). This would provide impetus to marker-assisted breeding on one
hand and enable gene discovery on the other for sustainable agriculture, and improving
rice yield potential (Ashikari and Matsuoka 2006). Realizing the immense potential of
GENOMICS, concerted efforts are essential for yield improvement under changing
climate conditions.
Sustained efforts have made possible to more than double the rice production
since the green revolution in the 1960s. There has been a gradual decline in the
annual growth rate of global rice production, while the population in rice-consuming
countries is increasing at a rate of 1.8 percent per year. Increasing rice yield to ensure
food security is a major challenge. Rice production is no longer keeping in pace with
population growth during last decade because of shrinking cultivable land area,
water scarcity, depletion of soil fertility, global warming (climate change), evolution of
new biotypes, pathotypes, etc. Hence, it is necessary to use innovative tools to
assist conventional methods in order to improve production and feed growing
population. The availability of the complete genome sequence of rice and the

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developments in the field of genomics has opened the door for speeding-up breeding
processes for increasing yields and minimizing production risks. High throughput
genomics is a promising approach in a holistic manner for mapping of genes/QTLs
associated with target traits, gene prospecting and allele mining for useful traits, and
re-sequencing of rice germplasm for discovery of SNPs, InDels, and precision breeding
through MAS approach.
The objectives of the chapter are a) identification of genes/QTLs associated with
resistance to brown plant hopper (BPH), pigmentation and antioxidants; b) association
mapping to identify genes/QTLs for seedling vigor and tolerance to drought stress;
c) gene prospecting and allele mining for tolerance to heat stress; and d) whole
genome re-sequencing of donors and elite rice cultivars.

2. IDENTIFICATION OF GENES/QTLS ASSOCIATED WITH

RESISTANCE TO BROWN PLANT HOPPER,
PIGMENTATION AND ANTIOXIDANTS
2.1. Brown plant hopper
Brown planthopper (BPH; Nilaparvata lugens Stal) is one of the most destructive
insect pests in rice-growing areas of Asia and south-east Asia. Both adults and
nymphs of the insect feed on rice sheaths by sucking sap from the phloem. All the
growth stages of rice plant in the field are vulnerable to BPH. Mild infestation leads to
yellowing of leaves, reduction in plant height, growth, vigor, number of productive
tillers and grain filling. Heavy infestation causes complete drying and death of plants,
a condition known as ‘‘hopperburn’’ (Sogawa 1982; Watanabe and Kitagawa 2000).
Brown planthopper also transmits rice tungro, grassy stunt and rugged stunt viruses
and causes indirect damage to rice plant (Ling et al. 1978; Hibino 1996; Rivera et al.
1996). The frequency of outbreaks and severity of damage have increased since
1990s because of year-round cultivation of semi-dwarf, photo-period insensitive,
genetically homogeneous varieties with greater use of fertilizers and insecticides.
Use of resistant varieties is one of the best options to reduce the BPH damage.
Systematic breeding programs have led to the identification of several donors, which
have been used to develop BPH resistant varieties and to identify genes/QTLs
associated with BPH resistance. Brown planthopper resistance is a complex trait
governed by both major and minor genes. Thirty-two major BPH resistance genes
have been identified using classical genetics and molecular approaches (Jena and
Kim 2010; Fujita et al. 2013; Wu et al. 2014; Wang et al. 2015a; Hu et al. 2016; Prahalada
et al. 2017). These genes have been mapped to six rice chromosomes 2, 3, 4, 6, 11 and
12. Eighteen genes, Bph1, bph2, Bph3, Bph6, Bph9, bph12, Bph14, Bph15, Bph17,
Bph18, bph19, Bph 25, Bph26, Bph27, Bph28, bph29, Bph30 and Bph32 have been
fine-mapped. In addition to major genes, many QTLs associated with BPH resistance
have been identified using different mapping populations and screening parameters
(Jena et al. 2010; Fujita et al. 2013; Deen et al. 2017; Mohanty et al. 2017). The major
genes Bph1, bph2, Bph3, Bph14, Bph15, Bph18 and QTLs QBph3 and QBph4
have been used for introgression into elite rice cultivars through marker-assisted

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breeding approach (Sharma et al. 2004; Jairin et al. 2009; Suh et al. 2011; Hu et al 2012;
2013; 2015; 2016). Xiao et al. (2016) individually transferred 13 genes/QTLs, Bph14,
QBph3, QBph4, Bph17, Bph15, Bph20, Bph24, Bph6, Bph3, Bph9, Bph10, Bph18
and Bph21 into cultivar 93-11 by marker-assisted backcross breeding (MABB). The
NILs were evaluated against BPH. All genes reduced BPH growth, development, and
showed antibiotic responses in seedlings. Only seven resistance genes, namely,
Bph3, Bph9, Bph14, Bph18, Bph26, bph29 and Bph32 have been cloned (Du et al.
2009; Tamura et al. 2014; Liu et al. 2015; Wang et al. 2015a; Ji et al. 2016; Ren et al. 2016;
Zhao et al. 2016b) ( Table 1).
Table 1. Examples of cloning of BPH resistance genes in rice.
S. No. Gene Protein product Function References
1 Bph3 Plasma membrane- Play a critical role in priming the Liu et al. 2015
localized lectin pattern-triggered immunity
receptor kinases. response to BPH infestation by
perceiving herbivore-associated
molecular patterns (HAMPs) or
damage-associated molecular
patterns (DAMP),or mediating
the downstream signaling events.
2 Bph9 Nucleotide-binding Activates salicylic acid and Zhao et al. 2016b
and leucine-rich jasmonic acid-signaling pathways
repeat (NLR) and confers both antixenosis and
containing protein. antibiosis to BPH.
3 Bph14 Coiled-coil Mediates resistance mechanism Du et al. 2009
nucleotide-binding through activation of salicylic
and leucine-rich acid(SA) signaling pathway and
repeat (CC-NBS- induces callose deposition in
LRR) protein. phloem tissue that inhibits BPH
feeding on the host plant.
4 Bph18 Coiled-coil Proteins are widely localized to Ji et al. 2016
nucleotide-binding the endo-membranes in a cell,
and leucine-rich including the endoplasmic
repeat (CC-NBS- reticulum, Golgi apparatus, trans-
LRR) protein. Golgi network, prevacuolar compartments
and recognize the BPH invasion at
endo-membranes in phloem cells.
5 Bph26 Coiled-coil Mediate sucking inhibition in the
nucleotide-binding phloemsieve element. Tamura et al.
and leucine-rich 2014
repeat (CC-NBS-
LRR) protein.
6 bph29 B3 DNA-binding Confers BPH resistance through Wang et al. 2015a
domain protein. activation of SA pathway and
suppression of jasmonic acid/
ethylene-dependent pathway.
7 Bph32 A short consensus The protein is localized in the Ren et al. 2016
repeat (SCR) plasma membrane of the cell and
domain protein. confers an antibiosis resistance
to BPH.

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 The primary sources of resistance to BPH have been reported from different
centers in India. Jena et al. (2002) identified OPA16938 RAPD marker linked to BPH
resistance present in IR54741- 3-21-22, an introgression line from Oryza officinalis.
Soundararajan et al. (2004) mapped six QTLs associated with seedling resistance,
antibiosis and tolerance on chromosomes 1, 2, 6, and 7 for BPH resistance using a DH
population (IR64 × Azucena). Genetics of BPH resistance revealed the presence of
two major genes, Bph3 and Bph6 in the donors Velluthacheera, T1471, T1426 and
T1432; Bph6 gene in ARC14529, ARC14771 and IR72; bph4 gene in ARC5984,
Manoharsali and Sonasali (Padmavathi et al. 2005). Deen et al. (2010) identified 3 BPH
resistance genes i.e., Bph22(t), Bph23(t) and bph24(t) from O. gaberrima, O. minuta
and O. rufipogon, respectively. Kumari et al. (2010) reported that two markers, RM3180
and RM2453 on chromosome 3 were linked with BPH resistance using a RIL population
derived between IR50 and Rathu Heenati. Deen et al. (2017) identified five major QTLs
associated with BPH resistance, qBphDs6 for damage score, qBphNp(48h)-1 and
qBphNp(72h)-12 for nymphal preference, and qBphDw(30)-3 and qBphDw(30)-8
for days to wilt contributing phenotype variance of 24.23, 8.69, 7.66, 4.55 and 10.48%,
respectively.
Behera et al. (2012)
assessed the genetic
relationship among 19 rice
cultivars differing in
resistance to BPH using 42
SSR markers. Genetic
similarities among cultivars
varied from 0.38 to 0.897 with
an average of 0.604. Seven
unique alleles were identified.
Jena et al. (2015) genotyped 48
rice cultivars including 39 Fig. 1. Two QTLs qBph4.3 and qBph4.4 on linkage
landraces using 22 gene- group8 (Chromosome 4) for BPH resistance were
linked markers of BPH identified in the resistant rice cultivar Salkathi. Left
resistance. Genetic diversity side of graph shows SSR markers and their positions in
analysis categorized all the cM. LG8 represents short arm of chromosome 4. Right
genotypes into 4 major side of graph shows two peaks corresponding QTLs
clusters with the 40% level of qBph4.3 and qBph4.4 with LOD score of 34.2 and
4.61, respectively. The qBph4.3 is a novel QTL.
genetic similarity. Mohanty et
Source: Mohanty et al. (2017).
al. (2017) identified two QTLs,
qBph4.3 and qBph4.4 linked to BPH resistance in resistant cultivar Salkathi (Fig. 1).
The qBph4.3 seems to be a novel QTL associated with BPH resistance. Brown
planthopper resistance in Sakathi has been successfully transferred into two elite rice
cultivars, Pusa 44 and Samba Mahsuri. The promising resistant breeding lines
developed from these varieties have been validated for the presence of these QTLs
using linked markers. Further, work is in progress for fine mapping and transfer of
these QTLs into elite susceptible cultivars, Pooja and Swarna.

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2.2. Anthocyanin and antioxidants

Colored rice genotypes (red, brown, purple, black) are the rich source of dietary
fiber, vitamins, phytic acids and phytochemicals such as phenolics (á-tocopherols,
tocotrienols and ã-oryzanol) and flavonoids (anthocyanins, proanthocyanidins).
These compounds are good source of natural antioxidants and grain color, which
help in decreasing the toxic compounds, oxidative stress and reduce the risk of
cardiovascular disease, type-2 diabetes, and also prevention of some cancers (Hudson
et al. 2000; Cicero and Gaddi 2001; Ling et al. 2001; Hu et al. 2003; Xia et al. 2003; Liu
2007; Yawadio et al. 2007; Arab et al. 2011; Walter et al. 2013). The colored genotypes
contain higher amounts of phytochemicals than non-pigmented genotypes (Goffman
and Bergman 2004; Shen et al. 2009). Anthocyanins and proanthocyanidins are the
primary pigments in colored rice. Among colored rice, black rice genotypes exhibit the
highest antioxidant activities followed by purple, red, and brown rice. The colour of
purple and black grains is due to the presence of anthocyanins (Reddy et al. 1995).
The phenolic compounds are mainly associated with the pericarp colour. The darker
the pericarp, higher the amount of polyphenols (Tian et al. 2004; Zhou et al. 2004;
Yawadio et al. 2007). The insoluble compounds appear to constitute the major fraction
of phenolic acids and proanthocyanidins in rice, but not flavonoids and anthocyanins.
Hence, rice should be preferentially consumed in the form of bran or as whole grain to
maximize the intake of antioxidant compounds. Phytic acid is vital for seed development
and higher seedling vigor. It is often considered as an anti-nutritional substance but
has the positive nutritional role as an antioxidant, anti-cancer agent, and lowering
heart and coronary diseases in humans (Bohn et al. 2008; Gemede 2014). The japonica
rice varieties are found to be richer in antioxidant compounds compared with indica
rice varieties. Fasahat et al. (2012) reported higher nutritional and antioxidant properties
of whole grains of O. rufipogon.
Two loci, Rc and Rd are involved in proanthocyanidin synthesis in rice pericarp.
When present together, these two loci produce red seed color. Rc produces brown
seeds in the absence of Rd, whereas Rd alone has no phenotype. Both genes have
been cloned and sequenced (Sweeney et al. 2006; Furukawa et al. 2007). Cyanidin-3-
glucoside and peonidin-3-glucoside are the two main pigments deposited in grain
pericarp of black rice (Abdel-Aal et al. 2006). Two loci, Pb (Prp-b) and Pp (Prp-a),
located on chromosome 4 and 1, respectively are required for the pericarp pigmentation
with anthocyanins of black rice (Yoshimura et al. 1997). Wang and Shu (2007) mapped
Pb gene on rice chromosome 4 responsible for purple color. Tan et al. (2001) identified
three, two and four QTLs for the color parameters of lightness (L), redness (a) and
yellowness (b), respectively. Jin et al. (2009) reported several QTLs responsible for
brown rice color, total phenolic and flavonoid contents in rice grain using a doubled
haploid population. Shao et al. (2011) identified 41 markers significantly associated
with QTLs for grain color and nutritional quality traits using 416 rice accessions
including red and black rice. Their study indicated that Ra (Prp-b for purple pericarp)
and Rc (brown pericarp and seed coat) genes control rice grain color and nutritional
quality traits. Maeda et al. (2014) identified three loci, Kala1, Kala3 and Kala4 on

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chromosomes 1, 3 and 4, respectively, which are associated with black pigmentation.
They introduced these loci into Koshihikari, a leading variety of Japan from black
rice, Hong Xie Nuo. Xu et al. (2016) identified loci for phenolic related traits and one
locus for ferulic acid in 32 red and 88 white pericarp accessions of rice using SNP
markers. Xu et al. (2017) identified 21 additive QTLs for anthocyanins (ANC) and
proanthcyanidins (PAC) using RIL population developed from red rice Hong Xiang1
(HX1) and white rice Song 98-131 (S98-131). Two new QTLs, qANC3 and qPAC12-4
were detected in several environments and explained significant phenotype variance.
The anthocyanin and gamma-oryzanol content of 160 pigmented rice genotypes
was evaluated by Sanghamitra et al. (2017). The purple grain type genotypes, namely,
Kalobhat, Mamihunger, Chakhao, Manipuriblack and Kalabiroin were identified with
rich source of anthocyanin content whereas Mamihunger, Chakhao and Kalobhat
were observed with rich source of gamma-oryzanol content compared to red and
brown grain type. Fate of anthocyanin and gamma-oryzanol content were also assessed
after processing, cooking and in different end user products of three pigmented rice
genotypes such as Chakhao, Mamihunger and Mornodoiga. The highest reduction
of anthocyanin and gamm-aoryzanol content (97% and 88%, respectively) was
observed in parboiled rice, whereas only 2-3% reduction in anthocynin and 70%
reduction in gamma-oryzanol content was observed in end use products like in popped
and puffed rice. Further, work is continuing to identify QTLs associated with
anthocyanin and antioxidants using RIL population developed from colored and
non-colored rice genotypes.

3. ASSOCIATION MAPPING TO IDENTIFY GENES/QTLS

FOR SEEDLING VIGOR AND TOLERANCE TO DROUGHT
STRESS
Association mapping is a powerful and promising approach for identification and
mapping of genes/QTLs associated with phenotypic traits in living organisms (Hall
et al. 2010; Stich and Melchinger 2010). This approach is increasingly being used in
plant species, e.g. maize, rice, barley, wheat, sorghum, sugarcane, sugar beet,
Arabidopsis, potato, soybean, grape, forest tree species and forage grasses
(Abdurakhmonov and Abdukarimov 2008). In association mapping approach, only
polymorphisms with extremely tight linkage to a locus that causes the phenotype
effect are likely to be significantly associated with the trait in a randomly mating
population, thus providing a much finer resolution than bi-parental mapping.
Conventional linkage analysis requires mapping populations (derived from a bi-
parental cross) that are difficult to develop and is time consuming. Association mapping
exploit the linkage disequilibrium (LD) already present in the natural population of
interest, allows a much higher resolution, permitting survey of large number of alleles
per locus, and has great potential for future trait improvement and germplasm security.
Several researchers have used association mapping approach for identification of
QTLs associated with different traits in rice, viz., grain yield and related traits (Agrama
et al. 2007; Fei-fei et al. 2016; Zhang et al. 2017), agronomic traits (Huang et al. 2010;

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Zhao et al. 2011; Zhou et al. 2012; Lu et al. 2015; Yano et al. 2016), stigma and spikelet
characteristics (Yan et al. 2009), flowering time and grain quality (Huang et al. 2012),
panicle architecture and spikelet’s/ panicle (Rebolledo et al. 2016), chlorophyll content
(Wang et al. 2015b), mesocotyl elongation (Wu et al. 2015), harvest index (Li et al.
2012a), leaf traits (Yang et al. 2015), seedling vigor (Anandan et al. 2016), amylose
contents (Jin et al. 2010), mineral element contents in whole grain (Huang et al. 2015),
aluminum tolerance (Famoso et al. 2011), salinity tolerance (Kumar et al. 2015), cold
tolerance (Pan et al. 2015; Pandit et al. 2017) and high temperature tolerance (Pradhan
et al. 2016).
3.1. Seedling vigor
The weeds are the major bottleneck and cause yield reduction up to 48%, 53% and
74% in transplanted, direct-seeded flooded and aerobic rice, respectively. Further,
manual weeding or spraying of herbicides incur additional cost of expenditure in rice
cultivation. However, application of herbicides to control weeds have been proven to
be effective, but in many cases, the intensive use may cause hazardous effect on
environment and possibility of development of herbicide tolerance in weeds. On the
other hand, the use of herbicides during monsoon time affects their efficiency.
Therefore, the use of weed-competitive varieties to suppress weeds might substantially
reduce herbicide use and labor cost. The rapid uniform germination and accumulation
of biomass during initial phase of seedling establishment is an essential phenotypic
trait considered as early seedling vigor for direct seeded situation in rice irrespective
of environment (Mahender et al. 2015). Early seedling vigor (ESV) trait has been
exploited in rainfed upland cultivar as those varieties are preferred over the others as
they have weed smothering effect. The most of high yielding rice varieties for irrigated
ecosystem are not suitable for dry direct seeded conditions as they are semi-dwarf in
stature with reduced seedling vigor (Mahender et al. 2015; Anandan et al. 2016).
Therefore, breeding rice varieties for direct seeded system combining high yield,
early vigor and strong weed competitiveness is very much necessary. Several QTLs
for seedling vigor and related traits have been reported in rice using bi-parental
mapping populations and well reviewed by Mahender et al. (2015). Recently,
association mapping strategies have been employed to identify QTLs for seedling
vigor using natural populations of rice (Dang et al. 2014; Wu et al. 2015; Anandan et
al. 2016; Lu et al. 2016). Dang et al. (2014) identified 18 SSR markers for three traits
such as root length, shoot length and shoot dry weight associated with seed vigor
using 540 rice cultivars and 262 microsatellite markers. Cheng et al. (2015) observed
significant natural variation of seed germination and seedling growth among 276
accessions under normal, drought and salt conditions. A total of 12, 14 and 9 simple
sequence repeat (SSR) markers associated with three traits were identified under
normal, drought and salt conditions, respectively using association mapping approach.
Wu et al. (2015) identified 13 loci associated with mesocotyl lengths of seedlings
grown in water in darkness and three loci associated mesocotyl lengths grown in 5 cm
sand culture using SNP array (Rice SNP50). Alpha-amylase precursor and ethylene-
insensitive3 are the genes found to be there in coding region. On the other hand, a
gene OsGA20ox1 was found to be associated with gibberellin (GA) biosynthesis

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from the fine mapping of major QTL qPHS3-2, which accounts for 26.2% phenotypic
variance (Abe et al. 2012). These promising QTLs and candidate genes associated
with seedling vigor would be useful for improving seedling vigour in high yielding
popular rice varieties by introgressing them through marker-assisted breeding
technique. Nagavarapu et al. (2017) validated the reported QTLs for seedling vigor in
a set of 47 indica cultivars. Six out of eight QTLs, qGR-1, qGP-6, qFV-3-2, qFV5-2
and qFV-10 were detected in genotypes showed high seedling vigor. The genotypes
Dinesh, Pooja and Sabita showed the presence of multiple QTLs indicating that these
genotypes have inherent capacity for early emergence with high seedling vigor.
Anandan et al. (2016) identified 16 SSR markers which were significantly associated
with early seedling vigor traits in 96 rice genotypes using association approach.
These genotypes were selected from 629 rice accessions based on their morphological
and physiological responses grown in the field under direct seeded aerobic situation.
Further, they have reported the pleiotropic effect of marker RM341 on chromosome 2
for shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Pandit et al. (2017)
conducted association mapping of cold tolerance using a panel of 66 rice genotypes,
and 58 SSR markers and 2 direct linked markers. These genotypes were selected
based on the screening of 304 indica rice germplasm to seedling stage chilling
tolerance. They identified nineteen SSR markers significantly associated with chilling
stress tolerance at 8 0C to 4 0C for 7–21 days duration. The QTLs identified to cold
tolerance, qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1,
qCTS12.1, qCTS-1b, and qCTB2 would be useful in molecular breeding program for
development of strongly chilling tolerant varieties.
3.2. Drought tolerance
There are several successful examples of identification of QTLs/genes for drought
tolerance using bi-parental mapping populations, but a few examples are available
using GWAS approach in rice (Courtois et al. 2013; Lou et al. 2015; Al-Shugeairy et al.
2015; Muthukumar et al. 2015; Ma et al. 2016; Phung et al. 2016; Swamy et al. 2017).
Courtois et al. (2013) identified 19 associations for deep root mass and the number of
deep roots in 168 traditional and improved japonica accessions using GWAS approach.
Al-Shugeairy et al. (2015) genotyped 371 cultivars of the Rice Diversity Panel using
Affymetrix SNP array containing 44,100 SNPs and identified one significant association
on chromosome 2 for drought recovery. Lou et al. (2015) performed genome-wide
association study and identified six QTLs linked to deep rooting for drought avoidance
in 180 recombinant inbred lines and an association mapping population containing
237 rice varieties using 10,19,883 SNPs. Phung et al. (2016) identified two associations
for root thickness and crown root number by genotyping 180 rice accessions of
Vietnam with 22,000 single-nucleotide polymorphism. Ma et al. (2016) identified 18, 5,
and 6 loci associated with plant height, grain yield per plant, and drought resistant
coefficient, respectively in 270 rice landraces and cultivars under contrasting moisture
conditions using GWAS approach.
Few association analysis studies have been reported in rice in India. Sing et al.
(2017) identified several QTL for early vigor and 8 related traits using 194 SNP markers

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and BILs derived from cross between Swarna and Moroberekan. Six genomic regions
containing QTLs for seedling vigor and related traits were identified. The QTLs located
in two QTL hotspot regions on chromosome 3 and 5 were expressed consistently in
field as well as glasshouse conditions. The majority of QTLs were clustered on
chromosome 3 (qEV3.1, qEUE3.1, qSHL3.1, qSL3.1, qSFW3.1, qTFW3.1, qRDW3.1) and
chromosome 5 (qEV5.1, qEUE5.1, qSHL5.1, qSL5.1, qSFW5.1, qSDW5.1, qTDW5.1).
Muthukumar et al. (2015) studied marker–trait associations using 1168 SSR markers
and 911,153 SNPs in 17 diverse rice lines from different geographical regions and
hydro-logical habitats. They identified 23 consistent associations with drought
tolerance traits. Swamy et al. (2017) genotyped 75 rice accessions with 119 highly
polymorphic SSR markers and identified 80 marker-trait associations for grain yield
(GY), plant height (PH) and days to flowering (DTF). Seven associations were identified
for GY under drought stress. Most of these associations identified were on
chromosomes 2, 5, 10, 11 and 12 and their phenotypic variance varied from 5 to 19%.
Massive screening work has been carried out to identify rice cultivars tolerant to
drought stress at vegetative stage at ICAR-National Rice Reseach Institute, Cuttack.
Screening of about 10,000 rice cultivars led to the identification of more than 250
tolerant genotypes at vegetative stage drought stress. Further, 384 genotypes
including 100 tolerant cultivars at vegetative stage drought stress were evaluated
under reproductive stage drought stress. An association mapping panel comprising
of 285 genotypes was developed based on the grain yield under reproductive stage
drought stress. Precise phenotyping of this association mapping panel genotypes
was carried out during Kharif 2016 and Rabi 2017. Further, work is in progress for
genotyping of association mapping panel by GBS approach, and to identify QTLs for
grain yield and related traits under reproductive stage drought stress. Two RIL
mapping populations have been developed from the tolerant cultivars, Sahabhagidhan
and Kalakeri, and susceptible cultivar IR20. The identification of QTLs under
reproductive stage drought stress is in progress.

4. GENE PROSPECTING AND ALLELE MINING FOR

TOLERANCE TO HEAT STRESS
Allele mining is the identification of nucleotide polymorphisms in the sequences
of interest genes to understand the diversity, evolutionary significance, effect on the
protein sequence and its functional impact on the organisms. This approach can be
effectively used for discovery of superior alleles through mining the gene of interest
from diverse genetic resources and development of allele-specific markers for use in
the marker-assisted selection. Next generation sequencing technologies has provided
enormous data of sequences of rice varieties. The sequences can be searched for
identification of homologous genes and its sequence variation. There are various
methods to identify the novel alleles of genomic regions. These include, amplification
of targeted region and sequencing through Sanger’s method of sequencing, TILLING/
EcoTILLING approaches, whole genome re-sequencing approaches, etc. All the novel
variants identified might not cause functional change in the organisms because most
of them would be occurring in the non-coding regions of the gene or could be

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synonymous substitutions. Thus, allele mining of genes within the coding and
promoter region could provide important information about the novel alleles of genes
in rice. Several genes have been identified related to grain yield, morphological and
quality traits, and tolerance to biotic and abiotic stresses. The allele mining studies
have been reported for a number of genes in rice (Table 2). So far, only one gene
Thermotolerant 1 has been reported to have novel allele conferring increased tolerance
to heat stress in rice. Thus, there is need to identify novel alleles for heat stress
tolerance in rice.

Table 2. Examples of allele mining of major genes in rice.

Novel alleles/ Efficient
S. No. Gene/QTL haplotype Source Phenotypic effect References
1 PsTol1 H17 O. rufipogan Increased shoot and Neelam et al.
root length. 2017
2 HKT1:5 7 major and 3 Aromatic lines Higher Na+ Platten et al.
minor alleles exclusion. 2013
3 Sub1A INDEL Meghi Stronger post Goswami et al.
submergence 2017
recovery.
4 TT1 Non-synony- Oryza Increased spikelet Li et al. 2015
mous glabberima fertility.
substitution
5 DREB1A, Alleles in - No association with Challam et al.
DREB1B 5' UTR cold tolerance. 2015
6 Pi54 9 new alleles Group of Varied patterns Vasudevan et al.
genotypes of resistance. 2015
7 Pi9 5 haplotypes Landraces Not performed. Imam et al. 2016
8 Pid3 6 haplotypes Indica Similar resistance Lv et al. 2017
spectrum.
9 Xa21, 2 alleles O. nivara Effective resistance Bimolata et al.
Xa26, xa5 source. 2015
10 Xa13 18 haplotypes - Not performed. Yu et al. 2016
11 Ghd7, 10-21 Combination A combination of Zhang et al.
Ghd8, Hd1 haplotypes of indica, strong, weak and 2015
japonica and non functional effect
Oryza on heading date, SSF
rufipogan for tropical condition.
alleles are
photosensitive.
12 DEP1 7 haplotypes Japonica Hap2 increased Zhao et al.
varieties. number of primary 2016a
and secondary
branches.
13 Gn1a, 2-5 haplotypes Habataki, Enhanced yield. Kim et al. 2016
OsSPL14, ST12, ST6,
SCM2, Aikawa1, YP9,
Ghd7,DEP1, Osmancik-97
SPIKE,GS5, and Kasalath.
TGW6

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Heat stress is one of the important abiotic stresses which cause spikelet sterility
up to 60% in rice during the flowering stage. Hence, it is considered as one of the
major threat to crop production (Teixeira et al. 2013). Rice is sensitive to heat stress
during gametogenesis and flowering stages. The cardinal temperature for heat stress
in rice is >35 °C (Prasad et al. 2006). It is reported that there would be negative impact
on rice yield due to warmer regime in future (Welch et al. 2010). Spikelet fertility under
heat stress is considered as the major trait for evaluating the response of rice genotypes
to heat stress. Nagina22 was identified as highly tolerant cultivar for heat stress
(Prasad et al. 2006; Pradhan et al. 2016). Some of the Oryza glabberima accessions
such as CG14 was also found to be tolerant because of early anthesis and pollination
during dawn compared to indica cultivars (Jagadish et al. 2008).
Many QTLs have been identified for heat stress tolerance in rice using F2, BIL and
RIL populations (Cao et al. 2003; Chang-Lan et al. 2005; Chen et al. 2008; Zhang et al.
2008; 2009; Jagadish et al. 2010; Xiao et al. 2011a; 2011b; Cheng et al. 2012; Ye et al.
2012; 2015; Buu et al. 2014; Tazib et al. 2015; Zhao et al. 2016c). These mapping
populations have been phenotyped at the time of heading in controlled environment
conditions or under high temperature condition by late planting in open field.
Poli et al. (2013) identified significant association of RM1089 with number of tillers
and yield per plant, RM423 with leaf senescence, RM584 with leaf width and RM229
with yield per plant using F2 population developed from IR64 and NH219 (N22-H-
dgl219). NH219 is a dark green leaf mutant of N22 (N22-H-dgl219), which showed
reduced accumulation of reactive oxygen species in leaf under 40°C heat conditions.
Prashant et al. (2016) evaluated fixed breeding lines for heat stress tolerance in field
condition. They indicated that spikelet sterility and yield per plant have to be taken as
a criteria for evaluating heat stress tolerant rice lines. The phenotypic variance of the
identified QTLs varied from 11% to 25% for spikelet fertility during heat stress in rice.
Shanmugavadivel et al. (2017) identified five QTLs on chromosomes 3, 5, 9 and 12 for
yield and percent spikelet sterility using 5K SNP array and RIL mapping population
developed from N22 and IR64. These QTLs explained phenotypic variation in the
range of 6.27 to 21.29%.
Pradhan et al. (2016) used association mapping approach to identify markers
associated with high temperature stress tolerance. A set 60 genotypes were selected
from 240 germplasm lines based on spikelet fertility percent under high temperature.
These lines were genotyped with two INDEL and 18 SSR linked markers. The marker
RM547 was associated with spikelet fertility while the markers like RM228, RM205,
RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress
tolerance were detected. A non-synonymous substitution in the HsfA2a gene in rice
was found to be specific to Aus ecotypes in rice (NRRI, Annual Report 2016).

5. WHOLE GENOME RE-SEQUENCING OF DONORS AND

ELITE RICE CULTIVARS
The availability of the complete rice genome sequence (Goff et al. 2002; Yu et al.
2002) and the advancement of next generation sequencing (NGS) technologies have

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provided opportunity for sequencing of germplasm, discovery of genome-wide DNA
variations such as SNPs and InDels, and mining information about diversity of genes
and alleles (Bentley 2006;Varshney et al. 2009; Davey et al. 2011; Gao et al. 2012).
These DNA sequence level variations can be associated with traits, and elucidate
genomic structure and composition (McNally et al. 2009; Chen et al. 2014). Millions of
DNA polymorphisms, including single nucleotide polymorphisms (SNPs), insertion-
and-deletion (InDels) and structural variant polymorphisms have been identified in
rice germplasm by using high-throughput sequencing methods and bioinformatic
tools (Table 3). The first SNP resource was developed based on the draft genome
sequences of the japonica and indica rice cultivars (Feltus et al. 2004). Numerous
DNA polymorphisms were identified by whole genome re-sequencing of a high quality
japonica variety Koshikari (Yamamoto et al. 2010); Omachi, a Japanese landrace used
for sake brewing (Arai-Kichise et al. 2011); restorer lines (IR24, MH63 and SH27)(Li et
al. 2012b); elite indica rice inbred lines (three CMS and three R lines) (Subbaiyan et al.
2012), two Korean rice varieties (Hwayeong and Dongjin) and three anther-derived
lines (BLB, HY04 and HY08) (Jeong et al. 2013), maintainer line (V20B) (Hu et al. 2014),
seven cultivated temperate and tropical japonica groups (Arai-Kichise et al. 2014),
two Korean japonica rice varieties (Junam and Nampyeong) (Jeong et al. 2015);
northern japonica rice variety Longdao24, and its parents Longdao5 and Jigeng83
(Jiang et al. 2017) and salt tolerant rice cultivar SR86 (Chen et al. 2017). Li et al. (2014)
re-sequenced 3000 rice accessions collected from 89 countries and identified 18.9
million SNPs.
The NGS techniques has been used for QTL mapping associated with different
traits, positional cloning, haplotype analysis and identification of seed purity of rice
varieties (Feltus et al. 2004; McCouch et al. 2010; Shen et al. 2010; Chen et al. 2014).
The genome-wide association studies for identification of QTLs associated with
agronomic and yield related traits have been carried out based on the genome re-
sequencing and SNP arrays (Huang et al. 2010; Zhao et al. 2011; Han and Huang
2013). Yang et al. (2017) used bulked segregant analysis combined with whole genome
re-sequencing technology to map quantitative trait loci (QTL) and candidate genes
for nitrogen use efficiency.
Jain et al. (2014) identified a total of 17,84,583 SNPs and 1,54,275 InDels by re-
sequencing of three rice cultivars (IR64-drought sensitive, Nagina22-drought tolerant
and Pokkali-salinity tolerant). Some of SNPs were identified in the differentially
expressed genes within known QTLs. The whole genome re-sequencing of high
yielding rice variety Swarna helped to understand genetic basis of low glycemic index
(Rathinasabapathi et al. 2015). Rathinasabapathi et al. (2016) re-sequenced Kavuni, a
traditional rice cultivar with nutritional and therapeutic properties, and identified
11,50,711 SNPs. Pathway mapping of these polymorphisms revealed the involvement
of genes related to carbohydrate metabolism, translation, protein-folding and cell
death. Analysis of the starch biosynthesis related genes revealed that the granule-
bound starch synthase I gene had T/G SNPs at the first intron/exon junction and a
two-nucleotide combination, which were reported to favour high amylose content
and low glycemic index.

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Table 3. Examples of whole genome re-sequencing of rice genotypes.

Sl No. Genotypes Re-sequenced DNA Polymorphism detected References
1 20 diverse rice cultivars. 160,000 SNPs were identified, McNally et al.
and revealed the breeding history 2009
and relationships among the 20
rice cultivars.
2 Omachi, a landrace of 132,462 SNPs and 35,766 IDELs Arai-Kichise
japonica rice, which is an were identified between the Omachi et al. 2011
important source for modern and Nipponbare genome.
cultivars.
3 50 rice cultivars(40 cultivated 6.5 million SNPs were identified. Xu et al. 2012
and 10 wild progenitors, Significantly lower diversity was
Oryza rufipogon and Oryza observed in cultivated rice as
nivara ). compared to wild rice.
4 6 elite indica rice inbred lines 2,819,086 DNA polymorphisms Subbaiyan
(three CMS and three R lines). were between the inbreds and et al. 2012
Nipponbare.
5 3 important restore lines Numerous SNPs, InDels and Li et al. 2012b
IR24, MH63 and SH27. structural variations were identified.
The results showed higher genetic
variations among restorer lines.
6 5 Korean rice accessions, 1,154,063 DNA polymorphisms Jeong et al.
including three anther culture were detected. Higher polymorphism 2015
lines (BLB, HY-04 and was found in anther culture derived lines.
HY-08), their progenitor
cultivar (Hwayeong), and an
additional japonica cultivar
(Dongjin).
7 6 cultivars including 5 Several of SNPs and InDels were Arai-Kichise
temperate japonica identified. et al. 2014
cultivars and 1 tropical
japonica cultivar
(Moroberekan).
8 A maintainer line V20B. 660,778 SNPs and 266,301 InDels Hu et al. 2014
were identified with respect to indica
reference genome 93-11.
9 3000 rice accessions Identified 18.9 million SNPs. Li et al. 2014
collected from 89 countries.
10 Three cultivars (IR64-drought 17,84,583 SNPs and 1,54,275 InDels Jain et al.
sensitive, Nagina22-drought were identified. 2014
tolerant and Pokkali-salinity
tolerant).
11 Two Korean japonica rice 352,478 SNPs and 45,645 InDels Jeong et al.
varieties(Junam and were identified between Junam and 2015
Nampyeong). Nampyeong.
12 Ten high yielding, Swarna, Several SNPs and INDELs were Behera et al.
Samba Mahsuri, MTU1010, identified. The number of SNPs and 2015
MTU1001, PKM-HMT, InDels varied from 23,23,105 (Samba
PR113, Pusa1121, Pooja, Mahsuri) to 31,27,894 (Swarna) with
Satabdi and Sahabhagidhan. an average of 27,52,180.

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Sl No. Genotypes Re-sequenced DNA Polymorphism detected References
13 Swarna 1,149,698 SNPs and 104,163 InDels Rathinasa-
were identified. 65,984 non- bapathi et al.
synonymous SNPs were identified in 2015
20,350 genes. It helped to understand
genetic basis of low glycemic index.
14 Kavuni, a traditional rice 1,150,711 SNPs were identified, of Rathinasa-
cultivar with nutritional and which 377,381 SNPs were located in bapathi et al.
therapeutic properties. the genic regions. 2016
15 PDK Shriram.(high grain) 2,337,784 and 2,471,741 SNPs and Behera et al.
and Heera (low grain). INDELs were identified in PDK 2016
Shriram and Heera, respectively.
1756 SNPs and 358 InDels were
identified in PDK Shriram while
1941 SNPs and 412 InDels were
identified in Heera among 41 yield
trait specific genes.
16 Northern japonica rice 361,117 SNPs and 81,488 InDels Jiang et al.
variety Longdao24, and its were identified between Longdao24 2017
parents Longdao5 and and Longdao5 while 428,908 SNPs
Jigeng83. and 97,209 InDels were identified
between Longdao24 genomeand
Jigeng83.
17 Salt tolerant rice cultivar 3,800,137 variants were identified, Chen et al.
SR86. of which 85% were SNPs and 3.3% 2017
were INDELs.

Behera et al. (2015) re-sequenced of ten high yielding mega rice varieties of India,
namely, Swarna, Samba Mahsuri, MTU1010, MTU1001, PKM-HMT, PR113, Pusa1121,
Pooja, Satabdi and Sahabhagidhan using NGS technology. They discovered a large
number of DNA polymorphisms between these varieties, which would be useful for
molecular breeding programs. Further, genetic relationship analysis indicated that
Sahabhagidhan is more closer to indica reference genome, 93-11 while Pusa1121 is
more closere to japonica reference genome, Nipponbare (Fig. 2). Behera et al. (2016)
conducted whole genome re-sequencing of PDK Shriram (high grain) and Heera (low
grain) rice cultivars and discovered a large number of DNA polymorphisms. The
distribution pattern and annotation of SNPs and InDels were studied at 41 yield trait
related genes. A total of 1756 SNPs and 358 InDels were identified in PDK Shriram
while 1941 SNPs and 412 InDels were identified in Heera among 41 yield trait specific
genes, which would be useful for basic and applied research.

6. KNOWLEDGE GAPS
Several rice cultivars have been sequenced and homology prediction identified to
more than 54,000 genes in the genome. But, only few genes have been identified, well
characterized and utilized in breeding programs for improving yield, grain quality,
input use efficiency, tolerance to biotic and abiotic stresses, etc. It is highly necessary
to identify more genes/QTLs from diverse genetic resources, characterize them,

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understand functions,
(a)
identify superior and
beneficial alleles, and
accumulate them in high
yielding varieties for
further improvement of
yield, grain quality, input
use efficiency, tolerance
to biotic and abiotic
stresses, and other
desired traits. Still, a
significant portion of
beneficial/ superior
alleles has not been
discovered and used in
(b) the breeding programs.
Salkathi is a highly BPH
resistant land race and
was used to introgress
resistance into popular
rice varieties Pusa44 and
Samba Mahsuri. Two
QTLs have been
identified in Salkathi but
mechanism of resistance
of these QTLs is not
known. Few QTLs for
antioxidant properties
Fig. 2. Genetic relationship between high yielding rice
and seedling vigor have
varieties based on the SNPs identified by whole genome
sequencing with respect to a) indica (93-11) and b) been identified and few
japonica (Nipponbare) reference genomes. Source: Behera genes have been cloned.
et al. (2015). However, clear cut
functions of those genes
are still not known. Several high throughput genomic tools are available to address
these problems.
The utilization of genome sequence information is meager though several rice
genotypes have been sequenced, due to lack of strong bioinformatics expertise and
facilities. Hence, human resource needs to be trained well to use NGS data efficiently.
Very few high throughput facilities are available in India for precise phenotyping of
germplasm for different traits and utilize them for allele mining, functional validation
and finally use in breeding programs to develop high yielding, value aided and climate
resilient rice varieties.

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7. WAY FORWARD
Concerted efforts are needed for identification and fine mapping of genes/QTLs
associated with traits like antioxidant properties, protein and micro nutrient contents
of grains, seedling vigor and other agronomic traits, input use efficiency, resistance/
tolerance to biotic and abiotic stresses and use them in molecular breeding programs
to increase value addition and climate resiliency in high yielding rice varieties. Further,
emphasis should be given for discovery of superior alleles for different traits, and
whole genome re-sequencing of key donors and elite cultivars has to be performed to
identify SNPs, INDELs, understand the structure and functions of key genes related
to yield traits, grain quality traits, tolerance to biotic and abiotic stresses, etc, and to
develop markers for effective utilization in MAS programs for rice improvement.

8. SUMMARY
Improvement through conventional approaches has met with considerable
success and rice production has doubled over the last 40 years. To feed growing
population by the year 2030 AD, the global demand for rice would increase by
40% requiring production of 858 million tons. Increasing rice yield to ensure food
security is a major challenge. Rice production is no longer keeping in pace with
population growth during last decade because of Shrinking cultivable land area,
water scarcity, depletion of soil fertility, globlal warming (climate change), evolution
of new biotypes, pathotypes, etc. Hence, we have to use innovative tools to assist
traditional methods in order to improve production and feed growing population.The
availability of the complete genome sequence of rice and the developments in field
of genomics has opened the door for speeding-up breeding processes for increasing
yields and minimizing production risks. Genomics tools have been used for
identification and mapping of genes/QTLs for target traits, whole genome sequencing
of donors and elite genotypes for discovery of SNPs, genome-wide association
mapping (GWAM), gene prospecting and allele mining, gene discovery for useful
traits, precision breeding through MAS approach. Several QTLs/genes for biotic and
abitic stresses, grain quality, early seedling vigor, input use efficiency, morphological
and yield traits have been idenrtified. Few of them have been fine mapped, cloned and
used in MAS breeding programs for developing climate regilient, input use efficient,
nutrient rich and value aided high yielding rice varieties.
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 Nutrient Management for Enhancing
Productivity and Nutrient Use Efficiency in Rice

AK Nayak, S Mohanty D Chatterjee, D Bhaduri, R Khanam, M

Shahid, R Tripathi, A Kumar, S Munda, U Kumar, P Bhattacharyya,
BB Panda and H Pathak

SUMMARY
Development of appropriate management strategy for enhancing nutrient use
efficiency, and ensuring environmental sustainability of rice production system is a
priority area of research. Considerable progress has been made so far from broad
based blanket nutrient recommendation to supply and demand based site specific
nutrient recommendation. The nutrient management researches in rice till dates mostly
focus on “4 R” stewardship i.e. right dose, right time, right source and right place of
nutrient application. Numerous technologies, tools and products such as soil test
crop response (STCR) based N, P, K recommendation, optical sensor based real time
N management, enhanced efficiency fertilizer materials have been developed and
evaluated in rice and rice based systems to ensure 4 “R” principles of nutrient
application and enhance yield and nutrient use efficiency. Further research is needed
to fine tune these technologies for its wider adaptability and also to redefine nutrient
management strategy in the context of climate change, next generation super, high
protein and abiotic stress tolerant rice. It is essential to devise ecological intensification
based nutrient recommendation that takes in to account ecological processes as well
as the interactions among themselves to reduce negative environmental impact of
chemical fertilizers.

1. INTRODUCTION
Rice is one of the input intensive crops in the world and input of nutrient contributes
approximately 20–25%to the total production costs of rice. At present rice production
alone consumes nearly 24.7 Mt of fertilizer (N + P2O5 + K2O) which accounts for
approximately 14.0 % of total global fertilizer consumption in a year. Scientists have
predicted that a hike of at least 60% in rice yield is essential in order to ensure food
and nutritional security of 9 billion populations that are expected to inhabit the globe
by 2050. With increasing demand for food production, demand for nutrients is likely
to increase further.
Despite several decades of research the average recovery efficiency of N, P and K
in rice is only 30-35%, 20-25% and 35-40%, respectively. At present, India imports
30% of nitrogenous, 70% of phosphatic and 100% of potassium fertilizer. Both N and
P fertilizers are highly energy intensive and at the same time also have very low use
efficiency. In addition, there are several drawbacks in the prevailing practices of
nutrient management such as non-judicious blanket nutrient application, skewed

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NPK ratio, and nutrient mining etc., that pose severe threats to the productivity and
sustainability of intensive rice production systems. At the same time inappropriate
use of these nutrients has several socioeconomic and ecological consequences such
as enhanced fertilizer cost, fossil fuel burning, greenhouse gas emission, pollution of
water bodies etc. Therefore an appropriate nutrient management strategy apart from
enhancing nutrient use efficiency, productivity and profitability should also aim at
enhancing eco-efficiency and environmental sustainability.
Voluminous research has been done to develop and optimize appropriate nutrient
management strategy for rice and rice based systems in varying agro-ecological
conditions. Most of the early researches focused on broad based blanket nutrient
recommendations for similar agro-climatic region. However, these recommendations
did not consider field-to-field variability of soil nutrient status which is often led to
either excess or deficit nutrient application resulting in loss of nutrient, reduced yield
poor nutrient response and low nutrient use efficiency. During past few years
tremendous progress has been made in the nutrient management research in order to
satisfy”4 R” criteria i.e. right dose, right time, right source and right place ,required for
enhancing nutrient use efficiency. This led to development of numerous tools and
technologies that can be used in rice cultivation across the agro-ecosystem such as
soil test crop response (STCR) based N, P, K recommendation, Site Specific Nutrient
Management (SSNM) using omission plot technique and targeted yield approach,
Real Time N Management (RTNM) using leaf colour chat, chlorophyll meter and
green seeker, use of enhanced efficiency fertilizer materials (EEFs) such as urea super
granules, coated urea, and nano-fertilizers etc.
Considering the fact that relationship between soil fertility status, nutrient use
efficiency and yield at farm level is highly scattered and show great degree of variation,
and a common nutrient management strategy may not be appropriate for farmers of
different agro-ecology and socioeconomic background. Efforts have been made to
upscale the data base with respect to soil fertility management from field to regional
level. Accordingly, management zones of rice cultivation have been delineated using
GIS, GPS and remote sensing tools.
Nutrient use efficiency depends on plant’s ability to uptake nutrient from soil
either native or applied and to convert it into final economic product and is controlled
by complex interactions of physiological, developmental and environmental processes
in soil-plant-atmosphere continuum. Multidisciplinary approach involving agronomy,
soil science, microbiology, plant physiology and genetic studies is being followed to
identify controlling factors of nutrient use efficiency of rice, developing efficient
genotypes and devising appropriate nutrient management strategy (Fig. 1). Apart
from that nutrient management research requires a thorough understanding of fate of
nutrients in soil, water, plant and atmosphere in emerging scenarios of climate change,
development of next generation rice (super rice, high protein rice, multi abiotic stress
tolerant rice etc.) and promotion of conservation agricultural practices for bringing in
new innovations in the management of N,P,K and micronutrients in rice.

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Nutrient Use Efficiency in Rice 223
 Objective of this
chapter is to discuss about
the progress, which have
been made so far in
management of nutrients
for enhanced productivity
and nutrient use efficiency
of rice and rice based
production system, and
how to fine tune the
existing technology for its
Fig. 1.Graphical presentation showing multidisciplinary
approach for understanding regulatory factors of nutrient
wider adaptability. This
use efficiency. chapter will also discuss
about the need of
redefining nutrient management strategy in the context of climate change, next
generation super, high protein and abiotic stress tolerant rice.

2. STATUS OF RESEARCH
2.1. Nitrogen
Nitrogen is one of the most essential and most limiting nutrient for rice production
and application of synthetic N fertilizer plays a crucial role in enhancing the yield.
Globally rice cultivation consumes approximately 9 to 10 million tons of fertilizer N in
a year which accounts for about 10% of the total fertilizer N production in the world.
However, only 30 to 40% of the applied N is recovered by the crop resulting in large
losses of reactive N, which not only negatively affects yield but also drains national
exchequer and pollutes environment simultaneously. Cost of remediation of the socio-
environmental side effects of N pollution such as global warming, ground water
pollution and eutrophication etc. is huge. Hence, enhancing N use efficiency of rice
has always been a researchable topic for
both plant nutritionist and environmental
scientists.
Studies on N management in rice
mostly revolve around four ‘R’ principles
of nutrient application i.e. right fertilizer
source, right dose, right time and right
place (Fig. 2).
Among inorganic sources of N, urea
is the most widely used nitrogenous
fertilizer in rice because of its high N
Fig.2. Four “R” approach of nitrogen
content and favorable physical
management for enhanced N use efficiency
properties. However, the major in rice.
disadvantage with urea is that once

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applied to waterlogged soils of low land rice, it undergoes rapid transformation

processes such as hydrolysis, nitrification, denitrification, leaching and volatilization
etc. resulting in loss of up to 50% of applied urea N.
Efforts have been made to develop slow release or controlled release urea fertilizers
by coating urea prills with less soluble chemicals such as sulfur, polymers and other
products like plaster of paris, resins and waxes. These coated urea products were
tested both in laboratories and in field condition with varying degree of effects on
urea hydrolysis and N recovery efficiency. Besides this several chemical and natural
inhibitors for inhibiting and/or slowing down the hydrolysis of urea (urease inhibitors:
NBPT - N-(n-butyl) thiophosphoric triamide – Agrotain, N-phenyl phosphorictriamides
(2-NPT), Hydroquinone (HQ), Phenyl phosphorodiamidate (PPD/PPDA)) and
biological oxidation of ammonical-N to nitrate-N (nitrification inhibitors: Nitrapyrin,
DCD, N (2,5 dichlorphenyl) succinic acid monoamide (DCS), 3,4-dimethylpyrazole
phosphate (DMPP)) have been identified and evaluated. The fertilizer products with
the coatings of less permeable material and one or more inhibitors as extra additive
within the formulation or as in the coating are known as enhanced efficiency fertilizers
(EEFs). The EEFs are generally designed to regulate either nitrification or urea
hydrolysis or both in order to reduce N loss and increase N uptake by plant. A
comprehensive analysis of hundreds of studies all over world with respect to
effectiveness of different EEFs showed that urease inhibitors could increase yield
and N use efficiency up to 9% and 29%, respectively and reduce in N loss up to 41%
in rice-paddy system (Li et al. 2017).
Presence of thin oxidized layer overlying reduced zone in soil is one of the reasons
behind rapid loss of N from the rice ecosystem in various forms when it is broadcasted
to surface soil. Studies on right place of N application indicated appropriate method
or place of N application may vary according to time and source of N application.
Basal incorporation of urea in puddled soil of transplanted rice has been observed to
reduce NH3 volatilization as compared to surface broadcasting of urea to flooded soil,
but its impact on yield depends on other factors like water management and tillage
practices during incorporation. Inter row band application of urea during top dressing
in direct seeded rice and deep (5-7 cm below surface) placement of USGs in reduced
zone in transplanted rice was found to be superior in terms of enhancing N use
efficiency and reducing N loss over surface broadcasting of urea. Considering the
drudgery and labor involved with manual deep placement method, several attempts
have been made to develop continuous operation type and non-continuous injector
type USG applicator for both basal and top dressing in transplanted rice. These
applicators, however, need to be fine-tuned to make those more user friendly and
efficient with respect to metering and uniform depth of application. Technique of
injecting dissolved urea into the upper soil layer, has also been developed which is
equally effective as deep placement of USG and at the same time less laborious and
can be used for top dressing too. Recent study on one-time root zone fertilization
(RZF) technique showed that basal application of urea into 10 cm deep holes dug at
a distance of 5 cm from the rice roots reduced fertilizer-N loss by 56.3–81.9% compared

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Nutrient Use Efficiency in Rice 225
to urea surface broad casting (Liu 2016). In addition to soil application, foliar spray of
urea has been suggested to avoid the complex interactions of urea in flooded soil of
rice. Its effect on grain N content mainly cultivar specific and varies with time of
application, however spraying of urea at flowering stage led to a more efficient dry
matter partition to the grain, higher grain number m-2 and finally increased grain yield
(Sarandon and Asborno 1996).
Synchronization of N supply with that of crop N demand is the key for enhancing
N use efficiency of crop, deciding time and rate of N application is an area of active
research in the field of nutrient management in rice. Timing of N application or the
decision on split application of N depends on the N requirement pattern of the rice
plant. The N absorption in early duration rice varieties is continuous from transplanting
to flowering after which there is almost no absorption. In medium and late duration
varieties the dry matter and N accumulation is vigorous from transplanting to maximum
tillering stage after which it slows down during the vegetative lag phase and again
becomes vigorous with onset of panicle initiation and continues little after flowering.
Thus there is a single peak of N requirement in early varieties and two peaks of N
requirement in medium and late duration varieties, suggesting the importance of
basal N application in early varieties and split application in medium and late duration
varieties. The number of split is also decided on the basis of soil texture. In soils of
relatively finer textures, N is applied in three splits with 50% at basal dressing, 25% at
21 days after transplanting (DAT) and the rest 25% at panicle initiation. But in soil of
lighter textures, N application in three splits of 25:50:25 proportions are considered
best. For hybrid rice, N is applied in four equal splits doses- 25% of N at basal
dressing, 25% at 21 DAT, 25% at PI and the rest 25% at panicle emergence. However,
in rainfed lowland direct seeded rice the entire dose of 60 kg N ha-1 along with 30 kg
P2O5 and 30 kg K2O ha-1 is applied in seed furrows at the time of dry sowing. Response
of crop to applied N is highly field specific and varies with soil condition hence
correct N recommendations requires information on N availability from all possible
sources and crop requirement. The site specific N management (SSNM)
recommendation based on indigenous N supply, expected N demand of crop and the
expected fertilizer N use efficiency resulted in an increase in N-use efficiency of
irrigated rice by 30–40% and grain yield by 7% in more than 100 field experiments in
Asia (Dobermann et al. 2002). Going a step further, ways and means were also devised
to address the real time need of crop which generally varies according to growth
stage and environmental condition. Hand held optical sensors such as chlorophyll
meter, green seeker etc. are promising real time N management tools which indicate
crop N status non-destructively on the basis of greenness of leaf. Recently leaf
colour chart (LCC) is being widely tested and promoted as an easy to use cheap and
farmer’s friendly diagnostic tool of real time N application. The extensive field research
in several parts of Asia indicated up to 25% saving of N in rice production could be
achieved by using LCC.
Crop simulation based decision support tools such as DSSAT, ORYZA-2000, Info
Crop have been developed to help determine N fertilizer recommendations matching

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with crop requirement. These tools consider complex interaction of N transformation

processes in soil-plant-atmosphere continuum and are useful to predict N management
option in different scenarios of agronomic management. Development of light and
portable hyper-spectral sensors and new generation satellites which obtain higher
resolution images offer the possibility to detect in season N status of crop on the
basis the normalized vegetation index to provide recommendation for larger areas at
affordable prices.
Nitrogen fertilizer is an integral component of green revolution in India and most
of the initial researches on N recommendation were related to agronomy trials on
yield response in different agro-climatic zone. Few studies on site specific N
recommendation have been initiated in several rice growing regions like Punjab, Odisha,
Bihar etc. Rice Crop Manger is such an initiative by IRRI in collaboration with ICAR
institutes that gives field specific N recommendation on the basis of past crop
management history. Recently Bijay-Singh et al. (2015) recommended a moderate
amount of N application at transplanting, followed by sufficient N fertilization at
active tillering, and an optical sensor-based N application at panicle initiation stage
for enhanced yield and N use efficiency in transplanted rice. However, the real time N
management tools like chlorophyll meter and green seekers etc. are confined to
experimental purposes only. Extensive studies on standardization and evaluation of
leaf colour chart based in season N application have been conducted in farmers’
fields in different parts of India.
Studies on use of EEFs for enhancing N use efficiency of rice in India are limited
to experimental stations only. Several attempts have been made for identification and
field scale evaluation of plant based natural inhibitors. Nimin, a tetraterpenoids
extracted from neem (Azadirachtaindica) cake and karanjin, a flavonoid obtained
from the seeds of the karanj (Pongamiapinnata) are reported to have nitrification
inhibition property. Technology has been developed to produce Neem coated urea
by coating urea prills with neem (Azadirachtaindica) oil emulsion.Field trials with
rice indicated reduced N loss, enhanced yield and N use efficiency with NCU as
compared to normal urea. Today according to the order of Government of India all
urea manufactured in India are coated with neem oil emulsion.
Development of appropriate N management strategy has always been an integral
component of rice research at ICAR-NRRI. Number of studies has been conducted to
understand fate of urea in low land rice under different improved N management
options. The time of complete urea hydrolysis in irrigated and rainfed rice ecosystems
was found to be 2-3, 5-7, and 7-14 days for broadcasting of urea onto flooded soil,
deep placement of USG in flooded soil and urea basal application in dry soil, respectively
(Nayak and Panda 2002). Relative ammonia volatilization and surface runoff loss from
rice field was estimated to be 0.4% and 6-8%, respectivelywith USG deep placement
and 6.0% and 78% with urea broadcasting on waterlogged soil (Nayak and Panda
2002). Subsurface placement of urea through thorough incorporation of applied urea
into wet soil by puddling in absence of any standing water and deep placement urea
mud balls in the reduced zone of submerged rice soil, also decreased N losses and

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improved N use efficiency in rice (Kabat 2001). Coating of urea with neemcake or
shellac for basal dressing also reduced ammonia loss (Mishra et al.1990). Nayak and
Panda (1999) tested efficacy of different nitrification inhibitors found that hydroquinone
was more effective in alluvial and laterite soils and alcoholic extract of neem cake was
better in black soil than dicyandiamide. In direct seeded rice, seed furrow placement
of urea produced higher grain yield than broadcasting method.
Yield response trials were conducted to optimize N dose for semi-dwarf rice in wet
season (40-80 kg ha-1), rainfed lowland direct sown rice varieties, (56-62 kg ha-1) and
hybrid rice (100 kg N ha-1 in kharif and 120-135 kg N ha-1 in rabi season). In addition
to this, nitrogen accumulation pattern of different rice cultivars was investigated in
different agro-ecological conditions to ascertain the pattern of N requirement and
decide number and time of split N application accordingly. Efforts have been made to
optimize N doses for several medium to long duration rice varieties grown at different
planting dates by crop simulation approach using of ORYZA 1N model.
Recently a five panel customized leaf colour chart (CLCC) was developed for real
time nitrogen management in rice of different agro ecologies by ICAR-NRRI. The
CLCC provides cultivar specific recommendation of basal as well as top dressing of N
(both time and dose) in terms of kg urea per acre for rainfed favorable lowland,
submerged and flood prone lowland, rainfed upland, and irrigated rice (Nayak et al.
2013). Field trials indicated yield advantages of 0.5-0.7 t ha-1with CLCC based N
application over recommended practice. Application of neem coated urea (NCU) on
the basis of CLCC reading enhanced yield and N recovery efficiency (REN) by 21.2-
22.9% and 16.3-18.0%, respectively, over conventionally applied urea (RDF-Urea) in
aerobic direct seeded rice (DSR) and by 14.6-15.9% and 11.6-14.6%, respectively in
puddled transplanted rice (PTR). Further, in aerobic direct seeded rice, NCU when
applied on the basis of leaf colour chart reduced NO3-N leaching and N2O-N emission
by 26% and 11-21%, respectively as compared to conventionally applied urea
(Mohanty et al. 2017). Web based nutrient management tool-rice crop manager (RCM)
was developed in collaboration with IRRI to give field specific recommendation for
the farmers of Odisha on the basis of past cropping and management history
information. Rice crop manager recommendation provided rice grain yield advantage
of 9.8 to 39.6% with an average of 22.6% over farmer’s practice (FFP). Remote sensing
and GIS tools were used to provide recommendation of N application for homogenous
management zone in few selected pockets of Odisha. Site specific N recommendations
of 66-100 kg ha-1 with an average of 80 kg ha-1 were computed using historical soil
data, yield target and expected agronomic N use efficiency. Site specific fertilizer N
recommendation (SSFN) map was generated for Ersama block, Jagatsingpur district
of Odisha using appropriate semi-variograms and interpolating SSNM values by
kriging.
Research has been initiated at ICAR-NRRI to fine tune technique of urea briquette
deep placement to make it more efficient and user friendly. The breakability of the
briquettes was reduced by mixing urea with oils of neem (Azadirachta indica) and
karanj (Pongamia pinnata). Apart from being good binding agent, the oils used

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contain active ingredients that reportedly inhibit nitrification activity in soil. Mixing
oil increased the strength of briquettes and reduced the breaking percentage to 2-5%
as compared to 25-30% of urea briquette without a binding agent. In addition to this,
agglomerated urea briquettes were prepared by mixing suitable amendments viz.
phospho-gypsum, fly ash, silica powder, neem cake and rice husk as filling materials
and biodegradable binding agents with urea (Nayak et al. 2017). Use of amendments
and binders improved the crushing strength of briquettes. Additionally, amendments
acted as filler material and reduced the concentration of urea in pellet which will
ensure its uniform distribution in the field. Efforts were also made to improve the
existing urea applicator and develop new prototypes. Manually pulled 2, 3 and 4 row
drum type urea briquette applicators for basal application, briquette applicator mounted
on conoweeder for top dressing, injection type briquette applicator for both basal
and top dressing are fabricated and tested in the field.
2.2. Phosphorous
About 50% of agricultural soils, on a global scale, are suffering from deficiency of
phosphorus (P), which has been majorly observed due to two prime factors, (i)
insufficient P replacement in agricultural soil, and (ii) P-fixing properties of a particular
soil causing P unavailability to plants. In highly weathered soils around the world,
mostly belongs to the orders Oxisols and Ultisols, P deficiency has been noticed as a
common factor hampering the agricultural production. Apart from the inherent soil
conditions to supply P, large imbalances in the rates of P fertilizer also exist, showing
the variations of lower or inadequate P application in many developing countries of
Asia, Africa and South America but adequate or excess P application in the Europe,
USA and few Asian countries (China, Japan and Korea) as reported by few analysis
over the years.
Response to P application is highly erratic due to direct and indirect influences of
several factors operating in the soil system on P availability to the plants. In general,
the response of lowland rice is usually lower than other dryland crops including
upland rice Reduced soil conditions normally increase the P availability to lowland
rice. Therefore, in many soils, P availability is not a yield-limiting factor for rice and
significant response of modern rice varieties to fertilizer P may be observed after
several years of intensive cropping. Thus management must focus on the buildup
and maintenance of adequate available P levels in the soil, so that P supply does not
limit crop growth. P fertilizer applications exhibit residual effects thus maintenance of
soil P supply requires long-term strategies on site-specific basis. Organically amended
plots (FYM, rice straw, and green manuring) in eastern India showed an improved
PUE than control. While others have found that effect of FYM application on P use
efficiency was not very prominent in irrigated rice rather it helps in recycling P.
Application of phosphorous solubilizing bacteria (PSB) to lowland rice ecology had
no significant impact while addition of phosphatic fertilizers and vermicompost
governed the soil P availability in the same occurrence (Kumar et al. 2016). Upland
rice-based crop rotation with maize and horse gram promoted native arbuscular
mycorrhizal fungi (AMF) colonization (in a tune of 10.4–38.8%) and ensured better P

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uptake (2.2–2.6 mg P g-1 plant) by rice crop which further reflected in higher grain
yield (Maiti et al. 2012).
Better phosphorus use efficiency (PUE) can be addressed through two clear-cut
approaches: 1. Genetically P efficient cultivars, and 2. P management by external
means. Scientists working in rice crop globally follow similar ways to enhance PUE.
Genotypes grown well at low soil P level but responded well to added P is the most
desirable trait for screening P efficient rice genotypes. The study further identified
two factors, shoot weight and P uptake, are the most crucial to identify P deficiency.
Moreover, PUE was identified higher in roots over shoots in rice grown under acid
soils that decreased with increasing levels of soil P (Fageria and Baligar1997). By
cutting edge approach of recent times, scientists have explored the possibility of
genetic manipulation in rice for improved PUE, including the identification of PSTOL1
(phosphorus starvation tolerance 1) gene, which is a key gene responsible for the
natural variation in phosphorus starvation tolerance, induce enhanced grain yield in
P-decient soil by promoting early root growth and Pi acquisition, over a range of
intolerant and tolerant rice genotypes like Kasalath (Gamuyao et al. 2012).
2.3. Potassium
In tall indica rice, there was limited response to K application in earlier years, but
with the introduction of high yielding varieties and intensive agriculture, response in
grain yield was recorded. The mean response of rice over several years in intensive
cropping systems of the long term fertilizer experiments ranged from 4 to 10 kg grain
for every kg of K2O applied. In view of high uptake of K by the high yielding varieties
of rice, application of a maintenance dose of 30 kg K2O ha-1 for lowland rice is suggested.
In light textured acid upland soils, K deficient areas, in biotic and abiotic stress
situations and in hybrid rice, split application of K or K top dressing along with N at
panicle initiation in addition to a basal dressing of K is beneficial for increasing rice
yield. Rice is mostly cultivated under submerged condition. Under such condition
potassium fertility level changes immediately after inundating the soils due to release
of soluble ferrous (Fe2+) and manganous (Mn2+) ions. These ions displaced K in the
exchangeable pools and released into the soil solution. Thus, availability of K increased
after submergence. However, contrasting reports are also available showing decrease
in K content due to the formation of sparingly soluble Fe-K complexes. Hence,
application of potassium along with other nutrients is very important for sustaining
rice yield.
Application of inadequate and unbalanced fertilizer excluding potassium is one of
the reasons for declining K nutrition in rice fields. In a long-term study in China, it is
observed that proper potassium fertilizer management control rice yield in the double
rice cropping system (Liao et al. 2013). It was further observed that the yield of both
early and late rice increased over time in the treatments that received fertilizer K or
combined application of fertilizer with rice straw. Decline in yield of rice is reported
when unbalanced fertilizers are applied (Liao et al. 2013). Rice removes large amount
of K from soil. Due to high K removal, a negative K balance prevail in rice and rice

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based cropping
system even after
recommended ferti-
lizer application.
Sharma et al. (2008)
reported a net
negative K balance
for nine different rice-
based cropping
systems (Fig. 3).
Fig. 3.Potassium balance in rice-based cropping systems Rice straw is a rich
(modified after Sharma et al. 2008). source of K, its
incorporation into
soil at the rate 5-10 t ha-1 markedly increases available K content and improves K
nutrition of rice crop. Therefore, effective straw management by returning a
considerable portion back into the field is another option for effective K management
(Bijay-Singh and Singh 2017). Split application of potassium in rice field increased the
yield and potassium use efficiency of rice in light textured soil. However in a long
term fertilizer experiment at NRRI, response to applied K was observed after 30 years
of rice-rice cropping, nevertheless treatment effects were most prominent on release
threshold concentration (RTC), followed by cumulative K release, K-release rate
constants, and K-fixation capacity. Rice cultivation without K fertilizer application
resulted in lower values of soil K parameters than the K fertilized treatments ( Debrup
et al 2018).
2.4. Micronutrients
Micronutrients more particularly Zn, B and Fe play key roles in growth and
metabolism of rice plant hence are essential for enhancing yield of low land rice. Zinc
deficiency is the most commonly observed micronutrient disorder in rice based
cropping system. In contrast, Fe toxicity is the major problem in the most wetland rice
soil in humid tropical regions of Asia due to drop of redox potential under submerged
condition which elevates the release of Fe(II) in the soil. However, in upland and
aerobic rice systems Fe could be a limiting nutrient for rice yield. Additionally, nutrient
mining and emerging trend of micronutrients deficiency in soils of many intensively
cultivated rice growing regions warrants for a judicious and need based micronutrient
application strategy in rice cultivation. Study on effect of micronutrient application
on rice yield showed number of tillers per square meter, spikelets per panicle and
paddy yield was maximum with combined use of zinc and boron and 1000-grain weight
was recorded highest where all three micronutrients (zinc, boron and iron) were applied
in combination. The maximum healthy kernel percentage was recorded where zinc
was applied along with iron (Qadir et al. 2009).
Flooding the soil alters availability of micronutrients like Fe, Mn and Zn which
interact among themselves and determine their uptake by plant. However, the soil test

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based approach is considered best for application of these nutrients. Among the
different available Zn fertilizers ZnSO4 is the most commonly used Zn fertilizer because
of its high solubility. In Zn deficient soil one time application of 20 to 25 kg ZnSO4 ha-
1
as basal has been recommended. However foliar spray of 0.5% ZnSO4 in 200 litre
water ha-1 has been suggested in emergency condition of Zn deficiency during rice
growth period. In calcareous soil incorporation of Zn fertilizer with green manure is
generally considered better than broadcasting.
Apart from upland condition, Fe deficiency also occurs in, calcareous, and alkaline
low land soil with low organic matter content. Management practices like application
of organic manure before sowing and green manuring with dhaincha before rice
transplanting have been proved beneficial to alleviate Fe deficiency in rice. Ponding
of water in nursery beds during dry spell and irrigating rice fields as soon as chlorosis
appears have also been suggested to deal with Fe deficiency. In addition to this
broadcasting of FeSO4.7H2O rate of the 30 kg Fe ha-1 as basal and spraying 1%
FeSO4.7H2O solution 2-3 times at 10 days interval have been recommended. Application
of lime (75% LR) along with Zn and other limiting elements such as K and Mn
ameliorated iron toxicity in some lowland iron rich rice soils (Shahid et al. 2014).
Manganese deficiency mainly occurs in alkaline and sodic soil with low organic
matter, leached and acid sulphate soils and degraded soils containing large amount of
soluble iron. Integrated application organic manures like FYM, compost or green
manure along with 25 kg MnSO4 ha-1 as basal could be the best management strategy
to address the problem of Mn deficiency in rice. In addition, spraying of 0.5% MnSO4
has been recommended for rapid correction of Mn deficiency.
Rice grown in highly weathered, acid upland, coarse textured sandy soils and
calcareous soils mostly suffers from B deficiency. Generally, soil test based application
of borax at the rate of 5-10 kg ha-1 as basal has been recommended for B deficient soil.
However, spraying of 0.2% boric acid or borax at pre flowering or heading stages has
been proved to be effective in taking care of hidden deficiency. For quick recovery
from B deficiency, spraying of borax or boric acid at the rate of 0.05% has also been
suggested.
2.5. Integrated nutrient management
Integrated approach of using both organic manures (Farm yard manure (FYM),
green manure (GM), crop residues, biological N2 fixation and biofertilizers) and chemical
fertilizers have been often recommended for managing soil fertility and nutrients in
intensive rice based cropping system to arrest the trend of yield stagnation and
minimize adverse environmental impact of chemical fertilizers. Numerous studies have
been conducted to ascertain the beneficial effects of organic manure application on
soil health and subsequent positive impact on growth and yield of rice. Sustainability
yield indices calculated for intensive rice production system often show comparatively
higher value when part of the recommended nutrient is applied through organic
sources such as FYM or GM than chemical fertilizer alone. Continuous application of
chemical fertilizers along with FYM to a 44 year old rice-rice system in tropical India

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resulted in improvement in soil physical and chemical properties and biological activity
leading to higher soil quality index and greater sustainability (Shahid et al. 2013).
Studies conducted at CRRI, Cuttack revealed that growing Azolla before rice
transplanting or after transplanting produces an additional grain yield of more than
0.5 t ha-1 and is equivalent to application of 30 kg of fertilizer-N. Free living bacteria
Azotobacter can fix 10-30 kg N ha-1 in aerobic soil, the associative bacteria Azospirillum
can fix 7 kg N ha-1; with its inoculation, grain yield increased by 8-30% over
uninoculated

3. KNOWLEDGE GAPS
Despite volumes of research and adoption of innovative technology, the N use
efficiency of low land rice has not been improved substantially. The recent approach
of SSNM along with RTNM has the potential to ensure efficient utilization of applied
N; however these technologies need to be simplified while retaining their effectiveness
to ensure large scale adoption by the small and marginal farmers growing rainfed rice.
Deep placement of urea super granules/urea briquettes in the reduced zone has been
proved to enhance N use efficiency and decrease N loss but in absence of a cost
effective efficient applicator for uniform application, deep placement technology has
not made any desired impact. Quantitative understanding of the complex interacting
processes taking place in soil as well as in plant that influence N use efficiency of rice
is still insufficient. Source sink relationship of super rice/next generation rice and
high protein rice is inadequately understood. Methods for estimation of various N
loss from rice ecosystem are yet to be standardized and up-scaled in different agro-
climatic conditions, the limited data generated following these methods are associated
with great degree of uncertainties. The fate of USG deep placement in light sandy
loam textured soil and in direct seeding rice in unpuddled soil, where substantial
amount of leaching takes place has not been properly known. Integrating satellite
based real time monitoring of soil and plant nutrient status with weather forecasting
for fertilizer recommendation advisory is another potential area of research. Similarly
,microbial processes like anaerobic ammonia oxidation and phyllospheric N fixation
which could have a bearing with N loss and N use efficiency of urea deep placement
is poorly understood.
Phosphorus is a unique element and indispensable for sustenance of crop plants,
microbes and ecosystem. In soil system major form of P is phosphate (PO43-) which
binds with the available cations (Ca2+, Mg2+, Al3+); however where rice grows in a
typical conditions (lowland, puddled, submerged, anaerobic) the availability of P and
its dynamics over time with changing pH and redox potential (Eh) is a researchable
issue. Moreover, the interaction of P ions with other abundant major (N, K) and
micronutrient ions (Fe, Zn, Cu, Mn) demands attention under low land/submerged
situation.
The major concern in K research is whether the ammonium acetate extractable K is
sufficient to justify the K supply for plant need. At present, additional parameters like

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the two categories of non-exchangeable K reserve viz. step-K and constant rate K
and the release and fixation threshold levels of K are important issues. Till date, there
is not much report available on the long-term effect of differential nutrient management
on potassium supply parameters under different cropping system. Role of micro and
macronutrients including K for ameliorating the biotic and abiotic stress in the context
of climate change is being focus of current nutrient management research
Studies indicated microbial inoculants can be efficiently integrated in a nutrient
management programme to reduce chemical fertilizer input and enhance nutrient use
efficiency; however the effectiveness and stability of the inoculants under diversified
agroclimatic condition is yet to be properly ascertained.

4. RESEARCH AND DEVELOPMENT NEEDS

4.1. Up scaling N recommendation
Though the leaf colour chart is being widely popular among the farmers as a easy
to use diagnostic tools for in season N application, it still is a qualitative indicator of
crop N status and provides a non-quantitative recommendation of N application and
not helpful for regional scale recommendations. More recently, some non-invasive
optical methods based on absorbance and/or reflectance of light by the intact leaf,
have been developed. These include ground-based remote sensors and digital, aerial,
drone and satellite imageries, which can be used for regional scale and quantitative
recommendations to overcome tedious soil and tissue testing. The remote sensing
(RS) based techniques have a great potential in formulating cost effective N
recommendations for reducing fertilizer doses and environmental risks and improving
nitrogen use efficiency and crop yield. But a very limited work has been done in this
field, as they have a greater future scope, emphasis should be given towards
improving and promoting these techniques. Remotely sensed data collected from
plant canopies can be used to formulate vegetation indices that may give an indication
of plant health. Several vegetation indices have been developed including, Normalized
Difference Vegetation Index (NDVI), Green Normalized Vegetation Index and infrared
to red reflectance ratio or simple ratio (SR). This provides opportunity for defining
fertilizer N algorithm for optimum N recommendation in different rice growing regions
of India on the basis of expected yields and achievable greenness of the leaves using
NDVI during the crop-growth period. Research can be directed to delineate N
management zone for rice indicating deficit, optimal and surplus region on the basis
of RS based Nitrogen Nutrition Index (NNI) approach by taking into consideration
the measured N concentration and predicted critical N concentration during growing
season.
4.2. Enhancing phosphorus use efficiency
Enhancing phosphorus use efficiency (PUE) and exploring the possibility of
harnessing the maximum share of P for crop nutrition from conventional (common
phosphatic fertilizers) and non-conventional fertilizer (oilseed cake, bone meal, fish

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meal, rock phosphate etc.) sources is essential to reduce the dependence on phosphatic
fertilizer for rice cultivation. Research is needed to exploit the potential of beneficial
soil microbes like AMF alone or in combination with PSMs for improving crop
productivity and reduced use of P-fertilizers. Interdisciplinary approach should be
followed to investigate the factors affecting P nutrition of rice crop for better
understanding of physiological/molecular basis, screening of better P-efficient
cultivars and simultaneously devising their management strategies to overcome the
problem of P deficiency. More research is needed to develop site specific nutrient
management practices for P nutrition in rice that can be easily adopted by the farmers.
4.3. Harnessing microbial resources for enhancing use efficiency of
potassium and micronutrients
Microbes play a significant role in cycling of nutrient in soil-plant-atmosphere
continuum. Strains of beneficial microbes that directly influence availability of nutrient
such as potassium solubilizing bacteria (KSB), Zn-solubilization microbes, siderophores
producing microbe have been identified. Most of the studies on these microbes are
confined to laboratories; research is needed to explore the possibility of using these
bacteria to enhance the use efficiency of both applied and inherent nutrients in field
scale. In addition, application of improved molecular tools (metagenomics, q-PCR
etc.) is needed to explore the untapped potential of rhizospheric and phyllospheric
microbial resources for their utilization to enhance nutrient use efficiency of rice.
4.4. Nutrient management under abiotic stress
Research has been carried out to develop single and multi abiotic stress tolerant
rice cultivars that can withstand drought, submergence or both to some extent. Advent
of submergence tolerant varieties like Swarna Sub1, IR-64 Sub 1 etc. make it necessary
to devise appropriate nutrient management strategy to enhance productivity and
reduce the yield loss. Some attempt has been made to develop nutrient management
recommendation for submerged rice of flood prone areas of eastern India and found
that application of additional (20%) basal P and post submergence N application
either as soil application or foliar spray (48 h after de-submergence) along with
additional potassium enhanced the submergence tolerance of both Sub-1 introgressed
HYV and its recurrent parent. More research is needed to understand the dynamics of
different nutrients in soil-plant system under various stress conditions and explore
the possibility of revival of stress affected crop through nutrient supplementation.
Till now most of the nutrient recommendations generated address only single stress
condition such as flood, drought and salinity. However, with emerging trend of frequent
occurrence of climatic extreme events it is essential to direct our research towards
developing appropriate nutrient management practice under multi abiotic stress
condition.
4.5. Nutrient management research in a changing climate scenario
Climate change variables including precipitation (amount and distribution),
temperature and atmospheric CO2 concentrations change rice productivity. Agricultural
productivity is potentially changed by associated changes in crop nutrient use.

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Understanding of crop-specific needs for achieving expected yields and soil-specific
nutrient supply characteristics is the primary basis for nutrient management
recommendations. In present scenario it is important to study the expected changes
in ambient CO2 concentration, temperature and precipitation which are expected to
influence the agriculture. Increases in air temperature and changes in precipitation
will significantly impact prevailing root zone temperature and moisture regimes.
Nutrient availability, root growth and development are primarily affected by soil
moisture and temperature. Limited work have been done to understand N and P
dynamics in soil and their subsequent acquisition by crop under elevated CO2 and
temperature condition, however, the nature and extent of the change in these two
parameters is highly site- and soil specific. At the same time little information is
available regarding impacts of elevated CO2on nutrient concentrations in solution-
phase, whose availability will also be indirectly mediated by temperature and moisture
changes. Research is needed to investigate the impact of elevated CO2 and temperature
on dynamics of different nutrient element in soil, availability and mechanism of their
acquisition by plant.
4.6. Nutrient management for next generation rice
Development of next generation rice based on the ideotype concept with a yield
target of 10-12 t ha-1(super rice) and high protein rice with protein content 10-12% are
frontier area of research in rice improvement. New plant ideotype necessitates
appropriate nutrient management practices for realizing the potential yields. Nutrient
response studies are needed for both super and high protein rice to ascertain their
requirement of different macro and micronutrients. Crop simulation models such as
WOFOST, QuEFTS (Quantitative Evaluation of the Fertility of Tropical Soil) and
Nutrient Decision Support System (NuDSS) will be helpful to calculate the nutrient
need of super rice on the basis of potential yield. Understanding source sink relationship
and site-specific nutrient management are promising options to estimate the nutrient
requirements of super rice based on attainable yields and indigenous nutrient supply.
Studies indicated amount of N uptake in super rice varieties could be as high as
18-20 kg N t-1of grain yield and most of the super rice is bred for a high N input
condition. Similarly, in case of high protein rice the N requirement could be different
than the normal rice. Uncertainties in the crop requirements for N, P and K and other
micro-nutrients may result in either excess or deficit application of fertilizers leading
to soil nutrient imbalances and associated negative environmental impact. Research
is needed to monitor the long term impact of cultivation of these next generation rice
on soil health and sustainability and at the same time efforts should be made to
develop appropriate nutrient management strategy that ensures environmental
sustainability while achieving its potential yield.

5. WAY FORWARD
Most of the straight and complex fertilizers currently being used in rice cultivation
are in use for last 50-60 years. Research is needed to identify and develop cheap
chemical and organic source of plant nutrients particularly customized fertilizer

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products specific to crop and region. Blanket recommendations of fertilizers for rice at
state and national level are in practice since long time. At present the nature of soil,
type of varieties, and environmental conditions have been changed from the time
when the fertilizer recommendation was made. Therefore, revised recommendation of
fertilizers are required keeping in mind the high level of exhaustion of soil nutrients by
high yielding varieties.
Progress has been made so far from blanket crop response based approach of
nutrient recommendation to need based site specific nutrient recommendation.
However, to enhance eco-efficiency of applied nutrient and minimize negative
environmental impact, it is essential to adopt ecological intensification based nutrient
management approach which takes into consideration ecological processes and the
beneficial interactions among different components of agro-ecosystem.
The 4 ‘R’ stewardship approach of nutrient management need to be relooked in
the context of development of sensor based precision real time monitoring system
and advent of next generation super, high protein, biofortified and climate resilient
rice. In the context of climate change, nutrient management strategy for enhancing
tolerance to biotic (disease and pests) and abiotic (drought, submergence, high and
low temperature) stresses need to be devised. In addition to this, it is essential to
develop nutrient management strategies for low input rice farming particularly in
difficult ecology.
Some emerging technologies like nano-technology, seed coating, liquid organic
fertilization etc. have potential to bring about substantial improvement in nutrient use
efficiency of arable crops. Both strategic and basic research is required to explore the
possibility of using nano-fertilizers for N and P nutrition of rice and at the same time
assess its undesirable side effects on soil flora and fauna. Liquid organic byproducts
of bioreactors that produce bioethanol has been identified as a good source of nutrient
and its use as a fertilizer is increasing in many developed countries. Recycling
bioreactor waste as a source of nutrient in rice production requires systematic research
and development support and involvement of extension machinery.
Production of EEFS in India is very limited, few companies produce SCU, PCU in
a small scale and inhibitors are mostly imported. Non availability of these products
and associated high cost prevent their wide scale use in rice cultivation. Government
policy support in form of fertilizer subsidy could address this problem. Coating seeds
with nutrients formulation is a promising technique to enhance nutrient use efficiency
and showed positive effect on P and N nutrition however this technique is in nascent
stage and require further investigation for it practical use.
References
Bijay-Singh and Singh VK (2017) Fertilizer management in rice. In: B.S. Chauhan et al. (eds.), Rice
Production Worldwide, Springer International Publishing. pp. 217-253 doi: 10.1007/978-
3-319-47516-5-10.
Bijay-Singh, Varinderpal-Singh, Purba J, Sharma RK, Jat ML, Yadvinder-Singh, Thind HS, Gupta
RK, Choudhary OP, Chandna P, Khurana HS, Kumar A, Jagmohan-Singh Uppal HS, Uppal

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 Assessing Energy and Water Footprints for
Increasing Water Productivity in Rice Based
Systems

R Tripathi, M Debnath, S Chatterjee, D Chatterjee, A Kumar, D

Bhaduri, A Poonam, PK Nayak, M Shahid, BS Satpathy, BB Panda
and AK Nayak

SUMMARY
Water is one of the important elements responsible for life on earth. Globally, three
major sectors i.e. agriculture, domestic consumption and industry compete for water.
India presently has the world’s second largest population and there is a net export of
agricultural products from India, which is likely to continue. These developments will
lead to a larger water demand for the agricultural sector in near future. Water
management is becoming a key issue affecting the availability and distribution of
already scarce fresh water to growing population. The data regarding water usage
and availability of water is not available which poses a challenge for sustainable
management and development of water resources. Hence, measurement and
quantification of the energy footprints, water footprints and water balance components
are fundamental for understanding the hydrological behaviour of a system for effective
water management. The objective of this chapter is to discuss the water footprints of
rice in different cultivation practices in comparison to other crops and discussing the
key challenges and issues related to the water management and water balance studies
particularly in river basins of India and need for advance methodologies for studying
water footprint, and energy balance components. Globally, water footprint of rice
paddy production is 784 km3 yr-1 with an average of 1325 m3 t-1. The mean water
footprint of cereals is about 1644 m3 t-1. Among them, the water footprint for millet is
comparatively large (4478 m3 t-1), while for maize it is comparatively small (1222 m3 t”1).
Water productivity differs with different cultivation systems and irrigation techniques,
which is discussed. The mean water footprint of rice (1673 m3 t-1) is close to the
average for all cereals together. In India there are about 20 river basins which are
presently the source of surface and ground water for many sectors including the
irrigation sector. There is a need to work out on the estimation of the water budget
components of the basin to go for proper utilization of water resources as water
resources and Indian riverine system may face water scarcity situation in near future
to come. In this chapter we have discussed the modern tools, techniques and models
such as remote sensing, GIS and hydrological models (such as METRIC and SEBAL)
which can be used for precise estimation of water budget components in these major
river basins.

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1. INTRODUCTION
Water is going to be one of the important issues concerning humanity in this
century and coming years. The world is already facing a crisis of water supply in
terms of both quantity and quality. Water is the most critical requirement of living
organisms, and it affects human behaviour in a very significant way. Water is regarded
as a gift of nature when available in plenty but becomes precious when its scarcity
occurs. Water is also a source of dispute and even conflict between its different
stakeholders and users. For 21st century, water management is becoming a key issue
since growing pressures are negatively affecting the availability and distribution of
already scarce fresh water to growing population. There are so many factors behind
diminishing water resources such as expanding populations, economic growth,
pollution and seasonal climatic conditions. Regular monitoring and forecasting the
global water cycle using modern techniques is becoming increasingly important for
efficient water management (Ray 2008).
Three major sectors i.e. agriculture, domestic consumption and industry are
competiting for water. Globally and in most major river basins, the biggest volumes
are withdrawn for irrigation purposes. Water use in agriculture is approximately 70%
worldwide. While populations are increasing at a faster rate, the available fresh water
resources are diminishing leading to greater scarcity. Precipitation is the major source
of fresh water, which is stored temporarily in natural areas or in man-made reservoirs.
Around 8% of the annual fresh water renewable resource is used, with 26% of
evapotranspiration of water and 54% of runoff (Ray 2008).
1.1. Global fresh water availability and growing pressure
Even though two-thirds of the global surface is covered by water, only 2.5% is
fresh water. This fresh water is not evenly distributed across the globe. Freshwater
resources are shrinking more rapidly now compared to previous decades due to
population explosion. Since 1970, world population has increased by 1.8 billion whereas
per capita water availability worldwide is a one third now. From 1970 to 2000, freshwater
usage by the agriculture increased by 175% which is consuming 70% of global fresh
water. Only an extremely small portion of the 1.36 billion m3 of global freshwater is
available for use. Various complex processes like evaporation and rainfall between
the sea and the land surface contribute very small quantities of freshwater, to the tune
of 40,000 km3 annually. Globally, in last 25 years, there is a decrease of 27 percent in
per capita water availability; in 1970 it was 10,000 m3 which declined to 7,300 m3 in
1995. Countries are regarded as water-stressed when the per capita annual freshwater
supply remains between 1,000 and 2,000 m3 and water scarce when the supply falls
below 1,000 m3. In India, over the past 50 years, per capita availability of fresh water
has declined from 3,000 m3 to 1,123 m3.
Loss of fresh water due to high evaporation rates is critical in tropical and arid
regions. In India, agriculture is mainly dominated by cereal crops such as rice and
wheat, and yield of cereals is sensitive to changes in temperature. The projected
temperature rise in the twenty-first century, therefore, will have serious implications

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Rice Based Systems 241
for India where high evapotranspiration rate and rising temperature, have profound
implications for freshwater management policies.
1.2. Fresh water withdrawal in India
Rainfall in India and sub-continental countries (Bhutan, Nepal, Bangladesh, and
Pakistan), is limited to three or four months of the year. This monsoon rain also
depends on the same riverine systems for freshwater. India currently withdraws a
little more than 26% of the available freshwater which is far less than Pakistan, with its
rate of 70%, is considered a high water stressed country. Whereas other South Asian
countries are using more than 40% of their available water resources. The annual
Indian evapotranspiration (ET) rate varies between 1,400 and 1,800 mm. It is highest
in west Rajasthan, some parts of Karnataka, Andhra Pradesh, and Tamil Nadu. In
some part of country, evaporation some time exceeds 1,800 mm.
With over a billion people, India presently has the world’s second largest
population and estimate of the population in the year 2050 is 1.7 billion. This is an
increase of approximately 50% in population in the coming 50 years. There is a net
export of agricultural produces from India, which has shown an increase in the past
decade and this trend is likely to continue. These developments will lead to a larger
demand in the total food grains production and ultimately more water for the agricultural
sector in near future.
1.3. Knowledge gap
In most cases data regarding water usage and availability of water is not available
which poses a challenge for sustainable management and development of water
resources. Hence, measurement and quantification of the energy footprints, water
footprints and water balance components is fundamental to understanding the
hydrological behaviour of a system for effective water management. In the assessment
of water resources and derivation of the water balance, it is important to understand
the spatial and temporal dynamics of water footprints, the different components
governing the surface energy balance such as evapotranspiration. This information
is crucial for planning and development of water resources infrastructure and also
agricultural planning. There is a strong need for studying the water and energy
balance for integrated water management at river basin scale along with the water
footprint of crops. Quantitative evaluation of water resources and their change on
the basis of the water balance approach under the influence of human activities are
possible if various components of hydrological cycle are studied. Additionally,
decision making on water management issues are strengthened by water balance
estimates.
Although small scale measurements of components of energy balance and
Evapotranspiration (ET) measurements over a crop canopy are done usually by
Lysimeters and Eddy Covariance approaches, large spatial scale measurements are
still not available. However, estimations of actual ET on large spatial scales would be
useful for many water resource applications including estimating agricultural water
use and monitoring water rights compliance.

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The objective of this chapter is to discuss the water footprints of rice in different
cultivation practices in comparison to other crops and discussing the key challenges
and issues related to the water management and water balance studies particularly in
river basins of India and need for advance methodologies for studying water footprint,
and energy balance components.

2. WATER FOOTPRINT CONCEPT AND CURRENT

SCENARIO
Currently, the ratio of volume of consumptive water use to the quantity of produce
of interest which is termed as water footprints may be used to indicate direct and
indirect utilization/appropriation of fresh water resources. Both consumptive water
uses i.e. the green and blue water footprints and the grey water footprint which is
required to assimilate pollution may be used for fresh water appropriations. Lower
water footprints from a management system indicate its efficiency to produce more
biological yield or product with less amount of water. The water footprint of a product
can be used to provide information to consumers about the water-related impacts of
products they use or to give policy makers an idea of how much water is being
“traded” through imports and exports of the product.
Some major determinants of the magnitude of the water footprint from any area are
(Chapagain and Hoekstra 2004):
 the average consumption volume per capita, generally related to gross income
 the consumption pattern of the inhabitants
 climate, in particular evaporative demand
 agricultural practices
2.1.Water footprints in rice production system
There are two major systems of rice cultivation: low wetland and upland cultivation
systems. Around 85% of the global rice harvest area is resulting from wetland systems
and around 75% of rice production is obtained from irrigated wetland rice (Bouman et
al., 2007). In Asia, paddy fields are generally prepared by tillage followed by puddling
where the top soil is saturated and water remain stagnated during most of the crop
growth period. Whereas, in the USA, Australia and Europe rice fields are dry and
flooding is done later.
Chapagain and Hoekstra (2011) made a global assessment of the green, blue and
grey water footprint of paddy, using a higher spatial resolution and local data on
actual irrigation. They reported that water footprint of rice paddy production globally
is 784 km3 yr-1 with an average of 1325 m3 t-1 (48% green, 44% blue, and 8% grey). They
also observed that the ratio of green to blue water varies significantly over time and
space. They estimated 1025 m3 t-1 of percolation in rice production. They reported that
the green water fraction is significantly larger than the blue one in India, Vietnam,

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Rice Based Systems 243
Indonesia, Thailand, Myanmar and the Philippines, whereas, in Pakistan and the USA
the blue water footprint is four times higher than the green constituent and the virtual
water flows which is related to rice trade internationally was 31 km3 yr-1. They also
reported that rice products consumption in the European nations was accountable
for evaporation of 2279 Mm3 of water and polluted return flows of 178 Mm3 across the
globe, annually mainly in Thailand, India, Pakistan and the USA and the water footprint
due to consumption of rice created moderately low stress on the water resources in
India as compared to that in Pakistan and the USA.
The calculated mean water depth used in cultivation of rice in each of the 13 major
rice-producing countries is presented in Table 1(Chapagain and Hoekstra 2011).
They calculated the total water use (m3 yr-1) for rice cultivation in each country by
multiplying the national harvested area of crop (ha yr-1) with the corresponding depth
of water (mm yr-1) used in rice fields. The water footprint of rice cultivation is thus
calculated as the sum of water evaporated from the crop fields and the volume of
water polluted in the process (Table 2)
2.2. Different Irrigation and tillage methods for reducing the water
footprints of rice
Water plays a major role in global agriculture. Due to rising demand of water
among various sectors, it is going to be a scarce commodity worldwide. Reduction of
crop water footprint is therefore very much essential which can be achieved by
lowering the crop water use from the crop fields. Work on improving the water
productivity of crop by reducing amount of applied irrigation water, which in turn
reduces the crop water footprint through adoption of various irrigation methodologies
like alternate wetting and drying, mulching, micro irrigation, namely, drip, sub surface
drip and sprinkler irrigation, are going on globally.

Table 1. Depth of water used in rice production (mm yr-1) for the 13 major rice-
producing countries for the period 2000–2004.
S.No. Countries Evaporation (green) Evaporation(blue) Pollution (grey)
1. China 228 302 73
2. India 314 241 34
3. Indonesia 260 217 53
4. Bangladesh 192 202 36
5. Vietnam 139 92 58
6. Thailand 252 149 31
7. Myanmar 297 133 18
8. Japan 219 258 39
9. Philippines 277 139 26
10. Brazil 260 220 20
11. USA 168 618 75
12. Korea, Rep. 232 253 55
13. Pakistan 124 699 26

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Table 2. Total national water footprint of rice production and percolation of water in
the 13major rice-producing countries (billion m3 yr-1) for the period 2000–2004.
National water footprint of rice production (evaporation + pollution)
Green Blue Grey Total
China 65.2 86.5 20.8 172.5
India 136.3 104.5 14.7 255.5
Indonesia 30.3 25.3 6.1 61.7
Bangladesh 20.4 21.5 3.8 45.7
Vietnam 10.5 6.9 4.3 21.7
Thailand 25.2 15.0 3.1 43.3
Myanmar 19.1 8.5 1.1 28..8
Japan 3.7 4.4 0.7 8.8
Philippines 11.2 5.6 1.0 17.9
Brazil 8.8 7.4 0.7 16.8
USA 2.2 8.0 1.0 11.1
Korea, Rep. 2.4 2.6 0.6 5.6
Pakistan 2.9 16.3 0.6 19.9

It was found that the moderate alternate wetting and drying technique was able to
increase grain yield by 6.1% to 15.2% and water productivity by 27% to 51% at the
same time reducing the amount of irrigation water applied by 23.4% to 42.6% when it
was compared with conventional irrigation practices (Yang et al. 2017). Alternate
wetting and drying of paddy fields under the System of Rice Intensification (SRI) was
found to be effective in increasing paddy yield by 78% with about 40% reduction in
total amount of applied water for irrigation, which also reduced the costs of production
compared to conventional continuous flooding (Sato and Uphoff 2007). Drip irrigation
method was found more effective with SRI to minimize water losses and also to
increase the rice yield based on field evaluation in India. It has been found that
adoption of SRI along with drip irrigation with a dripper spacing of 20 cm with plant to
plant spacing of 30 x 30 cm was able to give the highest net return (B:C ratio 3.23) with
highest water productivity of 0.90 kg m-3 and highest water-energy productivity of
7.85 kg kW h-1 as compared to conventional paddy cultivation (0.16 kg m-3 and 1.02 kg
kW h-1, respectively) under continuous flooding (Rao et al. 2017).
A study conducted on winter wheat in Northern China showed that deficit irrigation
reduced blue WF (by 38%) with an average yield reduction by 9% and increased
irrigation efficiency by 5%. It was also reported that the organic or synthetic mulching
practices reduced blue WF by 8% and 17%, respectively with the same yield level
with an improvement in water use efficiency by 4% and 10%, respectively. It was also
found that under the deficit subsurface drip irrigation (SDI) with organic mulching,
irrigation efficiency decreased blue WF by 44% and increased it up to 45% from 36%
as was found in case of sprinkler irrigation without mulching.
In a study, consumptive WF of different crops such as potato, maize, and tomato
were studied. Data on four irrigation techniques viz. furrow, drip, sprinkler, and

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Rice Based Systems 245
subsurface drip (SSD) with four irrigation strategies like full (FI), deficit (DI),
supplementary (SI) and no irrigation were analyzed under different mulching
treatments. Data from different countries were analyzed. Analysis revealed that water
footprint (WF) was found to be reduced to 8–10%, 13%, 17–18%, and 28%, respectively
under drip or subsurface drip irrigation, surface drip or subsurface drip with organic
mulching, and surface drip or subsurface drip in combination with synthetic mulching,
respectively as compared to the control (furrow irrigation, full irrigation, no mulching).
They reported that the water footprint of growing a crop was the lowest under drip
irrigation, followed by furrow irrigation, sprinkler irrigation and rain-fed condition. It
was also observed that growing crops with sprinkler irrigation system gave the largest
consumptive water footprints, followed by furrow irrigation, surface drip irrigation
and subsurface drip irrigation. This study interestingly gave the finding that furrow
irrigation was able to give less consumptive water footprint of crop as compared to
the sprinkler irrigation system, though irrigation efficiency of sprinkler irrigation is
higher than that of furrow irrigation.
2.3.Water footprint in different crops
In the past century the drawing of fresh water has been increased by 7 times due
to increase in population pressure and industrialization. At present, the agriculture
alone consumes around 85% of global blue water and 99% of global green plus blue
water (Hoekstra and Mekonnen 2012). The variation of water footprint was found
significant among crops and production regions. Crops having higher yield or biomass
generally have a less water footprint as compared to the crops having lower yield and
biomass. The mean global water footprint varied largely from sugar crops (197 m3 t”1),
vegetables (322 m3 t”1), fodders (253 m3 t”1), roots and tubers (387 m3 t”1), fruits (967 m3
t”1), cereals (1644 m3 t”1), oil seed crops (2364 m3 t”1) and pulses (4055 m3 t”1). The mean
water footprint of cereals is about 1644 m3 t”1. Among them, the water footprint for
millet is comparatively large (4478 m3 t”1), while for maize it is comparatively small
(1222 m3 t”1). The mean water footprint of rice (1673 m3 t”1) is close to the average for
all cereals together (Fig.1). Crops like soybean, sorghum and cotton has larger water
footprint than rice (Mekonnen and Hoekstra 2013).

Fig. 1. Global average water footprint (m3 ton-1) (a) green+blue (b) grey (modified after
Mekonnen and Hoekstra 2014).

Kar et al. (2014) has analyzed the water foot prints for maize crops, irrigated rice,
rainfed rice and water footprints of some winter crops (maize, groundnut, sunflower,

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wheat, potato) grown in rice fallow in Odisha. They reported a higher yield by 59%, 29
%, 33 %, 58 %, and 19% in respective crops when three irrigations was applied and
with four supplemental irrigation there was an increase of yield by 214%, 89%, 78%,
81% and 54%, respectively, for maize, groundnut, sunflower, wheat and potato over
two irrigation. They also reported that water footprints of the crops were less when
there was an increase in the crop yield at higher irrigation levels. They also estimated
the water footprints of crops like lathyrus, black gram, pea and chickpea under various
seeding or tillage methods in rainfed lowland rice fallow like relay (farmers’ practice),
one ploughing and sowing on same day, two ploughing in different days and sowing
after second ploughing, zero tillage and conventional tillage. They reported a less
blue water footprint under the tillage treatment, two ploughing in different days and
sowing after second ploughing (5941, 6754, 6678, 8500 m3ton-1 for lathyrus, black
gram, pea and chick pea, respectively), whereas the water footprint was maximum
under farmers’ practice (298, 8657, 12833, 9850 and 15455 m3ton-1 for lathyrus, black
gram, pea and chick pea, respectively).

3. WAYS TO MINIMIZE THE WATER FOOTPRINTS UNDER

DIFFERENT CROPPING SYSTEM
The crop evapotranspiration and thereby water foot prints in various crop
production system can be minimized by minimizing irrigation water losses through
adoption of modern scientific irrigation approaches like adoption of micro-irrigation
technology, adoption of conservation agriculture like SRI technique of rice cultivation
and mulching, precision land leveling techniques for uniform water application in
field, and optimal use of fertilizer in fields in order to reduce the grey water foot print.

4. THE PROJECTED FUTURE WATER DEMAND FOR

MAJOR RIVER BASINS OF INDIA
Different river basins have their reach in different states of India. Water demand in
industrial and domestic sectors besides the irrigation sector is on a rising trend day
by day. River basins are mainly the sources of water for all those sectors. Due to
rising water demands from various sectors many river basins are going to be water
scarce by 2050. It has been projected that several basins in India would deplete more
than 60% of potentially utilizable water resources that will be available in 2050, and
face acute water scarcities. Some of the major river basins like Indus and Ganga, will
have as high as 0.07181 billion m3 and 0.02425 billion m3 deficit water supply for
industrial and other sectors by 2050, whereas river basin like Mahanadi will be able to
supply 20% and 33% less water as compared to water available in 2010 for industrial
and other sectors due to a rising demand of water amongst various sectors (Gaur et al.
2011). This serious threat of water scarcity from various Indian river basins must be
dealt with priority.

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 In India there are about 20 river basins which are presently the source of surface
and ground water for many sectors including the irrigation sector. Among surface
and ground water, the availability of surface water is highly seasonal, whereas the
groundwater is a steady source of water throughout the year. In terms of water
availability from the river basins which comprises both the surface water and the
groundwater, groundwater constitutes on an average 50%, though inequalities exists
across river basins. As per estimation from the Ganga river basin, the share of
groundwater in the total water storage is about 64%, whereas, from basins like Krishna,
Mahanadi, Subernarekha, and Narmada it is about 35% or less. At present irrigation
sector in India is the most consumer of water from most of the river basins from India.
Due to rise in population the water demands in industrial and domestic sectors besides
the irrigation sector is increasing rapidly due to which many of the Indian river basins
are becoming water scarce. It is going to be more serious in 2050 when Ganga and
other river basins like Mahanadi and Pennar will also face severe water availability
problems (Gaur et al. 2011). Estimating the water balance components on river basin
scale will help in taking best water management measures especially in irrigation
sector to combat the water scarcity situation at basin level.

5. EVAPOTRANSPIRATION IN DIFFERENT RIVER BASINS

Evapotranspiration (ET) percentage for Narmada, Godavari, Cauvery and Krishna
basins, varies between 48.5 and 59.8% of precipitation. For these basins, overall ET
value is 58.3%. For the trans-boundary basins, such as Indus, Ganga and Brahmaputra,
ET is 23.1% of precipitation for Ganga and 71.7% for Indus basins. For these basins,
overall ET is 17.6%.
5.1.Water balance studies: Current status and future scenario
Based on hydrological simulation of Mahanadi River Basin and impact assessment
of Land Use and Land Cover (LULC) change on surface runoff generation through
use of hydrological model, an increased pattern in the annual flow of stream by 4.53%
was found in the Mahanadi river basin which was contributed to the reduction in
forest cover by 5.71% (Dadhwal et al. 2010). Water budget components estimation on
a point scale using basic water budgeting equation with the help of GIS was done in
the Lower Yamuna Basin, Delhi. Based on water balance estimation, it was found in
the study that all stations in the region are dry as the annual rainfall in the region
remains short of annual potential evapotranspirative demands (Ahlawat 2014).
Water resource assessment of Narmada Basin, India was done by using the
Variable Infiltration Capacity (VIC) hydrological model. It was observed that there
was a substantial increase in evaporation component by 0.56% whereas with a decrease
in runoff, base flow and stream discharge by 42.42%, 34.18% and 34% , respectively
in year 2005 in comparison with year 1975 due to change in LULC because of
construction of Indira Sagar Dam during the analysis period (Shiradhonkar 2015).
The water balance components of Chambal river basin using VIC model was
estimated. It was observed that the land use and land cover, soil and slope

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characteristics were the main parameters influencing the hydrological processes in

considerable manner. The annual runoff over the basin was 50% with a higher runoff
from areas having less vegetation, higher slopes. The runoff was also found to be
affected in considerable manner with respect to soil type and soil characteristics over
the area.
Impact study of Climate Change on the Hydrology of Mahanadi river basin was
done using Statistical Downscaling Model (SDSM). A decrease in precipitation pattern
for the time period 2020s and 2080s annually and seasonally was found from
downscaling of the precipitation in future scenarios through use of SDSM (Pandey
2015).
Impact of climate change on water balance in Krishna river basin was under taken
where the water balance components were estimated using semi-distributed
hydrological model namely Soil and Water Assessment Tool (SWAT). Based on climate
projections estimated that in the period 2041-70 (2050s) there will be increase in the
annual precipitation, surface runoff, water yield and actual evapotranspiration as
compared to the baseline simulation period (1961-1990) whereas no substantial change
for these parameters were observed by the model runs in 2020s (2011-2040).
The runoff, sediment and water balance components of Ken basin, India, were
estimated using remote sensing derived products (SRTM DEM), gridded precipitation
and temperature data (LANDSAT TM data), and using Soil and Water Assessment
Tool (SWAT) within a geographic information system (GIS) modeling environment. It
was found that evapotranspiration was more predominant which was around 44.6%
of the average annual rainfall falling over the area whereas the stream runoff was
34.7% and deep aquifer recharge is 19.5% for the river basin (Himanshu et al. 2017).
5.2. Estimating the evapotranspiration
For studying the water balance over a river basin, the most important, challenging
and variable component is the Evapotranspiration (ET) over the river basin.
Quite a few methods are used to measure or estimate ET, including hydrological
approach, micrometeorological method and plant physiological approaches. Eddy
covariance (EC) is the only direct and accurate measurement method which provides
latent heat flux (LE) and sensible heat flux (H) as independent variables. Globally
though works in this field has been done by researchers but literature availability on
works related to eddy covariance method from India are rare. Eddy covariance method
was used in Philippines for estimating the actual ET in direct-seeded rice field and it
was observed that the average growing season ET rate varied from 4.13 to 4.36 mm d-
1
in 2011 and 2012, respectively. They observed ET of growing rice in the range of
400–556 mm in Philippines. Timm et al. (2014) in Brazil reported that ET reached almost
7 mm d-1 at the end of the reproductive phase (flowering) of rice crop when leaf area
index was at its peak (4.57 m2 m-2). Hatala et al. (2012), using the eddy covariance
method, estimated daily evaporation up to 10 mm d-1 in a rice paddy field. In India,
Tyagi et al. (2000) reported an ET of 587mm in rice through eddy covariance method,
and the same was found to be 701mmthrough water balance approach.

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5.3. ET measurements over spatial scales
Because it involves the transfer of large quantities of water away from earth’s
surface, the combined effects of evaporation from soil and leaves and transpiration
from plants can have important implications for water resources. Small scale
measurements of evapotranspiration (ET) are already prevalent and well-established.
Eddy-covariance stations, for example, are frequently used to determine turbulent
fluxes, representative of a relatively small surface area, up to hundreds of meters.
Unfortunately, these measurements cannot be easily extrapolated over larger
landscapes due to heterogeneities in land characteristics such as elevation, vegetation,
and soil types (Choi et al. 2009).
A number of algorithms utilizing remote sensing to retrieve ET on a large scale
have been developed. In addition to providing estimates for larger scales than in situ
measurements, remote sensing is often inexpensive for the user to implement as many
of the satellite platforms are developed by the government and data are freely available
to the public. Two such operational ET modeling schemes include METRIC (Mapping
Evapo Transpiration at high Resolution with Internalized Calibration) and the Fusion
scheme made up of ALEXI (Atmosphere-Land EXchange Inverse model), DisALEXI
(Disaggregated ALEXI) and STARFM (Spatial and Temporal Adaptive Reflectance
Fusion Model).The basis for both the METRIC and Fusion modeling schemes is the
surface energy balance.

6. ENERGY BALANCE OVER RIVER BASINS COVERING

RICE CULTIVATION AREAS
Agro-ecosystem productivity rapidly responds to all the climatic variables like
atmospheric temperature, precipitation, humidity, solar radiation, and
photosynthetically active radiation (PAR). The formation of clouds and succeeding
precipitation is dependent on the heat fluxes which are governed by incoming and
outgoing radiations. The dynamics of heat fluxes are determined by the nature and
type of vegetation covering the soil. Therefore, the determination of a correct energy
balance (EB) mechanism is a crucial prerequisite to understand and model an
agroecosystem and its interaction with the climatic variables, which is associated
with the yield of the crop. Energy and mass transfer are two most important biophysical
processes that influence the EB in an agroecosystem. The lowland river basins are
mainly favoured for lowland rice and rice based cropping in eastern India. The lowland
rice has a unique characteristic, since it grows under semi-aquatic environment or
flooded environment. Such environment differs greatly from other upland based crop
ecosystem since a continuous water layer is maintained above the soil surface which
strongly influenced the surface EB components. Therefore, the exchange of carbon
dioxide, methane, water vapour and energy in flooded rice ecology varies to a great
extent and shows a close interrelationship between carbon cycle, hydrological cycle
and energy balance. Such differential nature of rice cultivation may modify the surface
runoff, groundwater storage, water cycle, surface energy budget and possibly the
microclimate of the region.

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Surface EB is mainly described by four types of energy fluxes, i.e. net radiation
flux (Rn), sensible heat flux (H), latent heat flux (LE), and soil heat flux (G) approaching
into or going out of the soil or water medium. The H is directed away from the surface
throughout the daytime, while it is in opposite direction during the evening and
nighttime. The LE is the result of evaporation and evapotranspiration at the surface.
The Rn is a consequence of radiation balance at the surface, a resultant effect of
upwell and downwell radiations. During the daytime, solar radiation is usually
dominated and Rn is directed towards the surface of the soil, while vice-versa at
nighttime. The G at the surface of soil was dissimilar with the soil beneath after certain
depth, and the G at the surface achieved better closure.
6.1. Land characteristics influencing energy balance
The nature of soil and land plays an important role in the EB by influencing
energy flux in the soil profile. These influences determine the change in soil temperature
in the soil profile, which ultimately control microclimate of the crop-soil-water
continuum. The thermal characteristic of soil varies with soil water content, maximum
and minimum air temperature, porosity, vapour pressure, saturated vapour pressure
and water vapour content. The ground surface gets heated more during the day by
insolation than layers underneath, resulting in temperature gradient between the
surface and subsoil on the one hand and surface and air layers near the ground on the
other. Within the soil this causes heat flow downward as a thermal wave, the amplitude
of which changes with depth. Estimation of soil heat flux (G) from the soil temperature
data can provide an understanding of the gain or loss of heat by the soil from the
atmosphere. The Bowen ratio method is an indirect method that has been widely
applied and tested in various environments to characterize the land. This ratio
describes the relationship between sensible (H) and latent heat (LE) fluxes and can be
used as a measure of evapotranspiration including tall vegetation. Surface albedo is
another important land characteristic which determines the surface energy budget
and inuences the distribution of radiation energy in earth–atmosphere system and
further regulates the atmospheric circulation patterns and hydrologic processes. It
strongly depends on soil moisture and temperature (Zheng et al. 2014). Surface
emissivity is a measure of the efficiency with which surfaces convert kinetic into
radiant energy.
6.2. Estimating energy balance using a single eddy covariance system
A field experiment was conducted using a single eddy covariance (EC) system to
study the surface energy budget and energy balance closure (EBC) in rice-rice ecology
at ICAR-National Rice Research Institute, Cuttack (Unpublished). Due to the presence
of standing water in the rice field, the average latent heat flux at surface and canopy
height was higher than sensible heat flux at surface and canopy height, respectively.
The average value of residual heat flux (R) was 10.3-12.0% higher in wet season
compared to dry season. Soil temperature (Tg) was highest in dry fallow, while the
skin temperature (Ts) was highest in dry season. Average Bowen ratio (B) ranged
from 0.21-0.60 and large variation in B was observed during the fallow periods as

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compared to the cropping seasons. The magnitude of aerodynamic, canopy and
climatological resistances increased with progress of cropping season was found
smallest during the fallow period. The actual evapotranspiration (ETa) measured during
both the cropping seasons was higher than the fallow period.
6.3.Remote sensing for energy balance studies
Satellite technologies are now helpful in quantifying the radiation and energy
exchanges between sun, earth, and space. Nevertheless, satellites cannot directly
measure the magnitude of the energy flows within the atmosphere and at the Earth’s
surface. Evapotranspiration is the most difficult hydrological flux to estimate or model
especially at regional or global scales for assessing the water resource base.
Evapotranspiration estimation based on weighing lysimeter, Energy Balance Bowen
Ratio (EBBR), eddy covariance techniques, pan-measurement, sap flow, scintillometer,
etc. are mainly based on complex models and equations. Moreover, these methods
are variable for local, field, and regional scales. These conventional methods can
provide the accurate estimates of ET over a homogeneous area. But natural
heterogeneity of the land surface and complexity of hydrologic processes do not
favor upscaling of such measurements. Remotely sensed images are a promising
source of data for mapping regional- and meso-scale patterns of ET on the Earth’s
surface. Remote sensing images with visible, nearinfrared, and thermal infrared bands
are used to retrieve the land surface temperature. These surface parameters estimated
from satellite data are used for simulating surface fluxes and ET.
6.4.Advantages of space technologies for energy and water balance
studies
Remote sensing data presents an interesting opportunity as it allows for the
quantification of key water balance components such as evapotranspiration. Space
technology applications have begun to permeate many aspects of life in our modern
societies. A growing number of activities–weather forecasting, global communications
and broadcasting, disaster prevention and relief–increasingly depend on the
unobtrusive utilisation of these technologies. The main advantages of using satellites
are summarised by Payne et al. (2006). Satellite data may be collected year-round and
can provide information when field data collection is not possible, due to remote
locations or bad weather conditions. This method also reduces cost when compared
to traditional field data collection methods in remote environments (landcover
classification for example). Remote sensing may be an option for supplementing more
intensive sampling efforts and help extrapolate findings. It is also possible to measure
elements of the global water cycle using diverse space-based systems. The estimated
residence time for water range from one week (e.g. biospheric water) to 10,000 years
(e.g. ground water) – hence the need for reactive, timely and long-term observations.
6.5.Limitations of remote sensing for energy balance studies
Uncertainties in the radiance measurement caused by atmosphere require the
corrections for the atmospheric effects. There is requirement of increasing accuracy

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of some land surface variables derived from remote sensing images for increasing the
accuracy of ET estimation. It’s very difficult to estimate the surface parameters such
as surface temperature from heterogeneous surfaces compared to homogeneous well-
watered vegetative surfaces. Differences in received radiances will occur due to the
differing amounts of soil and vegetation in the field of view when sensor viewing
changes from one angle to another.
Different models are used for different land surface characteristics. However, till
date, there is no universal model, which could be used throughout the world
irrespective of the changes in land surface characteristics, in the climate and terrain
without any modification or improvement to estimate the ET from satellite data.
Meteorological data which are collected at near-surface height required in most of the
ET models. These meteorological parameters are estimated at a satellite pixel
interpolation. Accuracy of the interpolation methods are required to be improved
while using the data for different climate and terrain conditions.
Nocturnal transpiration and dew may also affect significantly the ET estimation.
Nocturnal transpiration has been widely observed using sap-flow and gas exchange
measurements with ratios of night-time to day-time transpiration as large as 25%
being reported (Dawson et al. 2007). If nocturnal transpiration occurs at sites with
high LAI, this process could be an important source of error in remote sensing based
ET estimation because of its association with nocturnal vapor pressure difference
and wind speed. Adversely, at sites with low LAI, this process will tend to reduce this
source of error so that it may be ignored when considering daily TIR-based estimates
of ET.

7. WAY AHEAD AND FUTURE WORK SCOPE

To check the decline of surface and ground water resources in India it is highly
essential to adopt suitable agricultural techniques and agricultural management
practices for yield maximisation with less consumption of water. At present there is a
need for prioritising the appropriation of fresh water resources to different components
or crop production system, domestic and industrial sector to produce a particular
product or to complete one process requiring water from a particular management
system. The appropriation of water among different sectors or different crop production
systems is very difficult unless there are some sound methods or indices for quantifying
the water requirement from this production system.
There is a need to work out on the estimation of the water budget components of
the basin to go for proper utilization of water resources as water resources and Indian
riverine system may face water scarcity situation in near future to come. Remote
sensing, GIS and hydrological models are the modern tools that can be used for
precise estimation of water budget components in these river basins. As part of the
National Communication (NATCOM) project by the Ministry of Environment and
Forests, impact of the climate change on the water resources of Indian river systems
was quantified and the initial analysis revealed severity of droughts and intensity of

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floods in various parts of the country may get deteriorated. Governments must
increasingly ensure that farmers use water resources efficiently, and that they are
allocated among competing demands in a way that enables farmers to produce food
and fibre, minimise pollution and support ecosystems, while meeting social aspirations.
Also, the government should ensure the internal water-sharing issues based on
sound, internationally accepted principles. A failure to do so would create internal
water-related conflicts.
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M.Techdissertation (http://ethesis.nitrkl.ac.in/6676/1/Pooja_M.Tech_(R)_Thesis.pdf.;
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 Agro Ecological Intensification of Rice Based
Cropping System

BB Panda, BS Satapathy, AK Nayak, R Tripathi, M Shahid, S

Mohanty, D Bhaduri, R Khanam and PK Nayak

SUMMARY
Agroecological intensification of rice based cropping system mainly aims at
achieving maximum system productivity with minimum environmental impact by
managing and organizing crops in a way that they best utilize the available resources
(soil, air, sunlight, water, labour, equipments) and beneficial interactions among
themselves. Based on agro-ecological conditions, market and domestic necessities
and facilities available with farmers, the dominant rice based cropping systems
followed in eastern India are rice-rice, rice-wheat, rice-rapeseed/mustard, rice-
groundnut, rice-potato and rice-pulses etc. Cropping system research systematically
focused on development and management of site specific suitable rice based cropping
system particularly for rainfed regions of the country to ensure livelihood security of
the poor, small and marginal farmers. Ecological intensification is conceptualized to
increase crop yields per unit land, time, and other consumable resources used in food
production. Therefore, for improving the profitability, addressing biodiversity
conservation, climate change mitigation and long term sustainability we have to
exploit the food production system through ecological intensification of suitable rice
based cropping systems.

1. INTRODUCTION
Indian agriculture is largely dependent on rice based cropping systems.
Productivity enhancement of these systems has been proved as an important means
of achieving livelihood security, higher income, reduced poverty and employment
generation. Rice-based cropping system secures the livelihood of more than half a
billion farm families. Since Green revolution, the food grain production has increased
manifold in India with adoption of input responsive high yielding varieties. However,
urbanization and globalization and rapid economic growth has already brought a
considerable change in the food habits from staple food towards fruit, vegetables etc.
Hence, the per capita rice consumption has followed a declining trend and it seems
the trend would continue till 2030 indicating for an urgent attention toward diversified
and intensified cropping system. Adding to it cereal based cropping systems has
raised many uncommon issues now and continuation of the green revolution practices
has degraded the soil health and fertility, brought dominance of weed flora, soil
pathogen etc.
Rice-based cropping systems also produce and emit dominant green house gas
(GHG) methane that largely controlled by water and residue management practices.

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Further, the importance of prevailing rice based cropping system is now-a-days losing
ground due to decrease in factor productivity. Therefore, identification of suitable
rice-based cropping systems with higher resource use efficiency fitting to the local
agro ecological situation is the need of hour for improving the profitability and
employment generation in agriculture.
Diversification has been well reported as an alternative option for sustaining the
land productivity and enhancing farm income for achieving a stable agricultural
development. In eastern Indian states, rice-based cropping systems are the most
dominant system covering 43% of the country’s rice growing area. Rice-based systems
are intimately connected with development of water resources as rice is a big consumer
of water.
However, the natural resources are shrinking day by day making resource-use
efficiency an important issue while considering the suitability of any cropping system.
As rice is synonymous with life of eastern Indian people any alternation to the
existing system with a tendency to decline rice productivity will be neither sustainable
nor acceptable to the farmers. Therefore, component crop selection to be well
maneuvered to harvest the synergism among this crops for efficient utilization of
resources while mitigating the adverse environmental impacts.
In this chapter authors have tried to identify the issues associated with rice based
cropping system. Current station of diversification and intensification of the rice
based cropping system has been discussed. Further the optimal management options
indentified in different parts of the country and abroad has been explained. The
problem and management options for addressing rice fallows particularly in eastern
India has been summarized.
2. Agro-ecological intensification
Agricultural intensification aims at increasing the productivity of existing land
and water resources in the production of agriculture and allied products.
Intensification was generally associated with higher external inputs use earlier but
now defined as more efficient use of production inputs. Use of high yielding varieties
with higher resource/labour use efficiency resulted substantial productivity
enhancement. Better management practices has already brought in rice intensification
(SRI) in most of the rice growing countries raising the land, water, seed and labour
productivity (Hassan et al. 2015). However, ecological intensification (EI) is gaining
momentum now internationally. Ecological intensification is conceptualized as an
increasing crop yields per unit land, time, and other consumable resources used in
food production. It is particularly relevant for addressing biodiversity conservation
and climate change mitigation (Laurance et al. 2014). The original vision of ecological
intensification was based on narrowing the yield gap, soil quality improvement and
precise application of inputs (Cassman 1999).
An estimate says that India is home to more than 250 cropping systems. Based on
rationale of spread of crops; about 30 cropping systems have been identified as
important cropping systems. Among these, rice-based cropping system is the major

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257
cropping system practiced in India. In rice ecosystem of eastern India, rice-rice, rice-
wheat, rice-rapeseed/mustard, rice-groundnut, rice-potato and rice-pulses are
commonly practiced cropping sequences. With the introduction of stress tolerant
and short duration varieties, irrigation facilities and conservation practices there is
tremendous scope for crop intensification for increasing system productivity and
income of farmers. Diversification of crops and cropping systems having higher
water productivity, economic profitability and long-term sustainability with the
availability of modern management techniques may prove a better option in this
respect. Inclusion of legumes and oilseeds using intensification approach based on
resource availability can make a substantial enhancement in productivity and income
in addition to soil fertility improvement.
Rice based cropping system seems to be continued as the mainstay of Indian
agriculture. To achieve the livelihood security of the poor, small and marginal farmers,
we need to develop rice based system with higher productivity and profitability by
practising multiple cropping both in irrigated and rainfed ecologies. A number of
alternative cropping systems have already been identified (Table 1) for different regions
of the country and neighbouring countries. It is necessary to enhance the profitability
and sustainability of newly developed diversified and intensified cropping system
through appropriate management practices. Simply accelerating yield gains of existing
food production system leads to amplification of environmental degradation which is
not sustainable for ensuring food security. Therefore, we have to exploit the food
production system through ecological intensification of existing cropping systems.
2.1. Rice-wheat cropping system
Rice-wheat cropping sequence is the predominant cropping system covering
about 10.5 million hectares of area in the country with a major contribution to the
cereal production. Continuous adoption of rice-wheat sequence has led to weed flora
shift; disease and insect-pest build up, decline in factor-productivity, which ultimately
resulted in declining the system efficiency and productivity. Hence rice-wheat system
can be made sustainable and profitable following the ecological approaches. For
example, rice-vegetable pea-wheat-greengram sequence was a better system than
rice-wheat at Karnal, Haryana, whereas hybrid rice-gobhi sarson-okra system registered
maximum water productivity, production efficiency and rice equivalent yield compared
to the pre-dominant cropping system of the region i.e. rice-wheat and rice-chickpea in
clay loam soils of Jabalpur (MP). Desai et al. (2016) concluded that resource rich
farmers can diversify the existing rice- wheat- fallow system to rice-sorghum-sorghum
ratoon system for obtaining higher system productivity and profitability in south
Gujarat but resource poor farmers can adopt rice-sweet corn- black gram or rice-green
gram-groundnut cropping system for improving the soil fertility. In Punjab, maize-
potato-onion cropping system has been recommended as an efficient cropping system
for replacing existing rice-wheat system. Similarly, rice-wheat cropping system can
effectively be replaced with rice-vegetable systems with the inclusion of vegetables
like french bean, potato, cauliflower, rajmash, peas and garlic to fulfil the daily needs
of farmers and to get higher returns and better soil health. The rice-chickpea-vegetable

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cowpea cropping system can be suggested for diversifying rice–wheat system in the
irrigated situations of Kumaon Himalayas.
Intercropping of legumes, vegetables and other high value crops along with the
new crop establishment techniques i.e. FIRBS is the way towards farmer’s nutritional
security and economic growth (Naresh et al. 2017). Prasad et al. (2013) observed that
intercropping of potato with wheat and inclusion of greeengram seems more
productive, resource-use efficient and remunerative compared to rice–wheat or rice–
fallow systems under irrigated ecosystem of Jharkhand. Saha et al. (2010) reported
that rice-potato-blackgram and rice-maize (cob) + vegetable pea (1:2)-green gram
cropping system was superior to rice-wheat system in sandy clay loam soils of
Varanasi, UP.
Introduction of green manuring or leguminous crops in the existing rice-wheat
system in our neighbouring country Pakistan not only increased grain yields but also
improved the physio-chemical properties, organic matter contents and nutrients
availability. Unlike Pakistan, additions of cereal crops under cereal based cropping
system were also found most energy, environmentally and economically efficient
cropping systems for tropical region of Nepal (Pokhrel and Soni 2017).
2.2. Rice-rice cropping system
Next to rice-wheat, rice-rice is another extensively cultivated cropping system
spreading over 6 million hectares area in India. Poor resource use efficiency, micro
nutrient deficiency and deterioration of soil physical properties are major issues for
sustaining productivity of rice-rice cropping system. Sharma et al. (2016) suggested
for adoption of good agricultural practices and conservation agriculture for increasing
the productivity and income of rice based cropping systems. Baisya et al. (2016)
revealed that highest rice-equivalent yield and nutrient-use efficiency and productivity
can be achieved by cultivation of cabbage-greengram/blackgram in place of summer
rice. Under irrigated lands of Bihar, rice-tomato-bottle gourd, rice-potato–onion, rice–
coriander–lady’s fingers, rice–carrot–cowpea and rice–mustard–tomato cropping
systems are promising. However, in irrigated Chhattisgarh plains rice-potato-cowpea
system was most productive with rice-equivalent yield of (27.04 t ha-1 year-1),
production efficiency (83.97 kg ha-1 day-1), profitability (Rs. 320.36 ha-1 day-1), and
higher net return of Rs. 1,16,929 ha-1 year-1 as compared to other cropping systems
(Prasad 2016).
In rice-rice double cropped areas of Krishna–Godavari delta of Andhra Pradesh,
replacing dry season rice crop with maize recorded higher system productivity along
with economic efficiency whereas rice–mustard system recorded highest system
energy use efficiency (Rao et al. 2014). Sravan et al. (2014) observed that inclusion of
sunnhemp and blackgram is the best system for North Coastal Zone of Andhra Pradesh.
In the high rainfall zone of south Gujarat rice–fenugreek–okra system was most
productive and remunerative followed by the rice–onion–cowpea system.
Inclusion of high yielding mustard either under tilled or zero tilled relay
cropping can also bring substantial improvement of rice- rice cropping system (Hassan

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et al. 2015). Alam et al. (2017) opined that diversifying boro rice with wheat-mungbean
is economically superior to boro rice-aman rice system. A additional crop of pea as
green pod vegetable in rice–fallow–spring irrigated rice cropping system increased
farm productivity by 1·4-fold and income by four fold (Malik et al. 2017). However, in
non-saline areas of Bangladesh, the most profitable cropping pattern is rice -mustard-
jute and rice-potato-jute compared to rice-boro rice cropping system. Further
intensification of the double rice cropping sequence with addition of mustard,
mungbean in lowland rice ecosystem of Bangladesh can be done for higher productivity,
soil enrichment, economic benefit and employment.
In irrigated medium land of coastal Odisha rice-sunflower-greengram, rice-maize-
cowpea, rice-potato-sesame are found promising with highest rice equivalent yield of
18.8 t ha-1 which was recorded in rice-potato-sesame cropping sequence followed by
rice-maize-cowpea (18.2 t ha-1). Based on the research work done under different on-
farm trials in rice based cropping sequence, watermelon, chilli and sunflower found
promising crops for both medium and high salinity areas whereas, lady’s finger found
most remunerative under medium salinity condition after rice.
2.3. Rice-maize cropping system
Rice-maize cropping system are practised about in 3.5 million hectares areas in
Asia while it is grown in 0.53 million hectares in India. This system is developing very
first in Bangladesh, South and North India. Rao et al. (2014) reported that shifting
rice-rice double cropping in Krishna-Godavari delta areas of Andhra Pradesh to rice-
maize, recorded higher system productivity and economic efficiency whereas higher
system energy use efficiency was observed in rice-mustard and higher land use
efficiency was recorded in groundnut. Rice-rice or rice-fodder maize sequence had an
adverse impact on yield sustainability as it decreased the yield in low land rice
ecosystem of Karnataka but rice-soybean cropping sequence maintained/sustained
the rice yield on long term basis. Bastia et al. (2006) has concluded that rice-maize-
cowpea was the most productive and remunerative cropping system in Bhubaneswar,
Odisha.
2.4. Rice-pulse cropping system
Rice-pulse cropping system are dominant crop rotation in eastern India particularly
in Chhattisgarh, Odisha and parts of Bihar. Rice-blackgram, rice-greengram sequence
or as paira crop are popular and unique in rainfed lowland rice ecosystem of Odisha,
where these two tropical crops are grown in winter season after rice and it is subjected
to low temperature. Dwivedi et al. (2016) proved that rice-rice ratoon-greengram
sequence was best combination in terms of production and energy efficiency in
coastal Odisha. Growing of jute-rice-greengram offers more advantages than the
traditional cropping system as this system of crop intensification could improve soil
fertility and increase crop productivity. Sunnhemp-rice-black gram has also registered
the highest returns per rupee invested (2.52) and hence was suggested for Coastal
Andhra Pradesh.

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2.5. Rice-oilseed cropping system

Rice-oilseeds cropping sequences are considered as valuable cropping system
for food and nutritional security. In eastern India, rice-groundnut, rice-rapeseed/
mustard are predominant cropping systems. The rice-groundnut cropping system
can be replaced with rice-brinjal cropping sequence in mid-central table land zone of
Odisha as it provides maximum net return owing to higher system productivity
(Samant 2015). The finding by Lal et al. (2017) at NRRI, Cuttack demonstrated that
early sowing of dry season toria after rice is profitable and it ensures profitability of
rainfed rice based cropping system.
2.6. Rice-fallow
Rice fallow includes medium and low lands, which are kept fallow after kharif
paddy. The prevailing practice of leaving land fallow after harvest of rice is no more
economical and sustainable. Odisha accounts for around 10% (12.2 lakh ha) of the
total rice fallow of India (11.65 m ha). Utilization of fallow lands is likely to generate
considerable income and employment opportunities for the millions of small
landholders in the region. Efficient and proper utilization of rice-fallow lands in dry
season after a rice crop has the ability to meet the demands arises for food and
nutrition of the growing population. A number of short duration and moisture stress
tolerant crops and their improved varieties can be grown in these fallow lands as the
climatic and soil condition of the fallows varied from vary small duration to as long as
3 months. Pulses, because of shorter duration and their ability to grow under residual
moisture are good candidates for efficient utilization of fallows. However, knowledge
and technical gaps in management practices of pulses under fallows and different soil
conditions creates hindrance in its proper utilization. Adoption of early and mid early
rice varieties in wet season will have a greater window for raising a good crop in dry
season particularly the pulses and oilseeds having tolerance to low temperature.
However, energy requirement of different cropping systems varied a lot, different
crops and varieties may be suitable for specific locations while going for intensification
of the systems. Cultivation of no- till vegetable pea after rice harvest in rice- fallow
areas recorded higher green pod yield (5.89 t ha-1) resulting in 44 % less energy
requirements compared to conventional tillage (Singh et al. 2015). In another study,
Das et al. (2008) observed significantly higher net return in rice–french bean system
as compared to rice mono-cropping. Farmer’s net income enhanced by Rs.29,000 ha-1
and Rs 21,500 ha-1 over rice-fallow system due to inclusion of pea (vegetable) and
lentil, respectively, in the system following no tillage practice. Singh et al. (2014)
suggested that the suitability and profitability of cropping system varies not only
with soil type but also with soil series. For example rice–potato produced higher yield
in Lahangaon series whereas rice–pea in Teok series of Upper Brahmaputra valley of
Assam.
In rice fallows of eastern India, various pulses, viz. lathyrus, lentil, field pea,
blackgram, greengram, chick pea, fababean and oilseeds crops viz. linseed, mustard,
and niger etc. can be grown as utera crop. Selection of crop and varieties are important

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Table 1. Recommended intensified cropping systems for different regions.
Region Existing system Recommended system
Pakistan Rice-wheat rice–wheat–greengram–lentil
Nepal Rice-wheat Rice-lentil-maize, Rice-lentil-greengram
Bangladesh Rice- rice Rice-vegetable pea-rice
Non-saline areas of Satkhira Rice- rice Aman rice-mustard-jute
district in Bangladesh Aman rice-potato-jute
High Ganges River Flood plain Rice- rice Wheat-greengram- rice
of Bangladesh
Bangladesh Rice- rice Rice-mustard-rice
Sandy clay loam soil of Rice-wheat Rice-potato-blackgram, rice-maize
Varanasi (UP) (cob) + veg. pea (1:2) – green gram
cropping
Karnal, Haryana Rice-wheat Rice - vegetable pea - wheat-
greengram
Punjab Rice-wheat Maize-potato-onion
Clay loam soils of Rice-wheat Hybrid rice-gobhi sarson-okra
Jabalpur (MP) Rice-chickpea
South Gujrat Rice-wheat Rice-sorghum-sorghum ratoon
Rice-sweet corn-blackgram
Rice-greengram-groundnut
High rainfall zone of Rice-rice Rice–fenugreek–okra
south Gujarat
Krishna –Godavari delta Rice-rice Rice-maize, Rice – mustard
areas of Andra Pradesh,
North Coastal Zone of Rice-fallow Sunnhemp-rice-blackgram
Andhra Pradesh
Low land rice ecosystem Rice-maize Rice-soybeanRice-marigold
of Karnataka
Jharkhand (irrigated ) Rice-wheat Rice–potato + wheat (1:1)–
Rice-fallow greengram, Rice–potato–greengram
Irrigated medium land acid Rice-rice Winter rice–cabbage- greengram
soil situation of Assam Rice–chilli–blackgram
Irrigated ecosystem in Bihar Rice-rice Rice–tomato–bottle gourd, Rice–
potato–onion, Rice–coriander–lady’s
fingers, Rice–carrot–cowpea
Chhattisgarh plains Rice-rice Rice-potato-cowpea
Upper Brahmaputra Rice fallow Rice– potatoRice –pea
valley zone of Assam
Coastal plain zone of Odisha Rice-fallow Rice-ratoon-greengram, Rice-greengram/
blackgram
Rice fallow, Khurda Rice-fallow Rice-utera blackgram
District of Odisha

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criteria for getting the desire result from utrea crop. The results of on-farm trials
proved that the blackgram crop was the most feasible crop in coastal Odisha. Crops
like sunflower, groundnut, watermelon, lady’s finger can be raised with limited irrigation.
Medicinal crops like brahmi, bhrungaraj, bhukadamba, panmadhuri, juani, jalabrahmi
were found promising in rice based cropping sequence for increasing the profitability
of rice farmers. Sunflower found promising in coastal Odisha after rice with limited
irrigation.

3. MANAGEMENT OF RICE-BASED CROPPING SYSTEM

System productivity of different cropping sequences and systems depends on
optimum management of resources by considering system as one unit. Efficient crop
establishment methods followed by optimum management of water and nutrients
coupled with need based control of various biotic stresses particularly weeds are
prerequisites for sustainability of any production system.
3.1. Crop establishment
Crop stand establishment is the most critical operations for ensuring a good crop
particularly under rainfed situations. In rice-based cropping system; rice is commonly
established by transplanting. Huge amount of water and labour requirements for
transplanting reduces profit margins and become less remunerative. Puddling of land
makes the land unsuitable for subsequent crop production in transplanted rice. Thus,
the rice–rice and rice-wheat systems practised currently are unsustainable. Therefore,
management practices with reduced cost of production and increased productivity
and lower environmental ill effects are needed which can be achieved switching to
conservation agriculture (CA) practices. In heavy clay soils, where there is less chance
of land preparation, ‘zero tillage crop establishment’ following relay cropping or dibble
seeding in rows with crops like greengram, blackgram, lathyrus, linseed and lentil are
suggested for higher system productivity. Mulching with crop residues like rice straw
helps in moisture conservation and early establishment of crops.
From cropping system study in rice-wheat belt, drum seeding (wet bed, unpuddled)
resulted in higher grain yield of hybrid rice, whereas direct seeding (dry bed, unpuddled)
adopted in the preceding rice crop produced greater yield of wheat, chickpea and
Indian mustard. Direct seeding (dry bed, unpuddled) also increased the net returns
and benefit:cost ratio. Shweta and Malik (2017) recorded maximum mean grain (4.24 t
ha-1 ) and straw (6.24 t ha-1 ) yields of wheat in rice-wheat system when rice was
established through direct seeding and nutrient uptake (NPK) by the wheat crop was
highest under direct seeded rice due to rice establishment methods.
3.2. Energy management
Energy is the most critical inputs in agriculture and availability of the appropriate
energy and its efficient use are pre requisites for sustainable agricultural production.
Energy efficiency can be achieved through adaption of suitable cropping system
with integrated crop management practices. Energy use efficiency varies with cropping

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system, e.g system energy use efficiency was higher in rice–mustard followed by
rice–sunflower and rice–maize, while it was lowest in rice-black gram and rice-ragi
systems but rice–maize recorded the highest energy productivity followed by rice-
rice and rice–mustard and the energy productivity was lowest in rice-ragi and rice-
gingelly (Rao et al. 2014). Energy-use efficiency (EUE), in terms of total output energy/
total input energy, was significantly higher in rice–lathyrus cropping system followed
by rice–sunflower + greengram compared to other crop sequences as legumes require
much less energy than other crops (Walia et al. 2014). However, the suitability and
adaption of cropping system is more dependent on the total energy requirement than
the energy use efficiency particularly based on land holding size. For medium and
large farmers, jute–potato–rice, rice–potato–rice and rice–potato–sesame are suitable
due to higher system productivity but at the cost of higher consumption resulting
lower energy productivity. However, jute–wheat and jute–rapeseed–rice are considered
to be suitable for small and marginal farmers because of their moderate cost of
cultivation and net return with better energy use efficiency (Biswas 2017). Rice-
sunflower and rice-horsegram cropping systems were energy efficient systems with
high net energy despite of having low system productivity (Rautaray et al. 2017).
On the basis of productivity, profitability and energy use efficiency, rice–
potato–lady’s finger was found to be the best crop sequences for Indo-Gangetic
Plains of West Bengal. In red sandy loam soils of northern Telangana, rice-maize and
rice-sunflower cropping systems are sustainable cropping sequences as higher
production efficiency, input use efficiency and profit was achieved with lower energy
input than the other cropping sequences particularly rice-rice.
The energy and monetary budgeting of cropping systems should be done for
sound planning of sustainable systems. Rice-wheat system gained 27.7, 21.2, 17.2
and 10.8 per cent higher net return energy than soybean-wheat and pigeon pea-
wheat systems, rice-vegetable pea-wheat-green gram and maize-vegetable pea wheat
systems, respectively. Adaption of greengram and Sesbania as green manuring crop
in rice-wheat cropping systems increases the energy output of the system by 10 and
14% compared to rice-wheat summer ploughing system.
3.3. Nutrient management
Productivity and profitability of a cropping system depends mostly on nutrient
management practices. It is essential to have clear-cut idea about the nutrient
requirements of component crops, their uptake pattern, soil contribution and use
efficiency for developing the optimum nutrient management schedule of an intensive
rice-based cropping system. Long term fertilizer experiments indicated decreasing
trend of productivity in intensive rice based cropping systems with recommended
doses of fertilizers. Therefore, an alternative integrated nutrient management system
is required to maintain or improve soil fertility to achieve the desired levels of crop
productivity and improved physio-chemical and biological properties and SOC
sequestration through optimisation and integration of all available sources of plant
nutrients. The INM approach is more suitable in rice based cropping systems compared

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to other cropping systems as rice is predominantly grown under submerged soil

conditions with greater scope for using different nutrient sources.
Combinations of organic and inorganic fertilizer can augment SOC and other
nutrient accumulation and improve crop production under rice based cropping systems
(Hossain et al. 2016). Cow dung and manures when combined with NP fertilizer
increased SOC content by 0.30 Mg ha-1 yr-1 in a rice-wheat rotation. The INM strategy
have already results in economically viable, agronomically feasible and
environmentally sound sustainable crop production systems by improving soil fertility
and C sequestration, and reducing N losses and emission of greenhouse gases. High
yield in a rice-wheat cropping system can be obtained through integrated nutrient
management by including green manure, legume residues or loppings which can save
upto 80–120 kg N ha-1 or by applying them with 80 kg N ha-1, 1 t ha-1 more grain and
about 3t ha-1 more straw can be produced compared to plots receiving no organic
manures/residues. In rice + blackgram intercropping application of 15 kg N through
FYM and 20 kg N through chemical fertilizer (urea) + 40 kg P2O5 + 40 kg K2O yielded
37% higher REY than the recommended fertilizer dose (Mishra et al. 2012).
Under south Gujarat condition, Mansuri et al. (2016) observed that application of
50% recommended dose of nitrogen (RDN) through farmyard manure(FYM) and 50%
bio-compost through improved the availability of nitrogen, phosphorus and potassium
in soil. Similarly, application of 50% RDN through chemical fertilizers coupled with
50% RDN through green manuring of azolla or through farm yard manure to kharif
rice followed by supply of recommended dose of chemical fertilizers to summer rice
can be adopted for rice–rice cropping system in coastal Odisha to obtain higher and
sustainable yield and maintenance of soil health (Mishra et al. 2017).
Higher system productivity of rice-maize cropping system was achieved with
application of 50% NPK through fertilizers + 50% N through Glyricidia to rice and
75% RDF to succeeding maize crop. However, the uptake of these nutrients was more
with 50% N substitution either through FYM or Glyricidia to kharif rice, whereas
higher nutrient uptake by maize was recorded with 100% NPK supplied as inorganic
source. Kumar et al. (2017) suggested that replacing summer rice with maize in rice-
rice cropping systems is beneficial in limited irrigation when INM is followed with use
of locally available organic nutrient sources i.e. paddy straw/green manure crops.
Site Specific Nutrient Management (SSNM) is another potential option for
improving productivity, net income and nutrient use efficiency without depletion of
soil fertility in rice based systems in Indo Gangetic Plains. Site specific nutrient
management could improve the REY of system by 9.5 to 30%, over blanket
recommendation, soil testing based recommendation and farmers practice, respectively
(Singh et al. 2015). Site specific nutrient management has successfully been
demonstrated in India and proved to be of environmental friendly owing to its balanced
and need-based nutrient application.
Conservation agriculture involving zero- or minimum-tillage and crop residue
management are key technologies for agro ecological intensification of rice based

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cropping systems as it reduces the risk arise out of climate change while making the
production sustainable. Mulch can increase yield, water use efficiency, and
profitability, while decreasing weed pressure. Use of wheat residue in rice does not
have any adverse effect on rice yield if incorporated to soil. Further residue retention
under conservation tillage practices also enhanced the system yield in rice-wheat
cropping system (Yadav et al. 2017).
Application of 100% recommended dose of fertilizer to the preceding rice crop
along with the ‘P’ of blackgram to rice at sowing substantially may improve the seed
yield as well as net monetary benefit in rice-blackgram utera cropping sequence.
Application of blanket fertilizer reduced the yield and was economically unsuitable.
Further application of phosphorous to rice crop can enhance the grain and stover
yield of blackgram due to the residual effect.
3.4. Water management
Water availability is an important criterion for selecting components crops in a
cropping system particularly in dry season due to non availability of natural rainfall.
The water use efficiency can be increased by identification of appropriate crop
combinations. More so, agro ecological intensification of rice based cropping systems
largely depends upon water availability in dry season. In rice-based cropping system
crop water management in rice has a greater impact on the succeeding crop due to
change in water regime. Puddling is time consuming, capital intensive and requiring
more water and causes subsurface compaction, thereby is not conducive to the
succeeding crops. New technologies for saving water, such as alternate wetting and
drying, saturation soil culture, raisedbeds and aerobic rice found promising in
enhancing water productivity of rice cultivation in South Asia. However, in the coarse
texture soils of Punjab a good combination of water management practice and puddling
intensity can enhance the water productivity and sustain system productivity.
Flooding to field capacity throughout the rice crop considerably reduces the number
of irrigations and also gives higher water use efficiency. Besides, the depth of
submergence at 3–10 cm is sufficient for the optimum yield and control of most
weeds. Alam et al. (2017) observed that the wheat–mungbean–dry seed aman rice
system had a very large effect on water productivity and achieved the highest value
of 12–17 kg ha”1 mm”1. In sequential cropping, supplemental irrigation after rice had a
significant effect on grain yield of winter crops in rice based cropping system and
with two supplemental irrigation at tassel initiation and grain filling stage of maize,
peg initiation and pod development stage of groundnut, 50% flowering and grain
filling of sunflower, crown root initiation and jointing stage of wheat, stolonization
and tuberization of potato increased water use efficiency and productivity. Singh et
al. (2014) reported that higher field water use efficiency and yield of dry crops after
rice with two life saving irrigations in groundnut, lentil, rapeseed and potato
respectively. The water use efficiency of rice–lentil–greengram system was higher
than rice–wheat-greengram and higher rice equivalent yield was obtained in rice-
wheat-greengram and rice lentil greengram compared to rice-wheat system. Higher
water productivity and lower water use can be achieved in rice by soil mulching in

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combination with direct seeded aerobic condition. Further improvement in water

productivity can be achieved by reducing area under summer rice in Gangetic flood
plains of West Bengal by substituting with other food crops like wheat, maize and
pulses which is necessary for sustainability of agroecosystem security and economic
growth of the farmers. Enhancing water productivity through water saving
technologies is not individual farmer’s affairs. Mass awareness programme is required
to educate all the farmers of a village or region about modern technologies for water
saving as well as yield maximization using modern management practices.
3.5. Weed dynamics and management
Weeds are major biotic stress which affects crop production due to crop weed
competition. Weeds are dynamic in nature and weed infestation largely depends on
type of crop, cropping system and cultural practices. Cropping system intensification
in combination with new management practices has a great impact on the weed flora/
dynamics of the region. Cultural practices like crop rotation, crop geometry, moisture
regime, mulching, tillage practice influences the dominance of weed flora and its
distribution thus determines the weed control methods. Soni et al. (2012) concluded
that relative weed density and weed-flora differed from crop to crop from early stage
to maturity of crops. Thus, infestation of severe weeds viz., Phalaris minor in wheat,
Chichorium intybus and Rumex spp. and Medicago denticulata in berseem could be
minimized by intensified and diversified them with other crops with higher production
efficiency. Mishra and Singh (2012) revealed that Echinochloa colona L. and Cyperus
iria L. population density can increase in rice due to continuous zero-tillage in rice
wheat cropping system. Zero-tillage reduced the population of Avena ludoviciana L.
and Chenopodium album L. but increases the density of Medicago hispida compared
to conventional tillage systems.
Research results from Modipuram indicated a significant impact of stale seedbed
in reducing the weed incidence in rice-wheat system as compared to the traditional
seedbed preparation.Crop rotation using weed smothering and land covering crop
such as cowpea, soyabean and blackgram reduces the weed population a substantial
level. Similarly, intercropping systems involving rice and non-rice crops like greengram,
blackgram, pigeon pea or groundnut can help in suppressing the weeds in upland.
Intensification of rice-wheat system through inclusion of summer greengram though
produces comparable grain yield to summer cowpea or Sesbania green manuring but
recorded lower grasses and sedges and weed dry matter. Weed management by using
herbicides gaining popularity due to easiness and low-cost involvement, but
herbicides are highly crop specific and has residual effect on succeeding crop.
Therefore, selection of herbicides for weed management in cropping system particularly
in intercrops should consider about the selectivity and residual effect on succeeding
crops. In direct seeded rice-wheat cropping system, conventional tillage in both
crops and pre-emergence application of butachlor at 1.5 kg ha-1 followed post-
emergence application of + 2,4-D at 0.5 kg ha-1 in rice and isoproturon at 0.75 kg ha-1
+ 2,4-D at 0.5 kg ha-1 post-emergence in wheat produced maximum rice equivalent
yield and net returns as compared to other tillage practises and weed control method,

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respectively and thus ultimately reduce weed density and weed biomass under the
conservation tillage. Application of herbicide bispyribac sodium 25 g ha-1 at 15 days
after transplanting (DAT) followed by one hand weeding at 45 DAT can be
recommended for better weed control, growth and yield of transplanted rice without
significantly affecting the black gram growth and establishment (Parthipan et al.
2013).
In rice-wheat cropping system, the conservation tillage may have positive effect
on the suppression of weeds in wheat. By understanding the nature of weed seed
bank, various methods of integrated weed control should be formulated. The adoption
of recommended agronomic practices, understanding the nature of the weeds and
conservation agriculture can help the farmers to obtain the maximum productivity of
rice-wheat cropping system.
3.6. Environmental impact
Rice-rice cropping system is being seen as a major culprit due to higher methane
emission from anaerobic condition. However improved management practices such
as conservation tillage, crop residue retention and FYM incorporation to soil can
improve SOC accumulation which is a major agricultural strategy for mitigating
greenhouse gas emissions, enhancing food security and sustainability. Diversification
of rice-rice cropping system involving other dry crops can reduce the methane emission
from the system but there is possibility of increase in N2O from the soil. Therefore, net
global warming potential of the system may be balanced. However, Bhattacharyya et
al. (2014) reported that rice ecosystem acts as a net agricultural sink rather than a
polluter. Highest CH4 flux was recorded from rice-rice rotation plots and during wet
season, higher N2O flux was observed from rice-potato-sesame rotation. Higher global
warming potential (GWP) of rice-rice cropping system was recorded compared to rice
based cropping systems involving other dry crops. Therefore, rice-potato-sesame
cropping system was economically profitable and environmentally safe in eastern
Indian condition (Datta et al. 2011).

4. TECHNOLOGICAL KNOWLEDGE GAP

There is a great spatial variation in cropping intensity among the various ecosystem
and region of India. Punjab has the highest cropping intensity of 189%, followed by
Himachal Pradesh (188.1%), West Bengal (185.1%), Haryana (181.3%) and Uttar
Pradesh (157.7%). The intensity is low in dry, rainfed regions of Rajasthan, Gujarat,
Maharashtra and Karnataka (110-125%). As the average cropping intensity is low in
rainfed areas, there is an urgent need for intensification to achieve livelihood security
of farm families in those areas. At present, all crop diversification and intensification
are primarily based on increase in productivity only without considering the negative
impact on environment. Under input based production system, the cost of cultivation
is high and in increasing trend and very limited effort has been made to reduce the
cost of cultivation. Crop and soil management recommendation are based on individual
component crop basis without taking into consideration of carry over effect/mutual

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interaction with in the component crops in sequence/system both in time and space.
Eastern India is mostly rainfed with about 12.5 mha rice fallows but little effect have
been made to bring rice fallows under cultivation. Lack of suitable technology and
socio economic problem to bring fallow areas under cultivation are major concerns
for sustainability of rice ecosystem.

5. RESEARCH AND DEVELOPMENT NEEDS

Intensification and diversification of existing dominant cropping system of the
region like rice-rice, rice-wheat, rice-maize, rice-groundnut, rice-rapeseed cropping
system with inclusion of short duration pulses/oilseeds in sequence or as an intercrop
with due consideration of soil health and environment impact in irrigated ecosystem
is the need of the hour. Further, intensification of the existing rice-pulse/oilseed and
rice fallow cropping system in rainfed ecosystem has to be done through adoption of
resource conserving practices like minimum/zero-tillage, residue retention, mulching
etc. Reducing the cost of cultivation/production of the rice based cropping system
through farm mechanization, tillage, optimal/precise use of inputs, recycling/reuse of
resources can be tested and validated in farmer’s field. Development of best
management practices to increase resource use efficiency for existing and innovative
cropping systems are required for ensuring the sustainability. Developing/intensifying
rice fallows through crop adjustment, advancing sowing time for optimal utilization of
residual moisture and integrated crop management practices like seed priming, seed
treatment etc. maybe studied.

6. WAY FORWARD
There is a need to create awareness among the farming community for optimal
utilization of resources i.e. land, labour, water and energy and ensuring livelihood
security through adoption of agro-ecology based intensified cropping system.
Appropriate policy may be formulated to incentivise the farming community adopting
agro-ecologically intensified cropping system, ensuring availability of the inputs to
the farmers at right time. Developing irrigation facility with use of micro irrigation
system for efficient water use and enhancing the cropping intensity in the eastern
region is another important aspect of the cropping system research and development
which should be taken care of at appropriate stage.
References
Alam MJ, Humphreys E, Sarkar MAR and Yadav S (2017) Intensification and diversification
increase land and water productivity and profitability of rice-based cropping systems on
the High Ganges River Floodplain of Bangladesh. Field Crops Research 209:10-26.
Baishya A, Gogoi B, Hazarika J, Hazarika JP, Bora AS, Das AK, Borah M and Sutradhar P (2016)
Maximizing system productivity and profitability through crop intensification and
diversification with rice (Oryza sativa)-based cropping systems in acid soils of Assam.
Indian Journal of Agronomy 61(3):274-280.

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Biswas B (2017) Cropping system analysis for agricultural sustainability-productivity, economy,
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 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Integrated Rice-based Farming Systems for

Enhancing Climate Resilience and Profitability
in Eastern India

Annie Poonam, S Saha, PK Nayak, BS Sathpaty, M Shahid, AK

Nayak, R Tripathy, NN Jambhulkar, GAK Kumar, B Mondal, PK
Sahu, SC Giri, M Nedunchezhian, U Kumar and SK Lenka

SUMMARY
Majority of the rice farmers in eastern India possess small land holding (<1ha),
which is the only primary source of farm family income. Despite exploiting their land
extensively they often fail to achieve the target appreciably owing to high risk involved
in the natural calamity. Rice ecosystem in the eastern region is diverse and rich in
natural resources but the extremely fragileness of the ecosystem and small and marginal
land holdings call for diversification of the persisting/ conventional rice farming for
efficient resource management. Adoption of the most compatible multi-crop enterprises
into a small system holding would greatly improve the production system in the risk
prone ecology and will ensure sustainable food, economic and employment in the
small farm thus restricting the migration of farming community to the metro cities for
construction and other non-agriculture work.

1. INTRODUCTION
Farming family in tropical India is mainly dependent on rainfed farming with high
risk of weather uncertainty. In a constant struggle to survive, the small and marginal
farmers over the years have evolved techniques which have benefited them immensely.
But without knowing the scientific basis of such integration they have been practicing
the system for a long time.In India, traditionally, farming has been family based and
majority of them are smallholders. The success of farming family lies not in
‘specialization’ but in practicing farming to meet diverse household needs rather than
market opportunities alone. Hence, income from seasonal field crops alone in small
and marginal farms is hardly sufficient to sustain the farming family.
Rice being the staple food is grown in the country in around 43.5 million ha (Mha)
under various ecologies of which about 50% area is rainfed. More than 80% of the
rice farmers belong to small and marginal groups and the average per capita land
holding in India is only about 0.17 ha. In view of the population growth, competition
of land with industrialization and urbanization, declining farm holding size and the
dietary nutrition requirement of the farm families, it is necessary to look for the optimum
use of resources through shift from conventional rice farming to integrated farming
systems. Rice based farming system involving rice, other field and horticultural crops,
agro-forestry, fish birds livestock and further income generating enterprises will be

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Profitability in Eastern India 273
the right approach in this respect and will be more relevant in the risk prone rainfed
ecologies which are mostly located in the eastern part of the country. Because of
reducing per capita availability of land in India, there is no further scope for horizontal
expansion of land for increased food production. Hence, the best possible allocation
of resources and their intelligent management is important to reduce the risk related
to land sustainability. Integrated farming system is the potential approach and
powerful tool for management of vast natural and human resources in developing
countries including India to meet the various objectives of, competitiveness, food
security, poverty reduction and sustainability of small and marginal farmers.
Rice farmers in eastern part of India generally work in various risk prone
environments leading to low rice productivity. Available resources for modest
increment is due to lack of appropriate understanding of interaction and linkages
between the components under traditional rice farming system; manpower is
underutilized for employment and hence, rice growers are economically poor. Integrated
farming system (IFS) has been advocated as one of the tool for harmonious use of
inputs and their compounded response to make the agriculture in the region profitable
and sustainable.
The Indian economy is predominantly based on agriculture, which is facing a
serious challenge in terms of the sustainability and profitability of farming due to the
declining trend in size of land holding. The average size of the landholding has
declined to 1.1 ha during 2010-11 from 2.28 ha in 1970- 71. If this trend continues, the
average size of holding in India would be mere 0.68 ha in 2020, and would be further
reduced to 0.32 ha in 2030 (Agriculture Census 2010). As per estimates, more than
95% of the holdings will be under the category of small and marginal holders in 2050.
Hence, it is necessary to develop strategies and agricultural technologies that enable
adequate employment and income generation, especially for small and marginal farmers
who constitute more than eighty per cent of the farming community.
Under the gradual shrinking of land holding, it is needed to integrate land based
enterprises like minor livestocks, field and horticultural crops, etc. within the biophysical
and socio-economic environment of the farmers to make farming more profitable
(Behera et al. 2004). In addition, the dependence upon a few crops in combination
with a high biotic and abiotic risk of crop failure exposes the farmers to a high degree
of variability with respect to yield and income and therefore risks (Ashby 2001).
Further, few authors indicated that commercial farming systems are a threat to the
environment through a loss of genetic diversity and the possible negative impacts of
these systems and their associated inputs.
It becomes difficult for the small and marginal farmers to sustain with the single
farm enterprise unless resorting to integrated farming systems (IFS) for the generation
of adequate income and year round employment within their small farms (Mahapatra
1992). Decreasing land-man ratio, poor socio-economic condition of farmers, vagaries
of monsoon, new risks from environmental deterioration, population pressure and
rapidly changing agricultural input and output markets through globalization, high
degree of vulnerability in the rural area proved to be not sustained farmer’s livelihood

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274 Profitability in Eastern India
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mainly when they are solely dependent on traditional agriculture on their small piece
of lands. Therefore, agriculture diversification is utmost important for improving their
livelihood and reducing vulnerability.
1.1. Integrated farming system-a promising approach
Integrated farming system is the potential approach and powerful tool for
management of vast natural and human resources in developing countries, including
India to meet the multiple objectives of poverty reduction, food security,
competitiveness and sustainability of small and marginal farmers’ livelihood. The
approach aims at increasing income and employment from small-holding integrating
various farm enterprises and recycling crop residues and by-products within the farm
itself (Behera and Mahapatra 1999; Singh etal. 2006). Under the gradual shrinking of
land holding, it is necessary to integrate land-based enterprises such as dairy, fishery,
poultry, duckery, apiary, field crops, vegetable crops and fruit crops within the bio-
physical and socio-economic environment of the farmers to make farming more
profitable and dependable (Beheraetal.2004).Integrated farming systems are often
less risky, because if managed efficiently, they benefit from synergisms among the
enterprises, leading to diversity in produce and environmental soundness (Pullin
1998).
The objective of this Chapter is to analyze the traditionally practiced farming
systems nationally /internationally and how the progress has been made in terms of
different improved models/cropping systems for sustainable, food, nutrition,
employment generation and income of the small and marginal rice growers in diverse
agro-ecological situations.

2. STATUS OF RESEARCH/KNOWLEDGE
The cultivation of almost 90% of the world’s rice crops in irrigated, rainfed and
deep-water systems equivalent to about 134 million hectares offers a suitable
environment for fish and other aquatic organisms.The different integrations of rice
and fish farming–either on the same plot, on adjacent plots where by-products of one
system are used as inputs on the other, or consecutively – are all variations of
production systems that aim to increase the productivity of water, land and associated
resources while contributing to increased fish production. The integration can be
more or less complete depending on the general layout of the irrigated rice plots and
fishponds.
Asia accounted for about 90% of 672 Mt of rice produced in the world as of 2010
(FAO 2012). Rice farming in Asia used to be characterized by small scale, labour-
intensiveness and on-site recycling of green and animal manures. Although rice
farming is still labour-intensive in remote areas of Asian developing countries, it has
rapidly been mechanized and agrochemicals- intensive in the name of agricultural
modernization and green revolution. In fact, the so-called green revolution has largely
resulted from industrial monoculture, genetically modified crops and the excess use
of agrochemicals, which caused agricultural land degradation globally. Furuno

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Profitability in Eastern India 275
(2001)formulated the idea of systematically integrating rice with ducks, based on the
notion that two products highly complementary to each other can be jointly produced.
In the integrated rice–duck farming (IRDF) system, rice paddies provide food (weeds
and pests) for ducks, and ducks play a role in fertilizing rice plants.Integrated farming
systems are effectively systems that have traditionally been undertaken by farmers in
countries that include Indonesia, China, Malaysia, Vietnam, Rwanda and Thailand
(Praphan 2001). However, in many countries these traditional systems have been
replaced by the establishment of commercial cash and staple crop production systems
that have been promoted by governments (Ruaysoongnern and Suphanchaimart
2001).
As regards the general scale of rice–fish culture, China is the main producer with
an area of about 1.3 Mha of rice fields with different forms of fish culture, which
produced 1.2 Mt of fish and other aquatic animals in 2010. Other countries reporting
their rice–fish production to FAO include Indonesia (92000 t in 2010), Egypt (29 000 t
in 2010), Thailand (21000 t in 2008), the Philippines (150 t in 2010) and Nepal (45 t in
2010). Trends observed in China show that fish production from rice fields has
increased thirteen fold in the last two decades, and rice–fish culture is now one of the
most important aquaculture systems in China, making a significant contribution to
rural livelihoods and food security.
Rice–fish farming is being tried and practiced in other countries and continents
although to a lesser extent. Apart from Asia, activities have been reported from,
among others, Brazil, Egypt, Guyana, Haiti, Hungary, Iran (Islamic Republic of), Italy,
Madagascar, Malawi, Nigeria, Panama, Peru, Senegal, Suriname, the United States of
America, Zambia, and several countries in the Central Asia and Caucasus region.Rice-
fish systems are practiced in China, Egypt, India, Indonesia, Thailand, Vietnam,
Philippines, Bangladesh and Malaysia. The rice-fish systems are important in these
areas because they provide food security, reduce the impact of agriculture on the
environment, and may be less affected than conventional systems by climate change.
Integrated rice-fish production can optimize resource utilization through the
complementary use of land and water. This practice also improves diversification,
intensification, productivity, profitability, and sustainability of the rice agro-ecosystem.
In eastern India about 70% of farmer community comes under the marginal and
small farmer category (GOI 2009). Farmers under these categories are economically
poor and work in diverse risk prone environments. The income from rainfed rice crop
and other seasonal field crops on small and marginal farms is hardly sufficient to
sustain their family. Integrated farming system (IFS) has been advocated as one of
the tool for harmonious use of inputs and their compounded response to make the
agriculture in the region profitable and sustainable. Integrated farming systems aim at
an appropriate combination of farm enterprises like field crops, dairy, piggery, poultry,
apiculture, goatery, mushroom cultivation etc. for a productive, profitable and
sustainable agriculture. IFS interact appropriately with the environment without
dislocating the ecological and socio-economic balance on one hand and attempt to
meet the farmers need on the other. Thus, IFS is a reliable way of obtaining high

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276 Profitability in Eastern India
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productivity with substantial nutrient economy in combination with maximum

compatibility and replenishment of organic matter by way of effective recycling of
organic residues/ wastes etc. obtained through integration of various land based
enterprises (Gill et al. 2010; Sanjeev et al. 2011) An experiment on paddy cum fish
culture was started in west Bengal in 1945 in an area of 691.16 acres adjoining the
paddy fields and it was remarkably noted that the growth of tank fishes was slower
than those liberated in the paddy fields. The then rice committee of FAO in 1948
strongly advocated the practice of fish culture in the rice field for increased production
of rice. The farmers of the north-eastern part of India, which includes seven states viz.
Assam, Arunachal Pradesh, Nagaland, Meghalaya, Mizoram, Manipur and Tripura
cultivate rice as their staple food and a fish crop is traditionally raised only from the
paddies of rainfed lowlands (both shallow and deepwater). Traditional rice-fish
production systems have an important socioeconomic part in the life of the farmers
and fishers in the region. The practice of integrated farming system recorded higher
mean average net return (Rs. 3,06,875), gross return (Rs. 3,88,375) and benefit cost
ratio (4.58) over farmers practice.employment generation in the farming system under
Integrated farming system was 193 days in a year from the Bellari district of Karnataka
(Yogeesh et al.2016).Integration of various agricultural enterprises viz.,cropping, animal
husbandry, fishery, forestry etc. not onlysupplement the income of the farmers but
also help inincreasing the family labor employment through out the year (Jayanthi2002).
2.1. Improved integrated rice –fish farming system
Eastern India, in particular with about 5.6 m ha irrigated area and 14.6m ha rainfed
lowlands of the total 26.58 m ha rice area, offers high potential for rice-fish farming
system, especially in view of the resources, food habits and socio-economic needs of
the people. Rice-fish farming system with higher water and land productivity and
employment opportunities can ensure food, nutrition and livelihood security for the
farming communities, particularly for the largest groups of small and marginal farmers.
Rice-fish culture systems can be mixed or concurrent, sequential or rotational. However,
the techniques differ based on the physical, biological and socio-economic profiles
of the target agro-ecosystem.
2.1.1. Model I: Rice–fish–livestock-horticulture based farming system for rainfed
lowland areas: In order to improve and stabilize farm productivity and income from
rainfed water logged lowland areas, national Rice Research Institute, Cuttack has
developed an adoptable technology of rice-fish diversified farming system. Farm size
may vary from minimum of about one acre to one hectare or more. Field design
includes wide bunds (Dykes) all around, a pond refuge connected with trenches on
two sides(water harvesting come fish refuge system) and guarded outlet. The
approximate area allotments will be, 20 % for bunds, 13 % for pond refuge and trenches
and rest 67 % for main field. The pond refuge measures 10 m wideand 1.75m deep
constructed in the lower end of the field. The two side trenches of 3 m width and
average 1 m depth have gentle(0.5%) bed slope towards the towards the pond refuge.
Small low cost (Thatched/asbestos top)duck house and poultry unit are constructed
on bunds with a floor space of about 1.5 sq.ft. for each duck and 1 sq.ft. for each

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Profitability in Eastern India 277
 poultry bird. Poultry unit may be projected
upto 50% over the water in the pond refuge
to utilize the dropping as fish food and
manure in the system. In such case birds can
be housed in cages made of wire net. A small
goat house is made on the bund with floor
space of about 2 sq.ft for each animal (Fig. 1
and2).

Fig. 1.Rice –fish–livestock-horticulture i. Production Technology

based farming system for rainfed Production Technology broadly involves
lowland areas
growing of improved photo-period sensitive
semi tall and tall wet season rice varieties with field tolerance to major insect pest and
diseases. The suitable rice varieties are Gayatri, Sarala, CR Dhan 500, CR Dhan 505,
Jalmani, Varshadhan for Odisha, Sabita, Jogen, Hanseswari for West Bengal, Sudha
for Bihar, Madhukar and Jalpriya for eastern Uttar Pradesh and Ranjit, Durga and
Sabita for Assam. Management of insect pest in rice crop is done with the use of sex
pheromen traps, light traps and botanicals (Netherin/Nimbicidin spray at 1%). Indian
major carps (Catla, Rohu, Mrigal) Puntiussarana, exotic carps (common carp, silver
carp silver barb) and fresh water giant prawn (Macrobrachiumrosenbergii) fingerlings
of 3-4" size and prawn juveniles of 2-3" size are released in a ratio of 75 % and 25 %,
respectively at 10,000 per hectare of water area after sufficient water accumulation in
the refuge and in the field. Fish and prawn are regularly fed at 2% of total biomass
with mixture containing 95% of oil cake +rice bran (1:1) and 5% of fish meal. After rice,
various crops like watermelon, mung sunflower, groundnut, sesame and vegetables
are grown in the field with limited irrigations from the harvested rainwater. On bunds
different seasonal vegetables are cultivated round the year including creepers on the
raised platform, spices and pineapples are grown in shades. The fruit crops on bunds
include varieties of dwarf papaya, banana T x D coconut and arecanut. Flowers like
tuberose marigold etc. are also cultivated on the bunds. Both straw and oyster
mushroom cultivation are done in the thatched or polythene enclose. Bee rearing is
practice in 2-3 bee boxes on bunds. Agro-forestry component on the bund include
short term plantation of mainly Accacia spp. (A. mangium, A. auriculiformes). Animal
component constitutes improved breeds of duck, poultry birds and goats. Ducks are
raised in the rice field upto the beginning of flowering stage and later in an enclose in
pond refuge till the harvest of rice crop. Live Azolla is released @ 0.5 -1.0 t ha-1 and is
maintained to supplement duck feed and also to some extent fish feed, besides nutrition
to the rice crop. Fresh water pearl culture is integrated in the system using the host
mussel (Lamellidensmarginalis) which is normally available in the lowland rice
ecology. Components can however, be included in the system based on location –
specific requirements are grown along with the rice crop and later in the refuge after
the rice crop is harvested.

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ii. Productivity and economics

The rice fish farming system can annually produce around 16 to 18 t of food crops,
0.6t of fish and prawn, 0.55 t of meat, 8000-12,000 eggs besides flowers, fuel wood and
animal feed as rice straw and other crop residues from one hectare of farm. The net
income in the system is about Rs. 76,000 in the first year. Subsequently, this increases
to around Rs. 1,30,000 in the sixth year. This system thus increases farm productivity
by about fifteen times and net income by 20 folds over the traditional rice farming in
rainfed lowlands (Table 1). The rice fish system also generates additional farm
employment of around 250–300 man-days ha-1year-1.

Table 1. Cost of raising rice-fish-horticultural model in 1.0 ha area at NRRI.

Amount
S. No Particular (Rs.)
1. Construction of pond refuge and trenches and dykes (2000 cm x 35) 70,000
2. Constriction of platforms 16 No. @ 200/- 3200
3. Pit digging, planting of fruit and silvicultural plants (125-130 No.) 4000
4. Cost of seeds/seedlings/saplings 8,000
5. Cost of FYM/vermicompost 5000
6. Cost of fingerlings 8000
7. Cost of fish feed 5000
8. Small farm implements/equipments 5000
9. Labour 400 man days @ Rs. 150 60,000
Total 1,68,200

Fig.2. Layout and transverse section of rice based integrated farming system
for rainfed lowlands.

Integrated Rice-based Farming Systems for Enhancing Climate Resilience and

Profitability in Eastern India 279
2.1.2. Model II:Rice-fish-prawn-horticulture-agro-forestry based farming system
for deep water: With the aim of enhancing farm productivity in deep water areas (5-
100 cm water depth), a multi-tier rice-fish-prawn horticulture crops-agro-forestry based
farming system model has also been developed in 0.06 hectares area at NRRI, Cuttack.
i. Production Methodology
The design of the system includes land shaping in the form of uplands(tier I and
tier II) covering about 15% of field area followed by rice field area of 40% as rainfed
lowland (tier III) and deep water (tier IV). This rice field is connected to a micro water
shed cum fish refuge (pond) of 20% area for growing of fish and prawn with the rice
crop. Raised and wide bunds are made all around using 25% of the farm area. The
production technology includes growing of high yielding varieties of rainfed lowland
rice (Gayatri, Sarala)in teir III and deep water rice (Durga and Varshadhan) in tier IV
along with the fish and prawn during wet season. Dry season crops like sweet potato,
mung, sunflower, groundnut, vegetables are grown after lowland rice in tier III. Dry
season rice is cultivated after the deep water rice is harvested in their IV. Harvested
rain water in the pond refuge is used for irrigation of the dry season crops. Improved
varieties of perennial (mango, guava, sapota) and seasonal fruit crops (Papaya, Banana,
Pineapple) are grown in upland (tier I). Round the year different seasonal vegetables
and tuber crops (sweet potato, elephant foot yam, yam bean, colocasia and greater
yam) are cultivated in tier II(Upland). Agro-forestry (Acaciamangium) and plantation
crops (coconut and areca nut) are planted on the northern side of the bunds. Greater
yam is grown with the support of trunk of agro forestry tree. The productivity of the
system is about 8 t of rice crop per hectare, one tone of fish and prawn per hectare, 20-
25 t of vegetablesha-1 and 8.5 to 51.7 t of tuber cropsha-1. The cropping intensity in
this system greatly increases to 170% in field and 360% in the upland.
ii. Productivity and economics
Multi-tier rice fish horticulture based farming system can annually produce about
14-15 t of food crops, 1 t of fish and prawn, 0.5 -0.8 t of meat, 10000-12000 eggs in
addition to flowers and 3-5 t of animal feed from 1 hectare farm area. The productivity
of food crops further increases to 16-17 t besides, 10-12 t of fiber/fuel wood from eight
year onwards due to addition of produce from perennial fruit crops and agro-forestry
components. The net income in this system is around Rs. 1,00,000ha-1 in the first year.
This will increase to Rs. 1,50,000 or more from the eight year onwards.
2.1.3. Model III:Rice-based integrated farming system under irrigated condition:
With the objective of improvement of livelihood of small and marginal farmers, rice
based integrated farming system model for irrigated areas has been developed at
NRRI, Cuttack.
i. Production Methodology
About an acre of integrated farm area has been reoriented for the farming system
of which 30% of the area is converted to two rice plus fish fields of 600 sq.m area each
with a refuge of 15% area and another 30% area is developed into two nursery fish

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ponds of equal size of fingerlings rearing (Fig. 3). The remaining 40% (1500 m2) area is
utilized as bunds for growing vegetables, horticultural crops and agro-forestry. Three
rice crops are grown in the sequence of kharif rice (Sarla/Durga) followed by rabi rice
(Naveen/Shatabdi) and then summer rice(Vandana/Sidhant). Yellow stem borer pest
is controlled by using sex pheromone traps or by applying 1% Nethrin/Nimbecidine.
Fish culture is taken up with catla, rohu and mrigal species. The fish fingerlings are
reared in the two nursery ponds and are used for culture with rice crop in the system.
The excess fingerlings are sold out. On the bunds agro-forestry plants like teak,
Accacia, sisoo, neem, aonla and bamboo are planted on the northern and
southernbunds. Horticultural crops such as banana, papaya and arecanut are grown
on the bunds. Pineapple and spices are cultivated in the shade. Flowers like
marigold,hibiscus and jasmine are also cultivated in the western bund in 50m2 area.
Two plants of lemon and each of guava, jackfruit, mango and litchi are also planted on
the southern bund near the farm house to meet the household requirement. One
poultry and one duckery unit are integrated in the system in which 40 poultry birds
are raised during the dry seasons(October to April) and 20 ducks are reared during
the wet season (July to December).
ii. Productivity and economics
Three crop of rice yields 800 to 1000 kg of grain per year. Entire produce is sufficient
to cater the need of the small farm family. The straw is used for the cattle feed,
mushroom base and roof of the farm house. Rest of the straw is sold to earn Rs. 500-
1000 per year. After 2-3 months of rearing, fish fry worth of Rs. 4000-5000 is sold to the
other farmers. Fish are harvested according to the
need after the size becomes 250-300 g after 6
months or 0.5-1.0 kg after a year. The income from
fish rearing in the system is Rs. 20,000. Pulses
(mungbean, blackgram and pigeonpea) taken on Fig. 3. Transverse section of the
the slope and bunds are just enough to meet the rice based integrated farming
protein requirement of the farm family. system for irrigated area

2.2. On Station Research

2.2.1. Rice-ornamental fish culture: In order
to utilize the rice ecology for value added
aquaculture, the technique of breeding and
culture of ornamental fishes in irrigated
lowland rice field has been developed at
NRRI, Cuttack (Fig 4.). The rice field has been
renovated to make a pond refuge and raise
bunds all around. Ornamental fishes like Blue
gourami, Red gourami, Pearl gourami,
Guppies are bred and cultured with rice
(lowland varieties) crop during wet season. Fig. 4.Rice + ornamental fish system
During the dry season, rice (Naveen)cropwas under irrigated lowlands.

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Profitability in Eastern India 281
grown along with ornamental fishes with irrigation. About 25,000-6,00,000 ornamental
fishes ha-1were produced in the system, in addition to 3.5t and 5.0t of rice grain
during wet and dry seasons, respectively (Anonymous 1999).
2.2.2. Lowland weeds and their bio-control: Weed flora of different rainfed lowland
ecosystems were studied with special reference to rice-fish system at the farm of
NRRI, Cuttack revealed that with increase of water depth, the weed flora decreased
by 39% under rice–fish system indicating fish as a potential bio-control agent for
aquatic weeds.
The study conducted by Sinhababu et al. (2013) suggested that exotic carps
(grass carp, silver barb and common carp in order) were more effective than Indian
carps for control of weed in rainfed lowland rice fields and among the Indian carps,
rohu showed potential for weed control. Under the categories of grassy, sedges,
broadleaf and aquatic weeds total 13 major weeds were observed in the rice fields.
Grass carp reduced maximum weed biomass with weed control efficiency (WCE)of
63% at 60 days after transplanting (DAT) and 62% at 100 DAT followed by silver barb
and common carp (Table 2). Among the Indian carps, only rohu was effective in
control of weeds (WCE 23% at 60 DAT).

Table 2. Weed biomass and weed control efficiency (WCE) in rice alone and rice-fish
fields.
Weed biomass Weed biomass
(gm-2) WCE (%) (g m-2) WCE (%)
Treatments 60DAT 60DAT 100DAT 100DAT
Rice + grass carp 0.28d 63.34a 13.87d 62.31a
Rice + silver barb 0.32cd 60.54a 15.62cd 56.55ab
Rice + common carp 0.43c 46.89a 21.72c 41.81b
Rice + rohu 0.61b 23.10b 28.40b 23.22c
Rice + catla 0.77a 4.99c 32.86ab 8.49c
Rice + mrigal 0.76a 3.44c 31.75ab 11.23c
Rice 0.80a – 36.42a –
Source:Sinhababu et al. (2013)

2.2.3. Methane and nitrous oxide emission from rice–fish fields and refuge tank:
Datta et al. (2009) observed that CH4 emission from rice field plots sown with the two
rice cultivars, with or without fish, varied considerably (cv = 17%). Methane emission
was low in all the plots up to 30 days after sowing (DAS). Presence of fish resulted in
an increase in CH4 emission from both the rice cultivars with two sharp peaks recorded
at flowering and maturity stages of the rice crop. The mean CH4 emission (mg CH4 m-
2 -1
h ) from sowing till harvest followed the order: Varshadhan + fish (2.52) >Durga +
fish (2.48) >Durga (1.47) >Varshadhan (1.17). Cumulative CH4 emission was highest in
the treatment Varshadhan + fish (96.33 kg ha-1)while the lowest emission was reported
in field plots planted to cv. Varshadhan without fish (45.38 kg ha-1). Thus, percentage
increase in CH4 emission as a result of fish rearing was 112 in case of cv. Varshadhan
and 74 in case of cv. Durga. Methane emission from the pond refuge followed a similar

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pattern as that from rice fields. On the contrary, Unlike CH4, N2O emission flux from
rice fields exhibited a peak almost immediately after germination and stand
establishment, at 30–36 DAS and declined thereafter (Fig.2). As a whole,N2Ofluxeswere
comparatively low during the entire cropping period become greater only towards
maturity of the rice crop when the floodwater receded and the field started drying.
2.2.4. Physio-chemical parameters under rice fish system: Plots from an average of
28.51–28.94 °C in the different field plots in the morning (at 9:00 h) to around 32.23–
34.63 °C in the afternoon (at 15:00 h) (Table 1). Field plots without fish exhibited
significantly higher range of water temperature. The mean pH values also exhibited
significant differences (p<0.05) between the mean water temperature increased
considerably during the course of the day.
2.2.5. Fish Growth and Performance: Indian major carps, exotic carps and fresh
water prawn was reared at a density of 0.6m-2 (1 Prawn: 8 Fish) in the system. Among
the fishes, common carp was found to attain maximum size(2.4 kg) followed by Catla
(2.0 kg) and the prawn attained asize of 100 to 270g. Sampling and partial harvesting
indicated an estimated productivity of fish and prawn as 350 kg per ha per season
from the rice-fish system.
2.2.6. Validation and adoption in the farmer’s field: Since last two decades, rice-fish-
horticulture based farming system was developed in different villages/blocks of
Jagatsinghpur and Puri districts of Orissa, under different project funds. Recently
during 2014 and 2015 a farmer Sri.KunjoMullick, from Jagasinghpur district belonged
to small farmers category developed his rice growing farm into rice fish integrated
farming system under the guidance of NRRI experts. His rice field was prone to flood
during wet season due to poor drainage, back water and remain waterlogged for
nearly 4-5 months. Rise in salinity level was another problem during end march till
monsoon. The farmer mostly grew local rice varieties with low inputs and could get
very low rice produce (0.8-1.0 t ha-1) and hence could not sustain his livelihood. An
initial investment of Rs 72,000 was done by the farmer for establishment and shaping
of his rice area (Total 4 acres) into watershed/pond area of about 1 acre, where he was
advised to put the Indian major carps and the dug out soil was transformed into
raised dykes where the farmer took banana, coconut and vegetable crops like cowpea,
pumpkin, leafy greens, drum stick etc. Poultry and duckery was taken in the house
made with locally available materials. At the end of the year he could get the net
income of Rs. 1,50,000 with the cost benefit ratio of 1:2.08.

3. KNOWLEDGE GAPS
Traditional agriculture is known to cause environmental degradation because it
involves intensive tillage, when practiced in areas of marginal productivity.
Technologies and management strategies that can inflate productivity need to be
developed. At the same time, ways need to be found to preserve the natural resource
base. Within this framework, an integrated farming system represents a key solution
for enhancing overall production and safeguarding the environment through judicious

Integrated Rice-based Farming Systems for Enhancing Climate Resilience and

Profitability in Eastern India 283
and efficient resource use. Though many farmer, practices integrated farming system
traditionally in their homestead land but is not foolproof in combating climatic vagaries
and is mostly non interactive. The available resources in these areas, for modest
growth in land productivity is not utilized efficiently to reduce the risk related to land
sustainability vis-a –vis employment problem. Poor understanding of interaction and
linkages between the components under rice based integrated farming system is the
main reason for underutilization of resources and thereby unutilized rural employment
leads to poor economic condition of the farmer.The integrated nature of goal-based
modelling and the opportunity to play with the system might enhance learning about
the different components, their mutual relations and the potentials of the farm system.

4. RESEARCH AND DEVELOPMENT NEEDS

Climate change is already happening and its effects, especially on India’s rural
communities are particularly adverse. Although integrated crop–livestock systems
have been practiced globally for millennia, in the past century, farmers have tended
toward increased specialized agricultural production for better profitability, concerning
about natural resource degradation, stability of farm income, long-term sustainability.
Revitalizing integrated crop–livestock systems could foster crop diversity, better
managements of selected areas of the landscape to achieve multiple environmental
benefits. Integrated systems inherently would utilize animal manure, mutual benefits
of crop and livestock’s which enhances soil tilth, fertility, and C sequestration, and
adoption would enhance both profitability and environmental sustainability of farms
and communities. The system components combination complexity and potential for
public benefit justify the establishment of a new national or international research
initiative to overcome constraints and move toward greater profitability and
sustainability. The approach to climate-resilient agriculture will help increase the
response capacity of farmers and the resilience of the ecosystem, and reduce their
risks to climate change. The need is to highlight the key issues and understand the
practical challenges that must be addressed to build the capacities of rural communities
(small and marginal farmer’s) to participate and robustly adapt to mitigate the climate
change effects on agriculture.
In the climate change scenario, agriculture needs multi-sectoral and multi-agency
approach;well planned synchronised efforts for achieving sustainable agricultural
productivity and nutritional security and building resilience capacity of the people
and their livelihoods. Specific integrated farming system technology ‘package of
practices’ needs to be developed depending upon the farmers’ need and requirement
to the specific situation. Development of information system for providing timely,
accurate crop-weather advisories helps in minimizing risk and losses. Promoting/
reviving of indigenous crop varieties and reverse the loss of agro-biodiversity is
essential as indigenous crops are more resilient to climate variations and farmers
have better equipped knowledge for handling them, and traditional crops generally
meet the food preferences of communities. Reduction and proper utilization of waste
generating from agriculture practices and post harvest stages and their utilization
and value addition will reduce the carbon footprint.

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Weather-based locale-specific agro-advisories, contingent crop planning,

promotion of low external input technology, water budgeting, diversification for
livelihood security, conservation and promotion of indigenous varieties and
biodiversity need to be taken up in the respect of mixed integrated farming system are
to be relooked in the newer prospective for successful adoption of farming system in
the climate change scenario.
The way forward is to climate-smart sustainable integrated farming system. The
healthy soil, land and ecosystem with suitable ecosystem services are the main issues,
which will greatly contribute to conservation of precious resources (water, energy,
soil health, etc.),while decreasing the carbon footprint in agriculture. Good quality
storage facilities and marketing and value-addition of products would protect the
income of small-holder producers.

5. WAY FORWARD
The need for diversification of farming practice is thereby needed as the income
of farmers who depend solely on the produce of their traditional mono crop of rice
pattern is decreasing due to limited profit margin and changed food consuming habits.
Over the last two decades dietary pattern has been changed due to higher income
generation, change in food habit, population explosion has also changed the supply
and demand profiles of food. To meet the continuous rise in demand for food, stability
of income and diverse requirements of food grains, vegetables, milk, egg and meat
integrated farming systems (IFS) seems to be the feasible solution, thereby improving
the nutrition of the small-scale farmers with limited available resources. Integration of
different related enterprises with agriculture crops provides ways to recycle products
and by-products of one component as input of another linked component which
lessen the cost of production and thus raises the total income of the farm.Multiple
land use through integration of crops, minor livestock with aquaculture can result in
the best and optimum production from unit land area. In other words integrated
farming system can be practiced as micro business by farm youthfor achieving regular
income. Most of the constraints in agriculture can be removed by integration of
diverse enterprises which will solve most of the existing economic and evene cological
problems besides increasing productivity many-fold. Moreover,the expenditure on
fertilizers also declined due to availability of a good amount of manure, which resulted
into a saving of 50% expenditure on fertilizers as compared to arable farming (Tomer
et al. 1982). The prospect of improved research methods for the integrated farming
system is also an issue. This method should be tested in different agro-climaticzones
through out the country and improve it for wide-scale adoption with low invest
capital for small and marginal farmers as well as agri-enterprenuers.
References
Agriculture Census. (2010) Department of Agriculture & Co-operation, Ministry of Agriculture,
Government of India, New Delhi
Anonymous (1999) Annual Report (1998-99) Fish and Prawn production in the Rice-fish diversified
farming system pp69.

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Ashby JA (2001) Integrating research on food and the environment: an exit strategy from the
rational fool syndrome in agricultural science. Conservation Ecology. 5(2): 20.
Behera UK, Jha, KP and Mahapatra IC (2004) Integrated management of available resources of
the small and marginal farmers for generation of income and employment in eastern
India.Crop Research 27(1): 83-89
Behera UK and Mahapatra IC (1999) Income and employment generation of small and marginal
farmers through integrated farming systems.Indian Journal of Agronomy. 44(3): 431-
439.
Datta A, Nayak DR, Sinhababu DP, Adhya TK (2009). Methane and nitrous oxide emissions from
an integrated rainfed rice-fish farming system of Eastern India Agriculture Ecosystem and
Environment 129: 228–237.
Faroda AS, Yadav RS and Pal RN (1978) Comparative economics of specialized dairy farming,
mixed farming and arable farming. Journal of Research 8: 234-39.
FAO (2012) FAOSTAT, http://faostat.fao.org/site/339/default. aspx
Furuno T (2001) The Power of Duck (Integrated Rice and Duck Farming) Australia: Tagari
Publications.
Gill MS, Singh JP and Gangwar KS (2010) Integrated farming system and agriculture sustainability.
Indian Journal of Agronomy 54(2): 128-39.
Government of India (2009) Economic Survey of India, pp. 199-200. http://Indiabudget.nic.in
Jayanthi C (2002). Sustainable Farming System and lowland farming of Tamil Nadu.IFS Adhoc
scheme.Completion Report.
Kumar Sanjeev, Singh SS, Meena MK, Shivani and Dey A (2012) Resource recycling and their
management, under integrated farming system for lowlands of Bihar. Indian Journal of
Agricultural Science 82 (6):504-510.
Mahapatra IC (1992) Farming systems research challenges and opportunities. Eastern Indian
Farming System Research & Extension Newsletter 6: 3–10.
Praphan N (2001). Resilient of indigenous knowledge, fight to world crisis. Isan alternative
farming network, Ubonratchathani, Thailand.
Pullin RSV (1998) Aquaculture, Integrated Resources Management and the Environment. In:
Mathias JA, Charles AT, Baotong H (Eds.), Integrated Fish Farming. Proceedings of a
Workshop on Integrated Fish Farming, 11–15 October 1994, Wuxi, Jiangsu Province,
China.CRC Press, Boca Raton, Florida, USA.
Ruaysoongnern S and Suphanchaimant N (2001) land-use patterns and agricultural production
systems with emphasis on changes driven by economic forces and market integration. In:
Kam, S.P., Hoanh, C.T., Trebuil, G. and Hardy, B. (Eds.). Natural resource management
issues in the Korat basin of northeast Thailand: An Overview. Proceedings of the Planning
Workshop on Ecoregional Approaches to Natural Resource Management in the Korat
Basin, Northeast Thailand: Towards Further Research Collaboration, held on 26-29 October
1999, KhonKaen, Thailand. Los Banos (Philippines): International Rice Research Institute,
pp 67-77.
Shamim Al Mamun, FouziaNusrat and Momota Rani Debi (2011) Integrated Farming System:
Prospects in Bangladesh.J. Environ. Sci. & Nat. Resources4(2): 127-136.
Singh K, Bohra JS, Singh, Y and Singh JP (2006) Development of farming system models for the
north-eastern plain zone of Uttar Pradesh. Indian Farming 56(2): 5-11

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SinghKP, SinghSN, KumarH,KadianVSand SaxenaKK (1993) Economic analysis of different farming

systems followed on small and marginal land holdings in Haryana.Haryana J.Agron. 9:
122-125.
Sinhababu DP, Saha S and Sahu PK (2013) Performance of different fish species for controlling
weeds in rainfed lowland rice field. Biocon. Sci. &Tech. 23(12): 1362–1372.
Tomer SP, Sai Ram RK, Harika AS and Ganguly TK (1982) Comparative efficiency of dairy and
mixed farming systems. Forage Research. 8:93- 98.
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integrated farming system for enhancing the livelihood of farmers in Ballari district of
Karnataka. International Journal of Science, Environment and Technology 5(5):3630-
3634.

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 Resource Conservation Technologies under
Rice-based System in Eastern India

Mohammad Shahid, AK Nayak, R Tripathi, S Mohanty,

D Chatterjee, A Kumar, D Bhaduri, P Guru, S Munda, U Kumar,
R Khanam, B Mondal, P Bhattacharyya, S Saha, BB Panda and
PK Nayak

SUMMARY
During the period of green revolution intensive agricultural practices has improved
the yield of rice many folds, but put a big question on the sustainability of yield and
soil health. Conventional rice cultivation is highly intensive in terms of water, nutrients,
carbon and energy. With productivity stagnation and depletion of natural resources
in northwest India due to intensive cultivation have forced to put extra efforts for
increasing production and productivity in eastern India. Conventional crop
establishment methods such as puddle transplanted rice require large amount of
water, energy and labor, which are now becoming increasingly scarce and expensive.
To ensure sustainable production and food security, it is essential to identify rice
production systems with less irrigation water input. Recently, alternative resource
conservation technologies (RCTs) have gained the importance to reduce the cost of
cultivation and energy consumption, to sustain productivity, and to increase the
profit margin of farmers. Under the changing climate scenario resource conservation
technologies are viable options to shift production oriented to profit oriented
sustainable farming. Improved agricultural machines have been found to be very
effective on fields by reducing GHG emission. Increasing SOC in passive pool is one
of the moto of climate smart agriculture. Therefore, resource conservation technologies
may be considered as a realistic solution of the above-mentioned concerns.

1. INTRODUCTION
India has the biggest area (43.5 mha; 2015-16) under rice worldwide, producing
104.4 million tons of milled rice at productivity of 2.4 tons per hectare. Over the last six
decades the average production per year has increased by about five times and this
growth in agricultural production has come mainly from yield increase and to a lesser
extent from area expansion, which is projected to decline. Furthermore, in highly
intensive agricultural production areas, partial factor productivity is declining with
higher input use. Therefore, future expansion in production has to come from
productivity increase only through technological advancement. Post green revolution
era, the crop yields have even declined in some cases, for example in the grain-
producing areas of Punjab, where rice farming is characterized by intensive irrigated
agriculture. It is estimated that about 137 million tons of rice would require by 2050 in
India. Therefore, to sustain present status of production and to meet future food

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requirement, the rice productivity has to be brought to 3.3 tons per ha from the
current level.
With the evidence of productivity stagnation of rice and natural resources depletion
for the past decade in the northwest part of India, the country has compelled to put
extra efforts into increasing production and productivity in eastern India. A major part
of eastern India receives ample rainfall (1200-1700 mm), thus providing favorable
conditions for rice production. Out of the total rice growing area of the country,
eastern India covers about 67% with a production proportion of 59.5% and yield of
2.15 t ha-1 (Table 1), which is lower than the national average and uncertain because
of its dependency on monsoon and poor management practices. Trends of decline or
stagnation in productivity of rice even with the application of recommended levels of
N, P and K fertilizers in intensive rice based cropping systems, reduction of soil
health due to imbalance use of inorganic fertilizer, depletion of natural resources
particularly, water, nutrient and labour, several economic and environmental problems

Table 1. Region wise share of area, production, yield of rice in India (2012-14).
Zone Area in percent Rice Production Yield (t ha-1)
East 67.0 59.5 2.15
South 15.3 18.5 2.94
North 10.8 15.7 3.53
West 5.8 4.9 2.03
Total 100.0 (43.7)* 100.0 (105.8) 2.42
*Figures in parentheses indicate actual values (Area in million ha and production in million
tonnes) Data source: Directorate of Economics and Statistics, Ministry of Agriculture,
Government of India.

such as increasing cost of cultivation, fossil fuel burning, greenhouse gas emission,
pollution of water bodies in rice production system in India in general and eastern
India in particular have been manifested. Improved production technologies would
help to face the challenges to produce more food
at less cost and improve water productivity,
increase nutrient use efficiency and adapt the
effects of climate change in lowland ecosystem
in eastern India. So, there is dire need of an
energy, water and labor efficient alternate
system that helps to sustain soil and
environmental quality, and produce more at less
cost for sustainable and ecologically safe rice
farming (Fig. 1).
Recently, for achieving food security the
Fig. 1. General overview of
emphasis has been shifting from exploitative emergence of green revolution to
agriculture to conservation agriculture through sustainable agriculture (Srivastava et
the use of resource conservation technologies al. 2016).

Resource Conservation Technologies under Rice-based System in Eastern India

289
in order to preserve the natural resources as well as to efficiently use the external
inputs like water, chemical fertilizers and pesticides. Research efforts are focused, on
the refinement of resource conservation and conservation agriculture technologies,
to make the food production cost and energy efficient in order to increase the profit
margins of the farmers.
Over the past decades, extreme climatic events such as extreme precipitation as
well as extended drought periods or extreme temperatures have become more frequent
and stronger. These extremities greatly affect the agricultural production in the region.
Resource conservation technologies (RCTs) may help to adapt the production system
to the effects of climate change by improving the resilience and hence making them
less susceptible to aberrant climatic situations. The objective of this chapter is to
discuss recent advancements of the resource conservation technologies and
conservation agriculture both at international and national level with particular
reference to eastern India and their potential utilization in the region.

2. RESOURCE CONSERVATION TECHNOLOGIES AND

CONSERVATION AGRICULTURE
Resource conservation technologies (RCTs) and conservation agriculture (CA)
are the two approaches which often used synonymously. However, there is distinct
variation among the two. The resource conservation technologies refer to any of
those practices that enhance resource- or input- use efficiency. It has a wide dimension
and may include any agricultural practices that aim to conserve the natural resources
and improve their use efficiencies. Direct seeding of rice which saves water, energy
and labour may be considered RCTs. The varieties with high nitrogen use efficiency
and minimum tillage practices which save energy, labour and improve water
productivity may also be considered RCTs, as may land leveling practices that help
save water. There can be many more. In contrast the term “conservation agriculture”
(CA) according to the FAO, is an approach to managing agro-ecosystems for improved
and sustained productivity, increased profits and food security while preserving and
enhancing the resource base and the environment’ (Friedrich et al. 2012). Conservation
Agriculture has been based on the principles of holistic management of soil, water
and other agricultural resources so as to fulfill the objective of sustainable agricultural
production. CA is characterized by three major principles (FAO 2012):
 Minimal soil disturbance by direct planting through the soil cover without seedbed
preparation.
 Maintenance of a permanent soil cover by mulch or growing cover crops to
protect the soil surface.
 Diversifying and fitting crop rotations and associations in the case of annual
crops and plant associations in the case of perennial crops.
Usually under CA, 30% surface is essentially covered either by crop residues,
cover crops or biomass sourced ex-situ through agroforestry measures so as to cover

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the soil surface. This surface cover helps to physically protect the soil against agents
of soil degradation and provide food for the soil biota. Under the CA system, the
burning or incorporation of crop residues is strictly avoided. Another important
component of CA is zero tillage (ZT) technique, which restricts any kind of tillage
activity and sowing of seed without or with very little soil disturbance. Due to the
minimum soil disturbance in CA, soil biota and biological activities are not disturbed,
that is crucial for a fertile soil which supports healthy plant growth and development.
As the time passes, the soil biota acts as the agents of loosening of the soil and
mixing of the soil organic matter in zero tilled fields. Crop rotation involving leguminous
crop, which is another component of CA, helps to manage pest and disease problems
and improve soil quality through biological nitrogen fixation and addition of organic
matter.

3. STATUS OF RESEARCH/KNOWLEDGE - NATIONAL/

INTERNATIONAL
Globally, conservation agriculture using various RCTs is being practiced on about
125 M ha and the countries who adopted these technologies largely are USA (26.5 M
ha), Argentina (25.5 M ha), Brazil (25.5 M ha), Canada (13.5 M ha) and Australia (17.0
M ha) (Bhan and Behera 2014). In India, adoption of these technologies is still in the
initial phases and over the recent past, adoption of zero tillage and other technologies
has expanded to cover about 1.5 M ha (Jat et al. 2012). The use of zero-till wheat in the
rice-wheat system of the Indo-Gangetic plains is the major conservation agriculture
based technologies being adopted. In other crops and cropping systems, the
conventional agriculture based crop production systems are gradually shifting from
intensive tillage to minimum/zero-tillage operations. Many countries have now policy
decision to promote CA/RCT. In Europe, the European Conservation Agriculture
Federation, a regional lobby group uniting national associations in UK, France,
Germany, Italy, Portugal and Spain, has been founded. Resource conservation
technologies are also being adapted to varying extents in countries of southeast
Asia, viz. Japan, Malaysia, Indonesia, Philippines, Thailand, etc. The unique feature
that triggered the widespread adoption of RCTs in many countries is community-led
initiatives rather than usual research/government extension system efforts.
Most of the RCTs are already used by rice farmers of India especially northern
India i.e. Punjab, Haryana etc. But adoption level of these technologies in eastern
India is quite low possibly due to low level of mechanization and low availability of
irrigation water. In year 2016 in south Asia the adoption level of RCT technology are
direct seeded rice 22.54 %, zero till drill 11.21%, laser land levelling 6.51%, double no
till 0.21%, and turbo seeder 0.10 % (D’souza and Mishra 2018). Most RCTs have been
aiming at the two most crucial natural resources, water and soil. However, some of
them would also affect the efficiency of other production resources and inputs such
as labor and farm power or fertilizer. Some of the RCTs which are more popular and
being practiced in irrigated or rice-based cropping system are outlined below.

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3.1. Direct seeding
The shortages of labor and water, and depleting soil fertility issues are causing
increasing interest in shifting from puddling and transplanting to direct seeding of
rice (DSR). However, DSR is more preferred in the area with high wages and low water
availability. Major constraint in the adoption of direct seeding is the high infestation
of weeds, which is more difficult to manage under this system. There are in general
two types of direct seeding; (1) Wet-DSR, which refers to the sowing of sprouted rice
seeds either through broadcast or line sowing in puddled soil; and (2) Dry-DSR,
under which dry rice seeds are sown either through drilling or broadcasting in the
field that was prepared either by dry tillage or zero tillage or on a raised bed. One more
category of DSR is referred as water seeding where sprouted rice seeds are broadcasted
in standing water.
Wet-DSR is mostly practiced to manage the shortage of labour; however, increasing
scarcities of water, prompted to develop and adopt Dry-DSR. As far as yield is
concerned, differential response is observed for direct seeding of rice. In India, yields
were significantly lower (9.2–28.5%) in Dry-DSR than in conventional tillage
transplanting rice (CT-TPR). In Pakistan, yields of both Wet- and Dry-DSR were 12.7–
21.0% lower than CT-TPR. In Bangladesh and the Philippines, yields of CT-wet-DSR
were higher (8.6–18.5%) than those of CT-TPR, whereas in Nepal, Thailand, Combodia
and Laos, yields were similar to those of CT-TPR (Kumar and Ladha 2011). Studies
comparing CH4 emissions from different tillage and crop establishment methods but
with similar water management (continuous flooding/mid-season drainage/intermittent
irrigation) in rice revealed that CH4 emissions were lower with Wet- or Dry-DSR than
with CT-TPR (Kumar and Ladha 2011). The reported reduction in CH4 emissions was
higher in Dry-DSR than in Wet-DSR.
3.2. Bed planting
Bed planting is a system of crop production where the crop is grown on raised
beds, and furrows in between the beds are used for irrigating the crops. This system
has advantages of irrigation water saving, enhanced fertilizer use efficiency, better
weed management, and a reduced seed rate. Under bed planting system, significant
quantity of water is saved due to reduced evaporation and better distribution.
Additionally, the rooting environment is modified and aeration of the bed zone is
improved as compared with flat planting. Different type of bed plantings can be used
under different situations such as raised-bed transplanted rice, raised-bed drill-seeded
rice and permanent (double) bed-planted rice.
3.3. Minimum and zero tillage
Conventionally, tillage is done for the loosening of soil, preparation of seedbed
for good and uniform seed germination, management of weeds and incorporation of
crops left over, manures and fertilizers into the soil. While intensive tillage of the soil
has some immediate advantage, there are negative effects of continuous tillage on
soil quality which become more evident over the longer period. Soil organic matter

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(SOM) status is generally considered as the most dominating parameter for the
determination of soil quality and there is ample evidence of declining SOM with
tillage as compared to relatively undisturbed soil, which affects soil aggregation,
water availability, soil aeration, nutrient availability and soil microbial activity. Frequent
tillage tends to develop hardpan at the bottom of the plough layer which can restrict
water infiltration and root penetration. In recent years, considerable modifications
have taken place in tillage operations and several new concepts have been introduced
namely minimum tillage and zero tillage.
Minimum tillage involves considerable soil disturbance, though to a much lesser
extent than that associated with conventional tillage. It is aimed at reducing tillage to
the minimum necessary for ensuring a good seedbed, rapid germination, a satisfactory
stand and favourable growing conditions. Zero tillage (ZT) implies the sowing of
seed with the use of such tillage implements that open a narrow slit to drop the seed
and does not turn over the soil during the operation. Due to skipping of the intensive
ploughing that involves 3-4 tillage operations in traditional approaches, cost of
production is reduced and timely planting of subsequent crop is ensured.
Evidence on yield effects of zero tillage over conventional tillage is highly variable
and it was observed that zero tillage in combination with mulching resulted in initial
yield decline, and later on increase over the subsequent period (Baudron et al. 2011),
eventually exceeding yields in conventional tillage-based agriculture (Rusinamhodzi
et al. 2011). Other advantages of ZT over conventional tillage include better soil
health, energy saving and buildup of organic carbon. Zero tillage helps to mitigate
the effects of climate change through soil organic carbon sequestration and reduced
greenhouse gases emission. Various minimum and zero tillage operations used under
RCTs are minimum-till (non-puddled) transplanted rice, minimum-till (non-puddled)
dry drill-seeded rice, minimum-till drill-seeded rice with a power tiller–operated seeder,
minimum-till (non-puddled) dry drill-seeded rice+sesbania, zero-till (nonpuddled)
transplanted rice, zero-till drill-seeded rice, zero-till drill-seeded rice+sesbania and
double zero-till drill seeded rice.
3.4. Laser-assisted land leveling (LASER-level)
For surface-irrigated areas, a properly leveled surface with the required inclination
according to the irrigation method is absolutely essential. In the traditional method of
land leveling using eyesight, particularly on larger plots, getting accurate results are
difficult which lead to increased irrigation times, superfluous and inefficient water
use. Laser leveling is a process of flattening the land surface (± 2 cm) from its normal
elevation by using laser equipped drag buckets to achieve precision in land leveling.
By following this practice, a reduction in irrigation water and increase in yield of
wheat crop has been observed.
3.5. Alternate wetting and drying irrigation method
Alternate wetting and drying (AWD) is a method of water application during rice
cultivation which can be followed to reduce the water consumption in irrigated fields.
In this method, rice fields are alternately flooded and dried on frequent interval. The

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drying period of the soil in AWD vary according to the type of soil and the cultivar.
Alternate wetting and drying has been commonly used as a technology to save water
in many parts of the world for over a decade, however, unproductive water losses
could not be totally avoided due to the submergence of the field during irrigation
periods. The alternate wetting and drying technology not only saves water but can
greatly reduce emissions of methane.
3.6. System of rice intensification
The system of rice intensification (SRI) is a knowledge-based low-external input
technology which is developed in the 1980s in Madagascar and it benefit farmers
with small landholdings by giving higher yields without any harmful impact on natural
resources. It helps the rice farmers in increasing yield and provides some other benefits
such as saving of water and other inputs, if this is done in conjunction with other
changes in how they manage the plants, soil and nutrients. The main attributes of this
technology are transplanting of single young seedlings in a square pattern with
wider spacing, using organic manures and following alternate wetting and drying
irrigation method while keeping the rice soil moist during the vegetative growth
phase. This practice led to significant phenotypic changes in plant structure and
function and in yield and yield attributing characters. System of rice intensification
increased yields substantially (50–100% or more), while consuming only about half
as much water as conventional (Uphoff et al. 2011), whilst not needing the purchase
of additional external inputs. This technology has been proven to be resilient against
extreme weather events, pests, and diseases because of better plant vigor and root
structure. In recent years, many modifications in SRI has been noticed in different
parts of the world and it is asserted that the package of possible practices under SRI
have to be adapted to local conditions (Stoop 2011). Moreover, somewhat higher
labour requirement for SRI, poses the challenge to researchers and policymakers
concerned with the promotion of water saving rice technologies.
3.7. Cover crops and crop residues
One of the fundamental principles of the CA is to keep the soil surface covered.
This can be achieved either through growing cover crops or retention of crop residues
of previous crop on the soil surface. Cover crops are generally grown in between two
main crops to fill the gap period of harvesting one crop and establishing the next in
the fields where gap is too long. The vegetative biomass of cover crops helps to
protect the soil against the impacts of raindrops, provide shading of soil and preserve
the moisture loss. They may also benefit the main crops by providing mineral nutrition
through nitrogen fixation (legumes) and mineralization of other nutrients. Cover crops
may generate additional income through production of additional grain for human
food or extra fodder resources. There are different crop options such as grains, legumes,
root crops and oil crops that can be used as vegetative cover.
Crop residues are that portion of the crop which is left in the field after harvest, or
that part of the crop which is not used locally or traded commercially or discarded
during processing. More than 352 Mt of crop residues from various crops are produced

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annually of which major quantity is contributed by rice and wheat (Singh and Sidhu
2014). At many parts of the country especially the northern part, in situ burning of the
crop residues is a major concern that not only pollutes the environment but also
cause a loss of about 6 Mt of major nutrients. If managed properly, the crop residues
may become important source of nutrients and can also maintain or enhance soil
chemical, physical and biological properties along with preventing land degradation.
Some studies have found that recycling of crop residues in rice-wheat system increased
the rice as well as wheat yields by 13 and 8% and energy efficiency by 13 and 6%,
respectively with a decrease in cost of production, compared to residue retrieval,
whereas yield advantage was to the tune of 9 and 3% compared to residue burning
(PDFSR 2011). The major concerns in utilization of crop residues are the slow rate of
decomposition due to high C: N ratio of rice and wheat residues; obstruction during
tillage and sowing operation; and the increased incidence of disease limit its use.
3.8. Crop rotation and cropping system
Crop rotation is considered an essential component of the conservation agriculture
for achieving higher diversity in plant production. Growing diverse crops in sequence
not only maintain the higher soil microbial diversity but also help to explore the
different soil layers and recycle the nutrients that have been leached down to deeper
layers. Crop rotations involving legumes create favourable soil condition for the
proliferation of diverse soil biota, reduce input costs due to nitrogen fixation, provide
better distribution of water and nutrients through soil profile and help to manage
pests and diseases. Intensification of cropping systems such as increased number of
crops per year, double cropping, and addition of cover crops can increase soil C
storage under no-tillage (Luo et al. 2010). Efficient cropping sequences can contribute
to a great extent to sustain agricultural production.
3.9. Nutrient Management under RCT/CA
Eastern India is more agriculturally productive due to fertile soil, rainfall pattern
and plenty of available irrigation water, however more vulnerable to climate change.
Nutrient management is one of the prime options that are responsible for sustaining
crop productivity as well as maintaining soil quality. Under the periphery of resource
conservation technology, nutrient input in soil can be supplemented through:
integrated nutrient management (INM) and organic nutrient management (ONM).
Both the options can be suitable to improve the potential of yield under rice based
system of a specific agro-ecological region depending on the soil type, soil fertility
status and crop history.
An integrated nutrient management (INM) ideally combines both inorganic and
organic sources of nutrients in a balanced way. While inorganic nutrient forms readily
supplies plant essential ions and ensures better crop productivity; the organic forms
of nutrients, on the other hand, increase the nutrient use efficiency in soil and reduces
the chances of soil pollution due to excess use of factory generated chemical fertilizers.
Hence, the combination of both is often preferred for rice based farming system,
especially in the eastern Indian condition.

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 The sole organic nutrient management (ONM) is not as popular among the farming
communities of lowland rice system because of the uncertainty of the yield performance
of different rice varieties. But considering the sustenance of soil health, the locally-
available and cost-friendly investments of organic manures are sometimes preferred.
3.10. Weed management under RCT/CA
Economic factors and technology options have led to the change in rice
establishment method from traditional transplanting system to direct-seeding in Asian
rice systems over past few years. Weed infestation, however continues to be a major
bottleneck in this method because of simultaneous emergence of rice and weeds and
absence of standing water during early stages of crop growth to suppress germinating
weeds. Dry seeding of rice with zero tillage may further aggravate the weeds problem
because no tilling concentrates the weed seedbanks in the top layer of the soil that
results in a higher proportion of seed germination compared with conventional tillage
(Gallandt et al. 2004). Tillage also affects other soil growth factors such as temperature,
moisture, aeration and nutrients which affect weed infestation (El-Titi 2003).
Successful cultivation of direct-seeded rice, particularly under zero-tillage system
requires intensive use of herbicides. A variety of herbicides have been screened and
found effective for pre-plant/burn down, pre-emergence, and post-emergence weed
control in dry direct drill-seeded rice systems (Kumar and Ladha 2011). Because of
their high dormancy, the weeds of some weed species keep germinating throughout
the growing season. Pre- and post-emergence herbicides are imperative to keep weeds
under check (Kamboj et al. 2012). This practice of using pre- and post-emergence
herbicides is leading to pesticide load in the environment which is highly undesirable.
Therefore, cultivation practices should be evolved and designed in such a way that
the dual issues of weed management and rational use of pesticides are tackled
simultaneously.
3.11. Machineries used under RCT/CA
Improved agricultural machines have been found to be very effective on fields by
reducing GHG emission under precise land levelling, no tillage or zero tillage, sowing
machinery and subsequent efficient machinery for intercultural, harvesting and post
harvesting operations. Some of the machines that are commonly used are outlined
below.
3.11.1. Tractor drawn laser land leveler: The tractor drawn laser land leveller is used
for micro-levelling of fields and filling loose soil from higher elevation place to lower
place. Precision leveling increase yield by 20-30% and helps in control of weeds and
pests both in wet lands as well as up lands. This machine includes drag scraper, laser
transmitter, laser receiver, hydraulic control system, control panel and tripods stand.
3.11.2. Tractor drawn rotavator: Rotavator is an effective modern implement suitable
for all types and textures of soil. It effectively and economically replaces the combined
functions of cultivator, disc harrow, leveler and manual labour. It can be effectively
used as a puddler. It produces green manure by cutting roots/weeds in small fragments

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and mixing with soil. It creates better aeration and rapid germination of seeds.
Preparatory time of seedbed preparation between two crops reduces, hence it provide
opportunities for growing of second crop.
3.11.3. Direct rice seeder: Rice can be directly seeded either through dry or wet
(pregerminated) seeding. Dry seeding of rice can be done by drilling the seed into a
fine seedbed with a seed drill. Wet seeding is done through the use of drum seeder in
leveled puddled fields. Direct sowing of rice solve the problem of labour and water
scarcity. It gives saving of 12-35% of manpower and also reduction in methane
emission. Direct rice seeding methods results in higher economic return than
conventional transplanting.
3.11.4. Happy seeder: The Happy seeder is used for direct drilling of rabi crop in to a
combine harvested field (without straw removal/burning) in a single operation. The
rotating blades cut only that part of straw which is coming just in front of furrow
openers. These cutting blades are operated by PTO drive of tractor. It consists of two
units- one straw management unit and other sowing unit. The happy seeder cuts, lifts
and place the standing stubble and loose straw and sows the field in one operational
pass of the machine.
3.11.5. Tractor drawn zero till seed drill: This machine is used to sow the crop
directly into the uncultivated field just after the harvest of previous crop (rice) by
eliminating the tillage operation. It consists of fluted rollers for metering of seed and
fertilizer. The ground drive wheel supplies power through sprocket and chain for
metering of seed and fertilizer. The operation of zero till drill is energy efficient and
cost effective and it ensure timeliness of planting by avoiding repeated tillage
operations. It is suitable for sowing of wheat, gram, peas, soybean and linseed. The
machine is recommended for adoption by farmers for timely planting of crops viz.
wheat, gram, peas, soybean, linseed etc. during the brief turnaround time after harvest
of rice to increase the productivity and profitability of subsequent crop.
3.11.6. Straw reaper: It is a machine that cut threshes and cleans the leftover straw in
one operation. The stalks are conveyed into the machine by auger and guide drum
and reached to the threshing cylinder, where it cuts into small pieces. The short
fragments of stalks fall through the bars of the concave and the straw is collected in
an attached trolley and collected.

4. STATUS OF RESEARCH AT ICAR-NATIONAL RICE

RESEARCH INSTITUTE
ICAR-National Rice Research Institute (NRRI) has been in the forefront of
developing and refining resource conservation technologies for lowland rice in eastern
India. Many of the earlier works of the ICAR-NRRI was focused on improving the use
efficiency of the natural resources, increasing productivity of rice and reducing GHG
emission along with building up of carbon by developing the technologies related to
direct seeding, system of rice intensification, cropping system research involving

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legume crops, rice residue management, minimum tillage and zero tillage both under
transplanted and direct seeded conditions. The institute also worked upon the
designing and development of farm equipment for small and medium farmers related
to rice sowing and weeding. Some of the major findings are discussed below.
Saha (2005) reported that pre-emergence application of pyrazosulfuron ethyl +
molinate at 1.0 kg ha-1 supplemented with one hand weeding at 50 days after rice
sowing maintained a lower crop weed competition from the seeding of the crop till
maturity and registered the lowest weed density (3.2 m-2) in direct seeded rainfed
lowland rice. Moorthy and Saha (2003) reported that single application of butachlor
(2.0 kg ha-1), butachlor+safener (2.0 kg ha-1), quinclorac (1.0 kg ha-1) and fluchloralin
(1.0 kg ha-1) controlled weeds effectively and weed control efficiencies ranged from
63.5 to 71.6 per cent in rainfed lowland direct seeded rice. A supplementary hand
weeding controlled the weeds substantially as evidenced by comparable dry weight
of weeds recorded in these treatments with that of weed free check and higher weed
control efficiencies (82.1 to 85.3%).
Field experiment conducted to standardize the age of seedlings with different
crop densities for realization of higher yield in SRI indicated that 14-days old seedlings
planted at 16 hills m-2 gave significantly higher grain yield than conventional practice
(CRRI 2008). The yield potential of rice under SRI with different plant geometry and
age of seedlings was studied with the rice hybrid Ajay. Higher grain yield of 6.43 t/ha
was recorded with 8 days old seedlings planted at 25 cm x 25 cm spacing which was
5.75% and 14.4% higher than 14 and 21 days old seedlings at same spacing ( Lal et al.
2016).
In a field experiment it was observed that wet tillage recorded significant yield
advantage over the dry direct seeded practice, however, tillage depth had no
significant effect on yield. During dry season, greengram cv. PDM 54 produced 48%
higher yield in the plots where dry direct sown rice was grown in the preceding
season (CRRI 2012).
A study conducted at ICAR-NRRI on rice residue management revealed that
substitution of chemical N (25%) with crop residue to provide 60 kg N/ha gave
comparable grain and straw yields as that of chemical N. Superimposition of 60 kg
chemical N ha-1 (urea) on 2.5 t ha-1 crop residue increased the grain and straw yield of
rice over sole application of urea (CRRI 2011).
Field experiment was conducted with different resource conservation technologies
(RCTs) viz. minimum tillage, green manuring, brown manuring, wet direct seeding of
rice, zero tilled dry direct seeded rice and paired row dry direct seeded rice. The grain
yield varied in the range of 4.08 to 4.98 t/ha and the highest yield was obtained in the
paired row dry direct seeded rice with dhaincha. The input and output energy varied
in the range of 17.9-31.1 and 147.1- 190 GJ ha-1, respectively with highest input energy
in conventional system and lowest in zero tillage whereas highest output energy was
in paired row dry direct seeded rice dhaincha. The energy ratio (output/input) was
also found highest in the paired row rice with dhaincha treatment. There was significant

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amount of energy savings and net C gain in paired row dry direct seeded rice with
green manuring treatment compared to the rest of the treatments in this study (NRRI
2015).
A best bet climate-smart resource conservation technology (CRCT) involving the
‘package of primary land preparation with mould board plough (once in three year)
followed by soil pulverization by cultivator, dry direct seeding of rice and dhaincha in
paired row (15 cm spacing) with seed drill, dhaincha incorporation by cono-weeder at
25 DAS (alternatively knock down of dhaincha by 2,4-D, if standing water is not
available), 75% RDF of N and full doses of P and K as basal, customized leaf colour
chart (CLCC) based N application in two splits and mechanical harvesting by reaper’
was developed and validated in the farmers field and recommended for higher yield,
low energy and environment sustainability (Bhattacharyya et al. 2014).
In an experiment conducted at ICAR-National Rice Research Institute, Cuttack it
was observed that SOC stock was significantly higher by 5.3-9.7% in zero tillage
transplanted rice as compared to conventional rice cultivation (Dash et al. 2017).
Labile carbon pools are highly sensitive to cultivation practices, on the contrary total
carbon content does not change much. Therefore, carbon dynamics can be understood
by observing the changes in labile carbon pools under various RCT practices. Among
various RCT, residue incorporation and green manuring, in general, showed higher
quantity of readily mineralizable C, microbial biomass C, water soluble C, acid
hydrolysable carbohydrate and permanganate oxidizable C compared to other
techniques (Dash et al. 2017).
For small and medium farmers rice sowing and weeding equipment were developed
by ICAR-NRRI Cuttack. For sowing of pre-germinated seeds manual operated drum
seeders having four rows, six rows and power operated eight row seeder was
developed. Power tiller operated sowing machinery were developed which can be
used in sowing of rabi crop in rice crop residues. Manual and power operated weeders
were developed for weeding in wet land rice and dry land subsequent crops.

5. KNOWLEDGE GAPS
Intensive agriculture takes its toll on natural resources and on the environment.
This means that farmers have to produce more from less and deteriorating resources.
Keeping this in mind, the sustainability of rice farming under existing conditions in
eastern India is not assured without special efforts.
 Improper management of soil resource leads to degradation of the soil, resulting
in poor productivity. Soil quality assessment is, therefore, an important factor for
sustainable use of soil resources.
 Under zero tillage, the weeds emerge during the fallow just before the crop season
which makes the sowing difficult. Under this scenario, submergence of soil before
seeding or transplanting has its own advantages, viz., restricting the weed seed
germination under anaerobic condition, and decaying of emerged weeds. Intensive

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 research is required to be done on water seeding or mechanical transplanting in
standing water.
 The success of resource conservation technologies in eastern India depend on
two critical elements viz. residue retention on surface and weed control. Since
residues are generally used as fodder in rainfed, there is a need to determine the
minimum residue that can be retained without affecting the crop-livestock system.
 Any reduction in tillage intensity and frequency, poses serious concerns with
regard to weed management. Weed control strategies have remained challenging
for agricultural lands being switched to conservation tillage practices. Weed
management under zero tillage has been reported in many crops including cereals,
however, no comprehensive weed management strategy presently exists in
unpuddled transplanted rice.

6. RESEARCH AND DEVELOPMENT NEEDS

It is claimed that the full benefits of CA can be availed when all the three principles
(minimum soil disturbance, permanent soil cover through crop residues or cover
crops, and crop rotations) are followed i.e. the concept of CA is fulfilled. However,
there is probably no scientific report available on rice in India that proves this fact. A
thorough investigation on different components of conservation agriculture either
alone or in combination may help in the assessment of individual and combined
benefits that will lead to appropriately adjust the requirement at specific sites.
In eastern India, dominant rice ecology is the rainfed lowland. Under this ecology
moisture availability is enough and in general nutrient status is good, and if managed
properly it can support short duration rabi crop. Under such ecosystem, short-duration
pulse crop can be grown in sequence to the kharif rice crop. Short duration pulses
which have much lesser water requirement and require shorter duration can thrive
well under harsh climate and fragile ecosystems on one hand and can help to achieve
household food and nutritional security on the other, offer great promise towards
diversification of cropping systems.
In rice, it has been observed that strategies to reduce emissions of N2O often lead
to an increase in emissions of CH4. There is trade-off between these two gases. Both
gases have different global warming potential (GWP), hence our approach must be
focused on reduction of N2O emission, because N2O is having more GWP than CH4.
The RCTs measures with lesser emission of N2O need to be recommended for rice
based systems.
Some strides have been made for herbicide screening in DSR, however, research
is needed to evaluate the efficacy of different herbicides which can be effective for
weed control under zero-till systems. More research on weed management under
minimum tillage in a cropping system perspective is needed. Identification of critical
thresholds of tillage for various rainfall, soil and cropping systems, such that the
main objectives of rainwater conservation are not compromised. This will balance the
need for conserving soil and capture rainwater in the profile.

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Ecosystem services are crucial for the sustainable supply of food and fibre.
Unsustainable agricultural practices pose great threat to worldwide food supply due
to declining ability of the agricultural ecosystems to provide ecosystem services.
Assessment of ecosystem services under different RCT for long-term sustainability
of agro- ecosystems and their ability to provide increased production without
deteriorating the ecosystem services need to be done. With the accumulating evidence
on climate change, there has been interest in examining the greenhouse gas contribution
of production practices and products using life cycle assessment approach. The sole
application of mineral fertilizers could not maintain SOC stock while application of
organics proved essential for long-term sustainability of the rice based system.
Combination of rice residue and green manuring is adoptable soil amendment option
to sequester the soil organic C, yield sustainability and minimizing GHG emission.
Study on sustainability, C sequestration and ecosystem functioning for rice-based
system under organic nutrient management can help in understanding the ecological
footprint of the organic nutrient management. Application of optimum quantities of
inputs (mainly renewable energy) and utilizing positive synergies between the
agricultural crops will minimize the wastes of nutrients, water and locally available
organic wastes is the key principles for achieving sustainability. Strategies for low
energy inputs and synergy, conservation agriculture practices will minimize the
environmental impacts, making rice farming sustainable and eco-efficient. Crop residue
management is a challenge in rice farming and possible ways need to be explored for
fast decomposition of paddy straw.
Availability of machinery/equipment for promotion of RCTs is a prerequisite for
achieving targets of agricultural production. More user friendly technology need to
be developed for direct drilling of rabi crop in heavy paddy residue condition.
Development of specialised machineries such as paired row rice-daincha seeder is
required for doing the simultaneous operations in one go and save energy and labour.
Farm implements needed for seed and fertilizer placement simultaneously for ensuring
optimum plant stand, early seedling vigour in rainfed crops under minimum tillage.
There is a need to enhance the accessibility of smallholders to zero-till knowledge,
herbicides, and zero-till planters.

7. WAY FORWARD
Resource conservation technologies and conservation agriculture offer a new
paradigm for agricultural production different from earlier systems, which mainly
intended to achieve a specific production targets. Locally adapted RCTs appropriate
to resource availability of farmers and the biophysical condition hold potential to
improve management of natural resources and provide sustainable increases in
productivity. From the long-term field experiments, which were started at the beginning
of the green revolution era for developing nutrient management strategies and
understanding the nutrient mining, valuable information have been received to develop
future strategies. Appropriate long-term monitoring has to be continued, and be
relevant to future changes in tillage and water management practices. In addition,

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benefits of changes in the tillage system and stubble management to the soil ecosystem
need to be better understood. Zero-till, permanent bed-planting systems and new
non-puddled rice establishment techniques coupled with laser land levelling can go
a long way to increasing the use efficiency of this vital natural resource. Resource-
conserving technologies applied in isolation have advantages and disadvantages.
They are not universally applicable as the problems can sometimes outweigh the
benefits. However, by combining different resource-conserving technologies,
synergies can be created to eliminate the disadvantages of single technologies and
accumulate the benefits.
The increased use of chemical fertilizers to increase the production of food and
fibre is a cause of concern and it was realized that the soils which receive mineral
nutrients only through chemical fertilizers are showing declining or stagnating
productivity even being supplied with sufficient nutrients. In recent years, the
agricultural production system is facing the challenges of energy crisis, high fertilizer
cost and low purchasing power of the farming community which necessitates
rethinking on the alternatives. Unlike chemical fertilizers, organic manure and bio-
fertilizers are available locally at cheaper rates. They enhance crop yields per unit of
applied nutrients and provide a better physical, chemical and microbial environment
that is more conducive to higher productivity. The available quantity of animal manure
and crop residues cannot meet the country’s requirements for crop production.
Therefore, maximizing the usage of organic waste and combining it with chemical
fertilizers and bio-fertilizers in the form of integrated manure appears to be the best
alternative.
Mitigation options in the rice based cropping system may individually be of
limited scope, but they may achieve a discernable composite effect when implemented
in coordinated fashion. Mitigation programs will rely on win–win opportunities when
emissions can be reduced with another concomitant benefit such as higher yields,
less fertilizer, and water needs etc. Targeting one individual gas alone seems
inappropriate due to tradeoff effects in the emissions of CH4, N2O, and CO2. More
research is needed to combine geographic information, emission models, yield models
and socio-economic information to devise site-specific packages of mitigation
technologies. Many studies conducted on RCT shows reduction in cost of cultivation,
reduced incidence of weeds, saving in water and nutrient, increased yields and
environmental benefits. Still RCTs are not popular among farmers of eastern India.
These technologies need to be popularizing among farmers with the help of extension
departments.
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of conservation agriculture and current smallholder farming practices in semi-arid Zimbabwe.
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issues. International Soil and Water Conservation Research 2(4):1-12.

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Bhattacharyya P, Nayak AK, Din M, Lal B, Raja R, Tripathi R, Mohanty S, Shahid Mohammad,
Kumar A, Panda BB, Munda S, Gautam P and Mohapatra T (2014) Climate-smart resource
conservation technology (CRCT) for lowland rice ecologies in eastern India. CRRI research
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CRRI (2011) Annual Report 2010-11. Central Rice Research Institute, Cuttack, p. 21.
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in developing economies: The case of south Asia. Land Use Policy 70:221-223.
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carbon resource conservation techniques for energy savings, carbon gain and lowering
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Dynamics and management of Weeds in Rice

Sanjoy Saha, S Munda, BC Patra, T Adak, BS Satpathy,

P Paneerselvam, P Guru, N Borkar and S Chatterjee

SUMMARY
Weeds are serious problems for farmers of all hues and rice growing is no exception.
Problems associated with weed management in rice are mounting dramatically during
last few decades due to rapid changes in cultural practices of rice farming and also
because of reduced availability of affordable labour and shortage of water. Changes
in cultural practices viz., mechanized tillage, crop establishment by direct seeding,
increased herbicide use, variable water availability, mechanized harvesting, rice-rice
cropping sequence etc. led to shift from relatively easy-to-control sedges and
broadleaved weeds to more difficult-to-control grassy weeds including weedy rice.
New management strategies are required as no single method can solve all the problems
of weeds in rice cultivation. Manual weeding 2-3 times in a season by engaging more
than 100 person days ha-1 involves huge cost in weed control. Selection of suitable
rice varieties with proper management practices should be integrated with direct
control measures viz., mechanical weed control by using motorized weeder or by
application of safest herbicide with broad spectrum to reduce the cost on weed
management practices. The overall objective of modern weed management approaches
is to reduce the degree of direct control inputs. Therefore, further research is needed
for breeding weed competitive rice cultivars, herbicide tolerant rice. Also development
of power weeder with high operation efficiency is highly important. Along with these
technologies, emphasis on development and standardization of new and safe herbicides
should be given to make rice cultivation more profitable.

1. INTRODUCTION
Weeds are undoubtedly a major biotic constraint to rice production, causing 33%
of total yield losses in comparison to insects (26%) and diseases (20%). Extent of
dominance of weed is dependent on prevailing agro-climatic conditions, soil types,
water management, crop establishment practices, weed seed bank in soil and cropping
system adopted in different rice ecologies. Depending upon various factors, the yield
loss varies from 30% in irrigated to 70% in rainfed uplands (Saha and Rao 2011).
Beside this, weeds interfere with rice growth by competing for light, nutrients, water
and space and by creating a favourable habitat for the growth of various harmful
organisms such as insects and pathogens. Problems associated with rice weeds are
mounting dramatically due to changes in rice production systems in response to
changing climate and declining accessibility of labour and water. Weeds are dynamic
and new weeds keep emerging over a period of time owing to change in cropping
pattern and, practices of crop cultivation. Changing climate may also lead to weed
shifts, faster spread of invasive species and more competition to crops from weeds.

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Change in traits and growth behavior in response to climate change is expected to
make weed scenario more complex.
Access to supplementary irrigation has enabled crop establishment by direct
seeding in non-puddled, non flooded fields under dry condition and lowland rice
environment with limited water (Singh et al. 2006). Water and labour scarcity is also
pushing the farmers to opt for direct seeded systems. These non-puddled, non flooded
systems are threatened by heavy weed infestation. The absence of a seedling-size
advantage between rice and weed seedlings, as both emerge simultaneously, can
cause grain yield losses of 50–91%. Thus, weeds are the most severe constraints to
direct sown aerobic rice systems (Rao et al. 2007). The key to success of these
systems is efficient weed control techniques. Recently, weedy rice is emerging as
another serious threat to direct seeded systems. The spread of weedy rice became
significant all over the world mainly after the shift of rice cultivation from transplanting
to direct seeding. For farmers, weedy rice is a difficult-to-control weed/ plant as
strategy for its management is non-existent, and still remains elusive in non flooded
aerobic situations (Saha et. al. 2014). The conception of herbicide tolerant (HT) rice
may offer rice farmers a vital tool for controlling difficult to control grasses and mixed
population of weeds. It can also help to control wild and other weedy rice species and
provide an alternative tool for the management of those weeds that have already
evolved resistance to particular herbicides. It also makes way for the replacement of
some of the commonly used selective herbicides by new non-selective,
environmentally safe herbicides.
Traditionally, manual weeding is done 2-3 times in a season (more than 190 person
days/ha used) which involves huge cost in weed control. Additionally, seedlings of
grassy weeds (e.g., Echinochloa spp.) look similar to rice seedlings and it makes
hand/ manual weeding more tedious and difficult. Therefore, use of herbicides (and/
or bio-inoculants), or using machines (mechanical weed control) are considered as
alternative/supplement to manual-weeding and most economical way to manage weeds.
New safer herbicides need to be formulated and standardized for broad spectrum
weed control in rice under different situations. However, use of herbicides is deemed
with its own challenges like environmental pollution and herbicide resistance. In
absence of strict guidelines and its implementation, herbicides are being used in
excess, which cause water pollution through run-off, and negatively affect the soil by
affecting the microbes. Weed resistance to the herbicides used in rice is a relatively
new event. Since 1980s’, with the introduction of sulfonylurea herbicides, several
weed species have evolved resistance to herbicides due to continuous use of same
herbicide in the same field. Even multiple resistances (the resistance to more than one
type of herbicide action) have evolved in some cases. Low cost single row and
modified two row self-propelled power weeder may serve as an alternative to herbicide
with less drudgery. The machine has been designed and tested at ICAR-NRRI with
28-30% plant damage (CRRI Annual Report 2013-14). Further research is required to
design efficient implements (weeder) to cut down the energy and cost incurred for
manual weed control.

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An important factor of modern weed management strategy – is not to rely too

heavily on any one tactic. Current weed management technology consists of integration
of appropriate crop husbandry (agronomic practices) along with direct cultural and
chemical methods (Saha and Rao 2011). Thus, an integrated approach involving
appropriate crop husbandry along with some direct weed management practices viz.,
cultivation of weed competitive varieties, selection of herbicides and farm
mechanization. This chapter on weed management would give an insight on the
possibilities to tackle the threat called ‘weeds’ with the existing knowledge and
contemplate on what could be done further based on existing technologies. This
chapter also explores the challenges and responsibilities that lie ahead in future rice
production vis-a-vis weed management.

2. STATUS OF RESEARCH/KNOWLEDGE
2.1. Rice crop-weed interference
Among different categories of weed flora, grassy weeds are the most competitive
and usually the first group that emerges and grows simultaneously with the rice crop
for a considerable time period (7-70 days). Weeds that emerge before or simultaneously
with rice crop are far more competitive than those that emerge 2 to 3 weeks later.
Sedges and broadleaf weeds emerge subsequently at the later stages of crop growth.
While, under aerobic conditions, several flushes of weeds come up because the weed
seeds with differential dormancies germinate as and when conditions are favorable.
Initial slow-growth phase of the rice crop is critical when the weed growth is fast. The
weeds should be prevented at this particular stage until the crop enters the fast-
growth phase, the influence of weed competition can be greatly reduced. In case of
direct-sown rice, the initial 7-35 days is considered to be the most critical for crop-
weed competition. In uplands, since short duration varieties are grown, the proportion
of their life cycle infested by weeds is higher and hence the crop suffers more (Saha
and Rao 2011). Direct-sown rice in rainfed lowlands encounters similar situation as
that of uplands during the initial stage and experiences competition from mainly
grassy weeds and few sedges. However, with the accumulation of rainwater in crop
field during peak monsoon in lowlands, the crop faces competition from some non-
grassy broadleaf and aquatic weeds. In transplanted rice, weed problems are generally
of lower magnitude provided the puddling and water management are done properly.
Majority of weeds (about 60%) emerge within 7-30 days after transplanting (DAT)
and compete with rice plants till maximum tillering stage. About 15-20% of the weed
populations emerge in the period between 30-60 DAT and 20-25% of weeds emerges
later and are not important in yield reduction. While sedges and broad leaf weeds are
mostly predominant in irrigated ecology under both wet seeded and transplanted
cultures. In wet seeded system, the crop-weed competition is more intense (because
of similarities in age of rice and weed seedlings) than that of transplanted system
(where aged seedling with better competitive ability are raised). The ultimate loss in
grain yield due to competition with weeds is more in direct than transplanted rice
irrespective of growing season.

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2.2. Weed management under changing climatic scenario
It is expected that growth of C3 plants would be enhanced more by CO2 enrichment
as compared to C4 plants. Due to greater adaptability, weeds will achieve a greater
competitive fitness against the crop plants with a changed climate (Table 1). Probable
changes in the weed biogeography of agricultural systems pose challenges to
management. Environments with high degree of disturbance are more susceptible to
annexation by newly introduced plant species and are likely to reach a relatively
quick stability with emergent climatic factors. It is predicted that climate change can
reduce the effectiveness of current weed management practices. Agronomic practices
for particular crops are likely to change with time and space. New classes of herbicides,
cultivars, tillage system, irrigation techniques and seed sowing practices will influence
the geographic distribution of weeds and their invasiveness.
Under changed climatic scenario, temperature, precipitation, wind and relative
humidity may influence the efficacy of herbicides. Thicker cuticle development or
increased leaf pubescence, with subsequent reductions in herbicide entry into the
leaf is expected in drought situation. These physiological changes can interfere with
crop growth (reduced transpiration) and recovery after herbicide application. Overall,
herbicides are most effective when applied to weeds those are free from environmental
stress. For example, rising atmospheric CO2 concentrations can reduce the glyphosate
efficacy. High concentrations of starch in leaves in C3 plants grown under high CO2
environment might interfere with herbicide efficacy. Elevated temperature and higher
metabolic activity in C3 weeds tend to increase uptake, translocation and efficacy of
many herbicides, while moisture deficit, especially when severely depressing growth,
tends to decrease efficacy of post-emergence herbicides, which generally perform
best when plants are actively growing.
Table1. Crop/weed competition outcome at elevated CO2 conditions.
Weed species Crop Favored underelevated CO2
Amaranthus retroflexus (C4) Soybean (C3) Crop
Amaranthus retroflexus (C4) Sorghum (C4) Weed
Chenopodium album (C3) Soybean(C3) Weed
Taraxacum officinale (C3) Lucern (C3) Weed
Albutilon theophrasti (C3) Sorghum (C4) Weed
Taraxacum and Plantago (C3) Grasses (C3) Weed
Red rice (C3) Rice (C3) Weed
Echinochloa glabrescens (C4) Rice (C3) Weed
Source: Modified from Bunce and Ziska 2000

Mechanical and manual removal of weeds are the most widely used weed
management practices in developing countries. Mechanical control of perennial weeds
is likely to be adversely affected by elevated CO2. Elevated CO2 could lead to increase
in below ground carbon storage with subsequent increases in the growth of roots or
rhizomes. This may consequently help additional plant propagation with mechanical

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tillage (e.g. Canada thistle) (Ziska et al. 2004). Perennial grasses and sedges like
Cynodon dactylon, Cyperus sp. and Schoenoplectus articulatus propagate asexually,
hence, disking/harrowing would result in greater number of propagules. Increased
photosynthesis may stimulate more production of rhizomes and other storage organs
which will make control of perennial weeds more difficult. Biological control of weeds
is likely to be affected. Elevated CO2 could alter the efficacy of weed bio-control
agents by possibly changing the development, morphology and reproduction of the
target pest. Direct negative effects of high CO2 in environment would be related to
variations in C: N ratio and changes in the feeding habits and growth of natural
enemies.
2.3. Challenges of weed management in direct seeded/ aerobic systems
Dry direct seeding of rice (DSR) with subsequent aerobic soil conditions eliminates
the need for standing water, thus reducing the overall water demand and providing
opportunities for water and labour savings. Dry seeding of rice is now considered to
be an emerging production system in India and Asia because of a reasonable shortage
of water availability in agriculture. Despite the numerous benefits, DSR systems
adoption by farmers has been seriously inhibited by weed management tradeoffs.
The practice of DSR has resulted in a change in the relative density of weed species
in rice crops. In particular, Echinochloa spp., Ischaemum rugosum, Cyperus difformis,
and Fimbristylis miliacea are widely adapted to conditions of DSR (Rao et al. 2007).
Presence of Leptochloa chinensis and Dactyloctenium aegyptium is widely reported
from many areas, particularly in DSR.
Weed management in DSR is considered a serious threat and the risks of yield
losses is very high due to weed competition than in transplanted rice because (1)
early flooding suppresses initial flushes of weeds early in transplanted rice but not so
in DSR (2) rice seedlings in DSR are less competitive with concurrent emerging weeds
because of the absence of a size difference between the rice and weeds in DSR (Rao
et al. 2007). Although herbicides are important in reducing weed competition and
helpful in ensuring adequate yields under DSR, overreliance on herbicides poses
both economic and environmental risks. It can result in shifts in weed communities
and evolution of herbicide-resistant weed populations (Rao et al. 2007) that reduce
herbicide efficacy and increase costs, as newer and more expensive herbicides may
be required as the relatively fast emergence of “weedy” rice. This weed is
phenotypically similar to rice cultivars but exhibit undesirable agronomic traits, viz.
shattering. It is usually observed in areas where DSR is being practised, and this is a
serious concern to the rice production system sustainability.
In view of these weed management challenges in DSR, as well as the potential
problems associated with the overuse of herbicides, several recent works have
highlighted integrated weed management approach such as integration of use of
competitive cultivars, changes in seed rate, timing and geometry, use of residue
mulching, crop rotation, water and nutrient management, and mechanical methods
(Matloob et al. 2015; Rao et al. 2007). These works have also outlined the importance
of preventive measures which include seed predation, seed decay, and fatal germination

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as important components of integrated weed management in DSR. However, detailed
reviews on the potential of preventive approaches based on knowledge of the ecology
of weed species is limited in DSR system.
In our previous study at ICAR-National Rice Research Institute, it was observed
that grassy weeds viz. Echinochloa colona, E. crus-galli, Leptochloa chinensis,
Dactyloctenium aegyptium, Digitaria sanguinalis, Panicum repens etc. are the most
competitive weed-flora that emerge early and grow simultaneously with the rice crop
for a considerable time period in direct-sown rice. Sedges viz. Cyperus iria, C. difformis,
Fimbristylis mileacea etc. and broad leaved weeds Alternanthera sessilis, Ageratum
conyzoides, Ludwigia octovalvis, Sphenoclea zeylanica, Cleome viscosa etc.) emerge
subsequently at later stages of crop growth (Munda et al. 2017). Sometimes several
flushes of weeds come up as seeds present in soil germinate as and when conditions
are favourable in aerobic soil.
2.4. Hazard of herbicide resistance
Herbicide resistance is the inherent ability of a biotype of a weed to survive
herbicide application to which the original population was susceptible. Herbicide
resistance causes changes in the weed population because of resistant biotypes.
Resistant biotypes are build up when the herbicide to which those individuals are
resistant is used repeatedly. Herbicide-resistant weeds have been an issue since the
early 1970s, although it was described as a potential problem as early as 1957 by CM
Switzer. Like other organisms, random genetic mutations occur within plant populations.
These mutations are often at very low frequencies. For herbicide resistance, a single
plant in several million may have a mutation to survive herbicide treatment. Generally,
herbicide applications do not cause any genetic mutations. Applications create
selection pressure that favors the spread of resistant biotypes. Cross resistance can
occur within weed populations.
The development of herbicide resistance poses three serious problems:
i. Very expensive and time consuming to test for and develop alternative management
plans.
ii. Develop management techniques to continue utilizing current herbicides and
protect them against resistance development.
iii. Development of herbicide resistance in a biotype limits weed management options.
Factors that control development of resistant weeds are selection pressure, weed
biology and genetic factors. If herbicides with long soil residual activity are applied
repetitively, high selection pressure is placed for resistant biotypes of a weed. Some
weeds have high genetic variability i.e. many different varieties or biotypes exist
under the one species. They generally develop resistance quicker, as there already
exist resistant biotypes within a population. Seed longevity is another factor that
controls the development of herbicide resistance. Plant species that produce long-
lived seed tend to develop resistance early. This is because susceptible seeds from

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the seed bank germinate over many years adding variation to the population. The site
of action of the herbicide on the plant is governed by genetic factors. There are
differences pertaining to the frequency of mutations occurance at different biological
target sites within plants. Sites that have high frequency of mutation, tend to develop
quickly, for example resistance may develop with three or more years of continuous
use at the site of action of ALS and ACCase inhibitors. In contrast, the target site of
glyphosate do not mutate as frequently. Glyphosate resistance did not exist earlier,
but it took many years to develop (Neve et al. 2011).
In general, herbicide-resistant weeds are likely to develop in fields under
conservation tillage (minimum and no-till systems) as congenial environment is created
with repeated application of high dose herbicides. Because of the reduced tillage,
farmers rely primarily and, sometimes, solely, on herbicides for weed control, thereby
imposing constant selection pressures on weeds. However, the intensity of selection
pressure depends on herbicide family and type of tillage operation. Reports suggested
that an escalation in the use of ACCase-inhibitors in conservation-tillage did not
escalate the development of wild oat populations resistant to ACCase-inhibitors.
Also, the onset of glyphosate resistance in rigid rye-grass was delayed in a minimum-
tillage system.
2.5. Newly emerging weeds/weedy rice
During the last one decade, it was observed that Leptochloa chinensis emerged
as one of the dominant grassy weed species in rice-rice cropping sequence where the
rice field became wet during the major part of crop growing season. The dominance of
grassy weeds (>60% of total weed population) was recorded in DSR plots during
both wet and dry season. Leptochloa chinensis and Cyperus difformis were dominant
species occupying 56% of total weed population in this system (CRRI Annual Report
2014-15). Alternanthera philoxeroides, which generally occurs in irrigation channels,
water courses, wetlands during dry season (Feb-March) at high temperature, now
become an emerging weed in rice field, may be due to changes in atmospheric
temperature. Ludwigia adscendens, another weed generally occurs in wet lands or
irrigation channel, has now became another emerging weed in rice-rice system in
many States of eastern India, particularly lowlands due to continuous wet condition
of rice fields (CRRI Annual Report 2013-14).
Weedy rice is a troublesome weed in many rice growing regions. The extent and
type of competition imposed on cultivated rice by weedy rice depends on the structural,
biological and physiological features of weedy rice which shows a wide variability
among different populations (Londo et al. 2006). By definition, weedy rice is an
introgressed form of wild and cultivated rice (Oryza sativa L.). Weedy rice belongs to
the Oryza genus and sativa species as cultivated rice but with different form. It
appears as hybrid swarms due to introgression of genes between wild and cultivated
species in nature. In Asian rice, it is known as Oryza spontanea whereas in the
African context it is known as Oryza stapfii. The most common feature among extremely
variable weedy rice is their ability to disseminate seeds by early shattering. It is more
problematic in the direct-seeded rice than transplanted rice. The potential ecological

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risks associated with transgene escape through gene flow (or crosspollination) are
the foremost concerns. The spread of weedy rice infestations have been reported to
40-75% of the total rice area in Europe, 40% in Brazil, 55% in Senegal, 60% in Costa
Rica and 80% in Cuba. In Asia, infestation of weedy rice became an emerging problem
since 1980s. Its infestation was first reported in Malaysia in 1988, in the Philippines in
1990, and in Vietnam in 1994. Weedy rice infestation in Asia caused yield losses
ranging from 16 to 74%. Yield loss of about 1 t ha-1 was caused by infestation of 35
weedy rice panicles m-2 as reported in Malaysia. It was reported from USA that the
yield of cultivar New-bonnet was reduced by 219 kg ha-1 with one weedy red rice plant
in square meter. The competitive ability of one weedy rice plant was equivalent to
three rice plants (cultivar Mars).
Under a competitive environment, weedy rice competes well and utilizes resources
more efficiently than the cultivated rice varieties. Therefore, study of nutrient (NPK)
removal by weedy rice is essential to estimate the actual loss of nutrients from soil. In
Asia, some weedy rice accessions have been found to have greater nitrogen-use
efficiency for shoot biomass than cultivated rice (Dar et al. 2013). Researchers have
given due attention to the mechanism of nutrient losses in soil, particularly N, but
only few studies have been made on the impact of weedy rice competition on nutrient
use efficiency and other major nutrients P and K. Limited studies have been made on
the extent to which weedy rice populations, particularly of Indian subcontinent, can
compete with cultivated rice for the three major nutrients (NPK).
At ICAR- NRRI, five thousand thirteen germplasm including 41 wild rice accessions
collected from Assam and 139 wild and weedy rice accessions collected from Odisha
during 2012 were sown and transplanted along with check Swarna for characterization
and seed multiplication. One hundred and eighty wild and weedy rice were
characterized based on agro-morphological traits as per the descriptors. Study on
their genetic variation suggested that the genotypes selected for this study harbored
enough genetic divergence. However, an UPGMA dendrogram based on the genetic
relationships suggested a closer relationship of weedy and wild rice occurring within
the same regions (CRRI Annual Report 2013-14).

3. KNOWLEDGE GAPS
 Robust herbicide management technologies are not available to address the issues
of herbicide persistence in soil (causing environmental pollution) and herbicide
resistance in weeds. Greater strides need to be made to make herbicide use safer
for environment.
 Very little progress is made in the area of weed competitive rice varieties. Weed
competitive rice varieties could be a cost effective measure for suppressing the
weeds.
 Further research is needed regarding the development herbicide tolerant rice.
There is need to clearly understand the tradeoffs of herbicide tolerant rice.

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4. RESEARCH AND DEVELOPMENT NEEDS

Research and development needs have been broadly discussed under the following
heads:
4.1. Rational use of herbicides
In an agricultural system, the aim is to produce the highest yield achievable whilst
minimizing costs. Herbicides are one of the first labour and costs saving technologies.
Improved weed control with herbicides has the potential to improve crop yields.
Chemical weed control can provide a pro-poor technology for rice cultivation in Asia.
The herbicide use in the tropical countries is directly related to the cost and availability
of labour. The use of herbicides has gained importance due to rise in farm wages in
the recent years as a consequence of overall economic growth and growth in non-
farm employment opportunities, predominantly in Asia. Recent government mandates
such as the National Rural Employment Guarantee Act has created agricultural labor
shortages in India because guaranteed employment and wages mandated by the Act,
making hand weeding an unsuitable practice (Toth 2011).
While the role of herbicides in improving crop productivity has long been
recognized, the abuse of these chemicals has been among the major causes of
environmental pollution. Increasing concern has triggered research on the fate and
effect of continuous and massive use of pesticides to the environment. Smallholder
farmers face a number of problems associated with herbicide use, due to either an
inadequate knowledge about rate of application, or the optimum time for herbicides
application to control the weeds. A major cause of this is possibly serious lack of
information available to the farmers and the poor level of understanding. Often only
nominal precautions are taken for safe use of herbicides. Frequent herbicide application
has led to herbicide resistance within some weed populations. In the USA, Propanil
application for 30 years continuously, resulted in resistant Echinochloa sp. Continuous
use of Bensulfuron for four years resulted in resistance in four aquatic weed species.
The evolution of herbicide resistant weeds is a real threat to effective weed control
where herbicides are frequently used. Smallholder systems may be particularly
vulnerable as herbicides are often not used at appropriate times or dosages, which
may hasten the development of resistance. To prevent and manage existing herbicide
resistant biotypes requires an integrative approach. This may include research on
crop and herbicide rotation, standardization of herbicide mixtures (including tank mix)
and development of herbicide with short residual activity and intensive use of farm
machinery to reduce herbicide load.
Persistence of any pesticide is critical for weed control. Shorter than expected
activity (less persistent herbicide) can lead to poor weed control and require additional
action and expense by the farmer to supplement weed management. Residual activity
longer than expected (more persistent herbicide) can lead to problems with injury to
a subsequently crop and may cause non point pollution (Fig. 1). The persistence
depends on the characteristics of the pesticide itself or its metabolites. Volatility,
solubility, formulating agents, the method and site of application of pesticides

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 determine the persistence. Among the
environmental factors, particularly
temperature, moisture and wind determine
the dissipation of pesticide. Soil
characteristics like organic matter content,
soil pH, soil structure and texture, nutrient
content and its microbial population control
the persistence of any pesticide. So, further
Fig.1. Herbicide persistence in soil. research in required in this regard to
Source: http://ucanr.edu/blogs/blogcore/ developed herbicide which are safer to use
postdetail.cfm?postnum=5929
and which allow much greater plasticity in
application.
In rice, a number of herbicides like butachlor, pretilachlor, pendimethalin, oxadiazon,
anilofos, oxadiargyl etc. have been recommended as pre-emergence control of early
flashes of weeds. Pre-emergent herbicides are usually useful in direct-sown rice fields
to suppress the early flashes of weeds. These herbicides generally have narrow
spectrum of controlling annual grasses and some sedges. Their efficacy depends on
soil moisture and is ineffective in dry soil conditions. However, on light soils, heavy
rains may move the herbicide down in the soil to the germinating crop seeds and
cause severe injury. These herbicides also show severe phyto-toxic effects to rice
crop emergence under flooded condition immediately after herbicide application. Mild
phyto-toxicity may cause extension of flowering time and total duration of rice crop.
The high application rates of pre-emergent herbicides also show detrimental effect to
the beneficial microorganisms extant in soil.
In recent times, some new post-emergent herbicides with low dosages viz.,
bispyribac sodium, cyhalofop butyl, fenoxaprop-p ethyl, ethoxysulfuron, penoxulam,
azimsulfuron, flucetosulfuron etc. and herbicide mixtures like azimsulfuron + bispyribac
sodium, fenoxaprop-p ethyl + ethoxysulfuron, bensulfuron methyl + pretilachlor,
cyhalofop butyl + penoxulam, metsulfuron methyl + chlormuron ethyl etc. are showing
promise for controlling weeds in rice fields. The rate and time of application of these
new generation herbicides/ herbicide mixtures were standardized to keep the weeds
under control during first 5-6 weeks of rice crop establishment. Thus, low-dosage
high-efficacy post-emergent herbicides/ herbicide mixtures having broad spectrum
of weed control are expected to be an intervention to suppress the weeds during
critical period of crop-weed competition up-to 35-40 days of weed emergence (Munda
et al. 2017; Saha et al. 2016). Among herbicide tested at ICAR-NRRI, the lowest weed
biomass (9.0 g m-2) was recorded in the Azimsulfuron + Bispyribac sodium treated
plots with the weed control efficiency of 89% (ICAR-NRRI Annual Report 2014-15).
However, for successful control of weeds by herbicides, it is very much essential
for the users to know different types of herbicides, specific herbicides to control
different types of weed species, their doses and time of application, and safe handling
and accurate application technologies for effective and environmentally safe weed
control. Correct use of herbicides is essential to ensure that chemical residues on

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crops do not exceed the limits. Recommended herbicides generally do not pose any
threat to people, livestock, or rice crops if used correctly and if suggested precautions
are followed. However, the herbicides are potentially hazardous if not handled properly.
4.2. Weed competitiveness
Although, herbicides provide opportunity for relatively cheap control of weeds,
relieving farmers of a heavy financial burden, the over-reliance on chemicals has also
led to a number of environmental and agronomic concerns. The application of
herbicides is leading to the reduction of non-weedy species and having impacts on
biodiversity and ecosystem function. More notably, from a production viewpoint,
herbicide resistance is now a common phenomenon and widespread amongst many
problematic weed species in many countries, encouraged by the increasing
dependence only on a few selected herbicides. In response to these challenges, there
is new interest in the prospective for integrating non-chemical (or ‘cultural’) control
options into weed control strategies. Competitive rice cultivars would offer a relatively
cheap option in integrated weed management strategies. Many cultural methods can
be integrated but, competitive cultivars are a potentially attractive option in
comparison, because they do not incur any added costs. Breeding weed-competitive
cultivars requires easily used selection protocol, based on traits that can be measured
under weed-free conditions. Such cultivars may be more capable of reducing the
competitiveness of a weed species, produce chemical exudates (allelochemicals)
thereby reducing the economic burden by resisting weed growth and yield loss.
Competitive cultivars could reduce the seed return of a weed species and contribute
to medium to long-term weed management strategies, reducing the pressure on
herbicides and improving the sustainability of cropping systems.
Variability in cereal cultivars in their ability to restrict yield losses from weed
competition has been demonstrated in different crops. However, such comparative
studies are of limited value outside of the experimental pool of cultivars. It is important
that more practical approaches are developed that can be used to assess new cultivars
for various situations and guide crop breeding efforts in future. Two aspects of
cultivar competitiveness can be defined. The first is the ability of the crop to reduce
the fitness of a competitor, and the second is the ability of the crop to withstand the
competitive impact of neighbors (suppressive ability) and resist yield loss (tolerance
ability). A strong suppressive cultivar can reduce seed production capacity of weeds,
which could a viable long-term strategy in weed control. By contrast, tolerance means
yield will be maintained under weed pressure. Although cultivars with high competitive
ability have been recognized in many cereal crops (including wheat and barley),
competitiveness has not traditionally been considered a priority by rice breeders.
At NRRI, above hundred early maturing rice germplasms (95-115 days duration)
with five checks viz., Vandana, Anjali, Heera, Annada and Kalinga III were screened
for weed competitiveness during kharif 2014. The germplasms viz., IC 426096, RH 145-
55, Jhum Fulbadam, Deng-deng, IC 337590, IC 298485, IC 447256, CR 453 and DBT
2722 were found to be weed competitive (ICAR-NRRI Annual Report 2014-15). The
germplasms viz., IR 83929-B-B-291-2-1-1-2, IR 83750-B-B-145-4-174-3, IR-84899-B-184-

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18-1-1-1, IR-84887-B-153-33-1-1-3, IR-84887-B-157-38-1-1-3, IR 83750-B-B-145-4-174-2
and IR 82589-B-B-63-2-148-1 were found to be weed competitive at a different location,
Santhapur (CRRI Annual Report 2013-14).
A number of relationships between competitive ability of crop and plant traits
have been reported in the literature, viz. plant height, early vigour, tillering, canopy
architecture, belowground traits, and nutrient partitioning. These traits are not
independent of one another and have implications for other plant functions in addition
to weed competition, including yield potential and tolerance of stress. To realize the
potential of competitive crop cultivars, a faster, cheaper and simple-to-use protocol
for measuring the competitive potential of new cultivars is essential; it is likely that
this will not be based on a single trait, but will need to capture the combined effect of
multiple traits. Further work would be required to measure the trade-offs and recognize
win-win traits that improve competitive ability without negotiating other plant
functions.
4.3. Herbicide tolerant (HT) rice
Herbicide tolerant (HT) rice may offer rice farmers a vital tool to control broad-
spectrum of weeds. Rice varieties with an herbicide resistant gene would allow farmers
to use an herbicide that is more environmentally-friendly than those in current use
while simultaneously allowing better management of weeds. With HT-rice, farmers
get the flexibility to apply herbicides only when needed. Farmers can make decision
on input of herbicides with preferred environmental characteristics. HT-rice can control
the weed flora associated with rice, especially of wild and other weedy rice species
and also provide an alternative tool for the management of weeds that have already
evolved resistance herbicides, especially grassy weeds like Echinochloa spp. It
furthermore allows for the substitution of some of the currently used herbicides by
other non-selective herbicides having less detrimental effect to the environment like
glyphosate, glufosinate etc. Compared to other conventional herbicides used in rice,
imidazolinone, glyphosate and glufosinate are considered environmentally benign.
There is a negligible threat of residual effects of glyphosate in soil as it is strongly
adsorbed to the soil and crops. These herbicides can be used as post-emergent and
therefore their rates can be adjusted to the actual weed pressure. Compared to
conventional herbicides, HR-rice also provides a broader window herbicide application
in terms of time frame and therefore alleviates some of the usual concerns (time
pressure) for rice farmers. However, for season-long and broad-spectrum weed control,
appropriate herbicide programs need to be developed for HR-rice in relation to the
time of application, dose, herbicide mixture, and integration of non-chemical methods
to ensure the long-term benefits of HR-rice technology.
4.4. Exploring herbicides – microbe compatibility
In modern agricultural production, herbicide application is one of the inevitable
practices is being followed to minimize weeds problems in crop production. The
indiscriminate usage of herbicides is reported to affect a group of organisms such as
bacteria, fungi, nematodes, earthworms, termites and protozoa. The interaction

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between herbicides and soil biota is gaining practical significance since some of the
herbicide molecules have adverse effects to microbial activities in soil. Many scientific
evidences have revealed that the herbicides can cause both qualitative and
quantitative change in soil enzyme activity. However, positive relationship may still
exist with some herbicides molecules as noted in some studies. Herbicides application
has both positive as well as negative effect to microbial activities in soil in response
to different herbicides application.
Earlier, butachlor application was found to increase the reproductive ability of
bacteria, but it is affecting the multiplication of free living nitrogen fixing bacteria
particularly of Azotobacter sp. Some research findings indicated that application of
organophosphates herbicides gradually increased azotobacter, arthrobacter,
heterotrophic aerobic bacteria, actinomycetes and fungal counts. It is reported that
herbicide viz., MCPB, bentazon, MCPB + fluozifop-p-butyl., bentazon+fluozifop-p-
butyl, metribuzin, flouzifop-pbutyl+metribuzin, cycloxydin, and sethoxydin
significantly increased the population of soil fungi (4 to 10 times higher) as compared
uninoculated control, but these herbicides did not have any significant effect on
nitrogen fixing bacteria. Different herbicides viz., pendimethalin, oxyflourfen, pursuit
and pertialachlor application found gradually increased bacteria, fungi, actinomycetes
and rhizobia. Arbuscular mycorrhizal fungi (AMF) is beneficial symbiotic endophytic
fungi form a bridge between plants and soil and play a major role in the flow of energy
and mobilization of nutrients (particularly P) from soil to plants. Other beneficial
effects viz. plant growth promotion, inducing stress tolerance and enhancement of
crop yield have been established. The field application of diuron and trifiuralin
herbicides at recommended rates recorded minimal effects on AM fungi association.
In another study, trifiuralin and diuron had little adverse effect on AMF formation. As
the soil has mixed population of AM fungi, understating the side effects of herbicides
on these non-target microorganisms are very complex. Because species of AM fungi
differ in their response to a particular chemical, so no generalization can be made on
the toxicity of a chemical to AM fungi.
In rice cultivation, herbicide application is essential but there effects on non-
targeted organisms need to be studied in-depth. Moreover, information on proper
herbicide use is very important for preserving beneficial microbes in soil. Hence, it is
essential to study the effect of new herbicides on microbial properties in rice soils.
More research is needed to better understand the different aspects of microbe-
herbicide interactions. If we carry out some systematic studies on herbicides usage
and their influence on soil microbial properties in rice based cropping systems, it will
help to identify safe herbicides for rice cultivation, which in turn will preserve the soil
beneficial microbes.
One of the most popular rice herbicide, Bispyribac sodium was evaluated in rice
cv. Naveen at NRRI during 2015 under glass house condition to study its effect on
AM fungal association. The results indicated that application of Bispyribac sodium
even at double dose (600 ml ha-1) did not show any inhibitory effect to AM fungal
root colonization and sporulation in rice, the same treatment which recorded 33.3 and

Dynamics and management of Weeds in Rice

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9.09 % higher AM fungal colonization and sporulation respectively as compared to
recommended dose (300 ml ha-1). Similarly the AM fungi treated rice plants recorded
significantly higher soil microbial biomass carbon (261.2 - 266.6 μg g-1 soil) after 30
days application of bispyribac sodium as compared uninoculated control (results
unpublished).

5. WAY FORWARD
Wide variation in geographic, socio-economic, and agro-climatic conditions in
rice-growing areas have resulted in equally diverse and contrasting extremes of weed
control methods ranging from purely manual in developing countries to high-energy
input technology in developed countries with large commercial farms. However, no
single weed management strategy will solve all weed problems in rice. New
management strategies will be needed as the established methods may no longer
work in the changing environment. Current weed management technology consists
of integration of appropriate crop husbandry (agronomic practices) along with direct
cultural and chemical methods. It is also essential to develop weed database including
noxious weeds in different ecosystems to track the weed dynamics. Such information
will help to prepare list of weeds which are potential invaders and different models
can be made use for prediction of invasiveness. The overall objective of proper crop
management is to reduce the degree of direct control inputs. Thus, an integrated
approach involving appropriate crop husbandry (indirect weed management strategy)
including cultivation of weed competitive varieties and/or herbicide tolerant rice,
good land preparation, proper water and fertilizer management, appropriate seeding
rate/plant spacing, crop rotation is likely to improve rice grain yields. Future research
on direct weed management practices viz. selection of herbicides with robust herbicide
management strategy along with mechanical methods would bring about substantial
dividends.
References
Chauhan BS, G Mahajan, V Sardana, J Timsina and Jat ML (2012) Productivity and sustainability
of the rice-wheat cropping system in the Indo-Gangetic Plains of the Indian subcontinent
problems, opportunities, and strategies. Advances in Agronomy 117:315-369.
CRRI Annual Report (2013-14) Characterization of the germplasm for agro morphological traits
and molecular aspects. Exploration, characterization and conservation of rice genetic
resources, pp. 17-18
CRRI Annual Report (2013-14) Field performance of single row power weeder. Enhancing
Productivity, Sustainability and Resilience of Rice Based Production System, pp. 68-69.
CRRI Annual Report (2013-14) Screening of germplasm against weed Competitiveness. Enhancing
Productivity, Sustainability and Resilience of Rice Based Production System, p. 73.
ICAR- NRRI Annual Report (2014-15) Screening of early maturing germplasms for their weed
competitiveness. Enhancing Productivity, Sustainability and Resilience of Rice Based
Production System, p. 91.
ICAR- NRRI Annual Report (2014-15) Study on weed spectrum and efficacy of lowdose herbicide/
herbicide mixtures under varying seed rate in dry-direct sown rice. Enhancing Productivity,
Sustainability and Resilience of Rice Based Production System, p. 91-92.

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Kumar V and Ladha JK (2011) Direct seeding of rice: recent developments and future research
needs. Advances in Agronomy 111:297–413.
Londo J P, Chiang Y C, Hung K H, Chiang T Y and Schaal BA (2006) Phylogeography of Asian wild
rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice
Oryza sativa. Proceedings of National Academy of Sciences USA 103:9578"9583.
Mahajan G, Chauhan BS and Gill MS (2013) Dry-seeded rice culture in Punjab state of India lessons
learned from farmers. Field Crops Research 144:89–99.
Matloob, A, Khaliq, A and Chauhan, BS (2015) Weeds of direct-seeded rice in Asia problems and
opportunities. Advances in Agronomy 130:291–336.
Moss SR, Marshall R, Hull R and AlarconReverte R (2011) Current status of herbicideresistant
weeds in the United Kingdom. Aspects of Applied Biology 106:1–10.
Munda S, Saha S, Adak T and Jambhulkar N (2017) Weed management in aerobic rice role of
establishment methods and herbicides. Experimental Agriculture Doi: 10.1017/
S0014479717000576.
Neve P, J K Norsworthy, K L Smith, and I A Zelaya (2011) Modeling glyphosate resistance
management strategies for Palmer amaranth (Amaranthus palmeri) in cotton. Weed
Technology 25:335–343.
Rao AN, Johnson DE, Sivaprasad B and Ladha JK, Mortimer AM (2007) Weed management in
direct-seeded rice. Advances in Agronomy 93: 153–255.
Saha S, Munda S and Adak T (2016) Efficacy of azimsulfuron against complex weed flora in
transplanted rice (Oryza sativa) under rainfed shallow lowland. Indian Journal of Agricultural
Sciences 86 (2): 186–91.
Saha S, Patra BC, Munda S and Mohapatra T (2014) Weedy rice problems and its management.
Indian Journal of Weed Sciences 46(1):14-22.
Saha S and Rao KS (2011) Major weeds of rice. Research Bulletin No. 4, Central Rice Research
Institute, Cuttack, Orissa, India, pp. 1-63.
Singh S, Bhushan L, Ladha JK, Gupta RK, Rao AN and Sivaprasad B (2006) Weed management in
dry-seeded rice (Oryza sativa) cultivated in the furrow-irrigated raised-bed planting system.
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 Economic and Eco-friendly Use of Rice Straw

P Bhattacharyya, H Pathak, AK Nayak, P Panneerselvam, MJ Baig,

S Munda, D Bhaduri, S Satapathy, M Chakraborti, NT Borkar and
N Basak

SUMMARY
There are about 731 million tons of lignocellulosic rice straw generated in the
world every year. Every kilogram of harvested rice is accompanied by production of
about 1.0-1.5 kg of the straw. Assuming that 50% of crop residues are utilized as cattle
feed and fuel, the nutrient potential of the remaining residue is 6.5 million tonnes of
NPK per annum. In India about 16% of generated crop residues are burnt on farms.
Out of this 60% is paddy straw. Recent estimate showed that during November-
December, around 70% cause of air pollution in New Delhi and its surrounding cities
was straw burning. Not only Punjab and Haryana, straw burning is spreading over
other states, very rapidly. Primarily burning causes emission of CO2, CO, SOx, NOx,
particulate matter and CH4 which increases air pollution and GHGs/ Carbon footprint
tremendously.
It is a paradox that on one hand we have a shortage of animal feed, biofuel and
manures, and on the other hand considerable amount of crop residues are either
wasted or burnt. This is not only a big loss of natural renewable resources but at the
same time it is a source of greenhouse gas (GHG) emissions and environmental
pollution. However, these residues can effectively be used as mulch, for production
of manure, ethanol, bio-diesel, biochar, etc., and in conservation agriculture. In a
rough estimate, if 20% of world’s rice straw is used for production of ethanol annually,
about 40 billion litres could be generated, which is able to replace 25 billion litres of
fossil fuel based gasoline.
There are knowledge gaps on the economic technologies for in-situ and ex-situ
composting of straw, characterization of rice straw of available varieties for fodder
quality, cost effective small scale technologies for bio-energy production,
technologies for value addition of paddy straw in view of present day mechanized
agriculture and authentic database on contribution of straw burning in air pollution
and GHGs/ carbon footprint.
However, a huge potential to use paddy-straw in bio-energy production,
composting, as fodder and so on, can establish it as an important bio-resource.
Microbial composting, is an up-coming technology for agricultural wastes disposal
in which biodegradation of lignocellullosic matter like paddy straw is carried out
exploiting ligninolytic and cellulolytic microorganisms. Breeding of new varieties of
rice which not only provides good quality grains for human consumption but also
superior quality straw for feeding ruminant animals and producing biofuels with
increased efficiency is another innovative approach. At the same time there is an

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urgent need for popularizing the array of available technology such as use for power/
electricity generation, ethanol production, biochar production, composting and raw
material for paper mill/ board making industry.

1. INTRODUCTION
Rice straw is one of the most abundant lignocellulosic materials being produced
in the world (Total, 731 million tons; Africa, 20.9 million tons; Asia, 667.6 million tons;
Europe, 3.9 million tons; and America, 37.2 million tons) (Sarkar and Aikat 2013). Every
kilogram of harvested rice is accompanied by production of about 1.0-1.5 kg of the
straw. The major agro-residues in terms of volumes generated in India (in million
metric tons–MMT) are rice straw (112), rice husk (22.4), wheat straw (109.9), sugarcane
tops (97.8) and bagasse (101.3), which cumulatively amounts to approximately 620
million tons (Pandey et al. 2009). On an average these residues contain about 0.5%
N, 0.2% P2O5 and 1.5% K2O. Assuming that 50% of crop residues are utilized as cattle
feed and fuel, the nutrient potential of the remaining residue is 6.5 million tonnes of
NPK per annum.
In India about 620 million tonnes of crop residue is generated every year. About
16% of them are burnt on farms. Out of this 60%, paddy straw and wheat straw
accounted for 22%. Recent estimate showed that during November-December, around
70% cause of air pollution in New Delhi and its surrounding cities was straw burning.
Not only Punjab and Haryana, straw burning is spreading over other states, very
rapidly. Primarily burning causes emission of CO2, CO, SOx, NOx, particulate matter
and CH4 which increases air pollution and GHGs/ Carbon footprint tremendously.

2. RICE STRAW BURNING

The rice and wheat system (RWS) is one of the widely practiced cropping systems
in India. This cropping system is dominant in India where almost 90-95% of paddy
area in Punjab, Haryana and Western UP is under intensive Rice-Wheat-System
(RWS) (Ladha 2000). Widespread adoption of green revolution technologies and
high yielding varieties increased both crop yield as well as crop residue. In the RWS,
a short period of time is available between rice harvesting and wheat plantation and
any delay in planting adversely affects the wheat crop. This coupled with use of
combined harvester compels the farmers to burn the residue to get rid of it.
After harvesting, open burning of rice residues (both straw and husks) is a standard
practice in Asia. Open burning of rice straw residues has harmful environmental
effects. It causes greenhouse gas emissions (GHGE), including 0.7–4.1 g of CH4 and
0.019–0.057 g of N2O per kg of dry rice straw, and emission of other gaseous pollutants
such as CO2, SO2, NOx, HCl and, to some extent, volatile organic compounds (VOC)
and carcinogenic polycyclic aromatic hydrocarbons (PAH), dioxins and furans (Oanh
et al. 2011). It also affects the radiation budget of the earth. Intensive burning
contributes to the formation of Atmospheric Brown Cloud (ABC) that affects the air
quality and visibility (Kanokkanjana et al. 2011). Rice straw burning is also an important

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source of aerosol particles such as coarse dust particles (PM10) and fine particles
(PM2.5) (Chang et al. 2013), affecting regional air quality and reducing visibility as a
result of the gas and particle emissions. In November 2016, in an event known as the
“Great smog of Delhi”, air pollution spiked far beyond acceptable levels. Levels of
fine particle and sand-coarse dust particles hit 999 micrograms per cubic meter, where
as the safety limits for those pollutants are 60 and 100 micrograms, respectively, and
this event is chiefly attributed to the practice of open burning of rice straw in the
neighboring states of Punjab and Haryana.
Open burning of rice residues also results in loss of major nutrients. About 40%
nitrogen (N), 30 to 35 % of potassium (K) and 40 to 50 % of sulphur (S) are lost. This
is a critical and widespread issue in India, Bangladesh, and Nepal which is causing
depletion of soil K and Si reserves at many places (Dobermann and Fairhurst 2002).
Besides, the heating of the soil, kills the useful microorganisms of the soil causing
soil degradation including nutrient loss, depletion of soil organic matter (SOM), and
reduction in the presence of beneficial soil biota. Incorporation of rice straw into soil
without proper decomposition is creating another problem of decrease in production
efficiency and an increase in greenhouse gas emissions.
It is estimated that 22,289 Gg of paddy straw surplus is produced in India each
year out of which 13,915 Gg is estimated to be burnt in the field. Punjab and Haryana
alone contribute 48% of the total open field burning (Gadde et al. 2009). One year of
crop residue in Punjab contains about 6 million tonnes of carbon that on burning
could produce about 22 million ton of CO2 in just 15-20 days, says a study published
in Springer Briefs in Environmental Science (2014). The study also showed that CO
levels become critical in the area surrounding a burning field: concentrations of 114.5
mg m-3 or more were observed at 30 m from burning fields and 20.6 mgm-3at 150 m
away. The permissible limit of CO in ambient air is 4.0 mg m-3. Significant amounts (40–
50 μgm-3) of nitrogen oxide (NO2) and ammonia (NH3) were also recorded during
burning.
Open burning in the field affects life of human, animals, birds and other insects
below and above the earth. Burning at times also causes poor visibility and increases
the incidents of road accidents. Apart from humans and animals, residue burning also
adversely impacts the soil health. According to a presentation made by GV
Ramanjeneyulu, agriculture scientist and executive director of Hyderabad-based non-
profit Centre for Sustainable Agriculture, before the Punjab government, heat from
burning straw penetrates 1 cm into the soil, elevating the temperature to as high as
33.8-42.2°C. This kills the bacterial and fungal populations critical for a fertile soil. The
presentation also showed that the monetary cost of burning to Punjab farmers is
around Rs. 800-2,000 crore every year in terms of nutritional loss and Rs. 500-1,500
crore in the form of government subsidies on nitrogen, phosphorus and potash
fertilizers.
Recent environmental pollution caused by straw burning open up a challenge to
agricultural scientist as to how the crop residue may be better managed. What other
alternative economic avenues may be exploited that will enable environment friendly
usages of straw/crop residues. Integrated research approach should be addressed

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to use straw/crop residues in all possible options like, biochar conversion, bio-ethanol
production, better feedstock preparation for animals, as raw materials for paper
industries etc. In this chapter we discuss the international and national status of rice
straw management along with some alternative management strategies for in-situ
utilization of paddy straw, value addition in the light of fodder quality improvement
and substrate for mushroom production and few alternative avenues for utilization of
rice straw towards bio-energy production and ex-situ composting.

3. TECHNOLOGIES FOR STRAW UTILIZATION

China: China being a leading rice producer, has ample generation of rice straw,
contributing 62% of country’s total crop residues. Few technologies are already
available for utilizing the straw in the forms of fuel, feedstuff, manure and industrial
raw material. For a part of the country rice straw plays as the major energy source.
Since 1981, China had started a drive for better crop biomass resource and energy
conversion technology, encompassing rice straw which plays an important role (Liu
et al. 2011).
Pakistan: Farmers in Punjab, Pakistan adopt three main residue management practices,
including: i) the burning of rice residue after the rice harvest or ‘full burn’, including
the top part (pural) and the lower parts; ii) the removal of rice straw; and iii) the partial
or complete incorporation of rice residue into the soil using farm machinery (rotavators
and disc harrows).Though a negligible percentage of farmers followed the
incorporation of rice residue into the soil, and if assessed by area, the ‘full burn’
method ranks first. Around 58% of the area under rice cultivation was fully burned,
while the full removal of rice residue covered only 25% of the rice area in Pakistan.
The remaining area was either partially burnt or had rice residue incorporated into the
field.
Sri Lanka: In contrast, in Sri Lanka, straw is used for a number of purposes. Rice
straw is widely used as fodder, for the manufacturing of paper and paper boards and
for thatching the roofs of houses. Its use as mulches is also practiced in cultivation of
ginger and turmeric crops. A small amount of the straw is also used as a packaging
material. Only a handful of farmers add the straw back to the fields whereas a large
number burn the straw at the threshing site. Majority of farmers are unaware of the
value of rice straw as a fertilizer material and a sizable quantity of rice straw is wasted
in Sri Lanka primarily owing to this unawareness.
Bangladesh: Bangladesh produces around 43.85 million MT of rice residue (EPA,
2011). For residue management in Bangladesh, several practices are followed: (a)
burning in the field, (b) incorporating in the field and (c) removing from the field either
for burning along with cow dung or for feeding cattle. Report says complete (100%)
field burning of the residue is observed only in 3% of surveyed area, prevalent in
Narail, Khulna and Faridpur districts (Haider 2011). The farmers also remove or do not
burn residue instead keeping it for selling purpose. The main reason behind burning
the lower part of residue in the field is to use it as fertilizer thereby eliminating expensive

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operations like removal and cleaning of the land. Many farmers think that residue
burning in the field provides fertilizer to the field for the successive seasons. However,
higher removal cost is the main reason behind not removing the residue from the field.
Vietnam: In Vietnam, to chalk out the alternative rice straw management for future, a
study reported that deploying rice straw for biochar production and soil amendment
led to a lower climate change impact showing negative carbon footprint than open
burning of biomass in both spring and summer seasons’ rice cultivation (Mohammadi
et al. 2016). The Mekong Delta region has appeared to be potential hotspot for
bioethanol production from rice straw, producing 26 Mt rice straw yearly with an
estimated cost of 1.19 $ L-1. However, to lower down the production cost in terms of
energy cost, Diep et al. (2015) suggested few modifications in bioethanol plants, like
using residues for power generation and improving solid concentration of material in
the hydrothermal pre-treatment step.
Thailand: In order to discourage open burning of rice straw and to promote the
possibility of rice straw utilization for industrial applications, researchers of Thailand
proposed the use of rice straw based stoker boiler, a promising technology for heat
and power generation and an alternative to coal based power, with less emission of
NOx and chlorinated organic compounds (Suramaythangkoor and Gheewala 2010).
Japan: The Japanese cabinet launched “Biomass Nippon Strategy” for efficient
biomass utilization in Japan, though the amount of biomass resource is not very large
and limited production scale (Matsumura and Yokoyama 2005). In that scenario, power
generation from rice straw biomass (with a production potential of 12 Mt-dry year”1)
had a potential to supply 3.8 billion (kW) h of electricity per year, sharing only 0.47%
of the total electricity demand in Japan (Matsumura et al. 2005). In Japan, a long-term
trial has been successfully conducted using crop residue management in Fukuoka,
where soil quality showed beneficial impact under treatment of rice straw compost in
terms of greater accumulation of total C and N in the soil from rice straw compost, with
a declined value of metabolic quotient (qCO2) indicating better C utilization efficiency
by soil microbes (Tirol-Padre et al. 2005).
Korea: In Korea, rice straw (lingo-cellulosic fiber) is used along with waste tire particle
for manufacturing composite boards using as insulation boards, which showed good
acoustical insulation, electrical insulation, anti-caustic and anti-rot properties over
wood particle board (Yang et al. 2004). In another instance, regenerated cellulose
fibers (with a diameter of 10 to 25 ìm) were prepared by wet spinning in rice straw/N-
methylmorpholine-N-oxide solution (Lim et al. 2001).
India: India, the second largest rice producer in the world, produces nearly 130 million
tons of rice straw annually. Rice straw is fed to cattle and buffaloes in India since
ages. Rice straw is fed to cattle at home as basal diet in most areas where green fodder
is scarce. It is also used as feed for ruminants and has many other uses like manure,
thatching, purpose paper pulp, alcohol, mats, poultry litter and mushroom production.
Farmers are yet to realize the importance of rice straw as a form of manure and as a
profitable raw material for various industries. In the major rice growing states of

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Punjab and Haryana, farmers have tried various means of disposing the rice straw
while earning some income. Brick manufacturing companies, power companies, and
paper and packaging industries use rice straw as a raw material.
Punjab Agriculture University recommended various new technologies for straw
management. One of the promising one is to cut the straw in to small pieces and
scatter over the ground mechanically after harvesting by combined harvester followed
by direct sowing of the wheat with happy seeder in that field. In one day, up to 15-20
acres can be sown. The scattered straw helps not only in conserving the soil moisture
but also helps to operate happy seeder for direct drilling of wheat into the rice residue
in a single pass without burning the straw.
Applications of microorganisms as accelerators of biodegradation have shown
promising results. A consortium of Candida tropicalis (Y6), Phanerochaete
chrysosporium (VV18), Streptomyces globisporous (C3), Lactobacillus sp. and
enriched photosynthetic bacterial inoculum hasten the composting process of rice
straw by bringing C:N ratio down to 15:1 and achieving a total humus content of
4.82% within 60 days as reported by Sharma et al. 2014.
A combination of cow dung slurry @ 5% + Trichoderma harazianum @ 5 kg/ha
+ Pleurotus sajorcaju @ 5 kg/ha had significant influence in degrading rice straw as
evidenced through the activity of N- fixing and P- solubilizing microorganisms in the
soil. It was reported that nutrient enriched compost can be prepared by using the
consortium of fungal (Aspergillus nidulans, A.awamori, Trichoderma viride and
Phanerochaete chrysosporium) inoculants within 70-90 days by pit and windrow
methods.
Some existing microbial culture available in India for composting of rice straw are
listed in tabular form (Table 1).
On short-term basis, rice residue addition stimulates CH4 emission in next crop,
immobilizes available N, and may accumulate toxic material in soil. In general, no
consistent /significant effect of either incorporation or mulching of rice straw on N2O
emission was found, however, an increase in emission of N2O from field with mulch
compared to the incorporation was observed in subtropical rice-based cropping
system. Bhattacharyya et al. (2012) reported that the application of inorganic fertilizers
in combination with rice straw in tropical rice resulted in C build up, increase in
productivity and sequestration capacity of soil, although, it also resulted in higher
GHGs emissions. They recommended combination of inorganic fertilizer (urea) with
rice straw (1:1 N basis) for building of soil C (1.39 Mg ha-1), sustaining crop yield and
lower GHGs emission as compared to addition of rice straw/green manure alone.

4. ALTERNATIVE USE OF RICE STRAW

4.1. Conservation agriculture (CA)
Zero and/or reduced tillage is an important component of CA. It helps in increasing
soil organic matter by leaving the previous crop residues on the soil surface to decay,
which leads to increased soil nitrogen while conserving soil moisture and structure.

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Table 1. Existing composting technologies of rice straw available in India
Name of decomposing Type of microbes Recommended
microbial inoculants used dosage Source
TNAU Biomineralizer Consortium of 2.0 kg inoculum TNAU,
decomposing microbes per tonne of wastes Coimbatore
Effective micro- photosynthetic bacteria, EM solution
organisms (EM) Lactobacillus, accelerators @33.3 lit Indian Institute
Streptomyces, per pit (6’x4’x3’ LBH) of Soil Science,
actinomycetes, yeast i.e to produce 0.9 t Bhopal
compost
Institute of Biological Trichoderma harzianum 1.0 kg per 100 kg Indian Institute
Sciences (IBS) rapid (compost activators substrate of Soil Science,
composting technology should be prepared by Bhopal
mixing T.harzianum
with carbonaceous plus
nitrogenous materials)
Poultry waste compost Pleurotus sajar-caju 1.25 kg inoculum Indian Institute
per tonne of waste of Soil Science,
(1:1.25 ratio of paddy Bhopal
straw and poultry
dropping)
Phospho compost Fungal consortium IARI, Delhi
(Aspergillus niger,
A. flavus and
Trichoderma harazianum)
EM consortium Phanerochaete IARI, Delhi
chrysosporium VV18,
Streptomyces sp.C3,
Rhodotorula glutinisY6,
Lactobacillus plantarum
Biological Myrothecium roridum IARI, Delhi
delignification of LG 7, Trametes hirsuta
paddy straw and Streptomyces
griseorubens
Coimbatore/ Indore/ Cow dung slurry and 5-10 kg cow dung TNAU,
Bangalore method bone meal or cow dung in 2.5 to 5.0 I of water Coimbatore
slurry is applied layer and 0.5 to 1.0 kg fine
by layer bone meal sprinkled
over it uniformly per
layer

Leaving the residues on the field protect the soil surface from direct impact of wind
and rain drops hence reducing wind and water erosion and conserving soil moisture.
It also prevents germination of weeds. However, some disadvantages like, greater
risks of crop yield reductions or failure in initial year, increased possibility of pests
and diseases and difficulty in incorporating fertilizers may remain. But, with the advent
of second generation farm machineries like “Happy Seeder”, management of rice
straw in field became easy. The Happy Seeder is a machine that cuts and lifts rice

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straw, sows seeds into the bare soil, and deposits

the straw over the sown area as mulch (Fig. 1).
Combine harvesters are gaining popularity
day by day in India for timely harvesting of
paddy. By the combine harvested fields leave
high stubbles and straw in the field. For timely
sowing of next crop without burning of these
loose straw, chopping machine is used to pick
Fig. 1. Happy seeder them up and conveyed to serrated blade for
chopping cylinder, and the chopped straw are
then spread over the field.
Straw baling in the combine harvested paddy
field is considered as technically and
economically beneficial for animal feed, biofuel
and other industrial uses. Straw baling
technology is very useful for mechanized
collection of straw and can be done in less time.
It is convenient and economical for handing,
Fig. 2. Straw chopper and baler
transportation and storage of straw (Fig. 2) by
(Source: www.mikeprycemachinery.com)
straw bales.
4.2. Mulch
Rice straw could be used as mulch for other crops like wheat, maize, sugarcane,
sunflower, soybean, potato, chilli etc. In one side, it would improve crop yield in dry
land and water stress condition by conserving soil moisture and on the other hand,
could save irrigation water of about 7 to 40 cm. In light of reduction of GHG emission,
sowing of wheat with rice straw mulching in residual moisture (without pre-sowing
irrigation) could save about 20% irrigation water, which could save 80 KWh of
electricity and reduce emission of 160 kg of CO2 equivalent (Singh and Sidhu 2014).
4.3. Biochar
Controlled pyrolysis of crop residues (CRs) could produce biochar which not
only reduces GHGs emission but at the same time sequester C in soil for long time.
Biochar is a heterogeneous
substance rich in aromatic
carbon and minerals. It is
produced by pyrolysis of
sustainably obtained biomass
under controlled conditions
with clean technology and is
used for any purpose that does
not involve its rapid
mineralization to CO2 and may
eventually become a soil
Fig. 3. Conceptual flowchart of rice straw recycling
amendment (Fig. 3).
through biochar.

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 However, technological options and spatial field level data are required to fully
utilize or recognize its GHGs mitigation/adaptation potential. Biochar serves as a sink
for atmospheric CO2 because of its reactive surfaces and recalcitrant aromatic structure.
Further, during pyrolysis about 50% of C in rice straw is immediately released, which
could be effectively used as energy sources and the remaining recalcitrant is biochar
which sequester C in soil. So it is a win-win situation. On the other hand, 80-90% of C
of rice straw in original form is emitted as CO2 within 10 years, depending on soil and
environmental constraints. Therefore, recalcitrant biochar offers a prospect of
sequestering 40-50% of original rice straw-C having a huge greenhouse mitigation
benefit. However, India produces only about India 1.7 million tons of biochar/year
(Srinivasarao et al. 2013).
4.4. Rice straw as animal feed
In India, rice straw is used as fodder since time immemorial. In eastern part of the
country, it is the traditionally the most popular form of dry biomass which is given to
animals after they are chaffed and then mixed with green fodder or as basal diet in
animal sheds. In Punjab, Haryana and western Uttar Pradesh, rice straw is used
mostly as basal diet. However, the fact remain that it is the scarcity of good quality
feed and fodder in the country which forces the farmers to use paddy straw as fodder.
It is a poor quality feed in terms of protein and mineral content which are the two
important components of a fodder crop. On an average the crude protein content in
rice straw is as low as 4%. Although the crude fibre content is approximately 37% and
the total ash content is nearly 18%, the major fraction of them is lignocellulose and
insoluble ash. Due to these reasons, paddy straw is poorly palatable and thus its
intake by animals is low.
Rice straw-based animal feed block making machine: It is useful for making animal
feed blocks of size 20 cm x 20 cm by mixing rice straw with essential nutritional
elements. The machine is powered by 25 hp electric motor and has the capacity of 250
kg h-1. It is also available in 125 kg h-1 capacity with block size of 10 cm x 10 cm
operated by 10 hp electric motor. The self-life of the feed blocks is more than one year,
very economical to transport to distant places.
Feed block making procedure: The rice straws collected from farmers field are passed
through chaff cutter machine (15 hp
capacity) and are made into pieces of about
1 to 2-inch size. The essential mineral
mixtures (i.e. splitted maize grain, green
gram, black gram, horse gram and jiggery)
for increasing its nutritional quality and
chopped rice straw are placed in the mixing
machine (5 hp size) (Fig. 4). The output from
the mixing machine is then passed through Fig. 4. Mixing unit (Rice Straw + Other
the feed block making unit (25 hp size) ingredients) (Source: IARI, New Delhi)

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Fig. 5. Feed block making machine (after mixing Fig. 6. Feed block ready to use
with ingredients) (Source: IARI, New Delhi)

(Fig. 5) which then makes feed blocks of 3.5 kg each (Fig. 6), which are ready for
selling and are used for animal feeding (cow/buffalo).
4.5. Mushroom industry
Cultivation of edible mushroom is one of the cheapest and economically viable
processes for the bioconversion of lingo-cellulosic wastes. Mushrooms have capacity
to convert nutritionally less valued substances like rice straw in to valuable and
nutritious human food and animal feed. Various studies recommends the use of paddy
straw for cultivation of different types of mushrooms viz. Button mushroom (Agaricus
bisporus), Oyster mushrooms (Pleurotus spp.) and paddy-straw mushroom
(Volvariella volvacea, V.diplasia) in India.
Mondal et al. (2010) revealed that, highest biological and economic yield of Oyster
mushroom was obtained from rice straw as compared to other substrate materials
tested. The highest yield from rice straw appeared, due to comparatively better
availability of nitrogen, carbon and minerals from this substrate. The rice straw could
be used as substrate at a concentration of 15%: 60% in planted media of Oyster
mushroom production without any reduction in productivity of white Oyster
mushrooms (Utami and Susilawati 2017). It is one of the best substrate for cultivation
of milky white mushroom.
Paddy straw mushroom is the third most important mushroom cultivated in the
world and this mushroom can use wide range of cellulosic materials and prefers C: N
ratio of 40 to 60. North Eastern region and eastern India comprising of West Bengal,
part of Bihar, Jharkhand and Odisha has tremendous potential and scope for paddy
straw mushroom cultivation due to the easy availability of basic substrate (paddy
straw). Use of rice straw for cultivation of Volvariella spp. will decrease the
environmental problem and provide sustainable means of adding value to rice farmers
(Tripathy et al. 2011).
Cultivation of Pleurotus florida on rice straw has beneficial effect on digestibility,
degradability and increases the nutritional values for animal feed (Hadizadeh et al.
2015). Even the leftover of paddy straw after harvesting mushroom can be re-used as
manure (after composting) for other crops which would save expenses on chemical

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fertilizers. The proteinaceous, low lignin content of the spent rice straw from mushroom
production is a potential feed quality for ruminants (Kathrina et al. 2016). Edible
mushroom treated rice straw shows promise as feed resources for ruminant animals
either solely or in combination with other feedstuffs.
The physical and chemical properties of rice straw varies with variety, harvest
time, method of threshing and season of cultivation of rice crop which influences the
quality and productivity of mushrooms. There is consistent variation in the nutrient
value of rice straw associated with location and season for rice cultivars. Hand
threshed rigid and tall rice straw was found to be more appropriate than dwarf cattle
threshed and flexible straw against V. esculenta. Cellulose/lignin ratios in rice straw
were positively correlated to mycelial growth rates and mushroom yields.The physical
properties (moisture content, particle size, bulk density and porosity of rice straw
varies with rice varieties even though they were grown under same climatic conditions
using similar soil type and cultivation methods. Earlier findings revealed that paddy
straw derived from variety CR 1014, 1242, 141, T90 is good for preparing mushroom
beds. The role of extracellular enzymes like cellulases, hemicellulases and lignases is
pivotal to the production of any mushroom fruiting body which is affected by the
various nutrients and physical factors of the used substrates. There is a great scope
to evaluate the predominant rice varieties and available rice germplasms to establish
the rice varieties most suitable for economic and environment-friendly utilization of
rice straw for value addition.
4.6. Composting
Composting is a microbiological process carried out by succession of mixed
microbial populations with specific functions. High lignin content restricts the
enzymatic and microbial access to the cellulose in paddy straw. Many composting
technologies are available which requires nearly 60-75 days for complete
decomposition of paddy straw, but there is an absence of viable rice straw
decomposing methods within short period of time (45-60 days). At present, there is a
dearth of viable in-situ decomposition of rice straw residues at field levels. Hence, it
is essential to develop efficient microbial consortium to solve the aforesaid problems.
The composting of agricultural residues rich in lignocellulose like paddy straw
generally takes five to six months to obtain good and mature compost. Cellulose
degrading microorganisms hasten the biodegradation of crop residues such as straw,
leaves, trash etc. and such cultures have been used for composting of plant residues
but the time taken for composting is still too long. In nature, during decomposition of
lignocellulosic material many mesophilic, thermophilic and thermo-tolerant
microorganisms like fungi, bacteria and actinomycetes play a significant role at various
stages. Cellulose is the main polysaccharide in terrestrial ecosystems. Rice straw has
a cellulose content of 37-49%. It represents a huge source of energy for microorganisms.
In nature, most cellulose is degraded aerobically with the final product being CO2.
Cellulose is insoluble in water and therefore requires enzymatic degradation. The
ability of bacterial and fungal communities to degrade cellulose aerobically is
widespread among some soil microbial groups. Cellulose degrading bacteria are found

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in both filamentous (e.g. Streptomyces, Micromonospora) and non-filamentous (e.g.

Bacillus, Cellulomonas, Cytophaga) genera.
Cytophaga and Sporocytophaga are dominant cellulolytic microorganisms in
most of the composting processes; these are the aerobic mesophilic bacteria able to
degrade cellulose. Some mesophilic aerobic forms of Bacillus, like B. subtilis, B.
polymyxa, B. licheniformis, B. pumilus, B. brevis, B. firmus, B. circulans, B. megaterium
and B. cereus are also reported to behave as cellulose and hemicellulose degraders.
Similarly, actinobacteria (Streptomyces sp) has strong biodegradative activity, secreting
a range of extracellular enzymes and exhibiting the capacity to metabolize cellulose,
hemicellulose and lignin (Saritha et al. 2012).
Cellulose degradation is a common trait among fungi within both Ascomycota
and Basidiomycota. Aerobic cellulolytic fungi produce freely diffusible extracellular
cellulase enzyme systems consisting of endoglucanases, exoglucanases and â-
glucosidases that act synergistically in the conversion of cellulose to glucose (Lynd
et al. 2002). Hundreds of species of fungi are able to degrade lignocellulose. There are
mainly three types of fungi living on dead wood that preferentially degrade one or
more wood components viz. soft rot fungi, brown rot fungi and white rot fungi. In
majority of soils, 80 per cent of the fungal population belongs to the genera Aspergillus
and Penicillium. However, the most extensively studied lignocellulolytic fungi are
Trichoderma, Phanerochaete sp. and Pleurotus sp.
4.7. Biogenic silica from rice straw
Biogenic silica from rice straw has amorphous silica. It is having at least 3% of
silica and preferably more than 20% by weight of silica for use as an anti-caking
agent, excipient or flavor carrier. The straw is ground and the silica may be concentrated
by carbon reduction through enzymatic treatment or burning. In some instances an
antimicrobial treatment of the silica may be beneficial.
4.8. Alternate source of energy: Biofuel/biogas/bioethanol production
Rice straw being a ligro-cellulosic material is considered to be a potential source
of renewable energy. In this context synthesis of biofuel from rice straw, and mixing of
biofuels with convectional fuels could save the exploitation of fossil fuel thereby
reducing GHGs emission while helping to mitigate climate change. According to IPCC
data inventory (2014) about 25 billion tons of CO2 are generated by anthropogenic
activity every year, which could be reduced by lowering emission, enhancing sink or
removals and avoiding emission (through fossils fuels). All these three could be
effectively done, partially by suitable/effective management of rice straw. An increasing
trend has already been observed through 4th (2007) and 5th assessment (2014) report
of IPCC on the use of CRs as sources of feed stock for energy to displace fossil fuel.
CRs could be burnt directly or be processed further to generate liquid fuels like
ethanol or bio-diesel (IPCC 2007; IPCC 2014).
There is a huge potential to offsets fossil fuel by generating ethanol from bulk
CRs in general and rice straw in particular, with efficient commercial technologies.

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Potentially, 250-350 litre ethanol could be produced from each metric ton of dry CRs.
Considering only 20% of world’s rice straw is being utilized for this purpose, lead to
an annual ethanol production of 40 billion litres, which would be able to replace about
25 billion litre of fossil fuel based gasoline (Jeffery et al. 2011). As a result net GHGs
emission could be reduced to a tune of 70 million tonnes CO2 equivalent per year. But
large scale and small scale commercial machineries/technologies need to be developed
for harnessing this potential. However, for bio-energy perspective, residue would be
removed rather than returned to the soil (opposite to concept of conservation
agriculture). For that harvesting, threshing and transportation mechanism need to be
streamlined. Along with that, varieties having desirable straw characteristics should
be grown for biofuel production. Presently only 10% of the total rice residues in India
are used for bioenergy production (NAAS 2012).
4.9. Biogas
Biogas from rice residue in combination with animal excreta is an age old technology
in rice growing tropical world. But its use and efficiency has been declining over the
years, although, it has various benefits including plant nutrient addition to soil.
Further, fermented/composted biogas when used as manure in rice-paddy, generate
less CH4 as compared to addition of fresh organic manure. However, escalating fuel
price and climate change/environmental issue may re-stimulate its future (Singh and
Sidhu 2014).

5. KNOWLEDGE GAPS
 Lack of economic technologies for in situ composting.
 Absence of viable microbial inoculants for rapid in-situ/ex-situ decomposition of
paddy straw.
 Paddy straw is relatively less preferred by animals than wheat and crop residues
– lack of characterization of available variety/germplasm for fodder quality
 Lack of cost effective small scale technologies for bio-energy production.
 Less effort has been made for value addition of paddy straw in view of present
day mechanized agriculture.
 Lack of authentic database on contribution of straw burning in air pollution and
GHGs/carbon footprint.
 Lack of Cataloguing/prioritizing the causes of biomass burning required for policy
making to address the problem

6. WAY FORWARD
There is huge potential to use paddy-straw in bio-energy production, composting,
as fodder and so on, which can establish it as an important bio-resource. Microbial
composting, an up-coming technology for agricultural wastes disposal in which

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biodegradation of lignocellullosic matter like paddy straw is carried out exploiting

ligninolytic and cellulolytic microorganisms. Minimizing the time period for
decomposition is considered along with the other key factors viz. C/N ratio (25-30 is
optimum), temperature, aeration and moisture affecting the composting process and
quality. Therefore, nutrient amendments (urea, DAP, cattle, poultry, swine manures,
soybean residues, Jatropha Curcas) have been used for decreasing the C/N ratio of
rice straw. Based upon the aerobic or anaerobic types of composting process, aeration
is necessary and so is the moisture content.
Green revolution in the country was achieved through development of semi-
dwarf versions of traditional tall indica varieties. This led to a reduction of lodging
incidences by changing the centre of mass of the plants. However, the plant height
reduction also led to reduced biomass production from a unit area. In the quest for
higher yields, the selection of strong culms to sustain heavy panicles also lead to
selection of genotypes with higher amount of lignocelluloses in stems. In order to
develop varieties suitable for both grain production and better quality feed and biofuel,
the lodging resistance can’t be compromised which makes the matter more
complicated. Digestibility and saccharification efficiency of the straw depends on
the cell wall composition. With increased lignin content in shoots, the lodging
resistance of the culm increases, whereas, the fodder quality and saccharification
potential decreases substantially. Hence, an alternative mechanism where lignin
content can be reduced substantially without reducing the culm strength will be a
requisite.
Recently, in rice a mutant line “gold hull and internode2 (gh2)” have been identified
as lignin deficient. The GH2 (OsCAD2) gene encodes cinnamyl-alcohol
dehydrogenase (CAD) enzyme. Generally the mutants have lower lignin content and
are prone to lodging. A new natural mutation in the same gene was identified where
the lignin content was reduced to a great extent, although high culm strength was
obtained due to presence of strong, thick culms along with a thick layer of cortical
fibre tissue with well-developed secondary cell walls. The new rice variety developed
by this mutation produces high biomass suitable for forage and bioenergy and have
been named as Leaf star (Ookawa et al. 2014). Some other QTLs have also been
identified which increases lodging resistance in rice culms without increasing the
lignin or silica content. Rather some QTLs like prl5 and lrt5 (Kashiwagi et al. 2008 and
Ishimaru et al. 2008) increases the starch content in culms through carbohydrate re-
accumulation in stem after grain filling.
All the above discoveries have opened new avenues for breeders for developing
new varieties of rice which not only provides good quality grains for human
consumption but also superior quality straw for feeding ruminants and producing
biofuels with increased efficiency.
Paddy straw has economic potential but there is an urgent need to popularize the
array of available technologies for straw utilization such as use for power/electricity
generation, ethanol production, biochar production, composting and raw material for
paper mill/board making industry.

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 It is also necessary to develop machinery bank at block or district level equipped
with straw management machinery and help in capacity building of the farmers
regarding various uses of paddy straw management through various extension
strategies such as demonstration, field days and exposure visits. Development of
appropriate farm machinery to facilitate collection, volume reduction, transportation
and application of crop residues and sowing of the succeeding crop under a layer of
residues on soil surface is also the need of the hour.
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Rice mechanization in India: Key to enhance

productivity and profitability

PK Guru, N Borkar, M Debnath, D Chatterjee, Sivashankari M,

S Saha and BB Panda

SUMMARY
Rice mechanization contributes to sustainable increase in productivity and cropping
intensity. Without a review of patterns and progress in farm power availability farmers
would struggle to emerge from subsistence production. Present scenario of rice
mechanization including availability of farm machinery/implements for different field
operations starting from field preparation, sowing/transplanting, intercultural
operations, harvesting, threshing and post harvesting operations is compiled. Future
research areas are identified to enhance the mechanization level by performing field
operations timely, precisely, and efficiently. Precise and need based application of
inputs results in reducing cost of rice cultivation with optimal use of energy and
drudgery reduction in farm operations.

1. INTRODUCTION
Indian agriculture has made significant progress in the last five decades. However,
past some years stagnating net sown area, reduction in per capita land availability,
climate change and land degradation are posing serious challenges to it. India’s
population is increasing in a rapid rate which is likely to reach to 1.30 and 1.38 billion
by 2020 and 2030, respectively (Goyal and Singh 2002). Rapid increase in population
leading an immense pressure on Indian agriculture to produce more food in order to
get food and nutritional security. On the contrary, the average land holding size is in
a decreasing trend in India. The average estimated size of land holding in India would
be mere 0.68 ha in 2020, and would be further reduced to a low of 0.32 ha in 2030. With
all these challenges, India has the herculean task of ensuring food security for the
most populous country by 2050. Hence, farming should effectively address local,
national and international challenges of food, water and energy insecurity; issues
related to climate change; and degradation of natural resources. Farm mechanization
can play a key role in addressing these challenges for large as well as small-holder
farmers.
Farm machinery and equipment provide a package of technology to (i) increase
land productivity by improved timeliness of operations, reduced crop losses and
improved quality of agro-produce; (ii) increase efficiency of inputs used through
their efficient measurement and placement; (iii) increase labour productivity by using
labour saving and drudgery reducing devices, and (iv) reduce cost of cultivation.
Machinery is also important to harness available moisture at the time of tillage and
sowing, hence dryland areas also experienced growth in farm machinery. Farm machines

Rice mechanization in India: Key to enhance

productivity and profitability 337
like rotavator, ferti-seed-drill, raised bed planter and laser leveler boost water use
efficiency of little water/moisture that is available; thereby enhancing productivity in
dryland areas. There is a strong linear relationship between power available and
agricultural productivity. Improved agricultural tools and equipment are estimated to
contribute to the food and agricultural production in India by savings in seeds (15-
20%), fertilizers (15-20%), time (20-30%), and labour (20-30%); and also by increase in
cropping intensity (5-20%), and productivity (10-15%). International and national
experiences have established the benefits of engineering inputs in terms of enhanced
productivity by about 15% and reduction in cost of production by 20%, apart from
increase in cropping intensity (20%), timeliness in farm operations and drudgery
reduction.
Presently, India is the largest manufacturer of tractors in the world accounting for
about one third of the global production. India also has a big network of agricultural
machinery manufacturers. However, there is wide variation among the states at the
level agricultural mechanization. The highest concentration of tractors is in northern
India. After liberalization and with development of research prototypes of machines
manufacturing got a big boost particularly in Haryana, Punjab, Rajasthan, Madhya
Pradesh and Uttar Pradesh. Combine manufacturing is concentrated mainly in Punjab.
About 700-800 combines are sold annually. Combine harvesting of wheat, paddy and
soybean is well accepted by farmers in this area. The estimated levels of mechanization
of various farm operations in India are: 40% for tillage, 30% for seeding/planting, 37%
for irrigation and 48% for threshing of wheat, 5% for threshing of rest of the crops and
35% for plant protection (CIAE, Bhopal). There is close nexus between farm power
availability and increased productivity. The productivity of rice in Punjab, Haryana
and Western UP was more than other states namely Assam, Bihar, Jharkhand, eastern
UP, Chhattisgarh, Odisha, and West Bengal as these states had farm power availability
less than 1.50 kW per ha. The farm power availability in Indian agriculture and
productivity increased from 0.25 to 1.84 kW ha-1 and 0.52 to 1.92 t ha-1, respectively
over the years from 1951 to 2012. The predicted values of farm power availability and
productivity in India for the year 2020 is going to be increased to 2.2 kW ha-1 and 2.3
t ha-1, respectively (Mehta et al. 2014). In farm mechanization level India is lacking
behind other developing countries. Farm power availability in India is very low as
compare to the level of mechanization of United State (95%), Western Europe (95%),
Russia (80%), Brazil (75%) and China (57%) (Renpu 2014). One possible reason for
India’s low productivity in rice is the small size of individual farm holdings. The 2001
census found that 80% of farm holdings were less than 2 hectares in size, with 62%
averaging less than half a hectare. Just 1% of the holdings was classified as large
(over 10 hectares) and averaged 17.1 hectares. The overall average size of all holdings
was only 1.33 hectares. A more recent government report noted that small farms have
gotten even smaller, and that 85% of farmers lack access to farm inputs and credit.
This is not surprising as the rural population has grown but the available farm acreage
has not.
Farm mechanization is low in the rice-based farming systems in eastern India.
However, it is picking up and many of the small and big farm-machineries are now a

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common sight in eastern India. Even combine is also being used to harvest rice crop
in some parts of eastern India. Over these years there was rapid shift in farm power
uses from animal power to mechanical power. Mechanical power helps in timely farm
operations with less labour and cost, but reduction in animal uses on farms increases
the problem of crop biomass burning. In rice based cropping system managing rice
straw is a big challenge. Complete machinery package is needed to be introduced to
enhance the production and also it helps in minimize the input energy and cost
involved in rice based cropping system. The use of machinery for field preparation
operation for rice cultivation is high and most of the farmers of India are using tractor
with matching implements for deep ploughing and puddling operation. But the further
operation viz. sowing, transplanting, harvesting and threshing is done manually and
having very low level of mechanization. In India, the availability of draught animals
power has come down from 0.133 kW ha-1 in 1971-72 to 0.094 kW ha-1 in 2012-13,
whereas, the share of tractors, power tillers, diesel engines and electric motors has
increased from 0.020 to 0.844, 0.001 to 0.015, 0.053 to 0.300 and0.041 to 0.494 kW ha-1,
respectively during the same period. The rice transplanters market in India has grown
from about 550 in 2008-09 to 1,500-1,600 units in 2013-14. The industry is expected to
grow by more than 50 % in 2014-15 with Chhattisgarh, Odisha, Bihar and southern
states showing positive sign of adoption of technology (Mehta et al. 2014). The
objectives of the chapters are i) to study present status of farm machinery used in rice
cultivation in India; and ii) to identify future research area to enhance rice mechanization
in India.

2. PRESENT STATUS OF RICE MACHINERY IN INDIA

2.1. Tillage
On animal powered farms primary tillage is done by using Desi hal (Country
plough), and MB plough. Animal drawn plough is still used for tillage in Himachal
Pradesh, Assam, Bihar, UP, Odisha, West Bengal and Andhra Pradesh. Mostly these
ploughs are manufactured by local craftsman and their design differs from place to
place. Animal drawn disc harrow, spike harrow, spring type harrow, blade harrow, zig-
zag harrow, three and five tyne cultivators, clod crusher, chisel ploughs, sub-soilers,
scraper, bund former and wooden leveler are commercially available. On tractor powered
farms mould board plough (MB) and cultivators are two most commonly used
implements. Mould board plough is used for primary tillage operation and cultivator
is used for primary as
well as secondary tillage
operations (Fig. 1).
Tractor drawn disc
harrows are popular for
dry secondary tillage
operation. Now
rotavator is gaining a b
popularity due to its Fig. 1. Field preparation using tractor drawn MB plough (a)
capability for multiple and cultivator (b).

Rice mechanization in India: Key to enhance

productivity and profitability 339
operations in one time. Saving of 60-70 per cent in operational time and 55-65 per cent
in fuel consumption with single rotavator compared to the conventional method of
seed bed preparation with separate ploughing and harrowing operations have been
observed, besides conservation of moisture due to destruction of capillaries.
2.2. Puddling
Puddling operation is
performed to reduce deep
percolation of water, to
suppress weeds by
decomposing them and
to facilitate transplanting
of paddy seedlings by a b
making the soil softer (Fig. Fig. 2. Puddling using tractor rotavator (a) and animal drawn
2). In animal powered disc harrow (b).
farms for puddling
operation bullock drawn cono-puddlers, disc harrow-cum puddler, in power tiller or
tractor powered farms power tiller mounted cono-puddler, power tiller rotavator and
tractor drawn paddy disc harrow, cage wheel with cultivator and rotavator, are
machinery used for puddling which are commercially available.
2.3. Land leveling
In India rice farmer’s uses traditional land
leveling and laser land leveling for final field
preparation. Traditional land leveling includes
animal drawn leveler or tractor or even
bulldozers in the case of highly undulated
land. The accuracy of these implements is low,
which results in uneven distribution of
irrigation water. Laser land leveling is an Fig. 3. Tractor drawn laser land leveller
alternative to achieve higher level of accuracy
in land leveling. This gives uniform land for seed sowing or transplanting with uniform
distribution of irrigation water (Fig. 3).
2.4. Seeding, planting and transplanting
Rice is grown either by direct seeding i.e. broadcasting, drilling in dry soil, sowing
in wet soil or by transplanting. As per power availability (manual, animal, power tiller,
and tractor) on farms there are plenty of sowing implements developed and most of
them are for dry direct sowing of rice including one, two and three row manual seed
drill, three row animal drawn seed drill, self propelled hill seeder, power tiller and
tractor drawn seed drill (Fig. 4) for upland conditions for plain terrain whereas manual,
bullock drawn and power tiller drawn seed drills are suitable for hilly terrain. For wet
direct sowing of rice manual operated drum seeders are popular. The manual drum of
4-rows and 6-rows seeder being light in weight can be operated easily by female farm

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340 productivity and profitability
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

women in low land area.

Manual drum seeders of
4, 6 and 8-rows are
available commercially.
For transplanting of rice
manual operated a b
transplanter and power
operated transplanters Fig. 4. Tractor drawn seed cum fertilizer drill (a) and self
propelled eight row transplanter (b) in operation.
are commercially
available (Fig. 4).
2.5. Weeding
The weeds are more competitive with crops during the initial stages of their growth
(2-6 weeks after planting). Controlling weeds during this time is very essential for
realizing maximum crop yield. Manual uprooting of the weeds with hand in squatting
and bending postures is the
common practice for wetland
rice. For weeding in rice
hand hoe, finger weeder,
conoweeder animal drawn
weeder, power tiller operated
and self-propelled weeders a b
are commercially available Fig. 5. Weeding in rice with two row wet land weeder (a)
and used by the farmers and single row dry land weeder (b).
(Fig. 5).
2.6. Fertilizer application
Mostly manual
broadcasting of fertilizer is
performed by farmers.
However, for deep
placement of fertilizers for
higher efficiency of applied
nutrient (mostly N), deep
placement applicator are Fig. 6. Deep placement of urea briquettes.
used (Fig. 6).
2.7. Plant protection
Timely application of herbicides, pesticides and fungicides (collectively called
Crop Protection Products) at peak periods play a vital role in ensuring better yields
from a crop. The magnitude of this problem is further amplified due to shortage of
labour during this time. Different types of duster and sprayers have been developed
for operation by hand, a small engine, power tiller and also by using the tractor power
source. For application of pesticides, the farmers most commonly use hand

Rice mechanization in India: Key to enhance

productivity and profitability 341
compression sprayer, knapsack sprayers and power sprayers. Low volume and ultra
low volume (ULV) sprayers, which require comparatively smaller quantity of water,
are also in use.
2.8. Harvesting
For rice harvesting many technologies have been developed such as reaper,
combine harvester etc. but in eastern India still manual harvesting using sickle is
predominant method of paddy harvesting. It takes about 170-200 man hours to harvest
one hectare of paddy. Improved sickles, walk behind self-propelled vertical conveyor
reaper (Fig. 7), power tiller operated vertical conveyor windrower, animal drawn reaper,
tractor rear mounted reaper windrower, tractor operated straw combine, reaper binder
and combine harvester are available commercially. These harvesting equipments are
being used by famers for harvesting of paddy for plain field on custom hiring basis.
2.9. Threshing
Threshing is one of the most mechanized operations in rice cultivation. On animal
powered farms threshing by bullock treading is practiced on large scale in the country
but it is also time consuming and involves drudgery. Pedal operated thresher is used
for threshing of rice by the farmers of West Bengal, Odisha, Assam, Andaman, Bihar
and Jharkhand states. The output capacity, threshing efficiency and labour
requirement were 44 kg/h, 98.8% and 5 man-h/q, respectively. Power operated axial
flow thresher (Fig. 7) works on axial flow principle. It consists of spike tooth cylinder,
straw thrower, concave, sieve shaker and aspirator blowers. It is suitable for threshing
rice. It can be
operated with
power tiller, tractor,
engine and electric
motor. Axial flow
thresher operated
by single 1.5 kW
motor/power tiller
engine was
a b
developed for hilly
region. The Fig. 7. Threshing by power operated drummy thresher (a) and
capacities of power harvesting by reaper (b).
tiller and tractor
operated axial flow threshers are 3 to 5 q h-1 and 10 to 12 q h-1, respectively. Pedal
operated, animal drawn, power tiller operated, tractor drawn and electric motor
operated threshers are commercially available and have become very popular for
threshing operation in plain region.
2.10. Straw management machinery
Ministry of New and Renewable Energy (MNRE 2009), Govt. of India estimated
that about 500 MT of crop residue is generated every year. The surplus residues i.e.,
the residues generated, in excess of the less amount of residues used for various

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Profitability and Climate Resilience

purposes, are typically burned in the field or used to meet household energy needs
by farmers. Burning of crop residues leads to 1) release of soot particles and smoke
causing human health problems; 2) emission of greenhouse gases (GHGs) such as
carbon dioxide, methane and nitrous oxide causing global warming; 3) loss of plant
nutrients such as N, P, K and S; 4) adverse impacts on soil properties and 5) wastage
of valuable C and energy rich residues. There are several options which can be
practiced such as composting, generation of energy, production of biofuel and
recycling in soil to manage the residues in a productive manner. Generally, many
farmers are keeping rice straw in form of heap for feeding to animals. In north-western
(NW), India combine harvesting of rice and wheat is now a common practice, leaving
large amount of crop residues in the fields. Rice straw incorporation is practiced by
less than 1% farmers as it is energy and time-intensive. It is a common practice that
crop residue is burnt directly in the field, causing environment pollution. It is an
important challenge to manage the huge quantity of crop residue and its proper
utilization. Conservation agriculture (CA) practices in North India offers a good promise
in using these residues for improving soil health, increasing productivity, reducing
pollution and enhancing sustainability and resilience of agriculture. The technologies
(RCTs) involving no- or minimum-tillage, direct seeding, bed planting and crop
diversification with innovations in residue management are possible alternatives to
the conventional energy and input intensive agriculture. But most of the technologies
are for rice- wheat cropping system. In eastern India in irrigated lands rice-rice cropping
system is dominant. Here
farmers got paddy straw
two times in a year and no
energy efficient
technology is used by the
farmers. Paddy straw
management machinery
a b
available in India is straw
chopper cum spreader, Fig. 8. Happy seeder (a) and spatial till drill (b) in
happy seeder (Fig. 8), straw operation.
management system for
combine harvester and baler.
2.11. Water management in rice
To produce 1 kg of rice around 3000-5000 liters of water are often used which is
more than any other crop like wheat and maize (Satyanarayana et al. 2007). Generally
surface irrigation method, viz., check basin method is used for irrigating paddy crop.
Unfortunately, the efficiency of surface irrigation in India varies from 30-40% where
as in country like Australia the efficiency in surface irrigation ranges as high as
between 60-85% (Burton 2016). Fresh water for irrigation is becoming increasingly
scarce due to population growth, increasing urban and industrial development
(Bouman 2007; Belder et al. 2005). Any measure contributing saving in irrigation
water in rice will yield in large saving of water. Source of irrigation water may be either
surface water or ground water. Over the past three decades ground water has become

Rice mechanization in India: Key to enhance

productivity and profitability 343
the main source of growth in irrigated areas which at present accounts for over 60 per
cent of the irrigated area in the country (Gandhi et al. 2009). Generally, internal
combustion engine (IC) like diesel engines are used for pumping irrigation water in
India. It is a costly affair also the NOX gases released during use of IC engine for
irrigating crop has environmental pollution effect.
2.12. Post harvest management
Paddy after harvesting undergoes a series of processing operations to convert to
an edible form. The edible portion of paddy is the rice. The various unit operations
involved in the processing of paddy to rice include cleaning, drying, storage,
parboiling (optional) milling and polishing. Care should be taken at each one of these
unit operations to minimize the loss and maximize the head rice yield recovery. Use of
modern rice mill with the improved unit operations and equipments gives higher
return with improved quality. Spoilage in paddy occurs due to improper handling and
storage practices. Moisture content of paddy plays a major role in maintaining the
quality of the product. Recommended moisture content for harvesting is 20-25% and
safe moisture content for storage of paddy for 2 to 3 weeks, 8 to 12 months and more
than a year are 14-18%, 13% or less and 9% or less respectively. So, drying also plays
a major role in controlling the moisture level, thereby in deciding the quality of the
rice. Presently farmers are using open sun drying for drying of threshed paddy and
after drying storage in soil bins or concrete silos.
Rice milling is the oldest and the largest agro processing industry of the country.
Paddy grain is milled either in raw condition or after par-boiling, mostly by single
hullers of which over 82,000 are registered in the country. Apart from it there are also
a large number of unregistered single hulling units in the country. A good number
(60%) of these are also linked with par-boiling units and sun-drying yards. Most of
the tiny hullers of about 250-300 kg h-1 capacities are employed for custom milling of
paddy. Apart from it double hulling unit’s number over 2,600 units, under run disc
shellers cum cone polishers numbering 5,000 units and rubber roll shellers cum friction
polishers numbering over 10,000 units are also present in the country. Further, over
the years there has been a steady growth of improved rice mills in the country. Most
of these have capacities ranging from 2 t h-1 to 10 t h-1.

3. ICAR-NRRI DEVELOPED MACHINERY/IMPLEMENTS

FOR RICE CULTIVATION
For rice cultivation improved farm implements/machines were developed by ICAR-
NRRI Cuttack and popularized among farmers. These machines include bullock drawn
implements, manual drawn implements, power tiller operated machines, self-propelled
machines, weeding implements, transplanting implements, and post-harvest machines
(Fig. 9 and 10). Most of the machines are low cost and suitable for marginal and small
farmers. ICAR-NRRI developed farm implements/ machines for rice were
commercialized through MOU with private manufacturers. Farm implements/machines
were supplied to different states of the country. In last 10 years total 14 no. of farm
implements/machines were commercialized and around 4000 number of units were
sold.

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Table 1. ICAR-NRRI developed machinery for rice mechanization.

Tillage implements
Bullock Drawn two gang Field Capacity- 0.35 ha h-1
notch type disc harrow This implement can be used in light as well as heavy soils
by increasing and decreasing the weight by filling sand
inside the empty drum.
Price- Rs. 20,000/-
Bullock drawn drum type Field Capacity- 0.4 ha h-1
disc harrow Used for light as well as heavy soils by increasing and
decreasing the weight by filling sand inside the empty drum.
Price- Rs. 20,000/-
Sowing implements
One row manual seed drill Field capacity- 0.01 ha h-1
Saves 45 % time over manual seeding
Gives uniform row to row spacing
Price- Rs. 1500/-
Two row manual seed drill Field capacity- 0.019 to 0.022 ha h-1
Adjustable seed delivery rateuniform row to row space for
weeding operation
Price- Rs. 3000/-
Three row manual seed drill Field capacity- 0.03-0.04 ha h-1
Saving in seeds and labours in sowing of crops
Easy weeding and inter-culture operation
Price- Rs. 4000/-
Three row manual puddle Field Capacity- 0.15 ha h-1
seeder Adjustable seed rate, saving of seed and time of seeding
Price- Rs. 3500/-
Four row manual drum Field capacity- 0.030-0.034 ha h-1
seeder Reduced seed rate by 60-65 % as compared to broadcast
seeding.
Price- Rs. 4500/-
Six row manual drum seeder Field capacity- 0.04 ha h-1
Reduced seed rate by 55-60 % as compared to broadcast
seeding.
Labour requirement in weeding in drum seeder plots was
reduced by more than 70% due to use of mechanical weeders.
Price- Rs. 6500/-
Eight row manual drum Field capacity- 0.093 to 0.097 ha h-1
seeder (hyperboloid shape) Sowing of this method reduced seed rate by 50-55 % as
compared to broadcast seeding.
Price- Rs. 8500/-
Power tiller operated Field Capacity- 0.15 ha h-1
Multicrop seed drill One hactare area can be easily covered in single day by an
operator
About 70-80 % labour saving over manual operated sowing
implements
Price- Rs. 20,000/-
Contd....

Rice mechanization in India: Key to enhance

productivity and profitability 345
Power tiller operated seed Field capacity- 0.15 ha h-1
drill for rice and groundnut Different seed rates i.e. 30 to 100 kg/ha for rice and 40 to 135
kg/ha for groundnut could be achieved.
Price- Rs. 22,000/-
Self-propelled eight row Field capacity- 0.25 ha h-1
hill seeder Reduced drudgery involved in sowing in puddled field
condition
Uniform seeds per hill (3-4)Labour saving by 60% over
manual drum seeder application
Price- Rs. 60,000/-
Transplanter
Two row transplanter Field capacity- 0.02 ha h-1
Saving in labour by 40-45 % as compared to manual
transplanting
Gender friendly technology females can easily operate it
Price- Rs. 6500/-
Four row transplanter Field capacity- 0.03 ha h-1
Saving in labour by 55-60 % as compared to manual
transplanting
Price- Rs. 8500/-
Deep placement urea briquette applicators
Two row urea briquette Field capacity- 0.07 ha h-1
applicator Labour requirement- 15 man-h/ha
Price- Rs. 3500/-
Three row urea briquette Field capacity- 0.08 ha h-1
applicator Labour requirement- 12 man-h/ha
Price- Rs. 4500/-
Injector type urea briquette Field capacity- 0.03 ha h-1
applicator Labour requirement- 40 man-h ha-1
Price- Rs. 2000/-
Weeding implements
Wheel finger weeder Field capacity- 0.022 ha h-1
Saving in labour by 40-50% as compare to manual
weeding
Price- Rs. 700/-
Finger weeder Field capacity- 0.012 ha h-1
Saving in labour by 27-30% as compare to manual
weeding
Price- Rs. 320/-
Star-Cono-Weeder Field capacity- 0.013-0.017 ha h-1
Saving in labour by 30-32% as compare to manual
weeding
Price- Rs. 1900/-
Single row power weeder Field capacity- 0.025 ha h-1
Saving in labour by 50-55% as compare to manual weeding
Reduced drudgery during weeding operation
Price- Rs. 22,000/-
Contd....

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346 productivity and profitability
 Rice Research for Enhancing Productivity,
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Post Harvest and Processing machinery

Power rice winnower cum Capacity clean grain – 500 kg h-1
cleaner Cleaning efficincy- 98 %
Cost of operation Rs. 6 per quintal as compare to manual
cleaning Rs. 16 per quintal
Price- Rs. 20,000/-
Mini paddy parboiling unit Capacity-75 kg batch-1
Time required- 6 h per batch
Cost of operation Rs. 30 per quintal as compare to manual
Rs. 40 per quintal
Price- Rs. 6500/-
Manual rice winnower Capacity- 90 kg h-1
Cost of operation- Rs. 10/quintal
Price- Rs. 6000/-
Chaff and husk stove It consumes 1.5-2.0 kg husk in one batch burns for 45 min –1 hr
Price- Rs. 800/-
Power operated paddy Capacity- 3-4 q h-1
thresher Threshing efficiency- 98.5%
60% saving in labour requirement and 54% saving in cost of
threshing as compared to those of pedal type paddy thresher

Fig. 9. NRRI developed three row seed drill (a), six row drum seeder (b) and power
operated single row dry land weeder (c) in operation.

Fig. 10. Manual operated three row (a) and two row urea briquette applicators (b)

Rice mechanization in India: Key to enhance

productivity and profitability 347
4. FUTURE THRUST AREA
4.1. Mechanical rice transplanting
Transplanted paddy cultivation is considered to be better from crop management
and productivity point of view. Farmers of India used traditional methods of rice
transplanting involved more human work rather than use of advanced technologies.
Mechanical transplanter is most prominent option to avoid drudgery and time involved
during transplanting operation. For Indian conditions the present need is to mechanize
the small holding transplanting operation by introduction of low cost mechanical
transplanter. The transplanters are used for only limited period of 15-30 days in a year.
Therefore, farmers do not want to invest large amount on costly machines. To reduce
the cost and to overcome the problems associated with operation of manual
transplanter there is need to develop a small self-propelled type transplanter. The
transplanting mechanism and forward speed should be power driven and controlled
by the operator, so operator only needs to guide the transplanter. The existing popular
transplanters are needed to be modified for simultaneous application of urea in root
zone of rice and to reduce the nitrogen losses from field. Development of mechanical
transplanters for large mat type seedlings is needed so that it can be more popular on
custom hiring basis and easily available for small and marginal farmers. Nursery
seeder may be developed for sowing of paddy seeds in nursery trays. This gives the
uniform seedling population in trays and also the soil media selected becomes easy
for cutting by transplanter fingers and gives optimum seedlings per hill. Transplanter
capable for working under adverse field conditions viz. standing water on fields, less
prepared field, plant residue on surface, are needed to be developed. Root-wash type
seedlings transplanters need to be developed, so that the need of mat type nursery
can be eliminated. Precision transplanters can be developed for large farmers to save
time and to reduce the input cost.
4.2. Nitrogen management in rice cultivation
Urea, widely used nitrogenous fertilizer, is available in various forms like prilled
urea, pelleted urea, briquetted urea etc. Among these various forms prilled urea are
used in most of the cases. Owing to the problem of its larger surface area, only 30–
45% of the broadcasted prilled urea can be utilized by the plants and rest are lost in
the various sinks into the environment (Dong et al. 2012). To avoid this loss, the urea
is deep placed in reduced zone in rice field or slow release forms are used (e.g.
supergranules, urea mudballs, briquettes, coated urea). Some advantages of deep
placement using urea briquette applicator are: (a) higher yield and nitrogen use
efficiency (b) reduces loss of nitrogen (c) reduce greenhouse gas emission (d) less
labour cost (e) precise placement. Compared to the manual placement, use of machine
for deep placement of urea briquette is more precise and the most promising
technology. Precise urea briquette applicator can improve the placement and reduce
manual errors in placement depth.

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348 productivity and profitability
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4.3. Precision rice machinery

Developments in electronics, sensors, and information technology are now
permitting considerable up gradation of farm machinery in terms of minimizing the
wastage of inputs, reducing drudgery, improving the quality of farm produce and
making agriculture more environment-friendly. The input applicators such as seeders/
planters, fertilizer applicators, agro-chemical applicators and irrigation systems need
to take into account the spatial variability in the field while dispensing the precise
quantity of inputs. The present technologies of sensors, remote sensing, electronics,
and mathematical modelling permit their integration with machinery design to permit
the precision input applicators’ development. Development of pneumatic planter for
precise seed rate, precision fertilizer applicator based on site specific requirement,
precision mechanical transplanter, and variable rate chemical applicators need to be
developed for rice crop.
4.4. Paddy straw management machinery
To avoid burning of paddy residue, improved machinery need to be developed
and commercialized. A series of implements were developed in North India but still
these implements were not being used by the farmers. On-farm management of paddy
straw machines can save time, maintain soil health and remove the need of multiple
operations to be done to incorporate the paddy straw. Straw chopper, happy seeder,
combine with straw management system, half feed combine etc. are technology
available in the Indian market. These machines need to be tested and popularize in
different areas of the country.
4.5. Energy efficient machinery
Energy requirements in agriculture sector depend on the size of cultivated land,
level of mechanization, cropping pattern, and climatic conditions. Climate change and
environmental sustainability are the key issues, must be dealt with while producing
more food grains under use of various energy resources. These issues can be checked
through efficient utilization and conservation of energy at the most. Maximum benefits
in agricultural production can be drawn through optimal and proper utilization of
energy inputs involved in various farm operations available with farmers. As per the
size of land holding and method of crop cultivation, selection of energy efficient
technology is due important.
In present conditions, farm machinery available and used is mostly operated by
non-renewable sources of energy (Fossil fuels). Limited fossil resources emphasizes
the need for new sustainable energy supply options through use renewable energies.
Solar farming is slowly getting popularity and stationary agricultural tools such as
watering systems, dryers, green house etc. are available in market. There is a need to
give more emphasize on standardization and popularization of these technologies.
There is need to develop solar energy based farm machines/implements to replace the
fossil fuel based engines. Use of solar energy and modern micro irrigation techniques
in rice crop cultivation will help in increasing crop water productivity and yield besides
reducing cost of cultivation.

Rice mechanization in India: Key to enhance

productivity and profitability 349
 In rice cultivation use of machinery for field preparation is high and most of the
farmers of India are using tractor and power tiller with matching implements for deep
ploughing and puddling operations. But, for other operations viz. sowing,
transplanting, harvesting and threshing human labour or animals are used which
leads to higher use of energy input in rice production. Optimal use of energy sources
available in farm can reduce the input energy without affecting output. Based on the
energy footprints of rice cultivation improved package of practices through inclusion
of improved implements are recommended for cultivation of rice by different methods
viz. DDSR, transplanting and WDSR (Table 2).
Table 2. Improved cultivation practices for direct sown rice cultivation for optimal
energy use.
Farm type Dry direct sowing Transplanting Wet direct sowing
Animal Farm/ Bullock ploughing Bullock ploughing Bullock ploughing
small farm (MB Plough) x 1 + (MB Plough) x 1 + (MB Plough) x 1 +
(less than 2 ha) bullock disc harrow x 2; bullock disc puddler x bullock disc puddler
sowing by bullock 3; mat type nursery x 3; sowing by
drawn seed drill; preparation; Manual drawn six
weeding: chemical + transplanting by row cylindrical
mechanical + manual; manual transplanter; drum seeder;
FYM application by weeding: chemical + weeding chemical +
bullock cart; chemical mechanical + manual; mechanical + manual;
spray by hand FYM application FYM application
compression sprayer; by bullock cart; by bullock cart;
harvesting by improved chemical spray by chemical spray by
sickle; threshing by hand compression hand compression
manual pedal thresher; sprayer; harvesting sprayer; harvesting
transportation by bullock by improved sickle; by improved sickle;
trolley threshing by manual threshing by
pedal thresher; manual pedal thresher;
transportation by transportation
bullock trolley by bullock trolley
Mechanized Power tiller/ tractor - Power tiller/tractor - Power tiller/ tractor-
farm (more cultivator (2) + disc cultivator (2) + Disc cultivator (2) + disc
than 2 ha) harrow (2); sowing harrow (2); mat type harrow (2); sowing
with PT seed cum nursery preparation; with eight row cup
fertilizer drill/tractor transplanting by type power seeder;
drawn seed cum power transplanter; weeding with power
fertilizer drill; weeding weeding with power weeder + manual
with power weeder + weeder + manual weeding; manual
manual weeding; weeding; manual fertilizer application;
manual fertilizer fertilizer application; chemical spray by
application; chemical chemical spray by power sprayer;
spray by power sprayer; power sprayer; harvesting by reaper
harvesting by reaper and harvesting by reaper and threshing by
threshing by power and threshing by power operated
operated drummy thresher/ power operated drummy thresher/
harvesting by combine drummy thresher/ harvesting by combine
harvester; transportation harvesting by combine harvester;
by tractor trolley harvester; transportation
transportation by tractor trolley
by tractor trolley

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 Rice Research for Enhancing Productivity,
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4.6. Post harvest processing and value addition

Single pass rice mills with metal polisher need to be improved with rubber roll
sheller for better performance. Rice parboiling and drying system need to be improved
for better energy efficiency. Rice husk and straw can be properly utilized for energy
generation. Community level improved methods for drying, cleaning, milling, and
packaging can help in increase of farmer’s income. Value added products of rice (Rice
flour, puffed rice, rice flakes) have excellent commercial demands, to popularize these
values added products low cost and user friendly technology needs to be developed.

5. WAY FORWARD
 Development of decision support system and expert system for precise input
application and crop management for different agro-ecology regions of India
 Promoting establishment of more custom hiring centers with large machinery
tractor, combines, thresher etc is essential to enhance the mechanization level for
future of the industry.
 Testing facility of farm implements/machines need to be established in region
specific to maintain the quality and ensure safety.
 Community level improved methods of drying, cleaning, milling, and storage of
rice need to be promoted.
References
Belder P, Spiertz JHJ, Bouman BAM, Lu G and Tuong T P (2005) Nitrogen economy and water
productivity of lowland rice under water-saving irrigation. Field Crops Research, 93(2):169-
185.
Bouman BAM (2007) A conceptual framework for the improvement of crop water productivity at
different spatial scales. Agricultural Systems 93(1):43-60.
Burton M (2016) Water management issues at the farm level. Indian Irrigation Forum International
Commission on Irrigation and Drainage (ICID) India Water Week.
Dong NM, Brandt KK, Sørensen J, Hung NN, Van Hach C, Tan PS, and Dalsgaard T (2012) Effects
of alternating wetting and drying versus continuous flooding on fertilizer nitrogen fate in
rice fields in the Mekong Delta, Vietnam. Soil Biology and Biochemistry 47:166-174.
Gandhi V P and Namboodiri NV (2009) Groundwater irrigation in India: Gains, costs, and risks.
Indian Institute of Management Ahmedabad, Gujarat, India.
Goyal SK and Singh JP (2002) Demand versus supply of foodgrains in India: Implications to food
security. Paper presentation at the 13th International Farm Management Congress,
Wageningen, The Netherlands, July 7-12, 2002, p. 20.
Mehta CR, Chandel NS, and Senthilkumar T (2014) Status, Challenges and Strategies for Farm
Mechanization in India. Agricultural Mechanization in Asia, Africa, and Latin America,
45(4):18-23.
Renpu B (2014) Analysis of the Trends of Agricultural Mechanization Development in China
(2000-2020). ESCAP/CSAM Policy Brief, Issue No.1, 9-11.
Satyanarayana A, Thiyagarajan TM, and Uphoff N (2007) Opportunities for water saving with
higher yield from the system of rice intensification. Irrigation Science, 25(2):99-115.

Rice mechanization in India: Key to enhance

productivity and profitability 351
 Microbial Resources for Alleviating Abiotic and
Biotic Stresses and Improving Soil Health in
Rice Ecology

Upendra Kumar, P Panneerselvam, TK Dangar, A Kumar,

D Chatterjee, C Parmeswaran, SD Mohapatra, G Prasanthi,
K Chakraborty, P Swain and AK Nayak

SUMMARY
Abiotic and biotic stresses decrease the rice productivity; hence, there is an
urgent need to develop simple and low-cost microbial tools for management of these
stresses. Beneficial microbes present in soil and plant have huge potentials to alleviate
the stresses. We characterized few thermo/drought-tolerant microbes (Bacillus sp.,
Aspergillus oryzae etc.) to alleviate drought stress in rice and also developed
biocontrol formulations of Bacillus thuringiensis, Beauveria bassiana, Metarhizium
anisopliae and Skermanella sp. for managing rice leaf folder. We also explored the
potential of Azolla as biofertilizer and livestock feed. Cylindrospermopsis sp.
association in Azolla as abundant cyanobiont was first time documented which has
enlightened to rethink about Azolla-based biofertilizer strategies. Further, nutrient
profiling of different strains of Azolla suggested the prospects of Azolla microphylla
as suitable livestock feed. The efficient straw decomposing microbes (Bacillus,
Aspergillus, Trichoderma, and Streptomyces spp.) available with us, will be utilized
to develop a consortium to decompose paddy straw within one month. To explore the
beneficial role of Arbuscular mycorrhizal fungi and uncultivated microbial community
and understanding their structural and functional variations in rice ecosystem through
molecular approach are frontier research in future for sustainable rice production,
particularly in Eastern India. Overall, the present chapter deals the prospects of
beneficial microbes in alleviating abiotic and biotic stresses; improving nutrient use
efficiency and managing rice residues.

1. INTRODUCTION
Most of the cultivable lands around the world are severely affected by abiotic and
biotic stresses which are evident with one report that for every 1°C rise in day/night
temperature above 28/21°C declined the rice yield by 10%. Therefore, a wider range of
adaptations and mitigation strategies would be required to meet the challenge of
enhancing productivity of rice from affected lands. Beneficial microorganisms are
one of the best options to alleviate these stresses in agricultural crops, therefore, we
must explore the microbial potential particularly their unique properties of tolerance
to extremities, ubiquity, genetic diversity, and their interaction with crop plants for
sustainable rice production with higher yield stability (Grover et al. 2014; Kumar et al.
2017a).

Microbial Resources for Alleviating Abiotic and Biotic Stresses and

352 Improving Soil Health in Rice Ecology
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Rhizosphere is the place where microbial communications interact with plant roots
and effects higher numerical abundance and diversity of microbes compared to bulk
soil (root-free soil). Several reports indicated that microbial population in the
rhizosphere is highly influenced by differing physico-chemical and biological
properties of soil (Kumar et al. 2016; Kumar et al. 2017b). Soil harbours vastly diverse
of microbial communities, such as, bacteria, cyanobacteria (blue green algae), fungi
and actinomycetes (Kumar et al. 2017c). Of these, bacteria are ubiquitous in soil,
possibly because of having rapid growth rate and also have the ability to use a wider
range of substrate as carbon and/or nitrogen sources.
Most of the soil bacteria are adhered to soil particles and heavily influenced by
plant root exudates. Therefore, depending upon the nature of root exudates and soil
condition, the population of bacteria fluctuate in the vicinity of plant root and their
interactions are categorized into three types viz., beneficial, harmful and neutral.
Reports indicated that more than 80% bacteria are beneficial to the plants and these
are of two types-1) symbiotic bacteria which have a mutual relationship with the
plant, and 2) free-living bacteria in the soil, are often associated closely, on, or even
within the roots of plants. Plant growth-promoting rhizobacteria (PGPR) is another
term for beneficial free-living soil bacteria and sometimes referred as yield increasing
bacteria (YIB). Three most intrinsic characteristic need to be possessed by PGPRs,
namely, they must have ability i) to colonize the root, (ii) to survive, reproduce and
expressing plant-growth functions in the microhabitats of root surface under influence
of other microbiota, and (iii) finally, able to help in growth promotion of plant.
In general, application of PGPRs are commonly advocated in most of the crops for
making efficient and sustainable nutrient availability in plants and these can be grouped
in different categories based on their nature and function, such as, a) nitrogen-fixing
microbes: Azospirillum, Azotobacter, Rhizobium, Gluconacetobacter spp., Azolla-
cyanobiont (blue green algae) etc., b) phosphate solubilizing microbes; bacteria-
Pseudomonas striata, Bacillus megaterium, Bacillus subtilis etc., Fungi-Penicillium
sp., Aspergillus awamori etc., c) phosphorous mobilizing biofertilizers: Arbuscular
mycorrhiza fungi- Glomus, Gigaspora, Acaulospora, Scutellospora, Sclerocystis spp.
etc., d) silicate and zinc solubilizers: Pseudomonas, Bacillus spp. etc., e) potassium
solubilizer: Fraturia aurantia etc.
Based on the above background, the present chapter emphasizes on: 1) microbe-
mediated alleviation of drought and management of leaf folder under rice ecosystem,
2) status and research needs of Azolla as biofertilizer and livestock feed, 3) molecular
understanding of Azolla-cyanobiont association, 4) role of Arbuscular mycorrhiza
fungi (AMF) in rice and recent status of microbial consortia for paddy straw
decomposition, and 5) abundance and diversity of different structural and functional
genes related to biogeochemical cycling of major nutrients, such as, nitrogen (N),
phosphorus (P) and potassium (K) . The overall concept of whole chapter is represented
in Fig. 1.

Microbial Resources for Alleviating Abiotic and Biotic Stresses and

Improving Soil Health in Rice Ecology 353
 Fig. 1. Diagrammatic representation of overall viewpoints covered in this
chapter a) microbe- mediated management of rice leaf folder, b) drought, c)
paddy straw decomposition by microbes, d) role of AM fungi in rice, e)
bioprospects of Azolla and its cyanobionts, and f) assessment of microbial
community under rice ecosystem.

2. STATUS OF RESEARCH/KNOWLEDGE
2.1. Microbe-mediated alleviation of drought/moisture stress in rice
Most of the agricultural and agronomic practices are designated to optimize crop
growth by avoiding abiotic stresses (drought, saline, acidity, UV, nutrient etc.). Drought
or moisture stress is one of the most important abiotic stresses which usually occurred
due to the shortage of water. Plants are adversely affected by drought due to alteration
of its physiological processes, leading to decline in crop yield. Drought tolerant
plant-growth promoting microbes (PGPMs) is one of the alternatives to mitigate these
problems. Researchers have demonstrated some of the mechanisms of PGPMs by
which plants fight with drought or water stress. Table 1 represents few mechanisms
of PGPMs which helps in alleviating drought and/or moisture stresses in agricultural
crops including rice.
At ICAR-National Rice Research Institute (NRRI), Cuttack, we have attempted
some of the activities related to alleviating drought stress by PGPMs in rice. In this
connection, we screened a plant-growth promoting thermo-tolerant Bacillus sp. strain
TBB1 from Tarabalo hot springs of Odisha and evaluated its efficacy in rice. The
TBB1- treated plant showed better growth promotion in rice in terms of root length
and dry weight at the higher temperature. Additionally, ten thermo-tolerant plant
growth promoting fungi (PGPF) were also screened for PGP traits. Among them, the 6
potent thermo-tolerant PGPF were identified and submitted at National Center for
Biotechnology Information (NCBI), New York, USA and national fungal culture
collection of India (NFCCI), Pune, India with accession numbers KJ652020- KJ652025
and NFCCI 3438 - NFCCI-3443, respectively.

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354 Improving Soil Health in Rice Ecology
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Table 1. List of microbial genes responsible to alleviate drought or moisture stress

in agricultural crops including rice (Adapted from Bal et al. 2012; Meena et al.
2017 and Shekhar et al. 2017).
Name of the gene Source Host plant Role of the gene
ACC deaminase (acdS) Bacteria Rice, tomato, Decreased level of
canola, tobacco etc. ethylene under
drought/moisture stress
Oligosachharide Escherichia coli Rice Tolerant to drought
transferase
(ost A & ostB)
Early response to Paenibacillus Arabidopsis Tolerant to drought
dehydration 15 (erd15) polymyxa
Exopolysaccarides (eps) Rhizobium YAS34 Sunflower Tolerant to drought
strain
Trehalose 6-phosphate Yeast Tomato Tolerant to drought
systhase (tps1)
Levan sucrose (sacB) Bacillus subtilis Tobacco Tolerant to drought
Histidine Ammonia- Yeast Melon Tolerant to drought
Lyase (hal1)
Trehalose Pleurotus sajor- Tobacco Tolerant to moisture
phosphorylase (tp) caju stress
Mannitol-1-phosphate Escherichia coli Peanut Tolerant to drought
5-dehydrogenase (mtld)
Choline oxidase Arthrobacter Tomato Tolerant to drought
(codA or coxA) globiformis
Betaine aldehyde Escherichia coli Cotton Increased drought
dehydrogenase (betB) tolerance
Cold shock protein Escherichia coli Rice, arabidopsis Tolerant to water deficit
(cspA) and maize
Cold shock protein Bacillus subtilis Rice, arabidopsis Tolerant to water deficit
(cspA & cspB) and maize

2.2. Microbial formulations to manage rice leaf folder

The highest yield of any crop is based on the improved variety, appropriate pest,
disease management, and recommended fertilization. Adequate pest management is
essential for sustainable agricultural production. In the worldwide agriculture system,
the commonly used pesticides come under synthetic origin, such as, carbamate,
halogenated, organophosphorus etc. compounds. Excessive use of these synthetic
compounds led to creation of new strains of resistant besides environmental pollution.
Hence, biopesticides are considered as an alternative to synthetic pesticides that are
highly effective, target specific and reduce environmental risks. Up to now, there are
more than 3000 kinds of microbes are reported to cause diseases in insects. However,
further research is required to find out the remaining undiscovered or unidentified

Microbial Resources for Alleviating Abiotic and Biotic Stresses and

Improving Soil Health in Rice Ecology 355
microorganisms that are used in insect pest management. So far, nearly one hundred
bacteria identified as entomopathogens, among them Bacillus thuringiensis (Bt),
Metarrhizium sp. and Beauvaria sp. have got the maximum importance as microbial
control agents.
Rice is consumed by the one-third population of world, but the huge economic
loss of this crop is due to attack by many insect pests. Annually, pest accounted the
loss of more than 5% of the world total rice production, however, in India, the grain
yield loss of rice is accounted in the range of 21–51% due to insect attack and the
infestation varies depending on agro- climatic conditions. More than 100 species of
insects attack on rice crop, among them, rice leaf folder (RLF), Cnaphalocrocis
medinalis (Guenee) is considered as a serious insect pest. Earlier, the leaf folder was
considered as a minor pest of rice, but recently its importance has been increasing in
areas where modern high yielding varieties are grown. Managing leaf folder in rice is
challenging task and among different strategies, biopesticides can play important
role as a principal system to manage this pest.
Many microbial biocontrol agents have been documented, however, B.
thuringiensis is considered as one of the desirable alternatives to chemical pesticides
(Chatterjee et al. 2017). B. thuringiensis accounts for about 5-8% of total Bacillus sp.
in the environment. Till date, more than 130 species of coleopteran, dipteran, and
lepidopteran insects are found to be controlled by B. thuringiensis. So far, 71 serotypes
(84 serovars) of B. thuringiensis having a wide array of host range have been
commercially exploited directly as a native form or indirectly as transgenic microbes
or plants. Bacteria, especially B. thuringiensis and B. sphaericus are the most potent
and successful group of organisms for effective control of insect pests and vectors
of diseases. Similarly, Beauveria bassiana, and Metarhizium anisopliae are reported
to have strong biocontrol activity against rice leaf folder.
At NRRI, Cuttack, we are actively working since long to identify efficient
entomopathogens to manage rice leaf folder and finally able to identify the following
bacterial and fungal strains viz., B. thuringiensis, B. bassiana and M. anisopliae, and
formulations of these strains were also filed for Indian patents. In addition, recently
we have identified one efficient entomopathogenic bacterium (Skermanella sp.)
against rice leaf folder and pink stem borer.
2.3. Bio-prospects of Azolla for soil health improvement
Azolla is an aquatic fern and able to fix unlinked nitrogen (N2) directly from the
atmosphere by endosymbiotic cyanobacteria and is thus a very promising suppler of
nitrogen to aquatic ecosystems. It produces 10 to 20 t/ha/season of fresh biomass
and supplies 20 to 40 kg N/ha and also has the ability to improve the low nitrogen use
efficiency in rice (Yao et al. 2018). Azolla has several other important applications
which include organic manure, bioremediation, livestock feed, human diets and most
importantly in biofuel production. Therefore, to make Azolla technology very popular
among farming community a unique approach (sporocarp-based formulation of Azolla)
is required and further to resolve the controversial taxonomy of Azolla-cyanobiont
association, molecular methods may be helpful to explore the potentialities of Azolla.

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2.3.1. Sporocarp-based formulation of Azolla

Azolla technology is widely accepted throughout the world as efficient nitrogen
contributor in rice ecology through symbiotically associated cyanobacteria with them.
Sporulation and sexual reproduction of Azolla are essential for the survival of the
associations under adverse environmental conditions, such as tropical /sub-tropical
summers and temperate zone winters. Field observations and laboratory studies
indicate that sporulation in Azolla species is not simply a seasonal phenomenon
linked to photoperiod, rather, sporulation appears to be induced by the interacting
effects of environmental factors, including temperature, light intensity, nutrients, and
plant density. Furthermore, the conditions leading to the induction of sporulation are
not the same for all species (Brouwer et al. 2014).
As regards to the biomass production, and quantity of nitrogen fixation and
nutrient recycling, Azolla is highly efficient, cost-effective and ecologically sound
biofertilizer (Bhuvaneshwari et al. 2015). To produce Azolla inoculum in paddy fields,
larger scale of its vegetative fronds are required but there are several physical
constraints in Azolla production and utilization. The thick wall of megasporocarp can
withstand high temperature, drought condition, and pest attack. That is why, many
researchers were advocated to use sporocarp-based formulations of Azolla as
biofertilizers, however, most of the researchers have documented the sporocarp
production of Azolla only from a limited number of species, and therefore, it has to be
studied thoroughly in species available at NRRI Cuttack germplasm collections.
Earlier researchers have documented the mass production of Azolla and their role
in nutrient management in rice crop production at NRRI, Cuttack. They also have
attempted on induction of sporocarp in different species of Azolla and found that
some strains of Azolla are strongly sensitive to the environment and sporulate only
during winter months (November to March).
2.3.2. Bio-prospects of Azolla-cyanobiont
The available information on cyanobacteria association with Azolla is very poorly
characterized; the degree of their interaction with the host, their mode of inheritance
and patterns of co-evolution have not been fully investigated to date. Molecular
tools are one of the best alternatives to characterize this phenomenon, but the whole
genome sequence of Azolla is not yet available. Keeping the importance of Azolla in
a huge applicability in agriculture and industry, there is an urgent need to generate de
novo whole genome sequence data of Azolla to explore many possibilities. The genome
size of Azolla is tiny (750 Mb) as compared to other pteridophytes genomes (>10 Gb)
(Li and Pryer 2014), making it the perfect first genome to be sequenced in pteridophytes.
Azolla is a very good source of protein and hence, it may consider as one of the
important sources for cattle feed. Further, very limited reports are available on value-
added products and renewable energy from Azolla.
Most of the reports available on Azolla, pertaining to its importance as biofertilizer
and livestock feed. Nutrient profiling of A. microphylla was studied and its digestibility
as feed supplement in livestock was also evaluated using in vitro technique. Studies

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Improving Soil Health in Rice Ecology 357
also showed the abiotic stress tolerance response of Azolla against salinity and
ultraviolet radiations (UVB). Reports also indicated that A. caroliniana might be
used as a sorbent for removing toxic substances from paper mill effluent (Shivkumar
et al. 2015).
At NRRI, Cuttack, we are maintaining one hundred and two strains of Azolla
germplasms, we did nutrient profiling of six species of Azolla (A. pinnata; A.
filiculoides; A. rubra; A. microphylla; A. mexicana and A. caroliniana) and found
that they all have higher percentage of nutrient value (protein, antioxidants, iron,
calcium etc.) and least concentration of antifeedant value (acid and neutral detergent
fibres) which indicated that Azolla can be used as potential livestock feed (Kumar et
al. 2015). Furthermore, an Illumina-Miseq based Azolla-cyanobiont association in six
species (name mentioned elsewhere) of Azolla, was also characterized which revealed
for the first time that Cylindrospermopsis sp. was the most abundant Azolla-
cyanobiont and their diversity was dependent upon presence of Azolla fibre content.
Besides this, biomass production and mass multiplication of A. microphylla along
with biochemical constituents under various conditions were also analyzed.
2.4. Microbe-mediated paddy straw decomposition
In India, we are generating nearly 158 million tonnes of paddy straw every year
and recycling of these wastes properly, retrieve the considerable amount of nutrients
to the soil in addition to improving soil health and reducing greenhouse gas emission
to the environment. It has been frequently reported that the application of rice straw
to paddy fields increases methane emissions. Therefore, promotion of the oxidative
decomposition of rice straw in and out of the field is important for not only reducing
methane emissions but also enhancing the carbon stock in the soil.
Many research findings documented that the rice straw can be decomposed by
using the combination of microbes like a bacterial and fungal consortium. In rice field,
it was observed that application of decomposed rice straw decreases methane emission
(Takakai et al. 2017). In composting, bacteria play a major role as they make up 80-90%
of microorganisms found per gram of the compost. They can easily grow on soluble
substrates and have the capacity to attack more complex materials by releasing
extracellular enzymes. They contribute to a major proportion (80% of the total microbial
count) in compost and are responsible for degradation of a variety of organic materials
by releasing a wide range of enzymes. They are also responsible for the initial
decomposition.
Sannathimmappa et al. (2015) reported that treatment of rice straw with a
combination of cow dung slurry (5%), Trichoderma harizianum (5 kg/ha) and
Pleurotus sajor-caju (5 kg/ha) showed significant degradation of rice straw.
Researchers also reported that nutrient enriched compost can be prepared by using
the consortium of fungal (Aspergillus nidulans, A. awamori, T. viride and
Phanerochaete chrysosporium) inoculants within 70-90 days by pit and windrow
methods. In general, organic wastes are rich in lignin content which makes the
composting process a little challenging to the microbes for the degradation because

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of its complexity to degrade as well as it reduces the bioavailability of other cell wall
constituents. Some researchers have reported that fungi belonging to basidiomycetes
group are good at degrading lignin. Similarly, actinomycetes are found to grow
abundantly during the later stages of composting. Most frequently occurring
actinomycetes during the later stages of composting include Micromonospora,
Streptomyces, Nocardia, and Thermoactinomyces. The development of microbial
consortium based on bacteria, fungi and actinobacteria would be more effective for
decomposition of paddy straw than individual genus.
We have isolated nine strains from paddy straw and composting pit and evaluated
for their ability for decomposition of rice straw under microcosm experiment. The
results indicated that actinobacteria isolates (DA10, DA13, and DA9) degraded the
cellulose 72.7 to 81.6% higher than uninoculated control after one month of inoculation,
whereas, fungal (DF15, DF7 and DF19) and bacterial isolates (DB12, DB20 and DB23)
showed the cellulose degradation efficacy by 66.6 and 79.0% higher, respectively
compared to control. The bacteria, fungi and actinobacteria were identified as Bacillus,
Trichoderma, and Streptomyces spp., respectively.
2.5. Role of arbuscular mycorrhizal fungi (AMF) in rice
Arbuscular mycorrhizal fungi (AMF) are key components of soil microbiota and it
comes under phylum Glomeromycota which represents the most common and
widespread in terrestrial plant symbiotic association. The AMF is one of the most
beneficial microbes for agricultural crops because of its contribution in soil structure,
plant nutrition, disease resistance, drought and salinity tolerance (Auge et al. 2015).
Rice crop planted under upland area willingly associated with mycorrhizal colonization
but under lowland area or flooded conditions, colonization is infrequent due to the
anoxic environment. However, recent studies conducted at NRRI, Cuttack showed
that some of the species of AMF could colonize well under wetland condition of rice
(Sahoo et al. 2017).
AMF colonization in rice plant has been documented by Sahoo et al. (2017) and
this fungal association in rice found to enhancing P acquisition. The above findings
clearly indicated that the AMF association in rice plant is essential for plant growth
improvement. Plants acquire Pi by two mechanisms; i) directly via root epidermal
cells and root hair ii) through the extra-radical hyphae of AMF which delivers Pi
directly to colonized cells in the root cortex. It is well known that Pi is transported into
plant cells through membrane- associated Pi transporter proteins belonging to Pht
family. In rice, sequencing of rice genome has revealed 13 such phosphate transporter
genes. In AMF colonized rice roots, Pht 11 and Pht 13 exhibited altered expression.
Pht 11 is activated through symbiosis between AMF and rice, whereas, Pht 13 is
independent which is expressed both in AMF colonized roots and uncolonized roots.
So, Pht transporter protein Pht 11 is crucial for rice-AMF colonization. The phosphate
transporters not only contribute to Pi uptake but also for symbiotic association
(Glassop et al. 2007).
At NRRI, Cuttack, AMF association was studied in 72 different rice cultivars
including two low P tolerant checks viz., Kasalath and Dular, which were raised in P

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Improving Soil Health in Rice Ecology 359
deficient soil (< 6.0 – 8.0 ppm). The AMF root colonization was recorded in the range
of 20-90%, whereas, it was 80-90% in Kasalath and Dular cultivars. These two varieties
have the dominant unique type of vesicle-forming AMF colonization, which was not
observed in many low P tolerant varieties. This observation clearly indicates that
some genera of AMF may prefer the specific rice genotype of rice. It is well-known
fact that Kasalath and Dular possess the protein kinase gene pstol for phosphorus-
deficiency tolerance, thus these varieties having a unique kind of AMF root
colonization in P deficient soil, needs further in-depth investigation.
2.6. Abundance and diversity of structural and functional genes related
to biogeochemical cycling of nitrogen, phosphorus and sulphur under
rice ecosystem
Among all nutrient cycles in the earth, nitrogen (N), phosphorous (P) and sulphur
(S) are found to be dominant and soil microbes are playing a vital role to complete
their cycles. Assessment of these microbes are tedious because only small percentage
are cultivable and majourity of them are undetectable, therefore, molecular techniques
are to be used to monitor microbial populations in a variety of environmental samples
at concentrations previously considered undetectable because this technique bypass
cultivation dependent approach. Quantitative PCR (q-PCR) is one of the most
important molecular tools widely used in microbial ecology nowadays to assess
quantification of structural and functional genes within a complex community (Church
et al. 2005) or to monitor their gene expression (Zehr et al. 2007). In addition to q-PCR,
a metagenomic approach is also considered as a powerful molecular technique to
assess culture independent profiling of microbial communities in complex ecosystem
including rice.
At NRRI, Cuttack, culture based soil and plant microbial communities in rice have
been studied under influence of different management practices such as influence of
nitrogen fertilizers (Kumar et al. 2017a), non-target effect of chlorpyrifos (Kumar et al.
2017b) and even frequency of diazotrophs in aromatic rice cultivars (Kumar et al.
2017c), however, very limited study has been conducted to observe shift of microbial
community in NPS biogeochemical cycling at genetic level.

3. KNOWLEDGE GAPS
Based on the above information, we observed following problems which need to
be addressed in upcoming days.
 Water shortage is one of the major problems for rice cultivation and to mitigate
this problem, a plenty of information has been generated under in vitro but adequate
understanding and behavior of drought-tolerant microbial formulations are lacking
under in vivo condition.
 Though, we have many microbe-based biocontrol agents, however no effective
and consistent biocontrol agents are available till date for management of rice leaf
folder.

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 At present, the sporocarp-based primary inocula in place of vegetative propagules

is essentially required for Azolla large-scale mass production, but this technology
is not successful among farming community due to various reasons like time
bound sporulation frequency, extreme temperature, variable photoperiod, low light
intensity, soil pH, EC etc. These problems have to be resolved for making successful
sporocarp-based Azolla inoculum.
 In addition, the method of storage, self -life, mode of delivery of sporocarp-based
Azolla inocula are to be standardized.
 To date, whole genome sequence of Azolla is not available, hence it is difficult to
understand cyanobacteria-based nitrogen fixation process in Azolla and biomass
production under rice-based cropping system.
 Limited superior strains of Azolla are available for huge biomass & bioenergy
productions, as well as, suitable feed for livestock.
 No report are available about the exact biochemical pathway of Azolla
cyanobacterial-interactions and also systematic molecular approach to identify
different metabolite production in Azolla.
 Many ex situ composting technologies are available and it requires 75-90 days for
complete decomposition of paddy straw, but we do not have any viable in situ
rice straw decomposing methods within short period of time (45-60 days).
 Though, the AMF associations have been reported in many crops, the information
on rice is inadequate. Furthermore, it was reported that the plant growth
performance and nutrient uptake will vary from species to species, hence, there is
a need for selection of efficient AMF for better plant growth and development.
Some reports also indicated that AMF has host, as well as, ecological preference,
but this information in rice is not clear so far.
 In rice ecosystem, adequate information on abundance of soil microbial structural
(16S rRNA, ITS, AML) and nutrient mobilizing functional genes (nifH, amoA,
nirK, nosZ, phoD, soxB etc.) are not yet to be exactly quantified.

4. RESEARCH AND DEVELOPMENT NEEDS

Thermo-and drought-tolerant exopolysaccharide (EPS) producing plant growth
promoting bacteria and fungi are available at NRRI Microbiology laboratory and
these strains must be thoroughly characterized for different functional genes (acdS,
ostA/B, sacB, hal1, tp, tps1, mtdl, codA/coxA,cspA/B, betB etc.) related to drought
stress and efficient one must be formulated and evaluated under in vitro and in vivo
conditions in rice ecosystem to make a suitable microbial product which can alleviate
drought stress in rice.

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Improving Soil Health in Rice Ecology 361
 Six entomo pathogens strains (four B. thuringiensis and one each of B. bassiana
and M. anisopliae) were evaluated under laboratory and glass house conditions for
management of leaf folder and filed patent also. But these strains should be validated
for their efficacy and mode of delivery for managing rice leaf folder at farmers’ field. In
addition, bio-safety data should also be generated before commercialization. If we
develop an efficient bio-formulation for management of leaf folder, it will be one of the
potential components in organic cultivation of rice and also considerably reduce
insecticides usage in rice cultivation.
Though, the technology of Azolla as biofertizer is available for the farmers, but
not gaining much popularity in rice farming community due to huge inoculums
requirement (2-5 t/ha) in the form of vegetative inocula. Hence, the sporocarp-based
formulations will considerably reduce the initial inocula load to few liters per hectare,
if we successfully exploit the sexually propagated inocula of Azolla. Sporocarp-based
formulations will also ascertain the purity of strain which is not in case of earlier
methods of application. Sexually propagated inocula (megasporocarp) can withstand
adverse environmental conditions like high temperature, drought and pest attack.
Quantification of nif gene is one of the best alternatives to assess nitrogen fixing
ability of Azolla under various environmental conditions. Metagenome and
transcriptome sequencing of Azolla are other solutions to understand the co-evolution
pattern of Azolla-cyanobiont. Identification of cost-effective protein rich Azolla stains
for livestock feed is certainly needed to safeguard livestock health.
Straw burning problem has given a clue to develop the compatible lignocellulolytic
microbial consortium for rapid decomposition of straw residues. The development of
viable in situ partial or complete microbial decomposition of rice straw at filed levels
will retrieve the considerable amount of nutrients to soil, improves soil qualities,
decrease the greenhouse gas emission, suppress the population of stem borer and
soil borne pathogens in rice cultivation. When the farmer realizes the benefit of in situ
decomposition of rice straw in short periods (45-60 days), they will not burn the rice
straw.
To mitigate P deficiency, AMF colonization with rice roots can be treated as a
positive strategy for sustainable rice production. To unlock the potential of AMF for
sustainable rice farming, identification of key molecular players involved in the
colonization will open new vistas to design rice-AMF combinations with enhanced
AMF performance.
For better understanding and generating knowledge towards microbial role in rice
ecosystem, standardization of q-PCR protocol must be required to quantity different
structural (16S rRNA, ITS, AML etc.) and functional (nifH, amoA, nirK, nosZ, phoD,
soxB etc.) genes related to biological functions in paddy soil (Table 2). Finally, structural
and functional variations of microbial community under influence of rice varieties,
fertilizers and pesticides etc. are also essentially required for in-depth understanding
of microbial role under rice system.

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Table 2. Genes used for structural microbial community assessment and biological
functions of agricultural soil.
Microbial group/
Microbial genesPrimers enzymes Cycle Reference
16S rRNA F968/R1378 Total bacteria - Heuer et al. 2008
ITS FF390/FR1 Fungi - Vainio et al. 2010
act Act-878-a-a-19 Actinomycetes - Bredholt et al. 2008
Act-235-a-S-20
ps Ps-F/Ps-R Pseudomonas - Anuj et al. 2009
nif H NifH-F/NifH-R Nitrogenase reductase N Rosche et al. 2002
amoA (Bactria) AmoA1-F/ Ammonia N Hayden et al. 2010
AmoA (Archaea) AmoA-R monooxygenase
nirK NirK-FNirK-R/ Nitrite reductase N Yoshida et al. 2009
nos Z NosZ-FNosZ-R Nitrous oxide N Chon et al. 2011
reductase
pho D PhoD-F733/ Alkaline P Ragot et al. 2015
PhoD-R1083 phosphatase
soxB SoxB 710-F/ Sulphur oxidation S Tourna et al. 2014
SoxB 1184-R

5. CONCLUSION AND WAY FORWARD

Overall, the present chapter describes the different scenario of harnessing microbial
resources for soil, pest and residue management. The following microbe-mediated
works are essentially needed in future for sustainable development of rice crop
particularly in Eastern India.
 Microbial formulation and methodology are to be developed to alleviate drought
stress under rice cultivation system.
 The microbial consortium package should be developed exclusively for rice crop
residues and pest management.
 Sporocarp-based formulations are to be developed to reduce the initial inocula
load of Azolla in paddy field.
 Molecular markers are to be identified through meta-and transcriptome sequence
of Azolla for better understanding of Azolla-cyanobiont interactions.
 Latest molecular tools must be explored to understand the soil biological nutrient
cycling in paddy soil.
In conclusion, we urgently need a proper scientific research with technological
developments to meet the target of food and feed security for the increasing world
population. To achieve this goal an interdisciplinary approach is needed among
scientists in different fields. As the microbes are ubiquitous in nature so that harnessing
their diversified and pivotal potential provides an economical alternative for the
development of climate-resilient crops. To address the above-said task a global

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Improving Soil Health in Rice Ecology 363
approach is a prerequisite to understand all the distinctive properties of microbes and
it can be harnessed to fulfill the elevated demand for food, feed, and shelter. In the
present era of scientific advancement, it is very feasible to integrate different advanced
techniques in genomics and omics (transcriptomics, proteomics, metagenomics,
metabolomics etc.) for development of viable technology. Most importantly, the long-
term efficacy of stress tolerance and impacts associated with the use of microbes in
genetic engineering of plants need to be assessed thoroughly. Extension of
recombinant plant and microbial protocols would facilitate the validation process and
the development of stress-tolerant crops. The long-term and in-depth studies on
plant-microbe interactions are still needed to mitigate the elevated food and feeder
demand in the era of global climate change.
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Exploring New Sources of Resistance for Insect

Pest and Diseases of Rice

Mayabini Jena, PC Rath, AK Mukherjee, Raghu S, Guru P Pandi G,

Basana Gowda G, Prasanthi G, MK Yadav, MS Baite,
Prabhukarthikeyan SR, MK Bag, Srikant Lenka, Arvindan S,
Naveen Kumar Patil, SD Mohapatra, Annamalai M and T Adak

SUMMARY
In the present scenario of rice pest management, host plant resistance is playing
a pivotal role. It is the easiest way to reduce pesticide load in rice ecosystems as well
as to mitigate pest problem under adverse environmental conditions. With the
development of nitrogen responsive high yielding rice varieties and hybrids, several
insect pests and diseases assumed major status. Significant effort has been made in
the past to develop resistant varieties against different pests, particularly, brown
plant hopper, gall midge, blast and bacterial blight with identified resistant genes. But
gradually, most of the developed varieties have lost their resistance resulting in more
frequent and severe pest outbreaks. Therefore, again the search has began for new
resistant donors of different pests from the existing vast germplasm collection of the
country including those identified in the past. The mechanism of resistance in identified
genotypes has to be studied by assessing its effect on pest biology and behavior or
disease infection pattern. Molecular marker analysis of resistant genotypes (donors)
will give an indication of the presence of a known or new gene effective against the
particular pest. A set of donors should always be in place to be utilized in resistance
breeding programme for the development of pest resistant varieties, which will benefit
rice farmers of the country.
1. Introduction
Productivity of rice is facing severe threat from biotic stresses, particularly insect
pests and diseases, causing huge yield loss. Among the biotic stresses, insect pests
like yellow stem borer (YSB), gall midge, brown plant hopper (BPH), white backed
plant hopper (WBPH), and leaf folder are the major problems whereas among the
diseases, blast, brown spot, bacterial blight (BB) and sheath blight (ShB) are most
destructive to the crop. Recently, insects and diseases like case worm, swarming
caterpillar, mealybug, gundhi bug, false smut, bakanae and sheath rot have emerged
as the major problem in many rice growing areas of the country. Stored grain pests
also are gaining significant importance in causing post harvest losses among which
the rice weevil and angoumois grain moth are considered to be the most common
pests. Moreover, rapid change in the virulence characteristics of plant pathogen/
insect populations pose continuous threat to existing popular rice varieties as well as
for development of a virulent pathotype or biotype. Pesticide application has been
followed by farmers as the major option for pest management which in turn, is creating

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environmental pollution as well as health hazards by contaminating the food chain.
Host plant resistance has the potential to be an alternative for effective, economic
and ecofriendly means of pest management in rice independent of pesticide use. The
resistance of rice plant to biotic stresses may be an inherited one (Resistant through
donor) or it may be induced by application of an elicitor, activating the defense
mechanism of the plant.
Resistant sources/donors are most important as they are the key to success of
resistance breeding for developing pest resistant varieties. Keeping in view of the
emerging pest problems in rice and the role of resistant donors in controlling these
pests, the main objective should be to identify resistant donors against insect pests
and diseases from the vast gene pool of the country. This can be achieved by
evaluating large number of genotypes through standard screening techniques,
supported by study on their mechanism of resistance. Mechanism of plant resistance
against insects can be assured by biochemical analysis of the plant for its resistance-
imparting contents such as sugar, silica, phenol etc. as well as antixenosis, antibiosis
and tolerance studies. The resistance mechanism against diseases is to be ascertained
through study of virulence patterns. Molecular characterization of identified resistant
donors is necessary to look for the presence of resistance genes using reported
markers or identification of new genes, if any. In the case of induced resistance,
identification of effective elicitor/s is the prime need for inducing resistance in a
popular but susceptible rice variety.
2. Host plant resistance
Plant resistance is an inherited characteristic of a host that lessens the attack of a
pest, may it be the insect, disease, nematode or other organisms. As per the recent
pest management strategy through IPM, the use of resistant varieties should be the
major or syncing with other control measures. Host plant resistance provides an
efficient, economical, ecologically acceptable and safe means of crop protection.
Resistant cultivars are the most durable, economical and practical means of tackling
pest problems, being compatible with all other components of IPM. Besides
constitutive resistance, the plant resistance to pests can also be induced either by
endogenous or exogenous signaling molecules. Silicon, chitosan, plant growth
promoting rhyzobacteria (PGPRs), jasmonic acid (JA), jasmonoyl-isoleucine (JA-Ile),
salicylic acid (SA) and ethylene (ET) are some of the well known elicitors inducing
plant to put forth its resistance. These exogenous material or inducers are not directly
toxic or inhibitory to the pests but cause the plant to increase its level of resistance.
Though several donors have been identified in the past against several insects and
diseases and many varieties were developed by utilizing them, most of these donors
as well as varieties have lost their resistance in the present day scenario either due to
continuous exposure to the pest or due to development of more virulent population.
Screening data of released resistant varieties at National Rice Research Institute
(NRRI) gave an indication of gradual breaking down of their resistance.
The genotypes, still retaining the resistance are not popular among farmers due to
low yield or cooking quality or taste or are not utilized to develop new varieties due to

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their poor combining ability. Hence, identification of donors, resistant to different rice
pests, should be a continuous process to keep enough of such genotypes in store so
that the development of pest resistant varieties will be sufficient and continuous to
combat the pest situation in rice successfully. Further, the future challenge is to
exploit the elicitors of induced defense in rice for pest management especially for
borer pests. There is also a need to test the effect of foliar application of silicon on
natural enemy foraging and impact. The research should focus on studying the
integration of cultivar resistance and cultural controls, especially soil silicon
amendment, against the entire pest complex in rice.

3. STATUS OF RESEARCH
3.1. Host plant resistance against insect pests
3.1.1. Brown plant hopper: The International Rice Research Institute, Philippines
initiated studies on varietal resistance to BPH in 1966 with efficient mass- screening
techniques. The basic technique has been introduced in Japan, Korea, Taiwan, India,
Thailand, Sri Lanka, Indonesia and Solomon Island. The BPH resistant selections, IR
26 and IR 1561-228-3, were grown widely in the Philippines during 1974 and 1975.
Both cultivars have Bph1 gene for resistance. IR36 and IR38 which have the bph2
gene for resistance to BPH were released by the Philippine Government during 1976.
Varieties ASD 7 and Mudgo were resistant in the Philippines, Japan, Korea, Taiwan,
Thailand and Indonesia, but susceptible in India. The different reaction is due to
biotype formation. Biotype 1 in Southeast Asia (Philippines, China, Japan, Korea,
Malaysia, Taiwan, Thailand); Biotype 2 in Philippines, Solomon Island, Vietnam;
Biotype 3 in Southeast Asian countries (Philippines, Taiwan); Biotype 4 in South
Asian countries of India, Bangladesh and Sri Lanka are widely distributed. Afterwards,
though many resistant gene/QTLs were identified in different genotypes (Fujita et al.
2013), most of them have already lost their resistance against BPH population of
India.
Following extensive damage by BPH during mid 70s, breeding for resistance was
intensified in India which culminated in release of varieties like Jyothi in Kerala,
Sonasali, Vajram, Chaitanya in AP, Neela and Udaya in Orissa and Manasarovar
across the country. Some common donors were Ptb 33, Manoharsali, Rasi, Ptb 10, Ptb
20 etc. Afterwards, many BPH resistant varieties were released for different ecologies
all over India and were released in different states (Krishnamurthy et al. 1995). By
2006, more than 65 varieties were released with resistance/tolerance to the insect. But,
most of these varieties were developed keeping higher yield as the primary criteria
and were later found to be resistant/tolerant to BPH. Therefore, in most cases after
few years, the resistance breaks down and leading to the BPH menace. Several highly
resistant donors have been identified at NRRI, Cuttack through green house screening
according to the Standard Evaluation System during 2000-2016.
At NRRI, three thousand rice genotypes from NRRI Genetic resources were
screened for their resistant reaction to BPH under greenhouse condition during the

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years 2001 - 2016. More than 80 genotypes were found highly resistant with score 1.
Some of them are – CRRI accession numbers 35677, 35703, 34997, 35003, 35927, 35070,
35155, 35183, 35184, 35228, 35181, 34969, 34993, 34997, 35014, 38448, 38448, 38449,
38450, 38452, 38459, 38469, 38500, 38530, 38552 and 38552C. One hundred lines, evolved
from resistance breeding for BPH in the background of resistance from Salkathi
(CR.Ac.35181) and Dhobanumberi (CR.Ac.35184), 10 lines were highly resistant with
score ‘1’ whereas 36 lines showed resistance of score ‘3’. The lines are : CR 2711-76,
CR CR2712-22711-114, CR 2711-139, CR 2711-149, CR2712-2, CR 2712-11-1, CR 2712-
11-13, CR 2712-229, CR 2713-8 and CR 2714-2, out of which CR2711-114, CR 2711-76,
2711-139, CR 2711-149 and CR2712-2 were found highly resistant (Jena and Sahu,
2013). Out of seventy entries from IRRI screened at NRRI, IR69726-29-1-2-2-2, IR70454-
144-1-1-3-2 and IR72894-35-2-2-2 were found resistant. Out of 220 released varieties,
IR-64 MAS and Hazaridhan scored ‘1’ whereas CR-1980-1, Lalat MAS and Satyakrishna
showed resistance of score ‘3’. Six hundred farmers’ varieties of Odisha were evaluated
and 21 were highly resistant (Jena et al. 2006; 2015).
Molecular approach for BPH resistance was initiated at NRRI with a DBT sponsored
network project on “Identification and Functional Analysis of Brown Planthopper
Resistance Genes in Rice”. Under the programme, mapping population was developed
from the cross TN1/Salkathi. Phenotyping was made of 300 RIL populations under
artificial infestation conditions and the putative QTLs associated with the resistance
to BPH were identified (Mohanty et al. 2017).
The line CR2711-76 is also found to be resistant to multiple pests of rice (AICRIP
Report 2012-13) and having the resistant gene Bph 31 (Prahalada et al, 2017). Three
accessions of IRRI Philippines, IR 73382-80-9-3-13-2-2-1-3-B (IR 64 x O. rufipogon), IR
75870-8-1-2-B-6-1-1-B (IR64 x O. glaberrima) and IR77390-6-2-18-2-B (IR69502-6-SRN-
3-UBN-1-B x O. glaberrima) were found highly resistant against NRRI population of
BPH . After being used in popular varieties like MTU 1010 and Swarna, three lines
each from F3 lines of MTU1010/Swarna x IR 75870-8-1-2-B-6-1-1-B were highly resistant
against BPH. Four genotypes from Assam Rice Collection (ARC), ARC - 333, 356,
11324 and 11309 were also found highly resistant. Two accessions of doubled haploid
lines were highly resistant.
3.1.2. White backed planthopper: In general white backed planthopper (WBPH) has
not received as much research attention as BPH. However, 14 loci have been identified
for WBPH resistance. Since, it mainly occurs as a mixed population with BPH,
identification of single resistant donor is as important as identification of common
resistant donors for both. At IRRI, two resistant genes, Wbph7 and Wbph8 has been
identified from O. officinalis. Four varieties, IR48, IR52, IR60 and IR62 were reported
as moderately resistant. More than 300 cultivars resistant to WBPH have been
identified and 80 of them have been analyzed geneticlly (Brar and Khush, 2009). Four
donors (N22, ARC 10239, ADR 52 and Podiwi A8) have been identified at IRRI and
used to develop hopper resistant varieties. Several genes/QTLs have been identified
for resistance to the pest (Fujita et al. 2013).

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In India, O. officinalis, O. punctata, and O. latifolia showed high levels of

resistance to the pest. IR 2035-117-3 has been used in breeding programmes for S.
furcifera resistance (Padmavathi et al. 2007). Antibiotic Mechanisms of resistance to
S. furcifera include reduction in feeding on the resistant cultivar Rathu Heenati could
be attributed to the presence of certain water-soluble inhibitors in the plant. Low
chlorophyll, low sugar, low amino acid and high phenol content in the plant had
contributed for the resistance.
At NRRI, 167 rice genotypes from NRRI rice genetic resources and Punjab
Agricultural University (PAU) were screened under net house condition. The
genotypes IR 64 and TN1 were used as resistant and susceptible checks, respectively.
The entries IC568061, AC 111, AC 1066, AC 1073, AC 124, AC 1418 were found highly
resistant with score ‘1’ whereas 1552(2) and 1552(8) from PAU, IC567998, IC568060,
IC568065 and IC568082 were of score ‘3’. From 65 accessions reported resistant earlier
against WBPH at NRRI, only four accessions, i.e., AC 34222, AC 34264, AC 38468 and
AC 42425 were highly resistant at present against WBPH.
3.1.3. Yellow stem borer: Out of 17000 accessions screened against YSB at IRRI upto
1987, only about 40 O. sativa accessions and 80 wild rice accessions were found to
have resistance against yellow stem borer. From India, CO 7, CO 15, CO 21, Ratna,
TKM 6 and WC 1263 were identified as donors. Efforts were made to develop resistant/
tolerant varieties by using donors such as TKM6, CB 1, CB2 but none were good
combiners to produce desired level of resistance. Still, some accessions showed
moderate level of resistance which needs further evaluation. TKM 6 was found tolerant
against striped stem borer, Chilo suppresalis and was utilized in breeding programme.
The cultivars IR 36 developed at IRRI and Ratna developed at NRRI were having
highest level of resistance.
Thousands of entries have been screened at NRRI against yellow stem borer
(YSB). But most of them succumbed to the pest after continuous exposure for 2-3
years. One tropical japonica line WC-152 and a doubled haploid line SS-5 showed
zero SES score against YSB in consecutive two years of screening against the
susceptible check TN1 with damage score of 5. The inherent capacity of the pest to
adopt a variety after 2-3 years exposure as evident from the screening data of NRRI
for the past several years has not left avenue till now for choosing a highly resistant
donor. Seven hundred and ten rice cultivars from NRRI that were evaluated against
YSB in 2007, resistant cultivars with score 1 (below 5% white ear head) were NDR 402,
CR 580-5, LPR 256, LPR 85, LPR 14, LPR 96-10,LPR 56-49, LPR 50, Kariawa 4, TCA 12,
Bazail 65, Nali Hazara, Janaki, OR 1358-RGA-4, OR 1529-28-2, TKM 6, ARC 10660,
Litipiti, Daonara, Chadhei Nakhi, Dahijhil, Brahmanbojni, Mahalakshmi, Jogen, Punshi,
Triveni and Saket-4 as against Jaya the susceptible check with score 9 (28.1% WEH).
Those are to be screened again for confirmation of resistance.
3.1.4. Gall midge: Wide spread cultivation of some of the resistant varieties carrying
a single resistance gene has led to evolution of virulent populations, known to as
biotypes, that are capable of overcoming the resistance. Existence and emergence of

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new and virulent biotypes of the rice gall midge resulted in the breakdown of resistance
in many of the popular gall midge resistant varieties. So far, 11 resistance (R) genes
(designated Gm1 through Gm11) have been identified from different rice varieties
(Himabindu et al. 2010). Seven distinct gall midge biotypes, differing in their virulence
against these R genes have been reported (Vijaya Lakshmi et al. 2006). Using three or
four of these sources of resistance, more than 60 gall midge-resistant rice varieties
have been developed and released for commercial cultivation since 1975 (Bentur et al.
2003). Improved rice varieties carrying Gm1 or Gm2, however, have lost their resistance
against gall midge in most of the rice growing areas. Exceptionally, varieties deriving
resistance from Ptb21 have displayed resistance against five of the seven biotypes as
per AICRIP report, 2006. Keeping this in view, thorough screening of various available
rice germplasm is necessary in order to get new source of resistance.
Systematic evaluation of germplasm by NRRI for gall midge resistance during the
1950s - 1970s at hot spots such as Cuttack and Sambalpur in Odisha and at Warangal
in Andhra Pradesh under field conditions resulted identification of sources such as
Eswarakora, Ptb 18, Ptb 21, Siam 29, and Leuang 152 . Some accessions of wild species
of Oryza such as O. brachyantha, O. coarctata (now Porteresia coarctata), O.
eichingeri, O. granulata, and O. ridleyi were reported to be gall midge resistant.
None of the donors displayed resistance against all the six biotypes. Only
Orumundakan was resistant against 5 biotypes. Ptb 27, Dhanala 27, Ptb 18, Ptb 21,
ARC 5959 and 22 other accessions were reported resistant at NRRI during1964, 1965
and 1974. Also studies prior to 1975 suggested the prevalence of biotype 1 at NRRI as
differentials W1263 (with the Gm1 gene) and Leuang152 (Gm2) were resistant.
Subsequently, this population evolved into biotype 2 by acquiring virulence against
resistance conferred by the Gm1 gene. The present study shows resistance of W1263
whereas phalguna and ARC 5984 were susceptible. In recent years, all the known
gene differentials of gall midge having resistant genes 1, 2, 3, 4, 5, 6,7, 9,10 and 11
showed susceptible reaction to NRRI gall midge population (Biotype 2), either showing
breakdown of resistance or indicating a population change which is a researchable
issue.
3.1.5. Leaf folder: The rice leaf folder has recently emerged as an important insect
pest of rice in many Asian countries under changed climatic scenario. Management
of the pest with insecticides is becoming costly and there are reports of resurgence.
So, there is a need for the development of resistant cultivars to minimize the yield
losses. In India, the varieties like GEB 24 (a mutant of Konamani) and TKM6 , Ptb 33
were reported as resistant to leaf folder (Punithavalli et al. 2013). Similarly, TKM6,
GEB24, CO7, PTB33, ARC10982, Shete, Bir-Me-Fen, Kaohsiung Sen Yu 169, O.
rufipogon and O. brachyantha were reported as resistant genotypes. However, Ishaq
A. (2014) observed that Kaohsiung Sen Yu 169 was susceptible, TKM6, Ptb 33 and
GEB24 were moderately susceptible and only ARC10982 was moderately resistant
against leaf folder. Likewise, Genotypes like CR 56-17 and its donor parents GEB-24,
CR 190-103 and 294-548,Bundei, Harisankar, Sunakathi, Surjana, Juli and Sana chinamala
and Chandanpedi were identified as resistant varieties at NRRI during 1985 to 1998.
Genotypes such as RP 1746-1770-209; RP 2542-179-298; ARC 11281; RP 2543-136-

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277; RP 2572-3-340; RP 2572-5-342; RP 2572-24-7 were relatively less susceptible

while IR 8, IR 5 and TN 1 were highly susceptible. Three hundred sixty entries screened
for resistance against leaf folder under field condition showed AC 42738, IC 569085,
IC 569017 with less than 1% leaf damage and Konark, Rudra and Mahalakshmi had
less than 5% damage against 12.5% leaf damage in susceptible check TN1.Using the
biotechnological tools, two transgenic rice lines, expressing Cry1Ab, CpTI and Cry1Ac
showed significantly lower damage at different developmental stages. Further, studies
on mechanism of resistance need to be conducted to confirm either a tested rice
variety/line is resistant or susceptible to the pest.
3.1.6. Stored grain pests: There is common belief that the aromatic fine rice varieties
are more susceptible to insect attack. Khan and Halder (2012) reported Kalijira, an
aromatic fine rice variety (locally known as polao rice), to be less infested by the rice
weevil. The degree of susceptibility of the rice varieties from the highest to lowest
susceptibility was Lata (755) > Nazersail (695) > Minicate (654) > Pariza (482) >
Kataribhog (456) > Kalijira (402). Parboiled rice varieties were reported to be more
susceptible to stored pest infestation (Islam 2007).
At ICAR-NRRI, out of 20 rice varieties screened against S. cerealella multiplication,
only Annada showed tolerant reaction upto 90 days. Other varieties like Heera, Kalinga
III, Vandana, Sattari, Sneha, Dhaula, Naveen, Jaya, Indira, Saket-4, Tara, Kalinga III,
Pooja, Panidhan, Pusa Basmati-1, Basmati 370, Durga and Ratna were susceptible and
Tapaswini was highly susceptible to storage insects. So far many scientists in different
countries have sorted out countless varieties of cereals resistant against S.cerealella
to incorporate useful information in breeding programme.
3.1.7. Induced resistance: Silicon amendment conferred resistance to the rice leaf
folder (Han et al. 2015), by increased leaf abrasiveness against Spodoptera exempta
and Schistocerca gregaria. Nanosilica and Jasmonic acid were found to be effective
in controlling the pests like army worm (Stout et al. 2009). Soil incorporation of Si and
K present in fly ash mitigated the incidence of the rice stem borer, soil application of
Si reduced the percentage of white head caused by Chilo partellus in Parto cultivar
(Hosseini et al. 2012) and enhanced plant resistance to BPH (Yang et al. 2017). The
induced resistance by JA did not produce any phytotoxicity (Senthil-Nathan et al.
2009). Methyl Salicylate (MeSA) at 100 mg L-1 exhibited greater mortality against rice
leaf folder (Kalaivani et al. 2017).
3.2. Host Plant Resistance against Diseases
3.2.1. Blast: Yang et al. (2017) screened 358 rice varieties for the presence of 13 major
blast resistance (R) genes against M. oryzae using functional markers out of which
259 varieties were having one to seven R genes. Twenty-six SSR markers associated
with blast resistance in a set of 276 indica landraces from China and few from different
parts of the world were reported. Genome wide association mapping (GWAS) identified
16 LAFBR and 20 resistant cultivars with seventy-four candidate genes, which encode
receptor-like protein kinases, transcription factors, and other defense-related proteins
(Zhu et al. 2016). The identified markers associated with blast resistance can be

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validated for their effectiveness in a variety of genetic backgrounds and can be
helpful in the pyramiding of QTLs from different sources through marker-assisted
selection.
The genetic diversity for eight resistant genes against rice blast, was assessed in
landrace collections of Manipur, India and the presence of six to seven genes in rice
accessions from the North Eastern state of Manipur was related to high level of
resistance (Mahender et al, 2012). The rice blast resistant Pi9 gene was analyzed in 47
rice germplasm using the dominant STS marker 195R-1/195F-1 derived from the Nbs2-
Pi9 candidate gene and only six were positive for the Pi9 gene (Imam et al. 2013).
Molecular screening of Pi2 gene was carried out on 61 landraces of rice using gene
based marker NBS2P3 and NBS2R derived from Nbs4-Pi2 candidate gene that generates
a monomorphic band of 1.8 kb. Restriction digestion of PCR product with EcoR1
enzyme, however, revealed polymorphism between susceptible and resistant lines.
Out of 61 landraces, only five landraces had Pi2 gene type banding pattern. The five
landraces positive for Pi2 gene are from Sikkim and Jharkhand (Alam et al. 2015).
Phenotyping followed by genetic diversity study at NRRI, of eighty rice varieties
released by the institute, has been completed using molecular markers linked to twelve
major blast resistance (R) genes viz. Pib, Piz, Piz-t, Pik, Pik-p, Pikm Pik-h, Pita/Pita-2,
Pi2, Pi9, Pi1 and Pi5. Out of which, nineteen varieties (23.75%) showed resistance and
twenty one were moderately resistant (Yadav et al. 2017). Among the 1314 germplasm
accessions (ICAR-IIRR, NBPGR) evaluated for leaf blast resistance at Hazaribagh, 19
accessions (IC no. 245865, 246277, 246403, 246274, 454167, 121865, 199562, 218270,
245927, 246012, 246228, 246273 and 246659) were highly resistant (SES scores 0, 1, 2).
3.2.2. Bacterial blight: The most effective resistance gene Xa 21 was reported from
wild rice by Ikeda et al. (1990), which was effective against all the races of Xoo in
India. Long-term cultivation of rice varieties carrying single resistance gene has
resulted in a significant alter in pathogen-race frequency and consequential breakdown
of resistance. An example of this is failure of Xa4 which was integrated widely in many
high yielding varieties of rice via conventional breeding. Extensive cultivation of
varieties carrying Xa4 has lead to the predominance of Xoo races that can overcome
resistance conferred by this gene. One concrete solution to resistance breakdown is
pyramiding of multiple resistance genes in the background of modern high yielding
varieties. More than 36 resistance genes have been identified and designated in a
series from Xa1 to Xa41 till now. The effectiveness of R genes varies over locations
due to geographical structuring of the pathogen.
Oryza barthii found to have resistance against most of the races of Xoo in India
especially in the Eastern India. Works at NRRI, reported BR-4-39-51-2, BR-51-49-6,
IR3796-14-2, ARC-5925 & ARC 5943 as highly resistant and another 50 lines as resistant
to BLB kresek phase. A total of 5000 lines were screened for bacterial blight resistance
and 50 were resistant. Some of them are AC 36797, 35799, 36370, 36362, 35720, 36357,
36253, 35734, 36369, 35719, 35740, 36283, 35714 and 36294.
3.2.3. Brown spot: Three QTLs, qBS2, qBS9 and qBS 11 had been identified against
the disease in cultivar Tadukan with latest qBS 11 having major effect (Sato et al.

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2008). Satija et al. (2005) identified 15 Oryza sativa entries out of 124 classified as
resistant (less than 5% severity). Conversely, Hossain et al. (2004) identified one
resistant line out of 29 entries. Goel and Bala (2006) evaluated 219 wild rice accessions
with diverse origin belonging to 15 Oryza species encompassing all the six genomes
for their resistance to brown leaf spot and found that 15 lines were resistant while 78
lines were moderately resistant.
Synthesis of polyphenols and their oxidation products were observed to be
associated with the phenomenon of resistance. A high correlation has been existing
between the levels of phenols, lignin, flavonoids, silicon and oxidative enzymes in
rice leaf tissue and the susceptibility of rice lines Giza 180 and Arabi to brown spot.
However, Katara et al. (2010) identified 10 QTLs, some of which may be common to
those of Sato et al.
Work at NRRI revealed that, Out of 573 Assam rice collections (ARC) screened
against brown spot disease of rice, only 22 accessions were found moderately
resistant. Those are ARC – 5846,5918, 5956, 5550, 6017, 6058, 6101, 6110, 6170, 6622,
7080,7335, 10618, 10670, 10922, 10934, 11206,11434,11566, 11641, 11679 and 12006.
3.2.4. Sheath blight: Many workers employed various methods for testing varietal
resistance against this disease including (i) field tests using artificial inoculation (ii)
seedling test (iii) inoculation at different stages of plant growth (iv) tests in pots and
(v) sheath inoculation test. The results showed that, tall varieties with a few tillers
were more resistant than short varieties with many tillers and resistant genes were
located in tall varieties. In comparison with field ShB evaluation, the controlled chamber
or mist-chamber assays were simple, precise and more reliable methods in tagging
sheath blight resistance. Two wild rice species viz. Oryza australiensis and O. nivara
were resistant against R. solani. Among different red (Oryza sativa) and wild rice (O.
alta, O. lativa, O. grandiglumis and O. glubepatula) populations, none were found
resistant (Santos et al. 2002).
Work at NRRI revealed that, A tolerant donor CR 1014 has been identified for
disease, which has been utilized for developing mapping populations and transferring
the tolerance gene to mega variety ‘Swarna’. So far, out of 604 farmer’s varieties from
different parts of Odisha were screened by found that 31 varieties were found
moderately resistant, 56 varieties showed tolerant reaction. A total of 90 NRRI released
varieties were screened and 14 were moderately resistant and 16 were tolerant. Farmers
varieties such as Biradia Bankoi, Dhusara, Ganjamgedi, Kalaketiki, Panikoili, Rajamani-
K, Latamahu, Kendrapara-Kalama, Pasakathi, Tulasimali,Gangabhalu, Kandhamal-
Jhalaka, KanakChampa, K-Balisara-LaktiMarchi, LaxmiVilash, Magra-P, Bolangir-
Baidipali-Mahipal found moderately resistant/tolerant and NRRI varieties CR-1014,
IR 64 MAS,CR Dhan-306,CR Dhan-601, CR Dhan-701, Kalinga-III, Satyakrishna,
Gayatri, Reeta, Utkalprava, Geetanjali, Hanseswari, Binadhan 8, Varsadhan, Wita 9
found moderately resistant/tolerant. During 2012-13, 17 genotypes namely, Tapaswini,
Annapurna, Swarna, Swarna sub 1, Tetep,CR 1014,ADT 39, Manasarovar, IET 19346,
IET 20443, IET 19790, IET 20252, IET 17885, IET 17886, IET 19140, IET 20755 and IET
20216 were screened against the disease and results showed one genotype, CR 1014

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as moderately resistant, four genotypes Tetep, Manasarovar, IET 17886 and IET
20443 as tolerant and rest twelve genotypes were susceptible to highly susceptible.
3.2.5. False smut: The resistance of rice genotypes to false smut under natural disease
incidence was reported by various workers. Out of the seven rice genotypes screened,
IRAT 170 was highly resistant, Ex-China was resistant (disease severity score < 1% to
false smut), ITA 316 was moderately resistant (disease severity score <5%). Genotype
ITA 150 was susceptible, while ITA 315, ITA 335, and FARO 3 were highly susceptible
with disease severity scores >20%. The resistance level of Japonica type ranged from
20.37 to 92.90%, whereas, resistance level of Indica rice ranged from 68.15 to 83.21%.
Also hybrid rice showed similar Indica rice behaviour whereas their resistance level
ranged from 66.82 to 81.88% (El-Shafey 2013).
Seven varieties viz., Ptb 7, Ptb 23, Ptb 24, Ptb 32, Ptb 36, Ptb 42 and Ptb 46 were free
from disease when screened under field condition (Raji et al. 2016). Out of 20 varieties
screened, the varieties Harsha and Vaishak were found highly resistant and Makom,
Thekkancheera, Pavizham and Karthika were resistant and Kanakom, Revathi and
Prathyasha showed moderate resistance to the disease (Rashmi et al. 2016). Works at
NRRI revealed that, Ranjit and Luna Suvarna, were free from infection. Whereas CR
Dhan 907, CR Dhan 303, Nua Kalajeera, Ketakijoha, Nua Dhusara, Nua Chinikamini
have exhibited moderate resistance against false smut pathogen.
3.2.6. Bakanae: Rice materials carrying dwarf (d1) and semi-dwarf (d29, sd6 or sdq(t))
genes are useful in resistant breeding program. Recent studies have reported thirteen
genotypes with moderate or high resistance, five genotypes with medium resistance,
and one genotype with moderate resistance, respectively. Fiyaz et al. (2016) reported
eight highly resistant, four resistant, thirty-three moderately resistant genotypes
through high throughput screening protocol. Moreover, using inclusive composite
interval mapping, three quantitative trait loci, qBK1.1, qBK1.2, and qBK1.3, regulating
resistance of rice basmati to Fusarium fujikuroi were reported. Two quantitative trait
loci (QTLs) on chromosome 1 and 10 were found by an in vitro evaluation of the
Chunjiang 06/TN1 DH population (Yang et al. 2006). Despite of the necessity of
identifying resistance genes and the underlying mechanisms of resistant varieties
developed, genetic studies on bakanae disease resistance in rice need to be exploited.
3.2.7. Sheath rot: Sixty deep water rice entries were screened to sheath rot disease
and reported the cultivars viz., MDR40049, CN 1035-61 and OR-090-3-158 as resistant
with less than one percent infection. Of the rest, 32 showed moderate resistant and
other 25 showed moderately susceptible reaction. Sahu and Parida (1997) studied the
response of 60 rice breeding lines against sheath rot. Out of 60 lines tested, three lines
were highly resistant, 18 were resistant and 33 were moderately resistant to the disease.
Seed inoculation of rice varieties like BPT-5204, MAS-26 and MAS 946-1 by soaking
of seeds in conidial suspension (105 condial ml-1) of S. oryzae overnight was
standardized by Mahadevaiah et al. (2016). Twenty aromatic rice genotypes were
screened against sheath rot of rice. Less disease incidence were recorded viz., Boga
Jalsi, Boga Joha, Monika madhuri Joha, Tulsi Joha, Goul poriya Joha, Bokul Joha

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Monipuri Joha, Keteki Joha, and higher disease incidence were recorded viz., Kameni
Joha, Badshabhog, Jalsa Joha, Krishna Joha (Singh and Das 2015).
Inspite of the efforts at NRRI for last several years, the availability of resistant
genotypes for rice pests at present is very scanty except for BPH, blast and BB (Table
1). Therefore, we should continue evaluating genotypes to obtain resistant donors
for other pests, particularly for YSB and sheath blight, which are of economic
importance. Further, there is a need to evaluate previously identified genotypes against
different pest ecotypes, which may vary in reaction.

Table 1. Status of resistant genotypes identified against rice pests at NRRI, Cuttack.
Insect/Disease Source R/HR* genotype MR
BPH NRRI gene bank, breeding >60 -
lines of NRRI, IRRI
WBPH NRRI gene bank 07 -
Gall Midge NRRI gene bank, 10 01
Yellow stem borer NRRI gene bank - 03
Bacterial blight NRRI gene bank 43 -
Rice leaf Blast NRRI gene bank 35 -
Brown spot NRRI gene bank - 03
Sheath blight NRRI gene bank - 02
False smut NRRI gene bank 02 06
Tungro NRRI gene bank - 09
Angoumois grain moth NRRI gene bank - 01

4. KNOWLEDGE GAPS
Most of the varieties are developed keeping higher yield as the primary criteria
and were later found to be resistant/tolerant to pests like BPH. Therefore, in most
cases after few years, the resistance break down occurred leading to the havoc of
BPH menace. Several resistant donors were identified through screening, but the
detail of the mechanism operating for resistance is not worked out properly including
molecular basis of resistance. Though several resistance loci have been reported for
different pests, most of these are difficult to use during marker-assisted selection due
to thorough resolution of some genetic analyses, limited access to donor varieties,
and the widespread virulence of insect pests and diseases against certain resistance
genes. Resistant donors for most of the necrotrophic pathogens as well as insects
such as YSB, leaf folder, case worm and gundhi bug are not yet fully explored.
Phenotyping, genotyping, mapping, cloning and characterization of resistance genes
against emerging insect pests and diseases are yet to be done. Identification of broad
spectrum and durable resistance genes against major insects and disaeses are to be
continued. Gene pyramiding to combine major R genes against multiple diseases is to
be studied properly along with its impact on crop yield. There is a need to understand
the relative importance of both physical and biochemical defense mechanism of plant
against insect pests and diseases under induced resistance by different plant elicitors

Exploring New Sources of Resistance for Insect Pest and

Diseases of Rice 377
in rice. This is important for the pests where resistant donors are still lacking.
Resistance of the rice varieties (Seeds) to the infestation of stored insect pests is to
be exploited for reduction of infestation and also for formulating better storage options
for susceptible varieties.

5. RESEARCH AND DEVELOPMENT NEEDS

The first and foremost need is to screen a vast number of germplasm against
insect pests and diseases under high pressure to identify resistant donors. The
mechanism of plant resistance for each identified donor must be understood,
particularly against insects through biochemical, antixenosis, antibiosis and tolerance
study. Characterization of identified resistant donors for presence of resistance genes
using reported markers and identification of new genes, if any. The expression of
defense enzymes should be studied in susceptible and resistant lines, particularly,
studying the regulation of defense related genes.
The research should be focused to formulate strategies for improving rice pest
resistance through genetic studies, plant-pathogen interaction, identification of novel
R genes, development of new resistant varieties through marker-assisted breeding
for improving rice insect pest and disease resistance in India and worldwide.
Genotyping of resistant lines should be attempted by using SSRs, SNPs, and allele
mining for major resistance genes. Evaluation of the elicitors must be taken up for
induced defense in rice for pest management especially for borer pest and simultaneous
identification of genes responsible for defense. There is also a need to test for the
effects of foliar deposits of applied silicon on natural enemy foraging and impact. The
research should focus on studying the integration cultivar resistance and cultural
controls, especially soil silicon amendment, against the entire pest complex in rice. It
is necessary to know the resistance/susceptibility of stored rice varieties to the
infestation of insect pests, particularly to Sitophilus oryzae and Sitotroga cerealella
(Olivier), their occurrence and damage pattern under different storage conditions.
Resistant genotypes may be grown in pest endemic areas to assess their performance
under different environmental conditions.

6. WAY FORWARD
Exploring genetic diversity of rice cultivars for the presence of brown plant hopper
(BPH) resistance genes through screening of vast germplasm available at NRRI and
National Bureau of Plant Genetic Resource (NBPGR) will pave the way for resistance
breeding. At the same time, the valuable resistant genotypes already identified through
phenotyping and genotyping should be utilized to develop resistant varieties. They
are to be tested also for their reaction against other pests to obtain a multiple resistant
donor/variety. Since the susceptibility of rice genotypes to the infestation of stored
grain pests depends on the combination of many factors like grain hardness, nutritive
value, and natural resistance etc., studies are to be undertaken on these areas for
different popular varieties which occupy a greater space in national storage system.

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In addition, the factors comprising grain size and moisture content in rice might be the
reasons of severe infestation by the rice weevil population. These factors should
also be studied along with their management strategies. Important pests and diseases
like YSB, leaf folder, gundhi bug, sheath blight, brown spot etc., where resistant
genotypes are not available yet, induced resistance work should be in progress for
immediate protection of the plant.
The gene/QTL conferring resistance should be identified for further utilization in
marker assisted selection of resistant varieties which will quicken the process of
varietal development. Although incorporation and utilization of resistance to major
rice diseases have succeeded globally, with the currently available biotechnological
tools, it is feasible to identify major R genes as well as quantitative trait loci (QTLs)
conferring high level of partial resistance and achieve nearly complete resistance
against the major and emerging rice diseases.
Identification of donors needs a systematic and continuous evaluation of
genotypes for ascertaining their durable reaction. The identified donors can be utilized
as genotypes themselves or can be utilized in a breeding programme to develop
resistant varieties, may be for a single or for multiple pests. This is the most effective
and economic way of pest management system in rice to reduce production cost of
farmers as well as pesticide load from the environment.
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Bio-ecology of rice insect pests and diseases:
Paving the way to climate-smart rice protection
technologies

SD Mohapatra, Raghu S, Prasanthi G, MS Baite, Prabhukarthikeyan

SR, MK Yadav, Basana Gowda G, Guru P Pandi G, A Banerjee,
S Aravindan, NB Patil, S Chatterjee, S Lenka, Rajasekhara Rao K,
AK Mukherjee, MK Bag, PC Rath and M Jena

SUMMARY
The insect problem is accentuated in intensive rice cropping where the insects
occur throughout the year in overlapping generations. In India, about a dozen of
insect species are of major importance in rice but the economic damage caused by
these species varies greatly from field to field and from year to year. Insect pests
cause about 10-15 per cent yield losses. Estimation states that farmers loose an
average of 37% of their rice crop due to insect pests and diseases every year. This
chapter focuses on literature generated on various aspects of rice insect pests, diseases
viz., pest status and their distribution, bio-ecology, diversity, forecasting model for
real-time pest-advisory services, hyper-spectral remote sensing in pest damage
assessment, impact of climate change on insect biology, population structure and
epidemiology of different rice diseases.

1. INTRODUCTION
The rice plant is an ideal host for large number of insects and pathogens right
from nursery to harvest, but only a few of them are considered to be the serious pests
those cause economic losses by minimizing the attainable yields. About 800 insect
species attack rice starting from their production to consumption and the rest are all
friendly insects. Both the mature and immature stages of insect damage rice plants by
chewing leaves and root tissues, boring and tunnelling into stems or sucking sap
from stems and grains. The injury from feeding leads to damage showing symptoms
of skeletonized and defoliated leaves, dead hearts, white ear heads, stunted and
wilted plants and unfilled grains. Ultimately insect damage affects the plant physiology
leading to reduction in measurable yield, utility or economic return.
In India, about a dozen of insect species are of major importance but the economic
damage caused by these species varies greatly from field to field and from year to
year. These species include stem borers [yellow stem borer (Scriphophaga incertulas),
white stem borer (Scirphophaga innotata), pink stem borer (Sesamia inferens),
stripped stem borer (Chilo polychrysus), dark-headed stem borer (Chilo suppressalis)],
leaf folder (Cnaphalocrocis medinalis (Guenee), brown planthopper (Nilaparvata
lugens Stal.). In addition, species distribution and abundance vary among rice

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382 climate-smart rice protection technologies
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ecosystems within a given ecology. For

example, termites are primarily upland rice
feeders while others are more numerous and
damaging under lowland conditions. Some
species like yellow stem borer, leaf folder,
brown plant hopper may be abundant in all
rice-growing environments. Among the
biotic stresses insect pests cause about 10-
Fig. 1. Estimated yield losses due to 15 per cent yield losses. At National level,
different insect pests in rice in India stem borers accounted for 30% of the
(Modified from http://www.rkmp.co.in losses, while planthoppers (20%), gall midge
(15%), leaf folder (10%) and other pests
(25%) accounted for rest of the losses (Krishnaiah and Varma, 2018) (Fig. 1).
Among the various diseases reported, blast, bacterial blight, sheath blight, stem
rot, brown leaf spot and false smut were recorded to be the significant ones. Of these,
the sheath blight, bakane and false smut became important only after the green
revolution. Some of the diseases appeared in few pockets became major constraints
are sheath rot, seedling mortality by Sclerotium rolfsi. Primary source of inoculum are
internally seed borne, bacterial blight, blast, brown spot, sheath rot (fungal and
bacterial), seedling elongation, foot rot, seedling rot by F. moniliforme; externally
seed borne or as admixture in seed are sheath blight, false smut, seedling blight by
Sclerotium rolfsi. Some of the soil borne diseases are seedling elongation, foot rot
and seedling rot by F. moniliforme; sheath blight, false smut, seedling blight by
Sclerotium rolfsi. Besides the above, all the diseases may spread through collateral
host/stubbles of infected plant/diseased plant parts left in the field. Collectively, rice
diseases result in yield reductions of 10-15% in tropical Asia.
Crop losses due to arthropods, diseases and weeds across the world have
increased from about 34.9% in 1965 to about 42.1% in the late 1990s and the trend is
very alarming. Indian farmers face many biotic constraints in their mission to increase
rice production. This chapter focuses on literature generated on various aspects of
rice insect pests, diseases viz., pest status and their distribution, bio-ecology, diversity,
use of hyper-spectral remote sensing in pest damage assessment, impact of climate
change on insect biology, population structure and epidemiology of different rice
diseases.
Biodiversity conservation has always been major concern and in recent research
on this theme has been directed to areas under direct human influence such as
agricultural areas where biodiversity performs important functions for productivity
through recycling nutrients, regulating the micro-climate and the hydrological
processes (Mohapatra 2014). Majority of rice pests are controlled by a complex and
rich web of predators and parasitoids that live in or on the rice plant, rice water or soil.
The techniques to enhance the biodiversity will enable us to better utilizing the
ecological engineering method and opportunities for biodiversity conservation
associated with rice fields. There is a need to develop forewarning system, which can

Bio-ecology of rice insect pests and diseases: Paving the way to

climate-smart rice protection technologies 383
provide advance information for outbreak of insect pests and diseases. Limitation of
forewarning model for specific geographic locations could be overcome by the use of
satellite-driven weather and agromet data. Resultant systems shall enable appropriate
agro-advisory to minimize application of chemical pesticides, losses due to insect
pests and diseases, financial burden and environmental cost. Remote sensing gives
a synoptic view of the area in a non-destructive and non-invasive way which could
be effective and provide timely information on spatial variability of pest damage over
a large area. The role of hyperspectral remote sensing in pest surveillance can guide
scouting efforts and crop protection advisory in a more precise and effective manner.
A successful pest management plan requires information about a species biology
and lifecycle, how it interacts with other species. One pathogen lesion on one leaf
does not have a significant economic or ecological impact, however, during an epidemic
case even a single lesion leads to causes significant crop loss involves thousands or
millions of infections to their host plants. Epidemiology focuses on disease
progression, the multiplication of pathogen population through time and the movement
of pathogen population from plant to plant. Hence, it is important to understand the
population biology and epidemiology of pathogen in order to develop rational control
strategies.
To manage the above problems, the present chapter is discussed on the four
objectives.
i. Studies on the faunal diversity viz., insect pests, soil arthropods and natural
enemies in different rice ecologies
ii. Standardization of hyperspectral signature for candidate pests and develop satellite
based fore-warning model for major rice pests
iii. Studies on the population structure of pathogens in different rice ecologies
iv. Studies on the epidemiology of major and emerging rice diseases
1.1. Faunal diversity in rice field
Rice fields together with their contiguous aquatic habitat and dry land comprise
changing ecotones, harboring a rich biological diversity, maintained by rapid
colonization as well as reproduction and growth of organisms. The variety of
organisms inhabiting rice ecosystems includes micro, meso and macro invertebrates
(especially arthropods) inhabiting the vegetation, water and soil sub-habitats of the
rice fields. In addition, many species of amphibians, reptiles, birds and mammals visit
the rice fields for feeding from surrounding areas and are generally considered as
temporary or ephemeral inhabitants (Bambaradeniya et al. 1998). In relation to the rice
crop, the fauna and flora in rice fields include pests, their natural enemies (predators
and parasitoids) and neutral forms.
1.2. Lowland rice ecosystem
The rice plant is a host for insects as diverse in their feeding habit as polyphagous
grasshoppers and the virtually monophagous white backed plant hopper, Sogatella

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384 climate-smart rice protection technologies
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furcifera. Chakraborty et al (2016) profiled

the arthropods from the rice field of Upper
Gangetic Plain of West Bengal revealed
that that herbivores (41%) topped the list
followed by predators (21%), parasitoids
(16%), detrivours (13%) and plankton
feeders (9%). In predatory guild, spiders
Fig. 2. Abundance of arthropod natural were dominant group occupied over 41%
enemies in rice at Upper Gangetic Plain of followed by Coleoptera (29%), Hemiptera
West Bengal (8%), Odonata (8%), Diptera (5%),
Hymenoptera (6%) and Neuroptera (2%)
in descending order (Fig. 2). On-farm IPM trial on rice conducted in rainfed low land
ecosystem in the Pipili block of Puri district in Odisha revealed that under IPM regime,
predator like damsel fly, ground beetle (Paedarus sp.), spiders (Pardosa
pseudoannulata, Tetragnatha sp., Neoscana theisi) and mirid bugs were more
compared to farmers’ practice. The same trend was observed in case of parasitoid
complex comprising of Apanteles sp. and Cardiochiles sp. (Mohapatra et al. 2016).
Diversity indices of insect pests and natural enemies differed according to different
cultural practices, ecologies and crop growth stages. The highest abundance was at
reproductive stage and lowest was at mid tillering stage. They also found that
transplanted rice fields are richer both in
species diversity and species richness.
Bakar and Khan (2016) reported that early
tillering stage showed higher diversity in
terms of diversity index (1.48) compared
to other three stages (Fig. 3).
Evenness was also highest in the same
stage (0.826) indicating the highest
equability among insect pests in that
Fig. 3. Diversity indices, evenness and stage. The values of D also differed within
dominance of insect pests at different different stage and appeared as the
stages of rice at Bangladesh highest at early tillering stage (2.42) and
lowest at reproductive stage (1.08).
However, 3 diversity indices viz., diversity index (H), evenness (J) and D were
found highest at early tillering stage thus seemed to be more stable than other. Similarly,
they also reported that the diversity indices viz., diversity index (H), evenness (J) and
D of natural enemies in boro rice at different stages were found highest at seedling
stage and the lowest at early tillering stage (Fig. 4). Arthropod diversity study
undertaken at ICAR-National Rice Research Institute, Cuttack in semi-deep water
and irrigated low land ecologies revealed that in semi deep water rice ecology, spiders
(7.2/sweep) outnumbered the other predatory groups and were widely distributed
throughout the study area. The other major predatory arthropods include damsel fly
(5.9/sweep) and lady bird beetle (5.2/sweep).

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 Fig 4. Diversity indices, evenness and Fig. 5. Diversity of insect pests and
dominance of Natural enemies community at natural enemies in semi-deep water and
different stages of rice at Bangladesh irrigated rice ecosystems at NRRI, Cuttack

Among the parasitoids, Xanthopimpla sp., Carcelia sp., Stenobracon sp.

Apanteles flavipes, Brachymeria sp., Cardiochiles sp. were the predominant one
occurred (Fig 5).
Although the same trends were observed in the irrigated ecology, but the number
was comparatively lower than semi deep-water ecology. Diversity indices computed
in irrigated ecosystem were Simpson’s index [1/D] (10.48), Shannon-Wiener index
[H’] (2.62), Margalef’s index [M] (2.75) whereas in semi deep water ecologies the
Simpson’s index [1/D] (13.42), Shannon-Wiener index [H’] (2.78) and Margalef’s index
[M] (2.76). (NRRI Annual Report 2015-16).
1.3. Coastal rice ecosystem
Coastal rice ecosystem consists of both irrigated uplands and low lands. An
experiment conducted at Srikakulam district during kharif 2017 depicted that during
the first 30 days after transplanting significant yield losses occurred due to BPH,
WBPH and leaf folder in low lands of coastal ecosystem. The crop growth period
between 30-60 days after transplanting was most vulnerable resulting in major yield
losses (20-60%) mainly due to stem borer, leaf folder and brown planthopper. Beyond
sixty days after transplanting, the crop damage is inflicted by stem borer and leaf
folder causing 10 to 48% damage in coastal ecosystem. The other beneficial fauna
prevalent in the coastal ecosystems are coccinellid beetles (5 species), spiders (4
species), earwigs (3 species) and lacewings (2 species). The biocontrol agents include
egg parasitioids (2 species) in the coastal ecosystem in north coastal Andhra Pradesh.
1.4. Ratoon rice
A ratoon crop is potentially at risk from insect pests because it extends the time
period of host availability. With its shortened vegetative stage, a ratoon crop is
unsuitable to early season insects like whorl maggot, Hydrellia philippina and
caseworm, Nymphula depunctalis. Stem borer numbers are significantly reduced at
main crop harvest, but some survives to attack the ratoon crop. Leaf folder infestation
is higher at the vegetative stage on a ratoon crop than main crop. The lack of land
preparation in establishing a ratoon crop allows a high carryover of natural enemies,
particularly the predators which prevent significant build up of brown planthopper,
white backed planthopper and green leafhopper.

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The incidences of diapausing rice stem borer

larvae in the rice crop residues (stalks and
stubbles) investigated at ICAR-NRRI, Cuttack
from December 2016 to March 2017 revealed that
three predominant stem borer larvae diapaused
in the rice crop residues were Yellow stem borer,
Fig. 6. Relative abudance of different Scirpophaga incertulus, Striped stem borer,
species of stem borer Chilo supressalis and Pink stem borer, Sesamia
inference. The relative abundance of three
diapausing stem borers revealed that yellow
stem borer (40.8%) was most predominant
followed by Striped stem borer (36.2%) and Pink
stem borer (23%). The occurrence of stem borer
species was correlated with the height of the
stubble. The results revealed that 60% of the
total S. inferens and 17.6% of the total Chilo sp
recorded were concentrated to 9.8 and 7.0 cm
above the root zone, respectively, whereas 98%
of the Yellow stem borer larvae were
Fig. 7. Abundance of rice stem borer concentrated to the base of rice stubbles (Fig 6
in stubbles in ICAR-NRRI, Cuttack & 7).
It is clear that destruction of diapausing larvae of the above species of rice stem
borers during land preparation would be an effective cultural control method (NRRI
Annual Report 2015-16). During crop harvest, if rice stubble heights are adjusted to a
range of 5–10 cm, the survived stem borers can be reduced by 70–90%. Furthermore,
approximately 70% of the overwintering stem borers can be killed by ploughing and
irrigation. These measures can significantly decrease the initial population sizes of
stem borers.
1.5. Natural enemies
In agro-ecosystems, the associated natural enemies can perform important
ecological services, mainly biological control of crop pests. Naturally occurring
biological control has a potential role to play in the management of rice fields of
tropical south and south-east Asia and there is a need to emphasize the impact of
indigenous natural enemies as an essential part of IPM programme. Conservation of
the natural enemy fauna in situ for suppressing the pest population seems to be a
very good alternative. A study conducted at Cauvery command areas of Karnataka
by Parasappa et al. (2017) indicated that among the various predators, spiders and
mirids were the most important natural enemies. Among the odonata, damselflies
population was more compared to the dragonflies. Mirids Cyrtorhinus lividipennis
was considered as important, potential and efficient predator of BPH and WBPH.
Staphylinids were identified as Paederus fuscipes which is a predator on leafhoppers.
Rice insect predators in India belong to 25 families of 6 orders of class Insecta.
Among the predacious orders, Coleoptera ranks first and the family Coccinelidae is

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exclusively predacious with a few exceptions. Predaceous carabid beetles are generally
recognized as useful natural enemies against lepidopterous larvae in the rice fields.
There are 368 coleopteran species associated with rice and there is always confusion
about their herbivorous or beneficial role. Hymenopterous parasitoids associated
with rice are 524 species belonging to 181 genera exercising natural control. Among
the 419 organisms enumerated during the investigation, hymenopterans were by far
the most abundant representing 191 species followed by coleopterans and dipterans
representing 38 species each.
Predators are the most conspicuous and consume many preys during their life
span. Dragon flies and damsel flies are amongst the most conspicuous insects
associated with irrigated rice fields. They predate on adults of yellow stem borer and
leaf folders. Fourteen spp. of dragonflies and damselflies have been recorded from
rice field at Cuttack.
1.5.1. Spider: Spiders such as the wolf spider, Lynx spider, Orb spider are known to
consume a large number of prey and play an important role in reducing the densities
of plant and leaf hoppers in rice fields. Spiders are thus known as biological control
agents for phytophagous insects with some species being able to reduce the total
pest population by 22% per day. The predominant species of predatory spiders were
reported from rice fields of North–Eastern UP were Tetragnatha javana; Pardosa
pseudoannulata; Tetragnatha mandibulata, Pardosa birmanica, Hippasa holmerae,
Tetragnatha maxillosa,
1.5.2. Bird: In rice cultivation, many farmers have the practice of keeping dried tree
stumps in different localities in the field. Birds such as Drongos, Mynas and Kingfishers
use perches to feed on insects and caterpillars from the rice fields during daytime. At
night, different species of owls use these perches to prey upon rodents that contribute
to crop loss. Another group of birds that play a vital role in rice fields is the Egrets,
Herons and Water hen. These birds feed on worms, moths and caterpillars as well as
harmful soil organisms. Flock of cattle egret, Bubulcus ibis running behind the plough
or country plough is a very common sight in the rice paddy.
1.5.3. Earthworm: Earthworms are the most important soil dwelling organisms involved
in the process of soil formation and maintenance of soil health and help the composting
process. Earlier ten different earthworm species have been identified from different
habitats belonging to 4 different families. Lampito mauritii and Pellogaster
bengalensis were found to be ubiquitous. Among them, only L. maurtii was found in
all sites in high numbers
1.5.4. Duck: Ducks are generalist predators, feeding on stem borers, leaffolders,
grasshoppers, planthoppers and leafhoppers etc. Ducks have big appetite and on an
average one duck can consume more than 100 insects per hour thus decreasing pest
populations quickly, particularly in the early to mid-tillering stage of rice. The total
number of plant hoppers and leafhopper in duck fields were reduced by 63.9 and
77.3%. Rice–duck farming agro-ecosystem reduced 30.6% fertilizers and 59.4%
pesticides usage compare with conventional farming system.

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1.5.5. Fish: Fishes like carp, tilapia and catfish feed on plant and leaf hoppers, stem
borers or other insects like mosquito larvae and other aquatic insects that fall into the
water. Some fish also feed on the outer leaf of the leaf sheath, which contains plant
hopper and leaf hopper eggs.
1.5.6. Soil arthropod: Soil mesofauna which includes Cryptostigmatids, soil Acari
including Oriebatid and Cryptosigmatid mites and other invertebrates as important
reservoir of biodiversity and plays a pivotal role in determining many soil
characteristics. This diverse group of animals cover a range of taxa, the most important
being protozoan’s, nematodes, oligochaete worms (earthworms and enchytraeids),
mites, collembolans, millipedes, centipedes and a range of insects whose larval stages
complete their development in the soil. The presence of soil fauna increased the soil
organic carbon and also helps in decomposition of organic matter which led to an
increase in the yield of the crop by increasing the availability of nutrient. Some of soil
arthropods like ants and termites increased soil water infiltration due to their tunnels
and improved the soil nitrogen recycling of crop residues and plant productivity and
keeping the balance of soil carbon pool as well.

2. FORECASTING MODEL FOR MAJOR INSECT PEST

AND DISEASE
Weather-based forecasting systems reduce the cost of production by optimizing
the timing and frequency of application of control measures for minimizing crop loss
and reducing cost of plant protection. Forecast models provide an alternative to
calendar spray schedule to bring need-based protection, e.g., instead of sprays at 7-
14-day intervals to spray at precise time just when and where the pest is likely to
appear. Thus, precision pest management may bring down number of chemical
pesticide sprays to provide economic and environmental benefits. Finally, the system
of forecast should be taken as economically acceptable action as an integral part of
IPM package while growers should be capable and flexible enough to take due
advantage of a pest forewarning advisory.
2.1. Stem borer
Rice yellow stem borer, Scirpophaga incertulas recorded were used in conjunction
with the weather data of a particular location for development of weather-based
prediction categorized as to low, medium and high severity. The weather-based criteria
and prediction rules have been integrated online for forewarning S. incertulas
population levels. Forewarning of S. incertulas is specific for Cuttack location for
kharif season and being used for pest advisory services for the rice growers of the
region.
2.2 Rice blast
Savary et al. (2012) in Korea developed EPIRICE, a generic model for plant diseases
which was coupled with GIS. Manibhushanrao and Krishnan (1991) developed EPIBLA
(EPIdemiology of BLAst) model using multiple regression equation based on maximum

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temperature and maximum RH for simulation of leaf blast incidence. In their model
simulated incidence of blast made 7-day forecasts of disease progression in many
parts of India. The ICAR- NRRI, Cuttack operated a simple leaf blast forecasting
system based on empirical factors which interacted with rice varieties. Stages which
are most susceptible to rice blast viz. seedling, tillering and flowering were identified.
Kaundal et al. (2006) introduced a machine learning techniques model for forecasting
rice blast in India. Six weather variables were selected viz. temperature (max and min),
RH (morning & evening), rainfall and rainy days per week. Blast is mostly preferred
by particular air and soil temperatures, relative humidity (RH), hours of continuous
leaf wetness (LW), degree of light intensity, duration and timing of dark periods. All of
these have been considered as very crucial for development of the disease.

3. HYPER SPECTRAL REMOTE SENSING FOR PEST

SURVEILLANCE
At present, satellite remote sensing data are also being used in generating and
improving weather forecasts, providing crop estimate in terms of net sown area and
yield, issued in operational mode for the last few years with reasonable accuracy for
rice, wheat, mustard, potato, etc. Use of Remote Sensing (RS) and Geographic
Information System (GIS) could be explored for analysis of satellite-based agro-met
data products, mapping geographical distribution of pests and delineating the hotspot
zones. Super-imposition with causative abiotic and biotic factors on visual pest maps
can be useful for pest forecasting. Since, damaged plants increase reflectance
particularly in chlorophyll absorption band (0.5-0.7 cm) and water absorption bands
(1.45-1.95 cm), forecasting crop pests is possible by remote sensing.

4. CLIMATE CHANGE AND RICE INSECT PESTS

Current estimates of changes in climate indicate an increase in global mean annual
temperatures of 1 °C by 2025 and 3 °C by the end of the next century. The date at
which an equivalent doubling of CO2 will be attained is estimated to be between 2025
and 2070, depending on the level of greenhouse gases emission. Fifteen studies of
crop plants showed consistent decreases in tissue nitrogen in high CO2 treatments;
the decreases were as much as 30%. This reduction in tissue quality resulted in
increased feeding damage by pest species by as much as 80% (Coviella and Trumble
1999). In general, leaf chewers (Lepidoptera) tend to perform poorly whereas suckers
(aphids) tend to show large population increases indicating that pest outbreaks may
be less severe for some species but worse for others under high CO2.
Natural enemy and host insect populations may respond differently to the global
warming. There also instances where warmer conditions increase the effectiveness of
many natural enemy species and/or increase the vulnerability of their prey. In extreme
conditions, higher abundance of insect pests may partly be due to lower activity of
parasitoids or to disturbed parasitoid-pest relationship and decreased controlling
ability. However, parasitoids [Anagrus incarnatus and Apanteles chilonis] and

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predators (C. lividipennis), other than spiders (Pardosa astrigera and Tetragnatha
vermiformis) of rice insects breed two to three more generations a year. These facts
imply that the extent of biological control of rice pests by natural enemies will increase
in intensity under the global warming.
4.1 Carbon dioxide
The majority of plants, particularly those in the C3 category, which includes rice,
respond to increased CO2 levels by increasing productivity in the form of carbon
fixation. A CO2 induced reduction in host plant quality resulted in increased larval
consumption rates in order to obtain adequate dietary nitrogen in generalist. In the
majority of cases, increased feeding rates do not compensate fully for the reduced
quality of the diet, resulting in poor performance, slowing insect development and
increasing length of life stages which place them vulnerable to the attack by parasitoids.
However, the change in C:N ratio in the plant, phloem sap becomes more concentrated
at higher temperatures, and thus acts as a richer source of amino acids for sap feeders.
The concentration of a range of secondary plant compounds tends to increase under
drought stress, leading to changes in the attraction of plants to insects. The
atmospheric environment in the future is predicted to include correlated increases in
CO2 concentration and temperature. While crop biomass is predicted to increase in
response to elevated CO2 concentrations under many circumstances, it is also
recognized that crops and soils may subsequently become nutrient limited, especially
in terms of nitrogen availability.
4.2 Temperature
Insects are ecto-thermic organisms, the temperature of their body changes
approximately with the temperature of their habitats. Therefore, temperature is probably
the most important environmental factor influencing their behaviour, distribution,
development, survival and reproduction.
4.2.1 Yellow stem borer
Yellow stem borer took 8.1 mean days for hatching out into larvae at 30 °C. However
at higher temperature hatching period was found to be decreased. In the same way,
larval and pupal developmental period changes with increasing temperature. The
percentage incidence of dead heart and white ear heads were correlated negatively
with rainfall and minimum temperature, and positively with maximum temperature.
The percentage of white ear head correlated negatively with relative humidity.
Manikandan et al. (2013) reported that the number of eggs laid by YSB increased at
higher temperature. At 28.3 °C, the YSB laid 143 eggs, whreas it was increased to 176.5
eggs at 36 °C with a standard deviation of 6.6. Insect populations from environments
with higher temperatures may have higher fecundity and shorter growth stage. It is
reported that the incubation period of Scirpophaga incertulas decreases at higher
temperature, beginning at 30 °C and continuing up to 35 °C. Egg hatching percentage
of the YSB decreased at higher temperature and increased at lower temperature. The
egg hatching percentage was high (90.6%) at 30.6 °C followed by 28.3 °C. In contrast,
only 58.5 per cent of incubated eggs achieved emergence at 36.0 °C. The incubation
period of YSB eggs was 8.5 days at 28.3 °C, whereas it took only 5.75 days at 36 °C.

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The development time taken by the four larval instars varied significantly with respect
to the temperature.
4.2.2 Brown plant hopper
Brown plant hopper requires 6.7 mean days for hatching out into nymphs in
ambient condition. However, this period decreased significantly at higher temperature.
Decreased developmental duration of instars observed at increasing temperatures
might be connected with faster larval growth at these temperatures. Insects develops
faster will oviposit early and hence the population will grow earlier than expected.
The total life span at 38 °C decreased significantly than at 30 °C.
4.2.3 Leaf folder
Drastic changes in temperature can cause oxidative stress, which in turn trigger
the production of reactive oxygen species (ROS) derived from the metabolism of
molecular oxygen which cause oxidative harm to proteins, nucleic acids, lipids. Insects
produce a number of antioxidant enzymes for detoxifying ROS. Oxidative stress
enzymes viz., glutathione s-transferases (GSTs), catalase (CAT), superoxide dismutase
(SOD) play an inevitable role in detoxifying mechanism of ROS and contribute to
regaining the balance.
One response to warm stress is the formation of reactive oxygen species (ROS)
causing oxidative harm. The raised levels of SOD and GSTs movement, shown in a
period played an important role in battling of ROS in Neoseiulus cucumeris
demonstrated the contribution of these enzymes in host protection against thermal
stress. The ability of an insect without compromising the pace of its growth and
development to tolerate the thermal stress is an important adaptation to survive in
various climatic conditions (tropical, subtropical, and temperate), which is vital in
predicting insect outbreaks.
4.2.4 Stored grain pests
The stored grains maintained at a sufficiently low moisture level can be stored for
many years without any significant loss in quality. Optimum grain moisture for
development and reproduction of insects is 12.0 to 14.0 per cent. Generally, the dormant
stages-eggs and pupae of insects, eggs and resting stages of mites, and spores of
fungi can best resist desiccation while acting feeding stages may die out if conditions
are too dry.
Angoumois grain moth is one of the most serious pests of stored rice (paddy) at
post-harvest level. Three temperature zones are significant for growth and death of
stored product insects. At optimal temperatures (25-32 °C), insects have maximum
rate of multiplication. At sub optimal temperature (13-24 °C and 33-35 °C) where
development slows, and at lethal temperatures (below 13 °C and above 35 °C) triggered
the insects to stop feeding, develop slower, and eventually die. The more extreme
temperature, the more quickly they die. Each insect species, stage and physiological
state will affect the particular response to temperature. No stored-product insects can
survive freezing.

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Stored product insects breed faster at high humidity (65-80%) which is

approximately equal to 13.0 – 15.0 per cent moisture content of the grains. Above 80
per cent humidity or 15 per cent moisture content, mould growth start suppressing
insect multiplication. Rice weevils complete their life cycle in 25 days at 30 °C and
while they take about 94 days at 18 °C. At a temperature over 34 °C, insects usually
cannot develop. However, lesser grain borer Rhyzopertha dominica has the shortest
development period of 25 days at 36 °C with 80.0 per cent relative humidity and
longest development period of 106 days at 20 °C with 60.0 per cent relative humidity.
At 20 °C developmental activities of larvae and pupae of Tribolium castaneum ceased
and at 35 °C, it retarded significantly. The highest population increase of S. cerealella
occurred at 30 °C.
4.3 Elevated temperature and carbon dioxide
Earlier studies predicted that elevated CO2 and temperature exhibited a significant
positive effect on BPH multiplication and its population than ambient CO2 and
temperature (Pandi et al. 2016). Rice plants exposed to elevated conditions recorded
higher number of eggs (303.2 ± 35 eggs/female) whereas in the plants under ambient
condition (212.9 ± 21.5 eggs/ female) female laid significantly less number of eggs.
Thus, it was revealed that elevated condition stimulated fecundity of BPH by 29.5 %
compared to ambient. Quantification of honeydew was directly related to the sucking
rate; where only under elevated CO2 condition honeydew excretion was significantly
higher than ambient condition. In contrast elevated CO2 and temperature honeydew
excretion did not differ significantly from ambient condition. Further, developmental
period of nymphs and longevity of brachypterous females were significantly reduced
under elevated condition as compared to ambient. It has been observed earlier that
every degree rises in global temperature, the life cycle of insect would be shorter. The
quicker the life cycle, the higher will be the population of pests. Combined effects of
both elevated temperature and CO2 altered the plant phenology and pest biology and
aggravated the damage by brown planthoppr (BPH), Nilaparvata lugens.
4.4. Precipitation
Many pest species favour the warm and humid environment. Both direct and
indirect effects of moisture stress on crops make them more vulnerable to be damaged
by pests, especially in the early stages of plant growth. Some insects are sensitive to
precipitation and get killed or removed from crops by heavy rains. A decrease in
winter rainfall resulted in reduced aphid developmental rates because drought-stressed
tillering cereals reduce the reproductive capacity of overwintering aphids.

5. POPULATION BIOLOGY OF RICE PATHOGENS

5.1. Rice blast
Magnaporthe oryzae (63 isolates) collected, of which 16 (25%) were the mating
type MAT1-1 while 35 (56 %) were mating type MAT1-2. The MAT1-2 isolates
predominated in Jharkhand and Assam while MAT1-1 is more predominant in the

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isolates of Odisha. Both MAT1-1 and MAT1-2 were equally distributed in the isolates
of Meghalaya and Tripura. In another study forty six isolates of M. oryzae were
collected from various ecosystems of coastal Odisha, and the mating type analysis
showed that MAT1-1 mating type was dominating in all the ecosystems and MAT1-
2 was found to be present in uplands as well as in irrigated fields. Both mating types
could be found in the same field in irrigated ecosystem.
Recently, twenty isolates of M. oryzae were collected from Chhattisgarh and
categorized into three groups based on colony colour i.e., greyish blackish, greyish
and white, and in two group based on the texture of the colony as smooth and rough.
All the twenty isolates produced the characteristics symptoms of spindle shaped
lesion on susceptible plant. Among them, 5 isolates were found to be highly virulent,
8 were moderately virulent while, 7 were mild in nature. In phylogenetic analysis,
overall two major groups were formed. The Chhattisgarh (CG-2 and CG-43) blast
isolates along with Indian isolate were in one group whereas; isolates from Brazil,
Kenya, Japan and China were in a separate group.
5.2. Sheath blight
Sheath blight (ShB) of rice caused by Rhizoctonia solani Kuhn [teleomorph:
Thanatephorus cucumeris (Frank) Donk] is a major biotic constraint of rice in almost
all the rice growing tracts of India. Yield losses due to this disease were estimated to
range from 1.2 to 69.0% depending on the cultivar, environmental condition and crop
stage. The pathogen has a wide host range and can infect plants belonging to more
than 32 families and 188 genera. The weeds in and around the rice fields, water
channel and irrigation ponds may serve as source of primary inoculum of the fungus.
Natural occurrence of Rhizoctonia solani has been reported on sugarcane, weeds,
wheat, bajra, cash crops such as cotton, coriander, and turmeric. Sheath blight
pathogen survives from one crop season to another through sclerotia and mycelia in
the plant debris and also through weed hosts in tropical environments. Both mycelia
and sclerotia survive in infected plant debris. The disease severity was positively
correlated with sandiness of soil. Further, the disease incidence was highest in wet
soils with 50-60% water holding capacity (WHC) and lowest in submerged soils with
100% WHC.
The extent of damage of rice seedlings due to sheath blight incidence is dependent
on resistance levels among the rice strains, average daily temperature and frequency
of rain. Pot culture studies on the susceptibility of rice seedlings to R. solani revealed
that disease incidence and development was rampant on 20 to 30 days-old rice
seedlings compared to seedlings of 30 to 40 days old under artificially inoculated
conditions. Rice ShB symptom production under artificial condition depends on the
method of inoculation. Of different inoculation techniques such as single grain
insertion, single sclerotium insertion and mycelial suspension injection; single
sclerotium insertion was found most effective with highest ShB symptoms (68.5 to
80.0%), lesion length (2.45 to 4.75 cm) and percent disease index (32.5-43.5) followed
by single grain insertion technique.

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Maximum disease severity was observed when sheaths and leaves were inoculated
with 7-day-old propagules of the pathogen. The amount of R. solani inoculum plays
a major role in ShB disease development. Inoculum at the rate of 0.2 mg when placed
inside the leaf sheath with a few drops of sterile water induced single, discrete and
uniform-sized lesions irrespective of the inoculum type (mature, immature sclerotium,
and mycelium). Early infection on a healthy plant within 12 h is possible when mycelium
of the pathogen was used instead of sclerotial bodies. The ShB pathogen can infect
the rice crop at any stage of growth from seedling to flowering by different inoculum
sources. Three pathogens are found to cause ShB disease in rice. They are R. solani
(Thanatephorus cucumeris), R. oryzae-sativae (Ceratobasidium oryzae-sativae) and
R. oryzae (Waitea circinata). Combined inoculation with these pathogens resulted in
highest disease severity. Further, ShB incidence was maximum when treated with R.
solani, moderate with R. oryzae-sativae, and low with R. oryzae. Multiple linear
regression test was made between the percent disease incidence (PDI) and the weather
parameters indicating the highest contribution (61.05%) came from rate of evaporation,
while the other two weather parameters viz., maximum and minimum temperature
contributed 9.03% and 23.03% respectively.
5.3. Bacterial blight
The monitoring of pathotype is still an important tool for providing timely
information about the population structure of the pathogen and the effect of climate
change on population structure. In a recent study Yugander et al. (2017) reported that
bacterial blight pathogen, Xanthomonas oryzae pv oryzae has invaded into the newer
areas with more virulence. In fact the evolution of new races in plant pathogen is a
continuous process which requires regular monitoring. The change of climate especially
the increase of temperature with high humidity has helped the X. oryzae pv oryzae to
gain more virulence and that’s why newer areas were also invaded by this pathogen.
It is interesting to observe that different researchers have reported presence of different
pathotypes of X. oryzae pv oryzae in India (Nayak et al, 2008; Yugander et al. 2017) for
further study on the pathogen population infecting rice with the help of differentials
and molecular markers available.
5.4. Sheath rot
The rice sheath rot has gained the status of a major disease of rice and yield loss
varies from 3 to 85%. Rice sheath rot is a disease complex that can be caused by
various fungal and bacterial pathogens. Major pathogens associated with rice sheath
rot disease are fungi such as Sarocladium oryzae and Fusarium sp. belonging to the
Fusarium fujikuroi complex and the bacterial pathogen Pseudomonas fuscovaginae
(Bigirimana et al. 2015). S. oryzae is present in all rice-growing countries worldwide,
being very common in rainy seasons. The pathogen survives in infected seeds, plant
residues (straw and stubble), but also in soil, water or weeds when environmental
conditions are favorable. Helvolic acid and cerulenin are described as the major
secondary metabolites of S. oryzae and the pathogenicity determinant of the disease.
Temperature of 20-30 °C and relative humidity of 65-85% favour the sheath rot
development.

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 Sheath rot in rice has also been associated with Fusarium sp. belonging to the F.
fujikuroi complex. The complex is currently divided in three large clades, the African
clade, the Asian clade and the American clade. The main organisms associated with
rice are F. verticillioides from the African clade and the closely related species F.
proliferatum and F. fujikuroi from the Asian clade. Symptoms of rice sheath rot
caused by any of the members of the F. fujikuroi species complex are wide spread due
to their large variability and at least one of their members is found in any part of the
rice- growing world. Two categories of metabolites are involved in pathogenicity and
interaction with plants, gibberellins and mycotoxins. F. fujikuroi can survive up to 26
months in infected rice grains and 28 months in dried rice stubble. F. proliferatum can
survive in infected grains. Rice sheath rot causing Fusarium spp. have many hosts,
they can easily find alternate hosts in the environment, especially weeds.
5.5. False smut
Rice false smut caused by the fungal pathogen Ustilaginoidea virens (Uv) is
becoming a destructive disease throughout major rice-growing country. Information
about genetic diversity and population structure of the pathogen is essential for rice
breeding and efficient control of the disease. Recent reports applying genomic and
transcriptomic data have revealed single nucleotide polymorphism (SNP) and simple
sequence repeat (SSR) markers for the identification of Uv genetic diversity (Sun et
al. 2013). Earlier studies using PCR-based approaches, such as rDNA-ITS variability
amplified fragment length polymorphism (AFLP) and random amplification of
polymorphic DNA (RAPD), have identified very limited genetic diversity of Uv.
However, three SNP-rich genomic regions have been identified by comparative
genomics. Based on the analysis of the three SNP-rich genomic regions, significant
genetic diversifications were detected among populations from five major rice
production areas in China, and isolates from the same area showed considerable
DNA composition stability, which consistent with the conjecture that Uv may not be
an air-borne, but a water- and/or soil-borne pathogen. Consistent with this speculation
geography is more important than rice cultivar in constructing the genetic diversity
of Uv. Interestingly, genetic divergence is generally higher in isolates from inland
areas than from coastal areas. Genetic variation in north-east China is relatively low,
which may be a result of less active sexual reproduction. Survey of literatures reveals
that except Baite et al (2014) who reported that the genetic variability of Indian isolates
was related to geographical location as isolates from distantly related locations
possess higher genetic diversity; there is no other reports on population structure of
UV which is a good researchable issue that may be taken up in future.
5.6. Bakanae
In India, bakanae disease is also called as foolish seedling or foot rot because of
the variable symptoms, the pathogen produces. The disease is monocyclic with
pathogen producing conidia on infected plants and conidia will spread by wind and
water. The high production of conidia on infected or dead culms in the field coincides
with flowering and ripening of rice, when the conidia are able to infect or contaminate

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the seeds (Infected kernels develop a reddish color due to the presence of conidia,
and the whole seed becomes discolored when severely infected). The fungus can
also be isolated from asymptomatic seeds, if they are collected from a highly infected
rice field. Airborne ascospores have also been reported, as an infection source, at the
flowering stage of the crop. The fungus can infect seedlings at an early stage of
development, when it becomes systemic in the plant, but without any colonization of
the floral organs. The first 72 hours after seed germination are critical for the
development of the disease, which is favoured by high amounts of exudates (sugars
and amino acids) from germinating seeds.F. fujikuroi growth is also stimulated by
temperatures from 27 °C to 30 °C, and by higher levels of nitrogen in the soil.
Soil temperature also plays a crucial role in disease development, with more
prominent bakanae symptoms at 35 °C soil temperature. The application of nitrogen
to the soil stimulated the development of the disease and the effect was not modified
by the application of potassium or phosphorous. Relative humidity also plays an
important role in disease development with high humidity leads to elongation of the
culms, while low humidity causes rice plant stunting (Matic et al. 2016). Microconidia
and mycelia of the pathogen develop in vascular bundles, particularly in larger vessels
and in the xylem gaps, while the phloem and parenchyma do not seem to be infected.
The fungus overwinters in infected seeds, and these represent the main source of
inoculum for the following season. Progress in molecular taxonomy has shown that
there are around 50 species in the F. fujikuroi complex and the number keeps increasing.
The complex is currently divided in three large clades, the African clade, the Asian
clade and the American clade. The main organisms associated with rice are F.
verticillioides from the African clade and the related species F. proliferatum and F.
fujikuroi from the Asian clade.

6. EPIDEMIOLOGY
6.1. False smut
Epidemiological study of false smut pathogen is essential to gather information
for formulating appropriate management options. Till date there is no definitive pattern
of infection process, dissemination method and the influence of weather factor vis-à-
vis combination factors responsible for severe infection of false smut pathogen to
rice. Nessa et al. (2015) provided a broad but relatively clear picture of on the
epidemiology of rice false smut disease under natural environment and reported that
soil is the source of initiation of epidemic but did not recognize any long or short
distance primary or secondary source of infection. At Temperature 22-25 °C with no
less than 48 h of wetness duration considered necessary for successful infection of
sexual stage of FS pathogen Villosiclava virens and the highest level of disease
(92.9%) was obtained at 25 °C and 95% RH with 120 h wetness. Light can inhibit the
formation of secondary spores from chlamydospores. High level of nitrogen fertilization
increases rice foliar growth which allowed for higher humidity below the canopy and
created an environment favourable for the development of RFS. Additionally, irrigation
has been found to be a major factor which affects the development of RFS. Lower

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minimum and maximum temperature, high atmospheric humidity (92% and above)
before and during early part and less during later part of flowering favoured the
disease.

7. DIAGNOSTIC ASSAY
7.1. Rice blast
Highly sensitive and accurate methods for the early diagnosis of M. oryzae will
reduce quantum of loss. Traditionally, the major technique used to detect plant
pathogens is based on cultural and morphological observation. Consecutively, some
immunoassays and nucleic acid-based techniques have been developed for the
diagnoses of plant pathogens. The enzyme-linked immunosorbent assay is a sensitive
and specific method for the detection of plant pathogenic fungi. The most important
is the polymerase chain reaction (PCR) based detection methods that are more accurate,
sensitive and specific for diagnosis of blast disease. The quantification of M. oryzae
growth in rice plant was developed based on RNA-based northern blotting and
DNA-based real-time PCR.
7.2. Storage pathogen
Rice suffers from more than 60 diseases and most of the major diseases of rice are
seed borne. Fungi are the principal organisms associated with seed storage (Fakir
2000). Bacteria are also commonly carried internally or externally by the seeds. The
extremely seed borne diseases of rice are brown spot , bakanae , blast , sheath blight,
sheath rot , stem rot , false smut are major seed borne pathogens of rice. Bacterial
pathogens such as bacterial leaf blight and bacterial leaf streak are also taking a
heavy toll in terms of yield and quality by rapid spread and damage. Seed may be
infested, contaminated or infected. Seed infection may take place through the mother
plant, invasion through natural openings including the funicles and microphyles,
direct penetration of the seed or caryopsis or invasion from the pods or fruits.
Conventional detection and diagnosis methods coupled with molecular techniques
can add to the rapid and accurate diagnosis. In rice, a BIOPCR technique was used to
study survival of Xanthomonas oryzae pv. oryza in rice seed and track its progress in
planta following seed transmission. Quantitative real time PCR detection will definitely
help to quantify the pathogen load at an early stage so that further losses can be
minimized. Loop-mediated isothermal amplification (LAMP) offers as a field oriented
and user-friendly alternative to polymerase chain reaction (PCR). LAMP is less time
intensive than PCR and can be performed using heat-blocks, with results read by eye
under UV light.

8. KNOWLEDGE GAPS AND RESEARCH AND

DEVELOPMENT NEEDS
The biotic stresses are major contributors to reduction of crop yield. Increasing
ozone, CO2 and greenhouse gases in the farming atmosphere are possible reasons for

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increasing pest pressure and change in pest species to rice crop. Scientific tools and
techniques would ease the stresses endured by pest and diseases and shall provide
better initiatives amongst entrepreneurial initiative.
Biotic menaces are weather-dependent, weather-based prediction models could
be developed to manage these menaces. Forewarning models for major pests of rice
using satellite-based agromet product and surface data could be developed for
decision support system(s), which would reduce use of chemical pesticide on standing
crop. Besides, the measurement of insect developmental, survival and reproductive
responses to temperature poses practical challenges because of their modality,
variability among individuals and high mortality near the lower and upper threshold
temperatures. It will aid in the development of powerful tools for analyzing insect
population behaviour and response to challenging climatic conditions. It is important
to quantify and verify by critical experiments, the speculative relationships frequently
proposed between climatic factors and the population dynamics of rice insects. Future
experiments with population in controlled environments as well as statistical
correlations based on field data will permit a much clear understanding of the importance
of climate, and reveal the potential for improving pest control methodology through
this understanding

9. WAY FORWARD
With the available scientific knowledge, there is need for further strengthening
the research and development in the following areas:
 How temperature and other abiotic factors set the limits of distribution and define
abundance of insect species.
 The physical and biological components of our environment are all interrelated.
Thus, the rice fields need to be given the attention they need and deserve.
Preventing alien species from invading the rice ecosystem is very important.
Alien species often affect the conservation of endangered species by competition
and inducing additional chemical control applications.
 The importance and abundance of natural enemies have not previously been
investigated in different rice ecologies like upland, lowland, irrigated and deep
water. The current work will address the paucity of information on enemies of
paddy pests thriving in different rice ecologies and to have their comparative
diversity.
 Issues and problems about rice fields should be taught in schools. Students
should understand what is happening to a vital ecosystem such as rice fields so
that they could make a stand and help preserve an important part of our environment
and economy. Rice fields offer many benefits for all of us, like better rice and more
food and better environmental safety.

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10. CONCLUSION
The success of rice disease and pest management involves the understanding of
various aspects of rice insect pests, pathogens, their pest status, distribution, bio-
ecology, diversity, forecasting model for real-time pest-advisory services, hyper-
spectral remote sensing in pest damage assessment, impact of climate change on
insect biology, population structure and epidemiology of different rice pathogens.
These knowledge will reduce chemical pesticide application in rice, financial burden
and ultimately reduce environmental pollution.
References
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characterization of Ustilaginoidea virens isolates causing false smut of rice in India.
Indian Phytopathology 67 (3):222-227.
Bakar MA and Khan MMH (2016) Diversity of insect pests and natural enemies as influenced by
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Research 41(3):461-470.
Bambaradeniya CNB, Fonseka KT and Ambagahawatte (1998) A preliminary study of fauna and
flora of a rice field in Kandy, Sri Lanka. Ceylon Journal of Science (Biological Science)
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Bigirimana VP, Hua GKH, Nyamangyoku OI and Hofte, M (2015) Rice sheath rot: an emerging
ubiquitous destructive disease complex. Frontiers in Plant Science 6:1-16 (Article No.1066)
Chakraborty K, Moitra MN, Sanyal AK and Rath PC (2016) Important natural enemies of paddy
insect pests in the Upper Gangetic plains of West Bengal, India. International Journal of
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Coviella CE and Trumble JT 1999 Effects of Elevated Atmospheric Carbon Dioxide on InsectPlant
Interactions. Conservation Biology 13 (4): 700-712
Fakir GA (2000) An Annotated List of Seed-Borne Disease in Bangladesh. Seed Pathology Centre,
Dept. of Plant Pathology, Bangladesh Agricultural University, Mymensingh.
Kaundal R, Kapoor AS and Raghava GPS (2006) Machine learning techniques in disease forecasting:
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Krishnaiah K and Varma NRG (2018) Changing insect pest scenario in the rice ecosystem – A
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Manibhushanrao K and Krishnan P (1991) Epidemiology ofblast (EPIBLA): A simulation model
and forecasting system for tropical rice in India. In: Rice Blast Modeling and Forecasting
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Manikandan N, Kennedy JS and Geethalakshmi V (2013) Effect of elevated temperature on
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(12):5563–5566.
Matic S, Bagnaresi P, Biselli C, Orru L, Amaral Carneiro G, Siciliano I, Vale G, Gullino ML and
Spadaro D (2016) Comparative transcriptome profiling of resistant and susceptible rice
genotypes in response to the seed borne pathogen Fusariu fujikuroi. BMC Genomics
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Mohapatra SD, Rath PC and Jena M (2016) Sustainable management of insect pests and diseases
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M, Barman HN, Abdul Latif M and Galloway J (2015) Spatial pattern of natural spread of
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Parasappa HH, Narasa Reddy G and Neelakanth (2017) Rice insect pests and their natural enemies
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epidemics of rice diseases globally. Crop Protection 34:6–17.
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 Bio-intensive Management of Pest and
Diseases of Rice

AK Mukherjee, MK Bag, M Annamalai, T Adak, S Lenka,

Basanagowda G, Prasanthi G, Raghu S, M Baite,
Prabhukarthikeyan SR, NB Patil, PC Rath, Guru Prasanna Pandi G,
SRR Korada, N Basak, U Kumar, SD Mohapatra, S Bhagat,
A Banerjee, R Bhagawati and M Jena

SUMMARY
Biointensive approaches incorporating ecological and economic factors into
agricultural system and addresses public concerns about environmental quality and
food safety may be a sustainable approach. Different bio pesticides like biocontrol
agents and botanicals may help in the reduction of crop loss due to pests and diseases.
Different naturally occurring microbial agents which don’t have adverse effect on
crops but are toxic or growth retardant against the pathogen or insects have been
used as biocontrol agents (BCAs). Similarly different secondary metabolites or crude
plant extracts or oils which are not phytotoxic but toxic or repellant to the insects are
also being used for protection of crops against insect pests. The major problem of
using BCAs or botanicals for management of insect pests and diseases are that its
viability, wide spread efficacy, specificity, mass multiplication and sufficient source
of the product especially for the botanicals. However, extensive research works have
been undertaken to overcome the aforesaid problems that are discussed in details.

1. INTRODUCTION
Pests and diseases pose a serious threat to the rice production. To mitigate these
problems a significant amount of pesticide is used in conventional rice production.
This led to resurgence of newer biotypes/strains/isolates, development of acquired
pesticide resistance besides environmental pollution and health hazards. The
conceivable approach is therefore, the biointensive integrated pest management to
minimize the problem of pest and diseases vis-à-vis increasing rice production and
reducing environmental hazards.
‘Biointensive’ approaches actually incorporate ecological and economic factors
into agricultural system and addresses public concerns about environmental quality
and food safety. The benefits of implementing biointensive approaches include
reduced chemical input costs, reduced on-farm and off-farm environmental impacts,
and more effective and sustainable pest management. Biological control agents (BCAs)
are one of the most important components of biointensive approaches for rice pest
and disease management. Biological control of diseases and pests employs natural

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enemies of pests or pathogens to eradicate or control such population causing

economic loss. This can involve the introduction of exotic species, or it can be a
matter of harnessing whatever form of BCAs exists naturally in the ecosystem in
question. If a pathogen is kept in check by the microbial community around it, then
biological control is achieved. Biological control appears to take place on the plant
surface by the activity of epiphytic microflora. This is then an important consideration
when applying chemicals to plants, since there is a risk of killing natural antagonists
of pathogens other than the one being treated.
The BCAs include all kinds of biopesticides comprising living organisms and/or
their products that are used to suppress and manage pest populations. Food and
Agriculture Organization (FAO) has comprehensively put forth biopesticides as “A
compound that kills organisms by virtue of specific biological effects rather than as a
broader chemical poison”. Whereas, CABI has defined in more lucid term as
“Biopesticides use naturally occurring organisms, such as fungi, bacteria, viruses
and nematodes to control plant diseases and arthropod pests”. Environment Protection
Agency (EPA) has defined biopesticides as certain types of pesticides derived from
natural materials such as animals, plants, bacteria, and certain minerals. Biopesticides
fall into two major classes: firstly active biomolecules from plant, animal and
microorganisms and secondly microbial pesticides consist of a microorganism e.g. a
bacterium, fungus, virus or protozoan as the active ingredient. Biopesticides may be
bio-fungicides, bio-insecticides, bio-nematicides, entomophillic nematodes and bio-
rationals etc. Besides its controlling ability of pests and diseases, it has several
advantages like lower exposure, quick decomposition, remains virtually no residues
and allowing field for next crop immediately after application in the previous crop.
Biopesticides has expanding areas in the global pesticide market and is likely to grow
at a 15.6% compound annual growth rate (CAGR) from $1.6 billion in 2009 to $3.3
billion in 2014 (Ken Research Report 2015). About 63 Indian private companies
altogether registered 970 products. Indian government also intervened in this matter
and ICAR has 31 BCA production facilities while Department of Biotechnology
supported 22 and the Insecticide Act of 1968 was also simplified registration procedure
for speedier development of biopesticides. Demand for nature-based biopesticides is
increasing steadily in all over world because of increased environmental awareness
and the pollution potential and health hazards from many conventional pesticides.
Thus popularity of Biological control agents has increased significantly in recent
years, as extensive and systematic research has enhanced their efficacy. Several
research centres around the world are conducting research aimed at improving
techniques for the augmentation and application of biological control agents, with
the objective of getting better commercial and ready to use products. The National
Farmer Policy, 2007 is also treated at par with chemical pesticide for promotion and
utilization of BCAs. In the present book chapters authors have reviewed the use of
different BCAs, their efficacy, their adaptability, development and use of suitable
formulations of BCAs that provide higher competitive saprophytic ability to the
BCAs which help in maintaining viability of the BCA for longer duration.

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1.1. Modus operandi of biological control agents
The most common mechanisms for microbial antagonism of plant pathogens are
parasitism, predation, competition, induced resistance and production of antimicrobial
substances. Often, several mechanisms act together.
Competition exists between organisms that require the same resource for growth
and survival. Competition for space or nutrients usually takes place between closely
related species. Therefore, it can be effective to treat plants or seeds with a non-
pathogenic strain of a related species that can out-compete the pathogenic organism
or the treating species need not be closely related to the pathogen, as long as it uses
the same resources.
Parasitism be it hyperparasitism or mycoparasitism is well documented and is
affected by environmental factors, including nutrient availability. Formulations of
some parasitic species of fungi are available commercially for the control of fungal
plant pathogens in the soil and on the plant surface. Bacteria on the plant surface and
in the soil are also known to parasitize plant pathogens. Predation of plant pathogens
by invertebrates can also contribute to general biological control. Bacterial feeding
nematodes consume large numbers of bacteria in the soil and some amoebae are
known to attack yeasts, small spores and fungal hypha, although these organisms
are generally non-specific predators and their relative importance in biological control
is not well understood.
Induced resistance and cross-protection are two mechanisms of plant ‘immunity’
against a pathogen. In the case of cross-protection, an organism present on the plant
can protect it from a pathogen that comes into contact with the plant later. Induced
resistance is a form of cross-protection, where the plant is inoculated with inactive
pathogens, low doses of pathogens, pathogen-derived chemicals or with non-
pathogen species to stimulate an immune response. This prepares the plant for an
attack by pathogens, and its defense mechanisms are already activated when infection
occurs. It provides protection against a wide range of pathogens across many plant
species.

2. RESEARCH STATUS OF BIOLOGICAL CONTROL

AGENT
2.1. Rice diseases
Sheath blight (ShB) of rice caused by Rhizoctonia solani Kuhn {Thanatephorus
cucumeris (Frank) Donk} is one of the serious diseases and is prevalent in almost all
high yielding rice varieties growing area in India. A modest estimation of losses due
to sheath blight in India has been reported up to 54.3%. Currently, the disease is
managed mostly by application of systemic fungicides. No genetic resistance has
been reported for this disease and all the rice cultivars are susceptible to the pathogen.
As an alternative, biological control of plant pathogens gaining popularity in majority
of crops, its utilization in rice ecosystem is still at its infancy due to varied reasons.

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Rice, being a crop that is grown under inundated conditions, the survival, growth and
establishment of BCAs is questionable. However, effective management strategy of
sheath blight disease is feasible only when the BCAs those are in vogue in rice based
cropping systems survive, establish, proliferate and control sheath blight pathogen
and also have a synergistic growth promoting effect on the crop. Besides, the BCAs
should be able to induce systemic resistance thereby contributing to the disease
control. Bio-control agents/antagonists are considered as one of the effective and
eco-friendly means of management of diseases in different crops. Several fungi like
Trichoderma viride, T. harzianum, T. koningii (Das and Hazarika 2000); Aspergillus
niger, A. terreus, Gliocladium virens of rice field are found to be antagonistic against
R. solani (Gogoi and Roy 1993).
Among the fungal antagonists, Trichoderma spp. and Gliocladium spp. are widely
used in the management of rice ShB disease. These fungal antagonists are either
applied to rice seed, soil, as root dip and foliar spray for managing the disease. Foliar
application of Trichoderma spp. also was found very effective in reducing ShB severity.
Studies on field application of T. harzianumas talc + CMC based formulation reduced
disease severity by 52%. The bioagent was found effective when applied at 7 days
compared to simultaneous application with ShB pathogen (Khan and Sinha 2006).
The optimum dose of the bioagent was found to be 4 or 8 g L-1 and increased grain
yields were also reported (Khan and Sinha 2007). Spray application of the bioagent
was highly effective on rice seedlings that received 60 kg N + 60 kg P + 40 kg K /ha.
Further, Trichoderma spp. isolated from rice leaf was more effective compared to T.
virens isolated from rhizosphere (Khan and Sinha 2005). Mixed mode of application of
bioagent as soil treatment, root dipping, and foliar spray was found to be very effective
in reducing ShB severity over control. However, foliar application of the bioagent
alone was also effective under field conditions. Nagaraju et al. (2002) reported that
application of T. viride as root dip + spray was effective in reducing ShB severity by
59% under field conditions.
Mathivanan et al. (2005) reported that combined applications of T. viride and
Pseudomonas fluorescens was effective without any negative effects in reducing rice
ShB besides increasing number of productive tillers, higher grain and straw yields.
However, individual applications of bacterial and fungal antagonists separately had
more beneficial effects. Bhagawati and Roy (2005) proved that ShB disease suppression
at field level can be obtained by soil application of T. harzianum and T. viride at a pH
range of 5.1 to 6.0. A concomitant increase in plant growth and yield was obtained.
Further, it was reported that population levels of Trichoderma spp. are high and that
of R. solani are low in acid soils.
Among the bacterial biocontrol agents, plant growth-promoting rhizobacteria
(PGPR) offer a promising means of controlling plant diseases besides contributing to
the plant resistance, growth and yield in rice (Mew and Rosales 1992). Of the different
PGPR, fluorescent Pseudomonas and Bacillus spp. group of bacteria offer an effective
control of ShB besides inducing growth promoting effects and systemic resistance.
Bacteria isolated from rice seeds and rice ecosystem was able to effectively suppress

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ShB besides producing growth promoting effects. Two years pooled data of a field
experiment revealed that P. fluorescens product gave significant result over untreated
control but at par with carbendazim 50WP (check fungicide) treated plot (Bag and
Bandyopadhyay 2010). Seed treatment with these antagonistic bacteria resulted in
increased root and shoot length of seedlings.
Bacillus spp. are important gram positive PGPR in the biocontrol of rice ShB
disease. The bacterium produces endospores and microscopic studies revealed that
isolates of B. subtilis and B.megaterium exhibited effective inhibition against the
pathogens of ShB and bakane diseases of rice. The fermented product of Bacillus
strain Drt-11 was highly antagonistic to rice ShB pathogen, causing reduced sclerotial
germination (40-60% inhibition over control), reduced hyphal growth and colony
diameter (by 14%) besides increased rice seedling growth (Min and Hui 2006).
Sheath Rot (ShR) of rice is another emerging disease of rice caused by Sarocladium
oryzae now observed in almost all rice-growing ecosystems of the world and causing
yield losses of 3–85% depending on disease severity and complete suppression of
panicle exertion (Sundaramoorthy et al. 2013). In recent years, Fusarium species and
bacterial pathogen Pseudomonas fuscovaginae have been found to be associated
with rice sheath rot in making it more complex disease. The different species of
Fusarium forming complex are F. fujikuroi, F. verticillioides and F. proliferatum
cause various symptoms on different plant parts and are responsible of yield losses
of 40% in Nepal (Desjardins et al. 2000) and even upto 60% in Korea (Park et al. 2005).
Soil has enormous untapped potential antagonistic microbes i.e. Bacillus, fluorescent
pseudomonads and Trichoderma spp. Among them, Bacillus species have received
the most attention due to their antimicrobial and surfactant properties (Gross and
Loper 2009). Bacillus producing cyclic lipopeptides (CLPs) of the surfactin, iturin
and fengycin families and their antimicrobial activities are well studied (Vinodkumar
et al. 2017).
The combination of PGPR strains was more effective in reducing sheath rot disease
in rice plants compared to individual strains under glasshouse and field conditions
(Saravanakumar et al. 2008; Sundaramoorthy et al. 2013). Bag et al. (2010) observed
that a P. fluorescens product commercially available in the market reduced ShR disease
incidence significantly over the untreated control and at par with the check fungicide.
While another Trichoderma based BCA and Gaultheria extract based botanicals
also reduced the disease incidence, but below the fungicide check. The investigations
on induced systemic resistance (ISR) by PGPR demonstrated that several strains
protect plants from the plant diseases through the activation of defense genes and
expression of stress-related proteins. These induced defense responses are regulated
by a network of interconnecting signal transduction pathways viz., salicylic acid
(SA), jasmonic acid (JA) and ethylene (ET) which play key roles in activating defense
genes encoding peroxidase, polyphenol oxidase, catalase, superoxide dismutase,
chitinase, â-1,3-glucanase, lipoxygenase, proteinase inhibitors and phenylalanine
ammonia lyase (Van Loon et al. 2008).

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Bakanae or foolish seedling disease of rice caused by soil borne fungus Fusarium
fujikuroi, another emerging disease of rice causes yield losses of 20-50% in Japan,
15% in Eastern India and 3.7-14.7% in Thailand. Biocontrol agents like Trichoderma
releases a variety of compounds peroxidases, chitinases, b-1, 3-glucanases,
lipoxygenase-pathway hydro peroxide lyase and compounds like phytoalexins and
phenols that induce resistance responses to biotic and abiotic stresses (Harman et al.
2004; Cardona and Rodriguez 2006). Root colonization by Trichoderma harzianum
results in increased level of plant enzymes. Trichoderma has proved its efficacy to
control Fusarium fujikuroi (Hadwan and Khara 1990; Lin et al. 1994). P. fluorescens
and B. cereus isolates effectively control rice bakanae and foot rot disease when it
was applied to the seed, soil or as foliar spray (Kazempour and Elahinia 2007; Zhang
et al. 2010). Hossain et al. (2016) have shown that, root drenching with an endophytic
strain of Bacillus oryzicola YC7007 suspension reduced the disease severity of
bakanae significantly when compared with the untreated controls. Lakshmi Kumari et
al. (1972) observed that thermolabile, ether soluble fungistatic substance produced
by Azotobacter spp. inhibited growth and conidial germination of F. moniliforme.
Seed treatment and soil incorporation of Pseudomonas aureofaciens and other
antagonistic bacteria suppressed the growth of the pathogen (Lee et al. 1990). Kumar
et al. (2007) reported that P. fluorescens isolates PF-9, PF-13 and B. thuringiensis
isolate B-44 significantly reduced the fungal growth and bakanae incidence. Seed
treatment has been found more effective than spraying antagonistic isolates and
their efficacy was improved by combining the biological control agents (Lu et al.
1998). But still there is a lot of scope to identify new and potential biocontrol agents
and elucidating their role in interaction and control of bakanae disease.
False smut caused by Ustilaginoidea virens (Che.) Tak. (teleomorph Villosi clava
virens) is a serious disease of rice worldwide. Yield loss due to false smut ranged from
0.2 to 49.0 per cent in India (Dodan and Singh 1996). Presently, the control of rice false
smut disease mostly relies on fungicides. However, heavy reliance on fungicides is
not only harmful to the environment, but also increases the expenses for crop
production. Therefore, exploration of BCAs for management of false smut disease is
highly needed. Reports available from scanty literatures revealed that Trichoderma
viride have antagonistic potential against U. virens (Kannahi et al. 2016). Bioagent,
B. subtilis was reported to be effective against the disease (Liu et al. 2007).
2.2. Status of botanicals against rice insect pests
A study conducted by ICAR- NRRI in tribal areas of eastern India indicated that,
the insect pests of rice like yellow stem borer, brown plant hopper, case worm, gundhi
bug and other pests were effectively managed through the use of botanicals as
indigenous technology. They are mainly based on direct application of different plant
parts of neem (Azadirachta indica), karanja (Pongamia pinnata), parasi (Cleistanthus
collinus), mahua (Madhuca indica), kochila (Strichnos nux vomica), harida
(Terminalia chebula), sal (Shorea robusta), begunia (Vitex nigundo), wild sugarcane
(Sachharum spontaneum), turmeric and also organic matters like cow dung (Jena

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2012). Apart from direct application, the ITK-based botanical like Panimirch,
Polygonum hydropiper used as fish toxicant by the tribals, was also found effective
in controlling the notorious rice pests like BPH and case worm. Its toxicity was assessed
against fingerlings of Catla catla along with neem oil under rice-fish farming system
research (Das et al. 2005). The ITKs on neem, karanja, kochila, parasi and wild
sugarcane were evaluated in detail and their efficacy was ascertained (Jena and Dani
1994; Jena 1997; Jena and Dani 1997; Jena 2000; Jena 2005; Jena and Behera 2008).
The validation of ITKs on Parasi against YSB, case worm, gundhi bug and wild
sugarcane against case worm, were tested in the farmers’ field (Jena and Behera 2004;
Jena and Dangar 2004). Synergistic action of neem oil for enhancing the efficacy of
insecticides was also studied (Jena et al. 2004).
Methanol extract of Thevetia nerifolia leaf were evaluated against Spodoptera
litura (Fab.) and the results showed 53.8% larval mortality and only 29.6% pupation
and 22.3% adult emergence at 2.5% concentration level. Sub-fractioned extract with
solvents of different polarity indicated chloroform extract active in terms of increased
larval mortality (27.5-61.5%), reduced pupation (28.4-60.2%) and adult emergence
(19.8-52.8%) and the activity was found to be attributed to the glycosides present in
the extract (Ray et al. 2012). Leaf, stem and root extract of Thevetia peruviana (Pers)
Schum. in four organic solvents; petroleum spirit, ethyl acetate, acetone and methanol
on the adults of Callosobruchus maculatus F. effectively produced mortality and
their toxicity was in the order of solvents: petroleum spirit>ethyl
acetate>acetone>methanol and among the extracts, root extract was most toxic to C.
maculates (Mollah and Islam 2007). The antimicrobial potential of 50% ethanolic
extract of T. peruviana (kaner) leaves against some micro-organisms like
Staphylococcus aureus, Rhizobium sp., E. coli and Streptococcus sp. indicated that
the phytochemical extracts of T. peruviana exhibited significant activity at varying
dosages (50-150 mg/ml). It revealed that 50% ethanolic extract of T. peruviana leaves
can be used as a potential source of novel antibacterial agents against E.coli and S.
aureus (Naza and Agrawal 2015). Thus testing of Thevetia against leaf folder of rice
will give a new look on control of this insect pest.
Yellow stem borer, Scirpophaga incertulas is one of the most important insect
pests attacking rice from seedling to harvest stage. Farmers depend upon a large
number of insecticide applications, even though a lot of insecticide applications are
not effective. In recent years the use of synthetic insecticides in crop protection
programme around the world has resulted in disturbance in eco-bio-balance, pest
resurgence, pest resistance to pesticides and lethal effect to non-target organisms in
the agro-ecosystems in addition to direct toxicity to users. Therefore, it has now
become necessary to search for the alternative means of pest control, which can
minimize the use of synthetic insecticides. Botanical pesticides are the important
alternatives to minimize or replace the use of synthetic insecticides and several
botanicals have been reported as pesticides, antifeedants, insect growth regulators
and repellents (Jena 2012; Mishra 2014). Many botanicals were found effective against
various rice pests is listed in Table 1.

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Table 1. Botanicals tested against major rice pests.

S. No. Botanicals and their efficacy Rice pest Authors
1 Neem + Mahogony oil performed best in
reducing dead heart and white ear damage Stem borer Majlish et al. (2014)
2 In a field experiment, botanical neem Stem borer Islam et al. (2013)
extract reduced the dead heart to the tune
of 58.08% compared to control.
3 Neem seed kernel showed significant Stem borer Ogah et al. (2011)
reduction of stem borer damage (number
of white ear heads)
4 Pongamia pinnata, Nicotiana tabaccum, Stem borer Barman et al. (2014)
Citrus grandis
5 Seed extract of Annona squmosa, BPH Reddy and Urs (1988)
Sapindus trifoliates, Acacia concinna,
Hydrocarpus alpine, Gynandropsis
pentaphylla and Ocimum Gratissimum
bring down the oviposition rate
6 Oil and seed extracts of Pongamia BPH and Ramanuj and
glabra and Madhuca longifolia reduce WBPH Sundarababu (1989)
hatching rate
7 Leaf extract of Anona reticulate and BPH Telan et al. (1994)
vine extracts of Tinosphora rumphii
showed repellant action
8 Leaf extract of Andrographis paniculata Gundhi bug CRRI Annual report
and Coleus aromaticus protect the grain 1995-96
9 Seed oil extracts of Annona squamosa GLH Narsimham and
and mahua (M. longifolia) caused Mariappan (1988)
mortality
10 Plant essential oils of Eucalyptus sp Rice weevil Patil et al. (2016)
found to show contact, fumigant and
persistent toxicity and repellency activity

The major limitation in botanical pesticides’ usage is that their active principles
are easily degraded by the sun light or UV radiations and heat in open field conditions
(Ware and Whitacre 2004). Recent studies have shown that polymeric systems can
be used for the protection of pesticide molecules from natural degradation and for its
controlled release against the target pests (Campos et al. 2014). To avoid higher initial
dosages or repeated applications, many attempts were made to control the release
rate of biocides by encapsulating them mainly in polymeric carriers. Both biodegradable
and synthetic polymers can be applied as release rate controlling barrier materials of
biocides; however, the polymeric carriers are expensive due to their synthesis and
precursors, and they are thermally, dimensionally and chemically unstable.
For such protective and slow release, the following materials can be used.
 Biogenic silica nano particles could be used as an attempt to design cheaper and
cleaner controlled release systems compared to those prepared with polymeric
and synthetic silica as carrier material.

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 The nano particles of chitosan have good biocompatibility with other molecules
and have the potential for controlled release of the active molecules.
2.3. Infochemicals or semiochemicals for management of rice insect
pests
In recent years, to combat pest damage, the pest management tactics using
behavioural manipulation, including mating disruption, feeding disruption, oviposition
deterrence, use of attractants, and pre-release training, have become the focus of
research for pest control (Roitberg 2007; Phillips 1997). Successful mating disruption
technique has been demonstrated for pyralid storage moths under simulated storage
experiments (Sower and Whitmer 1977). Mating disruption, which prevents males
from finding females, is the most widely studied area of behavioural manipulation for
pest management (Roitberg 2007). Female moths emit a volatile pheromone that is
detected by males at distance to locate the sexually receptive female, and male antennae
have a large number of sensilla that contain olfactory receptor neurons specific to
components of the female sex pheromones (Schlamp et al. 2006). Ultrastructure of
antennal and ovipositor sensilla of S. cerealella and the location of the female sex
pheromone gland was determined by Ma et al. (2017). Seven types of antennal sensilla
were identified on both sexes, out of them the Sensilla trichodea was found significantly
more abundant on male antennae than on those of females, suggesting that these
sensilla may detect the sex pheromones. On the ovipositor, only Sensill achaetica of
various lengths was found. The sexual gland was an eversible sac of glandular
epithelium, situated dorsally in the inter-segmental membrane between the 8th and 9th
abdominal segments (Ma et al. 2017). The pheromone X-lure was found useful only
for monitoring S. cerealella (Akter and Ali 2016). Host-finding efficiency of natural
enemies in biological control programs could be improved with the use of kairomones
in mass-rearing or release protocols.
Among the stored grain pests, Angoumois grain moth, Sitotroga cerealella is
considered to be most destructive pests of cereal grains worldwide, particularly in the
tropics and warm temperate regions (Trematerra 2015). Its infestation starts in the
standing crop and continues in storage. Although there are many control strategies,
some effective, cheap and readily available strategy are the present need for safe
storage. Several approaches for managing S. cerealella include use of edible oils,
containers, synthetic chemicals, agricultural waste materials, plant derivatives, bacterial
protoxins, biopesticides, biocontrol enhancers and semiochemicals. Among these
methods, till now semiochemicals have not been identified for S. cerealella. By feeding
inside grains, S. cerealella is directly protected from chemical insecticides and causes
damage in both the field and storage condition (Fouad et al. 2014).
Gundhi bugs are also called stink bugs. An understanding of preference of gundhi
bugs to the host and mating behavior of adults is essential to identify semiochemicals
(infochemicals) to devise a trapping system. A detailed review on rice stinkbugs was
done by Litsinger et al. (2015). To detect a host plant, gundhi bugs first have to land
on it to determine whether the plant is of a preferred species or quality. Gunawardena

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and Ranatunga (1989) found gundhi bugs are attracted to the host plants probably
by odor, based on tests of steam distillates of milk-stage panicles. Kainoh et al. (1980)
using flight-tunnel experiments, suggested that adults can detect the odor of rice
plants when they fly close to a rice field, and aggregation on the panicles was mainly
due to an arrestant effect, exerted by the panicles at flowering. Adults examine the
plant closely through plant surface exploration using sensory apparatus such as
antennae where they walk about and/or tapping with the labium tip onto the surface
of the plant (Ishizaki et al. 2011).
Leal et al. (1996) pointed out that few out of the 35,000 species of Heteroptera
worldwide had sexual pheromones. The copious defensive secretions that
contaminated samples have hampered progress on gundhi bugs. A defensive alarm
pheromone has been identified from a related species, the bean bug Riptortus clavatus,
as well as an aggregation pheromone that enables second instar nymphs to find the
host food plant. In addition, bean bug males release semio-chemicals that attract both
males and females. Interestingly, the case of the gundhi bugs is just the opposite i.e.
only males are attracted to semio-chemicals that are produced and emitted by both
males and females. Although L. chinensis females can detect the male attractants, do
not elicit any attraction. Thus, both sexes produce attractants, but these are not true
sex pheromones.
Farmers also have used various materials that act as repellents to ward off gundhi
bugs. Farmers in Assam, India spread goat dung in rice fields (Deka et al. 2006), while
tribals of Arunachal Pradesh placed dried pomelo leaves in the field (Saravanan 2010).
Lefroy (1908) heard that farmers in Sri Lanka burn certain aromatic herbs and resinous
substances so the wind will carry the smoke into the rice crop to repel gundhi bugs
‘with considerable success’. A survey found 15% of farmers in Claveria, Philippines
burnt grass or rubber tyres and 2% burnt animal fat (goat) as repellents (Litsinger et
al. 2009). Other farmers set bonfires to repel the bugs by burning obnoxious plants
like Annona squamosa, Derris elliptica, betel nut Areca catechu, Gliricidia sepium,
Erythrina variegata, Pittosporumres iniferum, Pongamia pinnata, and Wikstroemia
ovata.
Many species of Alydidae that are attracted to pig carcass (Schaefer et al. 1983)
aggregate on rotting meat (Uichanco 1921) and the farmers used this practice to
attempt to control gundhi bugs. Gundhi bug adults were attracted to rotten fish,
mollusks, or shrimp (Otanes and Sison1941), dog meat or starfish (Litsinger et al.
2009), frog meat (Morrill et al.1991). Guimba et al. (2006) stated farmers to use golden
apple snail Pomacea canaliculata. Guimba et al. (2006) used baffle traps with rotting
meat and collected most of the gundhi bugs during flowering, but the numbers were
low.
2.4. Grain volatiles for attraction of Angoumois grain moth, Sitotroga
cerealella
To protect grains from the insect damages, tons of insecticides have been applied
to control the pests, which have resulted in environmental damage, pest resurgence,

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pest resistance to insecticides and lethal effects on non-target organisms. Furthermore,
because of cost, these pesticides are becoming increasingly inaccessible to the farmers,
particularly in developing countries. This fact, combined with the consumer’s demand
for residue-free food, prompted researchers to evaluate other alternative reduced-risk
control methods for stored-grain protection (Tang et al. 2009). To resolve the above
problems, new environmental friendly methods to control the insect damages have
become of utmost interest to the researchers.
Phytophagous insects generally utilize volatile semiochemical cues from the host
plants during one or more phases of the host selection process. Plant semiochemicals
may act as direct attractants for insects or they may synergistically enhance the
activity of pheromones produced by insects. However, little is known about
interactions among rice grain and insect herbivores. Stored-product insects present
a special situation for research on host plant volatiles because nearly all species are
intimately adapted to human-stored grains and grain products, truly non-
anthropogenic populations may not exist (Lindsley 1944).
Angoumois grain moths are serious destructive stored insect pests and frequently
found flying haplessly in stored house. Larvae penetrate seed coat and enter the
grain. In order to manage this pest through non-chemical especially semiochemical
approach, Vick et al. (1974) have identified sex pheromone components of this moth.
Subsequently several attempts have been made to improve the catching performance
of adult moths, but somehow results were not found satisfactory (Akter and Ali
2015). Volatile attractants for several beetle species that infest broken grain have been
identified from cereal grains and their products (e.g., Mikolajczak et al. 1984; Nara et
al. 1981; Pierce et al. 1990). Work on the maize weevil, Sitophilus zeamais, demonstrated
that odors from cracked wheat synergistically enhanced responses to male-produced
pheromone (Walgenbach et al. 1987). Based on the previous works, we are interested
to examine the behavioral activity of several grain-derived volatiles as attractants for
improving attraction and catching efficiency of moth.
2.5. Novel formulation of botanicals and bioagents for better efficacy
and higher shelf life
Of the estimated 0.5 million plant species that exist globally, nearly 10% have been
examined chemically and over 6,500 screened for anti-pest properties. In India,
products based on only three plants are registered under the Insecticides Act, 1968
(Table 2) (Parmar 2010).

Table 2. Botanical pesticides registered in India under the Insecticides Act, 1968.
Pesticide Key source plant
Pyrethrum Chrysanthemum sp. (ex. Cinerariaefolium, Coccinium etc.)
Neem Azadirachta indica
Nicotine (Export only) Nicotiana sp.

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Microbials as biopesticides include bacteria, fungi, nematodes, protozoa, viruses

etc. and the mass released macrobial parasitoids and predators which are used for
pest management. Their application is by inundative or inoculative means. The
microbials in use include bacteria (ex. Bacillus thuringiensis (Berliner),
entomopathogenic viruses (ex. nuclear polyhedrosis virus (NPV) and granulosis virus
(GV), entomopathogenic fungi, eg. Beauvaria bassiana, and others. A total of 13
products based on bacteria, fungi and virus are registered for use in India (Table 3).

Table 3. Microbial biopesticides registered for use under Insecticides Act, 1968.
Organism Formulation
Bacteria
Bacillus sphaericus 1.15%WP
Bacillus thuringiensis var. israelsensis 5% WP, 5% AS
Bacillus thuringiensis var. kurstaki 5 & 7.5% WP
Pseudomonas fluorescens 0.5& 1% WP
Fungi
Ampelomyces quisqualis 2% WP
Beauveria basssiana 1, 1.15, or 2.15% WP, 10% SC
Metarhizium anisopliae 1 & 1.5% WP
Trichoderma harzianum 0.5, 1 & 2% WP
Trichoderma viride 1% WP
Verticillium lecanii 1.15% WP
Virus
Hear NPV 0.43, 0.5, 0.64 & 2% AS
Spli NPV 0.5 & 2% AS
WP= Wettable Powder, AS= Aqueous Solution, SC= Suspension Concentrate,
WS= Slurry for Seed Treatment
(Wahab and Manjunath 2009)

3. KNOWLEDGE GAPS
The BCA formulations used India are based on mainly few microorganisms with
comparatively specific antifungal/antibacterial activity so there is a need for
identification of BCA with broad spectrum antifungal/antibacterial activity.
Application and grower acceptance of BCAs have been found slow to develop,
mainly due to the variation in efficacy under the range of environmental conditions,
likely to occur in the field. Better understanding of environmental parameters that
limit biological control is required.
Most of the formulations available in India are wettable powder and are clay
based. So, it reduces longevity of the active microbes by desiccating and by acting as
abrasive agent. These formulations also do not protect the active molecules from
external heat and UV light. These are having a very limited shelf life.
It has been indicated that slow progress in research on formulation and delivery
systems is a major hurdle to the development of biopesticide products. Besides the

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registration process for BCA in India is too complicated and at par with that of
chemical pesticide which needs to be changed.

4. RESEARCH AND DEVELOPMENT NEEDS AND THE

WAY FORWARD
It is essential to identify BCA which should have broad-spectrum antifungal/
antimicrobial activity and also should be effective over different geographical regions.
It is important to develop biocontrol formulation in such way that the BCA remains
viable, active and infectious for longer period but yet in dormant stage, safe, and easy
for application. The dormancy of bioactive molecules is exogenous, not constitutive,
so the key to prolonging their survival is to stop germination and to reduce metabolism
as much as possible. One possibility for stabilization is dehydration. Another problem
with biopesticides is limited shelf life due to its degradation in presence of UV light,
moisture, pH, etc. Economic feasibility of these product depends on market size and
spectrum of pests affected by the BCA, variability of field performance, costs of
production, and a number of technological challenges, including fermentation,
formulation, and delivery systems.
Essential oils have active ingredients towards many different biological activities
like antimicrobial against pathogens, repellents and antifeedent properties against
insect pests. These naturals can be exploited effectively using nano-emulsion
technology or the active ingredients can be released in a controlled fashion from the
nano-biomaterials. Similarly formulation can be taken up to have floating bioagents
to survive rice ecosystem. Controlled release technology will give a proper coat on
the biopesticides to render limited expose to environment. Limited exposure and
sustained release of biopesticides from controlled release matrices will be most
preferable.
Currently there is a lack of studies concern to the loading of active compounds in
inorganic supports such as the silica nanostructures and also, biogenic silica
nanostructures have not been explored as release rate controlling material of biocides.
Considering these both scientific gaps, the study concerning using biogenic silica
nanostructures as support for active compounds can provide an alternative for green,
controlled-release biocides.
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MS Baite, Naveenkumar B Patil, Prasanthi G, U Kumar,
P Panneerselvam, GP Pandi G, S Lenka, Basanagowda G,
SD Mohapatra, AK Mukherjee, Arvindan S, MK Yadav,
Prabhukarthikeyan SR and K Sankari Meena

SUMMARY
Pesticide is an indispensible part of modern agriculture. Over the years, new
researches from private and public organization are towards developing new molecules
or new formulations which are easy to use, economic and environmentally safe. The
pesticide poisoning and pollution are two major negative effects of pesticides.
Awareness programme should be included to obtain the optimize pesticide use. Proper
pest monitoring, protective clothing, application of pesticide at right time at right
dose and at right quantity should be integral part of pesticide application. Integrated
pesticide resistance management should be included in farm practices and both private
and public organization should take active participation in managing the problem.
Otherwise, there is a great chance that we may not have any pesticide option left in
pest management in near future. Genuine concerns on consumer and environmental
safety of pesticide uses should be dealt with scientific findings. Need of the hour is
to have a readymade pesticide detection kit at affordable price. Long term pesticide
uses and its effect on flora and fauna should be investigated and should be included
in cost-benefit ratio calculation.

1. INTRODUCTION
In India, around 40 per cent of the total cultivated area is treated with the pesticides.
Approximately, 65-70 per cent of the cultivated area treated with pesticides is irrigated.
The production of pesticides started in India in 1952 and at present, India is the fourth
largest global producer of agrochemicals after the US, Japan and China. These pesticide
industries had a value of USD 4.4 billion in financial year 2015 and are expected to
grow at 7.5% per annum to reach USD 6.3 billion by financial year 2020 (FICCI report
2016). Approximately 50% of the demand comes from domestic consumers while the
rest goes towards exports. Consumption of technical grade pesticides in India had a
steady growth over the years (Fig. 1). Andhra Pradesh (including Telangana),
Maharashtra and Punjab are top three states contributing to 45% of pesticide
consumption in India. Pesticides consumption in India is amongst the lowest in the
world at 0.6 kg/ha against ~13 kg/ha in China. Pesticide consumption is biased towards
insecticides (60% of the pesticide used is insecticide) in India as against 40% globally.
Among the crops, cotton and rice consume 57% of the total pesticide consumption.
Rice, a prevalent crop in south-east Asia is attacked by number of pests (Fig. 2) due
to favourable climatic conditions. 15-25% potential of rice production is lost due

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 different pests, weeds and diseases
(Table 1). It compels farmers to use
a major chunk of pesticides to
prevent/recover from pest attack. In
India, Central Insecticide Board and
Registration Committee has
Fig. 1. Pesticide use scenario over the years in recommended 90 pesticides or
value term (The expenditure on pesticide use combination product to tackle wide
was Rs.863 at all India level at constant 2013- range of pest problems. Most
14 price with highest use in the state of Punjab
benefits of pesticides are based only
(Rs.3340/ha) and lowest use in Jharkhand)
on direct crop returns. Pesticide
requirement/demand and import in India is presented in Table 2.

WBPH YSB larva Dead White ear Gallmidge Silver BPH GLH
and adult heart head adult shoot

Hopper Case Case Leaf Leaf folder Hispa Hispa Swarming

burn worm worm folder damage damage caterpillar
damage
Fig.2. Insect pest in rice and damage symptoms.

Table 1. Losses due to pest attack.

Approximate estimated Monetary value
Actual production lossin yield of estimated losses
Crop (milliontonnes) Percent In milliontonnes (millionRs.)
Cotton 44.03 30 18.9 339660
Rice 96.7 25 32.2 240138
Maize 19 20 4.8 29450
Sugarcane 348.2 20 87.1 70667
Mustard 5.8 20 1.5 26100
Groundnut 9.2 15 1.6 25165
Other oilseeds 14.7 15 2.6 35851
Pulses 14.8 15 2.6 43551
Coarse cereals 17.9 10 2.0 11933
Wheat 78.6 5 4.1 41368
Total/Average 17.5 863884
(Dhaliwal et al.2010)

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Table 2. Requirement/demand of pesticides and import of pesticides in India.

Pesticide demand MT(Tech. Grade)
2014-15 2015-16
2010-11 2011-12 2012-13 2013-14 provisional projected
54637 58368 53882 61153 64966 63154
Pesticide consumption MT(Tech. Grade)
55540 52979 45619 60282 57353 -
Source: Standing Committee on Agriculture (2015-2016) Sixteenth Lok Sabha Ministry of Agriculture and Farmers
Welfare (Department of Agricultural Research and Education) Twenty Ninth Report

Post harvest losses were estimated from 9 per cent in developed countries to 20
per cent or more in developing countries due to stored product insects. Concepts of
“a grain saved is a grain produced” and “hidden harvest” should be an integral part
to achieve food security. The most used fumigants are methyl bromide and phosphine.
Methyl brome is being phased out by many countries for its ozone-depleting nature.
Several reports pointed out that due to repeated use of phosphine led to the
development of pest resistance. Lack of new discoveries and strict fumigant
registration has added more challenges. There is an urgent need to evaluate and find
the most effective dose of fumigant against rice storage pests.
Despite the beneficial effects, there is genuine concern over the use of pesticides
and its impact to non-target organisms especially human being. This is because small
amounts of pesticide residues may remain in the crops, either resulted from the direct
use of pesticides on the crops or environmental contamination. In India problems
resulting from unregulated and uncontrolled usage are quite alarming. Over 98% of
sprayed insecticides and 95% of herbicides reach a destination other than their target
species, because they are sprayed or spread across entire agricultural fields.Runoff
and wind may cause non-point pesticide pollution and affecting other species. It is
relevant to know the concentration of pesticides presents in different matrices and if
there is certain scope to avoid the pesticide contamination.
1.1. Objectives
i. To generate baseline susceptibility data for the newer chemistry molecules against
insect pests and diseases.
ii. To study the mechanism of pesticide resistance and management of resistance.
iii. `To investigate long term effect of pesticides on soil flora and fauna
iv. To check pesticide related food and environmental safety issues

2. STATUS OF RESEARCH KNOWLEDGE

2.1. New molecules and assessing their effectiveness against insect-pests
Researchers are working tirelessly to develop safer molecules which could undergo
photo-degradation, microbial degradation as well as chemical degradation leaving

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very less amount of residues in the environment. Accordingly, many conventional
pesticides have been replaced by newer insecticides. These new group of insect
control insecticides includes neonicotinoids, spinosyns, avermectins, oxadiazines,
IGR’s, fiproles, pyrroles, pyridine azomethine, ketoenols and benzenedicarboxamides.
Most of these groups of pesticides play an important role in managing many arthropod
pests with good bioefficacy, high selectivity and low mammalian toxicity, which make
them attractive replacement for synthetic organic pesticides. These novel groups of
pesticides are likely to play an important role in IPM programme in future. Classification
and mode of action of new chemistry insecticides is presented in Table3.
Table 3.Classification and mode of action of new chemistry insecticides as per IRAC
(Insecticide Resistance Action Committee) (IRAC2015).
Chemical class Active ingredients Mode of action
Avermectins, Abamectin, Emamectin benzoate, Glutamate-gated chloride
milbemycins Lepimectin, Milbemectin channel allosteric modulators
Spinosyns Spinetoram, Spinosad Nicotinic acetylcholine
receptor allosteric modulators
Diamides Chlorantraniliprole, Ryanodine receptor
Cyantraniliprole,Flubendiamide modulators
Formamidines Amitraz Octopamine receptor agonists
Neonicotinoides Acetamiprid, Clothianidin, Nicotinic acetylcholine
Dinotefuran, Imidacloprid, receptor competitive
Nitenpyram, Thiacloprid, modulators
Thiamethoxam
Oxadiazines Indoxacarb Voltage-dependent sodium
channel blockers
Phenyl pyrazoles Ethiprole, Fipronil GABA-gated chloride channel
blockers
Pyridine azomethines Pymetrozine, Pyrifluquinazon Chordotonal organ TRPV
channel modulators
Tetronic and tetramic Spirodiclofen, Spiromesifen, Inhibitors of acetyl CoA
acid derivatives Spirotetramat carboxylase

Pesticide mixtures may be more effective against various life stages of arthropod
pests The primary benefits of mixed pesticide formulations are decreasing labour cost
by reduction of rounds of application, higher mortality of different groups of arthropod
pests having separate and distinct feeding habits and delaying resistance development
against a particular pesticide by various pests. Additive or synergistic effects of
insecticides in mixture with botanicals can be obtained to control insect pests (Table
4). Efficacy of insecticides as seedling root dip for YSB in dry season rice has been
worked out as effective and low cost technology (Jena 2004). Chemical control of
YSB has also been worked out, particularly, the oviposition deterrent activity. Thus
the evolution of materials continued with new chemical families discovered and
utilization of them in different formations will offer increased pest protection, reduced
persistence and less polution. Pesticide tested at ICAR-NRRI against insect pest are
presented in Table5.

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Table 4.Status of insecticide mixtures in controlling insect pests.

Pests Chemicals Authors
Nilaparvatalugens Buprofezin 23.1% + fipronil3.85% SC Chakraborty et al. 2017
(Brown planthopper)
Yellow stem borer Lowest per cent of dead heart recorded Neelakanth et al. 2017
in tricyclazole + chlorpyriphos
combination and white ear in
azoxystrobin + chlorpyriphos combination
Yellow stem borer Least per cent of dead heart (1.7%) in Prasannakumar et al. 2011
application of tricyclazole + fipronil

Table 5. Pesticides tested at ICAR-NRRI.

Pests Chemicals Authors
Hispa,leaf folder Phorate, carbofuran, beta cyfluthrin, Rath 2002
and yellow stem thiacloprid, phosphamidon,
borer monocrotophos
Termite, yellow stem Carbofuran, fenvalerate Rath 2005
borer and Gundhi bug
Termite, yellow stem Pyriphos,cypermethrin, phosphamidon, Rath 2006
borer and gundhibug monocrotophos, thiamethoxam,
imidacloprid, endosulfan, carbofuran
and phorate
Yellow stem borer Flubendiamide + buprofezin, Rath 2011; Rath 2012
and gundhibug monocrotophos, acephate,
flubendiamide,dinotefuron,buprofezin
Yellow stem borer Carbofuran,phorate,cartap,chlorpyriphos Rath 2013; Rath 2014
and gundhibug and monocrotophos
Yellow stem borer Sulfoxaflor,acaphate, dinotefuron, Rath et al. 2014;
and gundhibug thiamethoxam, triazophos, buprofezin, Rath et al . 2015
imidacloprid and monocrotophos
Rice hispa, BPH, ear Imidacloprid, bifenthrin, thiamothoxam, Jena and Dani 2011;
cutting caterpillar, indoxacarb Jena et al. 2000
leaf folder and
gundhi bug
Yellow stem borer Chlorantraniliprole Jena et al 2001

3. NEW MOLECULES AND ASSESSING THEIR

EFFECTIVENESS AGAINST DISEASES
Rice diseases cause crop losses about 12.2% of the attainable yield. A wide range
of rice diseases affect rice, like blast, sheath blight, bacterial blight, brown spot, false
smut and several virus diseases, including rice tungro, are of primary concern. As the
major rice diseases are caused by fungus, fungicides are important tool to control rice

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diseases.Globally 8.4% of fungicides market share is for rice.The rice fungicides can
be broadly classified in two categories viz., seed treating and foliar fungicides. Seed
treating fungicides have narrow to moderate spectrum of control. Major advantage of
seed treating fungicides is its high level of control at low dose and with low residue.
Tricyclazole at 0.2g/kg of seed effectively controlled leaf blast. Foliar fungicides are
highly effective in managing foliar diseases and those are grouped as per their mode
of action and chemical class.(a) Melanin biosynthesis inhibitors are highly effective
against rice blast disease; prevent melanin biosynthesis in appressoria of P. oryzae
and penetration to rice plants forming appressoria (e.g. tricyclazole, pyroquilon,
chlobenthiazone etc.) or scytalonedehydratase enzymes (carpropamid,
dichlocymetetc.).(b) Benzimidazole group fungicide (e.g. carbendazim, thiophanate,
thiabendazole etc.) was introduced during 1960s and early 1970s are single site
inhibitors of fungal microtubule assembly during mitosis, via tubulin-benzimidazole-
interactions. (c) Triazole fungicides (e.g. propiconazole, tebuconazole, hexaconazole,
difenconazole etc.), the largest class are highly systemic with mobility through xylem
and are known to have broad spectrum activity against major diseases like sheath
blight, sheath rot, grain discoloration etc. (d) MET II inhibitors (eg. thifluzamide and
flutalonil etc.) inhibit succinate dehydrogenase in fungi and highly effective against
sheath blight. These fungicides are systemic (Xylem mobile) and have good residue.
(e) Strobilurins, first synthetic group fungicides originally derived from mushroom
fungi, called Strobilurustenacellus. These fungicides are referred to as QoI fungicides
(Vincelli2002). Some of the other commonly used strobilurins against rice diseases are
fenamidone, kresoxim methyl, pyraclostrobin and trifloxystrobin either as stand-alone
or mixed with other multi-site inhibitor fungicides or triazoles like propiconazole.
As per Central Insecticide Board, Govt. of India, more than 30 fungicides have
been registered for use in rice and several new molecules are under testing.
Isoprothiolene and Tricyc1azole 75WP were more effective in controlling the blast
disease in nursery in comparision to Isoprothiolene, Tricyclazole, Edifenphos,
Hexaconazole and Mancozeb as seed treatment.In rice, strobilurin fungicide
trifloxystrobin in combination with tebuconazole are used against blast, sheath blight
and other foliar diseases (Bag et al. 2016). Tricyclazole and isoprothiolane are found
highly effective resulting in 87.9 and 83.8% reduction in neck blast and 33.8 and
29.9% increase in grain yield over check, respectively (Sachin and Rana 2011).
Optimum rate of azoxystrobin @ 125 g/ha are highly effective. Biswas and Bag
(2010) reported new QoI fungicides Kresoxim methyl, azoxystrobin,
metaminostrobinand trifloxystrobinand combinations with other groups were highly
effective against sheath blight of rice. Copper hydroxide fungicides reduced false
smut balls in harvested rice by 80% but yield was also often reduced significantly
while Bag et al (2010) reported effectiveness of new formulation of copper hydroxide.
Application of Metaminostrobin 20% SC + hexaconazole 5% SC was effective against
leaf blast and neck blast. Different pesticide tested against rice diseases are presented
in Table 6.

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Table 6. Literature on efficacy of fungicides in managing rice diseases.

S.No. Diseases Fungicides References
1 Blast Tricyclazole and Isoprothiolane Sachin and Rana (2011)
Kresoxim methyl,metaminostrobin and PrasannaKumar et al. (2011)
trifloxystrobin
Tricyclazole and azoxystrobin Kunova et al. 2013
Tetrachlorophthalide 30 WP, Ghazanfaret al. 2009
tebuconazole + trifloxystobin and
difenoconazole
Azoxystrobin and kresoximmethyl Chen et al.2015
Propiconazole Fang et al. 2009
2 Sheath Azoxystrobin and propiconazole Parsons et al.2009
blight Kresoxim methyl,metaminostrobin and PrasannaKumar et al.2011
trifloxystrobin
Thifluzamide PrasannaKumar et. al. 2012
Trifloxystrobin 25% + tebuconazole50% Bag2009
3 Brown Captan 70% + hexaconazole5% WP Kiranand Prasanna 2011
spot @ 0.2%
4 False Zineb and thiophanatemethyl Kannahi et al. 2016
smut Trifloxistrobin + tebuconazole Raji et al. 2016
Copper hydroxide Bag et al. 2010
5 Bakanae/ Carbendazim Bagga et al. 2006
Foot rot
6 Seedling Carbendazim 12% + mancozeb63%, Raghu et al. 2017
blight trifloxystrobin50% + tebuconazole25%.

4. PESTICIDE RESISTANCE-IT CAUSES, HOW TO

OVERCOME IT
Pesticide resistance is a reduction in the ability of an insecticide in achieving the
desired control. This is reflected in repeated failure of a pesticide expected level of
control of pests when used according to the product label recommendations. When
a pesticide is first used, a small proportion of the pest population may survive exposure
to the material due to their distinct genetic makeup. These individuals pass along the
genes for resistance to the next generation. Subsequent uses of the pesticide increase
the proportion of less-susceptible individuals in the population. Through this process
of selection, the population gradually develops resistance to the pesticide. It may be
behavioral, penetration,metabolic or/and altered target-site resistance.In addition,
failure to adhere to good farming practice such as crop rotation and cleaning of farm
equipment, which helps prevent the spread of pest seeds and spores, can exacerbate
the spread of resistance. Fungicides having single site action are more prone to
develop resistant mechanisms in the pathogen compared to those having multi cite
action. Status of insecticide resistance in India and world is given in Table 7.Thus,
industry has given emphasis in the research particularly areas of mode of action,
resistance risk, field monitoring for baseline sensitivity and sensitivity variations in
treated fields.

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Table 7.Status of insecticide resistance in India and world.
S. No. Resistance status Authors
1 In China field-collected populations of Nilaparvatalugens Zhang et al. 2016
had developed high levels of resistance to imidacloprid
(resistant ratio, RR = 233.3–2029-fold) and buprofezin
(RR = 147.0–1222). Furthermore, N. lugens showed moderate
to high levels of resistance to thiamethoxam (RR = 25.9–159.2)
and low to moderate levels of resistance to dinotefuran
(RR = 6.4–29.1), clothianidin (RR = 6.1–33.6), ethiprole
(RR = 11.5–71.8), isoprocarb (RR = 17.1–70.2), and chlorpyrifos
(RR = 7.4–30.7).
2 Most strains of N. lugens (except FQ15) collected in 2015 Mu et al. 2016
had developed moderate resistance to dinotefuran, with
resistance ratios (RR) ranging from 23.1 to 100.0 folds.
3 Field populations collected from different locations of Basanth et al. 2013
Karnataka (Gangavati, Kathalagere, Kollegala, Soraba and
Mandya) were studied for their susceptibility or resistance
to the insecticides and found that the populations from
Gangavati, Kathalagere and Kollegala exhibited higher
resistance to some of the old insecticides and low resistance
to new molecules.
4 Brown plant hopper population collected from east Krishnaiah et al. 2006
Godavari district of Andhra Pradesh exhibited 5- to
35-fold resistance to neonicotinoid insecticides like
imidacloprid, thiamethoxam and clothianidin.
5 Moderate levels of resistance were detected in the field Malathi et al. 2017
populations to acephate, thiamethoxam and buprofezin
(resistance factors 1.05–20.92 fold, 4.52–14.99 fold, and
1.00–18.09 fold, respectively)

4.1. Major factors that influence resistance development

 Continued and frequent use of one pesticide or closely related pesticides on a
insect pest population
 Use of application rates that are below or above those recommended on the label
 Poor coverage of the area being treated
 Frequent treatment of organisms with large populations and short generation
times
 Failure to incorporate non-pesticidal control practices when possible
 Simultaneous treatment of larval and adult stages with single or related compounds.
4.2. Steps to be taken to overcome it
The best strategy to avoid insecticide resistance is prevention. More and more
pest management specialists recommend insecticide resistance management programs

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as one part of a larger integrated pest management (IPM) approach. Monitoring is

one of the key activities in the implementation of an insecticide resistance management
strategy. Monitoring insect population development in fields to determine when
control measures are warranted. Monitor and consider natural enemies when making
control decisions in some cases. Insecticides should be used only if insects are
numerous enough to cause economic losses that exceed the cost of the insecticide
plus application. It is better to have an integrated approach to managing pests.Use as
many different control measures as possible. Avoid broad-spectrum insecticides when
a narrow-spectrum or more specific insecticide will work. Apply insecticides when the
pests are most vulnerable. Use application rates and intervals recommended by the
manufacturer Thus in nutshell the successful management of insecticide resistance
requires monitoring the levels of resistance and understanding the mechanisms
involved. Such studies are necessary to enhance the control efficiency by alternating
appropriate insecticides.

5. UNDERSTANDING ROLE OF PHOSPHINE IN RICE

STORAGE PESTS MANAGEMENT
Phosphine has been in commercial use as a grain fumigant since the mid 1950s.
However, Phosphine (from aluminium phosphide tablet and powder formulations) is
the only fumigant used for grain protection in India since 1970s. More recently its use
has expanded due to the phase-out of methyl bromide as they create ozone depletion.
Multiple phosphine applications (every 3 months during a storage period of 1 to 3
years) of grain stacks are common. Inadequacies in current fumigations such as use
of substandard gas proof sheets and sand stacks, shorter exposure periods (3 to 5
days), failure to measure gas levels, and poor maintenance of gas concentrations
during exposure period are major constraints of successful fumigation.
Phosphine fumigation is an effective method of eliminating insects in stored
commodities in many countries worldwide. It should be noted that there is little to be
gained by extending the exposure period if the structure to be fumigated has not been
carefully sealed and insects are not subjected to lethal concentration of phosphine. It
has been found that as regards technical performance, Quickphos (phosphine source),
when applied either in single or double dosage, exhibited in the control of stored-
product insects such as Rhyzopertha dominica, Sitophilus spp., and Tribolium
castaneum, yielding 100% mortality.Toxic hydrides produce by phosphine cause
changes to cellular and organismal physiology, including disruption of the sympathetic
nervous system, suppressed energy metabolism and toxic changes to the redox state
of the cell. It was recommended that at 1.0, 0.3, and 0.2 mg l-1 complete control can be
expected in 5, 10 and 14 days, respectively for field trial and eventual registration.
The main disadvantages of phosphine fumigant are that the treatment confers no
residual protection against re-infestation, once the commodity is again exposed, and
the fact that the most effective fumigants are all highly toxic to humans and other
non-target organisms. There is no doubt that good fumigation practices also prevent

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insect survival, which is assumed as preventing further insect resistance. Phosphine
resistance in grain beetle pests particularly in Rhyzopertha dominica, Tribolium
castaneum, Cryptolestes spp., has been elaborated. To prevent the development of
resistance, it is essential to avoid applications with sub-lethal doses. Depending on
fumigation circumstances, in particular low temperature and poor gas-tightness of
the container, it is important to use longer exposure to achieve pest mortality in all
parts of the fumigated commodities.In addition it is necessary to achieve a minimum
of 500 ppm for the control of normal insects and at least 1000 ppm when phosphine-
resistant insects are present as target end concentrations.

6. EFFECT OF PESTICIDES ON SOIL MICRO FLORA AND

FAUNA
In the present situation, pesticides application in agriculture becomes a necessary
evil which resulted in contamination of aquatic and soil ecosystems and thus affected
the microbial community inhabit of those ecosystems. Microbial communities are one
of the key drivers of assessing soil health and therefore for the advancement of
sustainable agriculture a proper understanding is to be required to visualize the
changes of soil microflora change under influence of chemical pesticides. Application
of higher dose of chemicals and fertilizers in agriculture actually warrants us to know
the real effect on soil microflora, but complete data are not available to justify the
actual impact of these on soil microbial communities. Besides, there are still multiple
issues which need to be addressed to estimate the effect of pesticides on microbial
communities in the soil in the future, and to make a broadly accepted agenda for risk
assessment in agro-ecosystems that include microbial indicators.
According to guidelines for the approval of pesticides, carbon or nitrogen
mineralization is the most important functional parameters to judge the side-effects of
pesticides on soil microorganisms under any systems (Kumar et al. 2017a). Some
microbial groups use applied pesticides as a source of energy and nutrients, whereas
other groups may be affected by toxic nature of the pesticides. A variation of soil
microbial community under influence of pesticides is a complex phenomenon and
thus provides an insight of two important implications of microbial diversity. Firstly,
a decrease in diversity must have resulted in the risk of alteration of their biological
response in a particular system. Secondly, alteration of microbial diversity itself
provides information about the intensity of such stressed ecosystem. Therefore, it is
necessary to be examined the non-target effect of pesticide on soil microflora and its
diversity under a particular system. Thus, we need to have a wider method to enumerate
soil microflora under pesticide exposure, and usage of latest molecular tools such as
qPCR and metagenome for better understanding the abundance and diversity of soil
microbial community under influence of long-term exposure of pesticides in agricultural
crops including rice.
In the past, a different array of cultivation-dependent and independent methods
were used to analyze the effects of pesticide exposure on soil microflora in the different

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ecosystem, however, under rice soils, it has been nominally investigated (Kumar et
al.2017b; Kumar et al. 2017c). Among all pesticides, 82% of the data refer to insecticides
and on an average, pesticide exposure resulted in the increased and decreased of
bacterial population by 17% and 25%, respectively, whereas, 58% of the cases no
significant change was noticed. The same trend continued to the actinomycetes
population, whereas results indicated that fungal groups were found to be most
sensitive to pesticides. Some reports also indicated that among the different groups,
nitrogen mineralization bacteria (ammonium oxidizers, denitrifiers, and nitrite oxidizers)
were seemed to be the negatively affected by the continuous application of chlorpyrifos
(insecticide) (Kumar et al. 2017a), while other bacteria were relatively less frequently
inhibited. The absence of inhibitory effect on populations of diazotrophs is in
agreement with a very low record of negative effects of pesticide application on
nitrogen fixation in soil (Table 8).

Table 8. Summarization of the data from published reports on the effects of pesticides
on microflora and microbial activities in wetland rice fields (Source: Dey 2012).
Population/Activity Pesticide tested* Effect**
MICROBIAL POPULATIONS F H I - = +
Actinomycetes 0 5 26 4 19 7
Fungi 0 1 25 7 18 1
Bacteria
Total bacteria in soil 0 5 15 4 13 3
Total bacteria in Phyllosphere 0 0 7 0 7 0
Total bacteria in rhizosphere 0 0 7 0 7 0
N cycle other than BNF 0 9 5 6 3 5
N2-fixing bacteria 0 1 20 1 15 6
Various Physiological groups 0 5 5 1 2 7
Miscellaneous groups 0 2 4 3 3 1
Total of Bacterial counts 0 22 63 15 50 22
SoilProperties(N,P,Kavailability) 3 7 0 1 0 8
Specific Enzymatic Activities
Amylase 0 1 8 0 8 1
Cellulase 0 0 8 0 8 0
Dehydrogenase 1 4 3 0 6 3
Dextranase 0 0 7 0 7 0
Invertase 0 1 14 0 15 0
Phosphatase 0 0 13 0 13 0
Urease 0 4 1 0 4 1
â-glucosidase 0 0 13 4 9 0
Others 0 0 2 0 2 0
Total of enzymatic activities 1 10 69 4 72 5

Contd....

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Population/Activity Pesticide tested* Effect**
MICROBIAL POPULATIONS F H I - = +
Microbiological activities
O2 uptake or CO2 Production 0 5 2 2 1 3
OMdecomposition/mineralization 1 2 1 0 4 0
Nitrification 2 6 15 14 6 2
Denitrification 9 9 12 4 16 0
N2-fixation (soil) 8 9 24 1 3 28
N2-fixation (rhizosphere) 0 0 32 13 10 9
Total microbiological activities 20 31 86 34 40 42
Grand total 24 76 269 65 199 85
I: insecticide; H: herbicide; F: fungicide; *Summary per microbiological groups and microbial
activities; ** - inhibition, =: no effect, +: enhancement

7. EFFECT OF CHEMICALS ON THE ABUNDANCE AND

DIVERSITY OF SOIL ARTHROPODS IN RICE ECOSYSTEM
Though not apparent to the naked eye, soil is actually one of the most diverse and
species rich habitats of the terrestrial ecosystem. The total number of described
species on earth (1,500,000) and 23 per cent are soil animals. Historically, most of the
efforts on biodiversity studies focused, especially on above ground plant and animal
species. However, the below ground biota supports much greater diversity of
organisms than does the above ground biota. The under agro-ecosystem, earthworms
were the most dominant organism in terms of biomass, while in terms of numbers, ants
and termites predominated.External agricultural inputs such as mineral fertilizers,
organic amendments, herbicides, fungicides and pesticides are applied with the ultimate
goal of maximizing productivity and economic returns, while side effects on soil
organisms are often neglected. Pesticides and fertilizers are integral part of agriculture
and studies related to their impact are well documented. Pesticides like Aldrin and
DDT, metal pollutants, Zn have adverse impact on soil fauna. Chlorpyriphos application
adversely affected beneficial arthropods like non-Sminthurid Collembolans, ants,
spiders and parasitic hymenoptera. Fertilizer application, pre emergence and post
emergence herbicides had some negative impact on the faunal activity. In Kentucky
blue grass turf, chlorpyriphos and isofenphos had the greatest impact on predacious
arthropods.

8. PESTICIDES RESIDUES IN SOIL-PLANT-WATER

SYSTEM
Upon application, pesticides undergo a very complex series of events. It may
reach to target site to kill the organisms or it may be transported into environmental
matrices through the air or water. Sometimes it may reach into the ground. Distribution
of pesticides depends on its nature and pertaining environment. It has been observed
that there is a significant knowledge gap about movement of pesticide and its fate in

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 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

the environment. Proper pesticide residue analysis across the globe in a network will
help to minimize the pesticide pollution. Every steps to be taken to release minimum
quantity of pesticides to save our environment.
Despite the health risks from pesticides, farmers believe it is indispensable for
higher production. It has been observed at farm level improper use of pesticides has
further contributed to the environmental and health problems resulting from pesticides.
Improper uses may be in the form high dosages, use of non-recommended pesticides,
inadequate pre-harvest intervals and cocktailing of pesticides. Untrained pesticide
shopkeepers play a critical role for improper and more use of pesticides. Most of
developing countries are unsuccessful to regulate the pesticide use and its market
despite its stringent laws.
Pesticides sprayed in field have a less chance to be quantified in rice grains. De-
husking and milling can remove residues at various extent as pesticides are mostly
contained in outer layer of grain i.e. bran. Pesticides are lipophilic in nature and there
is a greater chance they are contained in rice bran. There are very few pesticides can
translocate into the flour. But during grain storage, rice is invariably sprayed with
insecticides to reduce losses. This leads to pesticide contamination in food. In rice
ecosystem, large amount of standing water creates the probable problems of pesticides
contamination in ground and surface water. Leaching or runoff depends not only on
soil properties (clay content, organic matter content etc.) but also on pesticides
properties like solubility, residual half-life, etc. However, to maximize the benefits of
pesticide use at minimum human, environmental and economic cost, pesticides must
be strictly regulated and used judiciously by properly trained and appropriately
equipped personnel, ideally in tight integration with other complementary
technologies.
Continuous application of chlorpyrifos for 7 years did not affect most of soil
microbiota except nitrogen mineralizing microflora (Kumar et al. 2017a). Chlorpyriphos
degradation was faster under elevated CO2 (Adak et al. 2016). Changes in microbial
diversity indices confirmed that imidacloprid application significantly affected
distribution of microbes. The extent of negative effect of imidacloprid depends on
dose and exposure time (Mahapatra et al. 2017). Pretilachlor did not harm the soil
microbes at field dose but affected at higher dose (Sahoo et al. 2016). In-vitro experiment
has been carried out for number of pesticides namely butachlor, bispyribacsodium,
chlorantraniliprole, fipronil etc. to check their distribution in different environmental
matrices and effects on soil microbes.

9. KNOWLEDGE GAPS
In India, work on pesticide resistance and its management have not been given
much emphasis compared to developed countries. Recent reports of pesticide
resistance should be deeply understood to overcome the problem. Consumers are
concerned about the pesticide residue on their food. Simple but exhaustive analytical
method should be developed to quantify minimum quantity of pesticides. Short term

Optimization of Chemical Pesticide use in Rice

429
studies of pesticide poisoning were reported elsewhere. Our study on long term
effect of pesticide will provide inputs on structural and functional changes of soil
flora and fauna upon pesticide application.

10. RESEARCH AND DEVELOPMENT NEEDS

Based on the above observation, generation of baseline information of newer
chemicals about their effectiveness and variation in location should be investigated.
In addition to that, pesticide mixtures should be tried to overcome the resistance
problems. The mechanism of insecticide resistance should be studied for future
research. Impact of long-term pesticides on rice insect pests, soil fauna, microbes and
AM fungal associations in rice-rice cropping system should be determined. Loads of
pesticides in soil- plant- water system should be quantified to make a rice cropping
system more sustainable and eco-friendly.

11. WAY FORWARD

11.1. Managing pesticide resistance
The main purpose of resistance management is to prevent or at least slow down
the accumulation of resistant individuals in insect pest populations, so as to preserve
the effectiveness of available pesticides. The challenge is to reduce the selection
pressure for resistance while providing the necessary level of crop protection. There
is unfortunately no single resistance management prescription that can be applied
globally to all pesticides, insect pests and crops. Nor is resistance solely a technical
problem that can be readily overcome with the right new pesticide with a new mode of
action, or an adjustment in the way conventional pesticides are used. Managing
resistance requires: first, the use of rational pest control strategies based on the
principles of integrated pest management, which reduce pesticide use and hence the
selection pressure for resistance; and second, the implementation of a comprehensive
and tailor-made Resistance Management Plan (RMP) that is adapted to the pest, the
crop and the region.
11.2. Alternative of phosphine fumigations
Alternative to phosphine such as ethylformate, sulfurylfluoride and CO2-rich
atmosphere have been studied both at laboratory and field levels and efficacy proven.
However, these have not been used yet for grain preservation in India. Several plant
compounds have been studied but at laboratory level only. Overall, while there is an
appreciable change in Indian grain storage system by the use of silo bags substituting
CAP storage and by expanding storage capacity by erecting more metal silos across
the county, rigorous changes in fumigation of food grains are yet take place.
11.3. Cheaper methods to detect pesticide residue
Till date pesticides have been quantified through chromatographic methods
coupled to selective detectors, for example, GC-MS, LC-MS-MS. These methods are
efficient, sensitive and reliable. Major limitation of these techniques is time-consuming

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Profitability and Climate Resilience

and costly and need trained technicians. Cheap and easy methods which can reliably
detect pesticides in different food products into the homes have to be developed.
Considerable attention has been given to the development of biosensors for the
detection of pesticides as a promising alternative. Ready to use device like Electronic-
nose (e-nose) methods should be tested for rapid detection of pesticides. This will be
at low cost of detection. Scientists already developed an electronic nose gas-sensing
device. It was based on intrinsically conducting polymer (CP)-type. This device could
identify eleven insecticides representing eight different classes as well as can
discriminate them. Steps have been taken to have in-build library into the e-nose
based on electronic vapor signature patterns.
11.4. Moving towards greener chemicals and green practices in pesticide
usage
In recent years, neonicotinoids and diamides have been the fastest-growing class
of insecticides in modern crop protection, with widespread use against a broad
spectrum of sucking and certain chewing pests. This provides room for more
innovative technology to be developed in application of newer molecule pesticides.
Of such the technologies are 1) Employing pesticides as seed treatment to provide
protection to seedlings against insect pests, and 2) Using insecticides mixtures having
independent mode of action. Dermacor-X-100® (active ingredient, chlorantraniliprole)
seed treatment could be used as a valuable component of integrated pest management
program for stem borers in rice. Research for refined use of seed treatments is
anticipated. Status of insecticide seed treatment in controlling stem borers is presented
in Table 9.

Table 9. Status of insecticide seed treatment in controlling stem borers

Pests Chemicals Authors
Chilopartellus and Chlorpyriphos 20 EC (Seed treatment- Hedge et al. 2017
Sesamiainferens ST + Foliar spray-FS) was found best
among all the treatments
Stem borer complex Dermacor-X-100® (0.1 mg a.i per seed)
in rice in Texas seed treatment provided complete control. Way et al. 2009
(Eoreumaloftini and
D. saccharalis)
Chilopartellus Seed treatment with Spinosad 45%SC Vishvendra et al. 2017
spray @ 200ml/ha

12. CONCLUSIONS
Proper pest monitoring, protective clothing, application of appropriate pesticide
at right time at right dose and target species should be integral part of pesticide
application. Genuine concerns on consumer and environmental safety of pesticide
uses should be dealt with scientific findings. Need of the hour is to have a readymade
pesticide detection kit at affordable price. Long term pesticide uses and its effect on
flora and fauna should be investigated. Mass awareness among end users about
optimization of chemical pesticide use in rice is the need of the hour.

Optimization of Chemical Pesticide use in Rice

431
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 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Improving Protein Content, Glycemic Index,

Mineral Bioavailability and Antioxidant Value of
Rice

Awadhesh Kumar, SG Sharma, Nabaneeta Basak, Gaurav Kumar,

Lotan K Bose, Ngangkham Umakanta

SUMMARY
Rice grain quality is a multifaceted trait and is the prime determinant of consumer
choice and marketability of a variety. Thus, improving nutritional quality occupies an
important position in rice improvement programs. Climate change and its associated
consequences further emphasise upon development of nutrient packed rice grains to
cater to the nutritional needs of the millions of people, who are predominantly
dependent on rice. Currently available rice varieties are poor in grain protein content
which affects the health of rice eating population. Hence, enhancement of total protein
in rice grain along with increase in the amount of essential amino acids such as lysine
and threonine is of immense importance. Recent research at NRRI has led to release of
high protein rice varieties. Though milled rice is normally consumed, brown rice is
nutritionally superior as it is richer in nutrients including minerals. Unfortunately,
milling results in further reduction in the nutritional quality of rice. In addition, rice
contains phytic acid (PA), an anti-nutrient, which further restricts the bioavailability
of divalent cations. Thus, enrichment of mineral profile with reduction in PA content
is also a research priority. As rice is a carbohydrate rich grain, its glycemic index (GI)
is generally high, which makes it unsuitable for consumption by the diabetics. Hence,
research on low GI rice is a priority and has resulted in identification of low GI rice and
an insight into the factors that determine GI. The adverse effect of the changing
climate has seriously affected human health also due to an increase in production of
pollutants that tend to enhance the amount of reactive oxygen species. In recent
times, pigmented rice have received increased attention from consumers for their
inherently high content of bioactive compounds which provides antioxidative, anti-
inflammatory and other health benefits. Several pigmented rice with high anthocyanin
content have been identified. Recently, a cross between a pigmented rice and a white
rice has resulted in grains with an almost black endosperm at NRRI.
In view of the changing life style and global climate, it is imperative to identify and
develop high yielding rice varieties with better nutritional profile that suit even
diabetics and also ensure better availability of nutrients including minerals and
antioxidants.

1. INTRODUCTION
Rice, a dietary staple for half of the world’s population, accounts for 27% of
dietary energy supply, 20% of dietary protein and 3% of dietary fat. Removal of the
inedible husk of the paddy grain results in brown/unprocessed rice which is

Improving Protein Content, Glycemic Index, Mineral Bioavailability and

Antioxidant Value of Rice 435
nutritionally rich but has shorter shelf life. As a result, milling is carried out to remove
the aleurone layer. This leaves the starchy grain deficient in many nutrients including
protein, oil and micronutrients (vitamins and trace minerals) which are further lost
during washing and cooking. Thus identification and development of nutritionally
superior rice is a research priority to popularize consumption of rice varieties with
high grain protein content, mineral bioavailability and high antioxidant value. This
becomes more important in the context of changing climate, which demands that the
masses consume nutrient dense food. The objective of the present chapter is to
elaborate on the nutritional quality of rice particularly in relation to protein content,
glycemic index, mineral bioavailability and antioxidant value.

2. HIGH PROTEIN RICE

Milled rice is low (6-7%) in protein content (Juliano 1964). Over the past decades,
improvement in protein content of milled rice has been a key nutritional target in
breeding programs. The nutritional status of a variety is mainly dependent on its
protein content. Rice protein, when compared to that of other grains, is considered
one of the highest quality proteins. It has all eight of the essential amino acids with a
biological value of 86 (the BV of 70 or above indicates acceptable quality). Though, it
is a good source of aspartic and glutamic acids, it provides insufficient amounts of
lysine and threonine resulting in serious malnutrition.
The enrichment of rice grains with protein would have a positive effect on the
health of billions of people around the globe particularly the poor and the
malnourished. Scientists have been attempting to augment the protein content either
by N-fertilization or by genetic manipulations. Significant progress has been made in
understanding the factors affecting grain protein content and the complexity of
inheritance of the trait. Though, seed protein content has been known to show a
negative correlation with yield, the capacity to combine greater yield and high protein
content has been reported in cereals like wheat and oats (Vasal 2002). Exploitation of
the reservoir of genetic variability present in the landraces and germplasm for
conventional breeding programs is an effective method for improving protein content
of rice.
Rice seed storage proteins accumulate in two types of protein bodies-PB1 and PB
II. The former is indigestible and negatively affects protein quality. Grains richer in
prolamin fraction of proteins are not considered to be of high nutritional quality as
the fraction has low levels of lysine, arginine and histidine.
2.1. Achievements in high protein rice research
The trait for high grain protein content (GPC) has been transferred to high yielding
background of many cereals such as wheat and oat (Vasal 2002) and subsequent
marker validation has also been achieved. In case of rice, many QTLs along with the
associated markers have been identified for ensuing transfer of GPC to high yielding
background. But due to low heritability and significant influence of crop nutrient

Improving Protein Content, Glycemic Index, Mineral Bioavailability and

436 Antioxidant Value of Rice-
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

management practices, improvement of rice varieties for this quantitative trait through
simple breeding scheme was considered a real challenge. The ICAR-NRRI, Cuttack
pioneered research and developed two high protein rice varieties in 2016.
A wide range of variability observed by screening of world rice germplasm at
International Rice Research Institute indicated that GPC varied from about 5% to 18%
with an average of 9.5% which indicated the possibility for improvement of rice GPC.
Pedigree and long cycle recurrent selection were followed in earlier rice breeding
programmes at IRRI, Philippines and negative correlation between yield and protein
content was reduced to a significant level. However, the developed high protein lines
were not accepted either due to deviation in grain type and cooking qualities from the
adapted parent IR 8, or due to low stability of their protein yield. In a hybrid between
IR 64 and O. nivara, the expression of the prolamin band was much intense than the
parents. But the nutritional value of prolamin is inferior to that of glutelin for its low
digestibility and negative influence on cooking quality as it increases the hardness of
cooked rice. An inbred, high-protein, rice cultivar development project was initiated
at the Louisiana State University Agricultural Center in 2005. The rice ‘Frontière’
containing 11% protein (Reg. No. CV-150, PI 674794) was the first cultivar produced
by this project, which was released in 2015. It was developed from the cultivar Cypress
through induced mutation by means of cellular selection. It had excellent milling
quality (60.5% whole grain and 68.9% total milling yield), an average amylose content
of 21.8%, and an intermediate gelatinization temperature (Wenefrida et al. 2017).
Researchers from the University of Agricultural Sciences (UAS) developed a high
protein rice strain, which has 12 to 13% protein in grain and a 20% increase in the
amount of lysine, an essential amino acid (Satish Kumar 2016). A protein-enriched rice
variety developed by Indira Gandhi Krishi Vishwavidyalaya (IGKV) with over 10%
grain protein (which is 3% more than what is found in popular varieties) and 30 ppm
zinc (Rewari 2016).
The ICAR-NRRI, Cuttack has evaluated about 3000 rice germplasm for grain protein
content since 2004 and found wide diversity for the trait (5-15%). Two low yielding
germplasm from Assam rice collection (ARC10075 and ARC10063) with high grain
protein content (13-15%) in brown rice were identified (Table 1). The Institute has
developed protein rich lines in high yielding backgrounds of popular varieties Naveen

Table 1. High protein rice varieties identified by ICAR-NRRI, Cuttack.

Cultivars/ Crude Protein content Cultivars/ Crude Protein content
genotype (%) in brown rice genotype (%) in brown rice
PB-140 12.5-15.45 Bindli 11.93-13.8
CR Dhan-310 11.5-12.5 PB-84 12.2-13.8
ARC-10075 11.5-12.5 PLN-100 (CR Dhan311) 11.5-12.4
Kalinga-III 11.2-11.9 PB-177 11.8-13.59
PB-312 14.3-15.79 Naveen 7-7.5
Mamihungar 12.5-13.5 Swarna 6.9-7.5
PB-170 12.6-14.15

Improving Protein Content, Glycemic Index, Mineral Bioavailability and

Antioxidant Value of Rice 437
and Swarna, which suit irrigated and favourable rainfed system. Stability for yield and
protein yield were tested for three years. They were used in bulk-pedigree and
backcross breeding programme. The following two varieties were released in 2016 by
NRRI, Cuttack with high protein content:
 High Protein rice CR DHAN 310 was released by CVRC in 2016. This is the first
high protein (10.2%) rice variety at national level and has medium slender grains.
This is an introgression line (CR 2829-PLN-37) in Naveen background. The average
grain yield at national level was 4.5 t ha-1.
 Nutrient rich rice MUKUL (CR Dhan 311) (IET 24772: CR2829-PLN-100) was released
in Naveen background by SVRC, Odisha in 2016. It has high protein (10.1%) and
moderately high level of Zn (21 ppm). It is medium early (125 days) with long bold
grain. The average yield at national level was 4.1 t ha-1.
Higher quantity of both α-and β-glutelin in some of the high protein lines indicated
enhancement of nutritional quality of this variety. These breeding lines did not show
any significant changes in the intensity of prolamin band. Moreover, the prolamin/
glutelin ratio in high protein lines either
remained the same or was lower as
compared to Swarna, indicating that the
protein quality either remained the same
or was improved by the breeding process.
A simple and rapid method to
differentiate between the parent Naveen
(7.5% protein) and its high protein version
CR Dhan 310 was developed by ICAR-
NRRI. It was found that the xanthoproteic
test, the qualitative test used for
Fig. 1. Rapid color test (xanthoproteic test) confirming the presence of protein in a
to distinguish between low and high protein sample could easily distinguish between
grains the two varieties on the basis of intensity
of color produced (Fig. 1).
2.2. Challenges and way forward
Scientific knowledge regarding the process of nitrogen uptake, assimilation and
partitioning leading to the significant difference in high and low protein grains needs
to be analyzed. The amino acid profiling also needs to be carried out to identify
lysine/threonine rich varieties, because threonine forms a bigger part of the digestive
tract mucosal proteins. Screening of more germplasms should also be an integral part
of future program. The available germplasm is to be explored for nutrient dense rice
with higher protein content, biological value and better amino acid profile. Further
characterization of high protein rice cultivars/germplasm for resistant starch,
bioavailability of Zn, amino acid profile, antioxidant value and phytic acid needs to be
carried out. Biofortification using biotechnological approaches needs to be used as a

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438 Antioxidant Value of Rice-
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sustainable alternative to develop protein rich rice with higher amounts of lysine and
threonine to meet the daily nutritional requirements of humans.

3. GLYCEMIC INDEX OF RICE

The concept of glycemic index (GI) of foods developed by David Jenkins, Thomas
Wolever and colleagues at the University of Toronto in 1981 ranks the quality of
individual carbohydrate-rich foods on a scale of 1-100 by measuring how blood
glucose levels rise after someone eats an amount of food that contains 50 grams of
available carbohydrate. Foods are classified as low GI (GI, 55 or less), medium GI (GI,
56-69) and high GI (GI, 70 or more) types, when D-glucose is given a GI of 100. Foods
with a low GI score provide steady fuel to support energy levels and overall health,
while those with a high GI score are likely to provide an unhealthy quick rush of blood
sugar followed by a sharp crash. Refined, processed starches/fruits have higher GI.
Whole grains, high fiber foods, whole fruits, vegetables and legumes have lower GI.
People living sedentary lifestyle and overeating foods, especially rice are likely to
invite some health complications like type II diabetes and obesity. Presently, more
than 62 million individuals are diagnosed with diabetes in India, which may rise to
79.4 million by 2030. This would involve huge financial burden on treatment of people.
The GI value of rice varies from 48-92. A high dietary glycemic load (predominantly
from rice) has been associated with increased risk of type 2 diabetes mainly in Chinese,
Japanese and Indian populations. The development of low GI rice becomes a priority,
as rice is eaten by a large number of people, many of whom are diabetics, mainly with
type II diabetes.
3.1. Achievements
Rice is nearly 90% carbohydrate on dry weight basis. The average GI value of rice
(including the brown and milled grains) is 64 (Atkinson et al. 2008). Rice contains less
than 3% RS (mainly of type 5) which escapes digestion almost entirely and therefore,
its calories are unavailable for cells to use. RS positively influences the functioning of
the digestive tract, microbial flora, blood cholesterol level, GI and helps to control
diabetes (Fuentes-Zaragoza et al. 2010). The more the RS, the slower the digestion of
rice and consequently the lower is the GI. Several investigators have reported that
varieties with high-amylose content (AC) exhibit lower GI values than the low-amylose
varieties (Denardin et al. 2007). The GI and RS contents have been established as
important indicators of starch digestibility. Varieties with low GI and high RS content
tend to lower the glycemic response (GR) due to slow release of glucose in small
intestine, thus lowering the insulin response and controlling the rise in blood glucose
(Englyst et al. 1992). In a study of US men and women, a moderate inverse association
between diabetes risk and brown rice consumption was observed, although
contradictory reports have also been received (Sun et al. 2010). Dietary intervention
methods form the cornerstone of diabetes prevention/ management and are primarily
aimed at maintaining a low and stable postprandial blood glucose level. There is
evidence to suggest that low GI diets reduce the incidence of diabetes, hyperlipidaemia

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Antioxidant Value of Rice 439
and cardiovascular disease. Glycemic index values of milled rice of popular Indian
varieties are higher (70-77) compared to those of brown rice (50-87) as per the 2008
international GI table.
At the ICAR-NRRI, more than 100 rice
cultivars from different ecologies have
been evaluated for GI and RS content of
brown and milled rice. Further, the in vitro
method for GI estimation of Goni et al.
(1997) was improved (Fig. 2). Large
variations in the values of GI (60-70), RS
(0.35-2.57%) and AC (03.79-23.32 %) were
observed. Among the genotypes
studied, Mahsuri had lowest GI (60) and
highest RS (2.57%). The highest value
for GI (70) was found for Abhishek with
Fig. 2. Flow chart of in vitro GI estimation
protocol relatively low RS (0.83%). O. brachyantha
grains had the lowest RS content (0.35%)
with relatively high GI (69) (Fig. 3). Expression analysis of gbssI in developing grains
of three rice genotypes differing widely in GI, RS and AC resulted in maximum expression
in Mahsuri at middle stage showing a positive correlation between RS content and
gbssI expression (Kumar et al. 2017).

Fig. 3. Correlation between GI and RS values of different rice

genotypes

3.2. Challenges and way forward

Presently, very little information is available on GI values of processed, pigmented
and scented rice. Similarly, comparative studies on GI of brown and milled rice of
popular varieties are also rare. The role of degree of branching of amylopectin is also
not understood. There is little information available on how addition of different

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foods to rice affects the starch digestibility and GI value. An effective approach, to
help check diabetes would be to screen all available germplasm for GI, AC, fiber and
RS and popularize low GI rice among the rice eating population. Breeding for low GI
rice can also be attempted by transferring the trait to popular high yielding varieties.
As rice is often eaten with pulses, vegetables, curd, milk, cooking oils, and condiments
etc., their effect on GI of rice also needs to be studied. Effect of processing, soaking
and cooking methods on GI also needs attention.

4. ANTIOXIDANT VALUE OF RICE

Antioxidants, the substances found in foods and dietary supplements help protect
cellular constituents like proteins, lipids and DNA against the damage caused by
free-radicals including reactive oxygen species (ROS), which are routinely produced
during aerobic energy metabolism in our body. Brown rice (BR) or dehusked rice,
which is obtained when paddy (rough rice) is subjected to hulling is rich in bioactive
components such as dietary fiber, functional lipids, amino acids, vitamins, phytosterols,
phenolic compounds, gamma-aminobutyric acid (GABA), minerals and many
antioxidant molecules. Flavonoids, the water soluble polyphenolic molecules
containing 15 carbon atoms are a group of plant metabolites, which are thought to
provide health benefits through cell signalling pathways and antioxidant effects and
are divided into six major subtypes, which include chalcones, flavones, isoflavonoids,
flavanones, anthoxanthins and anthocyanins. Ramarathnam et al. (1989a; 1989b) first
identified the flavonoid isovitexin, alpha -tocopherol, and gamma-oryzanol in rice as
having antioxidant activities comparable to that of butylated hydroxyanisole, (BHA),
a common food preservative. To satisfy consumer’s needs, the rice grains are usually
milled into white rice, while the bran and husk are discarded. Most of the antioxidants
are confined to the bran layer and endosperm and thus are largely absent from the
milled rice. Pigmented rice is now gaining popularity because of its documented
health benefits. In addition to its high protein, vitamin, and fiber content, it is a good
source of a variety of phytochemicals including polyphenols, isoflavones,
phytosterols, and anthocyanidins that have several beneficial functions in human
health. The nutritional advantages offered by both brown and pigmented rice
necessitate their inclusion in the daily diet to a greater extent. Hence, characterization
of the colored and other rice for their antioxidant value needs to be a priority.
4.1 Achievement
Pigmented rice have been documented to be rich in protein, vitamins, fiber,
phytochemicals, such as polyphenols, isoflavones, phytosterols, and anthocyanidins
which provide several health benefits. They have been found to be high in bioactive
compounds like phenolics, tocols and sterol derivatives presenting antioxidant, anti-
inflammatory and other benefits. Polyphenols, such as phenolic acids, anthocyanins,
and proanthocyanidins, have been reported as the major antioxidants in rice. Generally,
white rice contains mainly phenolic acids; red rice is characterized by the presence of
procyanidins, whereas black rice is characterized by the presence of anthocyanins.

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Antioxidant Value of Rice 441
The distribution of phenolic acids exhibits varietal differences; rice bran had the
highest total phenolic content (TPC) among four different fractions of whole rice
grain. Overall, ferulic, p-coumaric, isoferulic, syringic, vanillic, sinapic, caffeic, p-
hydroxybenzoic, and protocatechuic acid are present in the whole rice grain, of which
ferulic acid is the most abundant phenolic acid in the insoluble-bound fraction. The
phenolic contents were positively correlated with the antioxidant capacity. In black
rice, anthocyanins accumulate in the outer layers as free forms and cyanidin-3-O-
glucoside and peonidin-3-O-glucoside have been identified in black rice bran as the
main anthocyanin components. Pang et al. (2018) studied the total phenolic content
(TPC), individual phenolic acid and antioxidant capacity of whole grain and bran
fraction of 18 rice varieties with different bran color. The levels of TPC in bound
fractions were found to be significantly higher than those in the free fractions either
in the whole grains or bran. The study also concluded that there is wider diversity in
the phenolics and antioxidant capacity in the whole grain and bran of rice.
Fourteen pigmented hill rice cultivars were studied for ascertaining the extent of
their nutritional and genetic diversity. The total phenolic content was almost 50%
higher in the pigmented rice as compared to non-pigmented rice. The range of DPPH
(2,2-diphenyl-1-picrylhydrazyl) scavenging activity of 14 pigmented hill rice cultivars
varied from 19.56% in Maichukik to 29.29% in Joradhan with an average value of
23.80%; no activity was detected in non-pigmented rice Vandana. Both the yellow
and black varieties of the medicinal rice Njavara had higher antioxidant activity, higher
bioactive compound content and higher anti-inflammatory activities than the staple
rice varieties. Kaur et al. (2017) reported strong positive correlation between total
phenolics and the antioxidant activity in non-pigmented rice varieties, whereas phytic
acid content was negatively correlated with the antioxidant activity.
Research at the ICAR-NRRI, Cuttack showed that the total anthocyanin content
(TAC), TPC and antioxidant activity (ABTS) differed significantly among the pigmented
genotypes with highest values of these parameters in the purple grain (Mamihungar),
whereas no significant difference between the colour groups (red and purple) was
observed for total flavonoid content (TFC), gamma-oryzanols and phytic acid content
indicating that value of these parameters depends on genotypes and not on kernel
color. A high correlation of TAC with TPC and ABTS suggests that the major
phytochemicals responsible for the tested antioxidant activities are phenolic acids
and anthocyanins (Sanghamitra et al. 2017). Recently, a cross between Manipuri
black rice and a white rice has resulted in grains with an almost black endosperm at
NRRI. The variety may provide health benefit due to its high antioxidant content.
4.2 Challenges and way forward
Although a large number of pigmented rice are grown in different pockets of
India, there is little information on the types of such landraces, their area of cultivation,
nutritional composition (especially with respect to antioxidant molecules) and the
possible health benefits. Total antioxidant activity is significantly contributed by
tocopherols, tocotrienols, and gamma-oryzanols (shown to reduce blood cholesterol
level). Hence, different pigmented and white rice need to be evaluated for individual

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antioxidant including gamma oryzanols. The genetic diversity found in the cultivars
may be considered as a need to select the best performers amongst themselves with
respect to the contents of nutritive and antioxidant principles as well as the antioxidant
activity. Promising candidates thus selected can be utilized for developing improved
lines in future breeding programmes.

5. MINERAL BIOAVAILABILITY
In Asia, rice serves as the major source of energy, protein, iron (Fe), zinc (Zn) and
calcium (Ca) in the diet. Fe and Zn are essential trace elements in human nutrition and
their deficiencies are major public health threats worldwide. Unfortunately, rice does
not furnish minerals adequately, because it contains only small amounts of Fe and
Zn, and the loss of minerals (particularly Fe) during milling is high. In addition, rice
contains phytic acid (PA), the most important anti-nutritional factor impeding
availability of divalent cations. Approximately 70% of total phosphorus in seeds
coexists with PA and its content typically accounts for 1% or more of seed dry weight.
As an anti-nutrient, high levels of PA can affect the bioavailability of essential minerals
such as Zn, Fe and Ca, as it is a strong chelator of divalent cations. The anti-nutritional
properties of PA can be further extended to human health, as it is considered to be the
most important anti-nutritional factor contributing to the iron deficiency suffered by
over 2 billion people worldwide. Phytic acid also has the potential to bind charged
amino acid residues of proteins, with the concomitant reduction of protein availability.
The undesirable properties of PA make the development and characterization of low
phytate crops a high priority in agricultural research.
Nearly 80% Indians consume rice as a staple food making it the major source of
carbohydrate and micronutrients such as Fe, Zn and vitamins. However, Fe and Zn
content of rice grains is low, which is further reduced significantly during processing
and by the presence of PA, which further limits their bioavailability. Micronutrient
malnutrition, particularly, Zn deficiency affects 49% of the world population that
accounts for 3-4 billion people, while over 2 billion people suffer from Fe deficiency
worldwide. It is thus necessary to improve net content and bioavailability of both Fe
and Zn from rice grain by identifying Fe, Zn rich and low PA rice cultivars.
5.1. Achievements
Kiers (2000) reported that though the cereals and legumes are rich source of
nutrients and antioxidants, they also contain indigestible constituents such as non-
starch polysaccharides, phenolic compounds, tannins and phytic acid. Brown rice is
richer than milled rice in terms of protein, fat, vitamins and minerals but also has
higher amounts of dietary fiber and phytate that may inhibit absorption of minerals.
Phytic acid, considered as a significant inhibitor of minerals can form strong complexes
with Fe and Zn in grains and limits the bioavailability of these microelements thereby
reducing the nutritional value (Raboy 2001). Phytate is indigestible to humans or
non-ruminants due to lack of appropriate digestive enzymes and is thus excreted as
sanitary sewage into waterways resulting in eutrophication of water bodies (Swick

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Antioxidant Value of Rice 443
and Ivey 1992). In addition, phytate also inhibits the enzymes (like amylase, pepsin
and trypsin) that digest food in the gut. Food fortification has been recommended as
one of the preferred approaches for preventing and eradicating Fe and Zn deficiency.
The bioavailability of minerals in rice can also be enhanced by selecting varieties with
inherently high mineral content and cultivating them under good agricultural practices
together with screening of lines with low PA and high mineral content. Considering
the world-wide deficiencies of Fe and Zn, research work has been initiated to find the
extent to which grain PA affects the bioavailability of Fe/Zn and to identify varieties
that exhibit highest bioavailability of the two minerals. Out of the 70 rice varieties
analyzed for PA content, six were evaluated for Fe and Zn bioavailability from brown
and milled rice. An inverse relationship was found between PA content and Fe/Zn
bioavailability in the brown rice of these varieties. Bindli, which had the lowest PA
(0.82%), showed highest Zn bioavailability (21%), while PB267, which had the highest
amount of PA (2.62%) showed low bioavailability of Zn (18%) and Fe (26%) (Kumar et
al. 2017). The bioavailability of Zn increased after milling because most of the amount
of this mineral is present in endosperm, while that of Fe decreased, most likely because
the major amount of Fe is found in the bran layer (Fig. 4 and 5).

Fig. 4. Total Fe content and its bioavailability in brown and milled rice of six
cultivars with contrasting PA content.

Fig. 5. Total Zn content and its bioavailability in brown and milled rice of
six cultivars with contrasting PA content.

5.2 Challenges and way forward

The information on PA value of brown and milled rice of most popular Indian
varieties is not available. Similarly, information about other compounds present in
rice grains which may affect minerals bioavailability along with PA is not available.
Screening of rice genotypes, identification of those with low PA and high mineral

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bioavailability and their popularization would help those suffering from micronutrient
malnutrition. Research needs to be initiated for the assessment of impact of certain
indigestible constituents such as non-starch polysaccharides, phenolic compounds
and tannins on minerals bioavailability. The minimum safe content of PA in seed
needs to be determined and studies on grain specific phosphorus transporter are
required to help develop low phytate lines.
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and Sharma SG (2018) Resistant starch could be decisive in determining the glycemic index
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reduce pollution. Trends in Plant Science 6:458-462.
Ramarathnam N, Osawa T, Namiki M and Kawakishi S (1989a) Chemical studies on novel rice hull
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developed-by-igkv-will-help-millions-of-undernourished-people/).
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Satish Kumar BS (2016) A more muscular rice variety takes on wheat. The Hindu, December 09,
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wheat/article16780286.ece).
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Profitability and Climate Resilience

Improvement of Photosynthetic Efficiency of

Rice: Towards Sustainable Food Security under
Changing Climate

MJ Baig, P Swain, K Chakraborty, A Kumar, KA Molla and

G Kumar

SUMMARY
According to various estimates, we will have to produce 40% more rice by 2025 to
satisfy the growing demand without affecting the resource base adversely. This
increased demand will have to be met from less land, with less water, less labor and
fewer chemicals. Most of our conventional crops, including rice and wheat, assimilate
atmospheric CO2 by the C3 pathway of photosynthesis, which takes place in the
mesophyll cells of leaves. Photosynthetically, these plants are underachievers because
on the one hand, they assimilate atmospheric CO2 into sugars but on the other hand,
part of the potential for sugar production is lost by respiration in daylight, releasing
CO2 into the atmosphere, a wasteful process termed photorespiration. C4 plants exhibit
many desirable agronomic traits: high rate of photosynthesis, fast growth and high
efficiency in water and mineral use. In this chapter we will discuss various aspects of
improvement of photosynthetic efficiency and creation of a C4 rice plant which has
the potential to generate substantially higher farm yields and make an important
contribution to global poverty alleviation efforts.

1. INTRODUCTION
Rice is an important food crop which feeds for more than half of the global
population. It accounts for 35-75% of the calories consumed by more than 3 billion
Asians as more than 90% of the world’s rice is grown and consumed in Asia which is
home to 60% of the human population. The crop is planted to nearly 154 million
hectares annually which makes up 11% of the total cultivated land on the earth.
About 75% of India’s poor people with low purchasing power live in rural areas and
nearly 60% of the cultivated area is under rainfed farming. According to various
estimates, we will have to produce 40% more rice by 2025 to satisfy the growing
demand without affecting the resource base adversely. This increased demand will
have to be met from less land, with less water, less labor and fewer chemicals. If we are
not able to produce more rice from the existing land resources, the hungry farmers will
destroy forests and move into more fragile lands such as hillsides and wetlands with
disastrous consequences for biodiversity and watersheds. To meet the challenge of
producing more rice from suitable lands, we need the rice varieties with higher yield
potential and greater yield stability. Most of our conventional crops, including rice
and wheat, assimilate atmospheric CO2 by the C3 pathway of photosynthesis, which
takes place in the mesophyll cells of leaves. Photosynthetically, these plants are

Improvement of Photosynthetic Efficiency of Rice: Towards Sustainable Food

Security under Changing Climate 447
underachievers because on the one hand, they assimilate atmospheric CO2 into sugars
but on the other hand, part of the potential for sugar production is lost by respiration
in daylight, releasing CO 2 into the atmosphere, a wasteful process termed
photorespiration. This is due to the dual function of the key photosynthetic enzyme,
Ribulose 1, 5-bisphosphate carboxylase/oxygenase (Rubisco). High CO2 favors the
carboxylase reaction and thus net photosynthesis, whereas high O2 promotes the
oxygenase reaction leading to photorespiration. Photorespiration reduces net carbon
gain and productivity of C3 plants by as much as 40%. This renders C3 plants less
competitive in certain environments. In contrast, with some modifications in leaf
anatomy, some tropical species (e.g., maize and sugarcane) have evolved a biochemical
“CO2 pump,” the C4 pathway of photosynthesis to concentrate atmospheric CO2 in
the leaf and thus overcome photorespiration. Therefore, C4 plants exhibit many
desirable agronomic traits: high rate of photosynthesis, fast growth and high efficiency
in water and mineral use.
The single cell C4 photosynthetic system has given us the clue that it may be
experimentally feasible to genetically engineer all C4 genes in a single cell of C3 plants,
say rice to enhance its photosynthetic activity and productivity. However, at the CO2
compensation point, net CO2 assimilation equals CO2 release through photorespiration
and mitochondrial respiration in light. In high CO2 and /or low O2, the oxygenase
activity of Rubisco is virtually absent, the flux through the photorespiratory carbon
cycle negligible and the CO2 compensation point close to zero. Rice being a C3 plant,
the first product of atmospheric CO2 fixation is the 3-carbon compound 3-
phosphoglycerate (3-PGA), which is produced during the Calvin cycle by Rubisco
(the only enzyme capable of net carbon assimilation) in the chloroplast stroma.
However, competition of O2 with CO2 at the active site of Rubisco results in a loss of
up to 50% of the carbon fixed in a process known as photorespiration. Oxygenation
of Ribulose-1,5-biphosphate (RubP) severely diminishes the efficiency of CO2
assimilation in rice under ambient air and results in the formation of 3-PGA as well as
2-phosphoglycolate (2-PGA). The latter is metabolized in the compartments of the
leaf cell, the chloroplast, the peroxisomes and the mitochondria, involving numerous
enzymatic reactions and transport processes. The overall photorespiratory cycle is
also linked to amino acid metabolism in that glycine, serine, glutamate and glutamine
are metabolized at high rates. Both CO2 and ammonia are released at equal rates in the
reaction catalyzed by the mitochondrial glycine decarboxylase complex. By introducing
the Escherichia coli glycolate catabolic pathway into rice, the loss of fixed carbon
and nitrogen due to photorespiration can be reduced to a great extent. Using step-
wise transformation with five chloroplast-targeted bacterial genes encoding glycolate
dehydrogenase, glyoxylate carboligase and tartronic semialdehyde reductase, the
plants may be generated in which chloroplastic glycolate is converted directly to
glycerate. This would reduce, but not eliminate, flux of photorespiratory metabolites
through peroxisomes and mitochondria. Such plants thus, may grow faster, produce
more shoot and root biomass, and may contain more soluble sugars, reflecting reduced
photorespiration and enhanced photosynthesis that correlate with an increased
chloroplastic CO2 concentration in the vicinity of Rubisco. These effects are evident
after over-expression of the three subunits of glycolate dehydrogenase but were
enhanced by introducing the complete bacterial glycolate catabolic pathway. Diverting

Improvement of Photosynthetic Efficiency of Rice: Towards Sustainable Food

448 Security under Changing Climate
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chloroplastic glycolate from photorespiration may improve the productivity of rice

with C3 photosynthesis.
Atmospheric CO2 concentrations has increased significantly in the past two
centuries, from 270 μmol mol-1 in 1750 to current concentrations which exceed 400
μmol mol-1. The primary effects of elevated CO2 levels in most crop plants, particularly
C3 plants, include increased biomass accumulation, although initial stimulation of net
photosynthesis rate is only temporal and plants fail to sustain the maximal stimulation,
a phenomenon known as photosynthesis acclimation. Increase in CO2 has double
effect on C3 (rice) plants such as an increase in leaf photosynthesis and a decrease in
stomatal conductance to water vapor. Elevated CO 2 levels increase net leaf
photosynthetic rate primarily by competitive inhibition of the oxygenase activity of
Rubisco and therefore photorespiration; and by acceleration of carboxylation because
the CO2 binding site is not saturated at the current CO2 levels. Rubisco catalyzes the
competitive reactions of RuBP carboxylation and RuBP oxygenation. It has long been
recognized that genetic modification of Rubisco to enhance its specificity for CO2
relative to O 2 would decrease photorespiration and potentially increase C 3
photosynthesis and correspondingly crop productivity. Although Rubisco has been
the primary focus of research to improve photosynthetic efficiency, it has been clearly
demonstrated that metabolic control of CO2 fixation rate is shared among different
enzymes in the pathway.
The enhancement of photosynthetic efficiency has emerged to provide a vital
opportunity to address the challenge of sustainable yield increases needed to meet
future food demand. Attaining higher photosynthesis rates for the same or decreased
use of water and nitrogen resources could be the crucial point to transform the
agriculture of the twenty-first century.
The CO2 concentrating mechanism, together with modifications of leaf anatomy,
enables C4 plants to achieve high photosynthetic capacity and high water and nitrogen
use efficiencies and ultimately high yield. As a consequence, the transfer of C4 traits
to C 3 plants is one strategy being adopted for improving the photosynthetic
performance of C3 plants. Improving the photosynthetic efficiency and creation of a
C4 rice plant has the potential to generate substantially higher farm yields and make
an important contribution to global poverty alleviation efforts.

2.PHOTOSYNTHESIS AND ITS CLASSIFICATION

Photosynthesis is the process by which plants, some bacteria, and some protistans
transform light energy into chemical energy.
The overall reaction of this process is: 6H2O + 6CO2—————> C6H12O6+ 6O2
2.1.C3 and C4 photosynthesis
The difference occurs in the second part of photosynthesis, the Calvin-Benson
cycle, which “fixes” CO2 into carbohydrates. As CO2 is used up by the normal Calvin-
Benson cycle, the balance of CO2: O2 inside the leaf alters in favor of O2, and Rubsico
starts to grab it instead. This both slows down photosynthesis and reduces its
carbon fixation overall.

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 The C4 plants have introduced an extra bit into the Calvin-Benson cycle, an extra
early reaction that fixes CO2 not into 3-carbon sugars, but 4-carbon compound called
oxaloacetate by plunking CO 2 onto a different receptor molecule
(phosphoenolpyruvate, or PEP) by way of the enzyme PEP carboxylase, which has
two advantages over Rubisco: it has no affinity for O2 at all, and it finds and fixes CO2
even at very low CO2 levels. Oxaloacetate has an advantage over 3PG, in low CO2
circumstances some of it degrades to form CO2 again in the mesophyll, the cells which
carry CO2 to Rubisco. As a result, the C4 plants can close their stomata to retain
moisture under hot, dry conditions, but still keep photosynthesis ticking over at
good efficiency.
2.2. Crassulacean acid metabolism (CAM) plants
Crassulacean acid metabolism plants (from “crassulacean acid metabolism”,
because this mechanism was first described in members of plant family Crassulacean)
are different kind of C4 plants. In the C4 plants described above, the fixation of CO2
into 4-carbon sugars and the further fixation of CO2 into 3-carbon sugars happen in
different cells, separated in space but at the same time in CAM plants, the two different
kinds of CO2-fixation reactions happen in the same cells, which separated in time. In
CAM plants the fixation of CO2into oxaloacetate happens at night, when it is cooler
and the stomata can open to ensure a plentiful supply of CO2, and then the oxaloacetate
is stored as malic acid. During the day, the stomata close to minimize moisture loss,
and the stored malic acid is reclaimed and turned back into CO2 to power the normal
Calvin cycle.
2.3. Single cell C4 photosynthesis
It has been thought that a specialized leaf anatomy composed of two distinctive
photosynthetic cell types (Kranz anatomy) is required for C4 photosynthesis, which
can function within a single photosynthetic cell in terrestrial plants. Borszczowia
aralocaspica (Chenopodiaceae) has the photosynthetic features of C4 plants yet
lacks Kranz anatomy. This species accomplishes C4 photosynthesis through spatial
compartmentation of photosynthetic enzymes, and by separation of two types of
chloroplasts and other organelles in distinct positions within the chlorenchyma cell
cytoplasm. The most dramatic variants of C4 terrestrial plants were discovered recently
in two species, Bienertia cycloptera and Borszczowia aralocaspica, each has novel
compartmentation to accomplish C4 photosynthesis within a single chlorenchyma
cell. The C4 photosynthesis in terrestrial plants was thought to require Kranz anatomy
because the cell wall between mesophyll and bundle sheath cells restricts leakage of
CO2. Recent work with the central Asian chenopods Borszczowia aralocaspica and
Bienertia cycloptera show that C4 photosynthesis functions efficiently in individual
cells containing both the C4 and C3 cycles. These discoveries provide new inspiration
for efforts to convert C3 crops into C4 plants because the anatomical changes required
for C4 photosynthesis might be less stringent than previously thought (Fig. 1 depicts
the different types of photosynthesis and process).

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Fig.1. Different type of photosynthesis (plants and process)

The present chapter focuses on the advantages offered by C4 plants over C3

plants under adverse climatic conditions. Further we have tried to explore the different
mechanism of increasing photosynthetic efficiency and conversion of C3 rice into C4
rice to ensure enhanced rice productivity under the changing climatic scenario.

3. ACHIEVEMENTS IN IMPROVEMENT OF
PHOTOSYNTHETIC EFFICIENCY OF RICE AND EFFORTS
TO CONVERT C3 RICE INTO C4 RICE
3.1.Improving light utilization efficiency by altering the plant architecture
Light use efficiency (LUE) plays a key role in determining the photosynthetic
efficiency of crop plants and thus has considerable impact on biomass production
and yield. Important components of LUE are canopy structure, nitrogen utilization,
photosynthetic capacity and CO2 diffusion rate. Modification of plant types or
architecture is thought to be an important strategy to enhance the photosynthetic
efficiency and potential yield of crops. Photosynthetic efficiency is found to vary
linearly with leaf nitrogen content, independent of the canopy position. Rice leaves
at early tillering stage under well fertilized N-treatments had higher photosynthetic
rates due to higher leaf N content leading to greater amounts of rate-limiting
photosynthetic proteins, which gave them an early head start and boost in productivity
and leaf area index (LAI), bringing increases in canopy light interception (Xue et al.
2016).
Plant architecture-the three-dimensional organization of the above ground plant
parts encompasses branching (tillering) pattern, plant height, arrangement of leaves

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and the structure of reproductive organs. Plant architecture is of major agronomic
importance as it determines the adaptability of a plant to cultivation, its harvest index
and potential grain yield. Rice plant architecture is mainly determined by tiller pattern,
plant height, leaf shape, arrangement and panicle architecture (Yang and Hwa 2008).The
canopy architectures of three typical hybrid rice cultivars were measured in field
condition using 3-D modelling methodology at four development stages from the
panicle initiation to the filling stage, where structural parameters of the rice canopies
were calculated and their light capture and potential carbon gain were simulated
based on a 3-D light model. The study showed that erect plant type with steeper leaf
angles allows light to penetrate more deeply with relatively uniform light distribution
in the canopy at higher sun elevation angles. The LUE at the higher leaf area index
could be enhanced by reducing mutual-shading (Zheng et al. 2008).
Ideotype breeding of rice, also known as modification of plant architecture, as per
Yuan’s (1997) model for rice, includes important morphological traits viz. medium
plant height for higher harvest index; moderately compact growth habit and moderate
tillering capacity for optimum panicles; top three functional leaves that are more
erect, thicker, longer and slight rolled for more efficient use of light energy and
photosynthesis; and heavy, droopy heavy panicle for more dry matter accumulation
(Yuan 1997). Improvement in the tiller angle makes plants more efficient at trapping
light for photosynthesis, which also allows plants to avoid some diseases by
decreasing humidity around plant canopy. The identification of tiller angle control
(TAC) gene QTL, which controls tiller angle, indicates the possibility of creating new
rice plant type with moderate tiller angle by altering the expression level of TAC via
transgenic approach.
3.2. Enhancing LUE by improving the leaf characters
Plant architecture, especially the arrangement of leaves and tillers in rice has
considerable effect on governing the LUE and photosynthetic efficiency. In a field
study with IR72, resulted linear relationship between leaf N concentration (on dry-
weight basis) and SPAD chlorophyll meter reading at mid tillering, panicle initiation
and flowering stages on the uppermost fully expanded leaves of both N-deficient and
N-sufficient plants. In rice, shading at grain filling stage increased the flag leaf
chlorophyll content and maximum efficiency of PSII photochemistry under dark-
adaption (Fv/Fm), but decreased the net photosynthetic rate, electron transport rate
(ETR), saturation irradiance (PARsat) and maximum electron transport rate (Jmax), which
resulted in sharp drop in grain yield mainly due to reduced spikelet filling and grain
weight (Wang et al. 2015).
3.3. Introduction of C4 enzymes in rice
Rice is a model C3 plant which operates Calvin cycle for fixation of atmospheric
CO2 into carbohydrate. The C4 cycle operating plants are suitable for the changing
climatic scenario to address the global food security issue. Hence, scientists took
initiative to transform rice into C4 plant, but the efforts made during last two decades
to introduce the C4 mechanism into rice to increase photosynthetic efficiency and
enhance yield did not meet with much success.

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Enzymes that play crucial role in C4 pathway have been cloned from C4 species
and over-expressed in transgenic rice plants.
3.3.1. Phosphoenolpyruvate carboxylase (PEPC): The key carbon fixing enzyme of C4
pathway is phosphoenolpyruvate carboxylase (PEPC), which catalyses the
carboxylation of PEP to form the four-carbon molecule oxaloacetate (Sage et al. 2004).
The C4 specific PEPC genes from maize and other C4 plants have been expressed in
rice. Over-expression of maize PEPC gene in transgenic rice plants has been found to
reduce O2 inhibition of photosynthesis and enhance photosynthetic rates compared
to untransformed plants. In another study, Jiao et al (2005) showed that maize PEPC
expression in rice increased photosynthetic capacity about 50% under high CO2
supply along with enhanced tolerance to photo-inhibition. The PEPC transgenic rice
plants also exhibited significant increase in carbonic anhydrase (CA) activity. Similarly,
when Indica rice was transformed with maize PEPC, the transgenic plants exhibited
significantly elevated photosynthesis rate, stomatal conductance and internal
CO2concentration, while no yield enhancement was observed. Chen et al. (2014)
demonstrated that PEPC enzyme activity and photosynthesis in transgenic rice can
be promoted by exogenous nitric oxide (NO) treatment. In a similar fashion,
photosynthesis of transgenic rice plants expressing maize PEPC gene was found to
be less sensitive to O2 inhibition (Agarie et al. 2002). Their results suggested that the
O2-insensitive photosynthesis in the PEPC transformants was caused by a Pi limitation
of photosynthesis. The sugarcane PEPC gene in rice has been demonstrated to increase
the rate of photosynthesis under high temperature, (Lian et al. 2014). Rice plant has
its endogenous C3 PEPC which plays an aplerotic role by replenishing the TCA cycle
intermediates that are withdrawn for nitrogen assimilation and for different
biosynthetic pathways (Izui et al. 2004). The C4 PEPC has evolved from an ancestral
non-photosynthetic C3 PEPC and during the course of evolution; C4 PEPC has
increased its kinetic efficiency as well as reduced its sensitivity to the feedback
inhibitors malate and aspartate. The reduction in inhibitor affinity and increased
kinetic efficiency of C4 PEPC are due to the substitution Arg(C3)884>Gly(C4) and Ala
(C3)
774>Ser(C4) respectively.
3.3.2. Malate dehydrogenase (MDH): Malate dehydrogenase catalyzes the reduction
of oxalate to malate in the second step of C4 cycle. Overexpression of sorghum NADP-
malate dehydrogenase enzyme in rice plant did not affect the photosynthetic CO2
assimilation rate.
3.3.3. Pyruvate orthophosphate di-kinase (PPDK): The regeneration of PEP, the
primary CO2 acceptor, from pyruvate is mediated by PPDK enzyme in the mesophyll
cell. Several studies described the development of transgenic rice expressing C4 specific
PPDK gene. PPDK activity in transgenic rice plant was greatly increased when intact
maize PPDK gene with promoter, intron and terminator was introduced, whereas
introduction of only chimeric cDNA construct resulted in slight increase in enzyme
activity. This indicates an important role for endogenous promoter, intron and
terminator for high level of PPDK expression. In another study, introduction of maize
PPDK gene in the rice IR 64 was shown to increase total nitrogen content of flag leaf
by 42.1%, CO2assimilation rate as well as other yield forming factors like dry weight

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and harvest index than the control plant (Zhang et al. 2010). No significant change in
carbon assimilation in transgenic upland rice was observed when C4 PPDK gene from
Echinochloa was expressed (Wang and Li 2008). The rice plant has its own PPDK
gene, but very low level of expression makes it difficult to detect PPDK activity, which
might be due to the absence of an operative regulatory mechanism like maize C4
PPDK. Except the weaker promoter strength for larger transcript, Rice C4-like PPDK is
very similar to the maize PPDK gene. It is evident from the previous studies that the
overexpression of C4-PPDK is not able to significantly impact the carbon metabolism
of transgenic rice leaves. This might be due to the freely reversible nature of PPDK
mediated reaction, which depends on other factors like concentration of substrates,
activators and inactivators (Miyao et al. 2003). However, Gu et al. (2013) showed that
maize PPDK expression in rice causes increase in leaf photosynthetic rate, higher
yield and enhanced drought tolerance.
3.3.4. NADP-dependent malic enzyme (NADP-ME): The NADP-ME catalyzes the
decarboxylation reaction, one of the key steps in C4 cycle, which increases CO2
concentration in the vicinity of Rubisco in bundle sheath cells. Transgenic rice plants
expressing NADP-ME from maize (Tsuchida et al. 2001) and sorghum (Chi et al. 2004)
have been reported. A rice- C3 specific isoform has also been over-expressed in rice
(Tsuchida et al. 2001). Although activity of NADP-ME has been found to be increased
significantly in transgenic rice, the transgene failed to increase photosynthetic
efficiency of transgenic rice (Tsuchida et al. 2001, Chi et al. 2004). Transgenic rice
expressing rice C3 specific isoform of NADP-ME did not exhibit any detectable
difference in plant growth (Tsuchida et al. 2001), increased levels of maize NADP–ME
enzyme in transgenic rice plants led to stunting and leaf photobleaching (Tsuchida et
al. 2001). The increased NADPH/NADP ratio and suppressed photorespiration has
been proposed as probable reason behind the enhanced susceptibility to
photoinhibition (Tsuchida et al. 2001). However, no change was observed in the
phenotype under normal growth condition of rice plant expressing sorghum NADP-
ME (Chi et al. 2004). In subsequent study the basis of increased photo-inhibition was
done and speculation were made that accumulation of C4 specific NADP-ME led to
NADP deficiency and photosystem I over-reduction, which in turn accumulates
reactive oxygen species (ROS) in the transgenic rice plants and makes the plant more
sensitive to photo-oxidation.
3.3.5. Phosphoenolpyruvate carboxykinase (PCK): Phosphoenolpyruvate
carboxykinase is an enzyme which also catalyzes the decarboxylation steps in C4
cycle like NADP-ME but in a different group of plants known as PCK type. Transgenic
rice plants expressing the C4-PCK gene from Urochloa panicoides have been
demonstrated to be able to partially change the carbon flow in mesophyll cells into a
C4-like pathway. In another study, Huang et al. (2008) demonstrated that expression
of maize PCK enzyme resulted in enhanced growth and yield of transgenic rice plant.
3.4. Pyramiding of transgenes
Although overproduction of single C4 enzymes in rice could alter the carbon
metabolism, but no remarkable improvement in photosynthesis and plant yield has

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been reported till now. Pyramiding of C4 genes is another viable option to positively
impact rice photosynthesis. Several studies have been conducted to simultaneously
express more than one C4 genes in rice. Enhanced stomatal conductance and higher
internal CO2 concentration were found to be associated with increased photosynthetic
efficiency (up to 35%) in transgenic rice plants co-expressing the maize PEPC and
PPDK genes. When PCK and PEPC genes were simultaneously overproduced, low
chlorophyll concentration and swollen thylakoid phenotype were observed in
transgenic rice. The result of the study suggested a little contributory effect of elevated
PEPC activity in combination with PCK activity on C4-like carbon flow. Interestingly,
ATP treatment of transgenic rice co-expressing PEPC and PPDK genes increased
net photosynthetic rate by 17 and 12% under high irradiance and high temperature,
respectively.
Enhanced drought tolerance, higher photosynthetic rate and higher yield were
observed in transgenic rice pyramided with PPDK and PEPC genes (Gu et al. 2013).
The co-over-expression of four C4 enzymes, viz., PEPC, PPDK, MDH and ME has
been studied. They developed transgenic rice plants with different combination of C4
enzymes and as well as with all four enzymes. Results of their study showed that only
the transgenic plants with all 4 enzymes exhibited some improvements on
photosynthesis, while other combinations of 2 or 3 enzymes could not show any
improvements. However, transgenic rice plants overproducing the four enzymes
exhibited slight stunting phenotype. They found that combinatorial expression of
ME with PEPC is the responsible factor for height reduction. A recent study showed
that pyramiding of CA, PEPC and PPDK genes in rice resulted in increased
photosynthetic efficiency and grain yield (Sen et al. 2017). The three genes in
transgenic plants also have been demonstrated to contribute towards increased root
biomass, wider leaves and stronger stalks.
3.5 Minimizing photorespiration in C3 plants like rice
The over production of PPDK, MDH or ME did not affect the rate of photosynthetic
CO2 assimilation, while in the case of PEPC, it was slightly reduced. The restoration of
CO2 assimilation was more at higher concentration which is an indication that
overproduction of the four enzymes in combination did not act to concentrate CO2
inside the chloroplast. Transgenic rice with different levels of the introduced enzyme
were compared and it was concluded that overproduction of a single C4 enzyme did
not improve photosynthesis of rice. Even, overproduction of the maize PEPC slightly
inhibited photosynthesis through stimulation of respiration in light and reduction of
the Rubisco activity. Expression of ictB gene of Arabidopsis and Nicotiana tabacum
in Cyanobacterium documented that photosynthetic rate was significantly faster
than the wild types. E. coli glycolate catabolic pathway was introduced into chloroplast
of Arabidopsis to reduce photorespiration. The plants had more shoot and root
biomass with more soluble sugar and enhanced photosynthetic rate. By applying
same principle, it was concluded that by relocating the photorespiratory CO2 (released
from mitochondria) into chloroplast, reduced energy cost by avoiding ammonia release.
It was shown to be the main factor that contributed to an improved photosynthetic
efficiency.

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 Expression of photorespiratory bypass genes in Camelina resulted in reduced
photorespiration and increased photosynthesis in both partial and full bypass
expressing lines. Expression of partial bypass increased seed yield by 50-57 %, while
expression of full bypass increased seed yield by 57-73 %, without any loss in seed
quality. The transgenic plants also showed increased vegetative biomass and faster
development compared with wild type.
At National Rice Research Institute, the research work is being done on two
aspects, namely, introduction of C4 genes in rice and reducing photorespiratory rate.
For minimizing photorespiratory effect, the possible strategy is the introduction of
bacterial (E. coli) glycolate catabolic pathway into rice chloroplasts to reduce the
loss of fixed carbon and nitrogen and maintain photorespiration in plant. Many bacteria
like E. coli can use glycolate as a sole carbon source. Five chloroplast-targeted
bacterial genes encoding GDH, GCL and TSR, have been amplified by PCR from E.
coli gDNA using suitable oligonucleotides and cloned in pGEMT vector. All sequences
are available from the E. coli K12 genome sequence (gi49175990). Rice Rubisco smaller
subunit (rbcs) transit peptide (~300 bp) nucleotide sequence has been also amplified
and cloned in pGEMT vector. The transit peptide sequence is used for tagging into
the GDH, GCL and TSR in order to facilitate transferring integrated genes product
from nuclear genome to chloroplast genome. This will generate plants in which
chloroplastic glycolate would be converted directly to glycerate. This would reduce,
though may not eliminate, flux of photorespiratory metabolites through peroxisomes
and mitochondria while increasing the rate of carbon fixation.
3.6. Photorespiratory CO2 scavenging mechanism
Though the CO2 released during the decarboxylation step of photorespiration in
mitochondria is not completely lost and can be re-fixed while passing through the
chloroplast by some plants, (photorespiratory CO2 scavenging mechanism), there is
barrier by chloroplast that can trap
photorespiratory CO2. This effect can
be enhanced by a tight association
between mitochondria and
chloroplast (Busch et al. 2013) (Fig.2).
3.7. Introducing cyanobacterial
CO2 concentrating mechanisms
(CCM) into chloroplasts
To introduce a cyanobacterial
CCM in to the chloroplasts of land
plant is another strategy to reduce
oxygenation process of Rubisco.
Cyanobacterial CO2 concentrating
Fig.2. Photorespiratory CO2 scavenging model:
inside the proteinaceous micro-
tight association between mitochondria and
chloroplast. compartment called the carboxysome
by which it suppresses the

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oxygenating reaction of Rubisco. An outer shell called â-carboxysome (composed by

several different proteins) encloses Rubisco and CA and maintains high CO2
concentration inside the micro-compartment and increases the catalytic efficiency of
the carboxylation reaction of the enzyme. A potential approach is the engineering of
a CCM into chloroplast of higher plant to express a functional cyanobacterial form of
Rubisco together with proteins involved in the enzyme’s assembly. However, the
engineered plants were able to survive only at high CO2 concentration. The transformed
plant expressed a rich amount of the foreign transporter but displayed the same CO2
assimilation rates as the wild type plant, indicating that the transporter had little or no
in vivo activity.
3.8. Photorespiratory bypass pathway
Despite some disadvantages, photorespiration has important role in plant because
it recovers 75% of the carbon from phosphoglycolate as well as efficiently removes
potent inhibitors of photosynthesis. Moreover, photorespiration dissipates excess
photo-chemical energy under high light intensities, thus protecting the chloroplast
from over-reduction. Instead of trying to reduce the photorespiration, the promising
idea is to engineer photorespiratory bypass mechanism by introducing the Escherichia
coli glycolate catabolic pathway to convert glycolate to glycerate directly in the
chloroplast without ammonia release. This pathway would metabolize
phosphoglycolate produced by RuBP oxygenation but minimize carbon, nitrogen
and energy losses and avoid the accumulation of photorespiratory intermediates.
Many studies suggested that this pathway requires less energy and shifts CO2 release
from mitochondria to chloroplast. Improved CO2fixation would not only increase the
productivity of crop but also simultaneously decrease consumption of water, fertilizer
and land.

Fig. 2. Photorespiratory bypass pathway: -GDH (Glycolate

gehydrogenase), GCL(Glyoxylate carboxyligase), TSR(Tartronic
semialdehyde reductase)

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 Fig. 3. Proposed diagrammatic scheme for introduction of bacterial glycolate
catabolic pathway in rice chloroplast to bypass photorespiration (GDC:
glycine decarboxylase; RuBP: ribulose 1,5-bisphosphate; RuBisCO:
ribulose 1,5-bisphosphate carboxylase-oxygenase; GDH: glycolate
dehydrogenase; GCL: glyoxylate carboxyligase; TSA: tartronic
semialdehyde reductase).

4. CHALLENGES
It is certainly a difficult job to achieve a similar level of photosynthetic efficiency
of C4 plants by transferring C4 specific genes in C3 plant. Lots of metabolic and
anatomical differences exist between C3 and C4 plants. Transferring the C4 metabolism
and anatomy to rice is undoubtedly one of the most ambitious crop engineering
approaches ever. There is no simple rule but coordinated activity of multiple enzymes
in different cell types in response to diverse environmental and metabolic stimuli are
required for a true C4 cycle engineering. When plants first evolved, photorespiration
was not a problem, because the atmosphere then was high in CO2 and low in O2. As a
byproduct of photosynthesis, O2 accumulated in the atmosphere and reached the
present level. Unluckily, current atmospheric CO2 levels limit photosynthesis in C3
plants, hence, due to its better mechanism C4 plants are able to maintain their
productivity even in adverse climatic condition. The introduction of C4 photosynthesis
into C3 species requires major changes in leaf anatomy and various genes required for
enzymatic reaction. For the development of peculiar subcellular anatomy, the genes
are unknown. Considering the lack of information of single cell C4 species, it is difficult
to bioengineer C4 metabolism in to C3 crop.

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5. WAY FORWARD
Although C4 leaves have close veins and high rates of photosynthesis, C4
photosynthesis is also naturally supported around widely spaced veins in maize
husk tissue, albeit at lower rates. Thus, a prototype C4 rice may be achievable with a
subset of C4 genes, but a good C4 rice will require substantial fine tuning of biochemistry
and anatomy. Particularly intriguing is the need for additional metabolite transport
across membranes of organelles in C4 photosynthesis. A functional C4-concentrating
mechanism in rice would allow for an approximately two-third reduction in Rubisco
levels, relative to wild-type rice, but Rubisco would be sequestered in bundle sheath
cells and ideally have a greater catalytic turnover rate. Antisense gene suppression
of key photosynthetic enzymes has illuminated C4 metabolism and engineering
strategies including the surprising phosphorylation of PEPC by the regulatory enzyme
PEP carboxylase phosphokinase is not needed for C4 function.
If the attempts to alter the photosynthesis of rice from C3 to C4 pathway by
introducing cloned genes from maize/sorghum to regulate the production of enzymes
responsible for C4 synthesis are successful, the yield potential of rice of our country
may increase by 30-35%. The single cell C4 photosynthetic system gives us hope to
genetically engineer all C4 genes in single cell of C3 plants (rice) to enhance its
photosynthetic activity and productivity.
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Abiotic Stress Tolerance in Rice: Physiological

Paradigm under Changing Climatic Scenario

P Swain, MJ Baig, K Chakraborty, N Basak, PK Hanjagi,

SK Pradhan, A Anandan, NP Mandal, K Chattopadhyay, JL Katara
and G Kumar

SUMMARY
Grown under diverse range of ecosystems, rice gets exposed to different
environmental stresses like drought, salinity, submergence, cold as well as high
temperature and lowlight. In the era of global climate change, rice cultivation especially
in the rain-fed ecology (rainfed upland, shallow lowland and lowland) faces multi-
facet problems. The changing climatic conditions make the rice crop vulnerable to
moderate to severe drought stress, germination stage oxygen deficiency (GSOD) or
submergence stress depending upon the timing of the natural events, and increase in
salinity level in coastal rice belts, lowlight stress situation due to heavy down pour or
prolonged cloudy weather conditions and heat stress due to increase in temperature
during dry spells mostly in grain filling period. Recent reports suggest more frequent
occurrence of such climatic extremities in many parts of the Indian subcontinent and
elsewhere. Yield improvement in such stressful environments could be achieved by
identifying secondary traits contributing tolerance to a particular stress or combination
of stresses and selecting for those traits in breeding programme. Land races, one of
the important components of the germplasm, serve as donors for different abiotic
stress tolerance and have broad genetic base which provides them wider adaptability
and protection from various stresses. So, identification of suitable donor and
secondary/putative traits for developing high yielding varieties through conventional
or molecular approaches with an added advantage of understanding stress tolerance
mechanism is of paramount importance in the present scenario.

1. INTRODUCTION
Rice is grown in different ecologies covering about 44.0 m ha throughout India.
Due to variations in geographic situations and rainfall pattern, the country experiences
different abiotic constraints. Climate change and irregularities in South-west monsoon
result in moderate to severe droughts in rainfed rice growing areas, submergence/
waterlogging even during reproductive stage in low lying areas, elevated temperature
regimes during both vegetative and reproductive stages and different intensities of
low light during the cropping period mostly in eastern Indian states.
Crop yield depends on specific climatic conditions and is highly affected by
climate variations. Estimation of the overall rice yield variation due to climate variability
over the last three decades showed that approximately 53% of rice harvesting regions
experiences the influence of climate variability on yield at the rate of about 0.1 t/ha per
year and approximately 32% of rice yield variability is explained by year-to year global
climate variability (Fig. 1).

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 The objectives of this chapter are
to outline the major abiotic stresses that
affect rice production and to
understand the tolerance mechanism
of each.
1.1. Drought
Water is an important factor in
agricultural and food production and
yet is a highly limited resource. Water
Fig. 1. Global rice yield variability due to
climate variability over the last three decades
deficit stress causes extensive loss to
(Ray et al. 2015). agricultural production worldwide,
thus being a severe threat to
sustainable agriculture. Out of 44.0 million ha area under rice in India, drought is one
of the major abiotic constraints in around 8.0 million ha of rainfed upland and rainfed
lowland situations. About 18% of total rice area of India and 20% of Asia are drought
prone. The irregularities in south-west monsoon do result in moderate to severe
drought in rainfed rice growing areas especially in eastern India. Drought is a
multifaceted stress condition with respect to timing and severity, ranging from long
drought seasons where rainfall is much lower than demand, to short periods without
rain where plants depend completely on available soil water (Lafitte et al. 2007).
Among the different environmental stresses, drought constitutes an important yield
limiting determinant. Food security and prosperity of India is challenged by increasing
demand and threatened by declining water availability thereby requiring crop varieties
that are highly adapted to dry environments.
1.2. Submergence
Submergence is a type of flooding stress, which is defined as a condition, where
the entire plant is fully immersed in water (a phenomenon termed as complete
submergence) or at least part of the shoot terminal is maintained above the water
surface (a phenomenon termed as partial submergence). Under submergence, plants
face a number of external challenges simultaneously or sequentially, which results in
multiple internal stresses that affect plant growth and survival. Submergence
substantially reduces the gas diffusion rate in the leaf tissue, restricting oxygen
uptake and forcing carbon inefficient carbohydrate metabolism via anaerobic route
(Panda et al. 2017). To add-on to the problem, turbid floodwaters also reduce light
availability, inhibiting underwater photosynthesis and leaf gas exchange. Limitation
of efficient gas exchange also restricts transpiration severely, possibly impeding the
absorption and transport of nutrients from the soil.
1.3. Salinity
Soil salinization is a worldwide problem for agriculture affecting 6% of total Earth’s
land, as a result of natural accumulation over long periods of time. However, agricultural
activity contributes to secondary salinization: 2% of all dry land is becoming salinized,
and more than 20% of irrigated soils are affected, mostly because of irrigation water

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containing small amounts of sodium chloride. Plants do vary in their sensitivity to

salinity stress. Although being the most sensitive amongst all the cereals, having a
threshold salinity level of only 3 dS m-1, rice show considerable variability across its
different species and also within different genotypes of the same species (Menguer
et al. 2017).
1.4. High temperature
The constantly rising temperature is one of the most detrimental problem
profoundly affecting plant metabolism. Heat stress in rice affects the anthesis and
grain filling stages of the crop. Even one degree rise in temperature above the optimum
temperature results in 7-10% loss in the yield of rice (Fahad et al. 2017). Apart from
yield, heat stress also has a negative influence on various grain quality traits and
reduces the sensory attributes. As the eastern part of India experiences early sunrise,
temperature often rise above 35°C during the time of anthesis in the months of April
and May. Consequently, late sown rabi season rice crop and timely sown long duration
cultivars are highly sensitive to elevated temperature stress in eastern India.
1.5. Lowlight
The low incidence of solar radiation coupled with fluctuating light due to over-
cast sky during the wet season is one of the major constraints for realizing the low
productivity in eastern and northeastern India. It induces high tiller mortality at
vegetative stage, reduction in spikelet number at reproductive stage and dry matter
production after flowering which drastically affects production. Rice yield during the
wet season is 65.2% of that of dry season. Rice that receives half of the sunshine has
27-37% less yield than rice receiving full sunshine (Murty et al. 1992). The future
increase in production has to come from these neglected regions as they harbour
huge area with low productivity. Tolerance to low light is genetically controlled, but
until recently little has been known about the genes involved. In order to design rice
genotypes with higher yield and greater stability under low light stress, evaluation of
rice germplasms tolerant to low light conditions is required along with a systematic
investigation of the mechanisms of tolerance to light stress.

2. PHYSIOLOGICAL AND BIOCHEMICAL BASIS OF

DROUGHT TOLERANCE
Though rice is a water loving plant, yet it can successfully be grown under upland
ecosystem due to its adaptability to low moisture conditions. However, its productivity
is much lower than what we get in irrigated/lowland ecologies. Drought tolerance is a
complex trait, which is a combined function of various morphological, biochemical
and molecular characters. Knowledge about these characters that maintain plant
growth and development during water stress conditions is paramount in
understanding stress response processes. Morphological traits viz., maintenance of
turgor, initiation of leaf rolling, cuticular wax, deep and coarse root with greater xylem
vessel radii and lower axial resistance to water flux are indicators of drought tolerance.

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Most physiological and metabolic processes are affected by water deficits which
include stomatal regulation, photosynthesis, translocation, PSII activity, chlorophyll
content, etc. Maintenance of these processes for prolonged period of time under
drought is a desired character. Since, ABA is an important component of signalling
under drought stress, efficient ABA signalling also ensures tolerance. Biochemical
parameters viz., proline and polyamine accumulation in plants increases under drought
stress. Further, the enhancement of the naturally occurring antioxidant components
(enzymatic and non-enzymatic) may be another strategy for reducing oxidative damage
and can be considered to be a vital mechanism of drought tolerance (Pandey and
Shukla 2015). In addition, a very large number of genes in rice are up- or down-
regulated by drought which not only enhances the plant survival in drought conditions
but also improves the crop productivity. Recently, many transcription factors (TFs)
have been identified in rice, the expression of which provides drought tolerance as
well as improves yield under stressful conditions. To facilitate the selection or
development of drought tolerant rice varieties, a thorough understanding of the
various mechanisms that govern the yield of rice under water stress condition is a
prerequisite.

3. PHYSIOLOGICAL AND BIOCHEMICAL BASIS OF HEAT

TOLERANCE
Rice is highly sensitive to heat stress particularly at flowering and post-flowering
stages. Exposure to short periods of heat stress coinciding with flowering has resulted
in significant yield losses in India, China and Japan. During anthesis heat stress leads
to irreversible reduction in spikelet fertility mainly by affecting sensitive physiological
processes such as anther dehiscence, pollination, and early fertilization events. To
minimize heat stress damage plants generally adopt three mechanisms viz., heat escape
(time of day of flowering, especially early morning flowering), heat avoidance through
transpiration cooling and heat tolerance through resilient reproductive processes
(Jagadish et al. 2010). High temperature may also hamper proper functioning of the
enzymes of nitrogen uptake and assimilation and also photosynthesis. Decline in the
activities of source and sink also significantly affects the growth and eventually the
economic yield of rice.

4. PHYSIOLOGICAL AND BIOCHEMICAL BASIS OF

SUBMERGENCE TOLERANCE
Rice plants tolerant to complete submergence usually exhibit very limited elongation
during submergence and often show tolerance to complete flooding, a strategy known
as quiescence. Some researchers believe that the ideal combination for adaptation to
complete flooding is submergence tolerance (survival under water) together with
some elongating ability. Under water photosynthesis and utilization of existing
carbohydrate reserve is found to be one of the most important factors for submergence
tolerance in rice (Das et al. 2009). Studies have shown that the differences in tolerance

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level were not necessarily associated with the initial carbohydrate status before
submergence but with the plant’s ability to maintain high levels of stored energy
through either slower utilization during submergence and/or greater underwater
photosynthesis.
The mechanistic understanding of molecular regulation of submergence tolerance
in rice has been advanced through functional characterization of key genes responsible
for acclimation to submergence stress in rice (Xu et al. 2006). Limited number of rice
genotypes possess inherent mechanism to tolerate a deep transient flash flood through
economization of energy reserves (quiescence strategy) (Fukao et al. 2008).
Quantitative trait locus (QTL) analysis and map-based cloning revealed that the
SUBMERGENCE1 (SUB1) locus, encoding a variable cluster of two or three tandem-
repeated group VII of ETHYLENE RESPONSIVE FACTOR (ERF-VII), regulate the
quiescence response (Xu et al. 2006). Most of the reported rice accessions were
found to contain SUB1B and SUB1C genes at the SUB1 locus, whereas SUB1A was
reported to contribute ~70% of submergence tolerance to some indica and aus rice
varieties (Singh et al. 2010).

5. PHYSIOLOGICAL AND BIOCHEMICAL BASIS OF

SALINITY TOLERANCE
Generally, salinity causes two types of stresses on plants: osmotic and ionic
stresses. The genetic basis of tolerance to ionic stress is much better understood
than that of osmotic stress. Between the two main sub-species of rice, it is observed
that Indica is more tolerant than Japonica. Tolerant Indica varieties are good Na+
excluders, absorb high amounts of K+, and maintain a low Na+/K+ ratio in the shoot.
Sodium, an integral constituent of our earth crust is naturally present in all soil
types. At lower concentration Na+ may promote growth in rice but eventually it
becomes toxic when present in high concentration in growing medium. Both Na+ and
K+ share high similarity in ionic as well as its physicochemical properties, but unlike
Na+, K+ are integral part of plant’s life and play essential role in growth and development.
Many basic physiological processes, which are essentially dependent on K+ shows
impairment due to hindrances in specific transport and interactions of K+ with enzymes
and membrane proteins (Britto and Kronzucker 2008). This may well be of diverse role
viz. short-term maintenance of membrane potentials to pollen tube development and
stomatal opening and closing (Dietrich et al. 2001).
Initially osmotic stress occupies the main position whereas with time more salt is
absorbed by the plant and ionic stress plays the leading role. Adaptation to salt
stress is to adjust with both osmotic and ionic stresses. Salt stress is cumulative.
With time injury symptoms increase. Susceptible cultivars die early compared to
tolerant cultivars in a salty environment. So, restricting the movements of ions such
Na+ or Cl- ions to growing meristematic tissues and young photosynthetic organs are
crucial for survival. Tolerant rice cultivars like Pokkali either absorbs low levels of
Na+ or restricts the movement of Na+ in comparison to K+ and thereby maintains low

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Na+:K+ ratio in shoot/leaf and protects the vital tissues (Kobayashi et al. 2017). High
Na+ in the cell cytoplasm impairs several physiological and biochemical courses of
action which restricts plant growth.

6. MECHANISM FOR LOWLIGHT TOLERANCE

Little is known about the mechanisms of low light tolerance in rice crop in terms of
physiological and molecular scale. When plants are shaded, the photo-assimilates
that fuel growth become limited; the growth of the stem is promoted to place the
leaves at a higher position, with better chances to capture light for photosynthesis.
This response involves enhanced growth when the available photo-assimilates are
already limiting.

7. MOLECULAR MECHANISM OF STRESS TOLERANCE

Drought is a main yield reducing factor for rainfed rice. The progress of rice
improvement is very slow. However, few yield QTLs under drought at reproductive
stage are valuable research advancement in drought breeding. As per the mapping
results, the yield QTLs qDTY1.1, qDTY2.1 and qDTY3.1 are effective under drought
stress (Dixit et al. 2014). Amongst these, qDTY1.1 was a consistent QTL showing
effect on per se yield under drought affected lowland ecology. The other two QTLs
also showed higher phenotypic variances for yield under drought situation. For
upland ecology, a QTL, qDTY12.1 has been detected showing very high additive
effects and found to be effective in drought breeding (Dixit et al. 2014). Another QTL,
qDTY3.2 exhibits a positive effect on yield under drought stress. Irrigated rice varieties
possess mostly surface spreading type root system. In rainfed farming, these varieties
are highly affected by moisture stress situations due to short drought spells. Hence,
a deeper rooting system escapes better under such situation. The QTL, Dro1 makes
the root to move downward by bending of the root in response to gravity. DEEPER
ROOTING 1 (Dro1) a major quantitative trait locus which helps in escaping drought
stress. Higher expression of Dro1 increases the root growth angle, whereby roots
grow in a more downward direction (Uga et al. 2013). Introducing Dro1 into a shallow-
rooting rice cultivar by backcrossing enables the resulting the recipient cultivar.
Variation in root growth angel in rice exists and may be may be controlled by a few
major QTLs and by several additional minor QTLs (Kitomi et al. 2015).
The yield loss due to flash flood is very high in lowland rice ecology. A major QTL
(Sub1) explaining about 70% of phenotypic variation for submergence tolerance has
been identified and fine mapped on chromosome 9 in the submergence tolerant
cultivar FR13A (Xu et al. 2000).

8. WORK DONE INTERNATIONALLY AND NATIONALLY ON

VARIOUS ABIOTIC STRESSES
Drought stress is a very important limiting factor at the initial phase of plant
growth and establishment. It affects both elongation and expansion growth (Shao et

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al. 2008). A soil water potential threshold of 20 kPa at 30 cm depth during the
vegetative stage was identified as the target for effective selection under vegetative
stage with grain yield reduction of about 50% compared to irrigated control trials
(Swain et al. 2017). Roots are crucial for nutrient and water acquisition and can be
targeted to enhance productivity under a broad range of growing conditions. A
dynamic root system is fine-tuned to soil moisture status and is known to regulate the
amount of water available to the plant depending on its distribution in the soil. Among
the root morphological traits, maximum root length, root diameter and root:shoot dry
weight ratio were found to be associated with drought resistance in upland conditions.
Root thickness was found to confer drought resistance, as roots are capable of
increasing root length density and water uptake by producing more and larger root
branches (Ingram et al. 1994). Shoot growth is reported to be more inhibited than root
growth when soil water is limited. This differential response/sensitivity of root and
shoot growth to low-water potential is considered as a mean of avoiding excessive
dehydration (Sharp and Davies 1989). Increased root:shoot ratio, high total root
length and high root elongation rates enable plants to maintain relatively high water
uptake (rates) under water stress conditions.
Photosynthetic ability has been regarded as important indicator of the growth of
plants, because of their direct link to net productivity. Drought causes not only a
substantial damage to photosynthetic pigments, but it also leads to deterioration of
thylakoid membranes. Chlorophyll pigment played important role in photosynthesis
and chlorophyll stability index is a measure of integrity of membrane of the pigments
found to correlate with drought tolerance. The strong relationship between drought
susceptibility index (DSI) and percent change in SPAD Chlorophyll Meter Reading
(SCMR) under water deficit condition indicate that higher chlorophyll concentration
is important for adaptation to water deficit conditions during grain filling period
(Talwar et al. 2011). DSI is also negatively related to yield under stress. Several
researchers have proposed the use of stomatal conductance (gs) as an indicator to
assess the difference between stomatal and nonstomatal limitations to photosynthesis
under water-limited environments. Regulation of leaf stomatal conductance (gs) is a
key phenomenon in plants as it is vital for both prevention of desiccation and CO2
acquisition. Cultivars that exhibited the highest values of total conductance to CO2
supported higher photosynthesis and yield under all levels of water availability (Gu
et al. 2013).
Proline as an osmo-regulatory solute acts as an osmo-protectant under drought
and salinity stress, its concentration increasing in stressed plants due to stimulation
of proline biosynthesis. In drought condition, some reactive oxygen species (ROS)
are created, and to overcome oxidative stress, plants develop enzymatic and non
enzymatic antioxidant defence mechanisms to scavenge ROS (Smirnoff 1993). The
most important antioxidant enzymes are super oxide dismutase (SOD), catalase (CAT)
and peroxidase (POD). SOD converts O2- into H2O2 and O2, while CAT and POD
scavenge H2O2 into H2O (Wang et al. 2009).

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 Significant genotypic variation has been documented in rice for heat stress induced
spikelet sterility. Variability in heat stress induced spikelet sterility has been explained
by air temperature, and interaction effect of air temperature and relative humidity on
plant tissue temperature. Large differences between the panicle and air temperature,
primarily due to vapor pressure deficit which is a function of prevailing temperature
and relative humidity (RH) have been reported (Yoshimoto et al. 2012). A recent study
showed that the effects of heat stress on sterility were due to the high temperatures
recorded in the organ itself and not that of the environment. Rice germplasms for high
temperature stress tolerance can be evaluated by employing field based high
temperature stress phenotyping to quantify the relationship between spikelet sterility
and air, leaf, panicle and canopy temperature in order to develop thermo tolerant rice
genotypes.
Internationally, the focus has also been on assessing quality parameters of rice as
affected by heat stress. It has been suggested that the temperature during grain
filling is an important factor influencing grain quality. It is seen that rice plants when
grown under high temperature have low amylose content compared to those grown
under low temperatures. It has been reported that high ambient temperatures in later
stages of development are responsible for reduction in spikelet fertility (Jagadish et
al. 2010) and reduced grain quality as the endosperm becomes chalky in texture
(Fitzgerald et al. 2009). Elevated temperatures during growing period have also been
shown to cause alterations in important physicochemical properties of rice starches
related to food processing quality. Studies report that high-temperature stress
suppressed the expression of the starch-synthesis-related genes GBSSI, BEIIb, SuSy2,
and AGPS2b to about 50 and 80% of that in the control conditions throughout grain
filling. Hakata et al. (2012) also reported that activation of α-amylase by high
temperature was a crucial trigger for grain chalkiness.
Importance of aerenchyma under long-term water-logging is well established and
studies showed that the short-term (7 days) exposure of rice plants to complete
submergence induced the formation of aerenchyma tissues in roots, a process much
faster in tolerant (FR13A) than in susceptible (IR42) genotypes (Nishiuchi et al. 2012).
Rice being a wetland crop is somewhat tolerant to anaerobiosis and such submergence
induced adaptive traits viz. aerenchyma formation and narrower leaves and leaf mass/
area probably helps them to withstand the ill-effect of anoxia during submergence
stress.
The variety Swarna possessing Sub1 has become very popular in rainfed lowland
ecologies in the country. Swarna-Sub1 was released by SVRC, Odisha and SVRC,
Uttar Pradesh and notified by Dept. of Agriculture and Cooperation, Ministry of
Agriculture, Govt. of India.
Rice has been reported to be relatively tolerant to salinity stress during germination,
active tillering and towards maturity, but sensitive during early seedling and
reproductive stages, where an addition of as little as 50 mM NaCl in the soil can
reduce rice yield significantly (Zeng et al. 2003). A range of transporters involved in

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reducing Na+ accumulation in shoots and in sub-cellular compartmentalization was

identified.
The high affinity potassium transporter (HKT), salt overly sensitive (SOS) and
Na+/H+ Exchanger (NHX) gene families are key players imparting salt tolerance in rice.
The HKT members are crucial determinants of tissue concentration of Na+. OsHKT1;5
was identified as the causative gene of Saltol, the major quantitative trait locus (QTL)
for salt accumulation in O. sativa genotypes (Ren et al. 2005). OsHKT1;5 is a plasma
membrane transporter that regulates partitioning of Na+ between roots and shoots by
efflux of Na+ from the xylem to adjacent parenchyma cells. Robust screening effort
including several O. sativa cultivars, landraces and O. glaberrima (AA genome)
genotypes, showed that salinity sensitivity is correlated with Na+ concentration in
the leaf blades. OsHKT1; 5 genotype was shown to be a major determinant for
tolerance: the more active the efflux transporter, which directs the Na+ exclusion from
the transpiration stream, the less Na+ is translocated to leaves.
Researchers across the world are trying to explore other species from the genus
Oryza for salt tolerance genes. O. rufipogon was shown to be salt tolerant when
compared to rice sensitive cultivars. Introgression lines derived from O. rufipogon×O.
sativa cross revealed 15 QTLs for salinity tolerance, 13 of which were derived from
the O. rufipogon parent (Tian et al. 2011). Over-expression of bHLH transcription
factors OrbHLH001 and OrbHLH2 from O. rufipogon resulted in Arabidopsis and O.
sativa salt tolerant lines (Chen et al. 2013). It was found that OrbHLH001 is able to
positively regulate the K+ transporter OsAKT1, suggesting that salt tolerance results
from maintenance of K+ homeostasis under high Na+ conditions (Chen et al. 2013).
At national level, very few discrete attempts had been made to compare the relative
salt tolerance capacity of rice genotypes of different ecologies of Indica type rice
genotypes belonging to O. sativa (Omisun et al. 2017). Salt tolerance in native
genotypes of north eastern India was attributed to efficient action of Na+/K+ co-
transporters, OsHKT2;1, OsHKT2;3 and OsHKT2;4, which is a predominant salinity
tolerance mechanism in O. sativa (Omisun et al. 2017).

9. WORK DONE AT NATIONAL RICE RESEARCH

INSTITUTE
To identify rice germplasm lines with built-in tolerance to vegetative and
reproductive stage drought, large number of rice germplasm including upland rice,
lowland rice, deep water rice, wild rice, aromatic rice and fixed lines are being screened
at ICAR-NRRI, Cuttack under field condition during dry season. Generally for large
scale screening experiments are conducted under field condition during dry season
where interference of rain is negligible during the cropping period. Wherever
controlled facility like rain-out shelter is available, screening is done in wet (kharif)
season also (Fig. 2). In this process, more than 10,000 germplasms were screened and
a good number of genotypes (>250) for vegetative and (>50) for reproductive stage

Abiotic Stress Tolerance in Rice: Physiological Paradigm under

Changing Climatic Scenario 469
 Fig. 2. Screening for drought tolerance under field and rainout shelter.

drought stress tolerance already have been identified in our institute. Ten genotypes
were identified tolerant to intermittent drought spells in rainfed upland conditions
yielding >2.0 t ha-1 with lower spikelet sterility (9.0–14.7%).
During evaluation for vegetative stage drought tolerance, morpho-physiological
changes viz. leaf rolling and death score based on standard evaluation system, plant
water status like Relative Water Content (RWC), Leaf Water Potential (LWP), membrane
stability index, water use efficiency and transpiration, chlorophyll content and
chlorophyll stability index, proline content, gas exchange parameters, chlorophyll
fluorescence, photosystem II yield, phenotyping for root morphological traits, Water
Use Efficiency (WUE) etc. are phenotyped. Better plant vigour, total protein content,
catalase and peroxidase activity under mild osmotic stress was observed in tolerant
genotypes AC 42994, AC 43030 and AC 43012.
Evaluations for key adaptive traits for vegetative and reproductive stage drought
tolerance are made in different experiments in field and controlled environments.
Genotypes maintaining high turgidity during severe stress (RWC>70%) and recovered
faster on re-irrigation had higher efficiency for drought tolerance. Significant negative
correlation between drought score vs. RWC (r= -0.78*) and drought score vs. Fv/Fm
(r= -0.610*) and significant positive correlation between RWC and Fv/Fm (r=0.710*)
indicates that plants having higher water content are able to harvest most of the
photon falling on the canopy and radiate less energy in the form of fluorescence (Fig.
3).

Fig. 3. Correlation of relative water content with drought score and Fv/Fm.

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The root:shoot ratio, maximum root length to shoot length ratio and root volume
were observed to be the most crucial morphological markers in determining drought,
tolerance in rice genotypes analyzed through biplot analysis. Among the thirteen
genotypes tested, AC-42994, AC-42997, AC-43020, CR-143-2-2, Ronga Bora and Bora
were found to possess desirable root traits and these genotypes can be used in the
breeding programme for enhancing drought tolerance in rice (Dash et al. 2017).
For reproductive stage stress tolerance, phenology, spikelet fertility/grain filling
per cent, yield and its components, relative yield reduction and drought susceptibility
index etc. used to be considered as important traits. Genotypes BVD-109 (2.15 t ha-1),
Kalakeri (2.08 t ha-1), IC 416249 (2.02 t ha-1) and CR 143-2-2 (1.90 t ha-1), AC 27675, IC
516130, Udayagiri, Indira, Vandana , AC-42994, Brahman-nakhi, AC-43006, Nania
Kalabora, EC 545088 and IC 337606 have been identified as promising having grain
yield of >1.5 t ha-1 with minimum yield reduction (18-45%) and low DSI (<0.65) at soil
moisture content of 9.8-13.3%.
Drought Susceptibility Index (DSI) was identified as a selection criteria for yield
under stress. The mean values of DSI close to or below one for grain yield (GY) in the
genotypes indicated their relative tolerance to drought (Fig. 4).

Fig. 4. Correlation between grain yield and DSI under control and stress conditions.

Under 55% field capacity, CR 143-2-2 (tolerant check) along with AC-43025, AC-
43037 and AC-42997 had highest water use efficiency coupled with slow transpiration
rate above VPD 5 kPa, low stomatal density with lower canopy temperature maintenance
(34.02 °C - 41.18 °C) (Fig. 5) leading to higher biomass production using less water
compared to susceptible check IR 64 (Dash et al. 2015).

Fig. 5. Canopy temperature and stomatal density in two contrasting genotypes.

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 Screening work carried out at NRRI identified three out of 30 advance breeding
lines CR 3564 -1-2-4-1-1, CR 3564 -1-1-1-1-1 and CR 3581 -1-1-1-1-1 and four out of 42
germplasm lines AC 39834, AC 39843, AC 39969 and AC 4391 as best heat tolerant
lines over 3 years with >80% spikelet fertility. Quality analysis of the heat stressed
samples were carried out and it was found under high temperature stress, amylose
content was high, gel consistency was low, alkali spreading value and grain breadth
did not change much, while length and L/B ratio reduced by 16% and 14%, respectively
as compared to ambient temperature.
The effect of high temperature on
grain yield and carbohydrate
accumulation was studied in seven
contrasting genotypes (N22, Ratna,
Annapurna, Satabdi, IR72, Lalat and
Naveen) grown in field at four different
dates of sowing at 10 days interval.
Grain yield was reduced under high
temperature stress to the tune of 43.7
Fig. 6. Carbohydrate accumulation pattern in flag to 47.9% in susceptible varieties like
leaves and panicles of tolerant and susceptible Naveen and Satabdi, while tolerant
varieties. variety Annapurna and N22 showed
very minimal 6.9 to 18.3% of reduction.
Accumulation of total sugar was reported to be very high in tolerant variety N22 as
compared to susceptible varieties suggesting the impaired carbohydrate mobilization
process due to high temperature stress (Fig. 6).
Significant progress has been made in submergence studies in rice at ICAR-
NRRI, Cuttack. The genotype, FR13A (vernacular name ‘Dhalaputia’, Odisha, India)
was identified from this institute as a true submergence tolerant genotype. FR13A is
the source of submergence tolerance gene/QTL (SUB1) which imparts submergence
tolerance. Extensive work was done with this genotype and mechanism of submergence
tolerance is now fairly understood. In other words, it can be said that NRRI (then
CRRI) and Odisha presented the SUB1 gene to the rest of the world. Genotypes with
SUB1 can withstand complete submergence depending on flood-water characteristics
up to 1-2 weeks. One of the key finding for submergence tolerance of rice identified
from here is that non-structural carbohydrates content before and after submergence
is important for providing energy for maintenance of key metabolic processes during
submergence and for regeneration and recovery of seedlings after submergence
(Panda et al. 2017). Studies have shown that the differences in tolerance level were
not necessarily associated with the initial carbohydrate status before submergence
but were rather associated with the plant’s ability to maintain high levels of stored
energy through either slower utilization during submergence and/or greater underwater
photosynthesis. The initial carbohydrate level before submergence was almost equal
in rice cultivars Gangasiuli and Raghukunwar, but Gangasiuli showed better survival

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472 Changing Climatic Scenario
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percentage (51%) than Raghukunwar (36%), with retention of higher chlorophyll and
non-structural carbohydrate contents during submergence.
The diversity in microsatellite markers in the Saltol-QTL region among 30
accessions from saline tracts was examined and validated by using 37 breeding lines
that were salt tolerant at the seedling stage and the diversity was assessed in terms of
morpho-physiological traits related to salt stress (at 12 dS m-1) which showed
moderately tolerant nature of the accessions collected from coastal areas in two
Indian states, West Bengal and Odisha and were distant from a Saltol-introgressed
line, namely FL478 (Chattopadhyay et al. 2014). Singh and Sarkar (2014) reported
chlorophyll fluorescence characteristics for distinction and characterization of salinity
tolerant and sensitive rice cultivars effective for Indian rice cultivars. Probing with
chlorophyll fluorescence technique, Sarkar and Ray (2016) reported, submergence-
tolerant rice (FR13A in this case) can withstand complete submergence even in saline
water and significantly longer duration of time. Chattopadhyay et al. (2014) reported
salt tolerant nature of genotype SR 26B, despite the most distant genotype from
Pokkali (known salt tolerant genotype) in the Saltol QTL region.

10. KNOWLEDGE GAP

In spite of extensive studies, there is still a strong need for more detailed
characterization of the response and acclimation mechanism of rice under drought
that is occurring in farmers’ fields. Less reduction in grain yield during drought is the
critical trait that plays an important role in tolerance against drought. Thus, yield
stability under drought conditions and increased crop water productivity should be
the target of all the approaches involved in drought tolerance. Molecular attributes
are key traits linked to yield under drought.
Heat stress by adversely affecting plant growth and development presents a
major challenge in today’s scenario. Evaluation of rice germplasms for high temperature
stress tolerance employing field based high temperature stress phenotyping to
quantify the relationship between spikelet sterility and air, leaf and panicle temperature
in the panel of germplasms under study and to identify high temperature stress
tolerant genotypes needs to be carried out. In addition, understanding the source-
sink relationship of structural and non-structural carbohydrates is required.
From the previous studies, it has been well documented that Sub-1 QTL accounts
for as high as 70% of the submergence tolerance in rice. But, there are a few rice
genotypes which can withstand submergence stress beyond 14 days. The mechanism
thereof needs to be identified. Also, researchers are trying to combine submergence
and anaerobic germination in rice to make rice cultivars tolerant to multiple abiotic
stresses suitable to rainfed low land ecologies. But, based on the current research
outcome, the mechanism of tolerance in these two stresses are almost opposite to
each other. So, how these genotypes would be working in case of multiple abiotic
stress situations need to be investigated.

Abiotic Stress Tolerance in Rice: Physiological Paradigm under

Changing Climatic Scenario 473
 Direct seeded rice suffers germination loss due to heavy rainfall in poorly drained
soils. Eastern India usually gets severe rains and cyclonic storm during grain maturity
stage. Therefore, tolerant QTLs like qAG9.2 and qAG7.1 for anaerobic germination
need to be pyramided in the mega variety. In addition, seed dormancy of at least one
week should be in the mega variety to avoid vivipary germination.
Although very good progress has been made in the area of salinity tolerance in
rice, but a lot of questions still remains unanswered. The ionic basis of Na+/K+
homeostasis and the role of ion specific transporter in different plant parts remains
elusive. Also, the mechanistic differences in salt tolerance in vegetative and
reproductive stages in rice need to be worked out in detail in order to develop salt
tolerant rice cultivars particularly tolerant to reproductive stage salinity stress.
Screening for contrasting germplasm lines for low light tolerance will help to
develop mapping populations to identify quantitative trait loci that can be used in
marker assisted breeding program for tailoring rice varieties. Analysis of molecular
processes together with engineering a new light receptor (modified phytochrome)
will mitigate the stress as well as reveal mechanisms to reduce the energy cost of light
stress in rice.

11. CONCLUSION AND WAY FORWARD

Higher production from abiotic stress situation is essential in this era of climate
change and thus poses a challenge to understand the adaptive mechanism and tailor
rice genotypes for optimum performance from limited use of resources.
The rainfed rice cultivation in the country is highly affected by the effects of
climate change. For this, it is essential to integrate crop physiology, molecular genetics
and breeding approaches to dissect complex abiotic stress tolerance traits, and develop
the next generation crops which can withstand the adverse climate and ensure food
security.
The high yielding varieties should be stacked with stress tolerant gene(s)/QTLs
for making them climate resilient. Thus, in mega varieties, multiple tolerant genes for
submergence, anaerobic germination, yield QTLs under drought, seed dormancy and
yield enhancing QTLs under drought need to be stacked to make them highly resilient
to the climate change.
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 Innovative Extension Approaches for
Increasing Income of Rice Farmers

SK Mishra, Lipi Das, GAK Kumar, NC Rath, B Mondal,

NN Jambhulkar, P Samal, BN Sadangi, SK Pradhan, S Saha,
PC Rath, AK Mukherjee, RK Sahu, PK Guru, CV Singh,
SM Prasad, S Bhagat, S Roy, R Bhagabati and K Saikia

SUMMARY
Social research on development and experimentation with new extension
approaches and models for faster dissemination of latest technologies and their wider
adoption has got more significance after Green Revolution during late 1960s in India.
These approaches vary widely from top-down and supply-led to bottom-up, demand-
led and participatory, mostly due to diverse agro-climatic regions, socio-economic
conditions and types of stakeholders. The ICAR-NRRI has been experimenting with
such five innovative extension approaches relating to (i) rice varietal popularization,
(ii) sustainable local seed system, (iii) rice value chain, (iv) gender sensitive extension
and (v) rice-based climate smart model village approach. The rice varietal popularization
strategy aims at shortening the time gap between the development of a new higher
yielding superior variety and its wide adoption by farmers. This would also help in
substitution of old mega varieties susceptible to various pests and diseases with
superior and multiple stress tolerant varieties in view of changing climate scenario.
The 4S4R model of local seed system has attempted to improve the local seed system
of villages through formation of farmer producer organizations (FPOs)/farmer interest
groups (FIGs) and capacity building of farmers in quality seed production of their
locally demanded varieties, in right time and at lower cost. This self-sufficient
sustainable seed system would help to address the various acknowledged demerits
of the public seed system. The rice value chain model developed through an MOU of
stakeholders from rice breeder to consumer would ensure rice growers to get fair price
of their produce, while benefiting all stakeholders and satisfying the consumers. The
gender sensitive extension approach in a rice-based farming system would help in
proper utilization of latent capacities of farm women and grooming them to lead
agrarian economy at par with their male counterparts. This approach would also help
to change the traditional mindset of the male-dominated society and create a healthy
societal climate boosting rural economic growth. The access to technologies and
productive resources by farmwomen has increased remarkably in our study area. The
rice-based climate smart model village approach through coordination and convergence
of all development departments alongside the farming communities has helped to
bring all stakeholders to a single platform for holistic planning of villages, execution
of action plans, monitoring of interventions and immediate remedial measures. This
approach would help to mobilize the farmers, farmwomen and rural youths, while
addressing issues relating to livelihoods, youth unemployment, market linkage and
changing climate.

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1. INTRODUCTION
Development of new approaches in agricultural extension in India and worldwide
is a continuous process with its focus on increasing productivity and profitability.
Since the Green Revolution during late 1960s, Indian agricultural extension has adopted
decentralized, participatory and demand-driven approaches, in which accountability
is geared toward the users (Kokate et al. 2009; Sulaiman and Hall 2008; Swanson
2009). While the call for demand-driven agricultural extension has existed for several
decades now, new modes of reaching out to farmers could have significant impact in
India, as they might better reflect the local information needs of farming communities.
The diverse nature of the Indian subcontinent, with its wide variety of agro-climatic
regions and broad range of socio-economic conditions in the rural population, calls
for agricultural extension approaches that are context-specific and situation-specific.
Extension organizations in general have been using a wide range of methods for
reaching individuals, groups and the wider public in rural areas with new information/
knowledge. Approaches to extension also vary widely from top-down and supply-led
to bottom-up, demand-led and participatory. Approaches also vary depending on the
mandate of the organization or the programme. Advances in information and
communication technologies (ICTs) have also provided new opportunities for
extension to reach more farmers in a short amount of time (Sulaiman et al. 2011). Five
such innovative extension approaches pertaining to (a) rice varietal popularization,
(b) sustainable local seed system, (c) rice value chain, (d) gender sensitive extension
and (e) rice-based climate smart model village approaches have been covered in this
chapter. Efforts have been made through the chapter to address various issues and
problems responsible for low income of farmers and share innovative ways, means
and extension solutions to get rid of those problems. The new ideas could be suitably
blended with existing extension models to hasten the extension service delivery in
any developing nations. The authors are of strong opinion that the information on
innovative extension approaches would be very useful to researchers, policy makers,
academicians, development professionals, agro-processing industries, scholars and
farmers at large.

2. CONSTRAINTS OF TECHNOLOGY TRANSFER AND

ADOPTION
The varietal development effort of the ICAR-NRRI has got an impetus in recent
past with an average of about six varieties per year (Table 1). But most of these
varieties are neither in state seed chain nor adopted by farmers due to their unawareness
or any other reason.
Table 1. No. of rice varieties developed by ICAR-NRRI since its inception.
Average no. of variety
Period No. of years No. of variety developed developed per year
1946-2000 54 57 1.05
2001-2010 10 28 2.80
2011-2017 7 40 5.71
Total 71 125 1.76

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of Rice Farmers 479
 A critical review of past studies reveals that the major reasons for slow spread and
adoption of new varieties by farmers pertain to (i) non-inclusion of recent varieties in
state seed chains, (ii) non-receipt of breeder seed indents from the state agriculture
departments, (iii) lack of sufficient quantity of quality seeds, (iv) lack of publicity and
awareness among farmers and extension personnel, (v) insufficient minikit trials and
demonstration programmes, (vi) lack of effort by central and state extension
machineries, (vii) absence of suitable seed production and distribution policy etc. It
is seen that a new rice variety takes about 6-8 years to be known or popular by the
farmers. But as per the existing government policy, all the subsidies cease for any
variety which is older than 10 years and those cannot be promoted through any
scheme with exception in case to case basis. To overcome this problem, the institute
has intensified its effort to fast spread and popularize newly released varieties in
various states through front line demonstrations and other transfer of technologies
methods with the active participation of various stakeholders.
As per the feedback information collected by this Institute from the rice growers
of our country, unavailability of quality seeds in sufficient quantity and in right time
is their most pressing problem. The formal system of seed production in India has
been fulfilling the need of the farmers. However, the system faces a number of problems
related to quality, quantity, timeliness, choice of variety, cost of seed production and
distribution. The solution lies in developing suitable local seed systems. In contrast
to formal seed sector, local seed system, if strengthened, can offer solutions to
overcome the constraints of formal (government) seed supply system. Local seed
system can produce seed according to local farmers’ need, in right quantity, of right
quality, with lower cost of production and supply and with timely delivery of seed to
farmers. Therefore, this institute has developed a self-sustaining local seed system
model, which needs to be validated before being replicated and adopted in a large
scale. This will help in accelerating the varietal replacement rate (VRR) as well as seed
replacement rate (SRR) in rice.
One of the major concerns of farmers is the absence of lack of proper marketing
facilities in almost all the states. Farmers are deprived of getting their minimum support
price (MSP) and are forced to sell at distressed price (less than 2/3rd of the MSP) to the
middlemen. To ensure fair price of their produce and maximize rice farmers’ income
and net profit, the ICAR-NRRI has been working on developing and refining a multi
stakeholders’ rice value chain (RVC) approach since 2014-15. Among the various
approaches to increase farm income and promote entrepreneurship, the prospect of
rice value chain assumes importance in agriculture and allied sectors (Das 2017). The
RVC, besides having the fundamental benefits, has some added prospective like (i)
rice will continue to dominate the farm production for various socio-economic and
cultural reasons in spite of poor financial gains and market glut, (ii) demand in the
national and international market for quality rice is quite apparent, (iii) apart from
farmers, other stake holders can join the chain leading to creation of additional
employment and (iv) quality and specialty rice varieties developed by research
institutes can spread quickly with less investment in extension.

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Gender issues in rice farming have always been a much talked topic of discussion.
Rice production is a labour-intensive activity, which involves both male and female
members. In eastern India, farmwomen perform up to eighty per cent of the work in
rice fields and are involved in almost all activities of rice farming. However, they are
often marginalized in business relations and have minimal control over access to
factors of production like land, inputs such as seed and fertilizer, credit and technology.
So, the question remains how to empower farm women, when the available statistics
speak volume of their poor condition worldwide. It is reported that unlike farmers,
only five per cent of current agricultural extension efforts and resources are directed
to farmwomen. Secondly, India is a country of continental size with a population of
over 1270 million, out of which about one third live in urban areas. Ready-to-eat
processed and packaged foods have become necessity and popular among this huge
urban population in recent years. Therefore, the Indian food processing industries
including rice is being termed as a ‘sun-rise industries’ and several efforts have been
made in the last few years to give a big thrust to this sector. The food processing
sector plays an important role in improving agricultural productivity, reducing post-
harvest losses, providing better nutrition, creating huge employment opportunities
and in improving food availability for the domestic market. Looking at the inherent
skills and expertise of Indian women in preparation of traditional rice based value
added products, we need to harness this vast pool of knowledge and skill, and
translate them into a commercial venture providing livelihood security, food and
nutritional security, and contributing to national economy. Therefore, we should
focus on some of these issues and strategies for commercialization of such rice based
processed value added products (VAPs) in an entrepreneurial mode and linking them
to the food value chain the country.
Several agencies are working for developing rural areas and village people. The
development takes place on the basis of quantum of efforts of agencies in their
respective areas of jurisdiction. The development is not always uniform. Piecemeal
approach, sporadic efforts and casual attitudes of development agencies often lead
to skewed growth and development. The visibility of efforts tends to disappear slowly
or fast depending upon the magnitude and quality of work, once the change agents/
development professionals withdraw their involvement. When different agencies
work independently in different directions in meeting the aspirations and expectations
of the village people, the focus of attaining sustainable rural development is lost.
This results in uneven development. Hence, this calls for an integrated extension
approach involving different stakeholders in ensuring holistic development of villages.
This can also lead to development of model villages where progressive agriculture
and empowered village society would be witnessed. Developing a rice-based climate
smart model village through convergence of all stakeholders namely, researchers,
development personnel, farmers, farm women, youths, farmers’ organizations and
NGOs etc is another innovative extension approach for inclusive development of all
available local resources in an integrated manner.

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3. STATUS OF RESEARCH
Regarding adoption of rice varieties in Bangladesh, Hossain (2012) reported that
the number of varieties grown in different seasons were 1091 (Aman/Kharif-535,
Boro/Summer–261 and Aus/Autumn-295). However, only a few varieties covered a
large proportion of area. The major varieties according to area coverage in Bangladesh
were BRRI Dhan 29 (37%) and BRRI Dhan 28 (23%) in dry season, while BR 11 (27%)
and Swarna (12%) in wet season. Similarly, the survey report also encompasses
findings from three major rice growing eastern Indian states namely, West Bengal,
Odisha and Jharkhand. The survey identified 226 rice varieties in West Bengal, a large
proportion of which were traditional varieties mostly grown in the aman season. The
most popular variety in the aman season was found to be Swarna (45% of the rice
area), whereas in the boro season it was IR 36 (27% area). The main source of seed for
aman varieties was farmers’ own seed, whereas, in the case of improved boro varieties,
it was seed traders. In case of Odisha, the number of varieties identified in the wet
season was 723, most of which were traditional varieties. On the other hand, the
number of varieties in the summer season was 29, all of which were improved varieties
grown under irrigated conditions. Variety Swarna (29.3%) was the most popular variety
in the wet season, whereas in summer it was Lalat (47.0%). In Jharkhand, altogether,
145 varieties were identified and the highest number was for medium land (71), followed
by lowland (55) and highland (19). In the highland, traditional variety Gora Dhan was
found to be the most popular, while in the medium land and lowland, improved varieties
namely IR 36 and Swarna respectively, were the most popular varieties.
Regarding primary traits for farmers’ varietal preferences, he reported that farmers
sought high grain yield from limited farm size as the most important trait in a new
variety. The responses of the farmers from Bangladesh, West Bengal, Odisha and
Jharkhand with respect to this higher grain yield trait were 96%, 100%, 100% and 73%
respectively. Farmers also looked for secondary traits like grain quality for a premium
price in the market, shorter maturity duration, lodging resistance, and higher milling
recovery.
The survey on adoption and diffusion of new varieties in Bangladesh, West
Bengal, Orissa and Jharkhand revealed that (i) If varietal performance is substantially
better than that of existing varieties, large farmers adopt and small and medium farmers
follow, otherwise, the variety is eliminated, (ii) Availability of seed of improved varieties
is a major constraint for fast-tracking diffusion (70% to 80% of the seeds are from
farmers’ own harvest or are exchanged with or purchased from neighbors), (iii) Once
farmers in a village are convinced of the superiority of a new variety, it takes 3 to 5
years to reach areas suitable for the variety, (iv) However, it may take a longer time to
reach a substantial portion of area because of information lag (extension system is
not highly effective, radio/television is a minor source of information, input dealers
are not targeted as information bearers), and (v) Once a variety is established, it is
difficult to dislodge it, unless new improved varieties have traits that are substantially
superior.

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For realizing optimum productivity of any crop in any production environment,

the choice of an appropriate variety is extremely essential (Lal 2010). He added that
the variety to be selected for cultivation must be adapted to the specific agro-ecologies/
production environments. Improper choice of the variety would result in low
productivity, even when adequate quantities of inputs are applied. It is equally
important to use the latest recommended varieties, since all varieties tend to lose
disease resistance on account of evolution of pathotypes/ biotypes of the disease.
For promoting newly released varieties, ICAR-NRRI has been producing breeder
seeds of rice as per seasonal indents received from various states through the
Department of Agriculture & Cooperation, Government of India and various other
organizations. In addition, truthfully labeled (TL) seeds are produced in the research
farm as well as in farmers’ field in a ‘Farmer Participatory and Buy-back mode’ for
direct sale to farmers through its own sale counter. In addition, limited varietal
demonstrations are conducted in selected clusters in the Odisha state. As part of the
varietal development programme, all India coordinated research project (AICRP) trials
are conducted in various states to test the efficacy and adaptability of the varieties.
Apart from these, minikit trials are conducted through various research initiatives like
institutional research projects, externally aided projects, and various programmes
like, Tribal Sub-Plan (TSP), Mera Gaon Mera Gaurav (MGMG), Farmer FIRST, BGREI,
NFSM, NICRA, KVKs etc to demonstrate and promote new varieties. The institute
also organizes and participates in national and international exhibitions showcasing
its latest varieties and rice production technologies. All trainee farmers and important
stakeholders coming from various states are also provided with seed minikits for their
respective local demonstrations and spread.
Paroda (2010) opined that for achieving desirable levels of seed replacement rate
(SRR), adequate seed needs to be produced first. Seed production programme should
be organized in each state under a comprehensive and integrated state seed plan
appropriate to region specific requirements. States should ensure production,
multiplication and replacement of seed and varieties to increase seed multiplication
ratio (SMR), seed replacement ratio (SRR) and variety replacement ratio (VRR)
progressively, particularly in respect of regionally important crops/varieties. While
delivering a special lecture during Indian Seed Congress 2013, Paroda (2013) mentioned
that promotion of hybrids/ HYVs in major field crops should be a high priority to
bridge the productivity gap and increase production. In this context, the private
sector has to play a major role. Immediate action is warranted for phasing out of all old
and obsolete varieties through de-notification and promoting only the best varieties
and hybrids suitable for specific regions, irrespective of whether they are from public
or private sector.
Sharma et al. (2013) stated that the present supply chain structure of rice in India
works on the traditional framework, which involves many intermediaries at supply
and distribution fronts. The current supply chain structure of rice in India is
somewhere lacking in efficiency and needs reforms. The traditional supply chain
structure faces the problems of inventory management, where either there is the

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overstocking which results in obsolescence and increased supply chain costs, or the
stock outs of the demanded varieties resulting in lost sales. Supply chain of rice in
India is also facing the supply chain problems related to procurement, distribution,
intermediaries collaboration, and logistics system which needs to be redesigned. In
spite of being the second largest producer in the world and a big consumer of rice,
which holds a significant presence in the global agri-food market, India fails to
contribute to the global food business to the level it deserves.
While analyzing value chain of rice and wheat in Uttar Pradesh state of India,
McCarthy (2008) viewed that high local, global and regional demand for rice and
wheat could greatly benefit smallholder farmers of both of these staple crops in the
rural areas of India. Small landholders, the major engines of production in India, can
take advantage of these growth trends to meet this demand and increase their incomes.
Taking advantage of these parallel trends will require farmers to increase production,
reduce post-harvest losses and market their crops in new ways. Amendments to the
restrictive state marketing channel (through mandis, or wholesale markets) are
beginning to allow farmers to access more profitable channels for their produce. The
mandi system does not reward farmers for higher-quality produce as alternative market
channels would, such as direct supply to supermarkets by establishing value chain.
The major actors in the rice and wheat value chains are input suppliers (including
manufacturers, wholesalers and retailers); producers; a large number of intermediaries
(including collectors, traders, commission agents, and brokers); wholesalers;
processors (including rice and flour millers); and retailers.
There is a growing body of evidence that promoting women’s rights over land
and natural resources are keys to enhancing women’s livelihood security and
promoting women’s empowerment. Land ownership is likely to have positive effects
on agricultural productivity, food security and children’s education (Agarwal 2003).
Moreover, technology research and innovations are rarely focused on women’s
specific needs and roles. As a result, farm women generally lack access to improved
technologies for use in farming activities, and the large majority of them still rely on
traditional, labour-intensive, drudgery-prone and time-consuming technologies. In
many countries, the menu of options available to farmers has become more diversified.
For instance, in Ethiopia the creation of a ‘women’s development package’ indicates
that agricultural officials are trying to improve their services to women (Tewodaj et al.
2009).
The ICAR-NRRI, which has been mandated to increase production and
productivity of rice-based farming systems in India, took up a project on ‘Gender
Mainstreaming in Rice’ during 12th plan period (2012-2017). A socially acceptable,
practicable and replicable approach was conceptualized based on the hypothesis
that, ‘if the inherent capacity of the farm women are explored and built up through
sensitization, gender gap identification, awareness, training, exposure to technologies,
access to family resources, group mobilization alongside the male counterparts of the
society and necessary organizational support, then all round development of the
farm women and household agricultural production and productivity can be achieved’.

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Under this approach, intense gender sensitization was a pre-requisite, which followed
capacity building programmes of women rice growers. Both men and women get
equal opportunity to exchange their experiences and feelings to provide community
support to women rice growers in many critical areas of gender gap. Finally the
approach ends in leaving the women in the family and evaluating the overall household
improvement in rice production and productivity in particular and gender issues in
general. The major activities, outputs, outcomes and experiences have been discussed
below under the approaches section.

4. KNOWLEDGE GAPS
Results of on-station, off-station and on-farm demonstrations, minikit trials and
farmers feedback on the institute developed varietal performance and their superiority
over local popular checks have been very encouraging over the years. Despite all
above efforts by the institute, varieties are spreading slowly and not reaching a wider
population as desired. One of the major shortcomings of the institute is production of
limited quantity of seed due to availability of limited area of about 30-40 hectares land
for seed production. On the contrary, state agricultural universities have been well-
placed due to their huge network of regional research stations within respective
states with vast area under seed production plan. Apart from superiority of varieties,
availability of large amount of quality seeds (foundation and certified seeds) is equally
essential to fulfill the seed requirements of state machineries to promote through
seed chains. Because of this reason, ANGRAU model of rice varietal diffusion and
popularization through distribution of sufficient minikits during initial 2-3 years of
their development has been a very successful model, as was shared by two of its
former Breeders-cum-Vice Chancellors namely, Prof. P. Raghava Reddy and Prof. Padma
Raju during the national level Brainstorming Workshop on “Rice Varietal Diffusion:
Estimation, Problems and Prospects” organized by MANAGE at Hyderabad during
19-20 May, 2017, citing examples of mega varieties like Swarna (MTU-7029), MTU-
1010, MTU-1001 and Samba Mahsuri (BPT-5204).
Another grey area is, farmers are not getting quality seeds in time at their door
step, even though rice seed market is growing faster in recent years. Rice seed
production and marketing is a very good enterprise in itself. Still, many Indian states
are facing very acute shortage of rice seeds with very less VRR and SRR. Rice seed
production technology and marketing can easily be promoted and adaptable, but
requires proper technical backstopping and active participation of farmers’
organizations. There is hardly any research or extension or organizational efforts to
make rice farmers self-sufficient with quality seeds at local level. Similarly, this institute
has developed some high protein, aromatic, export quality long slender and superfine
grain varieties, which can fetch higher remunerative market prices, benefitting the rice
growers. Developing and refining a multi-stake holder’s rice value chain (RVC),
involving all players starting from the rice developer to the consumer, can be a unique
and innovative proposition for this.

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 Indian farmwomen play a more significant role in rice sector contributing to
substantial increase in family income. They are traditionally skilled to prepare
thousands of value-added food products, so also rice based products. Encasing their
skills and involving in rice based value added enterprises and linking them to the
market can be a successful research endeavour. But, no such visible steps have been
taken so far at any level.

5. RESEARCH AND DEVELOPMENT NEEDS

In this section, various processes involved and experiences learnt in all the five
innovative extension approaches of NRRI, Cuttack have been discussed.
5.1. Approach-I: Rice varietal popularization strategy
The Institute is working on developing mechanisms to shorten the period between
varietal development and varietal spread leading to wide adoption, which can be
simplified in following concurrent activities. First of all, we need to identify existing
popular varieties and farmers’ preference in selected states for testing new and
comparable improved varieties through collection of primary as well as secondary
data from targeted areas. Accordingly, taking all criteria like ecology, duration and
farmers’ preference into consideration, a ‘Varietal Matrix’ can be prepared for all
‘popular but lower yielding varieties’ vis-a-vis ‘new, superior and higher yielding
varieties’ for replacement with better alternatives. Ecology wise district clusters should
be selected (may be, any one revenue block close to the district headquarters and
adjacent to a primary village road) and selection of about 15-20 innovative farmers per
cluster in consultation with state agriculture department officials and other
stakeholders. Varietal demonstration should be conducted by providing only 5-10 kg
seed minikits as critical inputs without altering farmers’ own crop management
practices. Planning for demonstration should be done in such a way that all the
districts may be covered in a maximum of 2-3 years in rotation.
These small scale on-farm demonstration may be done for participatory varietal
evaluation in consultation and collaboration with all stakeholders like, state
departments of agriculture (SDAs), state seed corporations (SSCs), state seed
certification agencies (SSCAs), farm science centres/ krishi vigyan kendras (KVKs),
state agricultural universities (SAUs), regional research institutes, farmer interest
groups (FIGs), private seed companies and dealers, non-governmental organizations
(NGOs) working in agriculture sector, media representatives and both demonstrating
and non-demonstrating farmers. Big size and clearly visible road side field boards
should be placed on the demonstration sites with details of varietal characteristics in
local language.
Capacity building programmes have to be conducted for various stakeholders
through training programmes, package demonstration, technical backstopping
through field visits/telephonic advisory/creating mobile social groups and conducting
field days at various stages of crop growth, especially in pre-harvesting stage

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associated with crop cutting experiments, with the principle of ‘Seeing is Believing’,
involving all the stakeholders including non-demonstrating farmers to showcase the
superiority of the new varieties. Participating farmers should be encouraged to share
their experiences to motivate fellow stakeholders. Best performing new varieties should
be upscaled through creating demand for breeder seed indents from next year onwards
and promotion of local seed production by government and private agencies for
making timely seed availability to farmers, and creating an institutional mechanism for
planning and production of adequate quantity of seed for minikit distribution. A
nodal officer along with a team of experts may be identified for continuous monitoring
at the institute as well as state levels.
Rigorous awareness campaign is required through electronic media, print media,
ICT tools like mobile apps/ social groups and distribution of extension leaflets in local
languages. Preparing success stories, recording of farmers’ reactions and overall
processes documentation are required for publicity and distribution. State level
workshops in the initial years must be conducted involving policy makers and senior
state development departments, officials to create awareness and convince key players
about the superiority of newly developed varieties. The non-conventional channels
(like seed companies, rice millers, traders and food processing industries) have to be
explored for spread of remunerative varieties. For fast spread of varieties, advisory
should be issued to participating farmers for not consuming the produced grains of
demonstrated plots during initial years, rather encouraging ‘farmers-to-farmers’
horizontal spread of seeds either through sale or on barter basis for rapid spread. As
part of the process, a good document should be prepared encompassing the workshop
proceedings, action points, demonstration details, crop cutting data vis-à-vis
comparative data on local varietal performance, feedback from farmers and other
stakeholders. The document should be widely circulated among important state and
central level officials & policy makers and action points should be followed up
accordingly.
5.2. Approach-II: Devising a self-sufficient sustainable seed system for
rice (4S4R)
The NRRI developed Self-sufficient Sustainable Seed System for Rice (4S4R)
model was conceptualized and developed in 2014-15 and since then it is being
implemented, tested and refined in Mahanga block of Cuttack, Odisha. However, the
model itself is general in nature harnessing the advantages of advancements in
information technology (IT) sector at various stages, like planning, execution,
monitoring, capacity building, support and marketing. The model tries to combine
best of the technologies and practices available with research institutions, universities
and IT institutions. Existing seed system was improved and supported by various
innovative interventions as follows.
 Facilitated farmers’ access to seed through (a) Awareness, (b) Training, and (c)
Capacity building;
 Introduced appropriate agricultural technologies in (a) Crop production, (b)
Integrated pest and disease management, (c) Introduction of improved varieties,
and (d) Seed health and storage management;

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 Improved disorganized local seed system through (a) Improved organization by
starting Farmer Producer Organisation (FPO), (b) Registering FPO under Company
Act 2013 (Old 1956) as Mahanga Agro Producers 4S4R Pvt. Ltd. on 30 April, 2017,
and (c) Providing support for establishment and sustainability; and
 Provided IT based solutions for (a) Expert system of seed production – ‘Paddy
SeedXpert’ was developed which is available at Google Play Store, (b) Used
remote sensing for identification of appropriate location for seed production, (c)
Used remote sensing and GIS maps to determine the seed requirement of the area,
(d) Linked financial institutions/KVKs of the districts to the Farmer Producer
Organisation (FPO), and (e) GIS mapping of seed availability and marketing.
This model has FPO in the centre of the activity at a block level (Fig. 1). The FPO
consists of i) seed producing farmers’ group, ii) seed processing enterprise and iii)
seed selling and marketing enterprise mainly catering the quality seed requirement of
the block at local level. The seed producing farmers’ group produces foundation/
certified seeds as per local demand from the breeder seed supplied by NRRI. Paddy
seed processing and packaging
machineries besides seed storage
godowns have been provided through
Rastriya Krishi Vikas Yojana (RKVY).
The sale outlet is part of the processing
unit. These two units have been
developed using entrepreneurship
development approach. Specialized
training programmes are imparted in the
area of FPO management and paddy
seed production which are followed by
required support to establish Fig. 1. Schematic representation of the 4S4R
processing and marketing unit(s). Model of NRRI.

The pivotal role in this model is being played by NRRI, being the specialized
institute for technology development in rice. The institute performs specialized roles
like, (i) supplying breeder seeds of locally preferred rice varieties. (Besides NRRI,
OUAT, Bhubaneswar also supplies breeder seeds to FPO as per the requirement of
the farmers), (ii) providing production and post-production technologies for quality
seed production, (iii) imparting training to KVK personnel involved in the project
activities, (iv) providing inputs for expert system development for seed production in
Odisha to IT Institution, (v) supporting in developing GIS-based tools for site (land)
selection for seed production, (vi) organising workshops at planning stage, portal
development stage and for capacity building to efficiently implement the project, and
(vii) coordinating various stakeholders in achieving the objectives of the project.
So far as the economic benefits of the model is concerned, the ‘Mahanga Agro
Producer 4S4R Pvt Ltd’, registered as part of the research initiative by NRRI with
participation of over hundred farmers, initially required nearly Rs. 31.94 lakhs as cost
of the project, but in the second year itself, the Break Even Point (BEP) was achieved

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with Rs. 87.0 lakhs sales realisation. The major challenges faced in implementing this
project are coordination among different stakeholders besides setting up FPOs at
block level and marketing of the paddy seed.
5.3. Approach-III: Developing a replicable rice value chain benefiting
all stakeholders
The main objective of the NRRI developed rice value chain (RVC) was to promote
large scale cultivation of high quality and specialty rice varieties of this institute in
contiguous patches, and to undertake it’s processing and trading, so that the
consumers have access to premium quality rice and all the parties involved in the
value chain are benefitted. During the planning phase of the RVC in 2014-15, several
brainstorming sessions, consultations
and focused group discussions were held
with all stakeholders including state
agriculture department to decide the
objectives, stakeholders, activities, links,
responsibilities of the partners and
benefits sharing. Finally, a chain emerged
in public-private-partnership (PPP) mode
with the involvement for five parties
including ICAR-NRRI, Cuttack (Fig. 2).
In consultation with all stakeholders, a
long slender grain aromatic inbred rice
variety ‘Geetanjali’ developed by NRRI
was selected for the rice value chain
during the initial year. The responsibilities
and benefits for each party were decided Fig. 2. Schematic representation of the
and agreed upon (Fig. 3) through a RVC Model of NRRI.
memorandum of understanding (MOU),
in brief as follows.

Fig. 3. Functions and Activities of RVC Actors.

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 1st Party (ICAR-NRRI, Cuttack): for supplying breeder seeds of ‘Geetanjali’,
technical backstopping, capacity building, hand-holding, overall coordination,
monitoring, and maintaining season-wise database.
 2nd Party (Sansar Agropol Pvt. Ltd., Bhubaneswar): A seed company for multiplying
the foundation or truthfully labeled seeds and supplying seeds to farmers groups/
rice growers at desired destination in time.
 3rd Party (Ananya Mahila Bikash Samiti, Sankilo, Nischintakoili, Cuttack): A farm
women group for mobilizing large number of farmers and producing large quantity
of grains.
 4th Party (Mahanga Krushak Vikas Manch, Mahanga, Cuttack): A farmers group
for mobilizing large number of farmers and producing grains. Apart from production,
these farmers groups were also involved to undertake survey of the rice ecology,
motivate farmers of various districts of the state to participate in the chain, monitor
the production and arrange lifting of production by the rice processor-cum-trader.
 5th Party (Sabitri Industries Pvt. Ltd., Mayurbhanj): Rice processor-cum-trader for
procuring grains from farmers’ point immediately after the harvest season ends, at
a price of at least 20 percent above the minimum support price (MSP) fixed by the
Govt. of India, making payments to growers within ten days of procurement,
ensuring quality processing, packaging, labeling with due credit to the variety
developer (NRRI) and marketing.
Intensive efforts were made for field monitoring, technical backstopping and
capacity building through farmers training, distribution of extension literature in local
languages and mobile advisory services through a monitoring committee comprising
of multi-disciplinary scientists and state line department officials. Workshops at
various stages of the cropping period (pre-kharif, pre-rabi and post-harvest etc) are
conducted for deciding varieties, finalizing seed and grain production plan, number
of farmers to be involved, recording feedback analysis, sharing experience, and
resolving issues with the participation of all stakeholders. As part of our initial effort
during rabi 2015-16, grain of Geetanjali variety was produced in three clusters totaling
166 acres of Khurda and Cuttack districts involving 82 farmers. The average yield of
the crop was recorded at 4.0-4.5 t/ha. After keeping for seed and household
consumption, 202 tons of paddy grains were sold by the participating farmers to the
rice processor/ miller (5th party) at the rate of Rs. 17,400/- per ton (i.e., 20% above
MSP) amounting to a total of Rs. 35.15 lakhs. Similarly, during kharif 2016 and rabi
2016-17, 136 tons of paddy grains were procured by the processor. The economic
analysis shows that the participating farmers got an overall net income advantage of
about 8-10 per cent over the non-participating farmers.
5.4. Approach-IV: Gender sensitive extension approach in rice farming
The gender sensitive extension approach in rice farming was designed and tested
in Sankilo village of Cuttack district with the involvement of over fifty participating

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farm women during 2012-17 and is being carried forward in an entrepreneurial mode
since then. The village was selected after making due consultations with the
households and finding the social climate relatively better in gender sensitiveness.
Preliminary meetings, gender sensitization programmes, gender gap analysis and
PRA studies were undertaken by involving both male and female key informants
separately to identify major gender issues in rice farming.
The major gender issues in rice farming identified included women-friendly
technologies, access to resources & information, labour sharing, benefit sharing,
capacity building, group mobilization, decision-making pattern, societal gender
mindset, constraints in farming, linkage with financial & marketing institutions etc.
Accordingly, suitable technological and institutional interventions were provided
and evaluated. The male heads of the families/ the legal owners of lands were sensitized
and motivated through personal contacts and close interactions to allocate about
half an acre rice growing land to all the participating family farm women to take up
crop demonstrations as per the advice of NRRI scientists and take independent
decisions on crop management. A women development group in the name of ‘Ánanya
Mahila Bikash Samiti’ was formed and registered after mobilizing all fifty farm women
for deriving maximum institutional benefits and for group sustainability. Intensive
awareness camps were organized and trainings imparted for desirable changes in
their skill, knowledge and behaviour with regard to the objective of the programme,
rice production technologies, market support and possible outcome of the project.
Demonstrations on rice production and crop management practices on popular
and suitable rice varieties based on women’s preference and market demand were
conducted in the allotted half acre land by each farmwoman during kharif seasons.
Apart from rice, during rabi seasons, technological interventions on cultivation of
high value vegetable crops, pulse crops and preparation of value added food products
were also given. Seeds and planting materials were provided free of cost as critical
inputs during initial years only. Improved rice production technologies like growing
of mat type nursery, seed treatment, line transplanting, use of rice transplanters,
balanced dose of fertilizer application and need based pesticides application were
provided along with technical backstopping in women’s perspectives. Similarly, for
harvesting and post-harvesting management, training-cum-demonstrations on
drudgery-reducing and women-friendly machines and technologies like NRRI rice-
parboiling unit and NRRI rice-husk combustor; and demonstration on paddy-straw
mushroom cultivation was also conducted for additional revenue generation and
family nutrition from rice by-products.
Looking at their acquisition of enough technical competencies and managerial
abilities, the group was made as a signatory to the NRRI developed rice value chain
for ensuring greater economic benefits of the participating women members. Reactions
of the farm women were recorded at regular intervals to assess the effects of
interventions and modify accordingly, if called for. The major impacts of the project in
terms of outputs and outcomes as found out through concurrent and end-term
evaluations are briefly outlined below.

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a) Change in attitude towards gender mainstreaming: Significant change in attitude
towards gender mainstreaming was established. The male members of the family
as well as in the village are now giving more importance and recognition to the
farm women in farm, family and community matters. More so, they were happy
and motivated to see and watch the success stories of their village in print and
electronic media. They are now allowing female members to attend agricultural
meetings and programmes outside.
b) Mindset of male members of family/society: Findings indicate that there was
major change in the mindset of male members of family/society towards women-
managed rice farming (90%). All the farm women were feeling recognized by other
members of the family as well as village due to their increased capacity in farm and
home management activities and leadership in organizing group and social activities.
c) Competency of farm women: As opined by the farm women, remarkable changes
in behavior of women rice growers were found with regard to agricultural
knowledge (100%), technical skill (93.33%), decision-making capacity (86.67%)
and undertaking group activities (76.67%). Improvement in skills in nursery raising,
handling farm implements, and disease and pest management were also observed.
d) Women friendly production technologies: Technologies with regards to raising
of mat-type seedlings for mechanical transplanting, seed treatment, mechanical
line transplanting and use of small farm equipments were found drudgery reducing.
Among the women-friendly farm machineries demonstrated, rice husk combustor,
finger weeder and 4-row manual drum seeder were perceived as more appropriate
by 85.71%, 70.37% and 57.14% farm women respectively. Paddy straw mushroom
cultivation as an income generating activity by converting rice byproduct (straw)
was also rated as more appropriate by 88.46 per cent farmwomen.
e) Perception about of demonstrated technologies: All the participating farmwomen
adopted scientific production practices based on their socio-economic feasibilities.
The analysis of the data shows that majority of the respondents had positive
perceptions with regards to comparative advantage of recommended/demonstrated
rice varieties over earlier grown varieties in terms of yield, resistance to pest/
diseases, tolerance to weeds/drought, labour saving, profitability and marketability.
f) Access to productive resources: Significantly increased access of women to farm
inputs was observed through the approach, as evident from the expansion of
allotted half an acre land to over one acre in many families by end of 2-3 years.
This expansion of area under the control of farmwomen signifies more trust and
confidence on women farmers by their male counterparts and a positive impact of
the project. Similarly, accessibility to family land (100.0%), seeds (100.0%), fertilizers
(100.0%), and money (45.45%) were found.
g) Entrepreneurial opportunities: Since, the farm women had their expertise in
preparing traditional value added food products (VAPs), they were encouraged
and supported to convert the traditional value added rice products into demand
driven marketable products through improved food technology process. A book

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on ‘Traditional Rice Foods - The Rich Heritage of India’ was also brought out
containing the processes of making over hundred traditional rice-based value
added products, primarily collected from the women group members.
h) Partnering in RVC: By working in groups, the women realized their inherent capacity,
developed friendly atmosphere and learnt the importance of working in groups in
the society. Accordingly the registered group also took up entrepreneurial activities
as a signatory to the NRRI rice value chain and in turn potential women
entrepreneurs were recognized.
i) Outstanding public recognition: Among others, one of the successful farm women
Smt. Rukmini Nayak of the group was conferred with ‘Best Innovative Farmer
Award’ during ‘Krishi Unnati Mela-2017’ at IARI, New Delhi and with ‘Best Farmer
Award’ during ‘Akshay Tritiya & Farmers Fair-2016’ at NRRI, Cuttack apart from
several other awards and recognitions, and received these awards from Hon’ble
Union Minister of Agriculture & Farmers Welfare, Govt. of India.
5.5. Approach-V: Developing a rice-based climate smart model village
through convergence
The National Rice Research Institute took up an initiative to demonstrate and
develop an extension approach for ‘development of a rice-based climate smart model
village’ with a broad objective of achieving all round development of Indian villages
in convergence mode with emphasis on sustainability and equity during 2012-17. It
was conceptualized as a holistic developmental model in a convergence mode
involving various stakeholders like NRRI scientists, line departments, development
departments, farmers associations, farmers, farmwomen, rural youths etc for achieving
capacity building and overall development of farming communities through agriculture
and allied activities.
The development of rice-based climate smart model village, evaluation of
interventions and recommendations were taken up in a rainfed cluster, namely
Gurujang-Guali of Tangi-Choudwar block of Cuttack district in Odisha. The cluster
was selected because most of the people were socio-economically disadvantaged,
the population comprised of mixed castes and livelihood, mainly dependent on rainfed
rice-based farming options and facing many adversaries of climate change. There
were about 100 farm families in the cluster with a total population of about 800. Based
on bench mark survey and PRA studies, suitable technological and institutional
interventions were provided and evaluated. Participatory technology demonstrations
on rice, vegetables, animal husbandry, fisheries, group vegetable farming by women
and allied activities were conducted. Capacity building of beneficiary farmers,
farmwomen and youth was done through training, farmers-resource persons
interactions, exposure visits and continuous technical backstopping. Village level
stakeholders’ meetings and workshops were organized by involving officers of the
stakeholders departments (agriculture, horticulture, animal husbandry, fisheries, soil
conservation, irrigation, panchayatiraj, cooperative etc), farmers and farm women of
the cluster and scientists of the institute for developing a holistic approach and

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mechanism of convergence among the departments. The priority needs of the cluster
were identified as rain water harvesting under watershed and minor irrigation
programme, control of wild buffaloes and stray cattle during rabi season and
management of weeds in rice and vegetable crops.
Seasonal and annual action plans developed for the purpose were monitored from
time to time for their effective implementation in a participatory and convergence
mode. The high yielding rice varieties namely Sahabhagidhan, Swarna Sub-1, Pooja,
Ketekijoha, Varshadhan, CR Dhan 304, CR Dhan 202 and Naveen were most liked due
to their various motivational traits. Climate resilient varieties namely, Sahabhagidhan
(drought), Swarna Sub-1 (submergence), Varshadhan (deepwater & waterlogged),
CR Dhan 202 (aerobic) etc. were introduced in the cluster and proved high adaptability
and acceptance by the farmers. Prior to project interventions, they were cultivating
HYVs of rice in about only fifteen per cent of rice growing area, which increased to
about ninety percent at the end of five years. Farmers were still growing some local
varieties due to their special grain and cooking quality.
The influence and benefits of group vegetable farming by women were very well
noticeable and might help formation of more women groups for vegetable farming.
The performance and impact were assessed which revealed that a very high percentage
(94%) of farmers of model village had well derived various socio-economic benefits
from the rice-pulse-horticulture-poultry-pond based production technologies
propagated by the institute. The farming habit has changed. The fallow back yard
lands of households have been covered under kitchen gardening or mushroom units
or poultry units and the drought prone lands have been covered with drought resistant
rice varieties or pulses. Apart from improvement in farming and socio-economic
conditions of the villagers, village sanitation has also improved with the support from
the block development department through construction of village pucca roads and
individual household safety toilets. A study conducted in the cluster to assess the
direction of changes revealed that significant positive changes had taken place with
respect to attitude towards hybrid rice, knowledge on high yielding varieties,
knowledge on rice cultivation, soil nutrient management, pest control and farm
mechanization. Youths have been motivated to assist parents in farming activities or
have taken up some kind of independent income-generating activities.

6. WAY FORWARD
As part of the institutional effort, cluster demonstrations were conducted during
kharif 2017 involving 60 farmers in Jharkhand (with CR Dhan 202 and CR Dhan 305);
24 farmers in West Bengal (with CR Dhan 201, CR Dhan 203 and CR Dhan 304) and
about 200 farmers in Odisha with 20 new rice varieties released for the state. The crop
cutting results of almost all the demonstrated varieties showed a grain yield
advantages of about 10-20% over all the existing popular varieties. A demand for
seeds of these varieties has been created among the farmers. There is need to upscale
these activities in convergence with other stakeholders in years to come.

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Information technology and FPO are effectively integrated in 4S4R model which
makes seed available at local level to ALL farmers according to their NEED, in right
QUANTITY, of right QUALITY, at lower COST and TIMELY delivery, which the
present formal seed system has FAILED to deliver. This project activity enriched the
subject on IT/ICT application in agriculture in general and dissemination of technology
in particular. This has involved expert systems, GIS, MIS, web-based applications
and mobile based methods for information dissemination. Another aspect that activity
this project contributed, is development of approach to form FPO as an extension
method for planned and organized transfer of technology and marketing.
The rice value chain approach has to be validated by widening the stakeholders’
base, involving more number of rice millers, processors, traders and farmers
organizations to generate competitiveness. Apart from long grain aromatic varieties,
high value non-aromatic and nutritionally enriched high protein, high zinc rice varieties
can be put into the chain. Nutritional rice varieties enriched with protein, iron and zinc
can be promoted through government welfare schemes like mid-day meal for school
children and Antyodoya AnnaYojana. Studies on marketing through e-national
agricultural marketing (e-NAM) portal could be explored.
Access to productive resources is critical for enhancing women’s economic
choices. Since, formal credit institutions rarely lend to this weaker sex, special
institutional arrangements has become necessary to extend credit to those who have
no collateral to finance their enterprise. In order to have access to credit, social,
institutional and government support is required. More than half of the farm labour is
contributed by farm women. Moreover, as evident from several literatures, they have
also proven their competencies over time and again to manage farm and home efficiently
and effectively at par with the male members of the society, provided they were
supported socially, economically, morally, technologically and institutionally. There
is a need to identify their hidden capacities and entrepreneurial abilities and link them
to the market. If they can be made technologically competent and socio-economically
empowered, they could be the efficient drivers in achieving accelerated agricultural
growth and development of the country in general and in boosting family income in
particular. Organizing women into groups has been proved to be a good intervention.
It can transform women from the status of ‘beneficiaries’ into ‘clients’, who are in a
long-term can have a reciprocal relationship with the institutions meant to serve
them.
The model village approach has successfully integrated all stakeholders in the
development of rural India in a participatory and convergence mode. In addition to
addressing the issue of socio-economic and agricultural development, climate issues
have been suitably addressed. The model needs to be validated and refined in other
parts of the country and should be replicated in bringing prosperity to the society.

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of Rice Farmers 495
References
Agarwal B (2003) Gender and Land Rights Revisited: Exploring New Prospects via the State,
Family and Market. Journal of Agrarian Change. 1(1& 2). London: Blackwell Publishing
LTD.
Das Lipi, Sharma SG, Samal P, Patnaik SSC, Sahu RK, Rath PC, Mishra SK, Panda BB and
Mukherjee AK (2017) Success Story on ‘Rice value chain in PPP mode for increasing farm
income and entrepreneurship’, 1-4. ICAR-NRRI, Cuttack.
Hossain M (2012) Rice varietal diversity, milling, and cooking in Bangladesh and eastern India: a
synthesis. In: ‘Adoption and diffusion of modern rice varieties in Bangladesh and eastern
India. (Ed. M. Hossain, W.M.H. Jaim, T.R. Paris, and B. Hardy), International Rice
Research Institute (IRRI), Philippines.
Kokate KD, Kharde PB, Patil SS and Deshmukh BA (2009) Farmers-led extension: Experiences
and road ahead. Indian Research Journal of Extension Education, 9(2):18–21.
Lal S (2010) Guidelines for selection of improved varieties/hybrids of rice, wheat and pulses for
NFSM states. Manual. DAC&FW, Ministry of Agriculture & Farmers Welfare, Govt. of
India, New Delhi.
McCarthy S, Singh DD, and Schiff H (2008) Value Chain Analysis of Wheat and Rice in Uttar
Pradesh, India, ACDI/VOCA for World Vision, Lucknow, India.
Paroda RS (2010) Revitalizing Indian Seed Sector for Accelerated Agricultural Growth. Foundation
Day Lecture delivered in the National Seed Association of India (NSAI) on 30 October,
2010.
Paroda RS (2013) Indian Seed Sector: The Way Forward. Special lecture delivered in the Indian
Seed Congress-2013, organized by NSAI on 8 February, 2013.
Sharma V, Giri S and Rai SS (2013) Supply Chain Management of Rice in India: A Rice Processing
Company’s Perspective, International Journal of Managing Value and Supply Chains
(IJMVSC), 4(1), March 2013.
Sulaiman VR, Kalaivani NJ, Nimisha Mittal and Ramasundaram P (2011) ICTs and Empowerment
of Indian Rural Women - What can we learn from on-going initiatives? CRISP Working
Paper 2011-001.
Sulaiman RV and Andy Hall (2008) The fallacy of universal solutions in extension: Is ATMA the
new T&V, LINK News Bulletin, September 2008, Learning Innovation Knowledge (LINK)
(www.innovationstudies.org).
Swanson B (2009) Changing extension paradigms within a rapidly changing global economy. Paper
presented at the European Seminar on Extension Education, Assisi, Italy.
Tewodaj M, Cohen MJ, Birner R, Lemma M, Randriamamonjy J, Tadesse F, and Paulos Z (2009)
Agricultural extension in Ethiopia through a gender and governance lens. IFPRI: Washington
D.C.

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Quantification of Yield Gaps and Impact

Assessment of Rice Production Technologies

Biswajit Mondal, P Samal, NC Rath, GAK Kumar, SK Mishra, Lipi

Das, NN Jambhulkar, PK Guru, MK Bag, SM Prasad, S Roy and
K Saikia

1. INTRODUCTION
It is projected that there would be 60% increase in demand for agricultural
production by 2050 (FAO, 2012), which is very large, but not unreachable. There is a
huge ‘yield gap’ and closing these gaps could improve not only the productivity but
also the efficiency of rice production. The term ‘yield gap’ has been commonly used
to refer to the difference between the average farmers’ yields and an estimate of a
reference yield or potential yield at a specific area in a given time. Maximum attainable
yield is the yield of experimental or on-farm plots with no physical, biological and
economic constraints and with known management practices at a given time and in a
given ecology. Potential yield (van Ittersum and Rabbinge 1997) can be defined and
measured in a variety of ways such as using crop growth models, maximum yield
trials, and other research experiments, or best yields from farmers’ fields (Lobell et al.
2009). Farm level yield is the average farmers yield in a given area at a given time in a
given ecology. Yield gaps exist because the best available production technologies
are not adopted in farmers’ fields which could be due to farmers’ personal
characteristics (e.g., lack of knowledge and skills, risk bearing ability), farm
characteristics (e.g., soil quality, land slope, poor road), and unsuitability of the
technology to farmers’ circumstances (e.g., labour-intensive, requirement of high
initial investment, poor access to inputs). Yield gap has two components, the first one
cannot be narrowed or not exploitable, because it is mainly governed by the factors
that are non-transferable such as environmental conditions. The second component
is mainly due to difference in management practices or farmer’s inefficiency level,
which is manageable and can be bridged. As average crop yields are critical drivers of
food prices, cropland expansion, and food security, yield gaps should be better
quantified and understood (Lobell et al. 2009). An experimental technique for identifying
and quantifying yield constraints in farmers’ fields was developed and validated by
Gomez (1977). It measures the potential yield, the actual yield, and the yields
corresponding to the addition or removal of test factors over and above the farmer’s
levels. In agronomy, there are many crop models that can incorporate location-specific
physical conditions to estimate crop growth and potential yields for particular crop
types, as well as for combinations of many crops. These crop models are often
developed using field and experimental data, thus providing reliable estimates of
plant growth and potential yields and very much useful tool when designing
agricultural systems for the maximisation of production outputs (de Koeijer et al.
1999; van Ittersum and Rabbinge 1997). However, economic, institutional and social

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Rice Production Technologies 497
factors are not associated in these models (de Koeijer et al. 1999), thus preventing
their usefulness in socio-economic analysis. Hence, a different approach is required
that integrates the experiments in farmers field into socio-economic analysis of
productive efficiency.
Impacts are the longer-term results produced by a programme or policy
implementation or adoption of a technology, which may be intended and unintended,
positive and negative, direct and indirect in nature. Impacts do not only refer to what
has happened-in some cases, the impact is in terms of preventing negative changes;
it also includes the reduction, avoidance or prevention of harm, risk, cost or other
negative effects’. An impact evaluation provides evidence about the results that
have been produced (or expected to be produced). It has to not only provide credible
evidence that changes have occurred but also undertake credible causal inference
that these changes have been at least partly due to a project, programme or technology.
There are different types of impact evaluation and categorized based on the period of
the exercise, like (a) ex-ante impact where evaluation undertaken before the programme
is initiated or the technology being adopted; (b) ex-post impact evaluation which is
conducted after a technology has been adopted by farmers in the target areas or a
programme being implemented fully; and (c) concurrent impact evaluation, which
gathers evidence about whether the programme is on track to deliver intended results
(during implementation process). Economic evaluations combine evidence about
stream of benefits and costs, through, (a) cost-benefit analysis, which transforms all
the benefits (positive impacts) and costs (resources consumed and negative impacts)
into monetary terms, taking into account discount factors over time, and produces a
single figure of the ratio of benefits to costs, and (b) cost-effectiveness analysis,
which calculates a ratio between the costs and a standardised unit of positive impacts
of different propositions or choices. For impact evaluation process, the standard
challenge is determining what would have happened in the absence of the programme/
technology for which evaluation is being undertaken. To understand the impact of a
programme/technology on a given indicator, information would ideally be available
from the beneficiaries and those same beneficiaries without the particular programme/
technology. The indicator could then be compared between these two situations to
examine if the programme/technology had an impact. However, beneficiary farmers
cannot be simultaneously in the project and out of the project making it necessary to
search for a substitute group of farmers to act as the counterfactual - that is, what
would happen in the absence of the programme/technology. To be a genuine
counterfactual, they would need to be exactly like the beneficiaries, or treatment
group, except they would have not received the benefit of programme/technology.
Thus, any differences in the indicator could be attributed to the particular programme/
technology. Agricultural programme are generally designed to improve production or
the returns to agriculture and therefore, impact evaluations of agricultural projects
focus on production-based indicators such as gross margins, crop prices, yields,
productivity, agricultural investment, spending on agricultural inputs, technology
adoption, changes in land use patterns, crop and varietal diversification and food for
home production. Collection of this type of information are challenging, beginning

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with the definition of the sample unit; in fact, while production is often linked to
multiple plots and crops, the decision-making process takes place at the household
level.
The primary objectives of this chapter are: (a) to briefly discuss the theoretical
and empirical issues related to yield gap analysis and impact assessment of modern
rice production technologies; (b) to explore the existing knowledge on quantification/
factors of yield gap as well as impact assessment of agricultural technologies; and (c)
to identify the gaps in knowledge, suggest research and development needs on yield
gap analysis and impact assessment of agricultural technologies.

2. STATUS OF RESEARCH
2.1. Research on rice yield gaps
2.1.1. Approaches to quantify potential yields and yield gaps: The factors that inhibit
farmers from getting potential yields with modern varieties may be physical, economic,
social, or any combinations of them. Physical conditions on some farms may prevent
the farmer from exploiting the full potential of the technology. Sometimes, high yields
may be physically possible but economically unprofitable. In some cases, social or
institutional problems may also exist. Farmers can’t acquire requisite inputs timely
due to lack of credit. Further, it is also likely that the technology may not be understood
by the farmers or by those directly advising them. The concept of yield gaps in crops
originated from different constraint
studies carried out by International
Rice Research Institute (IRRI)
during seventies. To measure the
potential yield, the actual yield,
and the yields corresponding to
the inclusion or withdrawal of test
factors over and above the
farmer’s yield, an experimental
technique was developed and
validated by Gomez (1977) in plot
experiments on sample farms. The
relative contribution of each
component to the difference
Fig. 1. The concept of yield gaps between an
between the potential yield and the
experiment station rice yield, the potential farm
farmer’s yield was then assessed yield, and the actual farm yield (Gomez 1977).
(Fig. 1). De Datta (1981) compared
a series of combinations of inputs of increasing intensity (management packages) to
establish the yield and profitability of different combinations and to indicate the
approximate intensity that is most attractive to farmers.
There are atleast four distinguished methods to estimate yield gaps at a local level
(Lobell et al. 2009): (a) field experiments, (b) yield contests, (c) maximum farmer yields

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Rice Production Technologies 499
based on surveys, and (d) crop model simulations. The first step associated with
each method is to estimate yield ceilings (potential yield: Yp) for a given crop in a
given location or region. Yield gap (Yg) is then calculated as the difference between
Yp and actual yield (Ya). Although field experiments and yield contests can be used to
estimate Yp for a given location and under a specific set of management practices,
they require well-managed field studies in which yield-limiting and yield-reducing
factors are eliminated (e.g., nutrient deficiencies, and diseases), and they must be
replicated over many years to obtain a robust estimate of average Yp and their variation
(Cassman et al. 2003). Field experiments and yield contests used as a basis for estimating
Yp must use sowing dates and cultivar maturities that are representative of the prevailing
cropping systems in the region of interest if they are to serve as benchmarks for these
systems.
Surveys among farmers to estimate maximum yields from upper percentiles
represent another approach to estimate Yp (Lobell et al. 2009). The best farmers’
yields of a given region may give a better idea of what actually can be achieved under
the normal edaphic conditions of that region (Lobell et al. 2009). It is also likely that
the use of maximum farmers’ yields as a proxy for potential yield is most appropriate
in intensively managed cropping systems, with high levels of fertilizers and pesticides,
where yield limiting factors such as nutrient deficiencies, insect attacks, diseases and
competition with weeds are virtually eliminated. However, even then it is still improbable
that a farmer reaches the water-limited yield potential, since optimal nutrient and pest
management is quite impossible to achieve and in many cases economically not
beneficial (Laborte et al. 2012). Moreover, under the conditions of family farms in the
tropics, farmers often cannot afford the best available technologies. If crop production
resources (including soil properties) and input levels have also been recorded, methods
such as the boundary line approach or frontier analysis can be used to identify the
highest yields for a given level of resource availability (Tittonell et al. 2008). However,
if obstacles prevent all surveyed farmers from realizing Yp, then Yg will be
underestimated. Such obstacles must operate at the same scale as the yield gap
analysis and could include lack of access to inputs, lack of markets, and lack of
knowledge or access to it.
Hoang (2013) has proposed a new analytical framework to examine productive
efficiency in crop production systems using the economic, institutional, physical,
social and technological factors of farm and the spatial heterogeneity. The novelty of
this framework is the incorporation of agronomic knowledge into economic production
frontier analysis. The framework has two stages; in the first stage crop growth and
economic production models are used to estimate potential and best practice output
levels. The framework has been applied to investigate the efficiency of rice production
using district-average farm data of eight districts in Sri Lanka (Hoang, 2013). This
empirical study yielded several important findings. Firstly, actual yields, on average,
achieved only 60% of potential yields, leaving a 40% yield gap. This gap was
decomposed into technical inefficiency (approximately 18%) and agro-economic
inefficiency (approximately 22%). Theoretically, it is possible to bridge gaps between
best practice and potential yields by providing optimal conditions for crop growth. In

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reality, however, it might not be economically optimal for farms to bridge these gaps
because the cost of marginal increments in yield might exceed the marginal gain (i.e.
revenues generated from incremental yields). To overcome limitations of the above
approaches, crop simulation models can be used to estimate Yp (Laborte et al. 2012).
These simulation models are mathematical representations of current understanding
of biophysical crop processes (phenology, carbon assimilation, assimilate partitioning)
and crop responses to environmental factors. They require site-specific inputs, such
as daily weather data, crop management practices (sowing date, cultivar maturity,
plant density), soil properties and specification of initial conditions at sowing, such
as soil water availability, and a model configuration that ensures nutrients to be non-
limiting. Grassini et al. (2015) presented an explicit rationale and methodology for
selecting data sources for simulating crop yields and estimating yield gaps at specific
locations that can be applied across widely different levels of data availability and
quality and it was used to estimate maize yield gaps in the state of Nebraska (USA),
and at a national scale for Argentina and Kenya. The aim of the suggested method
was to provide a transparent, reproducible, and scientifically robust guideline for
estimating yield gaps; guidelines which are also relevant for simulating the impact of
climate change and land-use change at local to global spatial scales.
2.1.2. Local studies to global relevance: It is essential to compare and assess different
methods of yield gap analysis across spatial scales from the field, to sub-national and
national scales, to identify key components that ensure adequate transparency,
accuracy, and reproducibility. Yield gap analyses for Southeast Asia helped to explain
yield trends in irrigated rice and revealed that nitrogen management had to be improved
to increase yields (Kropff et al. 1993). Global studies generally use empirical, statistical
approaches or generic crop growth models and a grid-based approach using global
datasets on climate, soils and sometimes agricultural land use and general crop
calendars. The statistical methods use highest yields within a defined climatic zone
(Mueller et al. 2012) or use a stochastic frontier production function (Neumann et al.
2010). They do not verify whether highest yields accurately represent the biophysical
potential yield limit as confirmed by either a robust simulation model or field studies.
The major limitation of this method is that it does not distinguish between irrigated
and rainfed crops; thus, many yield gap estimates for a given climatic zone are based
on irrigated crop yields-even in regions where the crop in question is grown almost
entirely under rainfed conditions. Global studies using generic crop growth models
utilize a single crop model to simulate generic crop yields for the entire globe. Often
global studies using generic crop growth models do not have the explicit aim to
estimate yield gaps; sometimes they aimed at estimating current yields and sensitivities
of these yields to variations in management or climate (Stehfest et al. 2007).
2.1.3. Yield gap estimates in rice: Yield gaps in rice were observed in various countries,
especially those of Asia region. Table 1 illustrates the rice yield gaps in India, Nepal,
Thailand, etc. as compiled by Mondal (2011). While it was only 3.38% in China and
27.78% in India, yield gap in other countries varied from 17 to 50%. According to a
study conducted by BRRI, the yield gap in rice in Bangladesh was about 1.74 t ha-1
and it was estimated that at least Tk. 1260 billion could be earned from the additional

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Rice Production Technologies 501
production annually by bridging the yield gap (BRRI 2011). In India, yield gap varied
from 15.50 to 60% with the national average gap of 52.30% in the irrigated ecosystem
(Siddiq 2000) and 2560 kg ha-1 for rainfed rice (Aggarwal 2008). Nirmala and co-
workers (2009) estimated 12.46% yield gap in rice in Raichur district of Karnataka,
between potential yield realized at research station and the yield that was reported at
the demonstration plot (yield gap I). Yield gap II, which is the difference between
potential farm yield (Yd) and the actual yield (Ya) was estimated to be 11.82%. Index
of yield gap, which is the ratio of the difference between potential yield (Yp) and
actual yield (Ya) to the potential yield (Yp) worked out to be 22.81%. Pushpa and
Srivastava (2014) quantified the gap between current and potential yields of major
crops namely wheat, rice and sugarcane in eastern region of Uttar Pradesh, and
identified the constraints that contribute to this yield gap. In the study area, yield
gaps exist in different crops ranging up to 53% and for rice the average gap was
estimated to be of 28.26%.

Table 1. Yield levels and yield gaps in rice of several countries of Asia region.
Irrigated/better
National average managed Yield gap Yield gap
Country yield (t ha-1) yield (t ha-1) (t ha-1) (%)
India 2.60 3.60 1.00 27.78
Nepal 2.50 4.20 1.70 40.47
Thailand 2.00 4.00 2.00 50.00
Vietnam 3.10 4.30 1.20 27.90
Indonesia 4.40 5.30 0.90 17.00
Philippines 2.80 3.40 0.60 17.65
China 5.70 5.90 0.20 3.38
Source: Mondal (2011)

2.1.4. Factors causing yield gaps: In general, factors causing yield gaps can be
classified as (RAP 1999): (a) biological factors: variety, soil fertility, management
practices (fertilizer, water, pest management, etc.); (b) socio-economic factors: social
and economic status of farmers, family size, farm holding, knowledge and education
level of farmers, contact with extension agents; (c) climatic factors: flood, drought,
salinity, etc. caused by climatic changes; (d) institutional/government policy related
factors: input/ output price, availability of inputs, credit supply, tenancy, etc.; and (e)
factors promoting technology transfer: research-extension linkage, training of extension
personnel on the new technology, their knowledge and education level about the
technology, demonstration of the technology, field visits and monitoring, etc. by
extension.
In a case study in Senegal (Ramaswamy and Sanders 1992), the causes of yield
gaps at field scale were identified using a basic cross-correlation analysis of yield
gaps against indicators of biotic and soil constraints and crop management. In fields
with a low water-limited yield potential, poor soil fertility was the main factor explaining
the yield gaps, while in fields with a relatively high water-limited yield potential, low

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soil fertility and weed infestation were the explanatory factors. Both low soil fertility
and weed infestation are likely to be directly related to the low purchasing power of
farmers and the resulting limited access to fertilisers and herbicides, and to the limited
availability of labour on their farms. Studies from other researchers (Perez et al. 1998)
in the same region mentioned water runoff as a key factor explaining observed yield
gaps. Even with improved access to fertilisers and other external inputs, closing the
yield gap in this region would require that farmers combine improved soil fertility and
weed management with water saving techniques at field and landscape level in order
to reduce production risks induced by rainfall variability, which are expected to increase
with crop intensification. Pushpa and Srivastava (2014) identified the causes of yield
gaps as: socio-economic, credit institutional/policy related factors, extension services
and lack of improved technology. In another case study in Vietnam, Husson et al.
(2004) used a similar approach as the one used in the Senegalese case study to
identify the main causes of variability of upland rice yields between fields. Here, the
major explanatory factors for yield differences were observed to be weed infestation
and soil fertility. In central Brazil, a detailed analysis of yield variations was carried
out by Affholder et al. (2003), where, the model STICS was used to simulate water-
and nitrogen-limited yield for each field. A cross-correlation analysis was performed
and observed that aluminium toxicity in soils, weeds and soil waterlogging were the
main factors explaining the gap between observed yields and simulated water- and
nitrogen limited yields.
2.1.5. Bridging the yield gap: Closing yield gaps to attain potential yields may be a
viable option to increase the global crop production. However, traditional methods of
agricultural intensification often have negative externalities. So, there is a need to
explore location-specific methods of sustainable agricultural intensification. Pradhan
et al. (2015) identified regions where the achievement of potential crop calorie
production on currently cultivated land will meet the present and future food demand
based on scenario analyses considering population growth and changes in dietary
habits. By closing yield gaps in the current irrigated and rain-fed cultivated land,
about 24% and 80% more crop calories can respectively be produced compared to
year 2000. They have also estimated the required fertilizers (N, P2O5, and K2O) to
attain the potential yields. Cui et al. (2013) achieved an increase in maize yield of 70%
in an on-farm experiment by closing the yield gap and evaluated the trade-off between
grain yield, nitrogen (N) fertilizer use, and GHG emissions. Based on two groups of N
application experiments in six locations for 16 on-farm site-years, an integrated soil-
crop system approach achieved 93% of the yield potential which is 70% higher than
existing crop management. Although the N application rate increased by 38%, N2O
emission intensity and the GHG intensity of the integrated system were reduced by
12% and 19%, respectively. Lobell et al. (2009) suggested that yields of 80% of its
potential are an approximate of the economic optimum level. Mueller et al. (2012)
presented a global-scale assessment of intensification prospects from closing ‘yield
gaps’ (differences between observed yields and those attainable in a given region),
the spatial patterns of agricultural management practices and yield limitation, and the
management changes that may be necessary to achieve increased yields. They found
that global yield variability is heavily controlled by fertilizer use, irrigation and climate.

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Rice Production Technologies 503
 Yield gaps caused by biological, socio-economic, and institutional constraints,
which can be effectively addressed through an integrated crop management (1CM)
practices. Transfer of the practices through extension agents could effectively help
farmers to minimize yield gaps. Timely planting, irrigation, weeding, plant protection,
and timely harvesting could account for more than 20% yield increase (Siddiq 2000).
However, input/output prices and employment opportunities influence farmers’
decision on the level of inputs to be applied.
2.2. Research on impact of rice production technology/training
2.2.1. Impact of rice production technology: Based on a survey conducted in
Maharashtra, India, Joshi and Bantilan (1998) observed partial and step-wise adoption
of different components of the technology that range between 31% for raised-bed
and furrow method of land management to 84% for improved varieties. The technology
also contributes in improving the natural resource base, and eases certain women
specific agricultural operations. Samal et al. (2009) assessed impact of three modern
rice varieties viz. Durga, Gayatri and Sarala in the submergence prone area of Odisha
state and indicated that the varieties have spread to 51% of the lowland area within
three years. The returns from all the three varieties were found to be attractive in
comparison to the traditional varieties in terms of additional return as well as
employment generation. Wu et al. (2010) assessed the impact of improved upland rice
technology on farmers’ well-being using propensity-score matching technique to
address the problem of ‘self-selection,’ because technology adoption is not randomly
assigned. It applies this procedure to household survey data collected in Yunnan,
China in 2000, 2002 and 2004. The findings indicated that improved upland rice
technology has a robust and positive effect on farmers’ well-being, as measured by
income levels and the incidence of poverty. Gauhan et al. (2012) in a study in stress-
prone rainfed area of Nepal indicated that the yield of newer generation modern rice
varieties (MVs) is not superior to that of old generation MVs despite their better
adaptability in rainfed conditions. They observed through censored regression that
favourable land type plays a key role in the adaptation of new generation modern
varieties. In Bangladesh, Islam et al. (2012), however, mentioned that the yield of MVs
and old generation MVs are not statistically different, which may explain the slow
varietal replacement in Bangladesh. Similar observation were made by Behura et al.
(2012) in Chattisgarh and Odisha, where the varieties released before 1990 like Swarna,
Lalat and Gayatri dominate most of the area. Bagchi and Bool-Emerick (2012) observed
in West Bengal that old generation MVs dominates during aman season while new
generation MVs occupy most rice areas during boro season.
2.2.2. Impact of training on rice production technology: Nakano et al. (2014a)
investigated impact of training provided by a large-scale private farm on the
performance of surrounding small-scale rice farmers in a rain-fed area in Tanzania.
They found that the training effectively enhances the adoption of improved rice
cultivation practices, and profit from rice cultivation by small-holder farmers. Several
other studies have shown that intensive training on rice cultivation can effectively
enhance the adoption of new technologies including modern variety, chemical fertilizer

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and improved agronomic practices, and productivity of rice cultivation increased

both in irrigated as well as rain-fed area (Kijima et al. 2012). However, improved rice
cultivation technologies are not widely adopted because of weak public extension
system (Nakano et al. 2014b).
2.2.3. Impact of investment on rice research: Assessment of economic impact of new
technologies delivers helpful information to justify investment efforts in research
and development to generate new technologies. Kumar and Rosegrant (1994) estimated
total factor productivity (TFP) of rice as 1.03%, which accounted about one-third of
output growth during the period of 1971-88. The marginal returns to public investment
in rice research in different regions were very high and the internal rate of return (IRR)
to public investment was 55%. They have shown that, contrary to popular perception,
rice research has paid handsome returns in India, even in the eastern region and
demonstrated that research productivity has not declined over time. Jha and Kumar
(1998) also propounded that rice research in India has been highly rewarding, generating
returns that are close to 30-50% and suggested to accord high priority to three major
issues: rice in eastern India, which essentially means rainfed (upland and lowland)
rice; sustainable irrigated rice production (in kharif as well as rabi season); and
improved efficiency in rice production. Agricultural research has contributed to
breaking the seasonal barrier in rice production in India. During recent periods, area
under the highly productive dry-season rice (boro) has been growing with the
expansion of small-scale groundwater irrigation. Huang et al. (1998) assessed the
contribution of research and technological change to the phenomenal growth in rice
yield in China raising rice seeds from 2.1 t ha-1 during early sixties to 6.1. t ha-1 during
late nineties.

3. KNOWLEDGE GAPS
Meeting future food demand requires a substantial increase in the yields obtained
from existing crop-land. Global analyses done earlier have suggested that these gains
could come from closing yield gaps - differences between yields from small-plot
research versus those in farmer fields. However, closing this gap requires knowledge
of causal factors not yet identified experimentally for different agro-ecological settings.
Potential yields vary with the cultivars, ecology as well as the agro-climatic region.
Precise knowledge on zone and ecosystem specific potential is a pre-requisite for
meaningfully determining the still untapped yield of the currently popular high yielding
varieties.
The impact evaluation methods and concepts has been poked with problems
both, methodological, such as econometric techniques and data availability, and
practical, such as ethical concerns, funding and weak incentives. Along with the
sound and robust data collection methods, the impact assessment toolkit has to be
evolved, particularly with regard to econometric methods. Because economic
evaluation is a predictive tool, it is difficult to determine accurately what a technology’s
benefits and costs will be in the future. One useful and simple way of gaining insight
into the impact of uncertain outcomes is a sensitivity analysis. Further, the empirical

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challenge in impact assessment using observational studies is establishing a suitable
counterfactual against which the impact can be measured because of self-selection
problems. To accurately measure the impact of technology adoption on improving
productivity of farm households, the exposure to the technology should be randomly
assigned so that the effect of observable and unobservable characteristics between
the treatment and comparison groups is the same, and the effect is attributable entirely
to the treatment. A coherent method is desirable to identify, quantify and value the
social advantages (benefits) and disadvantages (costs) in terms of common monetary
units. The benefit stream over time is brought together to a net present value (NPV)
by compounding or discounting. Unvalued effects/ impacts (intangibles) are described
qualitatively and weighed against valued items. However, integration of this value in
benefit stream is scarce or absent in existing literature about impact assessment of
agricultural technologies.

4. RESEARCH AND DEVELOPMENT NEEDS

There are two great challenges in regard to the agriculture in India and globally:
substantial increases in food demand must be met while decreasing agriculture’s
global environmental footprint. Closing yield gaps and increasing resource efficiency
are necessary strategies towards meeting these challenges, but certainly not through
unsustainable expansion of crop-land. The crucial role of nutrient and water
management towards sustainable cultivation should be encouraged. Agricultural
development programmes and policies must address the factors of yield limitation
while emphasizing management practices that maintains trade-offs between higher
production and environmental impacts. Changes to agricultural management to close
yield gaps should be considered in the context of climate change scenario, which is
expected to substantially impact yields and induce management adaptations.
Farmers need adequate amounts of quality inputs at the right time to obtain high
yields. It is also important that the fertilizer inputs are integrated with organic manures
for balanced use of nutrients. Resource-poor small but productive farmers representing
more than 80% of farm population are usually unable to purchase required quantities
of the inputs for better yield, therefore, they need to be supported by adequate and
timely supply of credit through simplification of lending procedures and revise
eligibility criteria. The action may also be taken for the expansion of rural bank branches
under public sector. The coordination of research and extension is essential and the
researcher should understand farmers’ constraints to high productivity and accordingly
develop integrated technological package (appropriate variety, timely planting,
fertilizer, irrigation, and pest management) for farmers in specific locations to bridge
the gaps. The extension service should ensure that the farmers apply correctly and
systematically the recommended technological packages through effective training,
demonstrations, field visits, monitoring, etc.
Impact evaluation provides information about actual accomplishments in the form
needed by the planners/ managers/ policy makers. For evaluation of a technology, all
basic data at all stages, i.e. from innovation to adoption by the end user and its’ uses

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are necessary. Hence, proper sampling technique is to be adopted for ensuring

representation of the users and the progress at various levels should be monitored.
For collection of data, a suitable questionnaire should be adopted and various
components such as productive, protective, environmental, etc. should be computed.
Evaluation process often seeks to analyze a situation to determine why some thing
happened, and suggest what might be done to correct undesirable situation.
Evaluation would ideally be a continuous process, starting at appraisal, continuing
with mid-term reviews and at termination, followed by an ex-post review, and ideally
a follow-up review 5, 10 or 15 years after the end of the life of the technology.
Evaluation indicators are designed to provide a standard against which we measure
or assess the progress of an activity against stated targets. They provide information
and describe the state of the phenomena, that are useful to monitor changes and
provide means to compare trends and progress over time. These are used as markers
of the progress towards achieving short-term, intermediate term or long term
objectives. It must be clear that indicators are not targets because targets are specified
results in terms of quantity and/or time. The selection of indicators is of crucial which
requires skill and experience. The main challenge in identifying indicators is to select
those that are sufficiently representative and at the same time easy to understand and
measure. It depends on the nature of the objectives and intended effects and impacts
of the technology. Ideal indicators should be of: specific (clearly and unambiguously
defined); measurable (either qualitatively or quantitatively); achievable (must be cost
effective to monitor; result should be worth the time and money it costs to apply
them); relevant (should be in consistency with the objectives and clearly reflect the
goals); and time-bound (should be quite sensitive to change in the situation to be
documented and sensitive to important changes such as in policy, programmes, and
institutions).
Before the mid-sixties, economists gave little consideration to the distributional
effects of technological changes. Hence, agricultural technologies tended to
recommend or encourage technological changes which were favourable to large-
scale farmers at the expense of small-scale farmers and farm labourers. In recent years,
in response to the growing number of agricultural critics, agricultural scientists
attempted to specifically account for some of the distributional effects of agricultural
technology. Although recent attempts to account for the distributional impacts of
technological change have significantly strengthened the credibility of economic
models, these models still do not take into account all the distributional effects (social,
economic or technical) arising from agricultural technology.

5. WAY FORWARD
Bridging yield gaps may not always be desirable or practical in the short term,
given marginal returns for additional inputs, regional land-management policies, limits
on sustainable water resources and socio-economic constraints (for example, access
to capital, infrastructure, institutions and political stability). However, use of precision

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agriculture techniques, conservation tillage, high-yielding hybrids, increased plant
populations and multifunctional landscape management can help to mitigate negative
environmental impacts of intensive agriculture. Additionally, use of organic fertilizers
is also helpful for improving soil carbon, enhancing soil biota and increasing water-
holding capacity. Social triggers of intensification used to differ across regions;
because of development interventions by governments or NGOs, market-driven
incentives for farmer investment, and land scarcity in regions which are not fully
connected to global markets. Hence, to close yield gaps technological solutions must
go hand in hand with lifting social and economic constraints through rights to land,
critical infrastructure, and links to the world market for food and raw materials.
Impact assessment plays an important role in both identifying and communicating
the implications of technology in economic terms starts from the planning process. In
the early stages of research planning, preliminary partial budget assessment of the
technology would assist planners and researchers in developing feasible management
practices as well as to reach a consensus in priority setting of research. Once a
consensus has been determined, further economic assessment will help to identify
expected impacts and the implications. To be useful to the planning process, the
economic implications of the particular technology/management practices must be
clearly communicated. The documentation and evaluation of the strategies will generate
evidences for prioritizing the technology for future research agenda. To communicate
these evidences in a form meaningful for comparison, a matrix summarizing the findings
of the assessment can be used. Further, impact evaluation relies on the construction
of a counterfactual situation to examine the outcome of a group in two states at the
same time, in and out the programme. A technology selected for the impact assessment
had to demonstrate that it carefully selected a group of non-participants that were
equally needy or deserving of the programme and were the same with regard to most
characteristics. Finally, considering the knowledge gaps, issues and needs, the impact
assessment of agricultural technologies/programmes should encompasses:
establishment of proper evaluation criteria, determining distributional consideration,
exact period of analysis based on economic life of the technology, identification of
relevant input and output, proper valuation and discounting of inputs (costs) and
outputs (benefits), and considering uncertainty and risks through sensitivity analysis.
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 Climate Resilient Production Technologies for
Rainfed Upland Rice Systems

D Maiti, NP Mandal, CV Singh, SM Prasad, S Bhagat, S Roy,

A Banerjee and BC Verma

SUMMARY
Upland rice accounts for about 13% and 13.5% respectively of world and Indian
rice growing areas. It is grown under diverse topography, climatic and soil conditions,
mostly as direct seeded, rainfed crop. Due to adverse topography (sloppy), poor soil
conditions and absolute rain dependence, it often suffers from drought at several
growth phases. Besides, poor soil nutrient conditions, biotic stresses like weeds,
diseases and insects, which also are accentuated by drought, are major challenges
for improving upland rice productivity. This chapter discusses progress of research
to address these constraints and suggests way forward based on knowledge gap
analysis.

1. INTRODUCTION
Upland rice is grown in around 15 Mha globally. Major upland rice areas are in
Asia (8.9 Mha) followed by Africa (3 Mha) and Latin America (3.1 Mha). Nearly 100
million people, globally, depend on it as their daily staple food (Arraudeau 1995). In
India it covers about 6.0 Mha under rainfed ecology. Major portion of upland rice
areas in India are in eastern and northeastern states.
Agricultural production system of upland ecology in India is mainly monsoon
dependent where rice is the major crop. However, rice productivity of the target
ecology is very poor owing to several constraints including moisture stress as the
most important followed by weeds, poor soil nutrient status and diseases (blast and
brown spot). The upland rice ecosystem is extremely diverse as it is grown on leveled
to gently rolling land (0-8% slope) and also on lands where slopes are greater than
30%. Soils vary from highly fertile volcanic and alluvial soils to highly weathered,
infertile and acidic type. Upland rice is grown at altitudes of up to 2000 m above MSL
and in areas with annual rainfall ranging from 1000 to 4500 mm. But erratic rainfall
frequently causes drought during growth periods and results in low and unstable
yields of upland rice (1–2 t ha-1), compared to irrigated lowland rice (>5 t ha-1). Improving
productivity of rice in the upland ecosystem is essential to meet food security needs
of impoverished upland communities leading to address the set national targets of (i)
Bringing Green Revolution to Eastern India (BGREI) and (ii) doubling farmers’ income.
In this context, the roadmap for improving rice production system of this ecology has
been set through: (i) breeding for drought-tolerant, high yielding rice variety; (ii)
developing climate resilient crop production technology including crop establishment,
nutrient management and (ii) establishing suitable crop protection schedule (Integrated

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Pest Management; IPM) including weeds, diseases and insects. All these components
under compatible integration would promote improvement of rice production system
of rainfed uplands. Thus, the objective of this chapter is to introduce the problems,
assesses present status of research and suggest way forward for improving upland
rice production system.

2. GENETIC ENHANCEMENT OF UPLAND RICE

Varietal improvement for upland rice at the international level has progressed
independently in tropical Asia, Africa and Latin America in collaboration with different
international agricultural research centers (Gupta and O’Toole 1986). Varietal
improvement in Africa is mainly through international programs as there were very
few national programs existed. Among the national programs, National Cereals
Research Institute, Ibadan in Nigeria is the pioneer in upland rice breeding in Africa
and developed many varieties, among them OS6 (FARO 11) became very popular
because of its drought tolerance. The Institute has specifically developed 63 rice
varieties that are low N and water use efficient, pest and diseases resistant for various
rice ecologies, with the recently released upland varieties FARO 58 and 59. In the
Ivory Coast the Ministry of Agricultural Research has released several useful varieties
including Moroberekan, before 1966. International Agricultural Research Centers
(IARCs) such as International Institute of Tropical Agriculture (IITA), IRAT (now
CIRAD; the French Agricultural Research and International Cooperation Organization),
WARDA (now Africa Rice) and International Rice Research Institute (IRRI) began
large scale testing of new varieties in 1976. These IARCs extensively collaborated
among themselves and kept developing and providing superior breeding lines to the
national programs to enhance their rice production. The varietal development program
in Africa revolutionized with the first NERICA (New Rice for Africa) rice variety (Jones
et al. 1997) developed by the Africa Rice Center (WARDA) from a cross between the
local African rice Oryza glabberima and the Asian type Oryza sativa. Total 18 NERICA
varieties were released with doubled average yield in sub-Saharan Africa. Development
of NERICA rice opened up new gene pools and increased rice biodiversity to scientific
community.
In Latin America, upland rice improvement program was initiated in Brazil at the
Instituto Agronomico Campinas (IAC), São Paulo during 1937. Since then, several
important cultivars have been released. Upland rice breeding program at the National
Rice and Beans Research Center (EMBRAPA/CNPAF) began in 1976 combining IAC
developed varieties with African germplasm 63-83, OS6, and LAC23 to broaden genetic
base and new varieties Cuiabana, Araguaia and Guarani were released between 1985-
1986.
In south and south-east Asia, IRRI collaborated with national programs of different
countries (Bangladesh, Cambodia, Indonesia, India, Thailand, Philippines etc.) to
help in identifying more productive cultivars. In the early part, upland rice breeding
in most of the countries was limited to collecting farmers’ varieties, purification, and
evaluation with limited hybridization. During this period many improved varieties

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from tall parents were released. Upland rice breeding in the Philippines began early
than any other countries and released varieties developed through hybridization.
Later in the 1970s, the University of the Philippines at Los Baños developed C22, UPL
Ri-3, UPL Ri-5, and UPL Ri-7 which have intermediate height, moderate tillering ability,
and good grain quality. Some of these varieties were introduced in other countries
though INGER program of IRRI and utilized by the breeders for varietal development
under national program. Upland rice improvement program at IRRI progressed in
collaboration with national programs and international institutes such as IITA,
WARDA, IRAT and CIAT (Gupta and O’Toole 1986). Larger numbers of crosses were
made at IRRI involving improved germplasm and traditional varieties and the lines
were distributed to partners for location specific selection.
Drought tolerance breeding started with use of secondary traits for the
improvement of drought tolerance in terms of grain yield under stress which met with
limited success because of several limitations. From the first decade of this century
the strategy changed towards direct selection for grain yield under stress for the
improvement of drought tolerance. It was demonstrated at IRRI that if the stress is
applied uniformly and consistently, yield under stress can be as heritable as yield
under control condition and resulted in significant gain in upland rice drought
tolerance (Bernier et al. 2007; Venuprasad et al. 2007; Kumar et al. 2008). For a more
intensive high input upland system, a new set of cultivars were developed for Asian
tropics with improved lodging resistance, harvest index and input responsiveness
(Atlin et al. 2006). These cultivars combined yield potential of high yielding lowland
rice with aerobic adaptation of upland rice and proved promise for water limited
environment. With the standardization of screening protocol for yield under drought,
large-scale conventional breeding and QTL identification programmes were started,
using yield as a selection criterion. This approach has led to the successful
development and release of 17 high-yielding drought-tolerant rice varieties in south
Asia, south-east Asia, and Africa.
In India, systematic rice improvement program began when ICAR-National Rice
Research Institute (ICAR-NRRI; formerly Central Rice Research Institute, CRRI) was
established at Cuttack, Orissa in 1946. Attempts to develop drought tolerant varieties
through hybridization began in Tamil Nadu and Kerala in 1955. The drought resistant
variety Co31 was released from Coimbatore, Tamil Nadu but this variety has long
growth duration and is photoperiod-sensitive. Initially selection from land races were
made to develop drought tolerant variety in India e.g., N22 from Rajbhog in Uttar
Pradesh, BR19 from Brown gora in Bihar and PTB10 from Thavala Kannan in Kerala.
The All India Coordinated Rice Improvement Project (AICRIP) initiated in 1965
organized a coordinated rice improvement program involving state agricultural
university/department with those of CRRI and other ICAR institutes and ushered
into a new era of rice breeding. This effort resulted in identification of drought tolerant,
long duration varieties like Lalnakanda41, CH45 etc. Subsequently, the focus shifted
to development of shorter duration (90-110 days), drought tolerant varieties to fit in
the southwest monsoon season of uplands. During next phase (1965-1970), short
duration, drought tolerant varieties like Bala, Annada (Orissa), Annapurna (Kerala),

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Cauvery (Tamil Nadu), Parijat (Orissa), Pusa2-21 (IARI), Rasi, Kanchan (Bihar) were
developed using the semi-dwarf gene. Later on, it was realized that tall varieties are
more appropriate to challenge the high weed pressure and first semi-tall variety Kalinga
III was released in 1983 from CRRI.. The momentum of upland rice varietal improvement
programme was intensified with the establishment of Central Rainfed Upland Rice
Research Station (CRURRS) of Central Rice Research Institute at Hazaribag during
early 1980’s. The first drought tolerant, early duration (90-95 days) variety Vandana
was developed in 1992 from this station, using drought tolerant aus and high yielding
indica genotypes (Sinha et al. 1994). Further efforts led to the development of varieties
like Anjali (2002), Virendra (2006), CR Dhan 40 (2008) and Sahbhagidhan (2011).
Simultaneous efforts at IGKV, Raipur and NDUA&T, Faizabad led to the development
and release of lndira Barani dhan-1 and Shushk Samrat, respectively. The collaboration
of DFID (Department of International Collaboration) with Birsa Agricultural University
at Ranchi developed two popular upland varieties BVD109 and BVD110 in 2005.
Subsequently, through Upland Rice Shuttle Breeding Network, linking centers in
eastern and western India working on upland rice, under the aegis of ICAR-IRRI
collaborative program, development of location specific upland rice varieties were
initiated in 2002 leading to development of variety Sahabhagidhan (Mandal et al.
2010). The success of Sahbhagidhan due to its resilience and higher productivity
under stress motivated the research group to identify QTLs that perform well under
stress. Several QTLs (DTY12.1, 2.2, 3.1, 4.1, 6.1 and 9.1) were identified at IRRI.
Breeding programmes at NRRI-CRURRS, Hazaribag focused on the transfer of these
QTLs to productive background, in collaboration with IRRI. The first drought tolerant
variety, developed through marker assisted selection (IR64 Drt1), where 2 major QTLs
(qDTY2.2 and qDTY4.1) for grain yield under drought stress have been introgressed
into popular variety ‘IR 64’ was released in 2014. Several institutions including CRRl,
lRRl, BAU and DRR were involved in phenotyping and advancement of the material
through multilocation testing. The Hazaribag centre has now moved on to combining
drought tolerance and blast resistance genes in productive backgrounds. Vandana
has been improved for drought and blast resistance with drought QTLs (12.1) and
blast R gene (Pi2). The developed lines are currently under multilocation testing.

3. MANAGEMENT OPTIONS FOR SUSTAINABLE RICE

PRODUCTION UNDER DIRECT SEEDED RAINFED
ECOLOGY
Direct seeding of rice refers to the process of establishing the crop from seeds
sown in the field rather than by transplanting seedlings from the nursery (Farooq et
al. 2011). Upland rice is grown in rainfed unbunded fields that are prepared and
seeded under dry conditions as other upland crops like maize and wheat. The upland
rice ecosystem differs from other rice production systems because the plants grow in
well-drained soils that are not flooded. Soils do not impound rainwater even for short
period of 2-3 days because of high porosity (soil) and sloppy topography. Rice is
more susceptible to drought than other crops owing to its shallow root system.

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Beside direct effects, drought also declines yield through poor nitrogen (N) acquisition.
Upland rice is typically a subsistence crop in India where farmers apply few or no
purchased inputs (Arraudeau 1995), and do most of the work using family laborers.
Joshi et al. (2013) reported that direct seeded rice (DSR) may be planted using any of
the three major methods viz., dry seeding (sowing dry seeds into dry soil), wet seeding
(sowing pre-germinated seeds on wet puddle soils) and water seeding (seeds sown
into standing water). Dry-DSR system is traditionally practiced under rainfed uplands
in most of the Asian countries.
Almost all the upland soils are low in nitrogen (N) and phosphorus (P) and have
high P fixation capacity. The soils are characteristically of high porosity and of low
fertility. In these soils, the productivity of the crop is not only low but also inconsistent.
Next to inadequate water and nutrient supply, weeds are the major constraint in
upland rice production system. Direct-seeded upland rice ecosystems are most
vulnerable to weed competition. Weeds reduce upland rice grain yield and quality.
Estimates of yield losses caused by weeds in upland rice range from 30 to 100%.
Hence, the production technology of rainfed upland rice revolves around crop
establishment, nutrient and weed management and likely shifts in weed flora due to
adoption of direct-seeded rice and crop diversification.
3.1. Crop establishment
To maintain good soil moisture and to maximize soil to seed contact, field should
be pulverized well under conventional tillage. For zero tilled direct seeded rice (ZT-
DSR), existing weeds should be burned down by using herbicides such as paraquat
@ 0.5 kg a.i. ha-1 or glyphosate @ 1.0 kg a.i. ha-1 (Gopal et al. 2010). Soil structure is
improved due to reduced compaction under zero tillage. Zero tillage beds also provide
the opportunity for mechanical weed control and improved fertilizer placement.
Uneven crop stand provides less competition to weeds compared to good crop
stand. Thus, ensuring good population through better land preparation and employing
seed invigoration approaches may help minimizing weed population. Seed priming
tools have the potential to improve emergence and stand establishment under a wide
range of field condition including DSR. Recent research on a range of crop species
showed faster germination, early emergence, and vigorous seedlings achieved by
soaking seeds in water for some time, followed by surface drying before sowing,
which may result in higher crop yield (Harris et al. 2000). In drought-prone areas, seed
priming reduced the need for a high seeding rate, although it (low seed rate) can be
detrimental if seeding takes place in soil that is at or near saturation (Du and Tuong
2002). Reviewed literature showed use of seed rates of up to 200 kg ha-1 to grow a DSR
crop. High seed rates are used mostly in areas where seed is broadcast with an aim to
suppress weeds (Moody 1977). High seed rates can, on the other hand, result in large
yield losses due to excessive vegetative growth before anthesis followed by a reduced
rate of dry matter production after anthesis and lower foliage N concentration at
heading leading to higher spikelet sterility. Moreover, dense plant populations at
high seed rates can create favorable conditions for diseases and insects and make

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plants more prone to lodging. Under good management, optimum seed rates for row
seeding 20 cm apart and broadcast were 300 and 400 seeds/m2 (67.5 and 90 kg ha-1 for
cv. Kalinga III), respectively (Singh et al. 2017).
Seeding depth is also critical for uniform germination. Therefore, rice should not
be drilled deeper than 2.5 cm to maximize uniform crop establishment (Gopal et al.
2010; Kamboj et al. 2012). Further, optimum time of planting results in improved
rainwater use efficiency by 40-50% and enhances the total productivity. To optimize
the use of monsoon rain, the optimum time for sowing DSR is about 10-15 days prior
to onset of monsoon (Gopal et al. 2010; Kamboj et al. 2012). Singh et al. (2017) reported
that an average increase of 25% grain yield when seeding date was advanced to first
fortnight of June in the red sandy loam soils of uplands. They further suggested that
varieties of 85-95 days would perform consistently better under advance seeding
though performance of 100-105 days varieties could be subject to even distribution
of rainfall during the cropping season.
3.2. Nutrient management
Applying a full dose of phosphorus (P), potash (K) and one-third nitrogen (N) as
basal at the time of sowing is the general recommendation for dry-DSR. Split
applications of N are recommended to maximize grain yield and to reduce N losses.
The remaining two-third dose of N should be applied in splits and top-dressed in
equal parts at active tillering and panicle initiation stages (Kamboj et al. 2012). In
addition, N application can be managed using a leaf color chart (LCC) (Kamboj et al.
2012).
Fertilizer management in direct seeded rice should aim at benefiting crop only, or
if not possible, benefiting crop more than weeds. Nitrogen fertilizer is usually applied
three times, at seeding, tillering, and panicle initiation stages, respectively, with a
total amount from 40 (Singh and Singh 2005) up to 200 kg N ha”1 (Yang et al. 2002) split
as 1/3, 1/3, 1/3 or 1/2, 1/4, 1/4 to synchronize with the demand of rice growth. Weeds
must be removed before N application, otherwise a greater weed growth and
competition would be created and rice yield would be even lower than when there is
no N application. However, timing of N application must accurately meet demand by
the rice plant, and that is often not feasible because of unpredictable rainfall. In
upland conditions, N recovery can also be affected by N loss from leaching. Singh
and Singh (2005) concluded that application of 1/4th N as basal in addition to two
splits (1/2 at 20 and 1/4 at 40 DAS) produced more grain and straw yield of upland rice
than the split application alone. When stale bed technique was adopted, application
of N at the time of sowing helped in increasing the early crop vigor and rapid coverage
of the field by the rice foliage with a consequent reduction in weed population (Murty
et al. 1986). Mishra et al. (1995) reported that growth and vigor of both rice and weeds
were less under Mussoorie Rock Phosphate at the early stage, but the growth of rice
increased at the late vegetative stage compared with the single superphosphate
application, without loss in grain yield. N application significantly influenced P uptake
in grain and straw. Shorter duration (100–110 days) upland rice varieties were found
to respond up to 18 kg applied P ha-1 in lateritic soils of eastern India.

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 Poor phosphorus (P) availability continues to be another major constraint for
agricultural productivity in drought prone rainfed uplands. On the other hand, it has
been reported that the well-drained, aerobic soil conditions of this ecology support
native arbuscular mycorrhiza (AM) activities which is known to promote higher P
acquisition by the associated plants. AM is symbiotic association between plant
roots and a special group of fungi (arbuscular mycorrhiza fungi; AMF). Sound
association of upland rice with AM-fungi forming mycorrhizal symbiosis was confirmed
long back by Brown et al. (1988). Partial dependence of upland rice on AMF for P
acquisition was also demonstrated (Saha et al. 2005). Exploitation of natural association
(AM) for improving P acquisition in upland rice was extensively attempted in upland
rice at CRURRS (Hazaribag) of ICAR-NRRI and has been reviewed (Maiti 2011).
Several native AM-supportive crop culture components for upland rice based
cropping systems (RBCS) were identified and judicious integration of the components
improved P nutrition of upland rice substantially with concomitant yield increase
(Maiti et al. 2011)
3.3 Weed management
Upland rice is directly sown in non-puddled, non-flooded soil, where weeds and
rice germinate simultaneously. The lack of ‘head start’ to rice over weeds and the
absence of floodwater make upland rice more weed infested than irrigated lowland
rice leading to yield loss ranging between 30-98% (De Datta and Llagas, 1984). There
is a diversity of floristic composition of weeds in different agro-climatic and edaphic
conditions. A mixture of annuals and perennials, grasses and broadleaf weeds,
intensifies the competitive effects of weeds in upland rice.
Mishra et al. (1995) reported from NRRI-CRURRS, Hazaribag that out of 30 weed
species observed, only 14 were important based on their abundance. Among the
important weeds, Echinochloa colonum was predominant in both coverage and
number. The major weeds in upland, however, are Echinochloa colonum, Eleusine
indica, Ageratum conyzoides, Cyperus rotundus, and Cynodon dactylon spp.,
Commelina benghalensis, Richardia brassilensis and Setaria glauca (Rafey and
Prasad 1995). Several methods are used to control weeds in the upland rice. While
direct methods are used to remove weeds completely from the upland fields; the
substitutive, preventive and complimentary measures generally minimize weed
populations to a manageable level. Preventive methods aiming at preventing weed
dispersal and build up of seed reserves in the soil include: (1) using weed-free seeds;
(2) maintaining clean fields, borders, levees and irrigation canals, and (3) cleaning
farm equipment to prevent weed transfer from one field to another (De Datta and
Baltazar, 1996). Good tillage and land leveling can remove weed vegetation at sowing
and suppress perennial weeds; provide fine soil to allow uniform and early rice
establishment; and permit uniform and easy irrigation and drainage (De Datta and
Baltazar 1996).
Direct physical control methods include removal of weeds by hand, with weeding
tools (hoe, scythe and spade), or with mechanical implements. Hand weeding, though
effective, is expensive, labor intensive and time consuming. Besides there are difficulties

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in procuring sufficient labor force for weeding operation in uplands as land preparation
and transplanting operations of medium and lowland rice coincide. Mechanical
weeding could be an alternative supplement to hand weeding. Hoe weedings plus
hand weeding at 14 and 28 days after rice emergence respectively in upland rice has
been observed to be the most suitable and economical weed-control practice.
Herbicides have the potential to offer an alternative to physical method of weed
control as they are less time-consuming and cheaper. However, relative efficiency of
such herbicides under upland situation is dependent upon the weed species, pattern
of weed emergence, soil moisture fluctuations and correctness of land preparation.
Singh et al. (2008) reported that application of pre-emergence butachlor @ 1.5 kg a.i.
ha-1 followed by a hand-weeding 30 DAS coupled with modified N and P application
schedule proved the best strategy for integrated weed management in rainfed upland
rice. Early post emergence spray of anilophos, pendimethalin, pretilachlor,
pyrazosulfuron etc. has also been found effective in controlling upland weeds.
However, one supplementary hand-weeding was found necessary in areas of heavy
weed infestation and especially where flushes of weed emerge at intervals (Pandey
and Singh 1982). Similarly, butachlor performed better when it was combined with
post-emergence application of the herbicide-propanil (Carson 1975).
Herbicides have been increasingly and broadly applied in agriculture since the
1940s. However, intensive and repeated use of herbicide causes problems of
environment pollution and resistant weed biotypes, which have aroused increasing
concerns. Weed resistant biotypes have appeared in the major rice producing nations
including China, India, Thailand and the Philippines. Reduced dependence on
herbicides may bring down the costs of crop production and retard the development
of herbicide resistance in weeds.
Differences in ability of rice cultivar to compete with weeds were initially reported
several decades ago. Tall, droopy-leafed and vigorous traditional cultivars were
reported to be more weed-competitive but lower in yield potential than short-statured,
erect modern ones (De Datta 1980). Early vigor is important for the direct-seeded
systems that increases stand establishment and weed competitiveness, both of which
are important components for high yields in direct seeded systems (Zhao et al. 2006).
Early vigor becomes more important when both rice as well as weeds emerges
simultaneously. Pre-sowing seed treatments have sown good promise for promoting
germination and early growth in several crops. Singh et al. (2017) reported that
integration of hormonal priming by GA3 @100 ppm with thermal hardening using
alternate temperatures of 43/28 oC improved rice productivity by influencing growth
and yield attributes of rice and reducing the weed pressure by increasing crop-
competitive ability. Intercrop systems are reported to use resources more efficiently
and are able to remove more resources than mono-crop systems, thus decreasing the
amount available for weed growth. Rice equivalent yield and economics indicated
overall advantages accrued from intercropping of pigeon pea and cowpea with rice in
4:1 and 4:2 row ratios, respectively (Singh et al. 2017).

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4. RICE BASED FARMING SYSTEMS FOR DROUGHT
PRONE RAINFED ECOLOGY
Integrated Farming System (IFS) approach is judicious mix of two or more
components while minimizing competition and maximizing complementariness with
advanced agronomic management tools aimed at sustainable and environment friendly
improvement of farm income and family nutrition. Integrated farming system involves
preservation of bio-diversity, diversification of cropping or farming system and
maximum recycling of residues. In general, farming system approach is based on
several objectives that include sustainable improvement of farm house hold systems
involving rural communities, enhanced input efficiency in farm production. It satisfies
the basic needs of farm families, improve their nutrition and raise family income through
optimum use of resources and proper recycling of residues within the system.
This approach is considered important and relevant especially for the small and
marginal farmers in rainfed areas. Due to erratic monsoons and climatic variability,
rainfed agriculture is becoming highly risk prone, particularly for resource poor farmers.
Therefore, development and adoption of location specific IFS module would minimize
risk beside other advantages. In IFS approach several components like crops,
livestocks, horticultural crops, poultry, mushroom, duckery, vermin-composting, apiary,
fisheries and other many enterprises get effectively integrated at the household level
with a view to optimize income and resource use.
The ICAR-NRRI, Cuttack has developed modules for rainfed lowland and irrigated
ecologies with rice- fish farming/ rice based farming systems. Inclusion of poultry,
duckery, goatery, etc. in those IFS modules has been done. Rice based farming system
including different enterprises to enhance the per unit area production of farming
community is the focus of the institute.

5. BIOTIC STRESS MANAGEMENT STRATEGIES FOR

RAINFED UPLAND
Upland rice suffers from several biotic stresses including diseases, insects and
weeds. Losses due to pest (diseases and insects) range between 10-30%. Negligence
of endemic areas can result in complete crop failures. Among the upland rice pests,
major diseases are: rice blast (Pyricularia oryzae), brown spot (Helminthosporium
oryzae/ Bipolaris oryzae), sheath rot (Sarocladium oryzae) and major insects are:
yellow stem borer (Scirpophaga incertulas), leaf folder (Cnaphalocrocis medinalis),
gundhi bug (Leptocorisa acuta) and termite (Odontotermes obesus) (Chauhan et al.
1991). Among important pests, this section has dealt with disease stresses which
account for major loss in upland rice. The weed component has been discussed in
section 3.3 of this chapter.
Rice blast caused by Magnaporthe oryzae is the most serious threat in uplands.
Occurrences of new races of the pathogen have resulted in frequent breakdown of
resistance causing 20–100% of crop losses despite utilization of many blast resistance

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genes in land races (Khus and Jena 2009). Despite more than 10 decades of dedicated
efforts, rice blast continues to be the most destructive disease of rice. Researchers
have been successfully tapping available wild sources for many genes in rice breeding
for useful traits such as blast resistance genes Pi9 from Oryza minuta, Pi-40(t) from
Oryza australiensis and Pirf2-1(t) from O. rufipogon. The introgression of broad-
spectrum blast resistance gene(s) from Oryza rufipogon into indica rice cultivar has
also been reported (Ram et al. 2007). Identification of QTLs for rice blast resistance
was initiated in cv. Moroberekan, a japonica rice cultivar cultivated in Africa. 373
QTLs for blast resistance have, so far, been identified (Sharma et al. 2012). Brown spot
of rice caused by Bipolaris oryzae (teleomorph – Cochliobolus miyabeanus) is
another serious disease for upland rice, causing significant crop yield loss, reported
to occur in all the rice growing countries. The disease has been reported to cause
enormous losses in grain yield (up to 90%) particularly under epiphytotic condition
as observed in Great Bengal Famine during 1942 (Ghose et al. 1960). In Indian uplands,
the disease is more severe in dry/direct seeded rice in the states of Bihar, Chhatisgarh,
Madhya Pradesh, Orissa, Assam, Jharkhand and West Bengal. The disease especially
occurs under moisture stress combined with nutritional imbalance, particularly lack
of nitrogen. The pathogen attacks the crop from seedling to milk stage. The fungus
may penetrate the glumes and leave blackish spots on the endosperm.
5.1. Management strategies for rice leaf blast
Among several management strategies, use of host plant resistance (HPR) is
most effective. However, along with use of resistant variety, several cultural and
chemical methods need to be integrated to reduce challenge of the fungus in order to
decrease chances of resistance breakdown. Recently, marker assisted backcrossing
(MAB) method has been extensively used for developing blast resistant variety.
Several researchers (Miah et al. 2017) developed blast resistant rice varieties using
MAB. Development of blast resistant upland rice varieties through conventional and
molecular breeding has been discussed in the section 2 of this chapter.
Beside conventional cultural methods like burning of diseased straw and residual
stubble, collection of disease free seeds, application of optimum N dose in splits, use
of multilines of mixtures of several near-isogenic lines (NILs) with uniform phenotypic
agricultural traits but different resistance levels can be used to control rice blast (Han
et al. 2015).
The efficacy of various fungicides has been reported by researchers around the
world. Variar et al. (1993b) identified suitable fungicide formulations (seed dressing
with tricyclazole followed by need based spraying of ediphenphos) for controlling
blast (both leaf and neck blast) in upland rice.
Recently, some botanicals were used for their antifungal activity against M. oryzae.
Aqueous extracts of Aloe vera, Allium sativum, Annona muricata, Azadirachta indica,
Bidens pilosa, Camellia sinensis, Chrysanthemum coccineum, processed Coffee
arabica, Datura stramonium, Nicotiana tabacum and Zingiber officinalis were used
by Hubert et al. (2015) for controlling rice blast disease in-vitro and in-vivo, without
any phytotoxicity.

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 Chaetomium cochliodes, a biological agent, was found effective as seed dresser
in the control of M. oryzae. Strains of Bacillus subtillis and Streptomyces sindenius
have good antagonistic activity against M. oryzae (Yang et al. 2008).
5.2. Management strategies for brown leaf spot of rice
In the past, resistance breeding efforts have been more emphasized on diseases
such as blast and bacterial blight with little focus on brown spot of rice. However,
efforts have been made towards searching for resistance to brown spot. Screening of
upland rice germplasm revealed partial and complete resistance to the pathogen
expressed in several genotypes under field conditions (Shukla et al. 1995). Bala and
Goel (2006) identified resistance sources from 15 wild rice accessions with diverse
origin. Subsequently, Katara et al. (2010) identified 10 QTLs, associated with brown
spot resistance. Resistance breeding using conventional and molecular methods is
now underway in different institutions including that of NRRI-CRURRS, Hazaribag.
Among several fungicides evaluated, seed treatment with tricyclazole (0.4%)
followed by spraying with formulation of mancozeb + tricyclazole and seed treatment
with thiram followed by spraying fungicide formulation of mancozeb + metalaxyl
proved highly effective against brown spot. Spraying the crop with mancozeb and
edifenphos also reduced disease considerably (Lore et al. 2007). Commercially available
antagonistic Pseudomonas and Trichoderma species can suppress diseases by direct
effect on the pathogen through mycoparasitism, antibiosis, and competition for
nutrients or by improving plant immunity. Plant extracts and botanicals have also
been found to be effective against brown spot disease. Aqueous leaf extract of Thuja
orientalis proved better for minimizing the incidence of B. oryzae and enhancing
seed germination and seeding growth (Krishnamurthy et al. 2001).
5.3. Management of sheath rot of rice
Sheath rot is an important disease next to blast and brown spot for upland rice.
Research on this disease under upland ecology was initiated in NRRI-CRURRS,
Hazaribag during early nineties. Based on information generated on perpetuation
mode and other ecological aspects of the pathogen in upland ecology, a low-cost
method of managing the disease below threshold level, in short duration varieties
under subsistence farming system, through mechanical separation of diseased seeds
using 20% common salt solution was developed (Maiti et al. 1995). Once the infection
from primary inoculums (from infected seeds) is managed the short duration varieties
(90-100 days) of uplands escape the secondary infection.
5.4. Integrated pest management for upland rice
Degree of pest(s) infestation, in upland rice, varies as drought occurs every year
during different phenological stages of crop growth (Variar et al. 1993a). Such
interactive effects necessitate modifications in the pest management schedules,
depending on the intensity of drought. Considering this, a suitable IPM package with
flexible options, to be implemented based on need based ad hoc decisions, for drought-
prone upland rice was developed after validation in farmers’ field (Maiti et al. 1996)

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and time to time up-gradation was made based on farmers’ feedback. Under favorable
uplands with wet DSR, same schedule with additional component for weed
management of using both early post emergence and need based post emergence
(betweed 20-30 DAS) is necessary (Maiti et al. unpublished).

6. KNOWLEDGE GAP AND WAY FORWARD

The complex rainfed upland ecology necessitates more focus on rice varietal
improvement with incorporation of multiple traits, governed by a combination of
minor and major genes, into elite high yielding varieties. This can be achieved using
diverse parents with desired traits following conventional pedigree breeding which is
very slow process.. In the current climate change scenario it is necessary to reduce
the time of breeding cycle because the farmers who use varieties bred very recently
are at least risk with respect to climate change. So, there is need to modernize the
upland breeding program with rapid generation advancement technology, genomic
prediction and recycling of new parents on the basis of field testing to increase the
genetic gain. The major limitation of drought stress breeding is the lack of suitable
screening methods for large volume of breeding population along with its environment
specific nature. Earlier studies tried to link secondary traits with drought tolerance.
However, recently direct selection for yield under drought and well-watered condition
has been accepted for drought tolerance in rice (Kumar et al. 2008).
Implementation and adoption of technology related to microbial support system
of nutrient management in crops is very poor owing to quality control issues. Such
support system, on the other hand, is very much required for upland rice farmers
which are poor and not capable of applying required amount of fertilizers in uplands.
Quality control is mainly policy issue and beyond purview of research. So, exploitation
of native beneficial micro-flora is an alternative to address this problem. Among
microbes, fungi are most effective in acidic soils of uplands. Native AM fungi have
been demonstrated to be exploited by manipulating crop culture components in favor
of these fungi for improving P nutrition of upland rice (Maiti et al. 2011). Another
innovative approach of exploiting native AMF flora could be through taking advantage
of potential of plant species (host) to harness ecosystem services rendered by native
AMF. This could be achieved by genetic manipulation of crop varieties for enhanced
AM response. The agronomic and genetic manipulations for enhanced mycorrhizal
nutrient acquisition and response are mutually inclusive and in combination could
exploit, to the full extent, AMF biodiversity in soil. The AM-responsiveness trait, in
rice, was demonstrated by the team working at NRRI-CRURRS, Hazaribag, to be
linked to QTLs (Toppo et al. 2013). Identification of such QTLs would promote
development of highly AM-responsive rice varieties.
By following the principles of integrated weed management system, herbicide(s)
use can be reduced beside economic returns. Integrated weed management systems
have the potential to reduce herbicide use (and associated costs) and to provide
more robust weed management over the long term. Successful weed management is
concerned with minimizing the impacts of weeds in the short term and simultaneously

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ensuring yield losses under an acceptable limit in the long term because of practices
being implemented. Hence, the most useful practices of weed control would provide
favorable stand establishment and growth for the crop, and that are simultaneously
unfavorable to the weeds through manipulation of agronomic practices like fertilizer
management, cropping system and seed treatment. Due to complimentary nature of
such agronomic practices, need is still felt to combine these practices to the most
direct methods of weed control, including hand weeding, mechanical weeding, and
herbicides. Research on rice based cropping systems has been done, so far, with the
perspective of improving productivity but there has been limited research on impact
of intercropping configuration on weed suppression as component of integrated
weed management.
Blast and brown spot are the major diseases in uplands. These biotic stresses get
accentuated under moisture stress (Variar et al. 1993a). So, genetic improvement of
upland rice for blast and brown spot diseases is imperative to stabilize the production.
The efficacy of blast resistance is increased when genes for partial resistance is
incorporated along with major genes. Two major genes for blast resistance, Pi2 and
Pi9 have been incorporated through MAS and haplotypes of Pi9 also have been
identified from Indian landraces (Imam et al. 2016). It is necessary to develop and
validate functional molecular markers for these two genes to facilitate their use in
MAB. Genetics of brown spot is poorly understood. QTLs have been reported for
resistance against brown spot disease but none of them explained large phenotypic
variation for this trait. Three QTLs for brown spot resistance have also been identified
at NRRI-CRURRS in Kalinga III/Moroberekan populations which need to be validated
for future use.
The new knowledge and technologies are not reaching most of the farmers due to
poor extension efforts in this area. The extension services in many countries is very
poorly trained and not equipped to handle delivery of new knowledge from researchers
to farmers. This lacuna should be urgently addressed. The technology delivery system
should be re-oriented to handle changing circumstances and to deliver complex,
knowledge-intensive technologies to farmers. There is a need to explore private sector
extension agencies in commercial farming areas and other service-oriented agencies
(NGOs) in food crop areas to extend new knowledge and technologies to farmers. The
effectiveness of different combinations of public, private, cooperative and NGO
extension agencies need to be further strengthened.
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Rainfed Upland Rice Systems 527
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Acronyms
2AP 2- Acetyl-1- Pyrroline
4S4R Self-sufficient Sustainable Seed System for Rice
ABC Atmospheric Brown Cloud
ABTS Antioxidant Activity
ADB Asian Development Bank
AFLP Amplified Fragment Length Polymorphism
AG Anaerobic Germination
AGP Anaerobic Germination Potential
AICRIP All India Coordinated Rice Improvement Project
AISPA All India Seed Producer’s Association
ALEXI Atmosphere-Land Exchange Inverse Model
ALS Acetolactate Synthase
AMF Arbuscular Mycorrhizal Fungi
AOSCA Association of Seed Certification Agencies
ARC Assam Rice Collection
AWD Alternate Wetting and Drying
BADH Betaine Aldehyde Dehydrogenase
BB Bacterial Blight
BCA Biocontrol Agent
BCM Billion Cubic Meters
BGREI Bringing Green Revolution to Eastern India
BHA Butylated Hydroxyanisole
BPH Brown Planthopper
BSP Breeder Seed Production
CA Conservation Agriculture
CAGR Compound Annual Growth Rate
CAM Crassulacean Acid Metabolism
Cas9 CRISPR associated protein-9 nuclease
CAT Catalase
CCM Carbon-dioxide Concentrating Mechanisms
CGR Crop Growth Rate
CIPK Calcineurin-Interacting Protein Kinase
CKM Cubic Kilometers
CLCC Customized LeafColour Chart
CLP Cyclic Lipopeptides
CM Cubic Meters
CMS Cytoplasmic Male Sterile

Acronyms
1
CR Crop Residues
CRCT Climate-Smart Resource Conservation Technology
CRISPR Clustered Regularly Interspaced Short Palindromic Repeats
CSP Common Symbiosis Pathway
CT Conventional Tillage
CVRC Central Variety Release Committee
DAC Department of Agriculture Cooperation
DAF Days After Flowering
DAP Days After Planting
DAS Days After Sowing
DFR Dihydro Flavonol Reductase
DH Doubled Haploid
DisALEXI Disaggregated ALEXI
DNA Deoxyribonucleic Acid
DSI Drought Susceptibility Index
DSN Disease Screening Nursery
DSR Direct Seeded Rice
DSSAT Decision Support System for Agrotechnology Transfer
DUS Distinctness, Uniformity and Stability
EBBR Energy Balance Bowen Ratio
EBC Energy Balance Closure
EEFs Enhanced Efficiency Fertilizers
EGMS Environment Sensitive Genetic Male Sterility
EI Ecological Intensification
EPA Environment Protection Agency
EPS Exopolysaccharide
ER Endoplasmic Reticulum
ERF Ethylene Response Factors
ES Ecosystem Services
ESV Early Seedling Vigor
ET Evapotranspiration
ETC Electron Transport Chain
ETR Electron Transport Rate
EUE Energy Use Efficiency
FAO Food and Agriculture Organization
FIG Farmer Interest Group
FIRBS Furrow Irrigated Ridge-till Bed-planting System
FLD Front Line Demonstration
FPO Farmer Producers’ Organization

Acronyms
2
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

FSS Formal Seed System

FYM Farm Yard Manure
GA Gibberellic Acid
GABA Gamma-Aminobutyric Acid
GBSS I Granule Bound Starch Synthase I
GCDT Global Crop Diversity Trust
GCL Glyoxylate Carboxyligase
GDC Glycine Decarboxylase
GDH Glycolate Gehydrogenase
GHG Greenhouse Gas
GHGE Greenhouse Gas Emissions
GI Geographical Indication
GI Glycemic Index
GIAHS Globally Important Agriculture Heritage System
GIS Geographic Information System
GLH Green Leafhopper
GM Green Manuring
GM GeneticallyModified
GMO GeneticallyModified Organism
GMS Genetic Male Sterile
GOT Grow-Out-Trail
GPC Grain Protein Content
GPS Global Positioning System
GSOD Germination Stage Oxygen Deficiency
GSR Green Super Rice
GST Glutathione s-Transferases
GV Granulosis Virus
GWAS Genome-Wide Association Study
GWP Global Warming Potential
HAR Hypernodulation and Aberrant Root Formation
HI Harvest Index
HLH Helix-Loop-Helix
Ho Heterozygosity
HPR Host Plant Resistance
HR Homologous Recombination
HRR Head Rice Recovery
HT Herbicide Tolerant
HYV High Yielding Variety
IARC International Agricultural Research Center

Acronyms
3
IC Internal Combustion Engine
ICAR Indian Council of Agricultural Research
ICIA International Crop Improvement Association
ICM Integrated Crop Management
ICT Information and Communication Technology
IFS Integrated Farming System
IGP Indo-Gangetic Plains
InDels Insertions and Deletions
INM Integrated Nutrient Management
IPCC Intergovernmental Panel on Climate Change
IPM Integrated Pest Management
IPR Intellectual Property Right
IRAC Insecticide Resistance Action Committee
IRC International Rice Commission
IRDF Integrated Rice–Duck Farming
IRRI International Rice Research Institute
ISR Induced Systemic Resistance
ISS Informal Seed System
ITPGRFA International Treaty on Plant Genetic Resources for Food and Agriculture
KRIBHCO Krishak Bharati Cooperative
KSB Potassium Solubilizing Bacteria
KVK Krishi Vigyan Kendra
LAI Leaf Area Index
LAMP Loop-Mediated Isothermal Amplification
LB Long Bold
LCC Leaf Colour Chart
LD Linkage Disequilibrium
LE Latent Heat Flux
LR Lime Requirement
LS Long Slender
LTS Long Term Storage
LUE Light Use Efficiency
LULC Land Use and Land Cover
LV Low Volume
LWP Leaf Water Potential
MAAL Monosomic Alien Addition Lines
MAB Marker-Assisted Backcross
MABB Marker-Assisted Backcross Breeding
MAS Marker Assisted Selection

Acronyms
4
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

MB Medium Bold
MB Mould Board Plough
MDH Malate Dehydrogenase
ME Malic Enzyme
METRIC Mapping Evapo Transpiration at high Resolution with Internalized Calibration
MGMG Mera Gaon Mera Gaurav
MGPT Marker Based Genetic Purity Testing
MMT Million Metric Tons
MoA Ministry of Agriculture
MOU Memorandum of Understanding
MS Medium Slender
MSI Membrane Stability Index
MSP Minimum Support Price
M TA Material Transfer Agreement
MTS Medium Term Storage
NAS Nicotianamine Synthase
NATCOM National Communication
NATP National Agricultural Technology Project
NBPGR National Bureau of Plant Genetic Resources
NCS National Collection from States
NCU Neem Coated Urea
NDVI Normalized Difference Vegetation Index
NERICA New Rice for Africa
NGB National Gene Bank
NGO Non-Governmental Organization
NGR New Generation Rice
NGS Next Generation Sequencing
NHEJ Non-Homologous End Joining
NIL Near-Isogenic Line
NIR Near Infrared Spectroscopy
NNI Nitrogen Nutrition Index
NPT New Plant Type
NPV Nuclear Polyhedrosis Virus
NPV Net Present Value
NRRI National Rice Research Institute
NSC National Seeds Corporation
NSP National Seed Project
NuDSS Nutrient Decision Support System
NUE Nutrient Use Efficiency

Acronyms
5
ONM Organic Nutrient Management
OSSC Odisha State Seed Corporation
OSSOPCA Organic Product Certification Agency
PA Phytic Acid
PAC Proanthcyanidins
PAH Polycyclic Aromatic Hydrocarbons
PAM Protospacer Adjacent Motif
PAP Purple Acid Phosphatase
PAR Photosynthetically Active Radiation
PCR Polymerase Chain Reaction
PEPC Phosphoenolpyruvate Carboxylase
PGA Phosphoglycerate
PGMS Photo-Sensitive Genetic Male Sterility
PGPM Plant Growth Promoting Microbes
PGPR Plant Growth Promoting Rhizobacteria
PGR Plant Genetic Resources
PPDK Pyruvate Orthophosphate Di-Kinase
PPP Public-Private-Partnership
PSB Phosphate Solubilizing Bacteria
PSM Phosphate Solubilizing Microbes
PSP Participatory Seed Production
PSTOL Phosphorus Starvation Tolerance
PUE Phosphorus Use Efficiency
PUL Pullulanase
Pup1 Phosphorus Uptake 1
qPCR Quantitative PCR
QTL Quantitative Trait Loci
QuEFTS Quantitative Evaluation of the Fertility of Tropical Soil
RAPD Randomly Amplified Polymorphic DNA
RBCS Rice Based Cropping System
RCM Rice Crop Manger
RCT Resource Conservation Technology
RDF Recommended Dose of Fertilizer
RDN Recommended Dose of Nitrogen
REY Rice Equivalent Yield
RFLP Restriction Fragment Length Polymorphism
RH Relative Humidity
RIL Recombinant Inbred Line
RKVY Rashtriya Krishi Vikas Yojana

Acronyms
6
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

RM Rice Microsatellite
RMP Resistance Management Plan
ROS Reactive Oxygen Species
rPGMS Reverse Photo-Sensitive Genetic Male Sterility
RTNM Real Time Nitrogen Management
RTV Rice Tungro Virus
RuBisCO Ribulose 1,5-Bisphosphate Carboxylase-Oxygenase
RuBP Ribulose 1,5-Bisphosphate
RVC Rice Value Chain
RWC Relative Water Content
RWS Rice and Wheat System
RZF Root Zone Fertilization
SAU State Agricultural University
SB Short Bold
SBE Starch Branching Enzyme
SCMR SPAD Chlorophyll Meter Reading
SDA State Departments of Agriculture
SDSM Statistical Downscaling Model
SES Standard Evaluation System
SFCI State Farms Corporation of India
SGSV Svalbard Global Seed Vault
ShB Sheath Blight
SHG Self Help Group
SMR Seed Multiplication Ratio
SNP Single Nucleotide Polymorphism
SOC Soil Organic Carbon
SOD Superoxide Dismutase
SOM Soil Organic Matter
SQI Soil Quality Index
SRI System of Rice Intensification
SRR Seed Replacement Rate
SSC State Seed Corporation
SSD Sub-Surface Drip
SSDC State Seeds Development Corporations
SSFN Site Specific Fertilizer Nitrogen
SSNM Site Specific Nutrient Management
SSR Simple Sequence Repeat
STARFM Spatial and Temporal Adaptive Reflectance Fusion Model
STCR Soil Test Crop Response

Acronyms
7
STMS Sequence Tagged Microsatellite
Sub1 Submergence1
SVRC State Variety Release Committee
SWAT Soil and Water Assessment Tool
TAC Total Anthocyanin Content
TFC Total Flavonoid Content
TGMS Thermo-Sensitive Genetic Male Sterility
TIL TeQing-into-Lemont Backcross Introgression Line
TN1 Taichung Native1
TPC Total Phenolic Content
TPR Puddled Transplanted Rice
TSR Tartronic Semialdehyde Reductase
ULV Ultra Low Volume
UNDP United Nations Development Programme
USG Urea Super Granule
VAP Value Added Product
VIC Variable Infiltration Capacity
VOC Volatile Organic Compounds
VRR Varietal Replacement Rate
WBPH White Backed Plant Hopper
WCE Weed Control Efficiency
WF Water Footprint
WOFOST World Food Studies
WUE Water Use Efficiency
Wx Waxy
YSB Yellow Stem Borer
ZT Zero Tillage

Acronyms
8
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

Editors and Authors

Editors
H Pathak, Director, ICAR-National Rice Research Institute, Cuttack, Odisha
AK Nayak, Head, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
Mayabini Jena, Head, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
ON Singh, Head, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
P Samal, Head, Social Sciences Division, ICAR-National Rice Research Institute, Cuttack, Odisha
SG Sharma, Head, Crop Physiology and Biochemistry Division, ICAR-National Rice Research
Institute, Cuttack, Odisha

Authors
A Anandan, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
A Banerjee, Scientist, NRRI Regional Station Central Upland Rice Research Station (CRURRS),
Hazaribag, Jharkhand
A Kumar, Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
A Kumar, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
AK Mukherjee, Principal Scientist, Crop Protection Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
Annamalai M, Scientist, Crop Protection Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
Annie Poonam, Principal Scientist, Crop Production Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
Arvindan S, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
BC Verma, Scientist, NRRI Regional Station Central Upland Rice Research Station (CRURRS),
Hazaribag, Jharkhand
Biswajit Mondal, Principal Scientist, Social Science Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
Basana Gowda G, Scientist, Crop Protection Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
BB Panda, Principal Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
BC Marndi, Senior Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
BC Patra, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
BN Sadangi, Principal Scientist and Head (Retd.) , Social Science Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
BS Satpathy, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
C Parameswaran, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha

Editors and Authors

1
CV Singh, Senior Scientist, NRRI Regional Station Central Upland Rice Research Station
(CRURRS), Hazaribag, Jharkhand
D Bhaduri, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
D Chatterjee, Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
D Maiti, Principal Scientist and Head, NRRI Regional Station Central Upland Rice Research
Station (CRURRS), Hazaribag, Jharkhand
DR Pani, Principal Scientist and Head, ICAR-NBPGR Base Centre, NRRI, Cuttack, Odisha
E Pandit, Student, Crop Improvement Division, ICAR-NRRI, Cuttack, Odisha
G Kumar, Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
GAK Kumar, Principal Scientist, Social Science Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
GP Pandi G, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
HN Subudhi, DR Pani, Principal Scientist, Crop Improvement Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
J Meher, DR Pani, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
JL Katara, Scientist, Crop Improvement Division, ICAR-National Rice research Institute, Cuttack,
Odisha
JN Reddy, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
K Ali Molla, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
K Chakraborty, Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
K Chattopadhay, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
K Rajsekhar Rao, Principal Scientist, Crop Protection Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
K Saikia, Senior Scientist, NRRI Regional Station Regional Rainfed Lowland Rice Research
Station (RRLRRS), Gerua, Assam
KB Pun, Principal Scientist, ICAR-Indian Agricultural Research Institute, New Delhi
L Behera, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
LK Bose, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
Lipi Das, Principal Scientist, Social Science Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
M Azharudheen, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
M Chakraborti, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
M Debnath, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
M Nedunchezhianm, Principal Scientist and Head, ICAR-CTCRI Regional Station, Bhubaneswar,
Odisha
M Shahid, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha

Editors and Authors

2
 Rice Research for Enhancing Productivity,
Profitability and Climate Resilience

MJ Baig, Principal Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
MK Bag, Principal Scientist, Crop Protection Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
MK Kar, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
MK Yadav, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
MS Baite, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
N Basak, Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
N Umakanta, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
NC Rath, Principal Scientist, Social Science Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
NK Patil, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
NN Jambhulkar, Scientist, Social Science Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
NP Mandal, Principal Scientist, NRRI Regional Station Central Upland Rice Research Station
(CRURRS), Hazaribag, Jharkhand
NT Borkar, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
P Bhattacharyya, Principal Scientist, Crop Production Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
P Guru, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
P Paneerselvam, Principal Scientist, Crop Production Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
P Sanghamitra, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
P Swain, Principal Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
PC Rath, Principal Scientist, Crop Protection Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
PK Hanjagi, Scientist, Crop Physiology and Biochemistry Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
PK Nayak, Principal Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
PK Sahu, Assistant Chief Technical Officer, Crop Production Division, ICAR-National Rice
Research Institute, Cuttack, Odisha
Prabhukarthikeyan SR, Scientist, Crop Protection Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
Prasanthi G, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
R Bhagabati, Principal Scientist and Head, NRRI Regional Station Regional Rainfed Lowland
Rice Research Station (RRLRRS), Gerua, Assam
R Khanam, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha

Editors and Authors

3
R Tripathi, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
Raghu S, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
RK Sahu, Senior Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
RL Verma, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
RP Sah, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
S Bhagat, Senior Scientist, NRRI Regional Station Central Upland Rice Research Station (CRURRS),
Hazaribag, Jharkhand
S Chatterjee, Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
S Lenka, Senior Scientist, Crop Protection Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
S Mohanty, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
S Munda, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
S Ray, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
S Roy, Scientist, NRRI Regional Station Central Upland Rice Research Station (CRURRS), Hazaribag,
Jharkhand
S Saha, Principal Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
S Samantaray, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
S Sarkar, Scientist, Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
SC Giri, Principal Scientist, ICAR-CARI Regional Station, Bhubaneswar, Odisha
SD Mohapatra, Principal Scientist, Crop Protection Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
Sivashankari, Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
SK Dash, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
SK Mishra, Principal Scientist, Social Science Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
SK Pradhan, Principal Scientist, Crop Improvement Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
SM Prasad, Principal Scientist, NRRI Regional Station Central Upland Rice Research Station
(CRURRS), Hazaribag, Jharkhand
SSC Pattanaik, Senior Scientist, Crop Improvement Division, ICAR-National Rice Research
Institute, Cuttack, Odisha
T Adak, Scientist, Crop Protection Division, ICAR-National Rice Research Institute, Cuttack,
Odisha
TK Dangar, Principal Scientist, Crop Production Division, ICAR-National Rice Research Institute,
Cuttack, Odisha
U Kumar, Scientist, Crop Production Division, ICAR-National Rice Research Institute, Cuttack,
Odisha

Editors and Authors

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