Animal biotechnology is the application of scientific
and engineering principles to the processing or
production of materials by animals to provide
goods and services to human kind.
Animal biotechnology includes livestock, poultry,
fish, insects, companion animals and laboratory
animals.
Transgenic technology
Gene knockout technology
Molecular genetics
Embryo transfer technique
In vitro embryo production
Modern vaccines
Molecular diagnostics
Nutritional biotechnology
A breed is a specific group of domestic animals having
homogeneous phenotype, behavior, and other
characteristics that distinguish it from other organisms
of the same species.
Therefore, breed is a stock of animals within a
particular species with distinctive characteristics, which
is produced by selective breeding.
Hence, each breed consists of unique appearance and
behavior when compared to another breed of the same
species.
Angus Tharparkar
Australian Charbray Red Sindhi
Chianiana Sahiwal
Ankole
Gir
Ongole
Jersey
Kangeyam
Boer (Sheep) Vechur
Thalichery (Sheep)
Exotic breeds Indigenous breeds
Kombai Aseel
Rajapalayam Chittagong
Kaikadi Kadaknath
Gaddi kuta
Busra
Brahma
German shepherd
Java
Golden Retriever Leghorn
Boxer Styrian
Great Dane Red cap
Dog Breeds Poultry breeds
In biology, a species is the basic unit of classification and a
taxonomic rank of an organism, as well as a unit of
biodiversity.
A species refers to the largest group of organisms in which
any two individuals of the appropriate sexes or mating types
can produce fertile offspring, typically by sexual reproduction.
The exchange of genes between the individuals of the
species or the gene flow is the major characteristic feature of
a species. The gene flow does not occur among different
species.
Speciation refers to the emergence of new species from the
existing species. It occurs due to physical, behavioral, and
reproductive isolation of different populations of the same
species.
Animal breeding is a branch of animal science that deals
with the evaluation of the genetic value of livestock using
different methods.
Animals with superior breeding value in growth rate,
egg, meat, milk, or wool production, and other desirable
traits are selected.
Animal breeding is performed to domestic animals in
order to improve desirable qualities and to better suit
human needs.
It is a group of animals used for the purpose of planned
breeding. In order to gain certain valuable traits in purebred
animals.
For example, when breeding cattle for milk, the “breeding
stock should be sound, milch, having longer lactation period,
higher productivity and reproductively efficient.
Breeding animals is common in an agricultural setting,
however, it is also a common practice for the purpose of
selling animals meant as pets, such as cats, dogs, horses,
and birds.
Environmental factors must be considered and controlled in
selecting breeding stock because it has greater effects on
performance.
There are two sources of variation namely, genetics
and environment. So, breeding progress requires
understanding these two.
Continuous selective breeding leads to homozygosity in a
population resulting a loss of variability.
Differences in the animals’ environment, such as amount of
feed, care, and even the weather, may have an impact on
their growth, reproduction, and productivity.
For example, only about 30 percent of the variation in milk
production in dairy cattle can be attributed to genetic effects;
the remainder of the variation is due to environmental effects.
Genetic variation is necessary in order to make progress in
breeding successive generations.
It refers to the Mating animals of the same breed for
maintaining such breed.
Opposite to the practice of mating animals of different
breeds, purebred breeding aims to establish and
maintain stable traits that animals will pass to the next
generation.
Such animals can be recorded with a breed registry, the
organization that maintains pedigrees
Generally, two ways of matings are prevalent:
Natural mating: It refers to mating of animals by natural
means.
Artificial insemination (AI): It is the technique in which
semen with living sperm is collected from the male and
introduced into female reproductive organ. So, mating is
done through artificial means.
Breeding or matting of the related animals is known as
inbreeding.
Inbreeding is often described as “narrowing the
genetic base” because the mating of related animals
produces offspring that have more genes in common.
Inbreeding is used to concentrate desirable traits.
Inbreeding is generally detrimental in domestic
animals.
Close breeding: Here animals are very closely related
and can be traced back to more than one common
ancestor. Examples: Sire to daughter, Son to dam,
Brother to sister.
Line breeding: Mating animals that are more distantly
related which can be traced back to one common
ancestor. Examples: Cousins Grandparents to grand
offspring, Half-brother to half-sister.
Increased inbreeding is accompanied by
Reduced fertility
Slower growth rates
Greater susceptibility to disease
Higher mortality rates.
It is breeding of unrelated animals. The effect of out
breeding is opposite of inbreeding because
heterozygosity is increased here. It is of two types –
Cross breeding: Crossbreeding involves the mating of
animals from two breeds. Normally, breeds are chosen
that have complementary traits that will enhance the
offspring's economic value. Superior traits that results in
the crossbred progeny from crossbreeding are called
hybrid vigor or heterosis. So, it is done to take
advantages of good qualities of two or more breeds. It is
mainly used by commercial producers.
Utilize the desired attributes of two or more
breeds.
Produce progeny better suited to target
markets while maintaining environmental
adaption.
Improve productivity quicker in traits which
are slow to change within a breed i.e.
environmental adaption, fertility and carcass
traits.
Take advantage of the production
improvements which arise from heterosis
(hybrid vigor) when breeds are crossed.
Heterosis is the production advantage that
can be obtained from crossing breeds or
strains, which are genetically diverse.
The new combinations of genetic material can
lead to production advantages over and
above the average of the two parent breeds
or strains.
To be of economic advantage, the new
production levels need to be above those of
either parent strain or breed.
The two breed cross system produces first cross,
or F1, progeny. In this system, the progeny
resulting from the cross of two breeds are usually
all sold for slaughter or to another commercial
breeder.
The system is most useful for situations in which
females of a specific breed are well adapted to a
given environment.
These adapted females can be mated to a sire of
another breed, resulting in heterosis for traits such
as growth, improved carcase, feed conversion
efficiency and vigour.
Two breed cross occurs where breed A and breed B are two purebreds and
the F1 progeny (AB) contains equal parts of the two breeds.
In a backcross system, Female F1 crossbred progeny
are mated to males of one of the parental breeds.
This breeding system takes full advantage of heterosis
for maternal traits such as fertility of the cow, milking and
mothering ability.
Continual backcrossing is the system used by producers
to upgrade or change from one breed to another without
having to buy purebred.
The backcross is obtained where all the females from a two breed
cross are mated to a purebred bull of either of the original breeds.
Three breed cross requires the input of three separate
breeds.
First cross females (F1 progeny) are joined with bulls of
a third unrelated breed.
This type of breeding takes advantage of both maternal
and individual heterosis and of the complementarities of
three breeds.
The progeny is generally considered to produce the
greatest lift in productivity, but it is influenced by the
quality of the purebreds maintained to breed the F1
females.
The three breed cross is obtained when all the females from a two breed
cross are mated to a bull of a third, unrelated breed. All the three breed
cross progeny are marketed.
Rotational crossbreeding (or) sequence breeding is
when males of two or more breeds are mated to
crossbred females.
Over a number of years, each breed will have
contributed its strengths and weaknesses equally.
Levels of heterosis achieved in rotational crossbreeding
depend on the number of breeds involved.
Increased heterosis in rotational systems is a result of
close to maximum heterosis being achieved in each
cross with the purebred.
Rotation breeding Starting at 50:50, and stabilises at 65:35 and giving
65 % heterosis from the last sire line used.
Development of a composite or synthetic breed results
from the crossing of two or more existing breeds.
The primary advantage of forming composite breeds is
that after the initial crosses are made, management
requirements are the same as for straight breeding.
The initial choice of breeds must be based on those
which have desirable traits for a particular environment
and for the target market.
The percentage of heterosis increases as more breeds
contribute in the initial mating program.
The heterosis will not be as high as that achieved with a
rotational crossbreeding program.
A simple approach to a composite breeding
Grading up is the breeding of animals of two different
breeds where the animals of an indigenous
breed/genetic group is mated by an improved pure
breed for several generations in order to get superior
traits of the improved breed.
Grading up is continuous use of purebred sires of the
same breed in a grade herd. By fifth generation, the
graded animals may reach almost purebred levels.
Grading up
Pure Thalichery Pure Boer
After 8th generation
100% Boer
Grading up - Change in the genetic composition
Number of generations Off-springs
1st Generation Percent replaced Percent non-descript
2nd “ 50 50
3rd “ 75 25
4th “ 87.5 12.5
5th “ 93.75 6.25
6th “ 96.87 3.13
7th “ 98.44 1.56
8th “ 99.22 0.78
off springs come closer to a 100% improved breed, as we go on breeding.
Chromosome Mapping
&
Identification of economically
important genes in Farm animals
The loci controlling quantitative traits are called
quantitative trait loci (or) QTL
The term quantitative trait loci is first coined by
Gelderman in 1975.
It is the region of genome that is associated with an
effect on a quantitative trait.
The example of QTL is milk production, which is
controlled by many genes.
It can be a single gene or cluster of linked genes that
affects the trait.
The traits are controlled by multiple genes, each
segregates according to Mendel's Laws.
The traits can also be affected by the environment to
varying degrees.
Many genes control any given trait and allelic variations
are fully functional.
Individual gene effect is small and genes involved can
be dominant or co-dominant.
The genes involved can be subject to epistasis or
pleotrophic effect.
To identify the region of the genome that affects the trait
of interest.
To analyze the effect of QTL on the trait.
To check the variation for the trait is caused by a specific
region of a DNA.
To test the gene action associated with QTL for Additive
effect or Dominant effect.
To identify the allele associated with favorable effect.
➢ Genetic marker is a general term used for any observable or
assayable phenotype or the genetic basis for assessing of the
detected phenotypic variability.
➢ Genetic markers are mainly classified based on physically
evaluated traits (morphological and productive traits), based
on gene product (biochemical markers) and based on DNA
analysis (molecular markers).
➢ Molecular marker also known as DNA marker and is defined
as a segment of DNA indicating mutations or variations, which
can be employed to detect polymorphism (base deletion,
insertion and substitution) between alleles of a gene for a
particular sequence of DNA in a given population or gene
pool.
High level of polymorphism
Even distribution across the whole genome (not
clustered in certain regions)
Clear distinct allelic features
Single copy and no pleiotropic effect
Cost efficient marker development and genotyping
Easy detection and automation
High availability and suitability to be multiplexed
Genome-specific in nature (especially with polyploidy)
Marker-Assisted Selection (MAS) is used for indirect
selection of superior breeding animals.
MAS depend on identifying association between genetic
marker and linked Quantitative traits loci (QTL).
The association between marker and QTL depend on
distance between marker and target traits.
As soon as markers linked to QTL have
been identified, they can be used in selection
programme. This use of marker in selection is called
Marker-Assisted Selection.
Testing for genetic defects e.g. BLAD.
Testing for single gene trait e.g. coat colour.
It is used to test multigenic trait or Quantitative trait e.g.
Milk production.
Growth performance
Milk production
Maternal ability
Carcass quantity and quality
Fertility
Reproductive efficiency
Inherited genetic defects
It contains 30 pairs of chromosomes.
The Human and cattle genomes are 83% identical.
Chromosome 1 – Birth weight
Chromosome 2 – Rib eye area and weaning wt.
Chromosome 4 – Tenderness
Chromosome 5 – Rib bone & ovulation rate
Chromosome 6 - Birth weight
Chromosome 7 – Trypano tolerance
Chromosome 8 – Back fat
Chromosome 9 – Behavior
Chromosome 12 - Birth weight
Chromosome 14 - Carcass weight
Chromosome 15 – Tenderness
Chromosome 16 - Birth weight
Chromosome 18 - Birth weight
Chromosome 19 – Ovulation rate
Chromosome 22 – Carcass weight
Chromosome 23 - Weaning weight
Chromosome 29 - Tenderness
Disease resistance
Product quality
Improve longevity
Feather pecking
Stress resistance
Desired behavior characteristics of animals
Non PCR-based or Hybridization based Molecular Markers.
The most common example of this type of marker is
Restriction Fragment Length Polymorphisms [RFLPs].
PCR-based DNA Markers these includes; Random Amplified
Length Polymorphic DNAs [RAPDs], Simple Sequence
Repeats or microsatellites [SSRs], Amplified Fragment Length
Polymorphisms [AFLPs].
DNA Chip and Sequencing-based DNA Markers. Single
nucleotide Polymorphisms [SNPs] is an example of these
types of markers.
Restriction Fragment Length Polymorphisms (RFLPs) was the
first form of DNA marker utilized to construct the first true
genomic map.
RFLP technology was first developed by Botstein and his co-
workers since 1980.
This hybridization based marker technology employed
synthetic oligonucleotides as probes, which are labelled
fluorescently to hybridize DNA
This technology used the restriction enzymes that cleave the
DNA at distinct site to observe the differences at the level of
DNA structure.
Differences are marked by using RFLP when the length of
DNA segments are different, this imply that the RE (restriction
enzymes) cleave the DNA at specific locations.
The change or polymorphism that take place as result of
mutation indicate creation or removal of the RE site and
produce new RE site.
The variations are determined by using hybridization probe.
In RFLP analysis, the choice of the DNA probe is very
crucial.
Gel electrophoresis is needed for the identification of RFLPs
to separate the DNA fragments of various lengths and to
transfer the fragments into a nylon membrane.
The radioactive labelled probe is applied to observe the
segments of DNA exposed to an X-ray Film.
This technique is normally employed in hybridization definition
of nucleic acid, detection and diagnosis, description of
polymorphisms on the gene construction of a genetic
linkage map and recombinant DNA technology in livestock
species.
Random Amplified Polymorphic DNA also called arbitrarily
primed PCR.
This technology utilizes an in-vitro amplification to randomly
amplify the unknown loci of nuclear DNA with a matching
pair of short oligo-primers, (8-10 base pairs) in length.
Multiple primers in the range of (5 to 21) nucleotides are
mostly used and has proven to be successful when detection
is combined with polyacrylamide gel electrophoresis.
The amplified products range from less than 10 to over a 100
depending upon the ratio and primer/template combination.
RAPD technology had been used to estimates the genetic
differences within or between the certain taxa of interest by
evaluating the occurrence or lack of each product, which is
directed by modification in the DNA sequence at each
locus.
RAPD technique offers a quick, simple, cheap and efficient
technique for producing molecular information.
Being highly polymorphic, only very small quantity of DNA is
needed to be amplified by PCR technique in the absence of
DNA sequence information.
This is the major reason why RAPD technique has been used
successfully in various phylogenetic and taxonomic
researches.
Microsatellites are two- to six-nucleotide repeats,
interspersed throughout the genome.
Microsatellites are highly polymorphic and abundant, often
found in non-coding regions of genes.
The most common dinucleotide motif in mammals is (CA)n,
where n is the number of repeats.
In avian species, the frequency of (CA) ≥10 is evaluated at
once every 140 to 180 kb, and that of (CA) ≥14 is one every
350 to 450 kb.
Microsatellites loci are also termed as short tandem repeats
(STR's), simple sequence repeats (SSR's) and simple
sequence tandem repeats (SSTR).
The microsatellites and minisatellites altogether make up the
variable number of tandem repeats (VNTRs).
The mutation rate of microsatellites is thought to be high and
there are often large numbers of alleles that vary in size at a
single locus.
The lengths of a specific microsatellite sequences tend to be
highly variable among individuals.
Slippage of DNA polymerase and mismatch repair during
replication appear to be the mechanisms generating diversity
of microsatellite length.
Microsatellite length variation is easily detected by the
polymerase chain reaction (PCR) using unique flanking
primer sequences.
Microsatellite derived markers represent a powerful way of
mapping genes controlling economic traits.
As soon as the simple repeat region is identified, by
sequencing its immediate flanking regions, specific primers
can be designed for PCR and for genotyping.
Normally, the size of a microsatellite PCR product is obtained
by electrophoresis in a denaturing polyacrylamide gel.
One of the two primers employed in the PCR is often labeled
with a fluorescent or radioactive tag.
This technique of detection usually works better but suffers
from an inherent weakness in determining the size of DNA
accurately.
More recently, there is an alternative to the gel-based
approach to determine the size of DNA products; there are a
series of technological advancement based on mass
spectrometry.
Microsatellite applications which includes, genetic
characterization studies, analysis of population structure,
estimation of genetic variability and inbreeding, determination
of paternity, phylogenetic relationships among populations,
disease diagnostics and forensic analysis.
AFLP method is a simple and inexpensive finger printing
technique which provide more valuable information by
producing multi-locus and consistent genomic fingerprints.
The basic idea behind AFLP polymorphism was the insertion
and deletion or substitution of nucleotides between and at
restriction sites.
The base substitutions are normally done at primer binding
sites during PCR as in the case of RAPD.
This technique is distinctive, as it enables the binding of
adaptors of known sequences to DNA segments that are
produced through the complete digestion of genomic DNA.
This ensure easy separation of the generated DNA fragments
following amplification the subset of entire fragments.
Analysis of fragment using automated sequencing machine
following gel electrophoresis.
AFLP technique offer an effective, fast and cost-effective
means for detecting a large number of polymorphic genetic
markers which are very consistent and reproducible.
The technique is considered as the most effective method
for molecular epidemiological studies of pathogenic
microorganisms and it is also used extensively in forensic
science.
The AFLP technology has been widely utilized in
identification of genetic polymorphisms, evaluating and
characterizing breed resources, measuring the correlation
among breeds, constructing genetic maps and identifying
genes in the main species farm animals.
Single nucleotide polymorphisms (SNPs) involve the
substitution of one nucleotide for another, or the addition or
deletion of one or a few nucleotides.
It comprise more than 90% of all variances between the
individuals; thus, they are the excellent genetic variation
resource for population studies and genome mapping.
SNPs type of marker are becoming highly attractive in
molecular marker development due to their abundance in the
genome of any organism (coding and non-coding regions).
SNPs have an ability to identifying hidden polymorphism
which is not commonly recognized by other genetic markers
and techniques.
There are four major reasons for the increasing interest in the
use of SNPs as markers for genetic analysis.
Firstly, they are prevalent and provide more potential markers
near or in locus of interest
Secondly, some SNPs are located in coding regions and
directly affect protein function. These SNPs may be directly
responsible for some of the variations among individuals in
important traits.
Thirdly, SNPs are more stably inherited than microsatellites,
making them more suited as long term selection markers.
Finally, SNPs are more suitable than microsatellites for high
throughput genetic analysis, using DNA microarray
technology.
There are a number of methods to detect SNPs.
The traditional gel-based approach uses standard molecular
techniques, such as sequencing, PCR, restriction digests and
various forms of gel elecrophoresis.
Microsatellite
Single locus marker
RFLP STR
DNA Fingerprinting RAPD
Multi-locus marker
AFLP
Identification of individuals is important in the domestic animals.
For e.g., for the control of semen used in artificial insemination, the
identification of cell lines and chimeras.
DFP using in skin samples allows the diagnosis of zygosity even
in species showing blood cell chimerism due to placental
anastomoses.
DFP also prove useful in investigating the phylogeny and genetic
structuring of populations in particular cases.
The control of inbred lines and determination of genetic
relationships have already been realized by DNA
fingerprints.
In poultry, highly discriminating oligonucleotides (CAG)5,
(CGAT)4 and (GT)8 have enough potential to differentiate
between individual chickens and strains.
Furthermore, the genetic makeup of inbred chickens can be
evaluated by establishing fingerprints.
Such data may be useful for selecting lines or individuals in
cross breeding programmes.
Genes involved in Milk production
Sl.No. Gene Gene name Function of gene Chromosome No.
1 ZNF232 Zinc finger protein 232 Regulating milk volume 5
Acetyl-CoA
2 ACACA Milk yield 19
carboxylase alpha
Influence
3 PRL Prolactin protein 23
Lactation performance
4 CSN1S1 Casein alpha s1 Controlled total milk yield 6
ADAM
metallopeptidase with Involved in the differentiation
5 ADAMTS20 5
thrombospondin type of mammary cells
1 motif 20
Genes involved in Composition of Milk
Sl.No. Gene Gene name Function of gene Chromosome No.
glycerol-3-phosphate biosynthesis of triglyceride
1 AGPAT6 27
acyltransferase 4 (milk fat)
Peroxisome
2 PPARγ proliferator activated Control milk fat yield 22
receptor gamma
3 CSN3 casein kappa Regulating protein content 6
solute carrier family Associated with lactose
4 SLC27A6 7
27 member 6 content
Play a central role in the
SREBP cleavage-
5 SCAP regulation of milk fat 22
activating protein
synthesis
Genes involved in Reproductive and Fertility Trait
Chromosome
Sl.No. Gene Gene name Function of gene
No.
Influence the ovarian
1 CDC25C cell division cycle 25C 7
development
2 PSEN2 presenilin 2 Influence the litter size 16
Related to semen
3 YBOX2 Y-box Binding Protein 2 19
volume
growth differentiation
4 GDF9 Related to follicular growth 7
factor 9
nuclear receptor
Critically involve in embryonic
5 NR6A1 subfamily 6 group A 11
development
member 1
Genes involved for Environmental adaptation
Sl.No. Gene Gene name Function of gene Chromosome
No.
Related to high-altitude
1 LEPR Leptin receptor 3
and fitness traits
Sodium/Potassium/C Responsible for hypoxia-
2 SLC24A4 21
alcium Exchanger 4 related cellular responses
Fibroblast growth Responsible for
3 FGF2 17
factor 2 thermotolerance
ADP ribosylation
Adaptation to different
4 ARFRP1 factor related protein 13
ecological environments
1
adaptation to oxidative
5 SR XN1 Sulfiredoxin 1 13
stress
