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Haplogroup diversity in the Indian population using 23 Y- STRs
Article in Annals of Human Biology · June 2022
DOI: 10.1080/03014460.2022.2091796
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Regional Forensic Science Laboratory Guru Ghasidas University
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Foresic science laboratory Sagar Madhya Pradesh Central forensic science laboratory Chandigarh India
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Annals of Human Biology
ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/iahb20
Haplogroup diversity in the Indian population
using 23 Y-STRs
Pankaj Shrivastava, Muktikanta Panda, Kamlesh Kaitholia, Shivani Dixit,
Ramkishan Kumawat, Hari Shankar, A. N. Sharma & Gyaneshwer Chaubey
To cite this article: Pankaj Shrivastava, Muktikanta Panda, Kamlesh Kaitholia, Shivani
Dixit, Ramkishan Kumawat, Hari Shankar, A. N. Sharma & Gyaneshwer Chaubey (2022):
Haplogroup diversity in the Indian population using 23 Y-STRs, Annals of Human Biology, DOI:
10.1080/03014460.2022.2091796
To link to this article: https://doi.org/10.1080/03014460.2022.2091796
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ANNALS OF HUMAN BIOLOGY
https://doi.org/10.1080/03014460.2022.2091796
RESEARCH PAPER
Haplogroup diversity in the Indian population using 23 Y-STRs
Pankaj Shrivastavaa,b , Muktikanta Pandab, Kamlesh Kaitholiac, Shivani Dixitd, Ramkishan Kumawate ,
Hari Shankarf, A. N. Sharmab and Gyaneshwer Chaubeyg
a
Biological Sciences Division, Regional Forensic Science Laboratory, Department of Home (Police), Government of MP, Gwalior, India;
b
Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, India; cDNA Unit, Regional Forensic Science
Laboratory, Department of Home (Police), Government of MP, Bhopal, India; dSchool of Life Sciences, Jaipur National University, Jaipur,
India; eDNA Division, State Forensic Science Laboratory, Jaipur, India; fDNA Fingerprinting Unit, State Forensic Science Laboratory,
Department of Home (Police), Government of MP, Sagar, India; gCytogenetics Laboratory, Department of Zoology, Banaras Hindu University,
Varanasi, India
ABSTRACT ARTICLE HISTORY
Background: A Y-STR polymorphism study is a convenient tool in molecular anthropology and foren- Received 11 January 2022
sic DNA analysis. Accepted 17 May 2022
Aim: Through standard ethical procedures, the proposed study explored the genetic scenario in male
KEYWORDS
lineage in Madhya Pradesh, a central Indian state, by Y-STR genotyping and haplogroup studies.
Y-STR; haplogroup; forensic
Subjects and methods: Five hundred and eleven unrelated male blood samples were directly ampli- analysis; population
fied, and fragment separation was done using capillary electrophoresis to generate a Y-STR profile for genetics; Madhya Pradesh
23 forensic relevant markers through PowerPlexV Y 23 multiplex system. The different statistical meth-
R
ods were applied for studying the forensic and genetics parameters. Subsequently, population com-
parison was performed by AMOVA, PCoA, and MDS plot, and Haplogroups were predicted with Whit
Athey’s haplogroup predictor tool.
Conclusion: These data represented the potential value of the PowerPlexV Y-23 multiplex system for
R
the forensic and human genetics application in the population of Madhya Pradesh, India.
Simultaneously the Haplogroup analysis revealed information about the multi-geographic origin as
well as multi-ethnic genetic affinities of the Madhya Pradesh population.
Background the whole state of Madhya Pradesh (Figure 1). Individuals
recruited for genotyping were those who came for regular
Madhya Pradesh is the second largest state located in
casework done in DNA Division, State Forensic Science
Central India (Figure 1). The Narmada and Sone river valleys
Laboratory (SFSL), Sagar, Madhya Pradesh, India. Written
demarcate the topography of Madhya Pradesh (Sonakia informed consent was obtained from the individuals during
1984). The state covers an area of 308 000 sq.km with a the biological sample collection for regular casework at the
population numbering 72 626 809. Hindi, an Indo-European Forensic Science Laboratory. All the samples are new sam-
group of languages with different dialects, i.e. Malwi, ples that were not genotyped and reported earlier. This
Bundeli, Bagheli, and Nimari is widely used by the residents. study was approved by the Institutional Ethics Committee,
The Gondi language which belongs to the family of Dr. Harisingh Gour Vishwavidyalaya (A Central University),
Dravidian language is commonly used by the indigenous Sagar, M.P., India-470003 vide letter number DHSGV/IEC/
communities of the state (INDIA POFMPIN 2011). This state’s 2021/2/02 of dated 3 November 2021.
unique geography and landscape have attracted many his-
torical and pre-historical migratory events and shaped the
present-day multicultural zone. In this study, we investigated Data collection
the male genetic portrait of this Central State of India to In the present work,
decipher the forensic scenario and genetic portrait. DNA was amplified directly (without DNA extraction and
quantitation) following the protocol used in previous studies
(Srivastava et al. 2019; Kumawat, Shrivastava, Shrivastava,
Sample
and Mathur 2020; Kumawat, Shrivastava, Shrivastava, Mathur,
A total of 511 unrelated healthy male individuals were Dash, et al. 2020; Kumawat, Shrivastava, Shrivastava, Mathur,
selected from different geographical regions that represented and Dixit 2020). These Y-chromosomes were multiplexed for
CONTACT Pankaj Shrivastava ecsdsjbp@gmail.com Biological Sciences Division, Regional Forensic Science Laboratory, Department of Home (Police),
Government of MP, Gwalior, 474011, India
These authors contributed equally to this work.
Supplemental data for this article is available online at https://doi.org/10.1080/03014460.2022.2091796.
ß 2022 Informa UK Limited, trading as Taylor & Francis Group
2 P. SHRIVASTAVA ET AL.
Figure 1. The geographical location of studied and compared populations.
23 short-tandem repeats (STR) loci using the PowerPlexV Y-
R
Results
23 system (Promega Corporation, Madison, WI, USA), a com-
The Y-STR haplotype data has been submitted to the YHRD
mercial forensic DNA kit. Capillary electrophoresis (CE) based
database (https://yhrd.org/) and an accession number
Genetic Analyser-ABI 3500 XL (Thermo Fisher Scientific) was
https://yhrd.org/YA004722 was obtained. Out of the 511
used for the amplified fragment separation. Subsequently,
samples, a total of 478 haplotypes were observed, of these
the Y-STR profile was generated by analysing the data in
445 were unique and 33 were seen twice (Table 1 and
GeneMapper IDXv1.6 (Thermo Fisher Scientific) software.
Table S1). The observed allele frequencies are mentioned in
Table S2. The highest Gene Diversity (GD) value was found
as 0.950 for locus DYS385a/b and the lowest for DYS391 i.e.
0.371 (Table S3). The haplotype diversity (HD) and the dis-
Data management and statistical analysis crimination capacity (DC) were noted as 0.999999999999
and 0.935, respectively, for the studied population. The
Using different descriptive statistics viz. Gene diversity (GD), polymorphic information content (PIC) and the random
haplotype diversity (HD), and allele frequencies for the match probability (RMP) values in the study population for
studied population were calculated using GenAlEx 6.0 soft- 23 alleles were observed as 0.99999999995894 and
ware (Peakall and Smouse 2006). Forensic parameters like 9.75 1013, respectively. The Rst distance matrix was used
discrimination capacity (DC) were calculated by the formula to draw the MDS plot (Figure 2), which revealed one major
DC ¼ hn , where h stands for the observed haplotypes count cluster along with a few outlier populations viz., South
and n is the total number of samples assigned into the Africa [African], Cape Town-South Africa, London-United
study. For genetic affinity analysis, both AMOVA and MDS Kingdom [British European], [Xhosa], United States
plots were generated through the online tool Y- [European American], China (Han), Balochistan (Hazara), Rio
Chromosome STR Haplotype Reference Database (YHRD) Negro-Argentina [European], Illinois-United States [African
(http://www.yhrd.org) (Willuweit and Roewer 2015). For the American], Sao Paulo-Brazil [European], and Uttar Pradesh.
construction of the Principal Component Analysis (PCA) plot, Further, the principal coordinate analysis (PCoA) plot (Figure
PAST software was used (Hammer et al. 2001). Previously 3) was drawn between components 1 and 2, which indi-
reported inland populations of India and other worldwide cated 95.5% variation among the compared populations.
populations were considered for AMOVA (Table S4) and MDS and PCoA were found to be consistent with
inter-population comparisons (Figures 2, 3). each other.
ANNALS OF HUMAN BIOLOGY 3
Figure 2. Multidimensional scaling (MDS) plot between studied and compared populations.
Figure 3. Principal component analysis (PCA) plot based on pairwise Fst values between studied and compared populations.
By using Whit-Athey’s tool (Athey 2006), a total of 461 (0.4%) were assigned to the bad haplogroup category. Out
individuals (i.e. 90.2%) out of the 511 were allocated to the of the 23 haplogroups, R1a (25.6%), H1 (20.0%), and R2
23 haplogroups. Forty-eight individuals (9.4%) were devoid (13.5%) were the major three haplogroups (Table 2) observed
of any haplogroup prediction and the other two individuals among the population of Madhya Pradesh, which accounted
4 P. SHRIVASTAVA ET AL.
Table 1. Forensic features of PowerPlexV Y-23 loci in a population of Madhya
R
for this study and Whit Athey for his help during the prediction of
Pradesh, India. the haplogroup.
PowerPlexV Y-23 loci
R
Number of observed haplotypes
1 (unique) 445
2 33 Ethical approval
Sample size 511
Number of haplotypes 478 The present work has been conducted according to the Ethical norm of
Proportion of unique haplotypes 0.930 the declaration of Helsinki (World Medical Association) (RICKHAM 1964).
Haplotype diversity (HD) 0.999999999999 Written informed consent was obtained from the individuals during the
Discrimination capacity (DC) 0.935
biological sample collection for the purpose of regular casework at the
Random match probability (RMP) 9.75 1013
Polymorphic information contents (PIC) 0.99999999995894 Forensic Science Laboratory. This study was approved by the
Institutional Ethics Committee, Dr. Harisingh Gour Vishwavidyalaya (A
Central University), Sagar, M.P., India-470003 vide letter no. DHSGV/IEC/
Table 2. In silico Y-chromosomal haplogroup assignments in the population 2021/2/02 of dated 3 November 2021.
of Madhya Pradesh were obtained using Whit Athey’s Y-DNA
Haplogroup Predictor.
Frequencies of Disclosure statement
Number of in silico Y-chromosomal
Haplogroup individuals haplogroup (%) No potential conflict of interest was reported by the author(s).
C2 2 0.4
E1b1a 5 1.0
E1b1b 9 1.8
G1 4 0.8
Funding
G2a 3 0.6
The author(s) reported there is no funding associated with the work fea-
G2 2 0.4
H1 102 20.0 tured in this article.
I 1 0.2
I2a 6 1.2
I2b 1 0.2 ORCID
J1 6 1.2
J2 2 0.4 Pankaj Shrivastava http://orcid.org/0000-0002-1647-2390
J2a 29 5.7 Ramkishan Kumawat http://orcid.org/0000-0002-7794-9615
J2a4 2 0.4
J2b 15 2.9
L 31 6.1
O1 7 1.4
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