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Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: Analysis based on 15 microsatellite markers

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Abstract

The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic level.

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References

  • Agrawal S., Muller B., Bhardwaj U., Bhattnagar S. and Khan F. 2002a Allele frequencies of microsatellite repeat loci in Bhargavas, Chaturvedis and Brahmins of North India.J. Forensic Sci. USA 47, 678–681.

    Google Scholar 

  • Agrawal S., Muller B., Bhardwaj U., Bhattnagar S. and Khan F. 2002b Distribution of allele frequencies of six STR markers in North Indians.J. Forensic Sci. USA 47, 682–685.

    Google Scholar 

  • Agrawal S., Muller B., Bhardwaj U., Bhattnagar S. and Khan F. 2002c Evaluation of six short tandem repeat in forensics: North Indian populations.J. Forensic Sci. USA 47, 686–689.

    Google Scholar 

  • Allchin B. and Allchin R. 1982 The rise of civilization in India and Pakistan. Cambridge University Press, Cambridge.

    Google Scholar 

  • Ashma R. and Kashyap V. K. 2002a Genetic study of 15 important STR loci among four major ethnic groups of Bihar, India.J. Forensic Sci. USA 47, 1139–1142.

    CAS  Google Scholar 

  • Ashma R. and Kashyap V. K. 2002b Genetic polymorphism at 15 STR loci among three important sup-populations of Bihar, India.Forensic Sci. Int. UK 130, 58–62.

    Article  CAS  Google Scholar 

  • Bhasin M. K., Walter H. and Danker-Hopfe 1994 People of India: An investigation of biological variability. In Ecological ethnoeconomic and linguistic groups. Kamla-Raj Enterprises, Delhi.

    Google Scholar 

  • Calafell F., Shuster A., Speed W. C., Kidd J. R. and Kidd K. K. 1998 Short tandem repeat polymorphism evolution in humans.Eur. J. Hum. Genet. 6, 38–49.

    Article  PubMed  CAS  Google Scholar 

  • CFSL 2002A national resource: Indian human population DNA repository. Central Forensic Science Laboratory, Kolkata.

    Google Scholar 

  • Chakraborty R., Walter H., Sauber P., Mukherjee B. N., Malhotra K. C., Banerjee S. and Roy M. 1998 Immunoglobin (Gm and Km) allotypes in nine endogamous groups of West Bengal, India.Ann. Hum. Biol. 14, 155–157.

    Article  Google Scholar 

  • Chattopadhyay P. and Kashyap V. K. 2001 Distribution of alleles of three tetrameric STR loci HUMHPRTB, HUMF13B, HUMLPL and other six PCR based loci HLADQA1, LDLR, GYPA, HBGG, D7S8, Gc in eight predominant populations of India.Forensic Sci. Int. UK 19, 134–137.

    Article  Google Scholar 

  • Chattopadhyay P., Dutta R. and Kashyap V. K. 2001 Allele Frequency data at nine fluorescent labeled STR loci in four tribal population groups in India.J. Forensic Sci. USA 45, 201–205.

    Google Scholar 

  • Chattopadhyay P., Dutta R. and Kashyap V. K. 2001 Population data for nine fluorescent based STR loci among four important tribal populations of India.J. Forensic. Sci. USA 46, 184–188.

    CAS  Google Scholar 

  • Das B., Ghosh A., Chauhan P. S. and Seshadri M. 2002 Genetic polymorphism study at four minisatellite loci (D1S80, D17S5, D19S20 and APOB) among five Indian population groups.Hum. Biol. 74, 345–361.

    Article  PubMed  Google Scholar 

  • Deka R., Shriver M. D., Yu L. M., Ferrell R. E. and Chakraborty R. 1995 Intraand inter-population diversity at short tandem repeat loci in diverse populations of the world.Electrophoresis 16, 1659–1664.

    Article  PubMed  CAS  Google Scholar 

  • Deka R., Shriver M. D., Yu L. M., Heidrich E. M., Jin L., Zhong Y.et al. 1999 Genetic variation at twenty-three microsatellite loci in sixteen human populations.J. Genet. 78, 99–121.

    Google Scholar 

  • Destro-Bisol G., Boschi I., Caglia A., Tofanelli S., Pascali V., Paoli G. and Spedini G. 2000 Micro satellite variation in central Africa: An analysis of intrapopulation and interpopulation genetic diversity.Am. J. Phys. Anthropol. 112, 319–337

    Article  PubMed  CAS  Google Scholar 

  • Dutta R. and Kashyap V. K. 2001 Allele frequencies of six STR loci among three predominant population groups of eastern India.Forensic Sci. Int. UK 119, 129–130.

    Article  CAS  Google Scholar 

  • Dutta R., Chattopadhyay P. and Kashyap V. K. 2000 STR data for AmpF1STR Profiler Plus loci among four predominant population of eastern India.J. Forensic Sci. USA 45, 353–1357.

    Google Scholar 

  • Eller E. 1999 Population substructure and isolation by distance in three continental regions.Am. J. Phys. Anthropol. 108, 147–159.

    Article  PubMed  CAS  Google Scholar 

  • Fairservis W. A. 1971 The roots of ancient India. Macmillan, New York.

    Google Scholar 

  • Gadgil M., Joshi N. V., Prasad U. V., Manoharan S. and Patil S. 1998 Peopling of India. InThe Indian human heritage (ed. D. Balasubramanian and N. Appaji Rao), pp. 100–129. Universities Press, Hyderabad.

    Google Scholar 

  • Gaikwad S. and Kashyap V. K. 2002 Polymorphism at fifteen hypervariable microsatellite loci in four populations of Maharashtra, India.Forensic Sci. Int. UK 126, 267–271.

    Article  CAS  Google Scholar 

  • Graber R. A. and Morris J. W. 1983 General equations for the average power of exclusion for genetic system ofn co-dominant alleles in one-parent cases of disputed parentage. InInclusion probabilities in parentage testing (ed. R. H. Walker), pp. 277–280. American Association of Blood Banks, Arlington.

    Google Scholar 

  • Guo S. W. and Thompson E. A. 1992 Performing the exact test of Hardy-Weinberg proportion for multiple alleles.Biometrics 48, 361–372.

    Article  PubMed  CAS  Google Scholar 

  • Hammond H. A., Jin L., Zhong Y.,et al. 1994 Evaluation of 13 short tandem repeat loci for use in personal identification applications.Am. J. Hum. Genet. 55, 175–189.

    PubMed  CAS  Google Scholar 

  • Hochberg Y. 1988 A sharper Bonferroni procedure for multiple tests of significance.Biometrika 75, 800–802.

    Article  Google Scholar 

  • Jin L., Baskett M. L., Cavalli-Sforza L. L., Zhivotovsky L. A., Feldman M. W. and Rosenberg N. A. 2000 Microsatellite evolution in modern humans: a comparison of two data sets from the same populations.Ann. Hum. Genet. 64, 117–134.

    Article  PubMed  CAS  Google Scholar 

  • Kashyap V. K., Sarkar N. and Trivedi R. 2001 Allele frequencies for the 15 STR loci of the Powerplex 16ℳ multiplex system in five endogamous populations of India.Forensic Sci. Int. UK 126, 180–188.

    Google Scholar 

  • Kashyap V. K., Guha S. and Trivedi R. 2002 Concordance study on 15 STR loci in three major populations of Himalayan state Sikkim.J. Forensic Sci. USA 47, 1163–1167.

    CAS  Google Scholar 

  • Lin Z., Cui X. and Li H. 1996 Multiplex genotype determination at a large number of gene loci.Proc. Natl. Acad. Sci. USA 93, 2582–2587.

    Article  PubMed  CAS  Google Scholar 

  • Malhotra K. C. 1978 Morphological composition of the people of India.J. Hum. Evol. 7, 45–53.

    Article  Google Scholar 

  • Mountain J. L., Hebert J. M., Bhattacharya S., Underhill P. A., Ottolenghi C., Gadgil M. and Cavalli-Sforza L. L. 1995 Demographic history of India and mtDNA-sequence diversity.Am. J. Hum. Genet. 56, 979–992.

    PubMed  CAS  Google Scholar 

  • Mukherjee N., Majumder P. P., Roy B., Dey M., Chakraborty M. and Banerjee S. 1999 Variation at short tandem repeat loci in eight population groups of India.Hum. Biol. 71, 439–446.

    PubMed  CAS  Google Scholar 

  • Nei M. 1973 Analysis of gene diversity in subdivided populations.Proc. Natl. Acad. Sci. USA 70, 3321–3323.

    Article  PubMed  CAS  Google Scholar 

  • Nei M. 1978 Estimation of average heterozygosity and genetic distance from a small number of individuals.Genetics 89, 583–590.

    PubMed  Google Scholar 

  • Nei M. and Roychoudhary A. K. 1974 Sampling variance in heterozygosity and genetic distance.Genetics 76, 379–390.

    PubMed  CAS  Google Scholar 

  • Panneerchelvam S., Vanaja N., Baskar D., Sivapriya V. and Damodaran C. 2001 Distribution of alleles of 12 STR loci in Tamil population (South India).Forensic Sci. Int. UK 119, 126–128.

    Article  CAS  Google Scholar 

  • Papiha S. S., Mastana S. S., Purandare C. A., Jayasekera R. and Chakraborty R. 1996 Population genetic study of three VNTR loci (D2S44, D7S22 and D12S11) in five ethnically defined populations of the Indian subcontinent.Hum. Biol. 68, 819–835.

    PubMed  CAS  Google Scholar 

  • Rajkumar R. and Kashyap V. K. 2002 Distribution of alleles of fifteen STR loci of the Powerplex 16ℳ multiplex in four predominant population groups of South India.Forensic Sci. Int. UK 126, 175–179.

    Google Scholar 

  • Reddy B. M., Sun G., Luis J. R., Crawford M. H., Hemam N. S. and Deka R. 2001 Genomic diversity at thirteen short tandem repeat loci in a substructured caste population, Golla, of southern Andhra Pradesh, India.Hum. Biol. 73, 175–190.

    Article  PubMed  CAS  Google Scholar 

  • Relethford J. H. and Jorde L. B. 1999 Genetic evidence for large African population size during recent human evolution.Am. J. Phys. Anthropol. 108, 251–260.

    Article  PubMed  CAS  Google Scholar 

  • Roychoudhury A. K. 1992 Genetic relationship of the populations in eastern India.Ann. Hum. Biol. 19, 489–501.

    Article  PubMed  CAS  Google Scholar 

  • Sahoo S. and Kashyap V. K. 2002a Allele frequency of data for Powerplex 16ℳ loci in four major populations of Orissa.J. Forensic Sci. USA 47, 912–915

    Google Scholar 

  • Sahoo S. and Kashyap V. K. 2002b Genetic variation at fifteen autosomal microsatellite loci in three highly endogamous tribal population of Orissa, India.Forensic Sci. Int. UK 130, 189–193.

    Article  CAS  Google Scholar 

  • Sambrook J., Fritsch E. F. and Maniatis T. 1989 Molecular cloning: a laboratory manual, 2nd edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

    Google Scholar 

  • Sarkar N. and Kashyap V. K. 2002 Genetic diversity at two pentanucleotide and thirteen tetranucleotide STR loci by multiplex PCR in four predominant population groups of Central India.Forensic Sci. Int. UK 128, 196–201.

    Article  CAS  Google Scholar 

  • Singh K. S. 1998 India’s communities.In People of India, National Series Volume (IV-VI). Anthropological Survey of India and Oxford University Press, Delhi.

    Google Scholar 

  • Sitalaximi T., Trivedi R. and Kashyap V. K. 2002 Genotype profile for thirteen tetranucleotide repeat loci and two pentanucleotide repeat loci in four endogamous Tamil population groups of India.J. Forensic Sci. USA 47, 1168–1173.

    CAS  Google Scholar 

  • Sitalaximi T., Trivedi R. and Kashyap V. K. 2003 Autosomal microsatellite profile of three socially diverse ethnic Tamil populations of India.J. Forensic Sci. USA 48, 211–214.

    CAS  Google Scholar 

  • Tahir M. A., Herrera R. J., Khan A. A., Kashyap V. K., Duncan G., Barna C., Budowle B., Rowold D. J., Sinha S. and Amjad M. 2002 Distribution of HLA-DQA1, Polymarker, CSF1PO vWA, TH01,TPOX, D16S539, D7S820, D13S317and D5S818 allele in east Bengali and west Punjabi populations from IndoPak subcontinent.J. Forensic Sci. USA 45, 1320–1323.

    Google Scholar 

  • Tandon M., Trivedi R. and Kashyap V. K. 2002 Genomic diversity at fifteen fluorescent labeled short tandem repeat loci in few important populations of states of Uttar Pradesh, India.Forensic Sci. Int. UK 123, 190–195.

    Article  Google Scholar 

  • Trivedi R., Chattopadhyay P., Maity B. and Kashyap V. K. 2002 Genetic polymorphism at nine micro satellite loci in four and altitude Himalayan desert human populations.Forensic Sci. Int. UK 127, 150–155.

    Article  CAS  Google Scholar 

  • Watterson G. A. and Guess H. A. 1977 Is the most frequent allele the oldest?Theor. Popul. Biol. 11, 141–160.

    Article  PubMed  CAS  Google Scholar 

  • Waye J. S., Presley L., Budowle B., Shulter G. G. and Fourney R. M. 1989 A simple method of quantifying human genomic DNA in forensic specimen extracts.Biotechniques 7, 852-f855.

    Article  PubMed  CAS  Google Scholar 

  • Weber J. L. and Wong C. 1993 Mutation of human short tandem repeats.Hum. Mol. Genet. 8, 1123–1128.

    Article  Google Scholar 

  • Weir B. S. 1992 Independence of VNTR alleles defined by fixed bins.Genetics 130, 873–887.

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. DNA Typing Unit, Central Forensic Science Laboratory, 30 Gorachand Road, 700 014, Kolkata, India

    V. K. Kashyap, Richa Ashma, Sonali Gaikwad & R. Trivedi

  2. Anthropological Survey of India, 27 Jawaharlal Nehru Road, 700 016, Kolkata, India

    B. N. Sarkar

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  1. V. K. Kashyap
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  2. Richa Ashma
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  3. Sonali Gaikwad
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  4. B. N. Sarkar
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Correspondence to V. K. Kashyap.

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Kashyap, V.K., Ashma, R., Gaikwad, S. et al. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: Analysis based on 15 microsatellite markers. J Genet 83, 49–63 (2004). https://doi.org/10.1007/BF02715829

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  • DOI: https://doi.org/10.1007/BF02715829

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