Cattle microsatellite markers successfully established diversity status of Arunachali yak (only registered yak breed of India)

HIMANI SHARMA; REKHA SHARMA; SONIKA AHLAWAT; P J DAS; S JAYAKUMAR; M S TANTIA

doi:10.56093/ijans.v88i9.83553

Authors

HIMANI SHARMA Senior Research Fellow, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
REKHA SHARMA Principal Scientist, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
SONIKA AHLAWAT Scientist, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
P J DAS ICAR-National Research Center on Pig, Rani, Guwahati, Asom
S JAYAKUMAR Scientist, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
M S TANTIA Principal Scientist, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India

https://doi.org/10.56093/ijans.v88i9.83553

Keywords:

Arunachali yak, Bottleneck, Cattle microsatellite, Genetic diversity, India, Polymorphism

Abstract

Yak diversity of the country has remained predominantly unexplored for a long time. Among the 169 registered livestock breeds of India, the sole representation from yak genetic resources is the Arunachali yak. This study for the first time investigated genetic diversity status of Arunachali yak using 26 bovine microsatellite markers. All the markers recommended for cattle except one (ILSTS05) amplified with yak genome. Allelic genotype pattern overlapped between yak and cattle across 25 microsatellite loci and a total of 233 alleles were detected in yak. The number of observed alleles across loci ranged from 3–16 with an average of 9.32±0.70. Observed heterozygosity (0.552±0.04) was less than the expected heterozygosity (0.648±0.035) pointing towards heterozygote deficiency in the population. In addition, positive value of FIS index (0.143±0.043) suggested considerable inbreeding. There was no indication of a recent bottleneck event in this population based on heterozygosity excess tests as well as mode-shift analysis. In summary, bovine microsatellite markers proved to be a valuable tool for characterization of Indian yak population. Arunachali yak represents an interesting gene pool with moderate level of diversity. Inbreeding in population calls for sincere efforts to formulate breeding policy so that this precious germplasm is conserved with substantial genetic diversity.

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References

th Livestock Census. 2012. All India Report. Ministry of Agriculture, Department of Animal Husbandry, Dairying and Fisheries, Krishi Bhawan, New Delhi.

Barcaccia G, Felicetti M, Galla G, Capomaccio S, Cappelli K, Albertini E, Buttazzoni L, Pieramati C, Silvestrelli M and Supplizi A V. 2013. Molecular analysis of genetic diversity, population structure and inbreeding level of the Italian Lipizzan horse. Livestock Sciences 151: 124–31. DOI: https://doi.org/10.1016/j.livsci.2012.11.022

Cornuet J M and Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001–14. DOI: https://doi.org/10.1093/genetics/144.4.2001

Das P J, Deori S S, Kumar J and Deb S M. 2016. Yak Genetic Resources of India Arunachali Yak. ICAR-National Research Center on Yak, Dirang, Arunachal Pradesh.

Dorji T, Goddard M, Perkins J, Robinson N and Roder W. 2002. Genetic diversity in Bhutanese yak (Bos grunniens) population using microsatellite markers. Proceedings of the Third International Congress on Yak, Lhasa, China, 4–9 September. pp. 197–201. International Livestock Research Institute (ILRI), Nairobi.

Hanotte O. 2000. Cattle microsatellite markers for amplification of polymorphic loci in Asian Bovidae. Proceedings of the 4th Global Conference on Conservation of Domestic Animal Genetic Resources, Kathmandu, Nepal, 17–21 August 1998. pp. 47–79.

ICAR-National Bureau of Animal Genetic Resources. http:// www.nbagr.res.in.

Luikart G, Allendorf F W, Cornuet J M and Sherwin W B. 1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity 89: 238– 47. DOI: https://doi.org/10.1093/jhered/89.3.238

Luikart G. 1997. ‘Usefulness of molecular markers for detecting population bottlenecks and monitoring genetic change’. Ph.D. Thesis, University of Montana, Missoula, USA. Miller D J. 1990. Grassland of the Tibetan Plateau. Rangelands 12: 159–63.

Miller D J and Steane D E. 1997. Conclusions. Proceedings of a Workshop on Conservation and Management of Yak Genetic Diversity. (Eds) Miller D G, Craig S R and Rana G M. pp 191–209. ICIMOD, Kathmandu, Nepal, 29–31 October 1996. DOI: https://doi.org/10.53055/ICIMOD.227

Minqiang Wang, Weigend S, Barre-Dirie A, Carnwath J W, Zhonglin L and Niemann H. 2003. Analysis of two Chinese yak (Bos grunniens) populations using bovine microsatellite primers. Journal of Animal Breeding and Genetics 120(4): 237–44. DOI: https://doi.org/10.1046/j.1439-0388.2003.00391.x

Nguyen T T, Genini S, Menetrey F, Malek M, Vogeli P, Goe M R and Stranzinger G. 2005. Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens). Animal Genetics 36(6): 484–89. DOI: https://doi.org/10.1111/j.1365-2052.2005.01357.x

Olsen S J. 1991. Confused yak taxonomy and evidence of domestication. Illinois State Museum Scientific Papers 23: 387–93.

Peakall R and Smouse P E. 2008. A heterogeneity test for finescale genetic structure. Molecular Ecology Notes 17: 3389–3400. DOI: https://doi.org/10.1111/j.1365-294X.2008.03839.x

Putman A I and Carbone I. 2014. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecology and Evolution 4: 4399–4428. DOI: https://doi.org/10.1002/ece3.1305

Qi X B. 2004. Genetic Diversity, Differentiation and Relationship of Domestic yak Populations—a Microsatellite and Mitochondrial DNA Study. p. 250. Lanzhou University, Lanzhou, P.R. China.

Ritz L R. 1997. ‘Genetic diversity in the tribe Bovini.’ PhD Dissertation, University of Berne, Berne, Switzerland. Ritz L R, Glowatzki-Mullis M L, MacHugh D E and Gaillard C. 2000. Phylogenetic analysis of the tribe Bovini using microsatellites. Animal Genetics 31: 178–85. DOI: https://doi.org/10.1046/j.1365-2052.2000.00621.x

Sambrook J, Fritsch E F and Maniatis P. 1989.Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York.

Sharma R, Kumar B, Arora R, Ahlawat S, Mishra A K and Tantia M S. 2016. Genetic diversity estimates point to immediate efforts for conserving the endangered Tibetan sheep of India. Meta Gene 8: 14–20. DOI: https://doi.org/10.1016/j.mgene.2016.01.002

Sharma R, Maitra A, Singh P K and Tantia M S. 2013. Genetic diversity and relationship of cattle populations of East India: distinguishing lesser known cattle populations and established breeds based on STR markers. Springerplus 2: 359–68. DOI: https://doi.org/10.1186/2193-1801-2-359

Xuebin Q, Jianlin H, Lkhagva B, Chekarova I, Badamdorj D, Rege J E and Hanotte O. 2005. Genetic diversity and differentiation of Mongolian and Russian yak populations. Journal of Animal Breeding and Genetics 122: 117–26. DOI: https://doi.org/10.1111/j.1439-0388.2004.00497.x

Xuebin Q. 2004. ‘Genetic diversity, differentiation and relationship of domestic Yak populations: a microsatellite and mitochondrial DNA study.’ PhD Dissertation, Lanzhou University, Lanzhou, China. pp. 96.

Yeh F C, Yang R C and Boyle T. 1999. POPGENE version 1.31, Microsoft Window-based free Software for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada.