Genomic divergence reveals unique populations among Indian Yaks

M. S. Tantia,Jayakumar Sivalingam,M. R. Vineeth,S. K. Niranjan,I. D. Gupta,T. Surya,Karanveer Singh,S. P. Dixit,D. Ravikumar

doi:10.1038/s41598-020-59887-3

M. S. Tantia, Jayakumar Sivalingam + Show 7 more

Open Access

https://doi.org/10.1038/s41598-020-59887-3

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Abstract

The present study focused upon identification of genome-wide SNPs through the reduced representation approach and to study the genomic divergence of the Indian yak populations. A total of 80 samples belonging to Arunachali yak (N = 20), Himachali yak (N = 20), Ladakhi yak (N = 20) and Sikkimi yak (N = 20) of India were used in the study. The results of the study revealed a total of 579575 high quality SNPs along with 50319 INDELs in the Indian yaks. The observed heterozygosity was found to be high in Himachali yak, followed by Arunachali yak, Ladakhi yak and Sikkimi yaks. The Sikkimi yaks was found to be genetically distant, followed by Ladakhi yaks which was observed to have some few individuals from Arunachali and Himachali yaks. Arunachali and Himachali yaks are found to get clustered together and are genetically similar. The study provides evidence about the genomic diversity in the Indian yak populations and information generated in the present study may help to formulate a suitable breeding plan for endangered Indian yaks. Moreover, the unique yak populations identified in the study will further help to focus attention for future characterization and prioritization of the animals for conservation purposes through the ddRAD approach.

Highlights

The present study focused upon identification of genome-wide SNPs through the reduced representation approach and to study the genomic divergence of the Indian yak populations
Indian yaks are classified into Arunachali yak, Himachali yak, Ladakhi yak and Sikkimi yak based upon the geographical area inhabitation and so far, only Arunachali yak has been described as a breed in India
The SNPs genotyped by this method could be used for studying genetic diversity, genetic introgression[6], QTL mapping, genomic selection[7,8], genome-wide association studies (GWAS)[9], population studies and identification of selective sweeps[10]

Summary

Introduction

The present study focused upon identification of genome-wide SNPs through the reduced representation approach and to study the genomic divergence of the Indian yak populations. The SNPs used in the array may not be geographically representative that results in ascertainment bias and inherently excludes detection of rare or population-specific variants[3], a major source of information for both population history and genotype-phenotype association. This may impair estimation of population parameters like diversity, population subdivision, recombination and the identification of causal mutations. In the present study, genome-wide SNPs identified through the reduced representation approach (ddRAD) were used to study genomic diversity as well the genetic polymorphism in the candidate genes responsible for high altitude adaptation in the Indian yak populations

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Results

Conclusion