Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

Abstract

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

Keywords:

• Yak
• whole genome sequencing
• genomic variants
• adaptation

Acknowledgements

The authors thank Indian Council of Agricultural Research, New Delhi and Director, National Bureau of Animal Genetic Resources, Karnal for providing the financial assistance for this study. Special thanks are due to Dr. PJ Das, ICAR-NRC Pig for providing yak samples.

Author contributions

R.K.V. planned and designed the study with inputs from A.K. and M.D. S.K.N and S.A. provided yak DNA for WGS. A.K. and M.D. generated the WGS data. A.K. analyzed the WGS data and drafted the manuscript. S.K.N., R.A., A.Kour, and MA revised the manuscript with inputs from all authors.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The raw data and .vcf file have been submitted to Sequence Read Archive (PRJNA803425) and European Variant Archive (PRJEB50815), respectively.