Whole genome resequencing reveals Y-chromosome variants in yak: key insights into genetic diversity and population structure

Abstract Yak, an economically important bovine species considered as the lifeline of the Himalaya. Indeed, this gigantic bovine is neglected because of the scientific intervention for its conservation as well as research documentation for a long time. The Y chromosome is widely recognized for its role in male traits, characterized by paternal inheritance, high mutation rate, and minimal recombination rate or reverse mutation. So, we investigated the Y-chromosome-specific variants in four yak populations namely, Arunachali, Himachali, Ladakhi, and Jinchuan through whole genome resequencing, we identified nearly 274828, 243143, 283774, and 194 228 SNPs, respectively. The intergenic regions held the highest proportion of SNPs, with Jinchuan yaks showing fewer SNPs due to intense selective breeding for reproductive performance and product quality. The Ts/Tv ratios were 1.57, 1.67, 1.55, and 1.99 for Arunachali, Himachali, Ladakhi, and Jinchuan yaks, respectively. SnpEff annotation indicated that most SNPs were intergenic, followed by intronic regions. Key genes identified included ASMT, ASMTL, and SRY, with significant roles in melatonin biosynthesis and male sex determination. Interestingly, we performed Linkage disequilibrium (LD) pruning, which retained only about 20% of SNPs, underscored the complexity of genetic analyses and highlighted the importance of careful LD criteria selection to avoid losing loci under selection. This pioneering mapping of Y-chromosome SNPs in yaks provides essential insights into their genetic landscape and underscores the critical need for precise LD pruning parameters to accurately assess genetic diversity and population differentiation.