Y-Chromosome SNPs Reveal Paternal Lineages and Candidate Circadian-Regulatory Variation in Indian YaksY-Chromosome SNPs Reveal Paternal Lineages and Candidate Circadian-Regulatory Variation in Indian Yaks

Yak (Bos grunniens), an economically and culturally important bovine species, is widely regarded as the lifeline of the Himalayan region. However, Indian yak populations remain comparatively understudied, with limited genomic resources to support conservation and genetic improvement. The mammalian Y chromosome, owing to its paternal inheritance, reduced recombination, and distinct evolutionary dynamics, provides a powerful framework for resolving male lineages and male-linked adaptation. In this study, we profiled Y-chromosome–specific variation in four yak populations—Arunachali, Himachali, Ladakhi, and Chinese Jinchuan—using whole-genome resequencing. We identified 274,828, 243,143, 283,774, and 194,228 Y-linked SNPs, respectively. Across populations, SNPs were most abundant in intergenic regions, followed by intronic regions; Jinchuan yak showed fewer SNPs, consistent with reduced diversity expected under intensive selective breeding. The transition/transversion (Ts/Tv) ratios were 1.57, 1.67, 1.55, and 1.99 for Arunachali, Himachali, Ladakhi, and Jinchuan yaks, respectively. Functional annotation using SnpEff indicated that most variants in Indian yaks occur in non-coding regions, while gene-based analyses highlighted key loci including ASMT, ASMTL, and SRY. Notably, ASMT and ASMTL participate in the melatonin biosynthesis pathway, implicating Y-linked (or PAR-adjacent) variation as candidate contributors to circadian regulation, a trait potentially relevant to adaptation under extreme high-altitude photoperiods. Finally, LD pruning retained only ~20% of SNPs, demonstrating that standard pruning parameters can substantially reshape Y-chromosome datasets and should be selected carefully to avoid loss of informative loci. Overall, this first Y-chromosome SNP resource for Indian yaks establishes a foundation for paternal haplotyping and population-genetic studies and motivates functional investigations into Y-linked contributions to chronobiological and high-altitude adaptation.