Paternal Lineage and Genetic Diversity of Jiuzhi Yaks Revealed by Y-Chromosome SRY Sequencing

Yak husbandry on the Qinghai–Tibetan Plateau relies on genetically resilient sire lines, yet the paternal ancestry of the locally prominent Jiuzhi breed has never been quantified. To resolve this gap, a 690 bp fragment of the Y chromosomal SRY gene was sequenced in 117 males spanning Jiuzhi (n = 12) and five neighboring Qinghai breeds and compared with three single individual public records that represent Qinghai Plateau, Tianzhu White, and Wild yaks. Alignment, haplotype calling, diversity indices, F_ST differentiation, AMOVA, multidimensional scaling, and TCS network analysis were performed. Thirty-two haplotypes were recovered; Jiuzhi yaks possessed twelve, and six of them had private alleles. Mean A + T content was 53.8%. Haplotype diversity was highest in Qinghai Plateau, Tianzhu White and Wild yaks and lowest in Larima yaks, while Jiuzhi diversity resembled that of Huanhu. Pairwise F_ST values indicated negligible differentiation between Jiuzhi and either Qinghai Plateau or Yushu yaks (F_ST ≈ 0) but pronounced divergence from Tianzhu White and Wild yaks (F_ST ≈ 0.97–0.99). AMOVA attributed 90.7% of molecular variance to among-breed differences, and multidimensional scaling clustered Jiuzhi with Jinchuan, Yushu and Huanhu. Network topology resolved two patrilineal clades, confirming dual paternal origins for Jiuzhi yaks. These data provide the first quantitative baseline for sire selection and conservation of Jiuzhi yaks and highlight close affinities with adjacent plateau breeds. Limitations include the use of single individual public sequences for Qinghai Plateau, Tianzhu White and Wild yaks (employed solely as phylogenetic anchors) and reliance on a single Y-linked locus; broader sampling and multilocus approaches will refine within-breed estimates.