Whole-genome resequencing reveals genomic characteristics and candidate genomic regions potentially associated with local adaptation of Leiwuqi yak (Bos grunniens)
Leiwuqi yak is an important indigenous yak genetic resource distributed in eastern Tibet, but its genomic characteristics and adaptive evolutionary features remain poorly understood. In this study, whole-genome resequencing was performed on 110 Leiwuqi yaks, and these data were integrated with publicly available genomic data from other domestic and wild yak populations to investigate the genetic diversity, population structure, and candidate genomic regions potentially associated with local adaptation of Leiwuqi yak. After quality control and variant filtering, a total of 19,966,141 high-quality SNPs were identified across all samples. Most SNPs were located in intronic and intergenic regions, with a transition/transversion ratio of 2.47. Although sequencing depth differed between newly sequenced (3.87×) and public (9.04×) data, all samples were processed through a unified pipeline with stringent filtering criteria. Genetic diversity analyses showed that Leiwuqi yak retained relatively abundant nucleotide diversity, whereas runs of homozygosity and genomic inbreeding coefficient analyses suggested possible effects of local isolation or recent inbreeding. Population structure analyses based on principal component analysis and ADMIXTURE revealed that Chinese domestic yak populations shared a broadly similar genetic background with wild yak, whereas Indian yak exhibited clear genetic differentiation. Although Leiwuqi yak did not form a completely independent genetic cluster at the genome-wide level, selective sweep analysis identified localized genomic differentiation in this population. A total of 466 protein-coding genes were detected within candidate selected regions. Functional enrichment analyses showed that these genes were mainly associated with the Wnt signaling pathway, NF-kappa B signaling pathway, pathways in cancer, light absorption, and receptor-mediated endocytosis. These findings suggest that developmental regulation, immune and stress responses, environmental perception, and cellular homeostasis may contribute to the adaptive differentiation of Leiwuqi yak. Overall, this study provides new genomic evidence for understanding the genetic uniqueness and adaptive evolution of Leiwuqi yak and offers a scientific basis for its conservation and sustainable utilization.