Genomic characterization of Sangsang yak reveals its genetic divergence from other yak populations

The yak ( Bos grunniens ) is a representative domestic animal of the Qinghai-Tibet Plateau and surrounding high-altitude regions, primarily distributed at elevations above 3,000 m across the plateau and its adjacent alpine and subalpine zones. Yaks provide humans with diverse resources including meat, milk, hides, wool, and labour, serving as a vital livelihood and economic pillar for pastoralists on the plateau. They constitute an indispensable component of the local livestock economy. The Sangsang yak is an indigenous breed endemic to the Sangsang region of Tibet. This study aims to elucidate its population genetic structure and evolutionary relationships, which holds important implications for the conservation of breed resources and the exploitation of favorable traits. The PCA results revealed that Sangsang yak was separated from other yak populations in the first and second principal components and exhibited a relatively independent genetic structure, which was further supported by the NJ phylogenetic tree. While population structure indicates genetic divergence, the genome-wide outlier analyses did not yield regions passing strict multiple testing corrections. Therefore, all detected genomic outliers are defined as purely suggestive candidate regions. These loci may be related to potential adaptive characteristics of Sangsang yak, including high-altitude tolerance and immune adaptation. The KIT gene was identified as a shared suggestive candidate locus across all comparison groups. This finding raises the hypothesis that Sangsang yak may have unique immune-related adaptive characteristics. This study utilized an integrated approach of whole-genome sequencing combined with population genetic analyses to systematically investigate and clarify the population structure and evolutionary characteristics of the Sangsang yak. Although no genomic regions reached statistical significance after strict multiple testing corrections, we obtained multiple suggestive outliers that may be associated with high-altitude tolerance and immune function. This research provides critical genomic insights for the scientific conservation and rational exploitation of Sangsang yak genetic resources.