Genetic Diversity Estimation and Genome-Wide Selective Sweep Analysis of the Bazhou Yak

The Bazhou yak, a major native meat yak breed in Xinjiang, China, is renowned for its fast growth rate, strong adaptability, and particularly high intramuscular fat (IMF) content. However, limited knowledge regarding its phylogenetic history and genomic composition has hindered its long-term conservation and utilization. This study evaluated the genetic diversity, population phylogenetics, and genome-wide selective sweep analysis (GWSA) of 100 newly obtained Bazhou yaks through genome resequencing, as well as 340 public yak genomes from nine other populations on the Qinghai-Tibet Plateau. The results revealed moderate diversity, lower genomic inbreeding levels, and rapid linkage disequilibrium (LD) decay in Bazhou yaks. Principal component analysis (PCA) and phylogenetic analysis showed a clear separation of Bazhou yaks from other yak populations, indicating the Bazhou yak as an independent genetic population. Furthermore, less genetic differentiation was found between the Bazhou yak and the Huanhu yak, while ADMIXTURE analysis revealed a common ancestral lineage between Bazhou yaks and Huanhu yaks, indicating an important genetic contribution of the Qinghai yak population to Bazhou yaks. The GWSA identified a total of 833 selected genes in Bazhou yaks using the top 5% interaction windows of both parameters (<i>F_ST</i>, <i>Pi</i> ratio, and XP-EHH). A significant number of these genes are related to fat synthesis and deposition, such as <i>MTOR</i>, <i>APOA1</i>, and <i>GPAT4</i>. In summary, this study sheds light on the phylogenetic status and distinctive genomic features of Bazhou yaks, which facilitates our understanding of the genetic basis of the IMF phenotype in Bazhou yaks.