Whole-genome resequencing reveals genetic diversity, population structure, and selection signatures in tibetan yak

The Tibetan yak is a keystone species in the Tibetan Plateau ecosystem. It serves as a vital source of livelihood for local herders and also represents a distinctive model for studying biological adaptation mechanisms to extreme high-altitude environments. The Xizang region harbors abundant genetic resources of yak. In recent years, superior genetic resources such as the Chawula yak (CWL), Jila yak (JL), and Niangya yak (NY) have been identified, showing unique germplasm characteristics. However, the genomic basis of their distinct genetic features and the differences among these populations have not been fully elucidated. To systematically elucidate the germplasm specificity, genetic structure characteristics of three yak populations, and their phylogenetic relationships with existing yak breeds/populations in the Xizang region, this study conducted whole-genome resequencing (WGRS) of CWL, JL, and NY. By integrating genomic data from 15 known yak populations, we performed a comprehensive analysis to clarify the genetic diversity, population structure, and phylogenetic position of these three groups within the Tibetan yak evolutionary framework. The study aims to identify candidate genes that may be associated with important traits, thereby providing a scientific basis for the conservation and sustainable utilization of yak genetic resources. We found that the CWL, JL, and NY exhibit richer genetic diversity, unique ancestral compositions, and a moderate level of genetic differentiation from other yak populations. Genetic structure and phylogenetic analyses showed that these three populations cluster into a distinct subclade with Yushu yak (YS) and wild yak (WY), while other domestic yak populations form a separate cluster. Further analysis indicated that CWL and NY were most closely related, while JL clustered with YS, which also contains WY ancestry. The genetic structure of yak populations in the Xizang region—including the CWL, JL, and NY populations—exhibits a distribution pattern that is not entirely geographically dependent, accompanied by complex patterns of gene flow between populations. Based on selection signal analysis ( F ST & P i ), we identified several candidate regulatory genes potentially involved in coat color formation ( KIF27 , MC1R , SLC24A5 , etc.), as well as meat production performance ( CP , ARPC2 , ATP1A2 , etc.). In addition, the study also revealed key pathways closely related to oxytocin, melanogenesis, neural development, growth and development, digestion and absorption, and immune regulation, which provided new clues for analyzing the mechanism of yak plateau adaptation and the genetic basis of economic traits. This study systematically revealed the population genetic structure and phylogenetic relationships of CWL, JL, and NY, identified candidate genes potentially associated with key traits, and demonstrating at the genomic level that these three groups possess unique genetic backgrounds and considerable breeding potential. These results provide valuable candidate genomic evidence to guide future selective breeding programs and functional validation studies.