The Yushu yak is one of China’s distinctive yak breeds, primarily distributed in the Yushu Tibetan Autonomous Prefecture of Qinghai Province and its surrounding areas. Yushu yaks are not only economically and culturally significant but also play a crucial role in protecting the ecosystem of the Qinghai-Tibet Plateau and promoting sustainable development. However, there are no clear records regarding the ancestry, population structure, and unique traits of Yushu yaks. Therefore, this study conducted an analysis of genetic diversity, population structure, and selection signals in Yushu yak populations, aiming to provide references for the conservation and utilization of the breed genetic resources. The results of the analysis showed that the Yushu yak population has high genetic diversity and low inbreeding coefficients, indicating a stable genetic structure. Population structure analysis revealed that the Yushu yak lineage is unique, with limited gene flow between domestic and wild yaks. Functional enrichment analysis of positively selected genes in Yushu yaks indicated prominent selection features related to growth and development as well as energy metabolism. Additionally, we classified the Yushu yak breeding bulls into family lineages based on kinship, which is essential for improving the efficiency of utilizing genetic resources and scientifically managing the population.

This study unveils the unique origins, evolution, and genetic variations of the Yangba cattle, an endangered breed in China, through a comparative genomic analysis involving 202 individuals from 21 domestic and international breeds. Genetic component analysis revealed that the Yangba cattle comprise four ancestral lineages: Eurasian taurine (18%), East Asian taurine (26%), Chinese indicine (39%), and Indian indicine (17%). Their high genetic diversity and low inbreeding coefficient set them apart significantly from mainstream commercial breeds. Gene introgression analysis indicated that the influx of genetic material from East Asian taurine has enhanced the Yangba cattle’s adaptability to environmental stress, while the introgression from Chinese indicine has endowed them with unique advantages in muscle development and tissue repair. A genome-wide selection scan identified strong positive selection signals for genes such as ABCC2, which is involved in immune regulation, and NCOA3, which plays a role in growth regulation, in the Yangba cattle. This study systematically elucidates, for the first time, the composite ancestral composition and mechanisms of adaptive evolution in Yangba cattle. These findings offer critical insights into the conservation and sustainable utilization of endangered cattle resources and underscore the importance of implementing effective breeding programs.