Genetic Diversity, Molecular Phylogeny and Selection Evidence of Jinchuan Yak Revealed by Whole-Genome Resequencing

Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield and reproductive performance. However, information about their overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes is limited. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak was distinguished as an independent population among the domestic yak population. Linkage disequilibrium analysis showed that the decay rate of Jinchuan yak was the lowest in the domestic yak breeds, indicating that the degree of domestication and selection intensity of Jinchuan yak were higher than those of other yak breeds. Combined with archaeological data, we speculated that the origin of domestication of Jinchuan yak was about 6,000 years ago (4,000-10,000 years ago). The quantitative dynamics of population growth history in Jinchuan yak was similar to that of other breeds of domestic and wild yaks but was closer to that of the wild yak. No significant gene exchange between Jinchuan and other domestic yaks occurred. Compared with other domestic yaks, Jinchuan yak possessed 339 significantly and positively selected genes, several of which relate to physiological rhythm, histone and the excellent production characters of Jinchuan yak. Our results provide a basis for the discovery of the evolution, molecular origin, and unique traits of Jinchuan yak.