Whole-Genome Resequencing Reveals the Uniqueness of Subei Yak

Abstract Background and aim: Subei yak is an essential local yak genetic resource recently discovered in the Gansu Province. Subei yak is a meat-and-milk breed with stable population genetic performance and high fecundity. However, its population structure and genetic diversity are yet to be reported. Therefore, this study aimed to identify molecular markers of Subei yak genome by whole-genome resequencing, and to analyze the population structure and genetic diversity of Subei yak.Results: This study screened 12,079,496 single nucleotide polymorphism (SNP) molecular markers in the Subei yak genome using whole-genome resequencing technology. Of these SNPs, 32.09% were located in the intronic region. The principal component analysis, phylogenetic analysis, and population structure analysis revealed that the Subei yak belonged to an independent group in the domestic yak population. The positive selection genes were annotated by comparing the Subei yak with other domestic yaks. The functional enrichment analysis showed that Subei yaks possessed prominent selection characteristics in terms of external environment perception, hypoxia adaptation, and muscle development. Further, Subei yak showed excellent muscle fat deposition and meat quality traits. Conclusions: Thus, this study will serve as a reference for discovering population structure, genetic evolution, and other unique traits of Subei yak and for expanding the genetic variation catalog of yaks.