Genetic Diversity, Adaptation, Wild Introgression, and Coat Color Mutation of Golden Yak

ABSTRACT The golden yak lives on the Qinghai‐Xizang Plateau with a golden coat and adapts to high altitudes and strong ultraviolet environment. The golden coat is a prominent phenotype in many domesticated species, contributing to the breeding of new strains and the promotion of national culture. However, the genetic basis underlying the phenotype of the golden yak remains unknown. This study collected 21 golden yak samples from the Yushu population in Qinghai Province (Golden Yushu yak) and 17 samples from the Jila population in the Xizang Autonomous Region (Golden Jila yak) and combined 45 published data of black, white, and wild yak. The genetic diversity of the golden yak was high, but the genomic runs of homozygosity coverage revealed inbreeding. Selective sweep analysis of Golden Jila yak highlighted the ABCC12 , MARK1 , FANCA , and TCF25 genes, which are involved in energy metabolism, hypoxia adaptation, and reproduction. Moreover, some genes involved in immune response and adaptation were of wild yak origin. In addition, an F ST , GWAS, and candidate gene sequencing revealed the previously reported MC1R mutation p.Gln34*, CM016709.1: c.100C > T, which is homozygous or heterozygous in all golden yak but not in black, white, or wild yak. The mutation took place in an MC1R sequence that originated from wild yak. Transcriptome analysis of skin samples revealed substantial differences between golden and black yak with a clear decrease in MC1R expression in golden yak.