Whole genome resequencing identifies genomic regions associated with fat-tail traits of sheep (Ovis aries)

The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. To characterize the origin, genetic diversity, and phylogeographic structure of wild and domestic sheep, we here analyzed the whole genomes of 247 sheep from 66 phenotypically and geographically representative domestic breeds and five wild species. Our results showed that domestic sheep display an east-to-west cline of the populations and the split among ‘East’ and ‘West’ populations occurs between 8.3~9.3 kyr. Moreover, we found no clear separation or geographical structuring existed between breeds in each continent-scale or among Chinese sheep populations due to human-mediated long-term gene flow induced by the human migration, commercial trade and extensive transport of sheep. We found that Mongolia and Kazakh populations in China are comparatively close to each other and Yunan is the most remote population exhibits the lowest nucleotide diversity. We also discovered many potential selective sweep regions associated with fat-tailed phenotype in modern sheep related to adipogenesis (PDGFD and BMP2) and formation of body structures (HOX gene family and VRTN). These findings substantially expand the catalogue of genetic variants in wild and domestic sheep and reveal new insights into the evolutionary history and domestic traits of fat-tailed sheep.