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.

家羊（Ovis aries）自全球范围内被驯化以来，一直是兼具经济与文化重要性的农场动物物种。为阐明野生与家羊的起源、遗传多样性及系统地理结构，本研究分析了来自66个表型与地理分布均具代表性的家羊品种，以及5个野生羊种的247份全基因组数据。研究结果显示，家羊种群呈现自东向西的种群渐变分布，“东”“西”两大种群的分化发生于距今8.3~9.3千年之间。此外，本研究未发现各大洲内部的家羊品种间，或是中国境内家羊种群间存在清晰的分化或地理结构，这一现象源于人类迁移、商业贸易及家羊大规模跨区域运输所介导的长期基因流。研究发现，中国境内的蒙古羊与哈萨克羊种群亲缘关系相对较近，而云南羊种群则是最为偏远的类群，其核苷酸多样性最低。本研究还在现代家羊中鉴定出诸多与肥尾表型相关的潜在选择性清除区域，这些区域涉及脂肪生成相关基因（PDGFD与BMP2）以及躯体结构形成相关基因（HOX基因家族与VRTN）。上述发现极大扩充了野生与家羊的遗传变异目录，并为肥尾羊的演化历史与驯化性状研究提供了新的认知。