Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep
Deyin Zhang, 兰州大学草地农业科技学院, 草地农业生态系统国家重点实验室, 农业农村部草牧业创新重点实验室, 草地农业教育部工程研究中心, 兰州大学草业科学实验教学中心, 甘肃 兰州730020, 中国, Xiaoxue Zhang, Fadi Li, Lvfeng Yuan, Xiaolong Li, Yukun Zhang, Yuan Zhao, Liming Zhao, Jiang-Hui Wang, Dan Xu, Jiangbo Cheng, Xiaobin Yang, Wenxin Li, Changchun Lin, Bubo Zhou, Weimin Wang, 甘肃农业大学动物科技学院, 甘肃 兰州730070, 中国, 甘肃省绵羊育种与繁殖生物技术工程实验室, 甘肃 民勤733300, 中国, 中国科学院兰州兽医研究所, 甘肃 兰州730046, 中国
Abstract
The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds, African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group, while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including <i>IFI44</i> and <i>IFI44L</i> genes and <i>PANK2</i> and <i>RNF24</i> genes, associated with immune response and visual function. Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation, energy metabolism, and growth development. Furthermore, the <i>IFI44</i> and <i>IFI44L</i> genes showed a common selection signature in the genomes of 30 domesticated sheep breeds. The <i>IFI44</i> c. 54413058 C>G mutation was selected for genotyping and population genetic validation. Results showed that the <i>IFI44</i> polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.