Skip to main content
Research article - Peer-reviewed, 2022

Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci

Lv, Feng-Hua; Cao, Yin-Hong; Liu, Guang-Jian; Luo, Ling-Yun; Lu, Ran; Liu, Ming-Jun; Li, Wen-Rong; Zhou, Ping; Wang, Xin-Hua; Shen, Min; Gao, Lei; Yang, Jing-Quan; Yang, Hua; Yang, Yong-Lin; Liu, Chang-Bin; Wan, Peng-Cheng; Zhang, Yun-Sheng; Pi, Wen-Hui; Ren, Yan-Ling; Shen, Zhi-Qiang;
Show more authors

Abstract

Domestic sheep and their wild relatives harbor substantial genetic variants that can form the backbone of molecular breeding, but their genome landscapes remain understudied. Here, we present a comprehensive genome resource for wild ovine species, landraces and improved breeds of domestic sheep, comprising high-coverage (similar to 16.10x) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, similar to 121.2 million single nucleotide polymorphisms, similar to 61 million of which are novel. Some display significant (P < 0.001) differences in frequency between wild and domestic species, or are private to continent-wide or individual sheep populations. Retained or introgressed wild gene variants in domestic populations have contributed to local adaptation, such as the variation in the HBB associated with plateau adaptation. We identified novel and previously reported targets of selection on morphological and agronomic traits such as stature, horn, tail configuration, and wool fineness. We explored the genetic basis of wool fineness and unveiled a novel mutation (chr25: T7,068,586C) in the 3 '-UTR of IRF2BP2 as plausible causal variant for fleece fiber diameter. We reconstructed prehistorical migrations from the Near Eastern domestication center to South-and-Southeast Asia and found two main waves of migrations across the Eurasian Steppe and the Iranian Plateau in the Early and Late Bronze Ages. Our findings refine our understanding of genome variation as shaped by continental migrations, introgression, adaptation, and selection of sheep.

Keywords

whole-genome sequences; genetic diversity; adaptive introgression; genetic selection; agronomic traits; migration

Published in

Molecular Biology and Evolution
2022, volume: 39, number: 2, article number: msab353

Authors' information

Lv, Feng-Hua
China Agricultural University
Cao, Yin-Hong
Chinese Academy of Sciences
Liu, Guang-Jian
Novogene Bioinformatics Institute
Luo, Ling-Yun
China Agricultural University
Lu, Ran
China Agricultural University
Liu, Ming-Jun
Xinjiang Acad Anim Sci
Li, Wen-Rong
Xinjiang Acad Anim Sci
Zhou, Ping
Xinjiang Acad Agr and Reclamat Sci
Wang, Xin-Hua
Xinjiang Acad Agr and Reclamat Sci
Shen, Min
Xinjiang Acad Agr and Reclamat Sci
Gao, Lei
Xinjiang Acad Agr and Reclamat Sci
Yang, Jing-Quan
Xinjiang Acad Agr and Reclamat Sci
Yang, Hua
Xinjiang Acad Agr and Reclamat Sci
Yang, Yong-Lin
Xinjiang Acad Agr and Reclamat Sci
Liu, Chang-Bin
Xinjiang Acad Agr and Reclamat Sci
Wan, Peng-Cheng
Xinjiang Acad Agr and Reclamat Sci
Zhang, Yun-Sheng
Xinjiang Acad Agr and Reclamat Sci
Pi, Wen-Hui
Xinjiang Acad Agr and Reclamat Sci
Ren, Yan-Ling
Shandong Binzhou Acad Anim Sci and Vet Med
Shen, Zhi-Qiang
Shandong Binzhou Acad Anim Sci and Vet Med
Show more authors

Sustainable Development Goals

SDG2 Zero hunger

UKÄ Subject classification

Evolutionary Biology

Publication Identifiers

DOI: https://doi.org/10.1093/molbev/msab353

URI (permanent link to this page)

https://res.slu.se/id/publ/115458