Home About Browse Search
Svenska


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

Lv, Feng-Hua and Cao, Yin-Hong and Liu, Guang-Jian and Luo, Ling-Yun and Lu, Ran and Liu, Ming-Jun and Li, Wen-Rong and Zhou, Ping and Wang, Xin-Hua and Shen, Min and Gao, Lei and Yang, Jing-Quan and Yang, Hua and Yang, Yong-Lin and Liu, Chang-Bin and Wan, Peng-Cheng and Zhang, Yun-Sheng and Pi, Wen-Hui and Ren, Yan-Ling and Shen, Zhi-Qiang and Wang, Feng and Li, Jin-Quan and Salehian-Dehkordi, Hosein and Hehua, Eer and Liu, Yong-Gang and Chen, Jian-Fei and Wang, Jian-Kui and Deng, Xue-Mei and Esmailizadeh, Ali and Dehghani-Qanatqestani, Mostafa and Charati, Hadi and Nosrati, Maryam and Stepanek, Ondrej and Rushdi, Hossam E. and Olsaker, Ingrid and Curik, Ino and Gorkhali, Neena A. and Paiva, Samuel R. and Caetano, Alexandre R. and Ciani, Elena and Amills, Marcel and Weimann, Christina and Erhardt, Georg and Amane, Agraw and Mwacharo, Joram M. and Han, Jian-Lin and Hanotte, Olivier and Periasamy, Kathiravan and Johansson, Anna Maria and Hallsson, Jon H. and Kantanen, Juha and Coltman, David W. and Bruford, Michael W. and Lenstra, Johannes A. and Li, Meng-Hua (2022). Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci. Molecular Biology and Evolution. 39 :2 , msab353
[Research article]

[img] PDF
13MB

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.

Authors/Creators:Lv, Feng-Hua and Cao, Yin-Hong and Liu, Guang-Jian and Luo, Ling-Yun and Lu, Ran and Liu, Ming-Jun and Li, Wen-Rong and Zhou, Ping and Wang, Xin-Hua and Shen, Min and Gao, Lei and Yang, Jing-Quan and Yang, Hua and Yang, Yong-Lin and Liu, Chang-Bin and Wan, Peng-Cheng and Zhang, Yun-Sheng and Pi, Wen-Hui and Ren, Yan-Ling and Shen, Zhi-Qiang and Wang, Feng and Li, Jin-Quan and Salehian-Dehkordi, Hosein and Hehua, Eer and Liu, Yong-Gang and Chen, Jian-Fei and Wang, Jian-Kui and Deng, Xue-Mei and Esmailizadeh, Ali and Dehghani-Qanatqestani, Mostafa and Charati, Hadi and Nosrati, Maryam and Stepanek, Ondrej and Rushdi, Hossam E. and Olsaker, Ingrid and Curik, Ino and Gorkhali, Neena A. and Paiva, Samuel R. and Caetano, Alexandre R. and Ciani, Elena and Amills, Marcel and Weimann, Christina and Erhardt, Georg and Amane, Agraw and Mwacharo, Joram M. and Han, Jian-Lin and Hanotte, Olivier and Periasamy, Kathiravan and Johansson, Anna Maria and Hallsson, Jon H. and Kantanen, Juha and Coltman, David W. and Bruford, Michael W. and Lenstra, Johannes A. and Li, Meng-Hua
Title:Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci
Series Name/Journal:Molecular Biology and Evolution
Year of publishing :2022
Volume:39
Number:2
Article number:msab353
Number of Pages:26
ISSN:0737-4038
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Evolutionary Biology
Keywords:whole-genome sequences, genetic diversity, adaptive introgression, genetic selection, agronomic traits, migration
URN:NBN:urn:nbn:se:slu:epsilon-p-115458
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115458
Additional ID:
Type of IDID
DOI10.1093/molbev/msab353
Web of Science (WoS)000767848900032
Alternative URL:https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab353/6459180
ID Code:27802
Faculty:VH - Faculty of Veterinary Medicine and Animal Science
Department:(VH) > Dept. of Animal Breeding and Genetics
Deposited By: SLUpub Connector
Deposited On:13 May 2022 06:50
Metadata Last Modified:13 May 2022 06:51

Repository Staff Only: item control page

Downloads

Downloads per year (since September 2012)

View more statistics

Downloads
Hits