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    Whole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important loci

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    Authors
    Feng-Hua Lv
    Yin-Hong Cao
    Guang-Jian Liu
    Ling-Yun Luo
    Ran Lu
    Ming-Jun Liu
    Wen-Rong Li
    Ping Zhou
    Xin-Hua Wang
    Min Shen
    Lei Gao
    Jing-Quan Yang
    Hua Yang
    Yong-Lin Yang
    Chang-Bin Liu
    Peng-Cheng Wan
    Yun-Sheng Zhang
    Wen-Hui Pi
    Yan-Ling Ren
    Zhi-Qiang Shen
    Feng Wang
    Yu-Tao Wang
    Jin-Quan Li
    Salehian-Dehkordi, H.
    Eer Hehua
    Yong-Gang Liu
    Jian-Fei Chen
    Jian-Kui Wang
    Xue-Mei Deng
    Esmailizadeh, A.
    Dehghani-Antezana, M.
    Charati, H.
    Nosrati, M.
    Štěpánek, O.
    Rushdi, H.E.
    Olsaker, I.
    Curik, I.
    Gorkhali, N.A.
    Paiva, S.R.
    Caetano, A.R.
    Ciani, E.
    Amills, M.
    Weimann, C.
    Erhardt, G.
    Amane, A.
    Mwacharo, Joram M.
    Han Jianlin
    Hanotte, Olivier H.
    Periasamy, K.
    Johansson, A.M.
    Hallsson, J.H.
    Kantanen, J.
    Coltman, D.W.
    Bruford, M.W.
    Lenstra, J.A.
    Meng-Hua Li
    Date Issued
    2022-02
    Date Online
    2021-12
    Language
    en
    Type
    Journal Article
    Review status
    Peer Review
    ISI journal
    Accessibility
    Open Access
    Usage rights
    CC-BY-4.0
    Metadata
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    Citation
    Feng-Hua Lv, Yin-Hong Cao, Guang-Jian Liu, Ling-Yun Luo, Ran Lu, Ming-Jun Liu, Wen-Rong Li, Ping Zhou, Xin-Hua Wang, Min Shen, Lei Gao, Jing-Quan Yang, Hua Yang, Yong-Lin Yang, Chang-Bin Liu, Peng-Cheng Wan, Yun-Sheng Zhang, Wen-Hui Pi, Yan-Ling Ren, Zhi-Qiang Shen, Feng Wang, Yu-Tao Wang, Jin-Quan Li, Hosein Salehian-Dehkordi, Eer Hehua, Yong-Gang Liu, Jian-Fei Chen, Jian-Kui Wang, Xue-Mei Deng, Ali Esmailizadeh, Mostafa Dehghani-Qanatqestani, Hadi Charati, Maryam Nosrati, Ondřej Štěpánek, Hossam E Rushdi, Ingrid Olsaker, Ino Curik, Neena A Gorkhali, Samuel R Paiva, Alexandre R Caetano, Elena Ciani, Marcel Amills, Christina Weimann, Georg Erhardt, Agraw Amane, Joram M Mwacharo, Jian-Lin Han, Olivier Hanotte, Kathiravan Periasamy, Anna M Johansson, Jón H Hallsson, Juha Kantanen, David W Coltman, Michael W Bruford, Johannes A Lenstra, Meng-Hua Li. 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.
    Permanent link to cite or share this item: https://hdl.handle.net/10568/116684
    DOI: https://doi.org/10.1093/molbev/msab353
    Abstract/Description
    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 (∼16.10×) whole genomes of 810 samples from 7 wild species and 158 diverse domestic populations. We detected, in total, ∼121.2 million single nucleotide polymorphisms, ∼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.
    CGIAR Author ORCID iDs
    Olivier Hanottehttps://orcid.org/0000-0002-2877-4767
    Joram Mwacharohttps://orcid.org/0000-0001-6981-8140
    CGIAR Action Areas
    Resilient Agrifood Systems
    CGIAR Impact Areas
    Poverty reduction, livelihoods and jobs
    CGIAR Initiatives
    Sustainable Animal Productivity
    Other CGIAR Affiliations
    Livestock
    AGROVOC Keywords
    genomes; genetics; animal breeding; sheep; small ruminants; loci
    Subjects
    ANIMAL BREEDING; GENETICS; SHEEP; SMALL RUMINANTS;
    Organizations Affiliated to the Authors
    China Agricultural University; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Novogene Bioinformatics Institute, China; Xinjiang Academy of Animal Science; Shandong Binzhou Academy of Animal Science and Veterinary Medicine, China; Nanjing Agricultural University; Kashi University; Inner Mongolia Agricultural University; Ningxia Academy of Agriculture and Forestry Sciences, China; Yunnan Agricultural University; Shahid Bahonar University of Kerman; Payame Noor University; State Veterinary Institute Jihlava; Cairo University; Norwegian University of Life Sciences; University of Zagreb; Nepal Agricultural Research Council; Empresa Brasileira de Pesquisa Agropecuária; Università degli Studi di Bari Aldo; Universitat Autònoma de Barcelona; Justus-Liebig-University Gießen; Addis Ababa University; International Livestock Research Institute; International Center for Agricultural Research in the Dry Areas; Chinese Academy of Agricultural Sciences; University of Edinburgh; University of Nottingham; International Atomic Energy Agency; Swedish University of Agricultural Sciences; Agricultural University of Iceland; Natural Resources Institute, Finland; University of Alberta; Cardiff University; Utrecht University
    Investors/sponsors
    National Natural Science Foundation of China; CGIAR Trust Fund; Chinese Academy of Sciences
    Collections
    • CGIAR Initiative on Sustainable Animal Productivity [567]
    • CRP Livestock genetics flagship [192]
    • ICARDA Articles in Journals [257]
    • ILRI articles in journals [6834]
    • ILRI livestock genetics program outputs [914]

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