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

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationChina Agricultural Universityen
cg.contributor.affiliationChinese Academy of Sciencesen
cg.contributor.affiliationUniversity of Chinese Academy of Sciencesen
cg.contributor.affiliationNovogene Bioinformatics Institute, Chinaen
cg.contributor.affiliationXinjiang Academy of Animal Scienceen
cg.contributor.affiliationShandong Binzhou Academy of Animal Science and Veterinary Medicine, Chinaen
cg.contributor.affiliationNanjing Agricultural Universityen
cg.contributor.affiliationKashi Universityen
cg.contributor.affiliationInner Mongolia Agricultural Universityen
cg.contributor.affiliationNingxia Academy of Agriculture and Forestry Sciences, Chinaen
cg.contributor.affiliationYunnan Agricultural Universityen
cg.contributor.affiliationShahid Bahonar University of Kermanen
cg.contributor.affiliationPayame Noor Universityen
cg.contributor.affiliationState Veterinary Institute Jihlavaen
cg.contributor.affiliationCairo Universityen
cg.contributor.affiliationNorwegian University of Life Sciencesen
cg.contributor.affiliationUniversity of Zagreben
cg.contributor.affiliationNepal Agricultural Research Councilen
cg.contributor.affiliationEmpresa Brasileira de Pesquisa Agropecuáriaen
cg.contributor.affiliationUniversità degli Studi di Bari Aldoen
cg.contributor.affiliationUniversitat Autònoma de Barcelonaen
cg.contributor.affiliationJustus Liebig University Giessenen
cg.contributor.affiliationAddis Ababa Universityen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationInternational Center for Agricultural Research in the Dry Areasen
cg.contributor.affiliationChinese Academy of Agricultural Sciencesen
cg.contributor.affiliationUniversity of Edinburghen
cg.contributor.affiliationUniversity of Nottinghamen
cg.contributor.affiliationInternational Atomic Energy Agencyen
cg.contributor.affiliationSwedish University of Agricultural Sciencesen
cg.contributor.affiliationAgricultural University of Icelanden
cg.contributor.affiliationNatural Resources Institute, Finlanden
cg.contributor.affiliationUniversity of Albertaen
cg.contributor.affiliationCardiff Universityen
cg.contributor.affiliationUtrecht Universityen
cg.contributor.crpLivestock
cg.contributor.donorNational Natural Science Foundation of Chinaen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.donorChinese Academy of Sciencesen
cg.contributor.initiativeSustainable Animal Productivity
cg.creator.identifierOlivier Hanotte: 0000-0002-2877-4767
cg.creator.identifierJoram Mwacharo: 0000-0001-6981-8140
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1093/molbev/msab353en
cg.isijournalISI Journalen
cg.issn1537-1719en
cg.issue12en
cg.journalMolecular Biology and Evolutionen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriGENETICSen
cg.subject.ilriSHEEPen
cg.subject.ilriSMALL RUMINANTSen
cg.subject.impactAreaPoverty reduction, livelihoods and jobs
cg.volume38en
dc.contributor.authorFeng-Hua Lven
dc.contributor.authorYin-Hong Caoen
dc.contributor.authorGuang-Jian Liuen
dc.contributor.authorLing-Yun Luoen
dc.contributor.authorRan Luen
dc.contributor.authorMing-Jun Liuen
dc.contributor.authorWen-Rong Lien
dc.contributor.authorPing Zhouen
dc.contributor.authorXin-Hua Wangen
dc.contributor.authorMin Shenen
dc.contributor.authorLei Gaoen
dc.contributor.authorJing-Quan Yangen
dc.contributor.authorHua Yangen
dc.contributor.authorYong-Lin Yangen
dc.contributor.authorChang-Bin Liuen
dc.contributor.authorPeng-Cheng Wanen
dc.contributor.authorYun-Sheng Zhangen
dc.contributor.authorWen-Hui Pien
dc.contributor.authorYan-Ling Renen
dc.contributor.authorZhi-Qiang Shenen
dc.contributor.authorFeng Wangen
dc.contributor.authorYu-Tao Wangen
dc.contributor.authorJin-Quan Lien
dc.contributor.authorSalehian-Dehkordi, H.en
dc.contributor.authorEer Hehuaen
dc.contributor.authorYong-Gang Liuen
dc.contributor.authorJian-Fei Chenen
dc.contributor.authorJian-Kui Wangen
dc.contributor.authorXue-Mei Dengen
dc.contributor.authorEsmailizadeh, A.en
dc.contributor.authorDehghani-Antezana, M.en
dc.contributor.authorCharati, H.en
dc.contributor.authorNosrati, M.en
dc.contributor.authorŠtěpánek, O.en
dc.contributor.authorRushdi, H.E.en
dc.contributor.authorOlsaker, I.en
dc.contributor.authorCurik, I.en
dc.contributor.authorGorkhali, N.A.en
dc.contributor.authorPaiva, S.R.en
dc.contributor.authorCaetano, A.R.en
dc.contributor.authorCiani, E.en
dc.contributor.authorAmills, M.en
dc.contributor.authorWeimann, C.en
dc.contributor.authorErhardt, G.en
dc.contributor.authorAmane, A.en
dc.contributor.authorMwacharo, Joram M.en
dc.contributor.authorHan Jianlinen
dc.contributor.authorHanotte, Olivier H.en
dc.contributor.authorPeriasamy, K.en
dc.contributor.authorJohansson, A.M.en
dc.contributor.authorHallsson, J.H.en
dc.contributor.authorKantanen, J.en
dc.contributor.authorColtman, D.W.en
dc.contributor.authorBruford, M.W.en
dc.contributor.authorLenstra, J.A.en
dc.contributor.authorMeng-Hua Lien
dc.date.accessioned2021-12-14T10:11:06Zen
dc.date.available2021-12-14T10:11:06Zen
dc.identifier.urihttps://hdl.handle.net/10568/116684
dc.titleWhole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important locien
dcterms.abstractDomestic 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.en
dcterms.accessRightsOpen Access
dcterms.audienceScientistsen
dcterms.available2021-12-10
dcterms.bibliographicCitationFeng-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.en
dcterms.issued2022-02-03
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherOxford University Pressen
dcterms.subjectgenomesen
dcterms.subjectgeneticsen
dcterms.subjectanimal breedingen
dcterms.subjectsheepen
dcterms.subjectsmall ruminantsen
dcterms.subjectlocien
dcterms.typeJournal Article

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