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_US
cg.authorship.typesCGIAR and advanced research instituteen_US
cg.contributor.affiliationChina Agricultural Universityen_US
cg.contributor.affiliationChinese Academy of Sciencesen_US
cg.contributor.affiliationUniversity of Chinese Academy of Sciencesen_US
cg.contributor.affiliationNovogene Bioinformatics Institute, Chinaen_US
cg.contributor.affiliationXinjiang Academy of Animal Scienceen_US
cg.contributor.affiliationShandong Binzhou Academy of Animal Science and Veterinary Medicine, Chinaen_US
cg.contributor.affiliationNanjing Agricultural Universityen_US
cg.contributor.affiliationKashi Universityen_US
cg.contributor.affiliationInner Mongolia Agricultural Universityen_US
cg.contributor.affiliationNingxia Academy of Agriculture and Forestry Sciences, Chinaen_US
cg.contributor.affiliationYunnan Agricultural Universityen_US
cg.contributor.affiliationShahid Bahonar University of Kermanen_US
cg.contributor.affiliationPayame Noor Universityen_US
cg.contributor.affiliationState Veterinary Institute Jihlavaen_US
cg.contributor.affiliationCairo Universityen_US
cg.contributor.affiliationNorwegian University of Life Sciencesen_US
cg.contributor.affiliationUniversity of Zagreben_US
cg.contributor.affiliationNepal Agricultural Research Councilen_US
cg.contributor.affiliationEmpresa Brasileira de Pesquisa Agropecuáriaen_US
cg.contributor.affiliationUniversità degli Studi di Bari Aldoen_US
cg.contributor.affiliationUniversitat Autònoma de Barcelonaen_US
cg.contributor.affiliationJustus Liebig University Giessenen_US
cg.contributor.affiliationAddis Ababa Universityen_US
cg.contributor.affiliationInternational Livestock Research Instituteen_US
cg.contributor.affiliationInternational Center for Agricultural Research in the Dry Areasen_US
cg.contributor.affiliationChinese Academy of Agricultural Sciencesen_US
cg.contributor.affiliationUniversity of Edinburghen_US
cg.contributor.affiliationUniversity of Nottinghamen_US
cg.contributor.affiliationInternational Atomic Energy Agencyen_US
cg.contributor.affiliationSwedish University of Agricultural Sciencesen_US
cg.contributor.affiliationAgricultural University of Icelanden_US
cg.contributor.affiliationNatural Resources Institute, Finlanden_US
cg.contributor.affiliationUniversity of Albertaen_US
cg.contributor.affiliationCardiff Universityen_US
cg.contributor.affiliationUtrecht Universityen_US
cg.contributor.crpLivestocken_US
cg.contributor.donorNational Natural Science Foundation of Chinaen_US
cg.contributor.donorCGIAR Trust Funden_US
cg.contributor.donorChinese Academy of Sciencesen_US
cg.contributor.initiativeSustainable Animal Productivityen_US
cg.creator.identifierOlivier Hanotte: 0000-0002-2877-4767en_US
cg.creator.identifierJoram Mwacharo: 0000-0001-6981-8140en_US
cg.howPublishedFormally Publisheden_US
cg.identifier.doihttps://doi.org/10.1093/molbev/msab353en_US
cg.isijournalISI Journalen_US
cg.issn1537-1719en_US
cg.issue12en_US
cg.journalMolecular Biology and Evolutionen_US
cg.reviewStatusPeer Reviewen_US
cg.subject.actionAreaResilient Agrifood Systemsen_US
cg.subject.ilriANIMAL BREEDINGen_US
cg.subject.ilriGENETICSen_US
cg.subject.ilriSHEEPen_US
cg.subject.ilriSMALL RUMINANTSen_US
cg.subject.impactAreaPoverty reduction, livelihoods and jobsen_US
cg.volume38en_US
dc.contributor.authorFeng-Hua Lven_US
dc.contributor.authorYin-Hong Caoen_US
dc.contributor.authorGuang-Jian Liuen_US
dc.contributor.authorLing-Yun Luoen_US
dc.contributor.authorRan Luen_US
dc.contributor.authorMing-Jun Liuen_US
dc.contributor.authorWen-Rong Lien_US
dc.contributor.authorPing Zhouen_US
dc.contributor.authorXin-Hua Wangen_US
dc.contributor.authorMin Shenen_US
dc.contributor.authorLei Gaoen_US
dc.contributor.authorJing-Quan Yangen_US
dc.contributor.authorHua Yangen_US
dc.contributor.authorYong-Lin Yangen_US
dc.contributor.authorChang-Bin Liuen_US
dc.contributor.authorPeng-Cheng Wanen_US
dc.contributor.authorYun-Sheng Zhangen_US
dc.contributor.authorWen-Hui Pien_US
dc.contributor.authorYan-Ling Renen_US
dc.contributor.authorZhi-Qiang Shenen_US
dc.contributor.authorFeng Wangen_US
dc.contributor.authorYu-Tao Wangen_US
dc.contributor.authorJin-Quan Lien_US
dc.contributor.authorSalehian-Dehkordi, H.en_US
dc.contributor.authorEer Hehuaen_US
dc.contributor.authorYong-Gang Liuen_US
dc.contributor.authorJian-Fei Chenen_US
dc.contributor.authorJian-Kui Wangen_US
dc.contributor.authorXue-Mei Dengen_US
dc.contributor.authorEsmailizadeh, A.en_US
dc.contributor.authorDehghani-Antezana, M.en_US
dc.contributor.authorCharati, H.en_US
dc.contributor.authorNosrati, M.en_US
dc.contributor.authorŠtěpánek, O.en_US
dc.contributor.authorRushdi, H.E.en_US
dc.contributor.authorOlsaker, I.en_US
dc.contributor.authorCurik, I.en_US
dc.contributor.authorGorkhali, N.A.en_US
dc.contributor.authorPaiva, S.R.en_US
dc.contributor.authorCaetano, A.R.en_US
dc.contributor.authorCiani, E.en_US
dc.contributor.authorAmills, M.en_US
dc.contributor.authorWeimann, C.en_US
dc.contributor.authorErhardt, G.en_US
dc.contributor.authorAmane, A.en_US
dc.contributor.authorMwacharo, Joram M.en_US
dc.contributor.authorHan Jianlinen_US
dc.contributor.authorHanotte, Olivier H.en_US
dc.contributor.authorPeriasamy, K.en_US
dc.contributor.authorJohansson, A.M.en_US
dc.contributor.authorHallsson, J.H.en_US
dc.contributor.authorKantanen, J.en_US
dc.contributor.authorColtman, D.W.en_US
dc.contributor.authorBruford, M.W.en_US
dc.contributor.authorLenstra, J.A.en_US
dc.contributor.authorMeng-Hua Lien_US
dc.date.accessioned2021-12-14T10:11:06Zen_US
dc.date.available2021-12-14T10:11:06Zen_US
dc.identifier.urihttps://hdl.handle.net/10568/116684en_US
dc.titleWhole-genome resequencing of worldwide wild and domestic sheep elucidates genetic diversity, introgression and agronomically important locien_US
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_US
dcterms.accessRightsOpen Accessen_US
dcterms.audienceScientistsen_US
dcterms.available2021-12-10en_US
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_US
dcterms.issued2022-02-03en_US
dcterms.languageenen_US
dcterms.licenseCC-BY-4.0en_US
dcterms.publisherOxford University Pressen_US
dcterms.subjectgenomesen_US
dcterms.subjectgeneticsen_US
dcterms.subjectanimal breedingen_US
dcterms.subjectsheepen_US
dcterms.subjectsmall ruminantsen_US
dcterms.subjectlocien_US
dcterms.typeJournal Articleen_US

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