Data from: Genome-wide SNP data unveils the globalization of domesticated pigs

dc.contributor.affiliationNational Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China* - Yang, Bin
dc.contributor.affiliationNational Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China* - Cui, Leilei
dc.contributor.affiliationCenter for Research in Agricultural Genomics - Perez-Enciso, Miguel
dc.contributor.affiliationFederal Scientific Center for Animal Husbandry named after Academician L.K. Ernst - Traspov, Aleksei
dc.contributor.affiliationWageningen University & Research - Crooijmans, Richard P. M. A.
dc.contributor.affiliationFederal Scientific Center for Animal Husbandry named after Academician L.K. Ernst - Zinovieva, Natalia
dc.contributor.affiliationUniversity of Illinois at Urbana Champaign - Schook, Lawrence B.
dc.contributor.affiliationRoslin Institute - Archibald, Alan
dc.contributor.affiliationChiang Mai University - Gatphayak, Kesinee
dc.contributor.affiliationUniversity of Göttingen - Knorr, Christophe
dc.contributor.affiliationAristotle University of Thessaloniki - Triantafyllidis, Alex
dc.contributor.affiliationAristotle University of Thessaloniki - Alexandri, Panoraia
dc.contributor.affiliationIndonesian Institute of Sciences - Semiadi, Gono
dc.contributor.affiliationUniversity of Nottingham - Hanotte, Olivier
dc.contributor.affiliationUniversity of Lisbon - Dias, Deodália
dc.contributor.affiliationUniversity of Ljubljana - Dovč, Peter
dc.contributor.affiliationUniversity of Helsinki - Uimari, Pekka
dc.contributor.affiliationAalborg University - Iacolina, Laura
dc.contributor.affiliationUniversity of Sassari - Scandura, Massimo
dc.contributor.affiliationWageningen University & Research - Groenen, Martien A. M.
dc.contributor.affiliationNational Key Laboratory for Pig Genetic Improvement and Production Technology, Nanchang, China* - Huang, Lusheng
dc.contributor.affiliationWageningen University & Research - Megens, Hendrik-Jan
dc.contributor.authorYang, Bin
dc.contributor.authorCui, Leilei
dc.contributor.authorPerez-Enciso, Miguel
dc.contributor.authorTraspov, Aleksei
dc.contributor.authorCrooijmans, Richard P. M. A.
dc.contributor.authorZinovieva, Natalia
dc.contributor.authorSchook, Lawrence B.
dc.contributor.authorArchibald, Alan
dc.contributor.authorGatphayak, Kesinee
dc.contributor.authorKnorr, Christophe
dc.contributor.authorTriantafyllidis, Alex
dc.contributor.authorAlexandri, Panoraia
dc.contributor.authorSemiadi, Gono
dc.contributor.authorHanotte, Olivier
dc.contributor.authorDias, Deodália
dc.contributor.authorDovč, Peter
dc.contributor.authorUimari, Pekka
dc.contributor.authorIacolina, Laura
dc.contributor.authorScandura, Massimo
dc.contributor.authorGroenen, Martien A. M.
dc.contributor.authorHuang, Lusheng
dc.contributor.authorMegens, Hendrik-Jan
dc.coverage.spatialAsia
dc.coverage.spatialEurope
dc.coverage.spatialGlobal
dc.date.accessioned2025-03-24T15:26:22Z
dc.date.issued2018-08-23
dc.date.issued2018-08-23
dc.descriptionBackground: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection. Results: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection. Conclusions: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation.
dc.identifierhttps://doi.org/10.5061/dryad.30tk6
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/11379
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectHolocene
dc.subjectAnthropocene
dc.subjectSus scrofa
dc.subjectpig
dc.titleData from: Genome-wide SNP data unveils the globalization of domesticated pigs
dc.typedataset
dc.typedataset
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