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dc.contributor.authorQanbari, Saber
dc.contributor.authorRubin, Carl-Johan
dc.contributor.authorMaqbool, Khurram
dc.contributor.authorWeigend, Steffen
dc.contributor.authorWeigend, Annett
dc.contributor.authorGeibel, Johannes
dc.contributor.authorKerje, Susanne
dc.contributor.authorWurmser, Christine
dc.contributor.authorPeterson, Andrew Townsend
dc.contributor.authorBrisbin, I. Lehr, Jr.
dc.contributor.authorPreisinger, Ruedi
dc.contributor.authorFries, Ruedi
dc.contributor.authorSimianer, Henner
dc.contributor.authorAndersson, Leif
dc.date.accessioned2021-01-29T21:19:33Z
dc.date.available2021-01-29T21:19:33Z
dc.date.issued2019-04-29
dc.identifier.citationQanbari S, Rubin C-J, Maqbool K, Weigend S, Weigend A, Geibel J, et al. (2019) Genetics of adaptation in modern chicken. PLoS Genet 15(4): e1007989. https://doi.org/10.1371/journal.pgen.1007989en_US
dc.identifier.urihttp://hdl.handle.net/1808/31309
dc.descriptionThis work is licensed under a Creative Commons Attribution 4.0 International License.en_US
dc.description.abstractWe carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5×10−6). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding.en_US
dc.publisherPublic Library of Scienceen_US
dc.rights© 2019 Qanbari et al.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.titleGenetics of adaptation in modern chickenen_US
dc.typeArticleen_US
kusw.kuauthorPeterson, Andrew Townsend
kusw.kudepartmentEcology & Evolutionary Biologyen_US
kusw.kudepartmentKU Biodiversity Instituteen_US
dc.identifier.doi10.1371/journal.pgen.1007989en_US
dc.identifier.orcidhttps://orcid.org/0000-0001-6866-2332en_US
dc.identifier.orcidhttps://orcid.org/0000-0003-2981-2582en_US
dc.identifier.orcidhttps://orcid.org/0000-0002-5670-2808en_US
dc.identifier.orcidhttps://orcid.org/0000-0001-7172-3263en_US
dc.identifier.orcidhttps://orcid.org/0000-0003-0243-2379en_US
dc.identifier.orcidhttps://orcid.org/0000-0002-7561-4512en_US
dc.identifier.orcidhttps://orcid.org/0000-0002-4657-1787en_US
kusw.oaversionScholarly/refereed, publisher versionen_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US
dc.rights.accessrightsopenAccessen_US


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© 2019 Qanbari et al.
Except where otherwise noted, this item's license is described as: © 2019 Qanbari et al.