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Genetics of adaptation in modern chicken
Univ Gottingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, Germany;AREEO, ABRII, Dept Anim Biotechnol, Karaj, Iran.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.ORCID iD: 0000-0003-2981-2582
Friedrich Loeffler Inst, Neustadt, Germany;Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany.ORCID iD: 0000-0002-5670-2808
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2019 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 4, article id e1007989Article in journal (Refereed) Published
Abstract [en]

We 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<2.5x10(-6)). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding. Author summary Domestic chickens (Gallus gallus domesticus) provide a critical resource for animal proteins for human nutrition worldwide. Chickens were primarily domesticated from the red jungle fowl (Gallus gallus gallus), a bird that still runs wild in most of Southeast Asia. Human driven selection during domestication and subsequent specialization into meat type (broilers) and egg layer (layers) birds has left detectable signatures of selection within the genome of modern chicken. In this study, we performed whole genome sequencing of 127 chicken including the red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken. Analysis of selection provided a comprehensive list of several tens of independent loci that are likely to have contributed to domestication or improving production. SNP by SNP comparison of allele frequency between groups of wild and domestic chicken showed a highly significant deficiency of the proportion of amino acid altering mutations. This implies that commercial birds have undergone purifying selection reducing the frequency of deleterious variants.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE , 2019. Vol. 15, no 4, article id e1007989
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Genetics and Breeding in Agricultural Sciences
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URN: urn:nbn:se:uu:diva-385576DOI: 10.1371/journal.pgen.1007989ISI: 000466866000009PubMedID: 31034467OAI: oai:DiVA.org:uu-385576DiVA, id: diva2:1325981
Funder
German Research Foundation (DFG), QA55/1-1Available from: 2019-06-17 Created: 2019-06-17 Last updated: 2019-06-17Bibliographically approved

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Rubin, Carl-JohanMaqbool, KhurramWeigend, SteffenGeibel, JohannesKerje, SusanneAndersson, Leif
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