Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
2014
Carneiro, Miguel | Rubin, Carl-Johan | Di Palma, Federica | Albert, Franck W. | Alföldi, Jessica | Barrio, Alvaro Martinez | Pielberg, Gerli | Rafati, Nima | Sayyab, Shumaila | Turner-Maier, Jason | Younis, Shady | Afonso, Sandra | Aken, Bronwen | Alves, Joel M. | Barrell, Daniel | Bolet, Gerard | Boucher, Samuel | Burbano, Hernan A. | Campos, Rita | Chang, Jean L. | Duranthon, Véronique | Fontanesi, Luca | Garreau, Hervé | Heiman, David | Johnson, Jeremy | Mage, Rose G | Peng, Ze | Queney, Guillaume | Gaillard, Claire | Ruffier, Magali | Searle, Steve | Villafuerte, Rafael | Xiong, Anqi | Young, Sarah | Forsberg-Nilsson, Karin | Good, Jeffrey M. | Lander, Eric S. | Ferrand, Nuno | Lindblad-Toh, Kerstin | Andersson, Leif | Broad Institute of MIT and Harvard (BROAD INSTITUTE) ; Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston] | Department of Evolutionary Genetics ; Max-Planck-Institut für evolutionäre Anthropologie = Max Planck Institute for Evolutionary Anthropology (MPI-EVA) ; Max-Planck-Gesellschaft-Max-Planck-Gesellschaft | Department of Animal Bredding and Genetics ; Swedish University of Agricultural Sciences = Sveriges lantbruksuniversitet (SLU) | The Wellcome Trust Sanger Institute [Cambridge] | University of Cambridge [UK] (CAM) | Génétique Physiologie et Systèmes d'Elevage (GenPhySE) ; Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT) ; Institut National Polytechnique (Toulouse) (Toulouse INP) ; Université de Toulouse (UT)-Université de Toulouse (UT) | Max-Planck-Institut für evolutionäre Anthropologie = Max Planck Institute for Evolutionary Anthropology (MPI-EVA) ; Max-Planck-Gesellschaft | Biologie du développement et reproduction (BDR) ; École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS) | Lawrence Berkeley National Laboratory [Berkeley] (LBNL) | Génétique Animale et Biologie Intégrative (GABI) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain] (CSIC) | U54 HG003067 NHGRI NIH HHS, WT095908 Wellcome Trust, WT098051 Wellcome Trust
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
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