Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro 1 Carl-Johan Rubin 2 Federica Di Palma 3, 4 Franck W. Albert 5, 6 Jessica Alföldi 3 Alvaro Martinez Barrio 7 Gerli Pielberg 7 Nima Rafati 8 Shumaila Sayyab 9 Jason Turner-Maier 3 Shady Younis 7, 10 Sandra Afonso 1 Bronwen Aken 11 Joel M. Alves 1, 12 Daniel Barrell 11 Gerard Bolet 13 Samuel Boucher 14 Hernan A. Burbano 15 Rita Campos 1 Jean L. Chang 3 Veronique Duranthon 16 Luca Fontanesi 17 Herve Garreau 13 David Heiman 3 Jeremy Johnson 3 Rose G Mage 18 Ze Peng 19 Guillaume Queney 20 Claire Gaillard 21 Magali Ruffier 11 Steve Searle 11 Rafael Villafuerte 22 Anqi Xiong 23 Sarah Young 3 Karin Forsberg-Nilsson 24 Jeffrey M. Good 5 Eric S. Lander 3 Nuno Ferrand 1 Kerstin Lindblad-Toh 7, 3 Leif Andersson 7, 9, 25
Abstract : 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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Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Franck W. Albert, Jessica Alföldi, et al.. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science, American Association for the Advancement of Science, 2014, 345 (6200), pp.1074-1079. ⟨10.1126/science.1253714 ⟩. ⟨hal-01193854⟩

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