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)
,
Véronique Duranthon
(16)
,
Luca Fontanesi
(17)
,
Hervé 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)
1
Centro de Investigaçao em Biodiversidade e Recursos Genéticos
2 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbiology
3 BROAD INSTITUTE - Broad Institute of MIT and Harvard
4 Vertebrate and Health Genomics
5 Department of Evolutionary Genetics
6 Department of Human Genetics
7 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbiology
8 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbioology
9 Department of Animal Bredding and Genetics
10 Department of Animal Production
11 The Wellcome Trust Sanger Institute [Cambridge]
12 CAM - University of Cambridge [UK]
13 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
14 Labovet Conseil
15 Max Planck Institute for Evolutionary Anthropology [Leipzig]
16 BDR - Biologie du développement et reproduction
17 Department of Agricultural and Food Sciences - Division of Animal Sciences
18 Laboratory of Immunology
19 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
20 Antagene - Animal Genomics Laboratory
21 GABI - Génétique Animale et Biologie Intégrative
22 CSIC - Consejo Superior de Investigaciones Cientificas = Spanish National Research Council
23 Science for Life Laboratory - Department of Immunology , Genetics and Pathology
24 Science for Life Laboratory - Department of Immunology, Genetics and Pathology
25 Department of Veterinary Integrative Biosciences
2 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbiology
3 BROAD INSTITUTE - Broad Institute of MIT and Harvard
4 Vertebrate and Health Genomics
5 Department of Evolutionary Genetics
6 Department of Human Genetics
7 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbiology
8 Science of Life Laboratory Uppsala - Department of Medical Biochemistry and Microbioology
9 Department of Animal Bredding and Genetics
10 Department of Animal Production
11 The Wellcome Trust Sanger Institute [Cambridge]
12 CAM - University of Cambridge [UK]
13 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
14 Labovet Conseil
15 Max Planck Institute for Evolutionary Anthropology [Leipzig]
16 BDR - Biologie du développement et reproduction
17 Department of Agricultural and Food Sciences - Division of Animal Sciences
18 Laboratory of Immunology
19 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
20 Antagene - Animal Genomics Laboratory
21 GABI - Génétique Animale et Biologie Intégrative
22 CSIC - Consejo Superior de Investigaciones Cientificas = Spanish National Research Council
23 Science for Life Laboratory - Department of Immunology , Genetics and Pathology
24 Science for Life Laboratory - Department of Immunology, Genetics and Pathology
25 Department of Veterinary Integrative Biosciences
Joel M. Alves
- Fonction : Auteur
- PersonId : 969750
Véronique Duranthon
- Fonction : Auteur
- PersonId : 737804
- IdHAL : veronique-duranthon
- ORCID : 0000-0001-8120-7481
- IdRef : 089031709
Hervé Garreau
- Fonction : Auteur
- PersonId : 1160367
- IdHAL : herve-garreau
- ORCID : 0000-0001-6195-1457
Claire Gaillard
- Fonction : Auteur
- PersonId : 736130
- IdHAL : claire-rogel-gaillard
- ORCID : 0000-0002-2174-1962
- IdRef : 154750417
Sarah Young
- Fonction : Auteur
- PersonId : 763962
- ORCID : 0000-0003-3862-3863
Résumé
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.