Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
Miguel Carneiro
,
Carl-Johan Rubin
,
Federica Di Palma
(1)
,
Franck W. Albert
(2)
,
Jessica Alföldi
(1)
,
Alvaro Martinez Barrio
,
Gerli Pielberg
,
Nima Rafati
,
Shumaila Sayyab
(3)
,
Jason Turner-Maier
(1)
,
Shady Younis
,
Sandra Afonso
,
Bronwen Aken
(4)
,
Joel M. Alves
(5)
,
Daniel Barrell
(4)
,
Gerard Bolet
(6)
,
Samuel Boucher
,
Hernan A. Burbano
(7)
,
Rita Campos
,
Jean L. Chang
(1)
,
Véronique Duranthon
(8)
,
Luca Fontanesi
,
Hervé Garreau
(6)
,
David Heiman
(1)
,
Jeremy Johnson
(1)
,
Rose G Mage
,
Ze Peng
(9)
,
Guillaume Queney
,
Claire Gaillard
(10)
,
Magali Ruffier
(4)
,
Steve Searle
(4)
,
Rafael Villafuerte
(11)
,
Anqi Xiong
,
Sarah Young
(1)
,
Karin Forsberg-Nilsson
,
Jeffrey M. Good
(2)
,
Eric S. Lander
(1)
,
Nuno Ferrand
,
Kerstin Lindblad-Toh
(1)
,
Leif Andersson
(3)
1
BROAD INSTITUTE -
Broad Institute of MIT and Harvard
2 Department of Evolutionary Genetics
3 Department of Animal Bredding and Genetics
4 The Wellcome Trust Sanger Institute [Cambridge]
5 CAM - University of Cambridge [UK]
6 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
7 Max Planck Institute for Evolutionary Anthropology [Leipzig]
8 BDR - Biologie du développement et reproduction
9 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
10 GABI - Génétique Animale et Biologie Intégrative
11 CSIC - Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain]
2 Department of Evolutionary Genetics
3 Department of Animal Bredding and Genetics
4 The Wellcome Trust Sanger Institute [Cambridge]
5 CAM - University of Cambridge [UK]
6 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
7 Max Planck Institute for Evolutionary Anthropology [Leipzig]
8 BDR - Biologie du développement et reproduction
9 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
10 GABI - Génétique Animale et Biologie Intégrative
11 CSIC - Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain]
Miguel Carneiro
- Fonction : Auteur
Carl-Johan Rubin
- Fonction : Auteur
Alvaro Martinez Barrio
- Fonction : Auteur
Gerli Pielberg
- Fonction : Auteur
Nima Rafati
- Fonction : Auteur
Shady Younis
- Fonction : Auteur
Sandra Afonso
- Fonction : Auteur
Samuel Boucher
- Fonction : Auteur
- PersonId : 948065
Rita Campos
- Fonction : Auteur
Véronique Duranthon
- Fonction : Auteur
- PersonId : 737804
- IdHAL : veronique-duranthon
- ORCID : 0000-0001-8120-7481
- IdRef : 089031709
Luca Fontanesi
- Fonction : Auteur
Hervé Garreau
- Fonction : Auteur
- PersonId : 1160367
- IdHAL : herve-garreau
- ORCID : 0000-0001-6195-1457
Rose G Mage
- Fonction : Auteur
Guillaume Queney
- Fonction : Auteur
Claire Gaillard
- Fonction : Auteur
- PersonId : 736130
- IdHAL : claire-rogel-gaillard
- ORCID : 0000-0002-2174-1962
- IdRef : 154750417
Anqi Xiong
- Fonction : Auteur
Sarah Young
- Fonction : Auteur
- PersonId : 763962
- ORCID : 0000-0003-3862-3863
Karin Forsberg-Nilsson
- Fonction : Auteur
Nuno Ferrand
- Fonction : Auteur
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.
Format du dépôt | Fichier |
---|---|
Type de dépôt | Article dans une revue |
Titre |
en
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication
|
Résumé |
en
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.
|
Auteur(s) |
Miguel Carneiro
, Carl-Johan Rubin
, Federica Di Palma
1
, Franck W. Albert
2
, Jessica Alföldi
1
, Alvaro Martinez Barrio
, Gerli Pielberg
, Nima Rafati
, Shumaila Sayyab
3
, Jason Turner-Maier
1
, Shady Younis
, Sandra Afonso
, Bronwen Aken
4
, Joel M. Alves
5
, Daniel Barrell
4
, Gerard Bolet
6
, Samuel Boucher
, Hernan A. Burbano
7
, Rita Campos
, Jean L. Chang
1
, Véronique Duranthon
8
, Luca Fontanesi
, Hervé Garreau
6
, David Heiman
1
, Jeremy Johnson
1
, Rose G Mage
, Ze Peng
9
, Guillaume Queney
, Claire Gaillard
10
, Magali Ruffier
4
, Steve Searle
4
, Rafael Villafuerte
11
, Anqi Xiong
, Sarah Young
1
, Karin Forsberg-Nilsson
, Jeffrey M. Good
2
, Eric S. Lander
1
, Nuno Ferrand
, Kerstin Lindblad-Toh
1
, Leif Andersson
3
1
BROAD INSTITUTE -
Broad Institute of MIT and Harvard
( 38338 )
- Cambridge, MA 02142
- États-Unis
2
Department of Evolutionary Genetics
( 469547 )
- Leipzig 04103
- Allemagne
3
Department of Animal Bredding and Genetics
( 430304 )
- Suède
4
The Wellcome Trust Sanger Institute [Cambridge]
( 232748 )
- Hinxton, Cambridge CB10 1SA, UK
- Royaume-Uni
5
CAM -
University of Cambridge [UK]
( 237843 )
- The Old Schools, Trinity Lane, Cambridge CB2 1TN
- Royaume-Uni
6
GenPhySE -
Génétique Physiologie et Systèmes d'Elevage
( 444812 )
- INRA Auzeville -
24, chemin de Borde-Rouge -
Auzeville Tolosane
31326 Castanet Tolosan
- France
7
Max Planck Institute for Evolutionary Anthropology [Leipzig]
( 308156 )
- Deutscher Pl. 6, 04103 Leipzig
- Allemagne
8
BDR -
Biologie du développement et reproduction
( 2183 )
- Bâtiment 440 Domaine Vilvert 78352 JOUY EN JOSAS CEDEX
- France
9
LBNL -
Lawrence Berkeley National Laboratory [Berkeley]
( 82005 )
- 1 Cyclotron Rd. MS 50A-1148, Berkeley, CA 94720
- États-Unis
10
GABI -
Génétique Animale et Biologie Intégrative
( 123239 )
- Domaine de Vilvert F-78252 Jouy-en-Josas
- France
11
CSIC -
Consejo Superior de Investigaciones Cientificas [España] = Spanish National Research Council [Spain]
( 106380 )
- Serrano 117, 28006, Madrid
- Espagne
|
Langue du document |
Anglais
|
Nom de la revue |
|
Volume |
345
|
Numéro |
6200
|
Page/Identifiant |
1074-1079
|
Date de publication |
2014
|
URL éditeur |
http://www.sciencemag.org/content/345/6200.toc
|
Audience |
Non spécifiée
|
Vulgarisation |
Non
|
Comité de lecture |
Oui
|
Localisation géographique du document |
INRA, UMR 1198 Biologie du Développement et Reproduction, Centre de Jouy en Josas
|
Public visé |
Scientifique
|
Version du document |
version éditeur
|
Indexation contrôlée |
|
Financement |
|
Domaine(s) |
|
DOI | 10.1126/science.1253714 |
ProdINRA | 265576 |
PubMed Central | PMC5421586 |
UT key WOS | 000340870900046 |
Origine :
Fichiers produits par l'(les) auteur(s)
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