Whole-genome resequencing reveals loci under selection during chicken domestication

Rubin , Carl-Johan
        . Department of Medical Biochemistry and Microbiology; Zody , Michael C.
        . Department of Medical Biochemistry and MicrobiologyBroad Institute of Harvard; Eriksson , Jonas
        . Department of Medical Biochemistry and Microbiology; Meadows , Jennifer R. S.
        . Department of Medical Biochemistry and Microbiology; Sherwood , Ellen
        . Department of Cell and Molecular Biology; Webster , Matthew T.
        . Department of Medical Biochemistry and Microbiology; Jiang , Lin
        . Department of Medical Biochemistry and Microbiology; Ingman , Max
        . Department of Genetics and Pathology, The Rudbeck Laboratory; Sharpe , Ted
        . Broad Institute of Harvard; Ka , Sojeong
        . Department of Neuroscience; Hallböök , Finn
        . Department of Neuroscience; Besnier , Francois
        . Department of Animal Breeding and Genetics; Carlbord , Örjan
        . Department of Animal Breeding and Genetics; Bed'Hom , Bertrand
        INRA
        , Jouy-En-Josas .
         UMR 1313 Génétique Animale et Biologie Intégrative; Tixier-Boichard , Michèle
        INRA
        , Jouy-En-Josas .
         UMR 1313 Génétique Animale et Biologie Intégrative; Jensen , Per
        . IFM Biology; Siegel , Paul
        . Department of Animal and Poultry Sciences; Lindblad-Toh , Kerstin
        . Department of Medical Biochemistry and MicrobiologyBroad Institute of Harvard; Andersson , Leif
        . Department of Medical Biochemistry and MicrobiologyDepartment of Animal Breeding and Genetics

Whole-genome resequencing reveals loci under selection during chicken domestication

2010

Rubin , Carl-Johan (Uppsala University(Suède). Department of Medical Biochemistry and Microbiology) | Zody , Michael C. (Uppsala UniversityMassachusetts Institute of Technology, Cambridge(Etats-Unis). Department of Medical Biochemistry and MicrobiologyBroad Institute of Harvard) | Eriksson , Jonas (Uppsala University(Suède). Department of Medical Biochemistry and Microbiology) | Meadows , Jennifer R. S. (Uppsala University(Suède). Department of Medical Biochemistry and Microbiology) | Sherwood , Ellen (Karolinska Institute(Suède). Department of Cell and Molecular Biology) | Webster , Matthew T. (Uppsala University(Suède). Department of Medical Biochemistry and Microbiology) | Jiang , Lin (Uppsala University(Suède). Department of Medical Biochemistry and Microbiology) | Ingman , Max (Uppsala University(Suède). Department of Genetics and Pathology, The Rudbeck Laboratory) | Sharpe , Ted (Massachusetts Institute of Technology, Cambridge(Etats-Unis). Broad Institute of Harvard) | Ka , Sojeong (Uppsala University(Suède). Department of Neuroscience) | Hallböök , Finn (Uppsala University(Suède). Department of Neuroscience) | Besnier , Francois (Swedish University of Agricultural Sciences(Suède). Department of Animal Breeding and Genetics) | Carlbord , Örjan (Swedish University of Agricultural Sciences(Suède). Department of Animal Breeding and Genetics) | Bed'Hom , Bertrand (INRA , Jouy-En-Josas (France). UMR 1313 Génétique Animale et Biologie Intégrative) | Tixier-Boichard , Michèle (INRA , Jouy-En-Josas (France). UMR 1313 Génétique Animale et Biologie Intégrative) | Jensen , Per (Linköping University(Suède). IFM Biology) | Siegel , Paul (Virginia Polytechnic Institute and State University(Etats-Unis). Department of Animal and Poultry Sciences) | Lindblad-Toh , Kerstin (Uppsala UniversityMassachusetts Institute of Technology, Cambridge(Etats-Unis). Department of Medical Biochemistry and MicrobiologyBroad Institute of Harvard) | Andersson , Leif(auteur de correspondance) (Uppsala UniversitySwedish University of Agricultural Sciences(Suède). Department of Medical Biochemistry and MicrobiologyDepartment of Animal Breeding and Genetics)

Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.

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