title: Whole-genome resequencing reveals loci under selection during chicken domestication.
abstract: 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.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-75123 Uppsala, Sweden.
authors.forename: Carl-Johan
authors.initials: CJ
authors.lastname: Rubin
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.forename: Jonas
authors.initials: J
authors.lastname: Eriksson
authors.forename: Jennifer R S
authors.initials: JR
authors.lastname: Meadows
authors.forename: Ellen
authors.initials: E
authors.lastname: Sherwood
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Webster
authors.forename: Lin
authors.initials: L
authors.lastname: Jiang
authors.forename: Max
authors.initials: M
authors.lastname: Ingman
authors.forename: Ted
authors.initials: T
authors.lastname: Sharpe
authors.forename: Sojeong
authors.initials: S
authors.lastname: Ka
authors.forename: Finn
authors.initials: F
authors.lastname: Hallböök
authors.forename: Francois
authors.initials: F
authors.lastname: Besnier
authors.forename: Orjan
authors.initials: O
authors.lastname: Carlborg
authors.forename: Bertrand
authors.initials: B
authors.lastname: Bed'hom
authors.forename: Michèle
authors.initials: M
authors.lastname: Tixier-Boichard
authors.forename: Per
authors.initials: P
authors.lastname: Jensen
authors.forename: Paul
authors.initials: P
authors.lastname: Siegel
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Leif
authors.initials: L
authors.lastname: Andersson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D005075:Biological Evolution; D002645:Chickens / Q000235:genetics*; D005260:Female; D056426:Genetic Loci / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion