title: Parallel Selection Revealed by Population Sequencing in Chicken.
abstract: Human-driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg-laying chicken along with pool sequences of three meat-type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or preimprovement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in "Ascites" in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement in chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to overconsumption of calcium in egg-laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders.
authors.affiliation: Animal Breeding and Genetics Group, Georg-August University, Göttingen, Germany sqanbar@gwdg.de.
authors.forename: Saber
authors.initials: S
authors.lastname: Qanbari
authors.affiliation: Institute of Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Seidel
authors.affiliation: Institute of Human Genetics, Helmholtz Zentrum München, Munich, Germany.
authors.forename: Tim-Mathias
authors.initials: TM
authors.lastname: Strom
authors.affiliation: Institute of Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.affiliation: Lohmann Tierzucht GmbH, Cuxhaven, Germany.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Preisinger
authors.affiliation: Animal Breeding and Genetics Group, Georg-August University, Göttingen, Germany.
authors.forename: Henner
authors.initials: H
authors.lastname: Simianer
mesh_terms: D000818:Animals; D001947:Breeding / Q000379:methods; D002645:Chickens / Q000235:genetics*; D005787:Gene Frequency; D056426:Genetic Loci; D049810:Genetic Speciation; D012641:Selection, Genetic
keywords: domestication; improvement; population differentiation; selective sweep