title: Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens.
abstract: Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells.
  
  
  
  We observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented.
  
  
  
  The extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.
authors.affiliation: Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden. mette.lillie@imbim.uu.se.
authors.forename: Mette
authors.identifier: 0000-0001-8714-0812
authors.initials: M
authors.lastname: Lillie
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
authors.forename: Zheya
authors.initials: Z
authors.lastname: Sheng
authors.affiliation: Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
authors.forename: Christa F
authors.initials: CF
authors.lastname: Honaker
authors.affiliation: Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
authors.forename: Ben J
authors.initials: BJ
authors.lastname: Dorshorst
authors.affiliation: Prestage Department of Poultry Science, North Carolina State University, Raleigh, NC, 27695, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Ashwell
authors.affiliation: Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Siegel
authors.affiliation: Department of Medical Biochemistry and Microbiology, Genomics, Uppsala University, Uppsala, 75123, Sweden.
authors.forename: Örjan
authors.initials: Ö
authors.lastname: Carlborg
mesh_terms: D000483:Alleles; D000818:Animals; D002645:Chickens; D004912:Erythrocytes / Q000276:immunology; D019143:Evolution, Molecular; D014644:Genetic Variation; D023281:Genomics; D006649:Histocompatibility Antigens / Q000235:genetics; D056724:Immunity, Humoral / Q000235:genetics*; D018125:Receptors, Transforming Growth Factor beta / Q000235:genetics; D012641:Selection, Genetic; D012756:Sheep / Q000097:blood
chemical_list: D006649:Histocompatibility Antigens; D018125:Receptors, Transforming Growth Factor beta
keywords: Antibody response; Pooled genome sequencing; Selective sweeps; Sheep red blood cells; Virginia chicken lines