title: Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.
abstract: BACKGROUND
  Artificial selection provides a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions where allele-frequencies have diverged during selection. To avoid false positive signatures of selection, it is necessary to show that a sweep affects a selected trait before it can be considered adaptive. Here, we confirm candidate, genome-wide distributed selective sweeps originating from the standing genetic variation in a long-term selection experiment on high and low body weight of chickens.
  
  
  RESULTS
  Using an intercross between the two divergent chicken lines, 16 adaptive selective sweeps were confirmed based on their association with the body weight at 56 days of age. Although individual additive effects were small, the fixation for alternative alleles across the loci contributed at least 40 % of the phenotypic difference for the selected trait between these lines. The sweeps contributed about half of the additive genetic variance present within and between the lines after 40 generations of selection, corresponding to a considerable portion of the additive genetic variance of the base population.
  
  
  CONCLUSIONS
  Long-term, single-trait, bi-directional selection in the Virginia chicken lines has resulted in a gradual response to selection for extreme phenotypes without a drastic reduction in the genetic variation. We find that fixation of several standing genetic variants across a highly polygenic genetic architecture made a considerable contribution to long-term selection response. This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.
authors.affiliation: Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. Zheya.Sheng@slu.se.
authors.forename: Zheya
authors.initials: Z
authors.lastname: Sheng
authors.affiliation: Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. Mats.Pettersson@imbim.uu.se.|Present address: Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden. Mats.Pettersson@imbim.uu.se.
authors.forename: Mats E
authors.initials: ME
authors.lastname: Pettersson
authors.affiliation: Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA. chonaker@vt.edu.
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, USA. pbsiegel@vt.edu.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Siegel
authors.affiliation: Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. Orjan.Carlborg@slu.se.
authors.forename: Örjan
authors.initials: Ö
authors.lastname: Carlborg
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D000483:Alleles; D000818:Animals; D001835:Body Weight / Q000235:genetics; D002645:Chickens / Q000235:genetics; D003433:Crosses, Genetic; D014644:Genetic Variation