Abstract
BackgroundArtificial 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.ResultsUsing 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.ConclusionsLong-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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0785-z) contains supplementary material, which is available to authorized users.
Highlights
Artificial selection provides a powerful approach to study the genetics of adaptation
Evaluated were the contribution of 106 selective sweeps, where the high and low weight selected Virginia lines were fixed for alternative alleles, to selection response [3, 4]
Here, we empirically confirm that the gradual response to long-term, bi-directional, single-trait selection in the Virginia chicken lines was, to a great extent, due to standing genetic variation across a highly polygenic genetic architecture in the common base population
Summary
Artificial selection provides a powerful approach to study the genetics of adaptation. A longstanding challenge in quantitative and evolutionary genetics has been quantification of the relative contributions from standing and emerging variation to long-term selection response [1, 2] While such results are very difficult to obtain in studies of natural populations, artificial. Subjecting populations to artificial selection provides an accelerated evolutionary process that may result in extreme phenotypes with accompanying changes across the genome [2,3,4] Using such experiments, the contribution by mutational variance to the evolution of quantitative traits can be quantified by, for example, measuring the release of genetic variance during selection experiments from an inbred founder population [5]. Whereas short-term contributions can be estimated based on the immediate selection response in a selection-experiment starting from outbred founders, long-term contributions of standing variation are more difficult to estimate due to confounding with effects
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