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Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment

Zheya Sheng, Mats E. Pettersson, Christa F. Honaker, Paul B. Siegel, View ORCID ProfileÖrjan Carlborg
doi: https://doi.org/10.1101/018721
Zheya Sheng
1Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Mats E. Pettersson
1Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Christa F. Honaker
2Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Paul B. Siegel
2Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Örjan Carlborg
1Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
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  • ORCID record for Örjan Carlborg
  • For correspondence: orjan.carlborg@slu.se
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Abstract

Artificial selection has, for decades, provided a powerful approach to study the genetics of adaptation. Using selective-sweep mapping, it is possible to identify genomic regions in populations where the allele-frequencies have diverged during selection. To avoid misleading signatures of selection, it is necessary to show that a sweep has an effect on the selected trait before it can be considered adaptive. Here, we confirm candidate selective-sweeps on a genome-wide scale in one of the longest, on-going bi-directional selection experiments in vertebrates, the Virginia high and low body-weight selected chicken lines. The candidate selective-sweeps represent standing genetic variants originating from the common base-population. Using a deep-intercross between the selected lines, 16 of 99 evaluated regions were confirmed to contain adaptive selective-sweeps based on their association with the selected trait, 56-day body-weight. Although individual additive effects were small, the fixation for alternative alleles in the high and low body-weight lines across these loci contributed at least 40% of the divergence between them and about half of the additive genetic variance present within and between the lines after 40 generations of selection. The genetic variance contributed by the sweeps corresponds to about 85% of the additive genetic variance of the base-population, illustrating that these loci were major contributors to the realised selection-response. Thus, the gradual, continued, long-term selection response in the Virginia lines was likely due to a considerable standing genetic variation in a highly polygenic genetic architecture in the base-population with contributions from a steady release of selectable genetic variation from new mutations and epistasis throughout the course of selection.

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Posted April 30, 2015.
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Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment
Zheya Sheng, Mats E. Pettersson, Christa F. Honaker, Paul B. Siegel, Örjan Carlborg
bioRxiv 018721; doi: https://doi.org/10.1101/018721
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Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment
Zheya Sheng, Mats E. Pettersson, Christa F. Honaker, Paul B. Siegel, Örjan Carlborg
bioRxiv 018721; doi: https://doi.org/10.1101/018721

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