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

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö - Genome Biol. (2015)

Bottom Line: 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.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.This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.

View Article: PubMed Central - PubMed

Affiliation: Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. Zheya.Sheng@slu.se.

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.

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Body weights at 56 days of age in the Virginia weight selected and Advanced Intercross Lines. Average body weights per generation are provided for females in the high and low body-weight selected lines and as sex-averaged weights in the Advanced Intercross Line. BW56: 56-day body weight
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Fig1: Body weights at 56 days of age in the Virginia weight selected and Advanced Intercross Lines. Average body weights per generation are provided for females in the high and low body-weight selected lines and as sex-averaged weights in the Advanced Intercross Line. BW56: 56-day body weight

Mentions: The base population for the Virginia lines was established in 1957 by intercrossing seven partially inbred lines of White Plymouth Rock chickens. The genetic variation entering the population thus represents a sample of the polymorphisms present when these partially inbred lines were founded. Since the founder population was established, the high (HWS) and low (LWS) body-weight lines have been bred with one new generation per year by single-trait, bi-directional selection for 56-day body weight [10–12]. The response to selection has progressed steadily throughout the experiment, resulting in an eight-fold difference in 56-day body weight after 40 generations of selection and currently, in the 57th generation, there is a 16-fold difference between the lines (Fig. 1). Genome-wide comparisons between the divergently selected lines have identified more than 100 candidate adaptive sweeps between them [3, 4]. The contribution to selection response of these candidate selective-sweep regions that originate from the standing genetic variation is still unknown. Here, we identified which of these candidate selective-sweeps contributed to adaptation and estimated their individual and joint contributions to the adaptive trait.Fig. 1


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

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö - Genome Biol. (2015)

Body weights at 56 days of age in the Virginia weight selected and Advanced Intercross Lines. Average body weights per generation are provided for females in the high and low body-weight selected lines and as sex-averaged weights in the Advanced Intercross Line. BW56: 56-day body weight
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4595211&req=5

Fig1: Body weights at 56 days of age in the Virginia weight selected and Advanced Intercross Lines. Average body weights per generation are provided for females in the high and low body-weight selected lines and as sex-averaged weights in the Advanced Intercross Line. BW56: 56-day body weight
Mentions: The base population for the Virginia lines was established in 1957 by intercrossing seven partially inbred lines of White Plymouth Rock chickens. The genetic variation entering the population thus represents a sample of the polymorphisms present when these partially inbred lines were founded. Since the founder population was established, the high (HWS) and low (LWS) body-weight lines have been bred with one new generation per year by single-trait, bi-directional selection for 56-day body weight [10–12]. The response to selection has progressed steadily throughout the experiment, resulting in an eight-fold difference in 56-day body weight after 40 generations of selection and currently, in the 57th generation, there is a 16-fold difference between the lines (Fig. 1). Genome-wide comparisons between the divergently selected lines have identified more than 100 candidate adaptive sweeps between them [3, 4]. The contribution to selection response of these candidate selective-sweep regions that originate from the standing genetic variation is still unknown. Here, we identified which of these candidate selective-sweeps contributed to adaptation and estimated their individual and joint contributions to the adaptive trait.Fig. 1

Bottom Line: 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.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.This provides new fundamental insights into the dynamics of standing genetic variation during long-term selection and adaptation.

View Article: PubMed Central - PubMed

Affiliation: Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. Zheya.Sheng@slu.se.

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.

Show MeSH
Related in: MedlinePlus