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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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Related in: MedlinePlus

Allele-substitution effects of selective sweeps associated with 56-day body weight (BW56) in the Virginia Advanced Intercross Line. The effects were estimated in the F15 generation of the AIL. Coloured bars indicate for selective sweeps with associations at a 5 % FDR and white bars selective-sweeps with associations at a 20 % FDR. Solid coloured bars indicate selective sweeps where the HWS derived allele increases body weight. Hashed coloured bars indicate selective-sweeps where the LWS derived allele increase body weight, that is, regions that are transgressive
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Fig3: Allele-substitution effects of selective sweeps associated with 56-day body weight (BW56) in the Virginia Advanced Intercross Line. The effects were estimated in the F15 generation of the AIL. Coloured bars indicate for selective sweeps with associations at a 5 % FDR and white bars selective-sweeps with associations at a 20 % FDR. Solid coloured bars indicate selective sweeps where the HWS derived allele increases body weight. Hashed coloured bars indicate selective-sweeps where the LWS derived allele increase body weight, that is, regions that are transgressive

Mentions: To estimate the contribution by the individual adaptive sweeps to the selected trait, additive, allele-substitution effects were estimated using a multi-locus association analysis. We found that the additive effects of the individual loci were generally small, and no individual locus had an additive allele-substitution effect greater than 29 g (or 0.2 σP) for the selected trait (Table 1; Fig. 3). The effects were similar for most of the loci when estimated in the F15 population (Fig. 3a). Most of the HWS derived alleles increased weight, however, two regions also had transgressive effects on the trait – that is, that an allele inherited from the LWS increased weight. The standing genetic variation in the base population for the Virginia chicken lines thus has contributed with alleles of small effect across a highly polygenic genetic architecture.Fig. 3


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)

Allele-substitution effects of selective sweeps associated with 56-day body weight (BW56) in the Virginia Advanced Intercross Line. The effects were estimated in the F15 generation of the AIL. Coloured bars indicate for selective sweeps with associations at a 5 % FDR and white bars selective-sweeps with associations at a 20 % FDR. Solid coloured bars indicate selective sweeps where the HWS derived allele increases body weight. Hashed coloured bars indicate selective-sweeps where the LWS derived allele increase body weight, that is, regions that are transgressive
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Allele-substitution effects of selective sweeps associated with 56-day body weight (BW56) in the Virginia Advanced Intercross Line. The effects were estimated in the F15 generation of the AIL. Coloured bars indicate for selective sweeps with associations at a 5 % FDR and white bars selective-sweeps with associations at a 20 % FDR. Solid coloured bars indicate selective sweeps where the HWS derived allele increases body weight. Hashed coloured bars indicate selective-sweeps where the LWS derived allele increase body weight, that is, regions that are transgressive
Mentions: To estimate the contribution by the individual adaptive sweeps to the selected trait, additive, allele-substitution effects were estimated using a multi-locus association analysis. We found that the additive effects of the individual loci were generally small, and no individual locus had an additive allele-substitution effect greater than 29 g (or 0.2 σP) for the selected trait (Table 1; Fig. 3). The effects were similar for most of the loci when estimated in the F15 population (Fig. 3a). Most of the HWS derived alleles increased weight, however, two regions also had transgressive effects on the trait – that is, that an allele inherited from the LWS increased weight. The standing genetic variation in the base population for the Virginia chicken lines thus has contributed with alleles of small effect across a highly polygenic genetic architecture.Fig. 3

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