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Originally published as Genetics Published Articles Ahead of Print on May 4, 2009.

Genetics, Vol. 182, 911-922, July 2009, Copyright © 2009
doi:10.1534/genetics.108.097030

Polymorphic Genes of Major Effect: Consequences for Variation, Selection and Evolution in Arabidopsis thaliana

John R. Stinchcombe*,{dagger},1, Cynthia Weinig{ddagger}, Katy D. Heath*, Marcus T. Brock{ddagger} and Johanna Schmitt§

* Department of Ecology and Evolutionary Biology and {dagger} Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada, {ddagger} Department of Botany, University of Wyoming, Laramie, Wyoming 82071 and § Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912

1 Corresponding author: University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada.
E-mail: john.stinchcombe{at}utoronto.ca

The importance of genes of major effect for evolutionary trajectories within and among natural populations has long been the subject of intense debate. For example, if allelic variation at a major-effect locus fundamentally alters the structure of quantitative trait variation, then fixation of a single locus can have rapid and profound effects on the rate or direction of subsequent evolutionary change. Using an Arabidopsis thaliana RIL mapping population, we compare G-matrix structure between lines possessing different alleles at ERECTA, a locus known to affect ecologically relevant variation in plant architecture. We find that the allele present at ERECTA significantly alters G-matrix structure—in particular the genetic correlations between branch number and flowering time traits—and may also modulate the strength of natural selection on these traits. Despite these differences, however, when we extend our analysis to determine how evolution might differ depending on the ERECTA allele, we find that predicted responses to selection are similar. To compare responses to selection between allele classes, we developed a resampling strategy that incorporates uncertainty in estimates of selection that can also be used for statistical comparisons of G matrices.