The Genomic Architecture of Interactions Between Natural Genetic Polymorphisms and Environments in Yeast Growth [Genetics of Complex Traits]

Gene-environment interaction (GxE) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting GxE have been reported, little is known about the general properties of GxE, and those of its underlying QTLs. Here, we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains, and the growth rates of these segregants in 47 environments, to identify growth rate QTLs (gQTLs) in each environment, and QTLs that have different growth effects in each pair of environments (gxeQTLs) . The average number of gxeQTLs identified between two environments is 0.58 times the number of unique gQTLs identified in these environments, revealing a high abundance of GxE. Eighty-seven percent of gxeQTLs belong to gQTLs, supporting the practice of identifying gxeQTLs from gQTLs. Most gxeQTLs identified from gQTLs have concordant effects between environments, but, as the effect size of a mutation in one environment enlarges, the probability of antagonism in the other environment increases. Antagonistic gxeQTLs are enriched in dissimilar environments. Relative to gQTLs, gxeQTLs tend to occur at intronic and synonymous sites. The gene ontology (GO) distributions of gQTLs and gxeQTLs are significantly different, as are those of antagonistic and concordant gxeQTLs. Simulations based on the yeast data showed that ignoring GxE causes substantial missing heritability. Together,...
Source: Genetics - Category: Genetics & Stem Cells Authors: Tags: Genetics of Complex Traits Source Type: research