Although the effect sizes of loci contributing to variation in mRNA transcript abundance are larger than the effects found in complex traits (which explain less than 1% of the phenotypic variance) effect sizes are relative to the population in which they are measured. A reasonable comparison for the rodent mRNA data is with the effect sizes of QTL found in crosses between inbred strains of mice. Remarkably, the median effect size of QTL is 12% (Flint et al. 2005), just under half that of the expression phenotypes. Therefore, even when we consider a phenotype that is directly linked to the genetic constitution of the organism, genetic architecture is not radically different from complex phenotypes.
