The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis

TLDR

Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs). The study shows that arbitrarily defined parameterizations of genetic effects can capture most genetic variation and argues that variance component analyses should not be used to infer the genetic architecture of quantitative traits. The authors demonstrate that arbitrary parameterizations of genetic effects, consistent with non-additive gene actions, can account for the majority of genetic variation. Many studies attribute a large proportion of quantitative trait variation to additive genetic variance, leading to claims that non-additive effects are unimportant, but this work reveals a logical flaw in using variance component magnitudes to infer the relative importance of additive versus non-additive gene actions.

Abstract

Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci (QTLs). Many studies have found a large proportion of quantitative trait variation can be attributed to the additive genetic variance (VA), providing the basis for claims that non-additive gene actions are unimportant. In this study, we show that arbitrarily defined parameterizations of genetic effects seemingly consistent with non-additive gene actions can also capture the majority of genetic variation. This reveals a logical flaw in using the relative magnitudes of variance components to indicate the relative importance of additive and non-additive gene actions. We discuss the implications and propose that variance component analyses should not be used to infer the genetic architecture of quantitative traits.