Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals. The genetic variance components are defined in terms of genotypic values reflecting underlying genetic architecture (additive, dominance and epistatic genotypic effects) and allele frequencies. However, the dependency of the definition of genetic variance components on the underlying genetic models is not often appreciated. Here, we show how the partitioning of additive and non-additive genetic variation is affected by the genetic models and parameterization of allelic effects. We show that arbitrarily defined variance components often capture a substantial fraction of total genetic variation regardless of the underlying genetic architecture in simulated and real data. Therefore, variance component analysis cannot be used to infer genetic architecture of quantitative traits. The genetic basis of quantitative trait variation in a natural population can only be defined empirically using high resolution mapping methods followed by detailed characterization of QTL effects.
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