title: Misspecification in Mixed-Model-Based Association Analysis.
abstract: Additive genetic variance in natural populations is commonly estimated using mixed models, in which the covariance of the genetic effects is modeled by a genetic similarity matrix derived from a dense set of markers. An important but usually implicit assumption is that the presence of any nonadditive genetic effect increases only the residual variance and does not affect estimates of additive genetic variance. Here we show that this is true only for panels of unrelated individuals. In the case that there is genetic relatedness, the combination of population structure and epistatic interactions can lead to inflated estimates of additive genetic variance.
authors.affiliation: Biometris, Wageningen University and Research Centre, 6702AG Wageningen, The Netherlands willem.kruijer@wur.nl.
authors.forename: Willem
authors.initials: W
authors.lastname: Kruijer
mesh_terms: D000818:Animals; D001419:Bacteria; D014644:Genetic Variation; D006801:Humans; D008957:Models, Genetic; D010944:Plants
keywords: epistasis; missing heritability; misspecification; nonadditive genetic variance