Additive genetic variance in natural populations is commonly estimated usingmixed models, in which the covariance of the genetic effects is modeled by agenetic similarity matrix derived from a dense set of markers. An important butusually implicit assumption is that the presence of any non-additive geneticeffect only increases the residual variance, and does not affect estimates ofadditive genetic variance. Here we show that this is only true for panels ofunrelated individuals. In case there is genetic relatedness, the combination ofpopulation structure and epistatic interactions can lead to inflated estimatesof additive genetic variance.
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