Reducing the bias of estimates of genotype by environment interactions in random regression sire models

The combination of a sire model and a random regression term describing genotype by environment interactions may lead to biased estimates of genetic variance components because of heterogeneous residual variance. In order to test different models, simulated data with genotype by environment interactions, and dairy cattle data assumed to contain such interactions, were analyzed. Two animal models were compared to four sire models. Models differed in their ability to handle heterogeneous variance from different sources. Including an individual effect with a (co)variance matrix restricted to three times the sire (co)variance matrix permitted the modeling of the additive genetic variance not covered by the sire effect. This made the ability of sire models to handle heterogeneous genetic variance approximately equivalent to that of animal models. When residual variance was heterogeneous, a different approach to account for the heterogeneity of variance was needed, for example when using dairy cattle data in order to prevent overestimation of genetic heterogeneity of variance. Including environmental classes can be used to account for heterogeneous residual variance.