Further insights of the variance component method for detecting QTL in livestock and aquacultural species: relaxing the assumption of additive effects

Abstract

Complex traits may show some degree of dominance at the gene level that may influence the statistical power of simple models, i.e. assuming only additive effects to detect quantitative trait loci (QTL) using the variance component method. Little has been published on this topic even in species where relatively large family sizes can be obtained, such as poultry, pigs, and aquacultural species. This is important, when the idea is to select regions likely to be harbouring dominant QTL or in marker assisted selection. In this work, we investigated the empirical power and accuracy to both detect and localise dominant QTL with or without incorporating dominance effects explicitly in the model of analysis. For this purpose, populations with variable family sizes and constant population size and different values for dominance variance were simulated. The results show that when using only additive effects there was little loss in power to detect QTL and estimates of position, using or not using dominance, were empirically unbiased. Further, there was little gain in accuracy of positioning the QTL with most scenarios except when simulating an overdominant QTL.