Use of genomic models to study genetic control of environmental variance

Vast amount of genetic marker information is being used to obtain insight into the genetic architecture of complex traits, for locating genomic regions (quantitative trait loci (QTL)) affecting disease and for enhancing the accuracy of prediction of genetic values in selection programmes. The genomic model commonly found in the literature, with marker effects affecting mean only, is extended to investigate putative effects at the level of the environmental variance. Two classes of models are proposed and their behaviour, studied using simulated data, indicates that they are capable of detecting genetic variation at the level of mean and variance. Implementation is via Markov chain Monte Carlo (McMC) algorithms. The models are compared in terms of a measure of global fit, in their ability to detect QTL effects and in terms of their predictive power. The models are subsequently fitted to back fat thickness data in pigs. The analysis of back fat thickness shows that the data support genomic models with effects on the mean but not on the variance. The relative sizes of experiment necessary to detect effects on mean and variance is discussed and an extension of the McMC algorithm is proposed.