The analysis we have given for estimating effects of dominance and epistasis is for the classical method using simple averages over genotypes weighted by their frequencies, which are the least squares estimates in the balanced case and the basis for the analysis of variance [14],[15],[16]. There are alternative parameterisations aimed at exemplifying more clearly the nature of the interactions, including that of ‘physiological epistasis’ [45]. Whilst such alternatives may be of use in the analysis and interpretation of gene or QTL mapping experiments where individual genotypes can be identified or predicted from linked markers, such alternative parameterizations are not feasible in analysis of populations using data solely on the quantitative traits, from which the estimates of genetic variance components and heritability are obtained. Further, as has been pointed out [46], although the estimated effects may differ, the variances explained by different models are generally the same in segregating populations.
