A comparison of two methods to estimate additive-by-additive interaction of QTL effects by a simulation study

Additive-by-additive epistasis plays an important role in the genetic architecture of complex traits. The parameter connected with the additive-by-additive interaction can influence decisions concerning usefulness of the breeding material for the generation of new genotypes with characteristics improved over the parental forms. This study presents comparisons of two estimation methods of additive-by-additive interactions of QTL effects by the Monte Carlo simulation study. In the first method we assume that we observed only the plant phenotype, while in the second method we have additional information from the molecular marker observations. The obtained results show that the additive-by-additive interaction effect calculated on the basis of the marker observations is always smaller than the total additive-by-additive interaction effect obtained from phenotypic observations only. The lack of influence of the distance between markers and the number of linkage groups on the estimation of effects of additive-by-additive epistasis interaction genes by the two methods shows that both these methods may be used for different genetic maps and for different plant species.