Analytical and numerical comparisons of two methods of estimation of additive × additive interaction of QTL effects

epistasis (additive × additive interaction) plays an important role in the genetic architecture of complex traits. this study presents analytical and numerical comparisons of two methods of estimation of additive × additive interaction of qtl effects. in the first method, we observed only the plant phenotype, while in the second method we have additional information from the molecular markers observations. in this study, two data sets were analyzed: i) 150 barley (hordeum vulgare l.) doubled-haploid lines derived from the cross steptoe × morex and ii) 145 doubled-haploid lines of barley obtained from the cross harrington × tr306. in total, 153 sets of observations were analyzed. the additive × additive interaction effect calculated on the basis of the marker observations is smaller than the total additive × additive interaction effect obtained from phenotypic observations only.