A Method for Marker-Assisted Selection Based on QTLs with Epistatic Effects

A method for marker-assisted selection (MAS) based on quantitative trait loci (QTLs) with epistatic effects is proposed. The efficiency of such method is investigated by simulations under a wide range of situations. In the presence of epistasis, MAS generally yields longer persistence response than that based exclusively on additive or additive and dominance. Neglecting epistasis could result in considerable loss in response, and more pronounced at later generations. In addition to population size and trait heritability, genetic variance configurations play an important role in determining both the short- and long-term efficiencies of MAS. MAS using breeding values not only achieves higher response, but also tends to have smaller standard error than other methods in most cases. Errors in QTL detection cause distinct reductions in responses to MAS in most cases. It is thus concluded that verifications of putative QTL and its magnitude of effect and accurate map chromosome location are imperative to realize the potentials of MAS.