A general framework for marker-assisted selection.

Early simulation studies have showed that the inclusion of epistatic components (especially the additive-by-additive effects) into marker-assisted selection (MAS) can improve selection efficiency for a short-term breeding program. In this study I extend Lande and Thompson's theory to incorporate both additive and non-additive effects into MAS with reference to the mass selection case. Four different indices are analytically examined in terms of the type of genetic components involved in the marker scores: phenotype-, general combining ability (GCA)-, and GCA and reciprocal effects-based marker scores. The phenotype-based marker index is applicable to any population of non-random mating, while the other three indices are applicable to the synthetic population derived from diallel crosses. All these indices may have higher selection efficiencies than the index with solely additive effects-associated markers as long as the detectable transient non-additive effects are present. The improvement in selection efficiency depends on the magnitude of non-additive variances and the proportion of them explained by markers. The index with the phenotype-based marker scores operates on the whole of the additive and non-additive effects, and has the largest selection efficiency. The indices with the GCA-based marker scores operate only on additive and additive-by-additive genetic variation and have relatively small selection efficiencies. Inclusion of the markers from organelle genomes can also increase selection efficiency, depending upon the proportion of the total genetic variation attributable to organelle genomes and the proportion of them explained by organelle genomic markers. Sharing of markers among different marker scores does not facilitate the improvement of selection efficiency.