Efficiency of multistage marker-assisted selection in the improvement of multiple quantitative traits

The application of marker-assisted selection (MAS) to breeding programmes depends on its relative cost and the expected economic return compared to conventional phenotypic selection. The relative efficiency of MAS can be increased through a two-stage selection scheme or through marker-based, multiple-trait improvement. However, the effectiveness of these alternatives has not been quantified. In this study, we evaluate the efficiency of MAS relative to conventional phenotypic selection and marker-only selection in multistage selection for the improvement of multiple traits. We further incorporate the costs of obtaining measurements on phenotypic characters and marker loci into the objective function to evaluate the efficiency of MAS with respect to the gain per unit cost. Deterministic analyses indicate that excluding costs, multiple-trait MAS can be used to increase the aggregate breeding values in quantitative characters and is expected to be more effective than conventional selection or single-trait MAS. Two-stage MAS has a slightly reduced gain because of culling in the first stage. If the objective function is to maximize the gain per unit cost, multiple-trait MAS is inferior to phenotypic selection in most of the selection schemes investigated when the cost ratio ( r ) of obtaining measurements on phenotypic characters to scoring marker loci is less than unity ( r ≤1.0) and the heritability ( h 2 ) is greater than 0.3. The efficiency of MAS increases as r increases and h 2 decreases. For MAS to be more effective, it is necessary to decrease further the cost associated with molecular marker assays.