Economic efficiency of one cycle of marker-assisted selection

The efficiency of molecular markers to improve genetic prediction has been proved by many studies. Nevertheless, the additional cost due to marker genotyping is seldom considered in the comparison between marker-assisted selection (MAS) and phenotypic selection. In the context of plant breeding, the relative cost efficiency of MAS in the first cycle of selection is evaluated through an analytical approach taking into account the effect of the experimental design (population size, number of trials, and replications per trial) on quantitative trait loci (QTL) detection. The same global cost is assumed for both methods. In a first step, the optimal allocation of the experimental resources is studied for each method before comparing them at their optimum. For traits sensitive to genotype x environment interactions, unreplicated trials are optimal for both methods but the optimal number of trials is different. It increases with the investment for phenotypic selection while it becomes nearly equal to one for MAS. The loss of efficiency due to non-optimal designs is evaluated. The expected economic return of MAS compared with phenotypic selection decreases with the cost of genotyping. When this cost is high, MAS interest is limited to traits with a low heritability, provided that the investment is high enough to evaluate a large population size, which is the necessary condition to explain with markers a large part of genetic variation. The maximal genotyping cost that is acceptable for MAS to be efficient is given for different values of investment and trait heritability.