The efficiency of molecular markers to improve genetic prediction has been
proved by many studies. Nevertheless, the additional cost due to marker gen
otyping is seldom considered in the comparison between marker-assisted sele
ction (MAS) and phenotypic selection. In the context of plant breeding, the
relative cost efficiency of MAS in the first cycle of selection is evaluat
ed through an analytical approach taking into account the effect of the exp
erimental design (population size, number of trials, and replications per t
rial) on quantitative trait loci (QTL) detection. The same global cost is a
ssumed for both methods. In a first step, the optimal allocation of the exp
erimental resources is studied for each method before comparing them at the
ir optimum. For traits sensitive to genotype x environment interactions, un
replicated trials are optimal for both methods but the optimal number of tr
ials is different. It increases with the investment for phenotypic selectio
n 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 co
mpared with phenotypic selection decreases with the cost of genotyping. Whe
n this cost is high, MAS interest is limited to traits with a low heritabil
ity, provided that the investment is high enough to evaluate a large popula
tion 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 tra
it heritability.