Power of tests for QTL detection using replicated progenies derived from a diallel cross

In crop species, most QTL (quantitative trait loci) mapping strategies use segregating populations derived from an initial cross between two lines. However, schemes including more than two parents could also be used. We propose an approach using a high-density restriction fragment length polymorphism (RFLP) map established on six F 2 populations derived from diallel crosses among four inbred lines and the phenotypic performances of two types of replicated progenies (F 3 and topcross). The QTL is supposed to be on the marker locus considered. Three linear model tests for the detection of QTL effects (T 1, T 2 and T 3) are described and their power studied for the two types of progeny. T 1 tests the global genetic effects of the QTL (additivity and dominance) and T 2 tests only additive effects assuming dominance is absent when it could exist. The models of these two tests assume that the main effects of QTL alleles are constant in different genetic backgrounds. The additive model of test T 3 considers the six F 2 populations independently, and T 3 is the equivalent of the classical mean comparison test if we neglect dominance; it uses only contrasts between the homozygote marker classes. The results show that T 2 is much more powerful than T 3. The power of T 1 and T 2 depends on the relative sizes of the additive and dominance effects, and their comparison is not easy to establish. Nevertheless, T 2 seems to be the more powerful in most situations, indicating that it is often more interesting to ignore dominance when testing for a QTL effect. For a given size of genetic effects, the power is affected by the total number of individuals genotyped in F 2 and the recombination rate between the marker locus and the putative QTL. The approach presented in this paper has some drawbacks but could be easily generalized to other sizes of diallels and different progeny types.