Marker-based inferences about epistasis for genes influencing inbreeding depression

We describe a multilocus, marker-based regression method for inferring interactions between genes controlling inbreeding depression in self-fertile organisms. It is based upon selfing a parent heterozygous for several unlinked codominant markers, then analyzing the fitness of progeny marker genotypes. If loci causing inbreeding depression are linked to marker loci, then viability selection is manifested by distorted segregation of markers, and fecundity selection by dependence of the fecundity character upon the marker genotype. To characterize this selection, fitness is regressed on the proportion of loci homozygous for markers linked to deleterious alleles, and epistasis is detected by nonlinearity of the regression. Alternatively, fitness can be regressed on the proportion of heterozygous loci. Other modes of selection can be incorporated with a bivariate regression involving both homozygote and heterozygote marker genotypes. The advantage of this marker-based approach is that "purging" is minimized and specific chromosomal segments are identified; its disadvantage lies in low statistical power when linkage is not strong and/or the linkage phase between marker and selected loci is uncertain. Using this method in the wildflower Mimulus guttatus, we found predominant multiplicative gene interaction determining fecundity and some negative synergistic (nonmultiplicative) interaction for viability.