Statistical power for detecting epistasis QTL effects under the F-2 design

Epistasis refers to gene interaction effect involving two or more genes. Statistical methods for mapping quantitative trait loci (QTL) with epistasis effects have become available recently. However, little is known about the statistical power and sample size requirements for mapping epistatic QTL using genetic markers. In this study, we developed analytical formulae to calculate the statistical power and sample requirement for detecting each epistasis effect under the F-2 design based on crossing inbred lines. Assuming two unlinked interactive QTL and the same absolute value for all epistasis effects, the heritability of additive × additive (a × a) effect is twice as large as that of additive × dominance (a × d) or dominance × additive (d × a) effect, and is four times as large as that of dominance × dominance (d × d) effect. Consequently, among the four types of epistasis effects involving two loci, ''a × a'' effect is the easiest to detect whereas ''d × d'' effect is the most difficult to detect. The statistical power for detecting ''a × a'' effect is similar to that for detecting dominance effect of a single QTL. The sample size requirements for detecting ''a × d'', ''d × a'' and ''d × d'' are highly sensitive to increased distance between the markers and the interacting QTLs. Therefore, using dense marker coverage is critical to detecting those effects.