Mapping epistatic quantitative trait loci with one-dimensional genome searches

The discovery of epistatically interacting QTL is hampered by the intractab ility and low power to detect QTL in multidimensional genome searches. We d escribe a nerv method that maps epistatic QTL by identifying loci of high Q TL by genetic background interaction. This approach allows detection of QTL involved not only ill pairwise but also higher-order interaction, and does so with one-dimensional genome searches. The approach requires large popul ations derived from multiple related inbred-line crosses as is more typical ly available for plants. Using maximum likelihood, the method contrasts mod els in which QTL allelic values are either nested within, or fixed ol er, p opulations. We apply the method to simulated doubled-haploid populations de rived from a diallel among three inbred parents and illustrate the power of the method to detect QTL of different effect size and different levels of QTL by genetic background interaction. Further, we show how the method can be used in conjunction with standard two-locus QTL detection models that us e two-dimensional genome searches and find that the method ma) double the p ower to detect fil st-ur der epistasis.