A one-dimensional mixed model genome scan approach for detecting QTL-by-genetic-background interactions in diallel and nested association mapping designs

Abstract QTLs in multi-parent population (MPP) designs can be modelled as having parent-specific or family-specific allelic effects. QTLs with family-specific allelic effects point to epistatic interactions. We present a one-dimensional genome scan approach by mixed models using design matrices based on IBD probabilities to identify parent-specific and family-specific QTLs. We fit both parent- and family-specific QTLs along a genomic grid of evaluation points and use an information criterion to decide on the nature of significant QTLs. This combined QTL detection procedure for parent- and family-specific jointly is more powerful than an existing approach testing for parent-specific QTLs only. We demonstrate the properties and application of our approach on simulated and real data.