A mixed model QTL analysis for a complex cross population consisting of a half diallel of two-way hybrids in Arabidopsis thaliana : analysis of simulated data

To improve QTL detection power for QTL main effects and interactions and QTL mapping resolution, new types of multi-founder crossing populations are created in plants and animals. Some recent examples are complex intercrossed populations in mice and Arabidopsis thaliana. For the latter, a set of eight accessions was intercrossed to produce four two-way hybrids that were subsequently intercrossed again in a half diallel fashion leading to six subpopulations of four-way hybrids, each subpopulation containing 100 individuals. Within each subpopulation, individuals were inbred for four generations via single seed descent. QTL mapping in the complex crosses requires new statistical tools. We present a first sketch of a QTL mapping methodology for the complex cross in Arabidopsis based on mixed model analyses. As experimental data were not yet available, we illustrate our methodology on simulated but realistic data.