Searching for interacting QTL in related populations of an outbreeding species

Many important crop species are outbreeding. Th e search for genes aff ecting traits is complicated by the fact that in each cross up to four alleles may be present at each locus. Th is paper is concerned with the search for interacting loci, perhaps in the presence of non-interacting loci. Th e material that is used consists of populations which have been obtained by crossing a number of parent individuals (e.g. using an incomplete diallel cross). In practice, parent individuals may be related by pedigree. However, in this paper it will be assumed that the parents are unrelated. Th e consequences of genetic relationships between parents will be shown. Th e approach has two goals: (1) fi nding loci that are possibly interacting with other loci, and also fi nding loci that behave additively; (2) fi nding parent individuals which segregate at the interacting loci, and which can be used to study interactions in greater detail. In this paper QTL analysis is carried out by means of regression on predictions of QTL genotypes. Th e research for this paper was carried out within the EU funded project Hidras, a collaborative eff ort of 11 European groups to breed high-quality, disease resistant apples.