Quantitative trait loci mapping in F-2 crosses between outbred lines

We develop a mixed-model approach for QTL analysis in crosses between outbr ed lines that allows for QTL segregation within lines as well as for differ ences in mean QTL effects between lines. We also propose a method called "s egment mapping" that is based in partitioning the genome in a series of seg ments. The expected change in mean according to percentage of breed origin, together with the genetic variance associated with each segment, is estima ted using maximum likelihood. The method also allows the estimation of diff erences in additive variances between the parental lines. Completely fixed random and mixed models together with segment mapping are compared via simu lation. The segment mapping and mixed-model behaviors are similar to those of classical methods, either the fixed or random models, under simple genet ic models (a single QTL with alternative alleles fixed in each line), where as they provide less biased estimates and have higher power than fixed or r andom models in more complex situations, i.e., when the QTL are segregating within the parental lines. The segment mapping approach is particularly us eful to determining which chromosome regions are likely to contain QTL when these are linked.