Complex Genetic Effects in Quantitative Trait Locus Identification: A Computationally Tractable Random Model for Use in F2 Populations

Methodology for mapping quantitative trait loci (QTL) has focused primarily on treating the QTL as a fixed effect. These methods differ from the usual models of genetic variation that treat genetic effects as random. Computationally expensive methods that allow QTL to be treated as random have been explicitly developed for additive genetic and dominance effects. By extending these methods with a variance component method (VCM), multiple QTL can be mapped. We focused on an F(2) crossbred population derived from inbred lines and estimated effects for each individual and their corresponding marker-derived genetic covariances. We present extensions to pairwise epistatic effects, which are computationally intensive because a great many individual effects must be estimated. But by replacing individual genetic effects with average genetic effects for each marker class, genetic covariances are approximated. This substantially reduces the computational burden by reducing the dimensions of covariance matrices of genetic effects, resulting in a remarkable gain in the speed of estimating the variance components and evaluating the residual log-likelihood. Preliminary results from simulations indicate competitiveness of the reduced model with multiple-interval mapping, regression interval mapping, and VCM with individual genetic effects in its estimated QTL positions and experimental power.