A method for multiple trait quantitative trait loci estimation in F₂ crosses between outbred lines

A new mixed model approach for analysing F2 crosses between outbred lines is proposed for multiple trait QTL mapping. The multiple trait F1 origin mapping technique models additive genetic effects in the F1 generation resulting in a significant reduction in the order of genetic covariance matrices and hence significantly reduces the number of mixed model equations. This property allows the rapid computation of Restricted Maximum Likelihood (REML) variance components over a number of quantitative traits. Furthermore allele substitution effects are modeled in the F1 generation using Best Linear Unbiased Prediction (BLUP). A simulation study is carried out on bivariate trait data to demonstrate the potential benefit of using multiple trait F1 origin mapping with multiple traits and to compare multiple trait QTL mapping with single trait QTL mapping. Analyses are performed by coupling the new approach with the computer software program ASREML providing a flexible and efficient tool for multiple trait QTL studies.