Mixed model analysis of quantitative trait loci

We develop a mixed model approach of quantitative trait locus (QTL) mapping for a hybrid population derived from the crosses of two or more distinguis hed outbred populations. Under the mixed model, we treat the mean allelic v alue of each source population as the fixed effect and the allelic deviatio ns from the mean as random effects so that we can partition the total genet ic variance into between- and within-population variances. Statistical infe rence of the QTL parameters is obtained by using the Bayesian method implem ented by Markov chain Monte Carlo (MCMC). This unified QTL mapping algorith m treats the fixed and random model approaches as special cases of the gene ral mixed model methodology. Utility and flexibility of the method are demo nstrated by using a set of simulated data.