A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. II. A simulation study.

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameters were estimated by marginal posterior means computed with a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), the event of linkage or nonlinkage, and the parameters (allele frequencies, QTL substitution effect, recombination rate, polygenic and residual variances). The analysis was evaluated empirically via application to simulated granddaughter designs consisting of 2000 sons, 20 related sires and their ancestors. Results obtained in this study and preliminary work on multiple linked markers and multiple QTLs support the usefulness of the Bayesian method for the statistical mapping of QTLs.