Mapping quantitative trait loci in a selectively genotyped outbred population using a mixture model approach

A mixture model approach is employed for the mapping of quantitative trait loci (QTL) for the situation where individuals, in an outbred population, a re selectively genotyped. Maximum likelihood estimation of mo del parameter s is obtained from an Expectation-Maximization (EM) algorithm facilitated b y Monte Carlo sampling using a Gibbs sampler. All individuals with phenotyp es, whether genotyped or not, are included in the analysis where both putat ive QTLs and missing marker genotypes are sampled conditional on known mark er information and phenotype. A simulation of a half-sib family structure d emonstrates that this mixture model approach will yield unbiased estimates of the allelic effects of a QTL affecting the trait on which selective geno typing is based. Unbiased estimates were also obtained for the QTL effect o n a correlated trait provided both traits were analysed jointly in a bivari ate model. The procedure is also compared with a standard linear model appr oach. The application of these methods is demonstrated for bovine chromosom e six, the data arising from two Holstein-Friesian families selectively gen otyped for protein yield in a daughter design.