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, are selectively genotyped. Maximum likelihood estimation of mo del parameters is obtained from an Expectation-Maximization (EM) algorithm facilitated by Monte Carlo sampling using a Gibbs sampler. All individuals with phenotypes, whether genotyped or not, are included in the analysis where both putative QTLs and missing marker genotypes are sampled conditional on known marker information and phenotype. A simulation of a half-sib family structure demonstrates that this mixture model approach will yield unbiased estimates of the allelic effects of a QTL affecting the trait on which selective genotyping is based. Unbiased estimates were also obtained for the QTL effect on a correlated trait provided both traits were analysed jointly in a bivariate model. The procedure is also compared with a standard linear model approach. The application of these methods is demonstrated for bovine chromosome six, the data arising from two Holstein-Friesian families selectively genotyped for protein yield in a daughter design.