Alternative models for QTL detection in livestock. II. Likelihood approximations and sire marker genotype estimations

In this paper, we compare four different methods of dealing with the unknown linkage phase of sire markers which occurs in the detection of quantitative trait loci (QTL) in a half-sib family structure when no information is available on grand-parents. The methods are compared by considering a Gaussian approximation of the progeny likelihood instead of the mixture likelihood. In the first simulation study, the properties of the Gaussian model and of the mixture model were investigated, using the simplest method for sire gamete reconstruction. Both models lead to comparable results as regards the test power but the mean square error of sib QTL effect estimates was larger for the Gaussian likelihood than for the mixture likelihood, especially for maps with widely spaced markers. The second simulation study revealed that the simplest method for sire marker genotype estimation was as powerful as complicated methods and that the method including all the possible sire marker genotypes was never the most powerful