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 unknow n linkage phase of sire markers which occurs in the detection of quantitati ve trait loci (QTL) in a half-sib family structure when no information is a vailable on grandparents. The methods are compared by considering a Gaussia n approximation of the progeny likelihood instead of the mixture likelihood . In the first simulation study, the properties of the Gaussian model and o f the mixture model were investigated, using the simplest method for sire g amete reconstruction. Both models lead to comparable results as regards the test power but the mean square error of sib QTL effect estimates was large r for the Gaussian likelihood than for the mixture likelihood, especially f or maps with widely spaced markers. The second simulation study revealed th at 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. (C) Inra/Elsevier, Paris.