An appropriate strategy to estimate variance components and breeding values in genetic models with quantitative trait loci (QTL) was developed for a dairy cattle breeding scheme by utilizing simulated data. Reliable estimates for variance components in QTL models are a prerequisite in fine-mapping experiments and for marker-assisted genetic evaluations. In cattle populations, only a small fraction of the population is genotyped at genetic markers, and only these animals are included in marker-assisted genetic evaluation models. Phenotypic information in these models are precorrected phenotypes [daughter yield deviations (DYD) for bulls, yield deviations (YD) for cows] estimated by standard animal models from the entire population. Because DYD and YD may represent different amounts of information, the problem of weighting these 2 types of information appropriately arises. To detect the best combination of phenotypes and weighting factors, a stochastic simulation for a trait representing milk yield was used. The results show that DYD models are generally optimal for estimating QTL variance components, but properties of estimates depend strongly on weighting factors. An example for the benefit in selection of using YD is shown for the selection among paternal half-sibs inheriting alternative QTL alleles. Even if QTL effects are small, marker-assisted best unbiased linear prediction can improve the selection among half-sibs, because the Mendelian sampling variance within family can be exploited, especially in DYD-YD models. Marker-assisted genetic evaluation models should also include YD for cows to ensure that marker-assisted selection improves selection even for moderate QTL effects (> or =10%). A useful strategy for practical implementation is to estimate variance components in DYD models and breeding values in DYD-YD models.