Mapping and analysis of dairy cattle quantitative trait loci by maximum likelihood methodology using milk protein genes as genetic markers.

Maximum likelihood methodology was used to estimate effects of both a marker gene and a linked quantitative trait locus (QTL) on quantitative traits in a segregating population. Two alleles were assumed for the QTL. In addition to the effects of genotypes at both loci on the mean of the quantitative trait, recombination frequency between the loci, frequency of the QTL alleles and the residual standard deviation were also estimated. Thus six parameters were estimated in addition to the marker genotype means. The statistical model was tested on simulated data, and used to estimate direct and linked effects of the milk protein genes, beta-lactoglobulin, kappa-casein, and beta-casein, on milk, fat, and protein production and fat and protein percent in the Dutch dairy cattle population. beta-Lactoglobulin had significant direct effects on milk yield and fat percent. kappa-Casein had significant direct effects on milk yield, protein percent and fat yield. beta-Casein had significant direct effects on milk yield, fat and protein percent and fat and protein yield. Linked QTL with significant effects on fat percent were found for kappa-casein and beta-casein. Since the beta-casein and kappa-casein genes are closely linked, it is likely that the same QTL was detected for those two markers. Further, a QTL with a significant effect on fat yield was found to be linked to kappa-casein and a QTL with a significant effect on protein yield was linked to beta-lactoglobulin.