Trait-based analysis in dairy cattle using blood group polymorphisms.

The potential of trait-based analysis to detect quantitative trait loci was investigated using blood group polymorphisms as the marker systems and milk and type traits in Holstein cattle as the quantitative traits. Within large half-sib families, animals were ranked on their predicted transmitted abilities or phenotypes, and blood group allele frequencies were compared between the upper and lower 5% tails of the distributions. Genotype frequencies within large families were also examined for evidence of selection. All of the major effects that had previously been detected using linear model analyses were identified by the trait-based analyses of a C blood group effect on rump angle, an L effect on milk yield and composition traits, an S effect on milk fat yield, and a direct effect of the M locus on milk and protein yields. These results provide additional support for the biological validity of these associations and also demonstrate the utility of trait-based analysis for the detection of quantitative trait loci within existing dairy breeding programs. However, just as in the linear model analyses, an analytical strategy should be utilized that allows the identification of the effects that are consistent across environments and genetic backgrounds.