Superiority of QTL-assisted selection in dairy cattle breeding schemes

The superiority of selection schemes employing information about a known quantitative trait locus (QTL) over conventional schemes is examined for dairy cattle breeding schemes. Stochastic simulation of a dairy cattle population with selection practices, structures, and parameters similar to the US Holstein population was implemented. Additive genetic effects were estimated by an animal model. Two schemes were compared: a QTL-assisted selection scheme in which the genotype of a known QTL was accounted for in the animal model as a fixed factor, and a QTL-free selection scheme in which the QTL was simulated but was not fit separately in the animal model. Under the QTL-assisted selection scheme, all animals in the mixed model were assumed to be genotyped for the QTL. The effect of using QTL information on the genetic response, the frequency of the favorable QTL allele, and the accuracy of evaluation were examined. Moreover, the effect was studied in four distinct paths of selection: active sires, proven young bulls, bull dams, and first-lactation cows. Average superiority values of 4.6, 7.6, 11.7, and 1.1% for genetic response were observed over 16 yr of selection for active sires, young bulls, bull dams, and first-lactation cows, respectively. Frequency of the favorable QTL allele changed faster in bull dams than males, and was the slowest in first-lactation cows. Finally, accuracy of evaluation under the QTL-assisted selection scheme was higher than under the QTL-free selection scheme. Young bulls of the QTL-assisted selection scheme on average had 0.049 higher accuracy, and first-lactation cows had on average 0.185 higher accuracy than corresponding animals of the QTL-free selection scheme.