Utilisation of marker assisted selection in a commercial dairy cow population

Abstract

Abstract Genetic and economic benefits of marker assisted selection (MAS) to a commercial dairy cow population were evaluated by calculating selection advance resulting from four pathways of selection. In addition to background polygenic effects, a single additive quantitative trait loci (QTL) was segregating. Three sizes of QTL were assessed; 0.5, 1.0 and 2.0 genetic standard deviations ( σ G ) (difference between homozygotes), at each of four starting QTL frequencies; 0.01, 0.10, 0.35 and 0.75 over a thirty year time horizon. No recombination existed between QTL and a marker. Two MAS strategies were evaluated by comparison to a breeding scheme that had no genotypic knowledge of the QTL, over a thirty year time horizon. Economic benefits were calculated from the returns of extra milk produced (accounting for increased feed costs) less identification costs of the QTL and subsequent genotyping costs. In both strategies increase in QTL frequency was not immediate and thus returns were received in the later years of the analysis. The MAS strategy that utilised knowledge of QTL genotype for bull dams and bull sires had superior genetic gain at all QTL sizes and frequencies. However, it was only profitable for a 1.0 σ G QTL at 0.1 and 0.35 frequencies, and a 2.0 σ G QTL at all except the highest frequency (0.75). Long-term genetic loss was observed. The second MAS strategy of progeny testing only homozygous and heterozygous QTL bulls required a QTL of size 1.0 σ G at frequencies of 0.1 or 0.35 or a 2.0 σ G QTL at frequencies of 0.01, 0.1 and 0.35 to be more profitable than the current breeding scheme. The choice of MAS strategy should depend on QTL size and frequency.