The use of marker haplotypes in animal breeding schemes

Information on marker haplotypes was used to increase rates of genetic gain in closed nucleus breeding schemes. The schemes were simulated for ten discrete generations: firstly five generations of conventional (non-MAS) and then five generations of marker-assisted selection (MAS). The inheritance of quantitative trait loci (QTL) alleles was traced by marker haplotypes with probability 1 - r. Emphasis was on extra genetic gains during the early generations of MAS, because it was assumed that new QTL were detected continuously. In the first generation of MAS, genetic gain was increased by 8.8 and 38%, when selection was, respectively, after the recording of the trait leg, selection for growth rate) or before (eg, fertility). The marked QTL explained 33% of the genetic variance, and r = 0.1. The extra genetic gain decreased with the number of generations of MAS as the variance of the QTL became more and more exploited. The extra response rates due to MAS increased more than proportionally to the variance of the QTL and they increased with decreasing heritabilities. When r increased from 0.05 to 0.2, the genetic gain from MAS decreased by only 7.7% (selection before recording). MAS was approximately equally efficient for sex-limited and non-sex-limited traits. In the case of a carcass trait, which is measured after slaughtering, extra response rates were up to 64%. If recording was after selection, additional genetic gains increased markedly with increasing numbers of offspring per dam, because markers rendered within-family selection feasible in this situation. It was concluded that the extra rates of gain from MAS can be large when there is a continuous detection of new QTL, and when selection is before the recording of the trait.