Linkage disequilibrium and selection response in two‐stage marker‐assisted selection of dairy cattle over several generations

Summary A stochastic simulation was carried out to investigate the advantage of marker-assisted selection (MAS) in comparison with traditional selection over several generations. The selection goal was a sex-limited trait or a linear combination of traits with a polygenic component, two unlinked additive QTL and a non-genetic component. The simulated QTL were moderate or large and the allele frequencies were varied. Two stages of selection among the male offspring were carried out. In the first stage marker information was used to select among full sibs (MAS) or one full sib was chosen at random. In the second stage young bulls were selected based on a progeny test. The response in total genetic gain was faster with MAS than with traditional selection and persisted over several generations. With a QTL of moderate size and initial allele frequencies of the favourable allele of 0.05 the response with MAS was 6% higher than with traditional selection in the sires selected after progeny test. MAS in a within-family two-stage selection scheme improved the genetic merit of selected bulls even when linkage disequilibrium between QTL and polygenes was initially increased.