Quantitative genetic variance associated with chromosomal markers in segregating populations

Use of chromosomal markers can accelerate genetic progress for quantitative traits in pedigree selection programs by providing early information on Mendelian segregation effects for individual progeny. Potential effectiveness of selection using markers is determined by the amount of additive genetic variance traced from parents to progeny by the markers. Theoretical equations for the amount of additive genetic variance associated with a marker were derived at the individual level and for a segregating population in joint linkage equilibrium. Factors considered were the number of quantitative trait loci linked to the marker, their individual effects, and recombination rates with the marker. Subsequently, the expected amount of genetic variance associated with a marker in a segregating population was derived. In pedigree selection programs in segregating populations, a considerable fraction of the genetic variance on a chromosome is expected to be associated with a marker located on that chromosome. For an average chromosome in the bovine, this fraction is approximately 40% of the Mendelian segregation variance contributed by the chromosome. The effects of interference and position of the marker on this expectation are relative small. Length of the chromosome has a large effect on the expected variance. Effectiveness of MAS is, however, greatly reduced by lack of polymorphism at the marker and inaccuracy of estimation of chromosome substitution effects. The size of the expected amount of genetic variance associated with a chromosomal marker indicates that, even when the marker is not the active locus, large chromosome substitution effects are not uncommon in segregating populations.