Using markers to reduce the variation in the genomic composition in marker-assisted backcrossing

Marker-assisted introgression or backcrossing is a widely used method to improve commercial breeding lines or study the effects of genes in a homogeneous genetic background. In this context, the recovery of the recipient parent genome is a major objective of backcrossing. Selection on markers has been shown to be very useful to accelerate the rate of recovery of the recipient parent genome in backcrossing. In this study we show how much information markers give on the true genetic composition of individuals by deriving the variance and estimating the distribution of the genetic composition of individuals sharing a known genotype at markers. These calculations enable predictions of the number of individuals carrying an ideal genotype at markers that must be produced to fulfil background selection objectives.