Backcrossing (or trait introgression) has long been a valuable strategy in plant breeding for a number of crops. The goal of backcrossing is to move a single trait of interest (e.g. disease resistance from a wild relative or a transgene from a donor line) into the genome of a commercially valuable variety without losing any part of the commercial variety's existing genome. The plant with the gene of interest is the donor parent, while the commercially viable variety is the recurrent parent.

Using DNA markers can accelerate a backcrossing program significantly. For example, most conventional corn backcrossing programs require 4-6 backcross generations before sufficient recurrent parent genome is recovered to release the line commercially.

Using markers allows a breeder to reach the same goal in 2 backcross generations thereby cutting 1-2 years of the product development cycle.

If linkage drag is a problem, markers that flank the gene of interest can be used to look for rare recombination events that break the linkage.

Marker-assisted backcrossing can be carried out with most marker types however IMP markers are particularly well suited to this task. Because each IMP reaction generates many, well distributed datapoints, it is possible to cover the genome by running only a handful (5-10) primers. IMP-assisted backcrossing can be carried out for a much lower cost compared to SSR markers.