Marker-assisted introgression using non-unique marker alleles II: selection on probability of presence of the introgressed allele

If marker alleles that identify a gene for introgression are not completely unique to the different base populations, the trait allele can be lost quickly during the process of backcrossing. This study considers ways to deal with incompletely informative markers in order to retain the desired allele. Selection was based on the probability of the presence of the desired (introgressed) trait allele, which was calculated for each marker genotype, using a single marker or a diallelic or triallelic marker bracket. The percentage of individuals retaining the introgressed allele was calculated over five generations of backcrossing, for selected fractions between 0 and 1, for marker alleles that could occur in both base populations. The best results were obtained with a rather large selected fraction, when all individuals, heterozygous and homozygous for the most desirable allele at the marker loci, were selected. Additional selection against marker homozygotes (which might have the highest probability of carrying the desired-trait allele, but produce uninformative gametes) altered the optimum selected fraction, making the selected fraction more consistently inversely related to a better retention of the desired-trait allele. A marker bracket was found to give a better retention of the desired-trait allele than a single marker and triallelic markers were better than diallelic markers, giving a retention of almost 50%. The earlier that preselection of parents (on informativeness) took place the better the overall result; preselection should occur preferably in the base populations. Preselection could make marker alleles unique to alternative base populations and markers would effectively become fully informative. Selection in the base populations might not be possible or not desirable, for example, because of the available number of individuals. This is unlikely to be a problem when parents are paired up to exclude any common marker alleles.