Introgressing multiple QTL in breeding programmes of limited size

The ability to enrich a breed with favourable alleles from multiple unlinked quantitative trait loci (QTL) of a donor breed through marker-assisted introgression (MAI) in a population of limited size was evaluated by considering the effects of the proportion selected, the size of the marker intervals, the number of introgressed QTL and the uncertainty of QTL position. Informative flanking markers were used to select progeny with the largest expected number of donor QTL alleles over five generations of backcrossing and five generations of intercrossing. In the backcrossing phase, with 5% selected and 20 cM marker intervals for three QTL, there were sufficient backcross progeny that were heterozygous for all markers, and QTL frequencies dropped below 0.5 only because of double recombinants. For higher fractions selected, longer marker intervals, and more QTL, frequency reductions from 0.5 were greater and increased with additional generations of backcrossing. However, even with 20% selected, three QTL, and marker intervals of 5 or 20 cM, mean QTL frequencies in generation 5 were 0.35 and 0.30, sufficient to allow subsequent selection of QTL in the intercrossing phase. After five generations of intercrossing, over 90% of individuals were homozygous for all QTL, and 85% when five QTL were introgressed. The higher the proportions selected, the longer the marker intervals, and larger numbers of introgressed QTL increased the number of intercrossing generations required to achieve fixation of QTL. Location of the QTL in the marked intervals did not affect QTL frequencies or the proportion of QTL lost at the end of the introgression programme. In conclusion, introgressing multiple QTL can be accomplished in a MAI programme of limited size without requiring that all individuals selected during the backcrossing phase to be carriers of favourable alleles at all QTL.