Combined detection and introgression of QTL in outbred populations

The method consisting in combining QTL mapping and gene introgression has been extended from inbred to outbred populations in which QTL allele frequencies vary both in recipient and donor lines in different scenarios and for which polygenic effects are included in order to model background genes. The effectiveness of the combined QTL detection and introgression procedure was evaluated by simulation through four backcross generations.The allele substitution effect is underestimated when the favourable QTL allele is not fixed in the donor line. This underestimation is proportional to the frequency differences of the favourable QTL allele between the lines. In most scenarios, the estimates of the QTL location are unbiased and accurate. The retained donor chromosome segment and linkage drag are similar to expected values from other published studies.In general, our results show that it is possible to combine QTL detection and introgression even in outbred species. Separating QTL mapping and introgression processes is often thought to be longer and more costly. However, using a combined process saves at least one generation. With respect to the linkage drag and obligatory drag, the results of the combined detection and introgression scheme are very similar to those of traditional introgression schemes.In QTL mapping designs such as those using F2 or backcross animals, the power to detect QTL is based on the assumptions that all genes affecting the trait of interest are biallelic with alternative alleles fixed in each parental inbred line and that there is no genetic variation within the line. In some plant species and laboratory animals, highly inbred lines are available that may fulfil this condition, but many important species are outbreeders: such as livestock (e.g., [1]), trees (e.g., [2]), fish (e.g., [3]), as well as most wild species (e.g., [4]).However, detecting a QTL is only the first step in genetic improvement programs. When a QTL with desirable characteristi