Enhancing backcross programs through increased recombination

ABSTRACT Introgression of a QTL by successive backcrosses is a strategy that can be used to improve elite lines (recurrent parent) by bringing in alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since one selects for the donor allele at the QTL, the elimination of the donor genome in the neighborhood of that QTL will be much slower (linkage drag). Using markers to monitor the genome around the QTL and in the background can accelerate the return to the recurrent parent genome. The success of an introgression will partly depend on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two aspects of recombination. Here, we assess, by simulation, their effect on the efficiency of introgression programs by studying the reduction of the linkage drag and the recovery of the recurrent genome. The selection schemes we simulate begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that when the QTL is in a region that was initially lacking crossovers, increasing the recombination rate can decrease the linkage drag nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region already rich in crossovers then increasing recombination proves to be detrimental. Key message In breeding programs, recombination is essential for introgression, but introducing more crossovers is beneficial only when the target is in a cold region, otherwise it is detrimental.