Targeted recombination refers to inducing or selecting for a recombination event at genomic positions that maximize genetic gain in a cross.

A previous study indicated that targeted recombination could double the rate of genetic gains in maize (Zea mays L.), a cross-pollinated crop for which historical genetic gains have been large. Our objectives were to determine whether targeted recombination can sufficiently increase predicted gains in self-pollinated species, and whether prospective gains from targeted recombination vary across crops, populations, traits, and chromosomes. Genomewide marker effects were estimated from previously published marker and phenotypic data on 21 biparental populations of soybean [Glycine max (L.) Merr.], wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and pea (Pisum sativum L.). With the predicted gain from nontargeted recombination as the baseline, the relative gains from creating a doubled haploid with up to one targeted recombination [RG(x1)] and two targeted recombinations [RG(x2)] per chromosome or linkage group were calculated. Targeted recombination significantly (P = 0.05) increased the predicted genetic gain compared to nontargeted recombination for all traits and all populations, except for plant height in barley. The mean RG(x1) was 211%, whereas the mean RG(x2) was 243%. The predicted gain varied among traits and populations. For most traits and populations, having targeted recombination on less than a third of all the chromosomes led to the same or higher predicted gain than nontargeted recombination. Together with previous findings in maize, our results suggested that targeted recombination could double the genetic gains in both self- and cross-pollinated crops.