Effective Recombination in Plant Breeding and Linkage Mapping Populations: Testing Models and Mating Schemes.

Recombination of standing genetic variation results in novel genetic combinations and is the most important genetic phenomenon for increasing variation in breeding material and for QTL localization in linkage mapping. Effective recombination events are those events that can directly be observed using polymorphisms in progeny and are always less than the actual and expected numbers of recombination events. For both trait introgression breeding and high resolution mapping (and cloning) of QTL, the development of particular recombination events is critical. Because effective recombination is increasingly the limiting factor in an experiment, this study sought to mechanistically model these events across various types of linkage populations created under different distributions and parameters. Using a simulation approach, the number of markers needed to view all effective recombination events, the mean number of events and the variance of all events were evaluated under a number of scenarios. These recombination models were then tested against the large Zea mays Nested Association Mapping (NAM) dataset. Although the NAM dataset had significant differences in the number of effective recombination events across different populations and chromosomes, model parameters that fit the observed data could be identified. A direct relationship between the number of effective recombination events per generation and two times the heterozygosity was also observed. Application of this study will likely be useful for breeders to identify the most efficient production of recombination events and geneticists to develop better linkage mapping populations.