UNLOCKING THE GENETIC DIVERSITY OF MAIZE: MEIOTIC RECOMBINATION AS A DRIVER OF EVOLUTION AND BREEDING POTENTIAL
Meiotic recombination is the main driver and maintainer of genetic diversity. The purpose of recombination is to break linkages; this leads to more favorable haplotypes and allows selection to act more efficiently. However, the impact of recombination per generation is limited due to the biased distribution of recombination events and the low rate of recombination per meiosis. Therefore, investigating the recombination landscape of a major crop is critical to understand how recombination can be better utilized to increase gains in plant breeding efforts. To this effect, I utilized plant breeding simulations and found meiotic mutants that have increases in recombination can increase genetic gain over time compared to a wildtype recombination landscape. Our data also show additive genetic variance is maintained longer in the population with increased recombination which demonstrates the long-term benefit of increased recombination – more genetic variation for selection to act on. Although increasing the recombination rate in major crops is currently only theoretical, the recombination rates of wild populations have been shown to increase naturally under specific conditions. Recombination rate evolution has little empirical evidence to support it, however, it has been hypothesized recombination rates increased during most crop domestication events. I first explored this phenomenon with an experimental crossover dataset, and found maize has a 12% higher genome-wide recombination rate, compared to teosinte, and that this increase came from the longest chromosomes. Then, to fully explore the variation between the maize and teosinte recombination landscapes, we used the population genomics approach of ancestral recombination graph (ARG) inference to obtain a saturated recombination map for both populations. The ARG-inferred data show that the longest maize chromosomes have more recombination in interstitial chromosome regions compared to teosinte. Additionally, we found that this increase came from reduced crossover interference and furthermore, from ARG-inferred selection signatures, we found evidence for selection acting on recombination-related genes involved in CO interference. We concluded indirect selection on CO interference-related genes caused maize COs to be re-positioned toward gene-rich regions shielding them from the Hill-Robertson effect. In conclusion, my studies highlight the importance of meiotic recombination as a driver of genetic diversity within maize.