Meiosis is a specialized cell division and fundamental to the gametogenesis. Meiotic recombination increases genetic diversity in a population. Meiotic recombination is initiated by programmed DNA double-strand breaks (DSBs) formation. The repair of DSBs leads to crossovers or non-crossovers via different DSB repair pathways. DSBs outnumber crossovers, thus only a few DSBs are repaired to crossovers. Anti-recombination factors restrict crossover number while interference causes even spaced crossover pattern by preventing coincidence of crossovers in the same pair of chromosomes. Intriguingly the DSBs and crossovers are non-uniform along chromosomes, typically occurring at narrow regions, called recombination hotspots. Plant meiotic recombination hotspots occur at gene promoters and terminators in euchromatin while heterochromatin is suppressed, indicating that chromatin structure influences recombination distribution (Choi et. al., 2013 Nature genetics, Choi et. al., 2018 Genome Research). Notably, the meiotic recombination process requires dynamic assembly and disassembly of meiotic protein complexes in time and space.
We aim to understand mechanistically how meiotic recombination is controlled by the interplay between meiotic proteins and the higher order of chromosome structure. To achieve this, we apply advanced methods of recombination measurements at different scales from single base-pair to genome (SPO11-oligonucleotide seq (~bp), pollen typing (~10 kb), fluorescent seed and pollen reporter systems (~1-5 Mb), genotyping-by-sequencing (genome)). Two key approaches are a genome-wide mapping of SPO11-oligonucleotides to determine meiotic DSBs sites in plants, and a forward genetic screen of crossover rate mutants via high-throughput fluorescent seed-scoring and tetrad analysis in Arabidopsis. We have developed "DeepTetrad", a deep learning-based image recognition package for pollen tetrad analysis that enables high-throughput measurements of crossover frequency and interference in individual plants. In addition, we are intensively using the CRISPR/Cas9 system, which enables us to edit genome and control gene expression for studying meiotic recombination in plants.
Importantly, our studies on meiotic recombination can help accelerate plant breeding for crop improvement by recombining or mapping useful genetic variations that occur spontaneously or by a result of mutagen in wild type plant accessions at particular areas and diverse domesticated varieties. New combinations of DNA variations contributing to crop productivity, disease resistance, fruit and grain quality can be generated by increasing crossover frequency between tightly linked alleles which had been hardly recombined along a chromosome. As soon as the useful DNA variations are identified by genetic mapping via increasing crossovers, a CRISPR/Cas9 system can be also applied to edit plant genomes of elite varieties.