| Meiotic recombination is responsible for the generation of nascent haplotypes, therefore providing the molecular framework for genetic variation in populations of sexually reproducing organisms. Despite this importance, the genomic and epigenomic determinants of meiotic crossover locations in plants genomes have remained poorly understood. Thus, high-resolution crossover maps (less than 5-kb intervals) were generated via empirical observations and the estimation of historical recombination rates, in potato and rice, respectively. Investigation of the underlying fine-scale genomic features revealed that crossovers were significantly associated with promoters (2-kb upstream gene transcription start sites) and the 1-kb downstream regions of genes. Coincident with their genomic organization, crossovers exhibited chromatin states consistent with active transcription, including increased chromatin accessibility and H3K4me3, consistent with observations in other model organisms. By accounting for the enrichment of crossovers relative to gene bodies, it was discovered that chromatin accessibility and H3K4me3 are intrinsic features of crossovers, regardless of the underlying genomic context. Interestingly, crossovers in both plant species were highly enriched with short repetitive DNA elements, namely the Stowaway family of MITE transposons. The presence of Stowaway transposons in crossover hotspots was accompanied by statistically greater peak recombination rates, suggesting that these elements may act as recombination enhancers. Furthermore, genomic and epigenomic analysis of these transposons within rice crossover hotspots revealed a linear relationship between counts of Stowaway transposons, increased chromatin accessibility, decreased DNA methylation, and signatures of genetic differentiation and diversity. Collectively, these results implicate the genomic, chromatin, and evolutionary features that underlie meiotic crossovers in plants. |
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