Meiotic recombination is associated with open chromatin in potato. Solanum tuberosum

Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic recombination maps have been developed in numerous plant species since late the 1980s, very few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic recombination. Using a whole genome sequencing based approach, we developed an ultra-high resolution reference-based haplotype map using two diploid potato clones as parents. The vast majority (~80%) of maternal meiotic recombination breakpoints were mapped to less than 2 kilobases. We demonstrate that these breakpoints reside in genomic regions of “open chromatin”, which were identified based on their hypersensitivity to DNase I digestion. The genomic regions spanning recombination breakpoints were significantly enriched with the TcMar-Stowaway family of miniature inverted-repeat transposable elements (MITEs). TcMar-Stowaways were also associated with features consistent with cis-regulatory function and their presence in gene promoters is concomitant with an increase in the local recombination rate. Collectively, our results suggest that maternal meiotic recombination breakpoints in potato are largely determined by the local chromatin status, marked by accessible chromatin, and are associated with TcMar-Stowaway transposons.