Meiotic Recombination Breakpoints Are Associated with Open Chromatin and Enriched with Repetitive DNA Elements in Potato

Meiotic recombination provides the framework for the genetic variation in natural and artificial populations of eukaryotes through the creation of novel haplotypes. Thus, determining the molecular characteristics of meiotic recombination remains essential for future plant breeding efforts, which heavily rely on recombination-mediated genetic variation. To date, very few genetic maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Using a whole genome sequencing based approach, we developed an ultra-high resolution reference-based haplotype map using a one-way pseudotestcross potato F₁ population. The vast majority (~80%) of meiotic recombination breakpoints were mapped to fine resolution. We demonstrate that “open chromatin” is an intrinsic feature of breakpoints and that breakpoints are significantly enriched in specific repetitive DNA elements. These breakpoint-associated repeats are characterized by features consistent with cis-regulatory function and their presence in gene promoters is associated with elevated local recombination rate. Collectively, our results suggest that meiotic recombination breakpoints are largely determined by the local chromatin status, and are associated with specific repeats in potato.