Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

Abstract Background Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Results Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents. The vast majority (81%) of meiotic crossovers were mapped to less than 5 kb. The fine-scale accuracy of crossover detection was validated by Sanger sequencing for a subset of ten crossover events. We demonstrate that crossovers reside in genomic regions of “open chromatin”, which were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified nucleosomes. The genomic regions spanning crossovers were significantly enriched with the Stowaway family of miniature inverted-repeat transposable elements (MITEs). The occupancy of Stowaway elements in gene promoters is concomitant with an increase in recombination rate. A generalized linear model identified the presence of Stowaway elements as the third most important genomic or chromatin feature behind genes and open chromatin for predicting crossover formation over 10-kb windows. Conclusions Collectively, our results suggest that meiotic crossovers in potato are largely determined by the local chromatin status, marked by accessible chromatin, H3K4me3-modified nucleosomes, and the presence of Stowaway transposons

Additional file 1: of Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

Figure S1. The distribution of alternate alleles across the haplotypes of RH and US-W4. Figure S2. Window-based haplotyping by Bayesian inference. Figure S3. Identification of crossovers by logistic regression. Figure S4. Crossover interval length by data set. Figure S5. Comparison of expected and observed crossover counts per chromosome. Figure S6. Evaluation of segregation distortion in the W4M6 population. Figure S7. Comparison of different chromatin data sets with recombination rates. Figure S8. Crossovers have higher DNase-seq and H3K4me3 levels than empirical distributions of nearby regions. Figure S9. Intergenic crossovers have enriched DNase-seq and H3K4me3 signals. Figure S10. DNase-seq and H3K4me3 levels over intergenic crossovers. Figure S11. Recombination rate is correlated with Stowaway element density. Figure S12. H3K4me3 and DNase-seq at Stowaway transposons. (XLSX 37 kb

M7_type_a_snps.hiconf

M7_type_a_snps.hicon

less_than_85cov_85id_at_least_500_bp_removed_contamination_transcripts

less_than_85cov_85id_at_least_500_bp_removed_contamination_transcript

M11_type_a_snps.hiconf

M11_type_a_snps.hicon

DM_v4.04_assembly

Contains 2 files: potato_dm_v404_all_pm_un.fasta and potato_dm_ChrUn.gff

M3_type_a_snps.hiconf

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