Fig. 5
Genetic and epigenetic control of crossover frequency within CTL3.9 and the HS6 hot spot. A Derived cleaved amplified polymorphic sequence (dCAPS) markers were used to map crossovers within HOTSPOT6 (HS6) and calculate cM/Mb. The numbers printed above the plot line show the number of crossovers identified in each interval. The midpoints of crossovers mapped by sequencing, as in Fig. 1, are indicated as purple ticks along the top axis. Gene annotation (red) is shown underneath, in addition to Gypsy/Ty3 (blue), LINE1 (dark blue), MuDR (green), hAT (pink), and Helitron (brown) transposon annotations. B Plots of the HS6 interval showing ONT-derived DNA methylation (%) in CG (red), CHG (blue), or CHH (green) sequence contexts, ChIP-seq enrichment (log2(ChIP/input)) for H2A.W6 (light purple), H2A.W7 (dark purple), H3K27me3 (blue), H2A.Z (blue), ASY1 (dark red), and REC8 (red), RNA-seq from floral (orange) and leaf (yellow) tissue, and SPO11-1-oligos (dark red). Information on chromatin datasets analyzed is available in Additional file 6: Table S2. C CTL3.9 crossover frequency (cM) in wild type, cmt3, met1-3/+, and HEI10, in an otherwise Col/Col homozygous background. Measurements from individuals are shown as circles. Horizontal blue lines represent the mean and the standard error of the mean. Red stars indicate samples which are significantly different from wild type using Wilcoxon tests, whereas “n.s.” indicates a non-significant difference. D As for C, but analyzing wild type, atxr5 atxr6, ligaseIV, mom1, and smc4-1 mutants in a Col/Col homozygous background. E As for C, but with genotypes in a Col/Ler hybrid background, and with the addition of recq4a recq4b. F Comparison of crossover frequency (cM/Mb) in wild type, recq4a recq4b and HEI10, generated by SSLP mapping in Col/Ler F2 populations. The position of the CTL3.9 T-DNAs is indicated by green and red vertical lines. The density of CEN178 on the forward (red) and reverse (blue) strands are plotted. Crossover counts per interval were compared between genotypes using chi-square tests. Asterisks indicate intervals that had significantly different counts between wild type and HEI10 or recq4a recq4b