Fig. 3
The fine-scale recombination landscape around Arabidopsis centromere 3. A Genetic strategy to recover crossovers within the CTL3.9 FTL interval. FTL T-DNAs encoding red and green fluorescent proteins are indicated by triangles. The parental chromosomes are from the Col (blue) and Ler (red) accessions. Fluorescent micrographs of CTL3.9/++ segregating seed are shown to the right. B Cumulative genetic map (centiMorgans, cM) relative to CTL3.9 genomic coordinates plotted against the Col-CEN assembly derived from KASP genotyping of selected recombinant seed. The blue diagonal line shows a linear relationship, with the red and green lines showing the CTL3.9 T-DNAs. The position of CEN178 satellite repeats are shown as red (forward) and blue (reverse) ticks on the x-axis, in addition to 5S rDNA (purple). C Crossover frequency (centiMorgan per megabase, cM/Mb, blue) plotted within CTL3.9 derived from KASP genotyping and compared to measurements from mapping-by-sequencing (purple) for the same intervals. FTL T-DNAs are indicated by red and green vertical lines. Col/Ler KASP marker positions are indicated as x-axis ticks. The horizontal dotted line shows the genome average cM/Mb. Map intervals with significantly higher (HOTSPOT, HS) or lower (COLDSPOT, CS) crossover counts are shaded pink and blue, respectively. The black and purple bars beneath show the NRZ and LRZs. D As for C, but the frequency of CEN178 satellite repeats on forward (red) and reverse (blue) strands per 10 kb is shown, overlaid with CENH3 log2(ChIP/input) enrichment (green) and GBS cM/Mb (purple). E As for C, but showing gene density per 10 kb (green), overlaid with %GC content (blue). ATHILA retrotransposon positions are indicated by x-axis ticks (red). F As for C, but showing the proportion of DNA methylation in 10-kb windows for CG (red), CHG (blue), and CHH (green) contexts. G cM/Mb values for CTL3.9 map intervals are presented as scatter plots compared against DNA methylation, H3K9me2, REC8, ASY1 ChIP-seq, Gypsy/Ty3 transposons, CENH3 ChIP-seq, genes, SPO11-1-oligonucleotides, H3K4me3, and H2A.Z. Spearman’s correlation coefficient is printed inset, where significant. Information on chromatin datasets analyzed is available in Additional file 6: Table S2