Fig. 6

Remodelling of the centromere-proximal crossover landscape in wild type, cmt3, and met1/+. A Genetic strategy to recover crossovers within the CTL3.9 centromeric FTL interval from cmt3 and met1/+ mutants. 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. B Cumulative genetic map (centiMorgans, cM) relative to CTL3.9 genomic coordinates against the Col-CEN assembly in wild type, cmt3, and met1/+. The blue diagonal lines show a linear relationship, with the red and green vertical/horizontal lines showing the location of 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 Plots of crossover frequency (centiMorgans per Megabase, cM/Mb) within CTL3.9 in wild type (black) and cmt3 (red) projected against the Col (upper) or Ler (lower) assemblies, with mean values shown by dotted horizontal lines. The position of KASP genotyping markers are indicated as black x-axis ticks, and CTL3.9 T-DNAs are indicated by red and green lines, and connected between the maps by lines. The LRZs (purple) and NRZ (black) as defined in wild type are shown as colored blocks above and below the plots. D As for C, but plotting wild type (black) and met1/+ (red) crossover frequency (cM/Mb). E CTL3.9 crossover frequency (cM/Mb) in wild type (upper), cmt3 (middle), and met1/+ (lower), with significantly high (hot spots, pink) and low (cold spots, blue) intervals shown by colored shading. F Plots of DNA methylation (%) across CTL3.9derived from BS-seq data in wild type, cmt3, and met1 [70, 71], colored according to CG (red), CHG (blue) and CHH (green) sequence contexts. The position of the flanking CTL3.9 T-DNAs are indicated by black vertical lines. Information on DNA methylation datasets analyzed is available in Additional file 6: Table S2