Fig. 4: Low-recombination haplotype blocks and their stability and selection during breeding and domestication.
a, Distribution of presence (red) or absence (blue) of low-recombination haplotype blocks (red) in each pseudo-molecule of the A (A01–A13) and D (D01–D13) subgenomes in Gh. Map positions (Mb) are indicated in the y axis. b, A low-recombination haplotype block near the pericentromeric region (~72 Mb) of chromosome A08 (bottom). The color indicates the coefficient of linkage disequilibrium (D′) from low (blue) to high (red) with the upper confidence bound (D′ = 0.90) for the recombination cutoff. The recombination rates (y axis; using locally estimated scatterplot smoothing (LOESS) regression, Methods and Supplementary Note) in Gb × GhF2 (blue), Gm × GhBC1F1 (green), Gt × GhBC1F1 (yellow) and the consensus (red) are shown above with the positions (Mb, x axis). Two elevated recombination events are detected in Gb × GhF2 (blue arrows) and one in Gm × GhBC1F1 (green arrow). c, The average percentage (%) of CG (circle), CHG (triangle) and CHH (cross) methylation in the recombination hotspots (red) and cold spots (blue) between Gb and Gh. The CHH methylation is clustered in the left lower corner, which is visible in an enlarged image (Extended Data Fig. 10a).
