Fig. 2: Genome-wide characterisation of haplotype blocks.

a Length (upper) and gene number (middle) of haplotype blocks sampled at 500 Kbp intervals across all 21 chromosomes (positions scaled to % of maximum chromosome length). Boxplots show distributions of 1% bins. Insets show boxplots for chromosomal compartments (bottom) based on recombination (R1 + R3 > R2a + R2b > C)¹⁵. Pairwise Wilcox test with Benjamini–Hochberg multiple testing correction was used for statistical analysis. b Leftmost heatmap shows % of the genome (top row) or chromosomes contained within haplotype blocks for all cultivars. Jagger values are highlighted (middle), with a breakdown of how many other cultivars share these Jagger haplotype blocks. Rightmost panel shows the physical positions of Jagger haplotype blocks. c Summary of highly conserved haplotype blocks across all cultivars (shared with ≥ 5 cultivars; positions scaled to % of maximum chromosome length per cultivar). Values based on haplotype blocks called using 5-Mbp bins. RHT-B1 is indicated by a red arrowhead.