Fig. 4

Gydle island containing the core yield region (defined by blue dotted lines, coordinates 671,200,000–675,300,000 bp). Assembled Gydle stage 2 sequences (orange, stage 2 with the genome segments based on BAC pools) aligned to Bionano maps (horizontal blue bars) in the top panel. The genome sequence within the bold dotted blue box in the top panel is the stage 3, finished, genome sequence region. The lower panel displays pairwise LD values (D’, [37]) between a total of 203 gene-based SNPs in same region across 863 diverse bread wheat accessions. Only common SNPs with high minor allele frequency (MAF > 0.3) are shown because common SNPs have high ability to define extent of LD and historical recombination patterns in diverse collections. The SNPs present within 2000 bp on either side of gene were included in this analysis. Color code: Bright red D’ = 1.0 and LOD > 2.0 (high LD); light shades of red indicate D’ < 1.0 and LOD > 2.0 (low-medium LD); white indicates D’ < 1.0 and LOD < 2.0 (no LD or complete decay)