Comparative sequence analysis showing differences in linkage disequilibrium (LD) and putative functional candidate gene content within haplotype blocks between homoeologous A-subgenome and C-subgenome QTL for (a,b) seed glucosinolate (GLS) and (c) erucic acid content on chromosomes (a) A02/C02, (b) A09/C09 and (c) A08/C03, respectively. Regions with strong (D’ = 1), high confidence LD (LOD > 2) are plotted bright red, lighter shades of red represent moderate LD (D’ < 1) with high confidence (LOD > 2), while light blue blocks represent weak, low confidence LD (D’ = 1, LOD < 2) and white blocks an absence of LD (D’ < 1, LOD < 2). Connecting lines show syntenic sequence alignments between the homoeologous QTL regions. Arrows show putative function candidate genes annotated to (a,b) glucosinolate biosynthesis or catalysis or (c) fatty acid or oil biosynthesis. Red arrows indicate genes under strong selection within conserved LD/haplotype blocks, whereas black arrows indicate that the corresponding gene at the homoeologous locus is not within a regions under strong selection. Gene names are given opposite the arrow positions on the homoeologue on which they are present.