Fig. 1: Characteristics of the GH06 and ZY821 genomes, phenotypes of the two parental lines and the two extreme bulks, and the QTL-seq results for the RILs.

a Circos plot showing the characteristics of the GH06 and ZY821 assemblies. I: Syntenic regions between the GH06 and ZY821 assemblies based on homology searches carried out with MCscan (python version). II: GC contents in non-overlapping 1-Mbp windows. III: Percent coverage of TEs in non-overlapping 1-Mbp windows. IV: Gene densities calculated based on the number of genes in non-overlapping 1-Mbp windows. V: Lengths of pseudo-chromosomes, with white and gray backgrounds representing the pseudo-chromosomes of GH06 and ZY821, respectively. Each ticket above the pseudo-chromosomes is on a scale of 10 Mbp. b Structural variation (SV) distribution between the GH06 and ZY821 genomes, with ZY821 serving as the reference sequence. c Schematic diagram of the technical roadmap for this study. The yellow- (Y1-Y25) and black-seeded (B1-B25) B. napus lines were used to construct the extreme bulks. Scale bar, 1.0 mm for GH06 and ZY821 and 0.5 mm for Y1–Y25 and B1-B25. d QTL-seq applied to the RIL populations identified the seed coat color locus. The permutation test was used for this analysis. Single nucleotide polymorphism (SNP)-index plots showing Δ(SNP-index) (in red) along the 19 chromosomes with statistical confidence intervals under the null hypothesis of no QTLs (green, P < 0.01; pink, P < 0.05). The red inverted triangle indicates the location of the significant locus.