Telomere-to-telomere genome assembly of yellow-seeded rapeseed reveals BnaSCC1 regulates seed coat color and oil accumulation.
Yellow-seeded rapeseed has higher oil content and seed quality than black-seeded varieties, but its genetic basis remains unclear. We report a telomere-to-telomere genome assembly of yellow-seeded rapeseed GH06 (981.18 Mb; contig N50, 56.93 Mb) generated with PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C sequencing. The GH06_SWU assembly shows high completeness, accuracy, and continuity, with 110,096 annotated protein-coding genes. Using GH06_SWU, GWAS of seed coat color in 504 accessions identifies a seed coat color-associated BnaSCC1 on chromosome A10. CRISPR-Cas9 knockout of BnaSCC1 inhibits seed coat pigmentation and increases seed oil content (SOC) by 3.37 percentage points on average. Multi-omics analyses show that BnaSCC1 disruption is associated with reduced flavanol glycoside accumulation, elevated triacylglycerol levels, and increased oil body number. Haplotype analysis links BnaSCC1Hap2 with lighter seed coat color, higher oil and oleic acid contents, and lower erucic acid content, supporting its use in marker-assisted breeding.