Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained large-effect mutations or structural variations. PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

油菜籽 ( Brassica napus ) 是世界上第二重要的油料作物，但其巨大的表型变异背后的遗传多样性在很大程度上仍未被探索。在这里，我们报告了八个欧洲油菜的测序、从头组装和注释加入。使用泛基因组比较分析，确定了数百万个小变异和 77.2-149.6 兆碱基存在和缺失变异 (PAV)。超过 9.4% 的基因含有大效应突变或结构变异。基于 PAV 的全基因组关联研究 (PAV-GWAS) 直接确定了以 ZS11（参考线）为供体的嵌套关联作图群体中角果长度、种子重量和开花时间的因果结构变异，这些变异未被单-基于核苷酸多态性的 GWAS (SNP-GWAS)，证明 PAV-GWAS 在识别性状关联方面与 SNP-GWAS 互补。进一步的分析表明，三个FLOWERING LOCUS C中的 PAV基因与开花时间和生态型分化密切相关。这项研究提供了资源，以支持更好地了解欧洲油菜的基因组结构和加速遗传改良。