It is now well established that a single reference genome is not adequate to represent the genetic diversity of a species thus necessitating the need for pangenomes. In this direction, eight accessions representing three different ecotypes of Brassica napus (Rapeseed) were sequenced by Song et al. to develop B. napus pangenome. Each accession was separately assembled using PacBio, Illumina and HiC data to obtain eight high quality B. napus reference genomes. The comparative analysis of these assembled genomes identified 1.87−3.93 million single nucleotide polymorphisms and 0.98−1.48 million small insertions/deletions. Considering the importance of structural variations in shaping plant genomes, the study extensively explored SVs in B. napus genomes. A significant number of SVs were identified including 7.5−15.6 Mb inversions (40 large inversions of >50 Kb), 39.7−49.1 Mb translocations and 77.2−149.6 Mb presence absence variations (PAVs). The genes within these PAV regions were enriched in defense response, signal transduction and response to stress. Further, a pangenome was constructed with a total size of  ~1.8 Gb containing 105,672 gene clusters, of which 56% were core, 42% dispensable and ~2% species-specific. In this study, PAV-based GWAS was carried out which helped in identification of causal variations for silique length, seed weight and flowering time which were missed by SNP-based GWAS. The study highlighted the association of PAVs with three FLOWERING LOCUS C genes related to flowering time and ecotype differentiation. The results of the study very well demonstrated the need and utility of pangenome, contribution of SVs in deciphering plant phenotype and advantages of PAV-based GWAS. Overall, the study provides an important resource for crop improvement and also serves as a roadmap for further plant pangenome studies. (Summary by Vanika Garg) Nature Plants (10.1038/s41477-019-0577-7)