Towards a Pangenome for Brassica napus Canola

With the increasing number of genome sequencing projects, there is growing evidence that a single individual is insufficient to capture the genetic diversity within a whole species due to gene presence absence variation. Therefore, the construction of a pangenome is essential as it can help us understand the variation within a species. The pangenome represents the complete set of genes for a given species. It is composed of core genes, which are present in all individuals, and variable or dispensable genes, which are present in some but not all individuals. Here we describe the construction of a pangenome for Brassica napus canola, which is one of the major oilseed crops in the world. There is currently only one public reference available for canola, which is the European winter variety, Darmor. While the availability of this genome reference can advance crop improvement, it is unknown how well it represents the genome diversity found in existing canola lines especially since extensive breeding has greatly reduced the genetic diversity present in those lines. We applied an iterative mapping and assembly approach to construct the canola pangenome. This is the first study of the Brassica napus canola pangenome and provides insight into canola genome diversity as a basis for genomics-based improvement of this important oilseed crop.