Brassica napus NRCDH4079 Genome Assembly and Annotation

A key challenge for the genetic improvement of canola (Brassica napus), one of the world’s most important oilseeds, is the limited natural variation for commercially important traits. The creation of new variation is further hindered by the lack of functional knowledge about genes controlling these traits. Ploidy and genomic duplications in canola complicate the effective transfer of functional insights from Arabidopsis. Here, we report a novel functional genomics platform for rapid gene/trait discovery and optimization. We established a double haploid population of 1,236 lines from EMS-mutagenized microspores of the spring-type canola line, NRCDH4079. A platinum-quality reference genome, gene annotations, and a gene expression atlas from developing seeds were generated for NRCDH4079. Exome sequencing of the mutagenized population resulted in the development of a 'TILLED' variant database, revealing 1,243 knockout mutations across 1,222 unique genes, along with 140,522 moderate-effect or modifier variants impacting 70,626 genes. Phenotypic analysis revealed significant variation in key seed traits, including oil, protein, and meal acid detergent fiber (ADF) content. Notably, the mutant variant DP125410314 exhibited increased protein and reduced ADF, two important traits for improving the meal composition of canola. Genetic mapping of this variant identified a homoeologous non-reciprocal translocation between A1 and C1 chromosomes associated with reduced ADF content, highlighting the role of structural variations in trait development. This work establishes haploid mutagenesis as a powerful tool for crop improvement in B. napus, with broader implications for other Brassica species. By enhancing our understanding of seed protein traits, it lays the foundation for canola varieties that meet future nutritional and market demands.