The Brassicaceae family contains some of the world’s most important economic and agronomic crops, which are utilised as edible and industrial oilseeds (e.g Brassica napus, B. juncea) and vegetables (e.g Brassica oleracea, Raphanus raphanistrum), along with the scientific model plant Arabidopsis thaliana and highly diverse wild species. Pathogens, such as Leptosphaeria maculans (causal agent of Blackleg) and Sclerotinia sclerotiorum (causal agent of Sclerotinia stem rot), severely affect production of crop species from the Brassicaceae. Plant genomes harbour resistance (R) genes, which play a role in plant immunity, where nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes are the most common type of R gene.
The identification of genes underlying quantitative trait loci is extremely challenging in complex genomes such as B. napus. Recent advances in next-generation sequencing (NGS) has enabled development of millions of SNPs. However, as an increasing number of genome sequences become available, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a species. We have examined the SNP diversity within NBS-LRR genes, and this allelic variation is strongly associated with phenotypic variation. However, we have also observed significant presence absence and copy number variation of R genes. We have developed Brassica pan genomes and using these the molecular analyses of candidate resistance genes using B. napus NGS data are presented. The difficulties associated with identifying functional gene copies within the highly duplicated Brassica genome will be discussed.
This analysis provides a valuable resource for the identification of R genes for enhanced crop protection through analysis of gene diversity and evolution linked to disease. Developing elite resistant cultivars where by the functionality of R genes from wild species is studied and introduced into commercial cultivars will enable continued resistance against pathogens, supporting future food security.