Gene Expression Dynamics of Blackleg Disease Development Revealed by Dual-RNAseq Approach in Differential Lines of Canola (Brassica napus)

Blackleg disease caused by the hemibiotrophic fungus Leptosphaeria maculans is responsible for significant yield losses in canola (Brassica napus) worldwide. Use of durable resistance source for the development of new cultivars is required for its effective management. The identification of genes underlying the host-pathogen interaction will be helpful to understand resistance mechanisms. Here we have used a host-pathogen dual-RNAseq approach to identify candidate disease resistance genes from canola and avirulence genes from L. maculans.  To understand the differential effect of major resistance genes, an isogenic line carrying a single Rlm2 resistance gene and the line Topaz DH16516 (no resistance) were inoculated with L. maculans isolate D5 carrying the corresponding AvrLm2 allele. A total of 96 cDNA libraries from five biological replicates of canola leaves collected at five different developmental stages were sequenced on Illumina Hiseq2000 sequencer. An average of 35 million reads per sample were obtained and mapped to Brassica napus and L. maculans reference genomes to identify differentially expressed genes across different conditions and genotypes. Several differentially expressed classically secreted effector proteins that appear to have a role in host-pathogen recognition and the subsequent primary response were identified. The atlas of gene expression provided here will be helpful to understand molecular crosstalk between canola and L. maculans that could be the basis for the deployment of novel strategies to overcome blackleg disease.