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While our understanding of the genetics underlying the  Brassica - Leptosphaeria  pathosystem has advanced greatly in the last decade, differences in molecular responses due to interaction between resistance genes and host genetic background has not been studied. We applied RNAseq technology to monitor the transcriptome profiles of  Brassica napus  ( Bn ) lines carrying one of four blackleg  R  genes ( Rlm2 ,  Rlm3 ,  LepR1  &  LepR2 ) in Topas or Westar background, during the early stages of infection by a  Leptosphaeria maculans  ( Lm ) isolate carrying the corresponding  Avr  genes. We observed upregulation of host genes involved in hormone signalling, cell wall thickening, response to chitin and glucosinolate production in all  R  gene lines at 3 day after inoculation (dai) albeit having higher level of expression in  LepR1  and  Rlm2  than in  Rlm3  and  LepR2  lines.  Bn-SOBIR1  (Suppressor Of BIR1-1), a receptor like kinase (RLK) that forms complex receptor like proteins (RLPs) was highly expressed in  LepR1  and  Rlm2  at 3 dai. In contrast  Bn-SOBIR1  induction was low in  Rlm3  line, which could indicate that  Rlm3  may function independent of  SOBIR1 . Expression of Salicylic acid (SA) related defense was enhanced in  LepR1  and  Rlm2  at 3 dai. In contrast to SA, expression of  Bn  genes with homology to  PDF1.2 , a jasmonic acid (JA) pathway marker, were increased in all  Rlm  and  LepR  lines at 6 and 9 dai. Effect of host genetic background on induction of defense, was determined by comparison of  LepR1  and  LepR2  in Topas vs Westar genotype (i.e. T- LepR1  vs W- LepR1  and T- LepR2  vs W- LepR2 ). In both cases (regardless of  R  gene) overall number of defense related genes at the earliest time point (3 dai) was higher in Tops compared to Westar. SA and JA markers genes such as  PR1  and  PDF1.2  were more induced in Topas compared to Westar introgression lines at this time point. Even in the absence of any  R  gene, effect of Topas genotype in enhanced defense, was also evident by the induction of  PDF1.2  that started at a low level at 3 dai and peaked at 6 and 9 dai, while no induction in Westar genotype was observed at any of these time points. Overall, variation in time and intensity of expression of genes related to defense, was clearly dependent on both  R  gene and the host genotype.

Dissecting R gene and host genetic background effect on the Brassica napus defense response to Leptosphaeria maculans