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Background  Stemphylium blight (SB), caused by  Stemphylium botryosum , is a devastating disease in lentil production. Although it is known that accessions of  Lens ervoides  possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in  L. ervoides . Therefore, a comprehensive molecular study of SB resistance in  L. ervoides  was needed to exploit this wild resource available at genebanks for use by plant breeders in resistance breeding.    Results  Microscopic and qPCR quantification of fungal growth revealed that 48, 96, and 144 h post-inoculation (hpi) were interesting time points for disease development in  L. ervoides  recombinant inbred lines (RILs) LR-66-637 (resistant to SB) and LR-66-577 (susceptible to SB). Results of transcriptome sequencing at 0, 48, 96 and 144 hpi showed that 8810 genes were disease-responsive genes after challenge by  S. botryosum . Among them, 7526 genes displayed a similar expression trend in both RILs, and some of them were likely involved in non-host resistance. The remaining 1284 genes were differentially expressed genes (DEGs) between RILs. Of those, 712 DEGs upregulated in LR-66-637 were mostly enriched in ‘carbohydrate metabolic process’, ‘cell wall organization or biogenesis’, and ‘polysaccharide metabolic process’. In contrast, there were another 572 DEGs that were upregulated in LR-66-577, and some of them were enriched in ‘oxidation-reduction process’, ‘asparagine metabolic process’ and ‘asparagine biosynthetic process’. After comparing DEGs to genes identified in previously described quantitative trait loci (QTLs) for resistance to SB, nine genes were common and three of them showed differential gene expression between a resistant and a susceptible bulk consisting of five RILs each. Results showed that two genes encoding calcium-transporting ATPase and glutamate receptor3.2 were candidate resistance genes, whereas one gene with unknown function was a candidate susceptibility gene.    Conclusion  This study provides new insights into the mechanisms of resistance and susceptibility in  L. ervoides  RILs responding to  S. botryosum  infection. Furthermore, we identified candidate resistance or susceptibility genes which warrant further gene function analyses, and which could be valuable for resistance breeding, if their role in resistance or susceptibility can be confirmed.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-2013-6) contains supplementary material, which is available to authorized users.

Using a transcriptome sequencing approach to explore candidate resistance genes against stemphylium blight in the wild lentil species Lens ervoides