Analysis of gene expression changes in wheat in response to Rhizoctonia cerealis infection using RNA-Seq

Bread wheat (Triticum aestivum L.) is the most widely grown crop in the world. Rhizoctonia cerealis, the causal agent of wheat sharp eyespot disease, has 21 become epidemic in many countries. In the present study, we performed transcriptome analysis in wheat infected by R. cerealis at 0, 12, 30, 70, and 98 h post-infection using R. cerealis-resistant and -susceptible genotypes (CI12633 and 'Yangmai15', respectively). We used quantitative real-time PCR to validate the Illumina gene expression data, and identified new gene annotations for 23,654 unigenes in the RNA samples from the resistant and susceptible cultivars. Comparing the same inoculation times, we found that the number of DEGs (differentially-expressed genes) increased gradually before 70 h and declined at 98 h in the two RNA samples. Furthermore, the expression of resistance-associated genes occurred earlier in CI12633 than in 'Yangmai15', and higher mRNA expression levels were detected in CI12633; this suggests that timing and relative expression levels of these genes are important in the CI12633-R. cerealis interaction. Functional annotations associated with sharp eyespot resistance included genes involved in energy production and conversion, posttranslational modification, protein turnover, chaperones, secondary metabolite biosynthesis, transport and catabolism, and defense mechanisms. The results of pathway enrichment analysis showed that the DEGs participate in glutathione metabolism, glycerophospholipid metabolism, lysine degradation, plant-pathogen interaction, glyoxylate and dicarboxylate metabolism, and other resistance-associated metabolic pathways. Disease inoculation experiments and the validation of in vitro antifungal activity of the candidate genes showed that the genes were up- or down-regulated in the resistant genotype CI12633 30 h after inoculation compared to its control, which validated the results of the RNA-seq analysis. The results of our study will help to understand the molecular basis of the host response to R. cerealis infection in wheat, and will also enable the future genetic improvement of sharp eyespot resistance in wheat through the incorporation of novel resistance genes.