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Background Rice sheath blight, caused by  Rhizoctonia solani  Kühn (teleomorph:  Thanatephorus cucumeris ), is one of the most severe diseases in rice ( Oryza sativa  L.) worldwide. Studies on resistance genes and resistance mechanisms of rice sheath blight have mainly focused on indica rice. Rice sheath blight is a growing threat to rice production with the increasing planting area of japonica rice in Northeast China, and it is therefore essential to explore the mechanism of sheath blight resistance in this rice subspecies. Results In this study, RNA-seq technology was used to analyse the gene expression changes of leaf sheath at 12, 24, 36, 48, and 72 h after inoculation of the resistant cultivar ‘Shennong 9819’ and susceptible cultivar ‘Koshihikari’ with  R. solani . In the early stage of  R. solani  infection of rice leaf sheaths, the number of differentially expressed genes (DEGs) in the inoculated leaf sheaths of resistant and susceptible cultivars showed different regularity. After inoculation, the number of DEGs in the resistant cultivar fluctuated, while the number of DEGs in the susceptible cultivar increased first and then decreased. In addition, the number of DEGs in the susceptible cultivar was always higher than that in the resistant cultivar. After inoculation with  R. solani , the overall transcriptome changes corresponding to multiple biological processes, molecular functions, and cell components were observed in both resistant and susceptible cultivars. These included metabolic process, stimulus response, biological regulation, catalytic activity, binding and membrane, and they were differentially regulated. The phenylalanine metabolic pathway; tropane, piperidine, and pyridine alkaloid biosynthesis pathways; and plant hormone signal transduction were significantly enriched in the early stage of inoculation of the resistant cultivar Shennong 9819, but not in the susceptible cultivar Koshihikari. This indicates that the response of the resistant cultivar Shennong 9819 to pathogen stress was faster than that of the susceptible cultivar. The expression of plant defense response marker  PR1b  gene, transcription factor  OsWRKY30  and  OsPAL1  and  OsPAL6  genes that induce plant resistance were upregulated in the resistant cultivar. These data suggest that in the early stage of rice infection by  R. solani , there is a pathogen-induced defence system in resistant rice cultivars, involving the expression of  PR  genes, key transcription factors,  PAL  genes, and the enrichment of defence-related pathways. Conclusion The transcriptome data revealed the molecular and biochemical differences between resistant and susceptible cultivars of rice after inoculation with  R. solani , indicating that resistant cultivars have an immune response mechanism in the early stage of pathogen infection. Disease resistance is related to the overexpression of  PR  genes, key transcriptome factors, and  PAL  genes, which are potential targets for crop improvement.

Gene expression analysis of resistant and susceptible rice cultivars to sheath blight after inoculation with Rhizoctonia solani