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

Abstract

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.

Cytological observation and transcriptome analysis reveal dynamic changes of Rhizoctonia solani colonization on leaf sheath and different genes recruited between the resistant and susceptible genotypes in rice

“…The fact that there were more DEGs in GD66 than that in Lemont at both 24 and 48 hpi indicated that the resistant genotype GD66 recruited more genes than the susceptible genotype Lemont in fighting against the pathogen. Our results are different from some previous reports that more DEGs were found in sheath blight–susceptible cultivars than that in sheath blight–resistant cultivars ( Zhang et al., 2017 ; Shi et al., 2020 ; Yang et al., 2022 ). It means that the GD66 may have different mechanism than other resistant cultivars during rice– R. solani interaction.…”

“…The transcriptome profiles between the susceptible cultivar Lemont and the moderately resistant cultivar Teqing in response to sheath blight disease were studied, and it showed that regulation of photosynthesis, photorespiration, jasmonic acid, and phenylpropanoid pathways contribute to rice resistance to R. solani ( Shu et al., 2019 ). Transcriptome analysis showed that the defense system in resistant rice cultivars involved the expression of PR genes, key transcription factors, PAL genes, and the enrichment of defense-related pathways ( Yang et al., 2022 ). Comparative transcriptome analysis suggested that photosynthesis, photorespiration, and jasmonic acid and phenylpropanoid metabolism played important roles in disease resistance ( Zhang et al., 2017 ).…”

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

“…The promoter analysis of these target genes helped to understand that the up-regulated genes were controlled by other WRKY proteins and the down-regulated genes were regulated by MYB and AP2/EREBP proteins (Qiu et al ., 2009). WRKY TF family are important regulators in defence response pathways against pathogen infection (Yang et al ., 2022). However, the promoter analysis in the entire genome will help to identify the possible target genes in the entire rice genome controlled by WRKY13 TF.…”

Identification and characterization of pathogenicity-related genes of Rhizoctonia solani AG3 during tobacco infection

“…Generally, AG1-IA primarily infects rice plants, AG2 infects cruciferous vegetables, and AG3 prefers solanaceous plants under natural conditions ( Hane et al., 2014 ). Rice SBD caused by AG1-IA and potato black scurf disease caused by AG3 have been widely investigated because of their economic and ecological importance in agriculture ( Zrenner et al., 2020 ; Yang et al., 2022 ). However, relatively few studies have examined the relationship between R. solani AG3 and other economically important crops, including tobacco.…”