The devastating sheath blight disease caused by Rhizoctonia solani Kuhn (teleomorph: Thanatephorus cucumeris) causes major yield loss in most rice growing regions of the world. In this study, two moderately tolerant and four susceptible genotypes of rice were selected for R. solani induced proteome analysis using two-dimensional polyacrylamide gel electrophoresis. Forty five differentially expressed proteins (DEPs) were identified and analyzed by Mass Spectrometry. Based on their functions, these proteins were classified into different groups, viz., photosynthesis, resistance and pathogenesis, stress, cell wall metabolism and cytoskeleton development associated proteins, and hypothetical or uncharacterized proteins. Expression of 14 genes encoding DEPs was analyzed by quantitative PCR which showed consistency in transcripts and genes expression pattern. Furthermore, the expression of 16 other genes involved in diverse biological functions was analyzed. Up-regulation of these genes in the tolerant genotype Pankaj during sheath blight disease suggested efficient genetic regulation of this cultivar under stress. Also, expression analysis of conserved microRNAs (miRNAs) and their target genes revealed important role of miRNAs in post-transcriptional gene regulation during development of rice sheath blight disease. Genome-wide discovery of miRNAs and further characterization of DEPs and genes will help in better understanding of the molecular events during sheath blight disease development in rice.

Sheath blight disease of rice caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris) remains a global challenge due to the absence of reliable resistance genes and poor understanding of pathogen biology. Pectin, one of the most vital constituents of the plant cell wall, is targeted by pectin methylesterases, polygalacturonases, and few other enzymes of fungal pathogens. In this study, we catalogued the expressed genes of the fungal genome from RNAseq of R. solani infected four rice genotypes. Analysis of RNAseq revealed 3325 pathogen genes commonly expressed in all rice genotypes, in which 49, 490, and 83 genes were specific to BPT5204, Tetep, and Pankaj genotypes, respectively. To identify the early and late responding genes of R. solani during plant cell wall degradation, a real-time PCR analysis of 30 pectinolytic enzymes was done at six different time points after inoculation. The majority of these genes showed maximum induction at the 72 h time point, suggesting that it is the most crucial stage of infection. Pankaj showed lesser induction of these genes as compared to other genotypes. Leaf-blade tissue and 45 days old-growth stage are more favorable for the expression of pectin degradation genes of R. solani. Additionally, the expression analysis of these genes from four different strains of R. solani suggested differential regulation of genes but no distinct expression pattern between highly virulent and mild strains. The implications of the differential regulation of these genes in disease development have been discussed. This study provides the first such comprehensive analysis of R. solani genes encoding pectin degrading enzymes, which would help to decipher the pathogen biology and sheath blight disease development.

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