Molecular characterization of sheath blight (Rhizoctonia solani) defense-responsive genes using QRT-PCR assay in rice (Oryza sativa L.)

Abstract

Sheath blight, caused by Rhizoctonia solani AG1-IA, is a significant fungal disease affecting rice crops globally. Breeding for sheath blight resistance remains a key strategy for sustainable disease management. However, the quantitative inheritance and lack of complete resistance sources have limited progress through conventional breeding alone. Recent advances in molecular breeding have accelerated resistance improvement by identifying and mapping multiple quantitative trait loci (QTLs). But, understanding plant defense mechanisms at the molecular level is critical for developing disease-resistant cultivars. So, transcriptome analysis has emerged as a powerful tool to uncover gene expression changes in response to biotic stress. This study focuses on identifying and validating candidate genes associated with sheath blight resistance in rice from available transcriptomic data through quantitative real-time PCR (qRT-PCR). Transcriptome data analysis previously showed thousands of differentially expressed genes (DEGs) during R.solani infection in two rice TN1 (susceptible) and Tetep (resistant/tolerant) genotypes for sheath blight disease. Among thousands of DEGs identified, 11 DEGs were selected based on their fold change value and their functional annotation and conducted qRT-PCR expression analysis to know the expression of the genes during interaction of R.solani with rice in both tolerant (Tetep) and susceptible (TN1) genotypes. All the identified 11 candidate genes were shown high expression in Tetep than the TN1. The findings demonstrated that resistance involves rapid activation of calcium signaling, MAPK pathways, cell wall reinforcement, and ethylene-mediated responses, along with coordinated upregulation of multiple defense-related genes. These candidate genes serve as valuable molecular markers and potential targets for marker-assisted selection, genetic engineering, or genome editing to develop sheath blight-resistant rice varieties, contributing to more sustainable disease control and food security initiatives.