Comparative Transcriptome Analyses of Gene Expression Changes Triggered by Rhizoctonia solani AG1 IA Infection in Resistant and Susceptible Rice Varieties

Abstract

Rice sheath blight, caused by Rhizoctonia solani, is one of the most devastating diseases for stable rice production in most rice-growing regions of the world. Currently, studies of the molecular mechanism of rice sheath blight resistance are scarce. Here, we used an RNA-seq approach to analyze the gene expression changes induced by the AG1 IA strain of R. solani in rice at 12, 24, 36, 48, and 72 h. By comparing the transcriptomes of TeQing (a moderately resistant cultivar) and Lemont (a susceptible cultivar) leaves, variable transcriptional responses under control and infection conditions were revealed. From these data, 4,802 differentially expressed genes (DEGs) were identified. Gene ontology and pathway enrichment analyses suggested that most DEGs and related metabolic pathways in both rice genotypes were common and spanned most biological activities after AG1 IA inoculation. The main difference between the resistant and susceptible plants was a difference in the timing of the response to AG1 IA infection. Photosynthesis, photorespiration, and jasmonic acid and phenylpropanoid metabolism play important roles in disease resistance, and the relative response of disease resistance-related pathways in TeQing leaves was more rapid than that of Lemont leaves at 12 h. Here, the transcription data include the most comprehensive list of genes and pathway candidates induced by AG1 IA that is available for rice and will serve as a resource for future studies into the molecular mechanisms of the responses of rice to AG1 IA.

Understanding sheath blight resistance in rice: the road behind and the road ahead

“…The study also reported improved sheath blight tolerance in transgenic rice plants overexpressing the RGB1 gene. The involvement of secondary messengers of rice in immune responses to R. solani has been reported in some comparative transcriptome and proteomic studies (Karmakar et al , ; Zhang et al , ). Several calcium/calmodulins signalling pathway genes ( OsCPK10 , OsCML16 , OsCML26 , OsCML27 , OsCML 31, OsCam1‐1 ) were differentially regulated at different time points after infection in response to ShB infection (Zhang et al , ) indicating the involvement of the secondary messengers, Ca2+ and calmodulin.…”

“…The involvement of secondary messengers of rice in immune responses to R. solani has been reported in some comparative transcriptome and proteomic studies (Karmakar et al , ; Zhang et al , ). Several calcium/calmodulins signalling pathway genes ( OsCPK10 , OsCML16 , OsCML26 , OsCML27 , OsCML 31, OsCam1‐1 ) were differentially regulated at different time points after infection in response to ShB infection (Zhang et al , ) indicating the involvement of the secondary messengers, Ca2+ and calmodulin. Wall‐associated kinases (WAKs) are known to bind several types of pectin, including oligomer generated by pathogen‐mediated cell wall degradation, and involved in pathogen‐responsive signal transduction pathways (Kohorn and Kohorn, ).…”

“…Similarly, WRKY80 was found to confer ShB tolerance through the activation of WRKY4 and JA/ET signalling pathway (Peng et al , ). Recent studies indicated the involvement of JA and phenylpropanoid metabolism in ShB disease resistance (Ghosh et al , ; Zhang et al , ).…”

“…Omics offers an attractive tool to get an overview of the collective response of genes in a host plant and how it reacts to a pathogen attack. Comparative transcriptomics has been performed to understand the extent and pattern of the differentially expressed genes (DEGs) between ShB‐susceptible (Lemont) and tolerant (Teqing) rice cultivars, wherein 4806 DEGs were identified (Zhang et al , ). Metabolic alterations and responsive transcripts during susceptible rice– R. solani interaction have been unravelled in a recent metabolomic and transcriptomic study (Ghosh et al , ).…”

Transcriptome analysis of rice leaves in response to Rhizoctonia solani infection

“…The differences in the molecular basis between the interaction of resistant and susceptible cultivars or species with the pathogens (23,24) suggests that RNA-Seq is an ideal tool to dissect the resistance mechanism of host plants (25).…”