Network-based integrative analysis of key regulatory genes involved in rice response to Meloidogyne graminicola in the susceptible cultivar IR64

Root-knot nematode infection caused by Meloidogyne graminicola is one of the most destructive diseases affecting rice, leading to reduced grain yield, leaf chlorosis, and ultimately plant death. In the present study, the molecular mechanisms underlying rice seedling responses to M. graminicola infection were investigated through transcriptome-based integrative bioinformatics analyses. Differentially expressed genes (DEGs) were analyzed using protein–protein interaction (PPI) network construction to identify key regulatory genes and major biological pathways associated with nematode stress. Hub genes were identified using the Cytoscape plugin CytoHubba based on topological network parameters, while significant subnetworks were extracted using the IPCA algorithm implemented in CytoCluster. Functional enrichment analysis revealed that the identified DEGs were predominantly involved in protein folding, ATP-dependent chaperone activity, and cellular stress response processes. Most hub genes belonged to the heat shock protein (HSP) family, suggesting their critical roles in chloroplast development, antioxidant enzyme regulation, and defense responses during pathogen-induced stress. Kyoto Encyclopedia of Genes and Genomes enrichment analysis further demonstrated that protein processing in the endoplasmic reticulum and RNA degradation pathways were significantly enriched during infection. Conserved domain analysis showed that the identified hub proteins contained functional domains associated with chaperone activity, ATP binding, and biotic stress responses, supporting their structural and regulatory roles in plant defense mechanisms. Furthermore, promoter motif analysis using Tomtom and GOMO revealed that their regulatory elements are mainly associated with plant growth, development, and responses to oxidative stress. These findings provide new insights into the molecular defense mechanisms of rice against M. graminicola and may contribute to the development of resistant transgenic rice cultivars.