Integrative gene network modeling and pathway analysis of rice transcriptomes in response to Meloidogyne graminicola infection

Abstract

Rice (Oryza sativa L.), a critical crop for global food security, is threatened by the root-knot nematode Meloidogyne graminicola. This study employed a systems biology approach to decipher rice’s molecular response to this pathogen. Analysis of transcriptomic data led to the construction of a protein-protein interaction network from 515 differentially expressed genes, identifying 27 central hub genes. Notably, most hubs were down-regulated, including receptor-like kinases and the metabolic enzyme nitrate reductase, suggesting a potential resistance-associated transcriptional reprogramming rather than a pathogen-mediated suppression strategy. Gene Ontology and KEGG enrichment analyses revealed significant disruptions in nitrogen metabolism, translation, and secondary metabolite biosynthesis pathways. Promoter motif analysis of hub genes identified conserved regulatory elements linked to two key functions: plasma membrane signaling and mitochondrial/ribosomal translation. This offers a transcriptional explanation for the coordinated gene suppression. Furthermore, in silico prediction identified specific microRNAs potentially targeting key hubs, suggesting an additional layer of post-transcriptional control. Our findings suggest a model in which the observed transcriptional changes may be associated with the disruption of both peripheral signaling and core cellular processes in the resistant genotype. However, these interpretations are hypothesis-generating and require experimental validation. The identified hub genes, regulatory motifs, and miRNAs constitute a valuable resource for functional studies and could potentially be explored as candidate targets in future breeding or biotechnological approaches, provided that experimental validation confirms their functional roles.