Integrative transcriptomic and metabolomic analysis reveals the molecular mechanisms of rice resistance to false smut disease

A serious danger to the world's rice supply is rice fake smut (RFS), which is brought on by the fungus Ustilaginoideavirens. Developing successful management measures requires an understanding of the molecular pathways that support rice resistance to this disease. To examine the mechanisms of resistance, a combined transcriptome and metabolome analysis of rice plants was carried out both before and after infections with strongly and weakly virulent strains of U. virens. A total of 8552 differentially expressed genes (DEGs) were found, with considerable enrichment in defensive signaling, cell wall modification, and immune response pathways, such as salicylic acid, Mitogen-Activated Protein Kinase (MAPK), and jasmonic acid. Resistant rice strains showed downregulation of genes linked to fungal susceptibility and upregulation of key resistance-related genes, such as receptor-like kinases, WRKY transcription factors, and Pathogenesis-Related (PR) proteins. Following fungal infection in resistant rice plants, metabolomic analysis identified 752 differentially accumulated metabolites (DAMs), with notable enrichment in amino acids, organic acids, secondary metabolites, and lipids. Pathway analysis of these DAMs identified key metabolic pathways involved in rice defense, including flavonoid biosynthesis, phenylpropanoid metabolism, and lignin biosynthesis. The combination of transcriptomic and metabolomic data revealed that the accumulation of defense-related metabolites and the coordinated regulation of defense genes effectively regulate rice resistance to fake smut. These results show possible targets for improving disease resistance in rice breeding programs and offer fresh insights into the molecular mechanisms underlying rice resistance to false smut.