Integrated Analysis of Transcriptomic and Metabolomic Responses in Rice Resisting False Smut

Abstract

Rice false smut, caused by Ustilaginoidea virens, is an important fungal disease that reduces both grain yield and quality. To dissect the molecular basis of resistance, we combined transcriptome sequencing and metabolite profiling in resistant and susceptible rice cultivars. Transcriptome sequencing revealed more than 8,500 genes with altered expression patterns after infection, while metabolite profiling detected over 700 significantly changed compounds. Resistant plants showed strong activation of immune regulators, including WRKY transcription factors, receptor-like kinases, and pathogenesis-related proteins, along with enhanced phenylpropanoid metabolism. Metabolite changes included higher levels of antifungal compounds (for example, sakuranetin, ferulic acid, caffeic acid, and luteolin). Network integration implicated salicylic acid, jasmonic acid, and MAPK signaling in coordinating cell-wall reinforcement and suppression of susceptibility pathways. Together, these findings highlight coordinated molecular and metabolic reprogramming that strengthens rice resistance to RFS, providing valuable candidate genes and metabolites for breeding programs.