Genetic diversity, haplotyping, integrative transcriptomic and metabolomic insights in Fusarium stalk rot of maize

Maize stalk rot is a major constraint to crop productivity, caused by a complex of Fusarium species. This study investigated the diversity, genetic structure and host-pathogen interactions associated with stalk rot in Indian maize. Phylogenetic analysis of isolates collected during 2022-2023 identified species from three major complexes: Fusarium fujikuroi (FFSC), F. incarnatum-equiseti (FIESC) and F. solani (FSSC), with F. verticillioides being the predominant pathogen. Genetic analysis using ITS, TEF-1α and RPB-2 markers revealed high within-population variability and moderate differentiation across populations. DNA polymorphism and neutrality tests suggested intense selection pressures and population expansion events, especially at the TEF-1α and ITS loci. Transcriptomic analysis of infected maize revealed 6948 differentially expressed genes. Upregulated genes were associated with fungal recognition, cell wall degradation and antimicrobial compound production, while downregulated genes indicated suppression of photosynthesis, protein folding and cytoskeletal functions. KEGG enrichment analysis highlighted significant changes in pathways related to lipid metabolism, secondary metabolite biosynthesis, oxidative stress and energy reallocation. Biochemical assays confirmed the elevated activity of plant cell wall-degrading enzymes (cellulase, β-glucosidase and pectate lyase), peaking at 4-6 days post-infection, supporting their role in tissue maceration. LC-MS/MS-based metabolite profiling revealed a clear metabolic shift in infected maize, characterized by an increased accumulation of secondary metabolites, including flavonoid glycosides and phenylpropanoids, in contrast to the dominance of primary metabolism in healthy tissues. These results provide a comprehensive understanding of the genetic, biochemical and metabolic responses of maize to stalk rot, underscoring the need for management and resistance breeding strategies targeting diverse Fusarium species.