Multi-omics reveals contrasting pod defense strategies associated with soybean resistance to Fusarium verticillioides.

Infection by Fusarium verticillioides causes field mold in soybean and reduces seed quality, yet the defensive role of pods as the first protective barrier remains poorly understood. Here, we compared a resistant cultivar (D49) and a susceptible cultivar (ND12). Phenotypic analysis showed that D49 exhibits stronger resistance to pathogen infection. Integrated transcriptomic and metabolomic analyses revealed that isoflavonoid and lipid biosynthetic pathways are specifically activated in the resistant genotype upon infection. Metabolite quantification demonstrated that isoflavonoids accumulate earlier and to higher levels in D49, whereas ND12 shows delayed and weaker induction. In addition, D49 undergoes dynamic remodeling of the cuticle wax barrier, characterized by reduced cutin monomers and increased wax accumulation, while ND12 displays a weaker structural response and a decline in wax content after infection. These results suggest that resistance is achieved through the coordinated action of early isoflavonoid accumulation and adaptive restructuring of the cuticle-wax barrier. Using WGCNA we found three candidate transcription factor genes (GmEGL3, BHLH149, and GmERF9) as potential regulators linking isoflavonoid metabolism and lipid barrier formation, providing molecular insights for soybean resistance breeding.