Transcriptomic and Metabolomic Explanation of the Interaction between Soybean and Root Rot Caused by Fusarium tricinctum

Soybean root rot (SRR), a severe soil-borne disease, hinders continuous soybean cropping, but the interaction mechanism between soybean varieties and Fusarium tricinctum (the dominant pathogen) remains unclear. Using buried root inoculation, 64 germplasms were screened: Heinong 531 (HN531) showed strong resistance, while Dongsheng 1 (DS1) was susceptible. Metabolomic and transcriptomic analyses revealed that phenylpropanoid and flavonoid biosynthesis pathways, including lignin and flavonoid production, were activated early during infection. Antioxidant response genes were rapidly upregulated. Notably, chlorogenic acid (CGA), a phenylpropane derivative sharing a pathway with lignin synthesis, exhibited high resistance potential. In vitro and pot experiments confirmed CGA’s role in SRR resistance, with 0.20 mg mL –1 achieving 60% inhibition while promoting soybean growth. This study identifies key pathways in soybean– F. tricinctum interactions, aiding resistance gene/metabolite discovery and biocontrol agent development.