IntroductionThe fungal pathogenFusarium verticillioides(Sacc.) Nirenberg (Fv) causes considerable agricultural and economic losses and is harmful to animal and human health.Fvcan infect maize throughout its long agricultural cycle, and root infection drastically affects maize growth and yield.MethodsThe root cell wall is the first physical and defensive barrier against soilborne pathogens such asFv. This study compares two contrasting genotypes of maize (Zea maysL.) roots that are resistant (RES) or susceptible (SUS) toFvinfection by using transcriptomics, fluorescence, scanning electron microscopy analyses, and ddPCR.ResultsSeeds were infected with a highly virulent localFvisolate. AlthoughFvinfected both the RES and SUS genotypes, infection occurred faster in SUS, notably showing a difference of three to four days. In addition, root infections in RES were less severe in comparison to SUS infections. Comparative transcriptomics (rate +Fv/control) were performed seven days after inoculation (DAI). The analysis of differentially expressed genes (DEGs) in each rate revealed 733 and 559 unique transcripts that were significantly (P ≤0.05) up and downregulated in RES (+Fv/C) and SUS (+Fv/C), respectively. KEGG pathway enrichment analysis identified coumarin and furanocoumarin biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction pathways as being highly enriched with specific genes involved in cell wall modifications in the RES genotype, whereas the SUS genotype mainly displayed a repressed plant–pathogen interaction pathway and did not show any enriched cell wall genes. In particular, cell wall-related gene expression showed a higher level in RES than in SUS underFvinfection. Analysis of DEG abundance made it possible to identify transcripts involved in response to abiotic and biotic stresses, biosynthetic and catabolic processes, pectin biosynthesis, phenylpropanoid metabolism, and cell wall biosynthesis and organization. Root histological analysis in RES showed an increase in lignified cells in the sclerenchymatous hypodermis zone duringFvinfection.DiscussionThese differences in the cell wall and lignification could be related to an enhanced degradation of the root hairs and the epidermis cell wall in SUS, as was visualized by SEM. These findings reveal that components of the root cell wall are important againstFvinfection and possibly other soilborne phytopathogens.