Transcriptomics and metabolomics reveal the molecular decoupling of Fusarium head blight Type II resistance from grain anthocyanins in pigmented bread wheat

Fusarium head blight (FHB) poses a major threat to global wheat production and food safety, necessitating sustainable disease management strategies. Pigmented wheat genotypes accumulate high levels of anthocyanins and other phenolic compounds, but whether grain pigmentation contributes to Type II FHB resistance remains unclear. Five pigmented bread wheat genotypes with blue aleurone (Skorpion and Purendo) or purple pericarp (Rosso, Vanilnoir and Indigo) were evaluated by point inoculation with Fusarium graminearum , together with resistant and susceptible non-pigmented controls. Disease progression, fungal biomass, deoxynivalenol accumulation, Fusarium-damaged kernels, and total phenolic content revealed marked variation among genotypes that did not consistently correspond to grain pigmentation. Vanilnoir displayed a resistant Type II phenotype comparable to Sumai3, whereas pigmented genotypes with similar grain coloration showed intermediate or susceptible responses. Early transcriptomic profiling used two complementary analyses: within-genotype FG-versus-mock comparisons to identify infection-responsive genes, and genotype × treatment interaction analysis in Vanilnoir–Rosso and Sumai3–Rebelde to identify genotype-dependent infection responses. Late-stage untargeted metabolomics at 21 dpi was performed across genotypes. Within-genotype analysis revealed shared infection-responsive functions involving phenylpropanoid metabolism, including 4CL , HCT , and COMT , redox and detoxification, and cell-wall-associated processes, while interaction analysis identified distinct genotype-dependent transcriptional responses involving pathogen perception and signaling components such as LRR-RLKs. Metabolomics further revealed genotype-specific remodeling of phenylpropanoid and flavonoid metabolism, whereas anthocyanin accumulation did not consistently track resistance. Overall, Type II FHB resistance was not consistently associated with grain pigmentation or anthocyanin accumulation. Resistant genotypes instead showed functional convergence through distinct transcriptional and metabolic responses.