Integrated metabolomic and genetic analysis reveals defense pathways in anthracnose-resistant tomato

Authors: LOPEZ-ORTIZ, CARLOS - West Virginia State University; HERNANDEZ-DE LIRA, INTY - West Virginia University; DUHAN, RITIK - West Virginia State University; Clarke, Christopher; BERNAL-GALEANO, VIVIAN - Oak Ridge Institute For Science And Education (ORISE); Stommel, John; BENDITO, VAGNER - West Virginia University; Hansen, Zachariah; RAHMAN, MAHFUZ - West Virginia University; GUTENSOHN, MICHAEL - West Virginia University; VERLINDEN, SVEN - West Virginia University; NIMMAKAYALA, PADMA - West Virginia State University; REDDY, UMESH - West Virginia State University

Submitted to: Plant Stress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/12/2026
Publication Date: 2/12/2026
Citation: Lopez-Ortiz, C., Hernandez-De Lira, I.O., Duhan, R., Clarke, C.R., Bernal-Galeano, V., Stommel, J.R., Bendito, V.A., Hansen, Z.R., Rahman, M., Gutensohn, M., Verlinden, S., Nimmakayala, P., Reddy, U.K. 2026. Integrated metabolomic and genetic analysis reveals defense pathways in anthracnose-resistant tomato. Plant Stress. 20. Article 101289. https://doi.org/10.1016/j.stress.2026.101289.
DOI: https://doi.org/10.1016/j.stress.2026.101289

Interpretive Summary: Anthracnose is a major disease of tomato that can cause severe post-harvest loss, impacting the economic viability of tomato production. While some varieties of tomato are resistant to anthracnose, no preferred commercial cultivars of tomato are fully resistant to the disease. Therefore, disease resistance traits need to be identified and moved into commercial tomato varieties. This project compared the composition of chemical compounds produced during ripening and anthracnose infection in disease-resistant and disease-susceptible tomato varieties. Multiple classes of tomato-produced compounds were identified that distinguish the disease-resistant tomato varieties from the disease-susceptible varieties. Genetic loci responsible for producing these compounds were often associated with known genetic regions previously associated with Anthracnose resistance. Tomato breeders may use the compounds to develop resistant varieties, ultimately helping farmers grow healthier, more resilient plants.

Technical Abstract: Anthracnose, caused by Colletotrichum species, is a major constraint to tomato (Solanum lycopersicum) production, particularly during fruit ripening. To investigate the metabolic and genetic basis of resistance, we performed widely targeted metabolomic profiling of the anthracnose-resistant accession PI 272636 and the susceptible cultivar ‘Rio Grande’ at mature-green and red-ripe fruit stages. Across developmental stages, more than 1,100 metabolites were differentially accumulated between genotypes. Although both genotypes remained symptom-free at the green stage, PI 272636 exhibited elevated accumulation of steroidal alkaloids, flavonoids, and phenylpropanoids, indicating constitutive metabolic differences prior to visible infection. At the red-ripe stage, resistance was associated with increased levels of glycosylated steroidal alkaloids, including lycoperoside C and acetoxytomatidine-related derivatives, as well as phenylpropanoids and flavonoids with established roles in plant defense. KEGG pathway enrichment highlighted flavonoid, phenylpropanoid, and sterol-derived metabolic pathways as key differentiators between resistant and susceptible genotypes. Integration of metabolomic profiles with QTL-seq data identified candidate loci associated with steroidal alkaloid metabolism, including genes encoding phosphomevalonate kinase, squalene synthase, a 2-oxoglutarate-dependent dioxygenase, and an ethylene-responsive transcription factor, as well as genes involved in hydroxycinnamic acid amide and flavonoid biosynthesis. Collectively, these results indicate that anthracnose resistance in PI 272636 is associated with coordinated differences in specialized metabolite composition across fruit development, supported by genetic variation in pathways contributing to steroidal alkaloid and phenylpropanoid metabolism, and provide candidate biomarkers and targets for breeding improved resistance in tomato.