Species-specific qpcr assays for colletotrichum fruit bitter rot and vegetable anthracnose detection and quantification

Overview

This solution offers species-specific quantitative PCR (qPCR) assays designed to detect and quantify multiple Colletotrichum species responsible for fruit bitter rot in apples and pears and anthracnose diseases in vegetables. The assays address a critical gap in crop disease management by enabling early identification of infective spores in the growing season, helping growers and crop protection professionals predict outbreaks, select effective fungicides, and mitigate fungicide resistance. The work builds on the identification of C. fioriniae, C. chrysophilum, and C. noveboracense sp. nov. as causal agents of apple bitter rot, with broader applicability to the many Colletotrichum species that vary in infection timing, virulence, and temperature optima.

Technical specifications

Key features:

• Species-specific primers and TaqMan probes designed for C. fioriniae, C. chrysophilum, and C. noveboracense based on 12-gene sequencing and five whole-genome assemblies
• Differentiation of target Colletotrichum species from closely related sister species and common rot fungi
• Quantitative capacity for measuring inoculum levels from spore sampling and infected plant tissue
• Application to spore sampling for determining infection timing across the growing season
• Potential to identify overwintering reservoirs and explain species-specific biology differences
• Foundation for modeling disease outbreaks under climate change-driven shifts in infection timing

How it works: Genome sequences of target Colletotrichum species are assembled, annotated, and comparatively mined to identify unique genomic regions. These regions inform the design of primers and TaqMan probes validated for specificity against referent strains and field-collected infected samples. The resulting qPCR assays detect and quantify pathogen DNA, providing a molecular tool for disease forecasting and management.

Technology readiness level

Currently at TRL 3–4 (proof-of-concept to laboratory validation). Gene sequencing has been completed for the three target species and primers/probes designed and tested for diagnostic specificity. Genome sequencing of five Colletotrichum isolates is underway to support assay development for C. chrysophilum and C. noveboracense. Future validation includes testing assays on infected plant samples and demonstrating quantitative performance. Funding of $15,000 for a one-year Postdoctoral Associate would advance the assays toward field deployment readiness for apple, pear, and vegetable growers, as well as crop protection industry partners.