Chip Digital PCR (cdPCR) to Identify and Quantify Botrytis cinerea Infection in Tomatoes

Botrytis cinerea is a fungal pathogen present in almost any environment, able to cause a severe postharvest disease on a wide range of crops, resulting in significant economic losses. Furthermore, B. cinerea is frequently found in plant tissues as a latent, asymptomatic infection that, when stimulated by favorable alterations in the environment or the physiology of the host, can swiftly develop into a significant symptomatic infection. In greenhouses, fields, and on propagation materials, the principal strategy adopted to control infection is the use of chemical fungicides or eco-friendly alternative methods. For the optimal success of conventional and biocontrol treatments, it is crucial to monitor the disease development and the fungal infection entity. The aim of this work was to develop a fast new method based on chip digital PCR (cdPCR) to estimate the extent of the B. cinerea infection in tomatoes. To better evaluate the amount of plant infection, a duplex assay able to co-amplify both fungal and host plant DNA was fine-tuned. The cdPCR assays were applied to quantify B. cinerea in tomato seedling samples, both naturally and artificially contaminated. The developed method offers sensitive detection, reliable identification, and precise pathogen quantification. The method can be used for B. cinerea diagnostics along the tomato production chain, starting from the seeds and transplanting seedlings to plants and crop residues in open fields and greenhouses. To the best of our knowledge, this is the first study directed at applying cdPCR to B. cinerea diagnosis in tomatoes.