High-Throughput Real-Time qPCR and High-Resolution Melting (HRM) Assay for Fungal Detection in Plant Matrices.

Crop producers are under great pressure to produce more and better food items. Effective control of crop pathogens is fundamental to guaranteeing food safety and reducing economic losses. Therefore, their identification throughout the production chain is of utmost interest. To achieve this goal, genomic analysis tools are currently being developed allowing to control crop production more effectively.Genomic analysis in some samples is difficult, mostly due to the sample's intrinsic characteristics, i.e., high levels of phenols, fatty acids (e.g., oleaginous fruits, such as olives), and carbon hydrates (e.g., honey), among others. Additionally, some samples yield very low DNA recovery with high content of contaminants, imposing protocol improvements to overcome these difficulties.Here we present protocols focused on qPCR and HRM to detect the presence of fungal pathogens collected from plant-derived samples.