SCAR-based real-time TaqMan PCR for early detection of Fusarium oxysporum in melon seedlings under greenhouse nursery conditions

Isolates of the fungus Fusarium oxysporum cause some of the most devastating plant diseases, leading to significant crop losses in both the greenhouse nursery and field environments. Because of this, tools that permit early pathogen detection are essential. This study develops such a tool. A specific primer set (FOX S and FOX R) and TaqMan probe (FOX TM) for F. oxysporum quantification were developed from an SCAR marker derived from RAPD-PCR. This system was used to monitor the presence of F. oxysporum in the substrate and the vegetative tissue of melon seedlings growing under greenhouse conditions. Detection and quantification data were obtained within 48 h with the new technique, compared to 5–6 days for the classical plate culture method, while also providing greater specificity and sensitivity.

► A set of primers and a TaqMan probe was designed from a SCAR marker.
► The system amplified all the isolates of F. oxysporum used in our experiment.
► Pathogen population was monitored in the organic growing media of melon seedlings.
► The pathogen was detected in plant tissues before the disease symptoms appear.
► This method was faster, more specific and more sensitive than classical approaches.