Detection and Quantification of Stagonosporopsis cucurbitacearum in Seeds of Cucurbita maxima Using Droplet Digital Polymerase Chain Reaction

Stagonosporopsis cucurbitacearum is an important seedborne pathogen of squash (Cucurbita maxima). The aim of our work was to develop a rapid and sensitive diagnostic tool for detection and quantification of S. cucurbitacearum in squash seed samples, to be compared with blotter analysis, that is the current official seed test. In blotter analysis, 29 of 31 seed samples were identified as infected, with contamination from 1.5 to 65.4%. A new set of primers (DB1F/R) was validated in silico and in conventional, quantitative real-time PCR (qPCR) and droplet digital (dd) PCR. The limit of detection of S. cucurbitacearum DNA for conventional PCR was similar to 1.82 x 10(-2) ng, with 17 of 19 seed samples positive. The limit of detection for ddPCR was 3.6 x 10(-3) ng, which corresponded to 0.2 copies/mu l. Detection carried out with artificial samples revealed no interference in the absolute quantification when the seed samples were diluted to 20 ng. All seed samples that showed S. cucurbitacearum contamination in the blotter analysis were highly correlated with the absolute quantification of S. cucurbitacearum DNA (copies/mu l) in ddPCR (R-2 = 0.986; p <= 0.01). Our ddPCR protocol provided rapid detection and absolute quantification of S. cucurbitacearum, offering a useful support to the standard procedure.

Automated summary

The aim of this study was to develop a rapid and sensitive diagnostic tool for the detection and quantification of the seedborne pathogen Stagonosporopsis cucurbitacearum in squash seed samples. The new set of primers was validated and showed effectiveness in PCR and ddPCR. The results demonstrated that ddPCR provided rapid detection and absolute quantification capabilities.