Measuring Pathogenic Soil Fungi That Cause Sclerotinia Rot of Panax ginseng Using Real-Time Fluorescence Quantitative PCR

Sclerotinia ginseng is the primary pathogenic fungus responsible for Sclerotinia rot of ginseng, which significantly reduces plant yield and quality. The density of sclerotia in the soil is closely associated with rot incidence and severity. Whole genome sequencing was conducted to obtain fungal frame maps. The specific primers, q2001F/q2001R, were screened out by pan-genomic analysis using the NCBI database. Recombinant plasmids containing amplicons obtained with this primer set were used as standard plasmids to construct a real-time fluorescence quantitative PCR system. The relationships between the cycle threshold (Ct) values and the soil sclerotium densities were determined by real-time PCR. Real-time PCR had a detection limit of 1.5 × 10−2 g·kg−1 soil for Sclerotinia rot causing fungal mycelium, and the relationship between the density of S. ginseng mycelium n (g·g−1 soil) and the Ct value was n = 10(40.048 − Ct)/6.9541. The detection limit of real-time PCR for measuring soil sclerotia was 3.8 × 10−5 g·g−1 soil, suggesting a sensitivity 100 times that of conventional PCR. The relationship between the sclerotium density n (g·g−1 soil) and the Ct value was n = 10(18.351 − Ct)/7.0914. Compared with the conventional PCR method, the fluorescent quantitative PCR method could detect the population of Sclerotinia spp. in soil more efficiently, accurately, and sensitively.