Development and Application of a TaqMan Probe-Based qPCR Detection Assay for Detecting Fusarium pseudograminearum

Fusarium crown rot (FCR) has become increasingly prevalent in China’s Huanghuai wheat-growing region, with Fusarium pseudograminearum emerging as the predominant causal pathogen. In this study, we developed a TaqMan qPCR assay targeting the conserved FpAH1 gene to specifically detect F. pseudograminearum. The assay’s specificity was verified against 12 Fusarium species and 10 other wheat pathogenic fungi, achieving an amplification efficiency of 105.3% (R² = 0.997) and a limit of detection (LOD) of 1 × 10² copies/μL. Using this assay, we monitored the monthly dynamics of F. pseudograminearum in wheat basal stems and top soil throughout two entire growing seasons (2023–2024 and 2024–2025) under three seed treatments: untreated control, tebuconazole-coated, and cyclobutrifluram-coated. Field dynamics showed that cyclobutrifluram treatment significantly suppressed F. pseudograminearum biomass in wheat plants, while tebuconazole-coated seeds exhibited no significant difference from the untreated control. Notably, F. pseudograminearum biomass surged sharply in the late growing stage across all three treatments. Top soil maintained relatively stable F. pseudograminearum biomass, comparable to the early-stage level in wheat basal stems, across all seasons. This study established a rapid and robust TaqMan qPCR assay for specific detection of F. pseudograminearum, with broad utility in related research and practice, and documented the pathogen’s cross-seasonal dynamics in both wheat plants and top soil. These characterized dynamics provide a theoretical foundation for refining Fusarium crown rot (FCR) control measures, exemplifying the assay’s practical value while highlighting its potential for broader applications.