Development and comparative evaluation of LAMP, nested PCR and Real-time PCR assays for detecting Fusarium tricinctum, a fungal pathogen of Zanthoxylum bungeanum.

Background: Zanthoxylum bungeanum is a highly valuable economic tree species in China, widely cultivated for its aromatic peel, medicinal properties, and industrial applications. In recent years, Fusarium tricinctum, a pathogen causing gummosis in Z. bungeanum, has severely impacted production in Sichuan and Gansu provinces. Early detection of this pathogen is challenging due to its prolonged incubation period and nonspecific symptoms, which often lead to significant crop losses and secondary infections by insects. Traditional methods of morphological identification are time-consuming and lack accuracy, necessitating the development of rapid molecular diagnostic tools.

Results: In this study, we screened potential target sequences from F. tricinctum and developed three rapid detection methods-loop-mediated isothermal amplification (LAMP), nested PCR, and real-time fluorescent quantitative PCR (qPCR) based on the CYP51C gene. All three methods demonstrated high specificity and effectiveness for early diagnosis of gummosis in Z. bungeanum. qPCR exhibited the highest sensitivity, detecting DNA concentrations as low as 3.1 fg/µL, which was tenfold more sensitive than LAMP and nested PCR. Additionally, qPCR enabled absolute quantification of the pathogen. Nested PCR showed exceptional stability and reliability, while LAMP provided rapid, cost-effective, and visually interpretable results, making it ideal for field applications.

Conclusions: These findings demonstrate the potential of molecular techniques to overcome traditional diagnostic limitations, providing practical solutions for early pathogen detection and sustainable disease management in Z. bungeanum. Among the methods, LAMP is optimal for field applications due to its simplicity, speed, and visual interpretation.