Research progress on nucleic acid amplification-based detection technologies for phytopathogenic fungi

Phytopathogenic fungi are highly diverse and globally distributed, posing a major threat to agricultural production worldwide. The annual losses caused by plant diseases can reach up to 30% of global crop yields, with over 80% of infections caused by fungal pathogens. The accurate identification of pathogenic fungal species is crucial for effective disease prevention and control. Thus, establishing accurate and rapid detection technologies for phytopathogenic fungi is crucial for implementing targeted control strategies and reducing agricultural losses. Molecular detection technologies based on nucleic acid amplification have recently become indispensable tools for pathogen detection. This review examines the principles and advancements of nucleic acid-based detection techniques, including thermal cycling-based methods (e.g., conventional PCR, real-time quantitative PCR, and droplet digital PCR) and isothermal amplification platforms (e.g., loop-mediated isothermal amplification and recombinase polymerase amplification), as well as CRISPR/Cas-assisted assays coupled with isothermal amplification (e.g., RPA-CRISPR and LAMP-CRISPR), with the aim of evaluating their strengths, limitations, and practical applicability in the rapid diagnosis and precision management of phytopathogenic fungal diseases. KEY POINTS: Nucleic acid amplification technologies enable rapid and sensitive detection of phytopathogenic fungi. Isothermal amplification and CRISPR/Cas-assisted platforms facilitate field-deployable and low-instrumentation diagnostics. Integrated workflows support early diagnosis and precision management of phytopathogenic fungal diseases.