CRISPR‐based platforms for the specific and dual detection of defoliating/nondefoliating strains of Verticillium dahliae

Abstract BACKGROUND Verticillium dahliae is a soil‐borne pathogenic fungus that causes Verticillium wilt disease on more than 400 plant species worldwide. Because of its broad host range and its ability to survive long term in the soil, there are few effective control measures for V. dahliae once it has become established. Accurate, sensitive, and rapid detection of V. dahliae is crucial for limiting pathogen entry into new regional environments and early management of Verticillium wilt. RESULTS In this study, we developed a method to detect V. dahliae based on recombinase polymerase amplification (RPA) and CRISPR/Cas technology and used fluorescence and lateral flow test strips to monitor the outcomes. Through the establishment and optimization of RPA–CRISPR/Cas13a detection, the sensitivity of the fluorescence method was 1 a m for genomic DNA (gDNA) within 20 min, whereas the sensitivity of the lateral flow strip method was 100 a m for gDNA in 30 min. The field applicability of RPA–CRISPR/Cas13a was also validated by the detection of V. dahliae on smoke trees ( Cotinus coggygria ) in Xiangshan Park, Beijing, China. Finally, diplex detection for defoliating and nondefoliating pathotypes of V. dahliae was established by combining CRISPR–Cas12a/Cas13a with specific target genes. CONCLUSION Taken together, this study achieved rapid, sensitive, and accurate detection of V. dahliae and the differentiation of defoliating and nondefoliating pathotypes and provides potential for field‐deployable diagnostic tools for rapid and ultrasensitive detection. © 2023 Society of Chemical Industry.