Molecular Detection of Phytophthora cinnamomi by RPA-CRISPR/Cas12a-Mediated Isothermal Amplification

Abstract

Background: Phytophthora cinnamomi is one of the soil-borne pathogens that causes root rot and stem rot in many plants globally. P. cinnamomi has serious economic, social, and environmental impacts, threatening natural ecosystems and biodiversity. Methods: In this study, a molecular detection method based on Recombinant polymorphic amplification (RPA) combined using the CRISPR/Cas12a system was developed for P. cinnamomi. The method was found to be highly specific for P. cinnamomi. Results: The results showed that 10 P. cinnamomi isolates were positive; however, 21 Phytophthora species, 4 Phytopythium species, 18 fungal species, and 2 Bursaphelenchus species were negative. In total, 10 pg·µL−1 of P. cinnamomi genomic DNA can be detected. The detection process is performed within 20 min at 37 °C, which makes it fast and convenient for use. Discussion: In conclusion, the RPA-CRISPR/Cas12a system in this study is a promising tool for the rapid and sensitive detection of P. cinnamomi in plant samples.