MOLECULAR DIAGNOSIS OF COLLETOTRICHUM KAHAWAE BY LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP)

Abstract

Colletotrichum kahawae, a very aggressive pathogen causing coffee berry disease (CBD), is specific to Arabica coffee (Coffea arabica) in Africa. This species is a significant quarantine pathogen in many countries which are still free from CBD. C. kahawae is morphologically similar to C. gloeosporioides but is phylogenetically and phenotypically distinct. Loop-mediated isothermal amplification (LAMP) is a simple, cost-effective, and rapid method for specific DNA-based detection. In this paper, the Apn2/MAT locus was selected as candidate marker, on whose basis species-specific primers were designed for loop-mediated isothermal amplification (LAMP) diagnosis of C. kahawae. The accuracy of this assay was tested using the type strains of other closely related species in the C. gloeosporioides species complex. The sensitivity of LAMP is high, with 8×10-2 pg μl-1 genomic DNA as the lowest detectable concentration. It offers a new and effective way for the rapid, specific and cost-effective diagnosis of severe fungal pathogens, thus representing a favourable option to conventional PCR and real-time PCR assays. LAMP diagnosis of C. kahawae is likely to provide a useful technological option for quarantine and disease management and control to prevent further spreading of this pathogen.