Molecular detection of Colletotrichum falcatum causing red rot disease of sugarcane (Saccharum officinarum) using a SCAR marker

Red rot disease of sugarcane caused by Colletotrichum falcatum is one of the most destructive diseases of sugarcane (Saccharum officinarum) worldwide. The pathogen spreads primarily through infected sugarcane setts and hence the use of disease‐free planting materials is essential for preventing disease development in the field. In the present study a polymerase chain reaction (PCR) assay was developed for accurate and sensitive detection of C. falcatum in planting materials. Randomly amplified polymorphic DNA (RAPD) analysis identified a 566 bp PCR fragment that was specific to C. falcatum. The DNA sequence of this fragment was determined and used to design oligonucleotides amplifying a 442 bp sequence characterised amplified region (SCAR). The specificity of the SCAR primers was evaluated using purified DNA from C. falcatum and other Colletotrichum spp. as templates in PCR. The results indicated that the SCAR primers were highly specific to C. falcatum since the 442 bp fragment was amplified only from DNA of isolates and races of C. falcatum but not from any other Colletotrichum spp. tested. The detection sensitivity of C. falcatum was 0.1 ng for genomic DNA of C. falcatum and 5 ng for DNA extracted from infected sugarcane tissue. This new PCR‐based assay is a convenient tool for detection of this important pathogen in seed canes to ensure production of sugarcane.