Genetic diversity of Colletotrichum graminicola isolates from India revealed by restriction analysis of PCR-amplified intergenic spacer region of nuclear rDNA

Sorghum anthracnose, caused by Colletotrichum graminicola (Ces.) Wilson, is a destructive disease responsible for as high as 50% loss in grain yield1. Management of this disease through host plant resistance has often been unsuccessful due to the hyper-variable nature of this fungus2. A rapid and reproducible tool for characterizing the pathogen genotypes would help researchers follow the shift in genetic make-up of the pathogen population, thus providing a dynamic picture of the interactions between the host and pathogen genotypes. This would, in turn, help devising strategies for management of this disease. Genetic variability in this fungus was earlier studied by using molecular tools like RFLP and RAPD3–7. RFLP is a reliable tool, but is cumbersome, time-consuming and requires large amount of DNA. RAPD,on the other hand, is simple and rapid, but often not reproducible and errorprone8. Restriction analysis of the intergenic spacer region of the rDNA repeats has been useful for variability studies in some fungi like Fusarium oxysporum9–11 and Pyrenophora graminea12. Once optimized (primer sequences and enzyme combinations), this technique combines the advantage of both PCR (simplicity and speed) and RFLP (reproducibility). The present communication reports on the successful use of the primer pair originally designed for F. oxysporum9 and identification of a single restriction enzyme, KpnI, which can be used for fingerprinting of C. graminicola populations