RAPID POPULATION ANALYSIS OF MAGNAPORTHE-GRISEA BY USING REP-PCR AND ENDOGENOUS REPETITIVE DNA-SEQUENCES

DNA samples from Magnaporthe grisea isolates were fingerprinted by usi ng repetitive element-based polymerase chain reaction (rep-PCR) with t wo outwardly directed primer sequences from Pod an element found in ap proximately 100 copies in the fungal genome. Variable length fragments , defining the sequences lying between these elements, were generated, and fingerprint patterns specific for individual strains were establi shed. ''Long PCR'' conditions, including higher pH (9.2) and increased extension time (10 min) were used to amplify DNA fragments ranging fr om 400 bp to longer than 23 kb. Polymorphisms specific to M. grisea st rains were generated, allowing inference of their genetic relationship s. Segregation analysis was used to confirm single-locus inheritance f or the fragments amplified by rep-PCR. Cluster analysis revealed robus t groupings that corresponded to previously determined MGR586 restrict ion fragment length polymorphism lineages of the rice-infecting strain s of the pathogen. We have also demonstrated the utility of rep-PCR to differentiate isolates that infect rice from those that infect nonric e hosts. DNA fingerprinting by Pot2 rep-PCR provides an efficient mean s to monitor the population dynamics of the blast pathogen. Because of the method's low cost and ease in application, it is now feasible to conduct large-scale population studies to understand the impact of hos t genotypes on pathogen evolution.