Movement of Xanthomonas oryzae pv. oryzae in Southeast Asia Detected Using PCR-Based DNA Fingerprinting.

ABSTRACT Two outwardly directed primers complementary to sequences in IS1112, a repetitive element isolated from Xanthomonas oryzae pv. oryzae, were used to fingerprint DNA from a set of 71 bacterial blight pathogen strains using polymerase chain reaction (PCR), PCR-based restriction analysis, and ligation-mediated PCR. To allow amplification of long DNA fragments, standard amplification conditions were altered to increase the pH, add dimethylsulfoxide, decrease denaturation time, and increase extension time. Bands ranging in size from 100 bp to 7 kb and in number from 13 to 48 bands per strain were amplified. The three methods revealed useful polymorphisms among individual strains and allowed their genetic relationships to be efficiently deduced. Good correlation was found between the major clusters obtained by the three methods. The PCR method gave the most robust clusters and was most efficient in terms of speed, simplicity, and economy. Using PCR and restriction fragment length polymorphism to compare strains of the bacterial blight pathogen from Indonesia and the Philippines, we found that, whereas there is regional differentiation of the pathogen populations, the predominant strains in the pathogen collections from both countries are closely related. This indicates the occurrence of regional movement, perhaps as a consequence of germ plasm exchange.