Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae is one of the most important rice diseases due to the severe epidemic and causing damage to rice fields in all parts of Thailand. X. oryzae pv. oryzae has high genetic diversity, as such it is difficult to breed any resistant rice cultivars for this disease. Therefore, the pathotype study of this pathogen is important for planning the use of resistance genes in rice breeding program for disease resistance. The pathotype screening is time consuming and laborious. Thus, the use of molecular techniques for pathotype differentiation to develop molecular marker will speed up the pathotype screening. In this research, 80 isolates of X. oryzae pv. oryzae from 12 provinces in northeastern Thailand were studied. PCR-based techniques, i.e. RAPD-PCR, rep-PCR, and IS-PCR, with survey and selected 15 primers were used. X. oryzae pv. oryzae isolates could be divided into 13 groups by cluster analysis in which isolate from 10 provinces were clustered into a large group. Three DNA fragments that specific to the pathogen in group I and group III were selected to develop molecular markers. Two primer sets, MG1 and MG2, were synthesized and used to test on all 80 isolates. The result showed that only the MG1 primer set could amplify a specific PCR fragment of the pathogen in group I. In conclusion, the pathogen isolates from northeastern Thailand had genetic diversity and were distributed to all parts of the region. A molecular marker was developed from this genetic diversity which is useful for pathotype screening. Thus, this information is importance for effective rice breeding program for bacterial left blight resistance.
