Xanthomonas oryzae pathovar oryzae causes a serious disease of rice in India and is endemic in all of the major rice-growing areas of the country. Sixty-seven X. oryzae pv. oryzae strains, collected mostly in 1994 and 1995, from 18 locations in India were analyzed by DNA fingerprinting methods using two separate repeat element probes from the X. oryzae pv. oryzae genome. These results show that strains belonging to a single pathogen lineage can be isolated from 16 of the 18 locations sampled; many of these locations are separated from each other by hundreds of kilometers and represent ecologically diverse rice-growing areas. Pathotyping analysis indicated that the strains in this lineage belong to pathotype 1b of X. oryzae pv. oryzae.

Genetic diversity among 42 Indian elite rice varieties, which is important for selection of parents for conventional breeding and hybrid program, was evaluated using three different types of DNA markers and parentage analysis. Random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers resulted in mean heterozygosity values of 0.429, 0.675 and 0.882 over all loci, respectively, and marker index values of 2.21, 4.05 and 5.49, respectively. The three molecular marker systems together provide wider genome coverage and, therefore, would be a better indicator of the genetic relationships among the 42 elite rice cultivars than those revealed using individual molecular markers. A total of 153 bands (91%) were polymorphic out of 168 bands amplified, considering all the markers together. The average genetic similarity coefficient across all the 861 cultivar pairs was 0.70 while the average coefficient of parentage was 0.10. Cluster analysis revealed that there was a very poor correlation (correlation coefficient <0.1) between dendrograms generated using coefficients of parentage and molecular marker generated genetic similarities, which can be attributed to selection pressure, genetic drift, sampling of loci and unknown relationships among supposedly unrelated ancestors.

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Xanthomonas oryzae pv. oryzae is the causal agent of bacterial leaf blight, a serious disease of rice. Spontaneous loss of virulence in X. oryzae pv. oryzae is associated with mutants that produce reduced levels of extracellular polysaccharide. Evidence is presented that these mutants accumulate in long-term stationary phase cultures but are not obtained from exponentially growing cultures. A number of independent spv (stationary-phase variation) mutants have been isolated and characterized. These mutants differ from each other with respect to the stability of the mutant phenotype, extent of loss of virulence, ability to outcompete wild type cells in stationary-phase cocultures, and hypersensitivity to hydrogen peroxide.Key words: stationary-phase variation, spontaneous loss of virulence, Xanthomonas oryzae.

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