Distribution of Xanthomonas oryzae pv. oryzae DNA Modification Systems in Asia

Xanthomonas oryzae pv. oryzae causes bacterial blight, the most important bacterial disease of rice in Asia (15, 16). Compared to the long history of rice cultivation, the deployment of genes for resistance to X. oryzae pv. oryzae in commercial rice cultivars is relatively recent. The introduction of these genes for resistance into rice is correlated with a change in the pathogenic diversity of X. oryzae pv. oryzae populations, that is, new races of the pathogen emerge and overcome deployed resistance (15, 17). These observations have stimulated much curiosity concerning the contribution of host genotype and other factors to the genetic diversity of the pathogen. Multilocus molecular markers have been used in conjunction with virulence typing to evaluate the diversity and structure of X. oryzae pv. oryzae populations within and between countries in Asia (1, 3, 6, 11, 12, 21, 27). In general, regionally defined pathogen populations in Asia were found to be distinct (1). This finding could be due either to slow pathogen migration or dispersal or to spatial partitioning of host genotypes (different cultivar preferences between regions). Although populations within a region generally were similar, in some cases genetically similar strains were detected in different regions, suggesting the migration of strains between countries, possibly as a consequence of germ plasm exchange (1, 6). Within one country, the Philippines, significant differentiation in populations was observed between different agroecosystems; that is, populations of X. oryzae pv. oryzae in the cool, mountainous highlands, where one crop of traditional varieties per year is grown, were different from those in the tropical lowlands, where two or three crops of semidwarf, early-maturing rice varieties per year are grown (3). Since several ecological factors in addition to host genotype likely influenced the genetic diversity of the pathogen population collected in that study (3), the magnitude of the contribution of any one of those factors to pathogen diversity is not clear. To more critically evaluate the genetic structure and movement of X. oryzae pv. oryzae populations throughout Asia and to understand some of the factors that influence the population structure of this pathogen, we have been investigating two X. oryzae pv. oryzae DNA restriction modification (R-M) systems (XorI and XorII) previously shown to be present in the pathogen (5, 28). R-M systems are particularly interesting for such studies, because they are thought to protect the bacterial genome from invasion by introduced bacteriophage or plasmid DNA (9) and thus may inhibit genomic variability due to DNA exchange on uptake. We cloned and sequenced two genes that are part of the XorII R-M system (xorIIM and xorII-vsr) (5). Not all X. oryzae pv. oryzae strains contained the XorI and XorII modification systems (5, 24), indicating that the systems might prove useful for developing an understanding of the origins of X. oryzae pv. oryzae genetic lineages and their distribution patterns. In this study, we determined the distribution of the two modification systems in a group of X. oryzae pv. oryzae strains collected from throughout Asia. Based on this information, we formulated a hypothesis on the geographic origin and historical migration of the DNA modification systems. In addition, we discuss the potential influence of these modification systems on the genetic stability of X. oryzae pv. oryzae populations.