Hierarchical analysis of spatial variation of the rice bacterial blight pathogen across diverse agroecosystems in the Philippines

A hierarchical analysis of variation was conducted for the rice bacterial blight pathogen in the Philippines. More than 1,200 strains were collected systematically from 13 sites along a 310-km transect spanning an indigenous rice-growing area in the mountainous region and the improved irrigated agroecosystem in the lowlands of the island of Luzon. Restriction fragment length polymorphism analysis using the transposable element IS1113 and restriction enzyme analysis using PstI were utilized to assess the genetic diversity and phylogenetic structure of the pathogen population. Nineteen haplotypes (distinct DNA fingerprints), grouping into three robust clusters, were defined using IS1113. PstI fingerprinting revealed greater diversity (46 unique haplotypes defined), but the phenogram derived from PstI data was not robust. Hierarchical analysis of genetic variation showed population substructuring within and between sites. For the entire transect, a high degree of genetic differentiation among sites was estimated, indicating geographic differentiation between pathogen populations in different agroecosystems. Reiterative subsampling of the PstI data set suggested that pathogen populations could be sampled less intensively by decreasing the number of samples collected per field without resulting in considerable loss of detected diversity. Nearly 80% of the haplotypes found by sampling 35 samples per field could be detected by sampling 18 samples per field. The results of this study have provided a thorough understanding of the population structure of the bacterial blight pathogen in the Philippines, which is one of the important prerequisites for designing effective and long-term strategies for resistance-gene deployment.