Molecular variability of rice tungro bacilliform virus genomes in tungro-outbreak areas in the Philippines

Genetic variation of rice tungro bacilliform virus (RTBV) genomes was analyzed from 288 natural field isolates from randomly collected leaf samples in Lanao del Norte and Zamboanga del Sur [Philippines], rice tungro-outbreak areas in the wet season of September, 1997. Visual scorings of symptoms and detection of tungro virus through double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) resulted to discripancies which were resolved through restriction analysis and DNA hybridization. Initial findings eliminated several fields found either with weeds, with low incidence of tungro infection or not in the reported outbreak area. Total DNA extracts from the final population of 135 isolates digested with EcoRV (genotypes) as well as mixed and "unclassified" genotypes were observed and they differed from the genome profiles of RTBV greenhouse variants G2 and L at the IRRI [International Rice Research Inst.] greenhouse. Six to nine genotypes (mixed and "unclassified" excluded) were detected in the four different outbreak fields with at least one to two predominant genotypes and these were not represented at equal frequencies. Statistical analyses such as Chi-square and Fisher's exact tests revealed no significant difference in terms of genetic composition exists among the RTBV populations from different locations (Lanao del Norte and Zamboanga del Sur) as well as from different fields within the same location (Lanao del Norte). Genetic composition of RTBV populations was also similar in the susceptible or apparently `resistant' varieties, suggesting that under the current conditions, the host variety exerted no apparent selection pressures as to which particular RTBV genotype is favored and hence predominate. Considering the potential sites for mutation in the viral genome, and therefore the variation that it would generate, it appears that there is a considerable constraint in variation based on the small number of genotypes observed in a population of 135 isolates