Inter- and intra-site genetic diversity of natural field populations of rice tungro bacilliform virus in the Philippines

The genetic structure of rice tungro bacilliform virus (RTBV) populations w ithin and between growing sites was analyzed in a collection of natural fie ld isolates from different rice varieties grown in eight tungro-endemic sit es of the Philippines. Total DNA extracts from 345 isolates were digested w ith EcoRV restriction enzyme and hybridized with a full-length probe of RTB V, a procedure shown in preliminary experiments capable of revealing high l evels of polymorphism in RTBV field isolates. In the total population, 17 d istinct EcoRV-based genome profiles (genotypes) were identified and used as indicators for virus diversity. Distinct sets of genotypes occurred in Isa bela and North Cotabato provinces suggesting a geographic isolation of viru s populations. However, among the sites in each province, there were few si gnificant differences in the genotype compositions of virus populations. Th e number of genotypes detected at a site varied from two to nine with a few genotypes dominating. In general the isolates at a site persisted from sea son to season indicating a genetic stability for the Focal virus population . Over the sampling time, IRRI rice varieties, which have green leafhopper resistance genes, supported similar virus populations to those supported by other varieties, indicating that the variety of the host exerted no appare nt selection pressures. Insect transmission experiments on selected RTBV fi eld isolates showed that dramatic shifts in genotype and phenotype distribu tions can occur in response to host/environmental shifts.