Sequence differences in rice tungro bacilliform virus

Rice tungro disease is the most important virus disease of rice. Information on virus variation can be crucial if conventional and biotechnology-based approaches are to be administered successfully. This study aimed to determine the level of genetic diversity and differentiations among different isolates of RTBV collected from different rice growing areas in the Philippines with recorded high tungro disease incidence and infer their phylogenetic relationships. Some 150 tungro-infected plants were obtained from four rice growing provinces: Isabela (ISA), Nueva Ecija (NEC), Negros Occidental (NOC), and North Cotabato (COT). Amplified PCR products with coat protein 1 (CP1) were purified and sent for single-pass DNA sequencing. Consensus sequences were generated using Staden Package and compared with GenBank using nucleotide Blast. Multiple sequence alignment and cluster analysis was conducted using MAFFT alignment procedure. BLAST query resulted to identity scores that ranged from 94-96% and E-value=0 which confirmed that the amplified sequences were indeed of rice tungro bacilliform virus origin. Highest nucleotide diversity was observed in ISA (PI=0.0564, THETA=0.0588) and lowest in COT (PI=0.0297, THETA=0.0265). Selection pressure on the coat protein genes at the province and national levels could be absent as indicative of non-significant Tajima's D values. The differences in the patterns of nucleotide diversity in RTBV across geographic regions may imply that the factors affecting nucleotide diversity could also vary within the provinces. Painwise FST (fixation index) tended to be lower for NOC with other provinces (0.2073-0.2878), except between ISA and NEC. Cluster analysis showed high heterogeneity among isolates from the same province and the degree of genetic differentiation between provinces. The isolates from Negros Occidental inclined to form a less tight cluster compared to other provinces due to its high variability. This information will be used in conjunction with varietal reaction patterns, spatial and genomic diversity monitoring to understand the RTBV evolution.