Collection of Rice Tungro-Infected Plants from Hotspots in the Philippines

  • Xavier Greg Caguiat Philippine RIce Research Institute
  • Frodie Waing Philippine RIce Research Institute
Keywords: breakdown, crop protection, nucleotide sequence, rice tungro bacciliform virus, rice tungro spherical virus


Tungro is one of the major rice pests causing as much 100% yield loss when unaddressed. Due to the onset of climate change and reports of breakdown of resistance, a study was designed to collect plants infected by tungro in selected tungro hotspots in the Philippines. Collection of tungro-infected plants were conducted in nine provinces: Isabela, Nueva Ecija, Laguna, Albay, Camarines Sur, Camarines Norte, Negros Occidental, Bukidnon, and North Cotabato.  A total of 400 suspected RTD-plants were collected. A total of 311 nucleic acid sequences (201 RTBV and 110 RTSV) were obtained and BLAST data yielded 83% to 100% identity with existing databases. Some sequences matched with RTBV strain RTBV-Ic, complete genome, RTBV isolate TB P194 gene, partial cds and some foreign isolates. Most of the samples were collected in Luzon while Mindanao had the least number of samples in terms of collected tungro-infected plants and the RNA extracted since it is highly dependent on the freshness of the plants. In the long run, knowledge on the genetic variation present in these organisms will help in disease management and development of rice tungro disease-resistant varieties.


Arboleda, M., Sta. Cruz, F. and Azzam, O. (1999). Preliminary analysis of genetic variation if rice tungro bacilliform virus in two provinces of the Philippines. Pages 11-16 in Chancellor TCB, Azzam O, Heong KL (Eds.). Rice Tungro Disease Management. International Rice Research Insititute, Los Baños, Philippines.
Azzam, O. and Chancellor, T.C.B. (2002). The biology, epidemiology and management of rice tungro disease in Asia. Plant Disease 86:88-100.
Bonfield, J.K. and Staden, R. (1996). Experiment files and their application during large-scale sequencing projects. DNA Sequence 6:109-117.
Cabauatan, P.Q., Cabunagan, R.C. and Koganezawa, H. (1995). Biological variants of rice tungro viruses in the Philippines. Phytopathology 85:77-81.
Cabauatan, P.Q. and Choi, I.R. (2008). The genetic and biological diversity of rice tungro viruses. Pages 81-91 in Tiongco ER, Angeles ER, Sebastian LS (Eds.). Rice Tungro Virus Disease: A Paradigm in Disease Management. Philippine Rice Research Institute, Munoz, Philippines and Honda Research Institute, Chiba, Japan.
Cabunagan, R.C., Angeles, E., Tiongco, E.R., Villareal, S., Truong, X.H., Astika, I.G.N., Muis, A., Chowdhury, A.K., Ganapathy, T., Chancellor, T.C.b, Teng, P.S., and Khush, G.S. (1996). Evaluation of rice germplasm for resistance to tungro disease. Pages 92-99 Chancellor TCB, Teng PS, and Heong KL (Eds.). Rice Tungro Disease Epidemilogy and Vector Ecology: the development of sustainable and cost-effective pest management practices to reduce yield losses in intensive rice-cropping systems. IRRI Discussion Paper Series No. 19. International Rice Research Institute, P.O. Box 933, Manila, Philippines.
Choi, I.R., Cabauatan, P.Q. and Cabunagan, R.C. (2009). Rice Fact Sheets:Rice Tungro Disease. International Rice Research Institute. Retrieved from
Dasgupta, I., Hull, R., Eastop, S., Poggi, P.C., Blakebrough, M.I. and Davies, J.W. (1991). Rice tungro bacilliform virus DNA independently infects rice after Agorbacterium mediated transfer. J Gen. Virol. 72:1215-1221.
De Los Reyes, J. 2000. Molecular Variability of Rice TUngro Bacilliform Virus Genomes in Tungro-outbreak Areas in the Philippines. Unpub. Thesis.
IRRI. (2009). Rice fact sheets: Rice tungro disease. International Rice Research Institute, Los Baños, Philippines.
Katoh, K., Kuma, K.I.m Toh, H. and Miyata, T. (2005). MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33:511-518.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007). "ClustalW and ClustalX version 2". Bioinformatics. 23 (21): 2947–2948. PMID 17846036. doi:10.1093/bioinformatics/btm404.
Lee, J.H., Muhsin, M., Atienza, G.A., Kwak, D.Y., Kim, S.M., De Leon, T.B., Angeles, E.R., Coloquio, E., Kondoh, H., Satoh, K., Cabunagan, R.C., Kikutchi, P.Q., Leung, S. and I.R Choi. 2010. Single nucleotide polymorphism in a gene for translation initiation factor (eIF4G) of rice (Oryza sativa) associated with resistance to rice tungro spherical virus. Mol. Plant-Microbe Interact. 23:29-38.
Hibino, H., Roechan, M. and Sudarisman, S. (1978). Association of two types of virus particles with penyakit habang (tungro disease) of rice in Indonesia. Phytopathology 68:1412-1416.
Hull, R. (1996). Molecular biology of rice tungro viruses. Ann. Rev. of Phytopathology 34:275-297.
Jena, K.K. and Mackill, D.J. (2008). Molecular markers and their use in marker-assisted selection in rice. Crop Science 48:1266-1276.

Librado, P. and Rozas, J. (2009). DNAsp v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451-1452.
Ling, K.C., Tiongco, E.R. and Cabunagan,R.C. (1983). Insect vectors of rice virus and MLO-associated disease. Pages 415-437 in Proc. First Intl. Workshop on Leafhoppers and Plant hoppers on Economic Importance. London, UK: Commonwealth Inst. Entomology.
Mangrauthia, S.K., Malathi, P., Agarwal, S., Ramkumar, G., Krishnaveni, D., Neeraja, C.N., Madhav, M.S., Ladhalakshmi, D., Balachandran, S.M., and Viraktamath, B.C. (2012). Genetic variation of coat protein gene among the isolates of Rice tungro spherical virus from tungro-endemic states of the India. Virus Genes 44:482-487.
Morrison, D.A.2009. A framework for phylogenetic sequence alignment. Plant Syst Evol 282:127-149.
Okonechnikov K, Golosova O, Fursov M, the UGENE team. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012 28: 1166-1167. doi:10.1093/bioinformatics/bts091
Ou, S.H. (1985). Rice disease. Second ed. Commonwealth Agricultural Bureau, Wallingford, UK. 33-47 pp.
Rivera, C.T. and Ou, S.H. (1965). Leaf hopper transmission of tungro disease of rice. Pl. Dis. Reptr. 49:127-131.
Saito, Y., Iwaki, M. and Usugi, T. (1976). Association of two types of particles of tungro-group disease of rice. Ann. Phytopathol. Soc. Jpn. 43:375.
Saitou, N. and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. and Evol. 4:406-425.
Sebastian, L.S., Tiongco, E.R., Tabanao, D.A., Maramara, G.V., Abdula, S. and Tabelin, E.B. (1999). Breeding for rice tungro disease resistance at PhilRice. Pages 23-29 in Chancellor TCB, Azzam O, Heong KL (Eds.). Rice Tungro Disease Management. International Rice Research Institute, Los Baños, Philippines.
Tagubase, J. 2004. Molecular Dynamics of Rice Tungro Bacilliform Virus (RTBV) Temporal Population in Response to Host Resistance. Unpub. Thesis.
Tamura, K., Nei, M. and Kumar, S. (2004). Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences (USA) 101:11030-11035.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol. Biol. and Evol. 28:2731-2739.
Umadhay, K.M.L., Yambao, M.L.M. and Azzam, O. (1999). Preliminary analysis of genetic variation of rice tungro spherical virus in the Philippines. Pages 17-21 in Chancellor TCB, Azzam O, Heong KL (Eds.). Rice Tungro Virus Disease Management. International Rice Research Institute, Los Baños, Philippines.
Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M. and Barton, G.J. (2009). Jalview v2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189-1191.
Yambao, M.L.M., Cabauatan, P.Q. and Azzam, O. (1998). Differentiation of rice tungro spherical virus variants by RT-PCR and RFLP. International Rice Research Notes 23:22-24
How to Cite
Caguiat, X. G., & Waing, F. (2018). Collection of Rice Tungro-Infected Plants from Hotspots in the Philippines. International Journal For Research In Agricultural And Food Science (ISSN: 2208-2719), 4(11), 07-17. Retrieved from