Noor Aidawati, Saipul Abbas, Elly Liestiany


Rice tungro bacilliform virus (RTBV) is a serious threat to rice production in various regions in Indonesia including South Kalimantan. Cautious and flexible management strategies are of utmost importance. This study investigates the genetic diversity within the P4 gene of RTBV in South Kalimantan, Indonesia, to inform targeted disease management strategies. The PCR method was used to amplify P4 gene fragments from RTBV samples collected from 2 locations, namely Karang Buah Village and Anjir Pasar Lama. The PCR results successfully detected fragments of 430 bp, which were then analyzed in sequence to identify genetic variations. The characterization results showed that the presence of significant genetic diversity among RTBV isolates. These variants include differences in nucleotides at specific positions in the P4 gene, indicating the adaptation of the virus to local conditions. These findings provide a solid basis for designing more precise control strategies, such as the development of rice varieties that are more resistant to certain RTBV variants or the implementation of more specific management measures.


PCR; P4 Gene; RTBV; Rice; Sequence Characterization

Full Text:



Abbas, S., S. Sulandari, S. Hartono and Y.A. Trisyono. 2020. Molecular Detections and Resistance Response of Six Rice Varieties to Tungroviruses from South Sulawesi. Jurnal Perlindungan Tanaman Indonesia, 24(1): 89.

Afandi, A., A. Wibowo, S. Loekito, S. Subandiyah, A. Hieno, K. Otsubo and K. Koji. 2022. Plant Pests Dis. Journal of Tropical Plant Pests and Diseases, 22(2): 90–99.

Bömer, M., A.I. Rathnayake, P. Visendi, G. Silva and S.E. Seal. 2018. Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology, 163(2): 533–538.

Cabauatan, P. Q., U. Melcher, K. Ishikawa, T. Omura, H. Hibino, H. Koganezawa and O. Azzam. 1999. Sequence changes in six variants of Rice tungro bacilliform virus and their phylogenetic relationships. Journal of General Virology, 80(8): 2229–2237.

Chisholm, P. J., S.D. Eigenbrode, R.E. Clark, S. Basu and D.W. Crowder. 2019. Plant-mediated interactions between a vector and a non-vector herbivore promote the spread of a plant virus. Proceedings of the Royal Society B: Biological Sciences, 286: 1911.

Dai, S., X. Wei, A.A. Alfonso, L. Pei, U.G. Duque, Z. Zhang, G.M. Babb and R.N. Beachy. 2008. Transgenic rice plants that overexpress transcription factors RF2a and RF2b are tolerant to rice tungro virus replication and disease. Proceedings of the National Academy of Sciences of the United States of America, 105(52): 21012–21016.

Das, A., D. Soubam, P.K. Singh, S. Thakur, N.K. Singh and T.R. Sharma. 2012. A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis confers broad spectrum resistance to Magnaporthe oryzae. Functional and Integrative Genomics, 12(2): 215–228.

Green, S. J., R. Venkatramanan and A, Naqib. 2015. Deconstructing the polymerase chain reaction: Understanding and correcting bias associated with primer degeneracies and primer-template mismatches. PLoS ONE, 10(5): 1–21.

Hibino, H. and P.Q. Cabauatan. 1987. Infectivity Neutralization of Rice Tungro-Associated Viruses Acquired by Vector Leafhoppers. Vol. 77.

Ingwell, L. L., S.D. Eigenbrode and N.A. Bosque-Pérez. 2012. Plant viruses alter insect behavior to enhance their spread. Scientific Reports, 2: 12-30.

Iswanto, E. H., D. Munawar and Rahmini. 2020. Resistance evaluation of modern rice varieties to brown planthopper Nilaparvata lugens STÅL. Journal of Tropical Plant Pests and Diseases, 20(2): 157–164.

Jones, R. A. C.. 2014. Plant virus ecology and epidemiology: Historical perspectives, recent progress and future prospects. Annals of Applied Biology, 164(3): 320–347. 10.1111/ aab.12123

Jones, R. A. C. 2021, Global plant virus disease pandemics and epidemics. Plants, 10(2): 1–41.

Jones, R. A. C. R.A. Naidu, R. A. 2019). Global Dimensions of Plant Virus Diseases: Current Status and Future Perspectives. Annual Review of Virology, 6: 387–409.

Kang, B. C., I. Yeam and M.M. Jahn. 2005. Genetics of plant virus resistance. Annual Review of Phytopathology, 43: 581–621. 10.1146/annurev.phyto.43.011205.141140

Karasov, T. L., G. Shirsekar, R. Schwab and D. Weigel. 2020. What natural variation can teach us about resistance durability. Current Opinion in Plant Biology, 56: 89–98. 10.1016/j.pbi.2020.04.010

Khanal, V. and A. Ali. 2019. First Complete Genome Sequence of Cucurbit Aphid-Borne Yellows Virus from Pumpkin in the United States. Microbiology Resource Announcements, 8(6): 13–14.

Medina-Puche, L. and R. Lozano-Duran. 2019. Tailoring the cell: a glimpse of how plant viruses manipulate their hosts. Current Opinion in Plant Biology, 52: 164–173.

Pouraziz, P., M. Yousefi, A.I. Santosa and D. Koolivand. 2023. Genetic Variation between Asian and Mediterranean Populations of Cucurbit Aphid-Borne Yellows Virus. Viruses, 15(8): 1-13.

Rajeswaran, R., V. Golyaev, J. Seguin, A.S. Zvereva, L. Farinelli and M.M. Pooggin. 2014. Interactions of rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery. Molecular Plant-Microbe Interactions, 27(12): 1370–1378.

Reen, J. K., K.P. Ramesha, D. Preeti, Revanasiddu and M. Ahirwar. 2019. Identification of single nucleotide polymorphism in GnRHR gene in Murrah bulls. Indian Journal of Animal Research, 53(9): 1172–1180.

Satterfield, D. A., T.S. Sillett, J.W. Chapman, S. Altizer and P.P. Marra. 2020. Seasonal insect migrations: massive, influential, and overlooked. Frontiers in Ecology and the Environment, 18(6): 335–344.

Wang, T., B. Li, C.E. Nelson and S. Nabavi. 2019. Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data. BMC Bioinformatics, 20(1): 1–16.

Wang, Y., H. Guo, H. Li, H. Zhang and X. Miao. 2012. Identification of transcription factors potential related to brown planthopper resistance in rice via microarray expression profiling. BMC Genomics, 13(1): 14-25.

Yee, S. F., C.H. Chu, E. Poili and M.S.H. Sum. 2017. Expression and the antigenicity of recombinant coat proteins of tungro viruses expressed in Escherichia coli. Journal of Virological Methods, 240: 69–72. j.jviromet.2016.12.001



  • There are currently no refbacks.

Copyright (c) 2024 Saipul Abbas

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Pakistan Journal of Phytopathology
ISSN: 1019-763X (Print), 2305-0284 (Online).
© 2013 Pak. J. Phytopathol. All rights reserved.