MOLECULAR IDENTIFICATION OF ONION YELLOW DWARF VIRUS IN ALLIUM FISTULOSUM AND ALLIUM SCHOENOPRASUM IN INDONESIA
Abstract
Virus infection in four edible Allium spp.: Welsh onion (Allium fistulosum), onion (Allium cepa), fresh chive (Allium schoenoprasum), and garlic chive (Allium tuberosum) cultivated in Indonesia had never been studied. Samples were obtained during field surveys in June – October 2023 at different production centers in Java Island, Indonesia, and then molecularly tested using a universal primer pair to amplify ± 700 bp of the 3′-end region of potyviruses. Six Welsh onion and four fresh chive samples were tested positive for Onion yellow dwarf virus (OYDV). Phylogenetic tree clustered the sequenced four Indonesian Welsh onion isolates (GenBank acc. no. OR772075 – 78) in a group together with other Welsh onion isolates from South Korea and Japan. Meanwhile, the four fresh chive isolates (OR772079 – 82) that were obtained were positioned in a separate group together with predominantly onion isolates from Europe and America. No significant recombination signal was detected on the compared isolates using Recombination Detection Program v5.30. Percentage identity analysis further determined the divergence of Welsh onion isolates to isolates from other hosts.
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Bag, S., H. F. Schwartz, C. S. Cramer, M. J. Havey. and H. R. Pappu. 2015. Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority. Molecular Plant Pathology, 16(3): 224-237. https://doi.org/10.1111/mpp.12177
Conci, V. C., A. Canavelli, P. Lunello , J. Di Rienzo, S. F. Nome, G. and Zumelzu, R. Italia. 2003. Yield losses associated with virus-infected garlic plants during five successive years. Plant Diseases, 87(12):1411–1415. https://doi.org/10.1094/pdis.2003.87.12.1411
Cremer, J., P. Campbell, V. Steele, D. Persley, J. Thomas, S. Harper. and C. Gambley. 2021. Detection and distribution of viruses infecting garlic crops in Australia. Plants, 10:1013. https://doi.org/10.3390/plants10051013
Fajardo, T. V. M., M. Nishijima, J. A. Buso, A. C. Torres, A. C. Ávila. and R. O. Resende. 2001. Garlic viral complex: Identification of potyviruses and carlavirus in central Brazil. Fitopatol. Bras, 26(3):619–626. https://doi.org/10.1590/S0100-41582001000300007
Gibbs, A. and A. Mackenzie. 1997. A primer pair for amplifying part of the genome of all potyvirids by RT-PCR. Journal of Virological Methods., 63(1-2), 9-16. https://doi.org/10.1016/s0166-0934(96)02103-9
Gupta, N., S. Islam, S. K. Sharma. and V. K. Baranwal. 2017. Complete genome sequence of an isolate of leek yellow stripe virus from garlic in India. Journal Plant Pathology, 99(3):793–797. http://doi.org/10.4454/jpp.v99i3.3945
Harti, H., S. H. Hidayat, Sobir and S. Wiyono. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas, 21(4):1697–1701. https://doi.org/10.13057/biodiv/d210451
Hidayat, S. H., Meliyana, R. Yulianingsih, D. Dinarti. and S. Nurulita. 2023. Incidence of main viruses infecting local garlic in Java, Indonesia. Journal Tropical Plant Pests Diseases, 23(2):7–15. https://doi.org/10.23960/jhptt.2237-15
Langeveld, S. A., J. M. Dore, J. Memelink, A. F. Derks, C. I. van der Vlugt, C. J. Asjes. and J. F. Bol. 1991. Identification of potyviruses using the polymerase chain reaction with degenerate primers. Journal of General Virology, 72: 1531-1541. https://doi.org/10.1099/0022-1317-72-7-1531
Mansouri, F., F. Krahulec, M. Duchoslav. and P. Ryšánek. 2021. Newly identified host range of viruses infecting species of the genus Allium and their distribution in six habitats in the Czech Republic. Plant Pathology, 70(6):1496–1507. https://doi.org/10.1111/ppa.13391
Martin, D.P., A. Varsani, P. Roumagnac, G. Botha, S. Maslamone, T. Schwab, Z. Kelz, V. Kumar. and B. Murrell. 2021. RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evolution, 7(1):veaa087. https://doi.org/10.1093/ve/veaa087
Muhire, B.M., A. Varsani and D. P. and Martin DP. 2014. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE, 9(9):e108277. https://doi.org/10.1371/journal.pone.0108277
Nurenik ., S. Hartono, S. Sulandari, S. Somowiyarjo and A. Kandito. 2021. Double infection of Onion yellow dwarf virus and Shallot latent virus in garlic from several regions in Indonesia. Journal of Perlind Tanam Indonesia, 25(1):40–47. https://doi.org/10.22146/jpti.62818
Santosa, A.I. and F. Ertunc F. 2020. Identification, molecular detection and phylogenetic analysis of four viruses infecting Allium cepa in Ankara Province, Turkey. Journal Plant Disease Protection, 127(4):561–569. https://doi.org/10.1007/s41348-020-00347-5
Santosa, A.I., F. Randa-Zelyüt, A. Karanfil, S. Korkmaz, S. Hartono and F. Ertunç. 2023. Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N. Virus Genes, 59(1):121–131. https://doi.org/10.1007/s11262-022-01956-y
Tamura, K. and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10(3): 512–526. https://doi.org/10.1093/oxfordjournals.molbev.a040023
Tamura, K., G. Stecher. and S. Kumar. 2021. MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution, 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120
Tsuneyoshi, T., T. Matsumi, K. T Natsuaki. and S. Sumi .1998. Nucleotide sequence analysis of virus isolates indicates the presence of three potyvirus species in Allium plants. Archives of Virology, 143(1):97–113. https://doi.org/10.1007/s007050050271
Verma, R. K., R. Mishra, N. M. Petrov, M. Stoyanova, A. Stoev, N. Bakardjieva and R. K. Gaur. 2015. Molecular characterization and recombination analysis of an Indian isolate of Onion yellow dwarf virus. European Journal of Plant Pathology, 143:437–445. https://doi.org/10.1007/s10658-015-0695-7
DOI: https://doi.org/10.33866/phytopathol.036.01.1054
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