Characterization of garlic virus A, garlic virus D, and onion yellow dwarf virus infecting onion
Abstract
Background: Allium cepa is one of the major vegetable crops cultivated in Saudi Arabia. This economically important crop faces several biotic stresses which adversely affect the quality and quantity of its production. Several virus groups (potyviruses, carlaviruses, tospoviruses, and allexiviruses) have been reported infecting Allium crops.
Methods: During the growing season of 2021-2022, a total of 81 onion samples exhibiting virus-like symptoms were collected from two different geographical regions in Saudi Arabia. The serological technique (ELISA) was used to detect the important allexiviruses and potyviruses. RT-PCR amplification of partial genome sequence was done using degenerate primers for allexiviruses and potyviruses and the phylogenetic trees were constructed using different bioinformatic tools.
Results: The results obtained from ELISA tests showed that 26% and 32% of onion samples were positive with both Garlic Virus A (GarV-A) and Onion yellow dwarf virus (OYDV) respectively. RT-PCR amplification and sequencing results showed that two allexiviruses, GarV-A, garlic virus D (GarV-D), and one Potyvirus (OYDV) were detected in both regions. Sequence data were deposited in the GenBank database with accession numbers, OQ397545, OQ397546 for GarV-A, OQ397547 for GarV-D, and OQ397548, OQ397549 for OYDV, sequentially. Phylogenetic tree analysis of these virus isolates showed making clades with closely related isolates of their respective viruses. Pairwise nucleotide sequence identity showed their similarity with GarV-A, GarV-D, and OYDV isolates reported earlier in the GenBank.
Conclusion: To the best of our knowledge, these two distinct allexiviruses (GarV-A, GarV-D) and one Potyvirus (OYDV) were isolated for the first time from an onion crop in Saudi Arabia.
Keywords: Allexiviruses; Potyviruses; Serological Detection; Allium cepa; RT-PCR; Sequence
Full Text:
PDFReferences
Friesen N, Fritsch RM, Blattner FR. Phylogeny and new intrageneric classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso: A Journal of Systematic and Floristic Botany, (2006); 22 (1): 372-395.
Abraham AD, Kidanemariam DB, Holton, TA. Molecular identification, incidence, and phylogenetic analysis of seven viruses infecting garlic in Ethiopia. European Journal of Plant Pathology, (2019); 155: 181-191.
Dossa FK, Miassi YE, Banzou K. Onion (Allium cepa) production in urban and peri-urban areas: financial performance and importance of this activity for market gardeners in Southern Benin. Current Investigations in Agriculture and Current Research, (2018); 3(2): 334-346.
Agricultural Production Survey Bulletin (2019), https://www.stats.gov.sa/sites/default/files/Agriculture%20Production%20Survey%202019%20EN.pdf, (Accessed: 9.9.2024).
Van Dijk P, Van der Vlugt RA. New mite-borne virus isolates from rakkyo, shallot and wild leek species. European Journal of Plant Pathology, (1994); 100: 269-277.
Maliogka VI, Dovas CI, Lesemann DE, Winter S, Katis NI. Molecular identification, reverse transcription-polymerase chain reaction detection, host reactions, and specific cytopathology of Artichoke yellow ringspot virus infecting onion crops. Phytopathology, (2006); 96(6): 622-629
Cafrune EE, Perotto MC, Conci VC. Effect of two Allexivirus isolates on garlic yield. Plant Disease, (2006); 90(7): 898-904.
Miller ME, Schwartz, HF. Stemphylium leaf blight and stalk rot: Compendium of Onion Garlic Diseases and Pests. 2008; 45-47. American Phytopathological Society
Shahraeen N, Lesemann DE, Ghotbi T. Survey for viruses infecting onion, garlic and leek crops in Iran. EPPO Bulletin, (2008); 38(1): 131-135.
Perotto MC, Cafrune EE, Conci VC. The effect of additional viral infections on garlic plants initially infected with Allexiviruses. European Journal of Plant Pathology, (2010); 126(4): 489-495.
King AM, Adams MJ, Carstens EB, Lefkowitz EJJ. Virus taxonomy:Ninth report of the International Committee on Taxonomy of Viruses. 2012; 1327. Elsevier
Dąbrowska E, Lewandowski M, Koczkodaj S, Paduch-Cichal E. Transmission of Garlic virus B, Garlic virus C, Garlic virus D and Garlic virus X by Aceria tulipae (Keifer) in leek. European Journal of Plant Pathology, (2020); 157: 215-222.
Karavina C, Ibaba JD, Gubba A, Pappu HR. First report of iris yellow spot virus infecting garlic and leek in Zimbabwe. Plant Disease, (2016); 100(3): 657-657.
Gera A, Kritzman A, Ganaim N, Raccah B. Transmission of tomato spotted wilt Tospovirus by F. occidentalis and analysis of the distribution of the virus in the field in Israel. In Proceedings of the Sixth International Symposium on Thysanoptera. (1998); 25-29.
Mahmoud SY, Abo-el-Maaty SA, El-Borollosy AM, Abdel-Ghaffar, MH. Identification of onion yellow dwarf Potyvirus as one of the major viruses infecting garlic in Egypt. American-Eurasian Journal of Agricultural & Environmental Sciences, (2007); 2(6): 746-755.
Bag S, Pappu, HR. Symptomatology of Iris yellow spot virus in selected indicator hosts. Plant Health Progress, (2009); 10(1): 41.
Mansouri F, Krahulec F, Duchoslav M, Ryšánek P. Newly identified host range of viruses infecting species of the genus Allium and their distribution in six habitats in the Czech Republic. Plant Pathology, (2021); 70(6): 1496-1507.
Clark MF, Adams A. Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. Journal of General Virology, (1977); 34(3): 475-483.
Daryono BS, Somowiyarjo S, Natsuaki KT. New source of resistance to Cucumber mosaic virus in melon. SABRAO Journal of Breeding and Genetics, (2003); 35: 19-26.
Chen J, Zheng HY, Antoniw JF, Adams MJ, Chen JP et.al. Detection and classification of allexiviruses from garlic in China. Archives of Virology, (2004); 149: 435-445.
Sokhandan-Bashir N, Ghasemzadeh A, Masoudi N, Khakvar R, Farajzadeh D. Degenerate primers facilitate the detection and identification of potyviruses from the northwest region of Iran. Iranian Journal of Biotechnology, (2013); 11(2): 115-122.
Sambrook J, Russell D. Molecular Cloning: A Laboratory Manual. 2001; Cold Spring Harbor Laboratory Press
Muhire BM, Varsani A, Martin DP. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS one, (2014); 9(9): e108277
Onion a vegetable with global market, https://www.dawn.com/news/275386/onion-a-vegetable-with-global-market, (Accessed: 10.9.2024). .
Anisuzzaman M, Ashrafuzzaman M, Ismail MR, Uddin MK, Rahim MA. Planting time and mulching effect on onion development and seed production. African Journal of Biotechnology, (2009); 8(3): 412-416.
Van Dijk P. Virus diseases of Allium species and prospects for their control. International Symposium on Alliums for the Tropics, (1993); 358: 299-306
Chen J, Chen J, Adams MJ. Molecular characterization of a complex mixture of viruses in garlic with mosaic symptoms in China. Archives of Virology, (2001); 146: 1841-1853.
Fajardo TV, Nishijima M, Buso JA, Torres AC, Ávila AC et al. Garlic viral complex: identification of Potyviruses and Carlavirus in Central Brazil. Fitopatologia Brasileira, (2001); 26: 619-626.
Paludan N. Virus attack on leek: Survey, diagnosis, tolerance of varieties and winter hardiness [variety trials, overwintering, Denmark]. Tidsskrift for planteavl, (1980); 84: 371-385.
Lot H, Chovelon V, Souche S, Delecolle B. Effects of onion yellow dwarf and leek yellow stripe viruses on symptomatology and yield loss of three French garlic cultivars. Plant Disease, (1998); 82(12): 1381-1385.
Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J et al. Methods in virus diagnostics: from ELISA to next generation sequencing. Virus Research, (2014); 186: 20-31.
Hadidi A, Flores R, Candresse T, Barba M. Next-generation sequencing and genome editing in plant virology. Frontiers in Microbiology, (2016); 7: 1325.
Jones S, Baizan-Edge A, MacFarlane S, Torrance L. Viral diagnostics in plants using next generation sequencing: computational analysis in practice. Frontiers in Plant Sciences, (2017); 8: 1770.
Singh J, Singh MK, Ranjan K, Kumar A, Kumar P et al. First complete genome sequence of garlic virus X infecting Allium sativum-G282 from India. Genomics, (2020); 112(2): 1861-1865.
Shahid MS, Sattar MN, Iqbal Z, Raza A, Al-Sadi AM. Next-generation sequencing and the CRISPR-Cas nexus: A molecular plant virology perspective. Frontiers in Microbiology, (2021); 11: 609376.
Prajapati MR, Manav A, Singh J, Kumar P, Kumar A et al. Identification and Characterization of a Garlic Virus E Genome in Garlic (Allium sativum L.) Using High-Throughput Sequencing from India. Plants, (2022); 11(2): 224.
Koo BJ, Kang SC, Chang MU. Survey of garlic virus disease and phylogenetic characterization of garlic viruses of the genus Allexivirus isolated in Korea. Plant Pathology Journal, (2002); 18(5): 237-243.
Wylie SJ, Li H, Jones MG. Phylogenetic analysis of allexiviruses identified on garlic from Australia. Australasian Plant Disease Notes, (2012); 7: 23-27.
Bereda M, Paduch-Cichal E, Dąbrowska E. Occurrence and phylogenetic analysis of allexiviruses identified on garlic from China, Spain, and Poland commercially available on the polish retail market. European Journal of Plant Pathology, (2017); 149: 227-237.
Taglienti A, Tiberini A, Manglli A, Rea R, Paoletti S et al . Molecular identification of allexiviruses in a complex mixture of garlic viruses in Latium (central Italy). European Journal of Plant Pathology, (2018); 150: 797-801.
DOI: http://dx.doi.org/10.62940/als.v11i4.2567
Refbacks
- There are currently no refbacks.