Detection of major viruses infecting shallot and molecular  characterization of Onion yellow dwarf virus from several  locations in Indonesia

Abstract. Harti H, Hidayat SH, Sobir, Wiyono S. 2020. Detection of major viruses infecting shallot and molecular characterization of Onion yellow dwarf virus from several locations in Indonesia. Biodiversitas 21: 1697-1701. Research was conducted to identify main viruses infecting shallot in several regions in Indonesia and to further characterize genetic variation of Onion yellow dwarf virus (OYDV). Field survey was conducted in Central Java (Brebes), East Java (Probolinggo), West Sumatera (Alahan Panjang), West Nusa Tenggara (Bima), and South Sulawesi (Enrekang). Virus detection from field samples was conducted by dot immunobinding assay. This detection confirmed that infection of OYDV, Shallot yellow stunt virus (SYSV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) has occurred in all field with incidence ranged from 20 to 93.5%, 2 to 93%, 21.5 to 80%, and 2 to 80.5%, respectively. The specific primers of Nib gene successfully amplified DNA fragments of OYDV from all locations. Sequencing of DNA fragments revealed that the amplified product was 351 bp. Sequence analysis indicated that the present OYDV isolates from Indonesia shared homology from 82 to 95%; and they had homology from 81 to 95% with OYDV isolates from other countries. The similarity of OYDV isolates from different geographical locations reflected the movements of seed bulbs among and within countries. The phylogenetic tree also revealed that OYDV isolates from different countries did not group together indicating their diverse origin.

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Identification and molecular characterization of onion yellow dwarf virus (OYDV) in Allium cepa crops in Poland

Progress in Plant Protection ◽

10.14199/ppp-2021-024 ◽

2021 ◽

Vol 61 (3) ◽

pp. 214-220

Keyword(s):

Phylogenetic Analysis ◽

Molecular Characterization ◽

Coat Protein Sequence ◽

Yellow Dwarf ◽

Dwarf Virus ◽

Onion Yellow Dwarf Virus ◽

Rt Pcr ◽

Pcr Products ◽

Yellow Dwarf Virus

Onion yellow dwarf virus is distributed worldwide significantly reducing yield of crops from the Allium genus. The aim of the study was the detection and molecular characterization of newly identified OYDV isolates infecting onions in Poland. The virus was detected by transmission electron microscopy and RT-PCR techniques using two pairs of diagnostic primers: OYDV-NibCPF1/R1 and OYDV-CPF2/R2. The specificity of obtained RT-PCR products was confirmed by Sanger sequencing and received viral coat protein sequence was used for phylogenetic analysis. The phylogenetic analysis was carried out using CP sequences of the new Polish onion isolate obtained in this study and 37 other sequences of OYDV retrieved from GenBank. The analysis revealed that the Polish OYDV isolate is the most similar to the OYDV isolates derived from onions from Argentina and Germany, which may indicate their common origin. Moreover, it was observed that the Polish onion and garlic isolates are very diverse and belong to different phylogroups.

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Molecular Characterization of Onion Yellow Dwarf Virus (Garlic Isolate) with Production of Virus-free Plantlets

International Journal of Virology ◽

10.3923/ijv.2012.61.70 ◽

2011 ◽

Vol 8 (1) ◽

pp. 61-70

Author(s):

Ahmed M. Soliman ◽

Sabry Y.M. Mahmoud ◽

Rehab A. Dawood

Keyword(s):

Molecular Characterization ◽

Yellow Dwarf ◽

Dwarf Virus ◽

Onion Yellow Dwarf Virus ◽

Yellow Dwarf Virus

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Molecular characterization of barley yellow dwarf virus in Tunisia

Acta Virologica ◽

10.4149/av_2014_03_214 ◽

2014 ◽

Vol 58 (03) ◽

pp. 214-222 ◽

Cited By ~ 2

Author(s):

M. BOUALLEGUE ◽

M. MEZGHANI-KHEMAKHEM ◽

D. BOUKTILA ◽

H. MAKNI ◽

M. MAKNI

Keyword(s):

Molecular Characterization ◽

Barley Yellow Dwarf Virus ◽

Yellow Dwarf ◽

Dwarf Virus ◽

Barley Yellow Dwarf ◽

Yellow Dwarf Virus

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Double Infection of Onion yellow dwarf virus and Shallot latent virus in Garlic from Several Regions in Indonesia

Jurnal Perlindungan Tanaman Indonesia ◽

10.22146/jpti.62818 ◽

2021 ◽

Vol 25 (1) ◽

pp. 40

Author(s):

Nurenik Nurenik ◽

Sedyo Hartono ◽

Sri Sulandari ◽

Susamto Somowiyarjo ◽

Argawi Kandito

Keyword(s):

Early Detection ◽

Latent Virus ◽

Yellow Dwarf ◽

Dwarf Virus ◽

Onion Yellow Dwarf Virus ◽

Rt Pcr ◽

Double Infection ◽

Specific Primers ◽

Shallot Latent Virus ◽

Yellow Dwarf Virus

Viruses have been a problem on garlic cultivations in various countries. There are several viruses reported infecting garlic. Genera Potyvirus and Carlavirus are the most common viruses found infecting garlic. Mixed infection on garlic is often designated as a “garlic viral complex”. These viruses can be transmitted through imported garlic seeds. Therefore, it is necessary to conduct early detection of garlic seeds to prevent the epidemic of these viruses. This study aimed to detect Onion yellow dwarf virus (OYDV) and Shallot latent virus (SLV) on garlic. Garlic samples were obtained from Enrekang, Magelang, Temanggung, Tawangmangu, and Yogyakarta. Total RNA was extracted from the samples and subsequently used for RT-PCR using two pairs of specific primers SLV-F/SLV-R and OYDV-F/OYDV-R. Primary pair SLV-F/SLV-R in amplicons sized 276 bp, while OYDV-F/OYDV-R in amplicons sized 112 bp. RT-PCR results showed that OYDV was found in all samples tested in this study. Meanwhile, double infections (OYDV and SLV) were found in eight out of ten samples tested. These results indicated that double infections on garlic were common in Indonesia.

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