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

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.

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

2020 ◽  
Vol 21 (4) ◽  
Author(s):  
Heri Harti ◽  
SRI HENDRASTUTI HIDAYAT ◽  
SOBIR ◽  
SURYO WIYONO
Keyword(s):  
Molecular Characterization ◽  
Virus Detection ◽  
Latent Virus ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Onion Yellow Dwarf Virus ◽  
Dna Fragments ◽  
Field Samples ◽  
Yellow Dwarf Virus

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.

scholarly journals Molecular characterization of barley yellow dwarf virus in Tunisia

2014 ◽  
Vol 58 (03) ◽  
pp. 214-222 ◽  
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

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

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.

scholarly journals Simultaneous Detection of Mixed Infection of Onion yellow dwarf virus and an Allexivirus in RT-PCR for Ensuring Virus Free Onion Bulbs

2010 ◽  
Vol 21 (1) ◽  
pp. 64-68 ◽  
Author(s):  
Sandeep Kumar ◽  
V. K. Baranwal ◽  
Subodh Joshi ◽  
Meenakshi Arya ◽  
S. Majumder
Keyword(s):  
Mixed Infection ◽  
Simultaneous Detection ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Onion Yellow Dwarf Virus ◽  
Rt Pcr ◽  
Onion Bulbs ◽  
Yellow Dwarf Virus

Molecular characterization and recombination analysis of an Indian isolate of Onion yellow dwarf virus

2015 ◽  
Vol 143 (3) ◽  
pp. 437-445 ◽  
Author(s):  
Rakesh Kumar Verma ◽  
Ritesh Mishra ◽  
Nikolay Manchev Petrov ◽  
Mariya Stoyanova ◽  
Antoniy Stoev ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Yellow Dwarf ◽  
Indian Isolate ◽  
Dwarf Virus ◽  
Onion Yellow Dwarf Virus ◽  
Recombination Analysis ◽  
Yellow Dwarf Virus

scholarly journals Occurrence and molecular characterization of wheat streak mosaic virus in wheat in Serbia

2020 ◽  
Vol 35 (2) ◽  
pp. 117-131
Author(s):  
Ana Vucurovic ◽  
Ivana Stankovic ◽  
Katarina Zecevic ◽  
Branka Petrovic ◽  
Goran Delibasic ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Wheat Streak Mosaic Virus ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Streak Virus ◽  
Nucleotide Position ◽  
Rt Pcr ◽  
Cp Gene ◽  
Yellow Dwarf Virus

The wheat streak mosaic virus (WSMV), vectored by the wheat curl mite, is globally distributed and threatens wheat production worldwide. Since its first occurrence in Serbia in the 1960s, WSMV presence has not been monitored. In 2019, a total of 62 samples of fi ve wheat cultivars from eight locations in Serbia were collected and tested for the presence of nine common wheat viruses: WSMV, barley yellow dwarf virus-PAV, -MAV, -SGV, and -RMV, cereal yellow dwarf virus-RPV, wheat spindle streak virus, brome mosaic virus, and soil-borne wheat mosaic virus, using individual or multiplex RT-PCR. WSMV was detected in 58.1% of the tested samples in seven wheat crops at five different locations. Species-specific primers failed to detect the presence of the other eight tested viruses. For further confirmation of WSMV, RT-PCR with the WS8166F/WS8909R primers covering the coat protein (CP) gene was carried out for both amplification and sequencing. The amplified product of the correct predicted size (750 bp) derived from four selected isolates, 98-19, 99-19, 102-19 and 120-19, was sequenced and deposited in GenBank (MT461299, MT461300, MT461301 and MT461302, respectively). Serbian WSMV isolates showed very high nucleotide identity (98.16-99.02%) and shared a deletion of triplet codon GCA at nucleotide position 8412- 8414 resulting in deletion of glycine amino acid (Gly2761). Phylogenetic analysis conducted on CP gene sequences revealed the existence of four clades, named A, B, C and D, and one recently introduced clade B1. All Serbian wheat WSMV isolates grouped into clade B together with other European isolates and one isolate from Iran. The results of this study provide the first insight into molecular characterisation of Serbian WSMV isolates, indicating their close relationship with other European isolates and existence of a single genotype in the country. Phylogenetic analysis also confirms the dispersal of WSMV isolates throughout Europe from a single locus.

scholarly journals Eliminasi Onion yellow dwarf virus melalui Kultur Meristem Tip pada Bawang Merah (Allium ascalonicum L.)

2017 ◽  
Vol 8 (1) ◽  
pp. 22
Author(s):  
Aqlima , ◽  
Bambang S. Purwoko ◽  
Sri Hendrastuti Hidayat ◽  
Diny Dinarti
Keyword(s):  
Tip Growth ◽  
Callus Formation ◽  
Block Design ◽  
Yellow Dwarf ◽  
Dwarf Virus ◽  
Onion Yellow Dwarf Virus ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Meristem Tip Culture ◽  
Yellow Dwarf Virus

<p>ABSTRACT<br />Meristem tip culture is culture of isolated meristem with 1-2 leaf primordia on suitable medium. This method is generally used to obtain free virus plant. Optimation of plant growth regulators (PGRs) was done to accelerate explant growth without callus formation and to avoid somaclonal variation in meristem tip culture. The aims of this study were to achieve the best combination of PGR for meristem tip growth and to evaluate meristem tip culture potential for Onion yellow dwarf virus (OYDV) elimination in shallot. This study used combination of PGRs 0.25 mg L-1 (2-ip, BAP, GA3, kinetin) with or without 0.1 mg L-1 IAA and medium without PGR. This research consisted of two experiments conducted separately. In experiment I, cv. Bima Brebes was used and experiment II cv. Tiron was used. Each experiment was arranged in completely randomized block design with single factor (PGR combination) that has 8 combination levels and 3 replications. The result showed that medium without PGR was the most efficient for meristem tip growth. Primary shoot was growing without callus formation. RT-PCR analysis showed that all of the tested samples were still infected by OYDV. Meristem tip culture method did not eliminate OYDV in both cultivars.<br />Keywords: Auxin, cytokinin, GA3, OYDV, RT-PCR</p><p>ABSTRAK<br />Kultur meristem tip merupakan kultur meristem yang diisolasi 1-2 primordia daun dan pada media yang sesuai. Metode ini umum digunakan untuk mendapatkan tanaman bebas virus. Optimasi terhadap zat pengatur tumbuh (ZPT) dilakukan untuk mempercepat pertumbuhan eksplan tanpa disertai pembentukan kalus untuk menghindari terjadinya variasi somaklonal pada kultur meristem tip. Penelitian ini bertujuan untuk mendapatkan kombinasi ZPT terbaik bagi pertumbuhan meristem tip dan untuk mengevaluasi potensi kultur meristem tip dalam mengeliminasi virus Onion yellow dwarf virus (OYDV) pada tanaman bawang merah. Penelitian ini menggunakan 0.25 mg L-1 (2-ip, BAP, GA3, kinetin) dengan penambahan atau tanpa 0.1 mg L-1 IAA serta media tanpa ZPT. Penelitian ini terdiri atas 2 percobaan terpisah. Percobaan 1 menggunakan cv. Bima Brebes dan Percobaan 2 menggunakan cv. Tiron. Masing-masing percobaan disusun berdasarkan rancangan kelompok lengkap teracak (RKLT) dengan 1 faktor, yaitu kombinasi ZPT yang terdiri atas 8 taraf kombinasi dan 3 ulangan. Hasil yang didapat menunjukkan bahwa media tanpa penambahan ZPT<br />merupakan media yang paling efisien untuk pertumbuhan tunas meristem tip. Tunas utama tumbuh tanpa disertai pembentukan kalus. Hasil analisis RT-PCR menunjukkan bahwa seluruh sampel yang dideteksi masih terinfeksi OYDV. Metode kultur meristem tip belum dapat mengeliminasi virus OYDV pada kedua kultivar bawang merah.<br />Kata kunci: Auksin, GA3, OYDV, RT-PCR, sitokinin</p>

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