scholarly journals Genomic variability in Potato virus M and the development of RT-PCR and RFLP procedures for the detection of this virus in seed potatoes

2010 ◽  
Vol 7 (1) ◽  
Author(s):  
Huimin Xu ◽  
Jeanette D'Aubin ◽  
Jingbai Nie
Keyword(s):  
Potato Virus ◽  
Rt Pcr ◽  
Genomic Variability ◽  
Seed Potatoes ◽  
Potato Virus M

scholarly journals First Report of Potato virus M and Chrysanthemum stunt viroid in Solanum jasminoides

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1359-1359 ◽  
Author(s):  
J. Th. J. Verhoeven ◽  
C. C. C. Jansen ◽  
J. W. Roenhorst
Keyword(s):  
Plant Species ◽  
Potato Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Test Plant ◽  
Rt Pcr ◽  
First Report ◽  
Chrysanthemum Stunt Viroid ◽  
Stunt Viroid ◽  
Local Lesions ◽  
Potato Virus M

In 2005, a plant of the ornamental crop Solanum jasminoides from the Netherlands was submitted for testing on viruses and viroids because of its intended use for propagation. Sap from this plant was mechanically inoculated to the test plant species Chenopodium quinoa, Nicotiana benthamiana, N. hesperis-67A, and N. occidentalis-P1 (3). N. hesperis-67A showed chlorotic local lesions and rugosity followed by vein necrosis, N. occidentalis-P1 showed necrotic local lesions and systemic leaf distortion, and the two other test plant species remained symptomless. Potato virus M (PVM) was identified by double antibody sandwich enzyme-linked immunosorbent assay using leaves from S. jasminoides and N. hesperis-67A. The plant of S. jasminoides was also tested for the presence of viroids by reverse transcriptase-polymerase chain reaction (RT-PCR) with universal pospiviroid primers Pospi1-RE/FW (2). This reaction yielded an amplicon of the expected size of 198 bp. The sequence showed 100% identity to an isolate of Chrysanthemum stunt viroid (CSVd; NCBI GenBank Accession No. AF394453). Subsequently, the complete sequence of our viroid isolate (GenBank Accession No. DQ406591) was determined from the amplicon obtained after RT-PCR using specific primers for the detection of CSVd (1). The viroid isolate from S. jasminoides consisted of 354 nucleotides and showed the highest identity (98.6%) to a chrysanthemum isolate of CSVd (GenBank Accession No. AB055974). Therefore, the viroid was identified as CSVd. To our knowledge, this is the first report of PVM and CSVd in S. jasminoides. Reference: (1) R. Hooftman et al. Acta Hortic. 432:120, 1996. (2) J. Th. J. Verhoeven et al. Eur. J. Plant Pathol. 110:823, 2004. (3) J. Th. J. Verhoeven and J. W. Roenhorst, EPPO Bull. 33:305, 2003.

scholarly journals High-throughput sequencing of Potato virus M from tomato in Slovakia reveals a divergent variant of the virus

2019 ◽  
Vol 55 (No. 3) ◽  
pp. 159-166 ◽  
Author(s):  
Miroslav Glasa ◽  
Katarína Šoltys ◽  
Lukáš Predajňa ◽  
Nina Sihelská ◽  
Jaroslav Budiš ◽  
...  
Keyword(s):  
High Throughput ◽  
Potato Virus ◽  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Rt Pcr ◽  
Tomato Plants ◽  
Virus Diversity ◽  
Group I ◽  
Potato Virus M ◽  
Intraspecies Diversity

High-throughput sequencing (HTS) analysis of tomato (Solanum lycopersicum) samples revealed the presence of Potato virus M (PVM) in this crop in Slovakia. Full-length genomes of three PVM isolates were obtained using both HTS and Sanger sequencing validation. While two isolates (T40 and T50) were shown to belong to major Group I, a divergent T20 isolate was phylogenetically unrelated to any known PVM variant, potentially representing a new phylogenetic group. Despite a relatively high intraspecies diversity (17.3 ± 0.3%), no evidence of recombination was detected in the dataset of available complete PVM sequences. Conventional screening of tomato plants in Slovakia using ELISA and RT-PCR further confirmed a frequent occurrence of PVM in this host. Developed RT-PCR showed its polyvalence to detect the PVM Group I isolates, however, in silico analysis of primer binding sites indicated its compromised use for Group II isolates. Our results further pinpoint the significance of HTS for unbiased unveiling of virus diversity and a need for continual optimisation of molecular detection tools.

scholarly journals Monitoring Current-Season Spread of Potato virus Y in Potato Fields Using ELISA and Real-Time RT-PCR

Plant Disease ◽  
2013 ◽  
Vol 97 (5) ◽  
pp. 641-644 ◽  
Author(s):  
Manphool S. Fageria ◽  
Mathuresh Singh ◽  
Upeksha Nanayakkara ◽  
Yvan Pelletier ◽  
Xianzhou Nie ◽  
...  
Keyword(s):  
Real Time ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Current Season ◽  
Seed Market ◽  
Polymerase Chain ◽  
Time Of Harvest

The current-season spread of Potato virus Y (PVY) was investigated in New Brunswick, Canada, in 11 potato fields planted with six different cultivars in 2009 and 2010. In all, 100 plants selected from each field were monitored for current-season PVY infections using enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) assay. Average PVY incidence in fields increased from 0.6% in 2009 and 2% in 2010 in the leaves to 20.3% in 2009 and 21.9% in 2010 in the tubers at the time of harvest. In individual fields, PVY incidence in tubers reached as high as 37% in 2009 and 39% in 2010 at the time of harvest. Real-time RT-PCR assay detected more samples with PVY from leaves than did ELISA. A higher number of positive samples was also detected with real-time RT-PCR from growing tubers compared with the leaves collected from the same plant at the same sampling time. PVY incidence determined from the growing tubers showed a significant positive correlation with the PVY incidence of tubers after harvest. Preharvest testing provides another option to growers to either top-kill the crop immediately to secure the seed market when the PVY incidence is low or leave the tubers to develop further for table or processing purposes when incidence of PVY is high.

Detection of potato virus M and potato virus S on test plants

1976 ◽  
Vol 19 (2) ◽  
pp. 131-139 ◽  
Author(s):  
A. Kowalska ◽  
M. Waś
Keyword(s):  
Potato Virus ◽  
Potato Virus S ◽  
Potato Virus M ◽  
Test Plants

scholarly journals Detection and genome characterization of Potato virus Y isolates infecting potato (Solanum tuberosum L.) in La Union (Antioquia, Colombia)

2016 ◽  
Vol 34 (3) ◽  
pp. 317-328 ◽  
Author(s):  
Pablo Gutiérrez S. ◽  
Mauricio Marín M. ◽  
Daniel Muñoz E.
Keyword(s):  
Solanum Tuberosum ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Seed Tuber ◽  
Rt Pcr ◽  
Potato Plants ◽  
Nextgeneration Sequencing ◽  
Prevalent Strain ◽  
Detailed Molecular Analysis

Potato virus Y (PVY) is one of the most severe viruses affecting the production of potato (Solanum tuberosum) in the world. This study presents a detailed molecular analysis using nextgeneration sequencing (NGS), IC-RT-qPCR and RT-PCR on the PVY isolates infecting seed-tubers and foliage of potato plants cv. Diacol-Capiro in La Union (Antioquia, Colombia). Analysis of incidence by IC-RT-qPCR in 15 random leaf samples of three cultivation plots and fifteen sprouting tuber eye-buds reveal infection levels between 13.4 and 80%; a higher incidence of 86.7% was observed in seed-tuber samples with threshold cycle (Ct) values as low as 24.3. Genome assembly from a bulk of foliage samples resulted in a consensus PVY genome (PVY_LaUnionF) of 9,702 nt and 399 polymorphic sites within the polyprotein ORF; while the assembled genome from sprouts of tubers has 9,704 nt (PVY_LaUnionT) and contained only six polymorphic nucleotide sites. Phylogenetic analysis demonstrates that the PVY isolates from leaf samples are in the recombinant PVYNTN group (sequence identity >99%); while those from tuber sprouts are in the PVYN/NTN group with identities above 95%. Sanger sequencing of viral capsid suggests the presence of a third variant related to PVYO, a prevalent strain reported in potato fields worldwide.

Prevalence and strain composition of potato virus Y circulating in potato fields in China’s north-central province Shanxi

Plant Disease ◽  
2021 ◽  
Author(s):  
Pengcheng Ding ◽  
Dexin Chen ◽  
Haixu Feng ◽  
Jiao Li ◽  
Hui Cao ◽  
...  
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Potato Production ◽  
Central China ◽  
Shanxi Province ◽  
Rt Pcr ◽  
Potato Leaf ◽  
Single Strain ◽  
North Central ◽  
Production Areas

Potato is an important crop in Shanxi province located in north-central China. During 2019-2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. Bio-chip detection kit revealed the presence of several potato viruses, and among them potato virus Y (PVY) was the most common one, reaching the incidence of 87.8% of all symptomatic samples. The immuno-captured multiplex reverse transcription (RT)-PCR was used to identify strains for all 280 PVY-positive samples, unveiling 242 samples infected with a single strain of PVY (86.4%) and 38 (13.6%) with a mixed infection. Of samples with a single-strain infection, PVY -SYR-II accounted for 102 (42.1%), followed by PVYN-Wi (33, 13.6%) , PVY -SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVYNTNa (20, 8.3%), PVYNTNb (19, 7.9%), and PVY -SYR-III (18, 7.4%). Seven isolates representing different recombinants were selected for whole genome sequencing. Phylogenetic and recombination analyses confirmed the RT-PCR based strain typing for all seven strains of PVY found in Shanxi. SXKL-12 is the first SYR-III strain from potato reported from China. However, unlike that in other known SYR-III isolates, the region positioned from 1,764 to1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, the PVYN-Wi isolate SXZY-40 also possessed a more divergent sequence for the region positioned from 6,156 to 6,276 nt than other N-Wi isolates known to date, sharing the highest identity of 86.6% with an uncharacterized Chinese PVY isolate, JL-11. Pathogenicity analysis of dominant strains PVY -SYR-II and PVYN-Wi in six local popular potato cultivars revealed that Kexin 13, Helan 15 and Jizhangshu 12 were susceptible to these two strains with mild mottling or mosaic symptoms expression, while three cultivars, Jinshu 16, Qingshu 9, Xisen 6 were found fully resistant.

scholarly journals Potato Virus Y Detection in Seed Potatoes Using Deep Learning on Hyperspectral Images

2019 ◽  
Vol 10 ◽  
Author(s):  
Gerrit Polder ◽  
Pieter M. Blok ◽  
Hendrik A. C. de Villiers ◽  
Jan M. van der Wolf ◽  
Jan Kamp
Keyword(s):  
Deep Learning ◽  
Potato Virus ◽  
Potato Virus Y ◽  
Hyperspectral Images ◽  
Seed Potatoes

scholarly journals Optimization and Application of a Multiplex RT-PCR System for Simultaneous Detection of Five Potato Viruses Using 18S rRNA as an Internal Control

Plant Disease ◽  
2006 ◽  
Vol 90 (2) ◽  
pp. 185-189 ◽  
Author(s):  
ZhiYou Du ◽  
JiShuang Chen ◽  
Chuji Hiruki
Keyword(s):  
Potato Virus ◽  
Internal Control ◽  
18S Rrna ◽  
Degradation Kinetics ◽  
Simultaneous Detection ◽  
Detection Sensitivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Potato Viruses ◽  
Das Elisa

Search for a host RNA molecule appropriate as an internal control for reverse transcription-polymerase chain reaction (RT-PCR) detection of viruses in potato (Solanum tuberosum) was conducted. The 18S ribosomal RNA (rRNA) was compared with the commonly used nad2 mRNA in terms of detection sensitivity and degradation kinetics. Detection of 18S rRNA was 5 magnitudes more sensitive than that of nad2 mRNA. The 18S rRNA also displayed degradation kinetics more similar to that of Potato virus X (PVX). Based on this result, reaction components and cycling parameters were optimized for a multiplex RT-PCR protocol for simultaneous detection of five potato viruses using 18S rRNA as an internal control. The protocol simultaneously amplified cDNAs from Potato virus A, PVX, Potato virus Y, Potato leaf roll virus, Potato virus S, and 18S rRNA. The multiplex RT-PCR protocol was able to detect all viruses in different combinations. The technique was 100-fold greater for detection of PVX than that of commercial double-antibody sandwich-enzyme-linked immunosorbent assay (DAS-ELISA), and also could detect viruses in some samples that DAS-ELISA failed to detect. This multiplex RT-PCR technique demonstrates a higher sensitivity of virus detection than DAS-ELISA.

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