Possible Escape of a Recombinant Isolate of Potato virus Y by Serological Indexing and Methods of its Detection

DREPP protein StPCaP1 facilitates the cell-to-cell movement of Potato virus Y and Potato virus S by inhibiting callose deposition at plasmodesmata

Plant viruses, constrained by their limited genomic coding capacity, rely significantly on host factors for successful infection. Disruption of these essential host factors can confer resistance to viruses, with such factors categorized as susceptibility genes or recessive resistance genes. Recent research has identified developmentally regulated plasma membrane polypeptide (DREPP) proteins as susceptibility factors integral to the cell-to-cell movement of potyviruses. In the present study, we demonstrated that the silencing of StPCaP1, a DREPP gene in potato, confers novel resistance to both Potato virus Y (PVY, Potyvirus) and Potato virus S (PVS, Carlavirus). Interaction and subcellular localization analyses revealed that the movement proteins (MPs) of PVY (P3NPIPO) and PVS (TGB1) interact with StPCaP1, recruiting it to plasmodesmata (PD). Furthermore, transcriptome analysis and experimental validation indicated that compared to wild-type (WT) controls, StPCaP1-silenced lines exhibit significantly increased glucose content and elevated expression levels of several UDP-glucosyltransferases (UGTs), which are potential components of the callose synthesis complex. These findings suggest that StPCaP1 participates in callose deposition, as evidenced by the increased callose deposition at PD and reduced PD permeability observed in StPCaP1-silenced lines. Additionally, we found that StPCaP1 expression in Nicotiana benthamiana led to reduced callose deposition at PD and promoted PVY-GFP cell-to-cell movement in NbPCaP1-silenced plants in a concentration-dependent manner, which suggests the changes in callose deposition at PD induced by StPCaP1 relates to viral cell-to-cell movement. This study provides a deeper understanding of DREPP-mediated viral movement and highlights potential targets for developing virus-resistant crops.

Insight into aphid mediated Potato Virus Y transmission: A molecular to bioinformatics prospective

Potato, the world's most popular crop is reported to provide a food source for nearly a billion people. It is prone to a number of biotic stressors that affect yield and quality, out of which Potato Virus Y (PVY) occupies the top position. PVY can be transmitted mechanically and by sap-feeding aphid vectors. The application of insecticide causes an increase in the resistant vector population along with detrimental effects on the environment; genetic resistance and vector-virus control are the two core components for controlling the deadly PVY. Using transcriptomic tools together with differential gene expression and gene discovery, several loci and genes associated with PVY resistance have been widely identified. To combat this virus we must increase our understanding on the molecular response of the PVY-potato plant-aphid interaction and knowledge of genome organization, as well as the function of PVY encoded proteins, genetic diversity, the molecular aspects of PVY transmission by aphids, and transcriptome profiling of PVY infected potato cultivars. Techniques such as molecular and bioinformatics tools can identify and monitor virus transmission. Several studies have been conducted to understand the molecular basis of PVY resistance/susceptibility interactions and their impact on PVY epidemiology by studying the interrelationship between the virus, its vector, and the host plant. This review presents current knowledge of PVY transmission, epidemiology, genome organization, molecular to bioinformatics responses, and its effective management.

Eukaryotic translation initiation factor 4E family member nCBP facilitates the accumulation of TGB-encoding viruses by recognizing the viral coat protein in potato and tobacco

Due to their limited coding capacity, plant viruses have to depend on various host factors for successful infection of the host. Loss of function of these host factors will result in recessively inherited resistance, and therefore, these host factors are also described as susceptibility genes or recessive resistance genes. Most of the identified recessive resistance genes are members of the eukaryotic translation initiation factors 4E family (eIF4E) and its isoforms. Recently, an eIF4E-type gene, novel cap-binding protein (nCBP), was reported to be associated with the infection of several viruses encoding triple gene block proteins (TGBps) in Arabidopsis. Here, we, for the first time, report that the knockdown of nCBP in potato (StnCBP) compromises the accumulation of potato virus S (PVS) but not that of potato virus M (PVM) and potato virus X (PVX), which are three potato viruses encoding TGBps. Further assays demonstrated that StnCBP interacts with the coat proteins (CPs) of PVS and PVM but not with that of PVX, and substitution of PVS CP in the PVS infectious clone by PVM CP recovered the virus infection in StnCBP-silenced transgenic plants, suggesting that the recognition of PVS CP is crucial for StnCBP-mediated recessive resistance to PVS. Moreover, the knockdown of nCBP in Nicotiana benthamiana (NbnCBP) by virus-induced gene silencing suppressed PVX accumulation but not PVM, while NbnCBP interacted with the CPs of both PVX and PVM. Our results indicate that the nCBP orthologues in potato and tobacco have conserved function as in Arabidopsis in terms of recessive resistance against TGB-encoding viruses, and the interaction between nCBP and the CP of TGB-encoding virus is necessary but not sufficient to determine the function of nCBP as a susceptibility gene.

Global Screening and Functional Identification of Major HSPs Involved in PVY Infection in Potato

HSP40 (also known as DnaJ), HSP70, and HSP90 are major heat shock protein (HSP) families that play critical roles in plant growth and development and stress adaption. Recently, several members of the three HSP families were reported to be widely involved in the plant host-virus interactions. However, their global expression profiles and core members recruited by viruses are largely unknown. In this study, a total of 89 StDnaJs were identified from a genome-wide survey, and their classification, phylogenetic relationships, chromosomal locations, and gene duplication events were further analyzed. Together with 20 StHSP70s and 7 StHSP90s previously identified in the potato genome, the global expression patterns of the members in 3 HSP families were investigated in 2 potato cultivars during Potato virus Y (PVY) infection using RNA-seq data. Of them, 16 genes (including 8 StDnaJs, 6 StHSP70s, and 2 StHSP90s) were significantly up- or downregulated. Further analysis using qRT-PCR demonstrated that 7 of the 16 genes (StDnaJ06, StDnaJ17, StDnaJ21, StDnaJ63, StHSP70-6, StHSP70-19, and StHSP90.5) were remarkably upregulated in the potato cultivar 'Eshu 3' after PVY infection, implying their potential roles in the potato-PVY compatible interaction. Subsequent virus-induced gene silencing (VIGS) assays showed that silencing of the homologous genes of StDnaJ17, StDnaJ21, StHSP70-6, and StHSP90.5 in Nicotiana. benthamiana plants dramatically reduced the accumulation of PVY, which indicated the four genes may function as susceptibility factors in PVY infection. This study provides candidate genes for exploring the mechanism of potato-PVY compatible interaction and benefits breeding work aiming to produce new cultivars with the ability to grow healthily under PVY infection.

Comparison of Mineral Oil, Insecticidal, and Biopesticide Spraying Regimes for Reducing Spread of Three Potato virus Y Strains in Potato Crops

In-field management of Potato virus Y (PVY) faces challenges caused by the changing availability and environmental acceptability of chemical agents to control aphid vectors of the virus and by proliferation of PVY strains with different symptoms and rates of spread. From 2018 to 2020, foliar spray treatments were compared in field experiments in New Brunswick, Canada, to measure effectiveness at reducing spread of PVY^O, PVY^N:O, and PVY^NTN strains. Mineral oil, insecticide, combined oil and insecticide spray, and a biopesticide (i.e., LifeGard WG) were compared. Insecticide-only and mineral oil-only treatments were not effective, but several combined oil and insecticide treatments and biopesticide treatments significantly reduced PVY spread. The biopesticide was proportionately more effective with recombinant PVY^N:O and PVY^NTN strains, possibly by exciting the plant's hypersensitive resistance response, caused naturally only in cultivar 'Goldrush' by PVY^O. Pesticide residue analysis showed that mineral oil increased the retention of pyrethroid insecticide in the potato foliage longer than with insecticide applied alone, which may explain the beneficial synergistic effect of combined sprays for reducing PVY spread. Tuber yields were generally unchanged in chemical insecticide treatments but were slightly lower in biopesticide treatment. The cost per PVY treatment was competitive across all effective treatments, including biopesticide; however, there was some revenue loss from lower yield with the biopesticide. This biopesticide is certified organic, however, and thus a small premium on the price for organic production could offset this yield deficit.

Susceptibility factor StEXA1 interacts with StnCBP to facilitate potato virus Y accumulation through the stress granule-dependent RNA regulatory pathway in potato

Plant viruses recruit multiple host factors for translation, replication, and movement in the infection process. The loss-of-function mutation of the susceptibility genes will lead to the loss of susceptibility to viruses, which is referred to as 'recessive resistance'. Essential for potexvirus Accumulation 1 (EXA1) has been identified as a susceptibility gene required for potexvirus, lolavirus, and bacterial and oomycete pathogens. In this study, EXA1 knockdown in potato (StEXA1) was found to confer novel resistance to potato virus Y (PVY, potyvirus) in a strain-specific manner. It significantly compromised PVY^O accumulation but not PVY^N:O and PVY^NTN. Further analysis revealed that StEXA1 is associated with the HC-Pro of PVY through a member of eIF4Es (StnCBP). HC-Pro^O and HC-Pro^N, two HC-Pro proteins from PVY^O and PVY^N, exhibited strong and weak interactions with StnCBP, respectively, due to their different spatial conformation. Moreover, the accumulation of PVY^O was mainly dependent on the stress granules (SGs) induced by StEXA1 and StnCBP, whereas PVY^N:O and PVY^NTN could induce SGs by HC-Pro^N independently through an unknown mechanism. These results could explain why StEXA1 or StnCBP knockdown conferred resistance to PVY^O but not to PVY^N:O and PVY^NTN. In summary, our results for the first time demonstrate that EXA1 can act as a susceptibility gene for PVY infection. Finally, a hypothetical model was proposed for understanding the mechanism by which StEXA1 interacts with StnCBP to facilitate PVY accumulation in potato through the SG-dependent RNA regulatory pathway.

Proliferation of Recombinant PVY Strains in Two Potato-Producing Regions of Canada, and Symptom Expression in 30 Important Potato Varieties with Different PVY Strains

Potato virus Y (PVY) exists as several strains with distinct symptomology and tuber yield effects in different potato varieties. Recently, new recombinant strains have proliferated and dominated local populations around the world. In this study, PVY^O, PVY^N:O, PVY^N-Wi, and PVY^NTN strains were tracked across Canada from 2014 to 2017, showing rapid evolution of populations away from the traditionally dominant PVY^O to recombinants PVY^N-Wi (western Canada) and PVY^NTN (eastern Canada). Simultaneously, 30 potato varieties were inoculated with PVY^O, PVY^N:O, and PVY^NTN in controlled greenhouse experiments. Foliar symptoms of primary (mechanical inoculation mimicking aphid infection) and secondary (tuber seedborne) infection were cataloged, and tuber yield measured. On average, and generally similar in primary and secondary infection, symptom expression and yield reduction were most severe with PVY^O, followed by PVY^N:O and PVY^NTN. Strong mosaic symptoms were most commonly expressed with PVY^O infection, and only seen with PVY^N:O or PVY^NTN in 15 and 3 varieties, respectively. Across variety-strain combinations, yield reduction was correlated with symptom severity, most strongly in PVY^O-infected plants (e.g., AC Chaleur, Beljade, Envol, Norland, and Pacific Russet), and four varieties exhibited tuber necrotic ringspot disease with PVY^NTN (AC Chaleur, Envol, Pacific Russet, and Yukon Gold).

Potato virus Y Transmission Efficiency from Potato Infected with Single or Multiple Virus Strains

There has been a recent shift in the prevalence of Potato virus Y (PVY) strains affecting potato with the ordinary strain PVY^O declining and the recombinant strains PVY^NTN and PVY^N:O emerging in the United States. Multiple PVY strains are commonly found in potato fields and even in individual plants. Factors contributing to the emergence of the recombinant strains are not well defined but differential aphid transmission of strains from single and mixed infections may play a role. We found that the transmission efficiencies by Myzus persicae, the green peach aphid, of PVY^NTN, PVY^N:O, and PVY^O varied depending on the potato cultivar serving as the virus source. Overall transmission efficiency was highest from sources infected with three virus strains, whereas transmission from sources infected with one or two virus strains was not significantly different. Two strains were concomitantly transmitted by individual aphids from many of the mixed-source combinations, especially if PVY^O was present. Triple-strain infections were not transmitted by any single aphid. PVY^O was transmitted most efficiently from mixed-strain infection sources. The data do not support the hypothesis that differential transmission of PVY strains by M. persicae is a major contributing factor in the emergence of recombinant PVY strains in the U.S. potato crop.

RT-PCR Differentiation, Molecular and Pathological Characterization of Andean and Ordinary Strains of Potato virus S in Potatoes in China

A survey of potatoes in a field in Hubei, China, for common potato viruses revealed that Potato virus S (PVS) was the most abundant virus. To unveil the strain identity of the virus, primers specific to the ordinary and/or Andean strains of PVS (i.e., PVS^O and PVS^A) were designed. RT-PCR using these primers successfully detected PVS^O and PVS^A in the samples. Sequence analysis of the amplicons confirmed the correctness of the RT-PCR assay. Two isolates, PVS HB24 and PVS HB7, representing PVS^O and PVS^A, respectively, were chosen for molecular and biological characterization. Both isolates contained a genome of 8,453 nt in length with six open reading frames. They shared a sequence identity of 79.5% at the complete genome sequence level. Phylogenetic analysis placed PVS HB24 and PVS HB7 to PVS^O and PVS^A clades, respectively. PVS HB24 induced chlorotic local lesions on the inoculated leaves but no visible symptom on the upper uninoculated leaves of Chenopodium quinoa after mechanical inoculation, whereas PVS HB7 induced both local and systemic symptoms on C. quinoa. ELISA and RT-PCR confirmed that PVS HB7 infected C. quinoa systemically whereas PVS HB24 failed to do so. Both isolates infected potato cv. Shepody and Solanum chacoense asymptomatically, but did not infect Nicotiana occidentalis and N. tobaccum cv. Samsun.

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

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.

Response of Potato Cultivars to Five Isolates Belonging to Four Strains of Potato virus Y

The responses of 14 potato cultivars to five Potato virus Y (PVY) isolates belonging to four strains (ordinary [PVY^O], tobacco veinal necrosis [PVY^N], N:O group [PVY^N:O], and nonrecombinant potato tuber necrotic [PVY^NTN]) were studied in primary and secondary infections. For the primary infection experiments, foliage symptoms were monitored daily after mechanical inoculation with a PVY isolate until harvest; and, for the secondary infection experiments, foliage symptoms were monitored regularly from plant emergence until harvest. Tuber symptoms (namely, tuber necrotic ringspots) were checked at harvest and monthly postharvest for up to 4 months. In both infections, symptoms varied significantly depending on potato cultivar and virus strain or isolate. In primary infections, local lesions occurred on inoculated leaves of 'AC Chaleur', 'Eramosa', 'Goldrush', 'Jemseg', 'Katahdin', 'Ranger Russet', and 'Yukon Gold' after inoculation with PVY^O isolates, followed by systemic necrosis on latterly emerged uninoculated leaves. In contrast, plants of 'CalWhite', 'La Rouge', 'Red LaSoda', 'Russet Burbank', 'Russet Norkotah', and 'Superior' did not exhibit any visible symptoms on inoculated leaves but developed mild to severe mosaic on latterly emerged leaves after infection with PVY^O isolates. In all cultivars, near-symptomless to mild mosaic was induced by PVY^N and mild to severe mosaic by PVY^N:O. PVY^NTN induced mild to severe mosaic in plants of all cultivars except AC Chaleur, 'Cherokee', and Yukon Gold, which developed visible systemic necrosis. Necrotic ringspots were observed in tubers of PVY^NTN-infected plants of AC Chaleur, Cherokee, and Yukon Gold. The tuber symptoms were also incited by PVY^N-Jg on Cherokee. In secondary infections, the symptoms were generally more severe than primary infections even though the symptom types did not alter. As in the greenhouse, a clear symptom severity pattern (PVY^O-FL > PVY^O-RB > PVY^NTN-Sl > PVY^N:O-Mb58 > PVY^N-Jg) was observed in AC Chaleur, Cherokee, Eramosa, Goldrush, Jemseg, Katahdin, Ranger Russet, and Yukon Gold in the field.

Strain specificity and simultaneous transmission of closely related strains of a Potyvirus by Myzus persicae

Potato virus Y (PVY), a Potyvirus, is transmitted by aphids in a nonpersistent manner. PVY severely affects potato production worldwide. Single and mixed infections of PVY strains, namely PVY(O), PVY(NTN), and PVY(N:O) are a common occurrence in potato systems. However, information available on the ability of aphids to simultaneously transmit multiple PVY strains, specificity associated with simultaneous transmission, and factors affecting specificity are limited. Aphid-mediated transmission experiments were conducted to test the ability of individual aphids to transmit multiple strains using a PVY indicator host. Preliminary results revealed that aphids can transmit at least two viral strains simultaneously. Subsequently, aphid-mediated transmission of three dual-strain combinations was tested using potato plants. Individual aphids transmitted two viral strains simultaneously for all three dual-strain combinations. In all aphid-mediated dual-strain infections involving PVY(NTN), the rate of PVY(NTN) infection was greater than the infection rates of the second strain and dual-strain combinations, indicating specificity associated with transmission of PVY strains. Results of aphid-mediated transmission experiments were compared with results obtained through mechanical transmission. In general, PVY infection rates from aphid-mediated transmission were lower than the rates obtained through mechanical transmission. Unlike aphid-mediated transmission, component strains in dual-strain inoculations were not eliminated during mechanical transmission. These results suggest that there may also be interference associated with aphid-mediated transmission of closely related PVY strains. Perhaps, the observed specificity and/or interference may explain the increase in the incidence of PVY(NTN) and other necrotic strains in recent years.

Transmission Efficiency of Potato virus Y strains PVYO and PVYN-Wi by Five Aphid Species

Potato virus Y (PVY) is a reemerging problem in potato production in North America. Although the "ordinary" strain, PVY^O, is still the dominant isolate in U.S. seed potatoes, the recombinant strain of the virus PVY^N-Wi (= PVY^N:O) has become widespread. An increase in the prevalence of a PVY strain could be due to differences in the efficiency of transmission by aphid vectors. The transmission efficiency by a clone of Myzus persicae was determined for five isolates each of PVY^O and PVY^N-Wi. An aphid transmission assay was developed based on the use of potato seedlings from true potato seed, allowing for greater control of plant age and growth stage. No apparent differences in transmission by M. persicae were observed. Single isolates of PVY^O and PVY^N-Wi were tested for their ability to be transmitted from potato to potato by five aphid species: Aphis glycines, A. gossypii, A. nasturtii, M. persicae, and Rhopalosiphum padi. Both PVY isolates showed a similar transmission phenotype in being transmitted efficiently by M. persicae but very poorly or not at all by A. glycines, A. gossypii, and R. padi. The aphid A. nasturtii transmitted both isolates with an intermediate level of efficiency. The data do not support a model for a differential aphid transmissibility being responsible for the increase in the prevalence of PVY^N-Wi.

Within plant distribution of Potato Virus Y in hairy nightshade (Solanum sarrachoides): an inoculum source affecting PVY aphid transmission

Potato virus Y (PVY) is vectored by several potato-colonizing and non-colonizing aphid species in a non-persistent manner and has a wide host range. It occurs naturally in several plant families. Myzus persicae and Macrosiphum euphorbiae are the most efficient potato-colonizing aphid vectors of PVY. Rhopalosiphum padi, a cereal aphid that migrates in large numbers through potato fields during the middle of the growing season, does not colonize potato plants but can transmit PVY. Hairy nightshade, Solanum sarrachoides, a prevalent annual solanaceous weed in the Pacific Northwest (PNW) of the United States, is an alternative host for PVY and a preferred host for M. persicae and M. euphorbiae. Hence, hairy nightshade plants might play an important role as an inoculum source in the epidemiology of PVY. We looked at titre accumulation and distribution of PVY(O), PVY(N:O) and PVY(NTN) in S. sarrachoides and potato after aphid inoculation with M. persicae and studied the transmission of PVY(O) and PVY(NTN), by M. persicae, M. euphorbiae and R. padi from hairy nightshade to potato plants. Virus titre at different positions on the plant was similar in S. sarrachoides and potato plants with strains PVY(O) and PVY(N:O). Titres of PVY(NTN) were similar in S. sarrachoides and potato but differences in titre were observed at different positions within the plant depending on the plant phenology. Percentage transmission of PVY(NTN) by M. persicae and M. euphorbiae was twice as high (46 and 34%, respectively) from hairy nightshade to potato than from potato to potato (20 and 14%). Percentage transmission of PVY(O) by M. persicae and M. euphorbiae was not affected by the inoculum source. No effect of the inoculum source was observed in the transmission of either PVY strain by R. padi. These results show that hairy nightshade may be an equal or better virus reservoir than potato and thus, important in the epidemiology of PVY.

Differential pathogenicity of two different recombinant PVY(NTN) isolates in Physalis floridana is likely determined by the coat protein gene

A previous study has identified two types of recombinant variants of Potato virus Y strain NTN (PVY(NTN)) in China and sequenced the complete genome of the variant PVY(NTN)-HN2. In this study, the complete genome of isolate PVY(NTN)-HN1 was fully sequenced and analyzed. The most striking difference between the two variants was the location of recombinant joint three (RJ3). In PVY(NTN)-HN1, like other typical European-PVY(NTN) isolates such as PVY(NTN)-Hun, the RJ3 was located at nucleotide (nt) 9183, namely the 3' proximal end of the CP gene (nt. 8571-9371), thus leading to most (the first 613 nucleotides from the 5' proximal end) of the CP gene (801 bp) with a PVYN origin and PVYN-serotype; whereas in contrast, the RJ3 in PVY(NTN)-HN2 was located at nt 8572, consequently leading to a CP gene of PVYO origin and PVYO-serotype. The varied genome composition among PVY(O), PVY(N), PVY(N:O), PVY(NTN_-HN1 and PVY(NTN)-HN2 made them useful for the investigation of possible roles of gene segment(s) in symptom formation on host plants. When Physalis floridana plants were infected with different PVY isolates, two types of symptoms were induced. PVY(N) and PVY(NTN)-HN1 induced mild symptoms (mainly mild mottling) whereas PVY(O), PVY(N:O) and PVY(NTN)-HN2 induced serve symptoms including leaf and stem necrosis, leaf-drop and stunting. These results, together with a previous study using artificial PVY chimeras, demonstrate that the CP gene, especially the 5' proximal segment (nt 8572-9183), and/or CP likely determine the pathogenicity of PVY in P. floridana.

Recognition and Molecular Discrimination of Severe and Mild PVYO Variants of Potato virus Y in Potato in New Brunswick, Canada

A field isolate of Potato virus Y (PVY) was collected in New Brunswick, Canada in 2007 due to unusual symptoms observed on different potato cultivars. To unveil the PVY strain identity, tobacco and potato bioassays, PVY^O and PVY^N-specific antibody-based enzyme-linked immunosorbent assays, and reverse-transcription polymerase chain reaction (PCR)-based genotyping were carried out. All the assays demonstrated that the isolate, designated as PVY^O-FL in this study, belonged to the PVY^O strain group. Greenhouse tests with the potato cvs. FL 1533 and Jemseg confirmed the severe nature of infection by PVY^O-FL. The complete genome sequences of PVY^O-FL and PVY^O-RB, the latter a mild PVY^O isolate, were determined. BLAST analysis revealed that the two isolates shared 97 and 98% sequence identities at the nucleotide and polyprotein levels, respectively. Further BLAST analysis unveiled that PVY^O-FL shared 99.7% nucleotide sequence identity with PVY^O-Oz, an isolate reported in New York, United States, whereas the PVY^O-RB isolate shared 99.2% sequence identity with PVY^O-139, a PVY^O isolate reported in New Brunswick, Canada. A phylogenetic tree of available, full-length sequences of PVY isolates demonstrated two subgroups within the PVY^O branch, one clustered with PVY^O-RB and the other with PVY^O-FL. Group-specific sense primers for differentiation of the two subgroups were developed and evaluated. A limited survey of potato tubers collected from a field plot at the Potato Research Centre, Agriculture and Agri-Food Canada, using the newly developed PCR primers, indicated that 65.3 and 2.4% of the PVY^O-positive tubers were infected with PVY^O isolates belonging to the PVY^O-FL and PVY^O-RB subgroups, respectively. Assessment of the pathogenicity of three representative isolates from each subgroup on the potato cv. Jemseg demonstrated that severe and mild symptoms were induced by the PVY^O-FL-like and PVY^O-RB-like isolates, respectively.

Expression of Potato virus Y cytoplasmic inclusion protein in tobacco results in disorganization of parenchyma cells, distortion of epidermal cells, and induces mitochondrial and chloroplast abnormalities, formation of membrane whorls and atypical lipid accumulation

Infection of plant cells by potyviruses induces the formation of cytoplasmic inclusions ranging in size from 200 to 1000 nm. To determine if the ability to form these ordered, insoluble structures is intrinsic to the potyviral cytoplasmic inclusion protein, we have expressed the cytoplasmic inclusion protein from Potato virus Y in tobacco under the control of the chrysanthemum ribulose-1,5-bisphosphate carboxylase small subunit promoter, a highly active, green tissue promoter. No cytoplasmic inclusions were observed in the leaves of transgenic tobacco using transmission electron microscopy, despite being able to clearly visualize these inclusions in Potato virus Y infected tobacco leaves under the same conditions. However, we did observe a wide range of tissue and sub-cellular abnormalities associated with the expression of the Potato virus Y cytoplasmic inclusion protein. These changes included the disruption of normal cell morphology and organization in leaves, mitochondrial and chloroplast internal reorganization, and the formation of atypical lipid accumulations. Despite these significant structural changes, however, transgenic tobacco plants were viable and the results are discussed in the context of potyviral cytoplasmic inclusion protein function.

Sequence characteristics of potato virus Y recombinants

Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem-loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination.

A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco

A novel Potato virus Y (PVY) isolate, L26, recovered from a Frontier potato line was initially typed as a PVY(NTN) strain using multiplex RT-PCR and serological assays. However, L26 induced mosaic and mild vein clearing symptoms in tobacco rather than vein necrosis characteristic of the PVY (NTN) strain. The whole genome sequence was determined for L26 and two other PVY(NTN) isolates, HR1 and N4, from Idaho that did induce vein necrosis in tobacco. The sequence of all three isolates was similar to typical European PVY(NTN) isolates that contain three recombination junctions in their genome. The sequence of the L26 genome was nearly identical to the genomes HR1, N4, and to a previously characterized PVY(NTN) isolate, 423-3, differing by only five nucleotides in the entire ca. 9.7-kb genome, only one resulting in a corresponding amino acid change, D-205 to G-205 in the central region of HC-Pro. Two "signature" amino acid residues, thought involved in induction of the vein necrosis syndrome in tobacco, K-400 and E-419, were present in the C-terminal region of HC-Pro of all three isolates. Multiple alignment of the whole genome sequences of L26 and other PVY(NTN) isolates whose phenotype in tobacco has been reported, suggests that a single nucleotide change (A-1,627 to G-1,627) resulting in the single amino acid change (D-205 to G-205) in the HC-Pro cistron of L26 correlates with the loss of the vein necrosis phenotype in tobacco. Secondary structure modeling of the HC-Pro protein predicts the G-205 residue, and the previously identified residues K-400 and E-419, would all be located on the exposed surface of the protein. Taken together, these data suggest that the vein necrosis genetic determinant of PVY in tobacco is complex and includes other element(s), in addition to the C-terminal fragment of HC-Pro.

Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers

Potato virus Y (PVY) is one of the most important viruses of potato world-wide, several strain groups are recognized. In the past two decades, novel PVY variants have appeared causing necrotic symptoms on potato tubers. Implicated are two groups of recombinant strains: PVY(N)W and PVY(NTN), and NA-PVY(NTN). While the first two are recombinants between PVY-N- and O-strains the latter is a recombinant between an N-strain and an unknown PVY strain or other Potyvirus. Available biological and molecular data on PVY suggest that classification of PVY strains has to be revised. Some drawbacks have been found with recently published primers used in RT-PCR based differentiation of PVY strains as some defined isolates could not be identified correctly. Consequently we developed new primers using both recently available sequences and newly generated complete sequences of PVY strains. The reliability of these newly developed primers and procedures was successfully demonstrated on nearly 100 biologically and serologically characterised PVY isolates.

The Occurrence of PVYO, PVYN, and PVYN:O Strains of Potato virus Y in Certified Potato Seed Lot Trials in Washington and Oregon

Totals of 960 and 286 certified potato seed lots from locations across North America were planted in trials in Washington and Oregon, respectively, in 2001 to 2003 and tested for strains of Potato virus Y (PVY). The incidence of PVY^O-infected lots averaged 16.4 and 25.9% in the Washington and Oregon trials, respectively. There was a general trend of increasing incidence of the PVY^O, PVY^N:O, and PVY^N strains during this period, as evidenced by more infected cultivars, sites of seed origin, and number of seed growers providing infected seed lots. In particular, there was a dramatic increase in seed lots with the PVY^N:O strain from 2002 to 2003. PVY^N:O, in contrast to PVY^O, which only causes yield reduction, also causes internal and external damage to tubers, making them unmarketable. In 2003, PVY^N:O occurred in seed lots originating in eight states and three Canadian provinces. The increased incidence of PVY^N:O was likely due to the difficulty in differentiating this strain from PVY^O. The prevalence of PVY in potato seed lots documented herein poses a threat to potato production in the United States and suggests that current measures to reduce the incidence of this virus are inadequate.

Improvement of Potato virus Y (PVY) detection and quantitation using PVY(N)- and PVY(O)-specific real-time RT-PCR assays

A Potato virus Y (PVY) single nucleotide polymorphism (A/G(2213)), recently identified as a molecular determinant of the tobacco leaf necrosis symptom induced by PVY(N) isolates, has been used as a target to develop two PVY group-specific (PVY(N) and PVY(O)) fluorescent (TaqMan-based) real-time RT-PCR assays. These procedures allow detection, characterisation, and quantitation of a wide range of PVY isolates in samples containing 10(3)-10(8) viral transcripts. Moreover, the high specificity of these two new assays make the simultaneous detection and the reliable quantitation of PVY(N) and PVY(O) isolates in mixed solutions, regardless of the Y(N)/Y(O) ratio, feasible. The high sensitivity (threshold of 10(3) copies per reaction) and the PVY group specificity of these two new PVY detection tools clearly improve previously published PVY detection tests and offer new opportunities for PVY research programs.

Biological and Serological Properties of Potato virus Y Isolates in Northeastern United States Potato

A survey of six potato viruses, Potato virus A (PVA), Potato virus M (PVM), Potato virus S(PVS), Potato virus X (PVX), Potato virus Y (PVY), and Potato leafroll virus (PLRV), was conducted in New York and Maine during 2002 and 2003. Leaf samples were tested by enzyme-linked immunosorbent assay and PVY-positive samples were further tested to determine whether a necrotic strain of PVY (PVY^N) or a strain able to induce necrosis in tobacco and in potato tubers (PVY^NTN) were present. In both years, PVY and PVS were identified in a majority of the samples, and mixed infections predominated in 83% of the symptomatic leaves in 2002. Of the total 394 PVY-positive samples, 3 reacted with monoclonal antibody (MAb) 1F5 and caused veinal necrosis (VN) in tobacco. Two of these isolates caused tuber necrosis in the potato cv. Yukon Gold. Three PVY isolates reacted with MAb 1F5 but did not cause VN in tobacco, and two caused VN but did not react with MAb 1F5. None of these eight isolates were able to overcome the Ry resistance gene in the potato cultivar Eva, but several were able to overcome the Ny resistance gene found in Allegany. PVY^N isolates were not widespread in the northeastern United States; however, several PVY isolates differed from both PVY^N and the ordinary strain of PVY and may represent strain recombinants.

Salicylic Acid Suppresses Potato virus Y Isolate N:O-Induced Symptoms in Tobacco Plants

ABSTRACT The effects of salicylic acid (SA) and 1-aminocyclopropane-1-carboxylic acid (ACC) on the systemic development of symptoms induced by a severe isolate of Potato virus Y group N:O (PVY(N:O)) in tobacco were investigated. Upon inoculation, the systemic development of symptoms in tobacco plants could be divided into three stages: virus incubation stage, rapid symptom-progress stage, and partial recovery and symptom-shifting stage. Treatment of seedlings with SA delayed the virus-induced necrosis in stems by 1 to 2 days. SA, not ACC, also significantly suppressed the symptom severity in stems. However, neither SA nor ACC treatment affected the partial recovery phenotype exhibited in the latterly emerged upper parts of the plants. Further analysis indicated that the accumulation of PVY was retarded by SA at the early stage of infection, and the effects were more profound in stems than leaves. Peroxidase (POX) activity and pathogenesis-related (PR) genes PR-1a and PR-1b were enhanced by PVY infection. SA not only increased POX activity in stems and PR genes in stems and leaves of mock-inoculated plants, but also elevated the activity of POX in both leaves and stems and the expression of PR-1a in leaves of PVY-infected plants. Together, the results suggest that systemic acquired resistance plays a key role in suppressing PVY(N:O)-induced symptom development through SA-mediated and ethylene-independent pathways. The symptom suppression was correlated with reduced replication/ accumulation of virus at the early stage of infection. The results also suggest that neither SA nor ethylene plays a role in the recovery phenotype.

Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Potato virus Y (PVY) is a serious potato pathogen that affects potato seed and commercial production crops. In recent decades, novel PVY strains have been described that cause necrotic symptoms on tobacco foliage and/or potato tubers. The major PVY strains that affect potato include PVY(O) and PVY(N), which have distinct serotypes that can be differentiated by immunoassay. Other economically important strain variants are derived from recombination events, including variants that cause tuber necrotic symptoms (PVY(NTN)) and PVY(O) serotypes that cause tobacco veinal necrosis (PVY(N)-W, PVY(N:O)). Although the PVY(NTN) and PVY(N)-W variants were first reported in Europe, apparently similar strains have been appearing in North America. Confirmation of the existence of these recombinant strains in North America is important, as is whether they spread from a common source or were derived by independent recombination. Whole genome sequencing can be used to positively identify strain variants and begin to address the issue of origins. Symptomology, serology, RT-PCR, and partial sequencing of the coat protein region were used to identify isolates of the PVY(NTN), PVY(N), PVY(NA-N), and PVY(N:O) for whole-genome sequencing. Sequencing confirmed the presence of PVY(NTN) and PVY(N) isolates that were >99% identical to European sequences deposited in GenBank in the 1990's. Sequences of the PVY(NA-N) and PVY(N:O) types were 99.0% and 99.5% identical to known sequences, respectively. There was no indication that recombinant strains PVY(NTN) or PVY(N:O) had different parental origins than recombinant strains previously sequenced. This is the first confirmation by whole-genome sequencing that "European"-type strain variants of PVY(N) and PVY(NTN) are present in North America, and the first reported full-length sequence of a tuber necrotic isolate of PVY(N:O).

Specific detection of the PVY(N)-W variant of Potato virus Y

PVY(N)-W is one of the variant populations of Potato virus Y (PVY). This variant is of concern in seed potato production and requires a specific diagnosis since it induces more or less symptomless infections and is not detectable easily in field inspections. Moreover, this variant is serologically indistinguishable from the common strain PVY(O). This study describes a simple and specific molecular detection test for the PVY(N)-W variant using a PCR protocol based on the recombinant point within the HC-Pro/P3 region of PVY(N) variants (PVY(NTN), PVY(N)-W). To avoid both detection of recombinant PVY(NTN) and PVY(N)-W isolates, a forward PVY(N)-like primer located in the HC-Pro region coupled to a reverse PVY(O)-like primer located in the NIa region was designed to amplify a specific PCR product of 4114 nt from PVY(N)-W isolates. This technique was assessed on 41 PVY reference and field isolates. Only isolates referenced as PVY(N)-W were amplified and gave the expected PCR product of 4114 nt, whereas no band was obtained from PVY(N), PVY(NTN) or PVY(O) isolates. In conclusion, this PVY(N)-W diagnosis tool is rapid, easy-to-use and suitable for large-scale testing in laboratories of seed potato certification.

Reverse Transcription Loop-Mediated Isothermal Amplification of DNA for Detection of Potato virus Y

A reverse transcription loop-mediated isothermal amplification of DNA (RT-LAMP) for detection of Potato virus Y (PVY) was developed. In this procedure, a set of four primers matching a total of six sequences of the coat protein (CP) gene of PVY were designed in such a way that a loop could be formed and elongated during DNA amplification. Using PVY CP complementary DNA clones as templates, the LAMP reaction was optimized by adjusting the concentrations of MgSO₄, dNTPs, and Bst DNA polymerase. The effects of fragment length of target DNA on LAMP also were investigated. Two-step and one-step RT-LAMPs were performed using RNA extracts of various PVY cultures, and the results were correlated with two-step reverse transcription polymerase chain reaction (RT-PCR) for detection of PVY. Further, the turbidity caused by precipitation of magnesium pyrophosphate formed in positive RT-LAMP reactions was used to measure the amplification by utilizing a time-saving spectrophotometric method. The one-step RT-LAMP-turbidity method gave results comparable with the two-step RT-PCR method for detection of PVY from potato leaf and tuber samples. Of the total 240 samples, 234 were diagnosed similarly by both methods.

Diversity Among Potato virus Y Isolates Obtained from Potatoes Grown in the United States

ABSTRACT Potato field isolates (Solanum tuberosum) of Potato virus Y (PVY) collected from the midwestern and western United States were characterized using serological, molecular, and biological assays. PVY field isolates were grouped into the previously defined categories: PVY(O), European PVY(NTN), North American PVY(NTN), and PVY(N:O) recombinant and four previously undefined groups. Studies reported here agree with published reports from Europe and elsewhere in North America as PVY isolates capable of causing veinal necrosis in tobacco indicator plants appear in high frequency. In contrast to European experiences, PVY tuber necrosis isolates have a PVY(O) coat protein rather than that of PVY(N). Several PVY(N:O) recombinant isolates induced potato tuber necrotic ringspot disease (PTNRD) in the highly susceptible potato cv. Yukon Gold. The PTNRD symptoms produced by these PVY(N:O) recombinants were atypical compared with lesions found on the same cultivar infected with either the European or North American PVY(NTN) isolates. These PVY(N:O) isolates produced a roughly circular, sunken necrotic lesion on the surface of the tuber instead of the typical external sunken ring pattern displayed by PVY(NTN) isolates. This study establishes the complex nature of PVY populations within the U.S. potato industry and clearly demonstrates the diverse nature of PVY in the United States.

Specific differentiation of recombinant PVY(N:O) and PVY(NTN) isolates by multiplex RT-PCR

The recombinant isolates of tobacco veinal necrotic strain of Potato virus Y (PVYN) and potato tuber necrotic group (PVY(NTN)) contain segments of the PVYO and the PVY(N) genome. Three major recombinant junctions (RJ) are present in the genome of the recombinant PVY(NTN) at sites HC/Pro-P3, 6K2-NIa, and the C-terminal region of CP gene and one RJ at HC/Pro-P3 site in some recombinant PVYN isolates (termed PVY(N:O)). Protocols for specific differentiation of the recombinant PVY(NTN) and PVY(N:O) from the non-recombinant PVYN are described. Specific primer pairs were designed to target the three RJs so that sense and antisense primers completely matched the nucleotide sequences at either side of the RJ. In a uniplex reverse transcription-polymerase chain reaction (RT-PCR), the first primer pair amplified a fragment of 641bp from the recombinant PVY(NTN) and PVY(N:O). The second and third primer pairs exclusively amplified fragments of 448 and 290bp, respectively from the recombinant PVY(NTN). In a multiplex (triplex) RT-PCR, when all three primer pairs were used simultaneously, the three fragments (641, 448 and 290bp) were amplified exclusively from the recombinant PVY(NTN), while only one fragment (641bp) was amplified from the PVY(N:O) isolates, clearly differentiating the two recombinant isolates. No amplification was observed from the non-recombinant PVY, including PVYO and North American (NA)-PVY(N/NTN). For further improvement of the multiplex RT-PCR, effects of cDNA preparation using specific antisense primers, random primers or oligo(dT) plus random primers were investigated. The cDNA prepared by random primer plus oligo(dT) increased the overall band intensity.