Potato Virus Y Strains Research Articles

Integrating Spectroscopy with Potato Disease Management

Spectral phenotyping is an efficient method for the nondestructive characterization of plant biochemical and physiological status. We examined the ability of a full range (350 to 2,500 nm) of foliar spectral data to (i) detect Potato virus Y (PVY) and physiological effects of the disease in visually asymptomatic leaves, (ii) classify different strains of PVY, and (iii) identify specific potato cultivars. Across cultivars, foliar spectral profiles of PVY-infected leaves were statistically different (F = 96.1, P ≤ 0.001) from noninfected leaves. Partial least-squares discriminate analysis (PLS-DA) accurately classified leaves as PVY infected (validation κ = 0.73) and the shortwave infrared spectral regions displayed the strongest correlations with infection status. Although spectral profiles of different PVY strains were statistically different (F = 6.4, P ≤ 0.001), PLS-DA did not classify different strains well (validation κ = 0.12). Spectroscopic retrievals revealed that PVY infection decreased photosynthetic capacity and increased leaf lignin content. Spectral profiles of potato cultivars also differed (F = 9.2, P ≤ 0.001); whereas average spectral classification was high (validation κ = 0.76), the accuracy of classification varied among cultivars. Our study expands the current knowledge base by (i) identifying disease presence before the onset of visual symptoms, (ii) providing specific biochemical and physiological responses to disease infection, and (iii) discriminating between multiple cultivars within a single plant species.

Validated reverse transcription droplet digital PCR serves as a higher order method for absolute quantification of Potato virus Y strains.

RNA viruses have a great potential for high genetic variability and rapid evolution that is generated by mutation and recombination under selection pressure. This is also the case of Potato virus Y (PVY), which comprises a high diversity of different recombinant and non-recombinant strains. Consequently, it is hard to develop reverse transcription real-time quantitative PCR (RT-qPCR) with the same amplification efficiencies for all PVY strains which would enable their equilibrate quantification; this is specially needed in mixed infections and other studies of pathogenesis. To achieve this, we initially transferred the PVY universal RT-qPCR assay to a reverse transcription droplet digital PCR (RT-ddPCR) format. RT-ddPCR is an absolute quantification method, where a calibration curve is not needed, and it is less prone to inhibitors. The RT-ddPCR developed and validated in this study achieved a dynamic range of quantification over five orders of magnitude, and in terms of its sensitivity, it was comparable to, or even better than, RT-qPCR. RT-ddPCR showed lower measurement variability. We have shown that RT-ddPCR can be used as a reference tool for the evaluation of different RT-qPCR assays. In addition, it can be used for quantification of RNA based on in-house reference materials that can then be used as calibrators in diagnostic laboratories.

Differential Spread of Potato virus Y (PVY) Strains O, N:O and NTN in the Field: Implications for the Rise of Recombinant PVY Strains in New Brunswick, Canada

Potato virus Y (PVY) is a major cause of yield and quality loss in potato crops worldwide. Recently, populations of PVY strains have shifted dramatically toward recombinant strains such as PVYNTN and PVYN:O. A 2010 to 2016 survey of PVY strains in commercial fields of New Brunswick (NB), Canada, and five field trials tracking PVY spread in NB and Manitoba, were conducted to study the current status of PVY strains and their relative rates of spread. In NB, PVYO dropped from 82% of infections in 2010 to 14% in 2016, replaced mostly by PVYNTN (64%) and PVYN:O (22%).In field trials with Russet Burbank and Gold rush varieties, PVYNTN spread most effectively compared to PVYN:O and PVYO. Strain-specific PVY spread varied with the potato variety, possibly due to selective PVYO resistance in Goldrush, mostly expressed at the plant-to-plant transmission level with little difference in transduction to tubers in infected plants. Relevance of in-field differences in spread of strains to changes in regional PVY populations, and potential mechanisms responsible, are discussed.

Potato Cultivar and Seed Type Affect the Development of Systemic Potato virus Y (PVYN-Wi) Infection

Potato virus Y (PVY) infection is one of the greatest challenges to seed potato production in the United States. To determine how cultivar and seed type affect the development of systemic PVY infection, Russet Burbank and Russet Norkotah Colorado 3 cultivars were grown from two types of pre-nuclear seed (i.e., plantlets and minitubers) and Generation 3 (G3) tubers and challenged with PVY strain Wilga (PVYN-Wi). Systemic PVY infection was measured by assaying spread of virus from the inoculation site to upper non-inoculated leaves. The Burbank cultivar had a lower incidence of systemic PVY infection compared to the incidence of systemic PVY that developed in the Colorado 3 cultivar. Furthermore, Burbank plants grown from G3 tubers had a lower incidence of systemic PVY infection, as compared to Burbank plants grown from plantlets. Together our results indicate that both cultivar and seed type affect the development of systemic PVYN-Wi infections post-inoculation.

A multigene phylogentic analysis of Potato virus Y and its application in strain identification.

The objective of this study is to develop a rapid and accurate multigene phylogenetic analysis to identify Potato virus Y (PVY) strains. The phylogenetic relationships of strains within the PVY species were evaluated with isolate-strain association using five datasets of concatenated sequences from the P1, HC-pro, VPg and CP genes to determine the best dataset for PVY strain identification. Results from phylogenetic analyses and Bayesian tip-association significance (BaTS) tests indicated that the major PVY strains could be distinguished using the P1, VPg and CP concatenated sequences datasets but not the remaining concatenated sequence datasets. Phylogenetic trees reconstructed from the concatenated sequences of P1, VPg and CP genes revealed that the ML and NJ trees had broadly similar topologies and that both were better than the maximum clade credibility tree (MCC). Additionally, the full genome of HLJ26, one isolate randomly selected for the multigene phylogenetic analysis, was clustered with high confidence among members of the PVYNTN-NW (SYR-Ⅱ) strain, which includes isolates of SYR-Ⅱ-2-8, SYR-Ⅱ-Be1 and SYR-Ⅱ-DrH. This suggests that it was a PVYNTN-NW (SYR-Ⅱ) isolate. Recombination analysis of this isolate identified four putative recombination joints in the P1, HC-pro/P3, VPg and the 5'-terminus of CP. This pattern is similar to that observed in the genomic structure of PVYNTN-NW (SYR-I), supporting the classification of this isolate as the PVYNTN-NW strain (SYR-Ⅱ). Simultaneously, two expected fragments of approximately 1 000 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consistent with the expected band pattern of the PVYNTN-NW (SYR-Ⅱ) strain. This further supports the utility of the multigene phylogenetic method in identifying PVY strains. We propose that the major PVY strains could be distinguished accurately using multigene phylogenetic analysis based on the concatenated sequences from the P1, VPg and CP genes.

Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures.

The potato virus Y (PVY) complex includes five non-recombinant strains and a growing number of recombinants. Up to now, the bulk of these PVY recombinants were found to be composed of genome segments coming from only two "parental" genomes, PVYO and PVYEu-N, with a small minority including segments from other parents, e.g. PVYC, PVYNA-N, and a segment of the recombinant strain PVY-NE11. Here, comprehensive analyses of 396 whole genomes of PVY isolates from 34 countries and a variety of hosts revealed 28 isolates to be rare or novel recombinants. When subjected to a thorough recombination analysis, these 28 PVY isolates were found to represent 25 poorly sampled PVY recombinant structures, ten of which had not been recognized previously. Nine of the ten novel structures carried parental sequences from PVYNA-N or PVY-NE11 strains recombined with PVYO and PVYEu-N sequences, while seven of the new structures contained sequences from three different parents. The number of known PVY recombinant patterns now stands at thirty six. These recombinant structures present a challenge for PVY strain typing, but may shed light on interactions between PVY and host resistance genes.

POTATO VIRUS Y: AN EVOLVING PATHOGEN OF POTATO WORLDWIDE

Potato virus Y (PVY) is one of the important diseases of potato throughout the world wherever potatoes are grown. Yield losses in potato due to PVY are upto 70% if infection occurs at initial growth stages of plants. More than eight PVY strains have been reported worldwide which differ from each other based on symptoms they produce in the infected host plants and at their genetic makeup. In recent past years, new necrotic strains of PVY have emerged which are more damaging as they produce necrotic rings and arms on the tubers of infected plants. With increasing aphid population during last decade, incidence of PVY epidemics has increased worldwide. Managing PVY is difficult as some strains do not produce symptoms on infected potato plants and disease diagnosis becomes difficult. In Pakistan, work on strain differentiation of PVY and their aphid vectors are lacking and there is need of molecular research to identify PVY strains which are present in Pakistan.

Sequential acquisition of Potato virus Y strains by Myzus persicae favors the transmission of the emerging recombinant strains

In the past decade recombinant strains of Potato virus Y (PVY) have overtaken the ordinary strain, PVYO, as the predominant viruses affecting the US seed potato crop. Aphids may be a contributing factor in the emergence of the recombinant strains, but studies indicate that differences in transmission efficiency of individual PVY strains either from single or mixed infections, although variable, are not generally significant. Multiple strains of PVY are present in all potato production areas and common in many potato fields. Therefore, it is likely that individual alate aphids moving through a potato field will sequentially encounter multiple strains as they “taste test” multiple potato plants while looking for a suitable host. This study examined the transmission likelihood and efficiency of three common PVY strains when acquired sequentially by individual aphids. Green peach aphids (Myzus persicae, Sulzer) were allowed a 2–3min acquisition access period (AAP) on potato leaves infected with PVYO, PVYN:O or PVYNTN, followed by another 2–3min AAP on a second potato leaf infected with a different PVY strain before being transferred to healthy potato seedlings for a 24h inoculation access period. All possible combinations of the three strains were tested. Strain-specific infection of the recipient plants was determined by TAS-ELISA and RT-PCR 3–4wk post-inoculation. The recombinant strains, PVYN:O and PVYNTN, were transmitted more efficiently than PVYO when they were sequentially acquired regardless of the order acquired. PVYN:O and PVYNTN were transmitted with similar efficiencies when they were sequentially acquired regardless of the order. The recombinant strains appear to preferentially bind to the aphid stylet over PVYO or they may be preferentially released during inoculation. This may contribute to the increased incidence of the recombinant strains over PVYO in fields or production regions where multiple PVY strains are detected.

Dynamics of PVY strains in field grown potato: Impact of strain competition and ability to overcome host resistance mechanisms

Potato virus Y (PVY) is the most important viral pathogen affecting potato crops worldwide. PVY can be transmitted non-persistently by aphids that do not colonize the host plant, resulting in a rapid acquisition and transmission of the virus between plants. PVY exists as a complex of strains that can be distinguished according to their pathogenicity, serology and genomic analysis. While virus incidence remains low in Scottish seed potato crops, PVY has become the increasingly prevalent virus. The monitoring of PVYN and PVYO serotypes has revealed a recent shift towards PVYN which now accounts for more than 90% of all PVY cases. A survey of the molecular diversity of PVYN isolates indicated that 80%–90% belong to the recombinant European (EU)-NTN group, with North-American (NA)-NTN and non-recombinant EU-N variants accounting for the remainder. The shift from non-recombinant to recombinant PVY isolates is a common trend observed worldwide. Surveys of a range of PVY isolates representing the main strain and phylogenetic groups suggest that PVY has the ability to overcome hypersensitive response-mediated resistance with significant differences between isolates of the same strain group. Contrastingly, genes mediating extreme resistance (Ryadg, Rysto) provide efficient resistance to PVY transmission to progeny tubers. Transmission experiments in field conditions of PVY isolates representing the three main molecular groups (PVYO, PVYEU−NTN, PVYNA−NTN) indicate that PVYEU−NTN has the highest transmission rate. Our results suggest that PVYEU−NTN isolate has a competitive advantage over PVYO and PVYNA−NTN isolates which is likely to be an important factor in shaping the evolution of viruses and the population dynamics of PVY.

Occurrence of Diverse Recombinant Strains of Potato virus Y Circulating in Potato Fields in Egypt.

Potato is one of the staple crops in Egypt, grown under irrigation almost continuously year-round. Potato virus Y (PVY) has been reported as one of the main viruses affecting potatoes in Egypt, but limited information is available on PVY strains circulating in potato fields in the country. From 2014 to 2016, virus surveys were conducted in several potato-growing governorates of Egypt, and PVY-positive samples were found to represent at least five distinct recombinant PVY strains, including PVYNTN and PVYN-Wi. Whole genome sequences were determined for four isolates representing strains PVY-SYR-III (Egypt7), PVY-261-4 (Egypt11), PVYNTNa (Egypt35), and a novel recombinant named Egypt24 that combined molecular properties of strains PVY-261-4 and PVY-Wilga156var. At least three recombinants found in Egypt in potato were previously found associated with potato tuber necrotic ringspot disease (PTNRD). The identification of multiple recombinant types of PVY in potato in Egypt, including the novel recombinant Egypt24, suggests a wide presence of PTNRD-inducing virus strains in the country.

Phylogenetic study of recombinant strains of Potato virus Y

Potato virus Y (PVY) exists as a complex of strains, including a growing number of recombinants. Evolution of PVY proceeds through accumulation of mutations and more rapidly through recombination. Here, the role of recombination in PVY evolution and the origin of common PVY recombinants were studied through whole genome analysis of 119 newly sequenced PVY isolates largely from U.S. potato, and subsequent combined phylogenetic and recombination analyses with an additional 166 whole PVY genomes from the GenBank database. Two novel PVYC recombinants were sequenced and identified, along with one novel PVYN:O recombinant. Sequence diversity in the parental sequences made it possible to trace the origins of all recombinant types of PVY, which also showed remarkable sequence diversity in most cases. The results suggested that the common recombinant PVY strains originated more than once, from different parental sequences.

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 PVYO declining and the recombinant strains PVYNTN and PVYN: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 PVYNTN, PVYN:O, and PVYO 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 PVYO was present. Triple-strain infections were not transmitted by any single aphid. PVYO 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.

Comparative genetic diversity of potato virus Y populations based on coat protein gene.

Potato virus Y (PVY) is an important plant pathogen with a wide host range including economically important crops of potato, tobacco, tomato, and pepper. The coat protein gene has been commonly used in studying molecular biology of plant viruses including PVY. In this study, we used a large dataset of CP sequences from isolates collected across the world to assess the detailed molecular evolution of PVY populations with a focus on the Iranian PVY population. Phylogenetic analysis showed that the world PVY population had two major lineages (O:C and N:NTN); each comprising several divergent sublineages. Results showed that the Iranian PVY isolates were distributed across the tree suggesting polyphyletic origin of the Iranian PVY population. Statistical analysis revealed great genetic differences between pairs of the PVY phylogenetic populations. Host populations and also geographical populations of PVY were genetically differentiated. The extent of the genetic diversification among PVY host and geographical populations were mild or moderate. Purifying selection was detected on the CP gene sequences of the PVY populations, suggesting that most of the mutations in the gene were harmful, thereby were eliminated by natural selection. We also detected a variety of recombination patterns to occur along the CP gene of the PVY strains. A significant number of the Iranian PVY isolates were found to be recombinant. Different analyses suggest that Iranian PVY population is highly diverse. In conclusion, results of this study demonstrated that different factors including mutation, host adaptation, geographical distinction and selection pressure shaped the genetic structure of the PVY populations.

Priming Potato with Thiamin to Control Potato Virus Y

Potato virus Y (PVY) is a major potato pathogen affecting potato yields worldwide. Thiamin, a water-soluble B vitamin (vitamin B1) has been shown to boost the plant’s immunity, thereby increasing resistance against pathogens. In this study, we tested different concentrations of thiamin (1 mM, 10 mM, 50 mM, 100 mM) and multiple thiamin applications (once, biweekly and monthly) on potato resistance to PVY in Ranger Russet potatoes. Plants were mechanically inoculated with PVYN:O. This PVY strain is known for causing well-defined foliar symptoms. We collected leaflets weekly through April and May 2015 and tested them with an enzyme-linked immunosorbent assay specific to PVY as well as by real time quantitative RT-PCR. These assays allowed us to determine the presence and level of PVY in different parts of the plants. We found that the highest thiamin concentration treatment (100 mM) produced the lowest virus level in potatoes across all dates and leaflet samples. Also, it was found that multiple applications of thiamin had a positive effect on reducing virus level, especially when thiamin was applied every four weeks.

Graphical genotyping as a method to map Ny(o,n)sto and Gpa5 using a reference panel of tetraploid potato cultivars

Key messageThe method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable.Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus. The method is illustrated with cultivars resistant to Potato virus Y (PVY), while simultaneously selecting for the absence of the SNPs in susceptible clones. SNP data will then merge into an image which displays the coordinates of a distal genomic region on the northern arm of chromosome 11 where a specific haplotype is introgressed from the wild potato species S. stoloniferum (CPC 2093) carrying a gene (Ny(o,n)sto) conferring resistance to two PVY strains, PVYO and PVYNTN. Graphical genotyping was also successful in showing the haplotypes on chromosome 12 carrying Ry-fsto, another resistance gene derived from S. stoloniferum conferring broad-spectrum resistance to PVY, as well as chromosome 5 haplotypes from S. vernei, with the Gpa5 locus involved in resistance against Globodera pallida cyst nematodes. The image also shows shortening of linkage drag by meiotic recombination of the introgression segment in more recent breeding material. Identity-by-descent was found to be a requirement for using graphical genotyping, which is proposed as a non-statistical alternative method for gene discovery, as compared with genome-wide association studies. The potential and limitations of the method are discussed.

Strain-Specific Resistance to Potato virus Y (PVY) in Potato and Its Effect on the Relative Abundance of PVY Strains in Commercial Potato Fields.

Potato virus Y (PVY) is a serious threat to potato production due to effects on tuber yield and quality, in particular, due to induction of potato tuber necrotic ringspot disease (PTNRD), typically associated with recombinant strains of PVY. These recombinant strains have been spreading in the United States for the past several years, although the reasons for this continuing spread remained unclear. To document and assess this spread between 2011 and 2015, strain composition of PVY isolates circulating in the Columbia Basin potato production area was determined from hundreds of seed lots of various cultivars. The proportion of nonrecombinant PVYO isolates circulating in Columbia Basin potato dropped ninefold during this period, from 63% of all PVY-positive plants in 2011 to less than 7% in 2015. This drop in PVYO was concomitant with the rise of the recombinant PVYN-Wi strain incidence, from less than 27% of all PVY-positive plants in 2011 to 53% in 2015. The proportion of the PVYNTN recombinant strain, associated with PTNRD symptoms in susceptible cultivars, increased from 7% in 2011 to approximately 24% in 2015. To further address the shift in strain abundance, screenhouse experiments were conducted and revealed that three of the four most popular potato cultivars grown in the Columbia Basin exhibited strain-specific resistance against PVYO. Reduced levels of systemic movement of PVYO in such cultivars would favor spread of recombinant strains in the field. The negative selection against the nonrecombinant PVYO strain is likely caused by the presence of the Nytbr gene identified in potato cultivars in laboratory experiments. Presence of strain-specific resistance genes in potato cultivars may represent the driving force changing PVY strain composition to predominantly recombinant strains in potato production areas.

Biological and molecular characterization of a tomato isolate of potato virus Y (PVY) of the PVYC lineage.

An isolate of potato virus Y (PVY), PVY-H14, was collected on the island of Oahu, Hawaii, from tomato plants exhibiting stunting and necrotic lesions on leaves. PVY-H14 triggered the hypersensitive resistance response in potato cultivars King Edward and Maris Bard, typical of a PVYC strain, and was unable to infect systemically the four tested cultivars, Desiree, Maris Bard, King Edward, and Russet Norkotah. Phylogenetic analysis of H14 and the whole genomes of 31 PVY isolates of non-recombinant strains of PVY placed PVY-H14 in the same clade with PVYC and several unclassified PVY isolates from tomato and tobacco.

The movement of potato virus Y (PVY) in the vascular system of potato plants

Potato virus Y (PVY) is responsible for major viral diseases in most potato seed areas. It is transmitted by aphids in a non-persistent manner, and it is spread in potato fields by the winged aphids flying from an infected source plant to a healthy one. Six different PVY strains groups affect potato crops: PVYC, PVYN, PVYO, PVYN:O, PVYNTN, and PVYN-Wi. Nowadays, PVYNTN and PVYN-Wi are the predominant strains in Europe and the USA. After the infection of the leaf and accumulation of the virus, the virus is translocated to the progeny tubers. It is known that PVYN is better translocated than PVYO, but little is known about the translocation of the other PVY strains. The translocation of PVY occurs faster in young plants than in old plants; this mature plant resistance is generally explained by a restriction of the cell-to-cell movement of the virus in the leaves. The mother tuber may play an important role in explaining mature plant resistance. PVY is able to pass from one stem to the other stems of the same plant through the vascular system of the mother tuber, but it is unknown whether this vascular link between stems is permanent during the whole life of the plant. Two greenhouse trials were set up to study the spread of PVY in the vascular system of the potato plant. The PVY-susceptible cultivar Charlotte was used for both trials. It was demonstrated that all stems growing from a PVY-infected tuber will become infected sooner or later, and that PVYN-Wi translocates more efficiently to progeny tubers than PVYNTN. It was also demonstrated that the progressive decay of the mother tuber in the soil reduces the possibility for virus particles to infect healthy stems through the vascular system of the mother tuber. This new element contributes to a better understanding of the mechanism of mature plant resistance.

Surveys of aphids and potato virus y in potato fields in wallonia, belgium : a four year overview

Populations of Potato virus Y (PVY) and aphids were characterized in potato seed and stock production fields in southern Belgium (Wallonia) from 2009 to 2012. More than 40 aphid species were identified using yellow pan traps. Four thousands potato leaf samples collected in 87 plots from 29 fields were analysed for the presence and typing of PVY strains by RT-PCR. PVY was detected in 26%, 20% and 60% of the seed plots tested from 2009 to 2011, respectively. A higher prevalence of PVY was observed in plots of stock potatoes (60% in 2010 and 67% in 2011). The N/NTN strain of PVY was predominant, representing 70-99% of the strains.

A Mutant eIF4E Confers Resistance to Potato Virus Y Strains and is Inherited in a Dominant Manner in the Potato Varieties Atlantic and Russet Norkotah

Potato Virus Y (PVY) is one of the most important pathogens affecting potato production worldwide. Here we tested the efficacy of engineered resistance against PVY in two popular susceptible potato varieties, Russet Norkotah and Atlantic. This resistance is based on the expression of a modified potato eIF4E gene containing mutations homologous to those in the recessive resistant allelic variant found in pepper. The expression of this eIF4E variant conferred differential resistance responses against three prevalent PVY strains including PVYO, PVYN:O and PVYNTN in the five tested transgenic lines. When resistance was established, the virus was not detectable in the inoculated leaves, the newly emerged leaves, nor in the sprouted tubers. Some strains were restrained to a low but detectable level in some of the potato lines. Crosses between transformed and wild type lines demonstrated that the engineered resistance gene was inherited in a dominant manner.