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In this study, the impact of culture media filtrate of QD3 actinobacterial isolate on two potato cultivars, Spunta and Diamond, infected with potato virus Y (PVY) was investigated. Various parameters, including infection percentage, PVY virus infectivity, disease severity scoring, PVY optical density, photosynthetic and defense-related biochemical markers, enzymatic profiling, phenolic compounds, proline content, salicylic acid levels, and growth and yield parameters, were assessed to elucidate the potential of the QD3 actinobacterial isolate culture filtrate in mitigating PVY-induced damage. The physiological and biochemical characteristics of the QD3 actinobacterial isolate, including its salinity tolerance, pH preferences, and metabolic traits, were investigated. Molecular identification via 16S rRNA gene sequencing confirmed its classification as Streptomyces fradiae QD3, and it was deposited in GenBank with the gene accession number MN160630. Distinct responses between Spunta and Diamond cultivars, with Spunta displaying greater resistance to PVY infection. Notably, pre-infection foliar application of the QD3 filtrate significantly reduced disease symptoms and virus infection in both cultivars. For post-PVY infection, the QD3 filtrate effectively mitigated disease severity and the PVY optical density. Furthermore, the QD3 filtrate positively influenced photosynthetic pigments, enzymatic antioxidant activities, and key biochemical components associated with plant defense mechanisms. Gas chromatography‒mass spectrometry (GC‒MS) analysis revealed palmitic acid (hexadecanoic acid, methyl ester) and oleic acid (9-octadecanoic acid, methyl ester) as the most prominent compounds, with retention times of 23.23 min and 26.41 min, representing 53.27% and 23.25%, respectively, of the total peak area as primary unsaturated fatty acids and demonstrating antiviral effects against plant viruses. Cytotoxicity assays on normal human skin fibroblasts (HSFs) revealed the safety of QD3 metabolites, with low discernible toxicity at high concentrations, reinforcing their potential as safe and effective interventions. The phytotoxicity results indicate that all the seeds presented high germination rates of approximately 95–98%, suggesting that the treatment conditions had no phytotoxic effect on the Brassica oleracea (broccoli) seeds, Lactuca sativa (lettuce) seeds, and Eruca sativa (arugula or rocket) seeds. Overall, the results of this study suggest that the S. fradiae filtrate has promising anti-PVY properties, influencing various physiological, biochemical, and molecular aspects in potato cultivars. These findings provide valuable insights into potential strategies for managing PVY infections in potato crops, emphasizing the importance of Streptomyces-derived interventions in enhancing plant health and crop protection. [ABSTRACT FROM AUTHOR]

Excellent germplasm resources are the foundation for cultivating high-quality, disease-resistant, and stress-tolerant varieties. In this study, simple sequence repeat (SSR) markers were used to identify 138 potato accessions collected from worldwide, and genetic cluster analysis was used to characterize the genetic diversity of the tested germplasm resources. The Potato virus Y (PVY) resistance of these potato accessions was identified by artificial friction inoculation combined with molecular marker detection, and potato accessions with different PVY resistance were screened based on disease index and incidence rate. Using SSR markers, 138 potato accessions were identified, and the results showed that the genetic distances between the tested potato germplasm resources ranged from 0.025 to 0.660, and the genetic similarity coefficients ranged from 0.489 to 0.975. The 138 accessions could be clustered into five subgroups using Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Among them, Z173, Biyin No. 4, Suyin No. 2, XN995, XN987, Biyin No 22, Bibiao104, Sarpo mira, XN996, XN979, Desiree, RUNSHI, Actrice, Jia 1219, Heyin No 12, and Moyin No.1 have relatively distant genetic relationship with another 122 accessions. Based on the disease index, the following different accessions were screened: five highly resistant, 11 resistant, 45 moderately resistant, 35 susceptible, and 42 highly susceptible. Fourteen resource materials with good resistance (disease index ≤ 33.74%, and a grading of high resistance (HR) or medium resistance (MR); incidence rate ≤ 67.58%) were identified. By combining genetic cluster analysis and PVY resistance identification, six accessions showed PVY resistance and had distant genetic relationships with other accessions selected which provided important materials for disease resistance breeding and quality improvement of potato. In this study, the genetic diversity and PVY resistance of global potato germplasm resources was explored, and potato germplasm materials with important utilization value were screened. The results obtained in this study could provide important references for the research and utilization of global potato germplasm resources. [ABSTRACT FROM AUTHOR]

Aphids are phloem‐feeding insects that reduce crop productivity due to feeding and transmission of plant viruses. When aphids disperse across the landscape to colonize new host plants, they will often probe on a wide variety of nonhost plants before settling on a host suitable for feeding and reproduction. There is limited understanding of the diversity of plants that aphids probe on within a landscape, and characterizing this diversity can help us better understand host use patterns of aphids. Here, we used gut content analysis (GCA) to identify plant genera that were probed by aphid vectors of potato virus Y (PVY). Aphids were trapped weekly near potato fields during the growing seasons of 2020 and 2021 in San Luis Valley in Colorado. High‐throughput sequencing of plant barcoding genes, trnF and ITS2, from 200 individual alate (i.e., winged) aphids representing nine vector species of PVY was performed using the PacBio sequencing platform, and sequences were identified to genus using NCBI BLASTn. We found that 34.7% of aphids probed upon presumed PVY host plants and that two of the most frequently detected plant genera, Solanum and Brassica, represent important crops and weeds within the study region. We found that 75% of aphids frequently probed upon PVY nonhosts including many species that are outside of their reported host ranges. Additionally, 19% of aphids probed upon more than one plant species. This study provides the first evidence from high‐throughput molecular GCA of aphids and reveals host use patterns that are relevant for PVY epidemiology. [ABSTRACT FROM AUTHOR]

Summary: Ethylene response factors (ERFs) have been associated with biotic stress in Arabidopsis, while their function in non‐model plants is still poorly understood. Here we investigated the role of potato ERF StPti5 in plant immunity.We show that StPti5 acts as a susceptibility factor. It negatively regulates potato immunity against potato virus Y and Ralstonia solanacearum, pathogens with completely different modes of action, and thereby has a different role than its orthologue in tomato. Remarkably, StPti5 is destabilised in healthy plants via the autophagy pathway and accumulates exclusively in the nucleus upon infection. We demonstrate that StEIN3 and StEIL1 directly bind the StPti5 promoter and activate its expression, while synergistic activity of the ethylene and salicylic acid pathways is required for regulated StPti expression.To gain further insight into the mode of StPti5 action in attenuating potato defence responses, we investigated transcriptional changes in salicylic acid deficient potato lines with silenced StPti5 expression. We show that StPti5 regulates the expression of other ERFs and downregulates the ubiquitin‐proteasome pathway as well as several proteases involved in directed proteolysis.This study adds a novel element to the complex puzzle of immune regulation, by deciphering a two‐level regulation of ERF transcription factor activity in response to pathogens. [ABSTRACT FROM AUTHOR]

Calibrachoa, an ornamental native plant from South America, is propagated by stem cuttings, and vegetative propagation causes frequent occurrence of viral diseases. The purpose of this paper was to use a cloning technique for calibrachoa “Pampa Salmon INTA”, like meristem culture, to generate Potato virus Y free plants, a virus that usually infects this cultivar. Cloning plants by using the apical meristems (0.2–0.5 mm long) were cultured in Murashige and Skoog (½ concentration) medium supplemented with 0.01 mg. L-1 6-benzyladenine. Seventy-four percent (74%) of regenerated plants were virus-free through reverse transcription polymerase chain reaction analysis. Finally, meristem culture is a quite efficient method to generate virus free plants, so this is the first report regarding a cloning method of viral free plants of calibrachoa. [ABSTRACT FROM AUTHOR]

BACKGROUND: Potato virus Y (PVY) is a prominent representative of plant viruses. It can inflict severe damage upon Solanaceae plants, leading to global dissemination and substantial economic losses. To discover new antiviral agents, a class of planar chiral thiourea molecules through the key step of N‐heterocyclic carbene‐catalyzed nitrile formation reaction was synthesized with excellent optical purities for antiviral evaluations against plant virus PVY. RESULTS: The absolute configurations of the planar chiral compounds exhibited obvious distinctions in the anti‐PVY activities. Notability, compound (S)‐4u exhibited remarkable curative activities against PVY, with a half maximal effective concentration (EC50) of 349.3 μg mL−1, which was lower than that of the ningnanmycin (NNM) (EC50 = 400.8 μg mL−1). Additionally, The EC50 value for the protective effects of (S)‐4u was 146.2 μg mL−1, which was superior to that of NNM (276.4 μg mL−1). Furthermore, the mechanism‐of‐action of enantiomers of planar chiral compound 4u was investigated through molecular docking, defensive enzyme activity tests and chlorophyll content tests. CONCLUSION: Biological mechanism studies have demonstrated that the configuration of planar chiral target compounds plays a crucial role in the molecular interaction with PVY‐CP, enhancing the activity of defense enzymes and affecting chlorophyll content. The current study has provided significant insights into the roles played by planar chiralities in plant protection against viruses. This paves the way for the development of novel green pesticides bearing planar chiralities with excellent optical purities. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Summary: The interactions among plant viruses, insect vectors, and host plants have been well studied; however, the roles of insect viruses in this system have largely been neglected.We investigated the effects of MpnDV infection on aphid and PVY transmission using bioassays, RNA interference (RNAi), and GC‐MS methods and green peach aphid (Myzus persicae (Sulzer)), potato virus Y (PVY), and densovirus (Myzus persicae nicotianae densovirus, MpnDV) as model systems.MpnDV increased the activities of its host, promoting population dispersal and leading to significant proliferation in tobacco plants by significantly enhancing the titer of the sesquiterpene (E)‐β‐farnesene (EβF) via up‐regulation of expression levels of the MpFPPS1 gene. The proliferation and dispersal of MpnDV‐positive individuals were faster than that of MpnDV‐negative individuals in PVY‐infected tobacco plants, which promoted the transmission of PVY.These results combined showed that an insect virus may facilitate the transmission of a plant virus by enhancing the locomotor activity and population proliferation of insect vectors. These findings provide novel opportunities for controlling insect vectors and plant viruses, which can be used in the development of novel management strategies. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is a highly diverse and genetically variable virus with various strains. Differential evolutionary routes have been reported in the genus Potyvirus, caused by natural selection pressure, mutation, and recombination, with their virulence being dependent on different environmental conditions. Despite its significance and economic impact on Solanaceous species, the understanding of PVY's phylogeography in Kenya remains limited and inadequately documented. The study centers on the molecular characterization of a Kenyan PVY isolate, GenBank accession number PP069009. In‐depth phylogenetic analysis unveiled a strong evolutionary association between the Kenyan isolate and isolate [JQ924287] from the United States of America, supported by a robust 92% probability. Recombinant analyses exposed a mosaic‐like genetic architecture within the Kenyan isolate, indicating multiple gene recombination events. Selection pressure scrutiny identified specific sites under selective pressure, with evidence of positive/diversifying and negative/purifying selection. Population genetics analysis revealed a calculated nucleotide diversity (π) of 0.00354881, while analysis of molecular variance (AMOVA) unveiled a structured genetic landscape with an øST value of 0.45224. The extensive haplotype network depicted the possibility of diverse PVY strains occurring across continents. This analysis provides valuable insights into the genetic diversity and distribution of PVY globally, highlighting the importance of understanding evolutionary dynamics for effective management and control strategies of PVY on a global scale. [ABSTRACT FROM AUTHOR]

Background: Although potato virus Y (PVY) is the most serious virus-infecting potato plants worldwide, the losses concurred by it remain unmanageable due to the lack of efficient anti-PVY agents. Hence, the objective of this study was to assess the antiviral properties of secondary metabolite compounds obtained from culture filtrates of four Trichoderma spp. isolates. The assessment was conducted using computational methods, including molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis, as well as molecular dynamics simulations. The aim was to develop novel and effective agents for combating PVY. Results: The GC–MS analysis of the studied Trichoderma spp. secondary metabolites revealed 24 compounds with relative amounts exceeding 10%. Molecular docking was then performed using MOE software to evaluate the activity of these compounds against the PVY protein coat (PDB-ID: 6HXX). Ningnanmycin and ribavirin, known plant virus inhibitors, were employed as reference ligands for comparison. Among the compounds tested, C9, C10, C13, and C19 exhibited superior docking scores, root mean square deviation (RMSD) values, and binding modes compared to the reference ligands. In addition, these compounds successfully passed the ADMET analysis. Further investigation focused on compounds C13 and C19, which underwent in-depth analysis through MDs for 100 ns. The MDs trajectories demonstrated that both complexes exhibited favorable stability, compactness, and binding modes throughout the simulation period. However, the C19/PVY-CP complex outperformed the C13 complex in all calculated parameters such as RMSD, root mean square fluctuation (RMSF), radius of gyration (RoG), solvent-accessible surface area (SASA), and intermolecular hydrogen bonds. Interestingly, these findings aligned with the results obtained from the docking analysis, indicating that C9 and C10 possess high potential against PVY, as they exhibited binding modes like that of C19. Conclusion: These promising outcomes provide a solid foundation for considering the potential use of compounds C9, C10, C13, and C19 as antiviral agents. Further experimental validation and in-depth studies are warranted to assess the efficacy and safety of these compounds and their potential as antiviral therapeutics. To our knowledge, this is the first report to study the biological activities of the Trichoderma-based bioactive compounds against PVY using computational techniques. [ABSTRACT FROM AUTHOR]

Manipulating evolutionary forces imposed by hosts on pathogens like genetic drift and selection could avoid the emergence of virulent pathogens. For instance, increasing genetic drift could decrease the risk of pathogen adaptation through the random fixation of deleterious mutations or the elimination of favorable ones in the pathogen population. However, no experimental proof of this approach is available for a plant-pathogen system. We studied the impact of pepper (Capsicum annuum) lines carrying the same major resistance gene but contrasted genetic backgrounds on the evolution of Potato virus Y (PVY). The pepper lines were chosen for the contrasted levels of genetic drift (inversely related to Ne, the effective population size) they exert on PVY populations, as well as for their contrasted resistance efficiency (inversely related to the initial replicative fitness, Wi, of PVY in these lines). Experimental evolution was performed by serially passaging 64 PVY populations every month on six contrasted pepper lines during seven months. These lines exhibited highly divergent evolutionary trajectories, ranging from viral extinctions to replicative fitness gains. The sequencing of the PVY VPg cistron, where adaptive mutations are likely to occur, allowed linking these replicative fitness gains to parallel adaptive nonsynonymous mutations. Evolutionary trajectories were well explained by the genetic drift imposed by the host. More specifically, Ne, Wi and their synergistic interaction played a major role in the fate of PVY populations. When Ne was low (i.e. strong genetic drift), the final PVY replicative fitness remained close to the initial replicative fitness, whereas when Ne was high (i.e. low genetic drift), the final PVY replicative fitness was high independently of the replicative fitness of the initially inoculated virus. We show that combining a high resistance efficiency (low Wi) and a strong genetic drift (low Ne) is the best solution to increase resistance durability, that is, to avoid virus adaptation on the long term. Author summary: Given their high evolutionary potential, viruses are notoriously difficult to control by drug treatments or by breeding resistant hosts. In plants, resistance genes targeting viruses become often rapidly inefficient due to virus mutational escape. Manipulating the evolutionary forces imposed by the plant on the virus population, like selection and genetic drift, could help control virus adaptation and prevent resistance breakdown. Theoretically, a plant genotype imposing low selective pressures could slow down the fixation of adaptive viral mutations, while a plant genotype imposing strong genetic drift could decrease virus fitness by favoring the random fixation of deleterious viral mutations and/or the elimination of favorable ones. Using experimental evolution, we studied the effect of plants imposing contrasted levels of genetic drift on the emergence of resistance-adapted virus mutants. Results indicate that the level of genetic drift during plant colonization, in part controlled by the genetic background of the plant, and the plant resistance level are the main drivers of the virus evolutionary trajectories, which varied from fast adaptation to extinction. Consequently, it is possible to achieve high resistance efficiency and durability by breeding plant genotypes through the introduction of major-effect resistance genes exerting a strong selection on virus populations into a genetic background increasing genetic drift. [ABSTRACT FROM AUTHOR]

The ability to initiate sprouting soon after harvest to enable direct tuber testing for potato virus Y (PVY) could aid in acquiring more rapid results compared to the traditional winter grow out tests currently used. Methods to break dormancy for PVY detection using laboratory direct tuber testing by ELISA in commercially produced Ranger Russet, Clearwater Russet, and Umatilla Russet seed lots were tested over two years and compared to leaf testing results obtained from the winter grow out and spring grow out. At harvest, three 400 tuber samples from each cultivar were obtained for the trial and included (1) untreated control (UTC), (2) application of cold aerosol smoke, or (3) application of Rindite. Tuber samples were held at 18.3 C and sprout development was monitored weekly. Treatments were direct tuber tested for PVY when one treatment of that cultivar achieved three sprouts elongating to six millimeters. A fourth 400 tuber sample was collected, treated with Rindite, and included in the Idaho winter grow out plots in Waialua, Hawaii and leaves were sampled and evaluated for PVY using ELISA. Laboratory tested seed was stored and planted in a spring grow out (Kimberly, Idaho) and leaf samples were analyzed for PVY by ELISA. Rindite treated tubers had greater sprout rating and number of sprouts elongating compared to UTC tubers and tubers receiving the smoke treatment at time of PVY testing. Smoke had a greater sprout rating but did not always significantly differ in the number of sprouts elongating compared to the untreated tubers. Overall, estimates of PVY prevalence from direct tuber testing showed limited significant differences to those obtained in the winter grow out for each cultivar, year, and PVY incidence. However, in year two, the incidence of PVY in the winter grow out (7% PVY) significantly differed from direct tuber testing (16% PVY) in Ranger Russet. In both years, the spring grow out PVY results for all cultivars were not significantly different than the direct tuber testing, except in year one the Ranger Russet direct tuber tested UTC showed 10% lower PVY detection compared to the spring grow out. This study identified a novel dormancy breaking treatment to promote earlier and accurate PVY detection by direct tuber testing using ELISA and provided data to support direct tuber testing for post-harvest evaluation of PVY in seed certification. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is a major tobacco (Nicotiana tabacum L.) pathogen that causes severe crop losses. We studied the influence of meteorological factors and a population of twelve aphid species on the development of PVY in field-grown tobacco from 1996 to 2010 in Poland. Three PVY-susceptible tobacco varieties were used in the study. The mean virus incidence ranged from 18% in 2010 to almost 99% in 1996, 2004, and 2009. For determining the relationship between tobacco plant infection and meteorological conditions and aphid populations, logistic regression analysis was used. It was found that the probability of PVY infection is significantly dependent on the average air temperature, relative humidity, number of days with an average temperature of at least 25 °C, and the abundance of Aphis fabae and Brachycaudus helichrysi. The probability of infection of tobacco plants with potato virus Y decreased with increasing air temperature and relative humidity. In addition, with each subsequent day with a temperature of at least 25 °C, the risk of infection decreased by 24%. Furthermore, it was often observed that high populations of Aphis fabae and Brachycaudus helichrysi were associated with a high incidence of virus infection in tobacco plants. [ABSTRACT FROM AUTHOR]

Virus diseases represent important economic threats to seed potato production worldwide, yet relatively little is known of their epidemiology at the landscape‐scale. In this study, data was compiled from the Scottish national seed potato classification scheme on the incidence of 10 different potato viruses for the years 2009–2022. A co‐occurrence analysis identified that 12 virus species pairs occurred together more often than expected by chance, and potato blackleg was positively associated with eight potato viruses. ArcGIS was used to investigate spatial and spatiotemporal variation in incidence rates of the three most prevalent viruses (potato virus Y, potato leaf roll virus and potato virus A), and this revealed prominent geographic differences in long‐term disease outcomes. Focusing on potato virus Y as the most commonly occurring single infection, interpretable machine‐learning techniques were used to investigate the influence of key crop, management and environmental factors on patterns of incidence in space and time. The results showed that health characteristics of seed stocks were among the most important predictors of incidence, along with blackleg infection, several management features, cultivar resistance, distance to the nearest seed and ware crop, temperature variables and several soil features. This approach provides a comprehensive overview of potato viruses in Scotland, a deeper understanding of epidemiological risk factors at the landscape‐scale and a forecast model that could serve as the basis of a decision support tool for improved management of potato virus Y. [ABSTRACT FROM AUTHOR]

Diversifying agricultural systems by growing more than one crop species in an area can decrease pest and disease pressure and increase crop yields. However, there is a lack of information on how crop diversity at larger spatial scales influences pest and disease pressure. Here, we investigated how landscape‐scale crop diversity affects aphid vector communities and prevalence of non‐persistently transmitted potato virus Y (PVY).To test the influence of landscape‐scale crop diversity on PVY prevalence and aphid communities, we conducted a field study during the 2020 and 2021 field seasons in the San Luis Valley, Colorado, where we quantified aphid communities and PVY incidence at multiple sites. We then determined the association between aphid species richness and abundance and PVY incidence with landscape variables (crop diversity metrics and percentage cover of crop species) within 1, 2 and 3 km buffers from study sites.Higher crop diversity (measured as Shannon Diversity Index) led to decreased aphid species richness at a 3 km buffer in the 2021 field season. We only detected a positive association between percentage of alfalfa crop cover and aphid species richness in 2020 and aphid abundance in 2021 within a 1 km buffer.Higher crop diversity led to increased PVY incidence at a 2 km buffer in 2021 and 3 km buffer in 2020 and 2021. At a 3 km buffer in 2021, we found a positive influence of crop species richness on PVY incidence and a negative influence of crop species evenness on PVY incidence. Also in 2021, we found a positive influence of percentage of potato (virus host) on PVY incidence and a negative influence of percentage of barley (virus non‐host) on PVY incidence.Synthesis and applications. In summary, we found that landscape‐scale crop diversity impacts plant virus prevalence at spatial scales of >1 km. This suggests that potato growers could reduce PVY prevalence by geographically isolating potato fields from other potato or other PVY hosts. Crop diversity had a negative influence on aphid vector communities, so growers could reduce risk of virus spread by aphid vectors by using certified potato seed in a diversified landscape. [ABSTRACT FROM AUTHOR]

Viral diseases cause significant economic losses in tomatoes worldwide. This detect conducted a comprehensive survey in tomato (Lycopersicum esculentum L.) fields in Hamedan and Tehran provinces in Iran to detect and determine the incidence of tomato-infecting viruses. Using specific antibodies, collected symptomatic samples (348) were analyzed by Double antibody sandwich (DAS)-ELISA. According to the DAS-ELISA experiment, we found that 26.14% of collected samples were infected Arabis mosaic virus (ArMV), 36.78 % with Cucumber mosaic virus (CMV), 10.63% with Potato virus Y (PVY) 3.44 % with Tomato bushy stunt virus (TBSV), 7.18 % with Tomato spotted wilt virus (TSWV), and 2.87% with Tomato yellow leaf curl virus (TYLCV). Furthermore, double and triple infections were also observed in 15.08 and 6.03% of samples, respectively. CMV was the most prevalent among other tested viruses. Moreover, our findings showed that CMV was present in multiple infections of different samples. Serological diagnoses were confirmed by reverse transcription-polymerase chain reaction tests (RT-PCR) using a pair of primers that are specific for the detection of CMV and resulted in a DNA fragment of the expected size (540 bp). These results confirmed the DAS- ELISA experiment. Furthermore, in this study, we introduced a rapid method that facilitates the diagnosis of CMV in infected samples. Our findings can be used for control strategies and rapid diagnosis of viral infection in plants. Moreover, the outcome of this research can be used for the preparation of resistant cultivars against important viruses in tomatoes. [ABSTRACT FROM AUTHOR]

We had previously reported that a plum pox virus (PPV)‐based chimera that had its P1‐HCPro bi‐cistron replaced by a modified one from potato virus Y (PVY) increased its virulence in some Nicotiana benthamiana plants, after mechanical passages. This correlated with the natural acquisition of amino acid substitutions in several proteins, including in HCPro at either position 352 (Ile→Thr) or 454 (Leu→Arg), or of mutations in non‐coding regions. Thr in position 352 is not found among natural potyviruses, while Arg in 454 is a reversion to the native PVY HCPro amino acid. We show here that both mutations separately contributed to the increased virulence observed in the passaged chimeras that acquired them, and that Thr in position 352 is no intragenic suppressor to a Leu in position 454, because their combined effects were cumulative. We demonstrate that Arg in position 454 improved HCPro autocatalytic cleavage, while Thr in position 352 increased its accumulation and the silencing suppression of a reporter in agropatch assays. We assessed infection by four cloned chimera variants expressing HCPro with none of the two substitutions, one of them or both, in wild‐type versus DCL2/4‐silenced transgenic plants. We found that during infection, the transgenic context of altered small RNAs affected the accumulation of the four HCPro variants differently and hence, also infection virulence. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is a common and devastating pathogen of potato worldwide and insecticide control alone for aphid vectors is not effective due to the rapid transmission of the virus by aphids following probing. Three Ry genes for extreme resistance to PVY have been identified and are used in potato breeding programs for the development of PVY-resistant varieties. Tightly linked molecular markers have been developed for all three genes and are used for marker-assisted selection (MAS). However, some varieties with known extreme resistance to PVY do not amplify any molecular markers for these resistance genes. Sante and its progeny Bistra are examples of two varieties with extreme resistance to PVY and yet have no amplification of Ry associated molecular markers. The source of PVY resistance in Bistra was mapped using SNP genotyping of 190 of its progeny which had been characterized for response to PVY infection using a N-Wilga strain. A major QTL was found on the proximal end of chromosome 11, in close proximity to Ryadg, one of the three known extreme resistance genes for PVY. However, no known markers which detect Ryadg amplify in Sante or Bistra which indicates they may possess a currently unidentified resistance gene, or the genetic linkages of molecular markers typically associated with the presence of Ryadg no longer exist due to recombination between the gene and its associated molecular marker primer annealing sites. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is one of the most important constraints to potato production worldwide. There is an increasing occurrence of recombinant PVY strains PVYNTN and PVYN-Wi and a decline in the incidence of the nonrecombinant PVYO. We hypothesized that this may be due to the ability of these recombinant strains to antagonize and/or outcompete PVYO in mixed infections. To determine this, we investigated interactions between PVYO and three recombinant PVY strains common in North America: PVYNTN, PVYN-Wi, and PVYN:O. Overall, our study showed that these interactions are tissue-dependent. Specifically, PVYNTN, the main causal agent of potato tuber necrotic ringspot disease (PTNRD), was found to be more adaptable than PVYO, especially in potato leaves due, at least in part, to the Ny gene that confers hypersensitive resistance (HR) to PVYO. Furthermore, PVYN-Wi was found to repress PVYO in potato tubers but act synergistically in potato leaves. The PVYO-induced foliage necrosis in cultivar 'Ranger Russet' was observed to be more severe in plants co-infected by PVYN-Wi and PVYN:O, respectively, resulting in plant death. Strikingly, this PVYO -induced necrosis was suppressed by PVYNTN in doubly infected plants. These interactions may, at least partially, explain the decreasing incidence of PVYO in United States potato production regions, especially given that many cultivars contain the Ny gene, which likely limits PVYO enabling PVYNTN and PVYN-Wi to outcompete. We also found that replication and cell-to-cell movement of these PVY strains in tubers at 4 °C was similar to levels at ambient temperature. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is one of the most important constraints to potato production worldwide. There is an increasing occurrence of recombinant PVY strains PVYNTN and PVYN-Wi and a decline in the incidence of the nonrecombinant PVYO. We hypothesized that this may be due to the ability of these recombinant strains to antagonize and/or outcompete PVYO in mixed infections. To determine this, we investigated interactions between PVYO and three recombinant PVY strains common in North America: PVYNTN, PVYN-Wi, and PVYN:O. Overall, our study showed that these interactions are tissue-dependent. Specifically, PVYNTN, the main causal agent of potato tuber necrotic ringspot disease (PTNRD), was found to be more adaptable than PVYO, especially in potato leaves due, at least in part, to the Ny gene that confers hypersensitive resistance (HR) to PVYO. Furthermore, PVYN-Wi was found to repress PVYO in potato tubers but act synergistically in potato leaves. The PVYO-induced foliage necrosis in cultivar ‘Ranger Russet’ was observed to be more severe in plants co-infected by PVYN-Wi and PVYN:O, respectively, resulting in plant death. Strikingly, this PVYO -induced necrosis was suppressed by PVYNTN in doubly infected plants. These interactions may, at least partially, explain the decreasing incidence of PVYO in United States potato production regions, especially given that many cultivars contain the Ny gene, which likely limits PVYO enabling PVYNTN and PVYN-Wi to outcompete. We also found that replication and cell-to-cell movement of these PVY strains in tubers at 4 °C was similar to levels at ambient temperature.

Besides increasing plant growth, several Plant Growth Promoting Rhizobacteria (PGPR), can enhance tolerance to biotic and/or abiotic stresses of numerous plant species. While cultivated plants are frequently subject to combined stresses in the field, there is limited knowledge of the effect of PGPR on plants undergoing simultaneous stress conditions. Therefore, we tested the beneficial properties of the halotolerant PGPR Serratia sp. strain C2, previously shown to enhance salt stress tolerance in barley, on tomato plants exposed to salinity, to Potato Virus Y (PVY) infection, and both stresses simultaneously. In our experimental conditions, C2 inoculation improved tomato tolerance to salt stress and positively correlated with a 46–68 % decrease in the level of PVY RNA compared to non-inoculated tomato plants. Morphometric, physiological and biochemical analyses (e.g., chlorophyll, sugar and proline accumulation, oxidative stress status and NDVI) indicated that C2 treatments had beneficial effects on tomato growth under simple and combined stress conditions. This is the first report of a PGPR enhancing tolerance not only to individually induced salinity and PVY infection, but also to both stresses in combination. Moreover, the expression analysis of selected genes involved in stress responses and RNA silencing-mediated antiviral immunity suggests that C2 can interfere with distinct defence response pathways to enhance stress tolerance in tomato. These pioneering results support the perspective of using PGPR as multi-spectrum and multi-host biostimulants for improving plant growth and protection from biotic, abiotic, and combined stresses to promote sustainable crop production in the face of environmental changes.

Trans-acting small interfering RNAs (tasiRNAs) are 21-nt phased (phased siRNAs) resulting from successive DCL-catalyzed processing from the end of a double-stranded RNA substrate originating from the RDR of an AGO-catalyzed cleaved RNA at a micro RNA target site. Plant tasiRNAs have been synthesized to produce synthetic tasiRNAs (syn-tasiRNAs) targeting viral RNAs that confer viral resistance. In this study, we engineered syn-tasiRNAs to target potato virus Y (PVY) infection by replacing five native siRNAs of TAS1c with 210-bp fragments from the coat protein (CP) region of the PVY genome. The results showed that the transient expression of syn-tasiR-CPpvy2 in Nicotiana benthamiana (N. benthamiana) plants conferred antiviral resistance, supported by the absence of PVY infection symptoms and viral accumulation. This indicated that syn-tasiR-CPpvy2 successfully targeted and silenced the PVY CP gene, effectively inhibiting viral infection. syn-tasiR-CPpvy1 displayed attenuated symptoms and decreased viral accumulation in these plants However, severe symptoms of PVY infection and a similar amount of viral accumulation as the control were observed in plants expressing syn-tasiR-CPpvy3. syn-tasiR-CPpvy/pvx, which targets both PVY and potato virus X (PVX), was engineered using a single precursor. After the transient expression of syn-tasiR-CPpvy/pvx3 and syn-tasiR-CPpvy/pvx5 in N. benthamiana, the plants were resistant to both PVY and PVX. These results suggested that engineered syn-tasiRNAs could not only specifically induce antiviral resistance against one target virus but could also be designed for multi-targeted silencing of different viruses, thereby preventing complex virus infection in plants.

This article presents a genomic dataset that combines different genotyping techniques to analyze the genetic traits of tetraploid potato clones. The dataset focuses on resistance to diseases and pests and provides valuable information for potato researchers and breeders. The dataset includes genotyping data from genotyping-by-sequencing, SolCAP array, and PCR markers, and consists of 27,148 high-quality SNPs. The research was funded by various organizations and there are no conflicts of interest. Additionally, the document provides a list of references that cover topics related to potato genotyping and resistance to pathogens, which can be useful for researchers studying potato genetics and breeding for disease resistance. [Extracted from the article]

Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding. [ABSTRACT FROM AUTHOR]

The control of potato virus Y (PVY) induced crop failure is a challengeable issue in agricultural chemistry. Although many anti‐PVY agents are designed to focus on the functionally important coat protein (CP) of virus, how these drugs act on CP to inactivate viral pathogenicity, remains largely unknown. Herein, a PVY CP inhibitor ‐3j (S) is disclosed, which is accessed by developing unusually efficient (up to 99% yield) and chemo‐selective (> 99:1 er in most cases) carbene‐catalyzed [3+4] cycloaddition reactions. Compound ‐3j bears a unique arylimidazole‐fused diazepine skeleton and shows chirality‐preferred performance against PVY. In addition, ‐3j (S) as a mediator allows ARG191 (R191) of CP to be identified as a key amino acid site responsible for intercellular movement of virions. R191 is further demonstrated to be critical for the interaction between PVY CP and the plant functional protein NtCPIP, enabling virions to cross plasmodesmata. This key step can be significantly inhibited through bonding with the ‐3j (S) to further impair pathogenic behaviors involving systemic infection and particle assembly. The study reveals the in‐depth mechanism of action of antiviral agents targeting PVY CP, and contributes to new drug structures and synthetic strategies for PVY management. [ABSTRACT FROM AUTHOR]

Background: Potato virus Y (PVY) is among the economically most damaging viral pathogen in production of potato (Solanum tuberosum) worldwide. The gene Rysto derived from the wild potato relative Solanum stoloniferum confers extreme resistance to PVY. Results: The presence and diversity of Rysto were investigated in wild relatives of potato (298 genotypes representing 29 accessions of 26 tuber-bearing Solanum species) using PacBio amplicon sequencing. A total of 55 unique Rysto-like sequences were identified in 72 genotypes representing 12 accessions of 10 Solanum species and six resistant controls (potato cultivars Alicja, Bzura, Hinga, Nimfy, White Lady and breeding line PW363). The 55 Rysto-like sequences showed 89.87 to 99.98% nucleotide identity to the Rysto reference gene, and these encoded in total 45 unique protein sequences. While Rysto-like26 identified in Alicja, Bzura, White Lady and Rysto-like16 in PW363 encode a protein identical to the Rysto reference, the remaining 44 predicted Rysto-like proteins were 65.93 to 99.92% identical to the reference. Higher levels of diversity of the Rysto-like sequences were found in the wild relatives of potato than in the resistant control cultivars. The TIR and NB-ARC domains were the most conserved within the Rysto-like proteins, while the LRR and C-JID domains were more variable. Several Solanum species, including S. antipoviczii and S. hougasii, showed resistance to PVY. This study demonstrated Hyoscyamus niger, a Solanaceae species distantly related to Solanum, as a host of PVY. Conclusions: The new Rysto-like variants and the identified PVY resistant potato genotypes are potential resistance sources against PVY in potato breeding. Identification of H. niger as a host for PVY is important for cultivation of this plant, studies on the PVY management, its ecology, and migrations. The amplicon sequencing based on PacBio SMRT and the following data analysis pipeline described in our work may be applied to obtain the nucleotide sequences and analyze any full-length genes from any, even polyploid, organisms. [ABSTRACT FROM AUTHOR]

Tobacco vein necrosis (TVN) is a complex phenomenon regulated by different genetic determinants mapped in the HC-Pro protein (amino acids N330, K391 and E410) and in two regions of potato virus Y (PVY) genome, corresponding to the cytoplasmic inclusion (CI) protein and the nuclear inclusion protein a-protease (NIa-Pro), respectively. A new determinant of TVN was discovered in the MK isolate of PVY which, although carried the HC-Pro determinants associated to TVN, did not induce TVN. The HC-Pro open reading frame (ORF) of the necrotic infectious clone PVY N605 was replaced with that of the non-necrotic MK isolate, which differed only by one amino acid at position 392 (T392 instead of I392). The cDNA clone N605_MKHCPro inoculated in tobacco induced only weak mosaics at the systemic level, demostrating that the amino acid at position 392 is a new determinant for TVN. No significant difference in accumulation in tobacco was observed between N605 and N605_MKHCPro. Since phylogenetic analyses showed that the loss of necrosis in tobacco has occurred several times independently during PVY evolution, these repeated evolutions strongly suggest that tobacco necrosis is a costly trait in PVY. [ABSTRACT FROM AUTHOR]

Global environmental issues shift crop production to the new conditions. This increases all kinds of biotic and abiotic stresses, beside others also plant diseases. Such changes are also in Kazakhstan where potato production is dramatically increasing, and crop is growing in regions with continental climate. Problems with potato virus type Y (PVY) need cultivars with better resistance. Introduction of silencing small interfering RNA (siRNA) is new technology. In vitro experiment was done on potato (Solanium tuberosum L.) local cultivar Izolda. Results show significant effect of siRNA in decreasing mortality and occurrence of PVY symptoms and allow expansion of potato cultivation to continental climate conditions, where are faced with new virus problems. [ABSTRACT FROM AUTHOR]

Transcription factors belonging to the family of ethylene response factors (ERFs) in plants function in disease resistance to pathogens. One of the tobacco ERF genes, NtERF5, inhibits the accumulation of tobacco mosaic virus (genus Tobamovirus) when overexpressed in tobacco carrying the resistance gene N. Here, we report that NtERF5 can function as a transcriptional activator through binding of the GCC-box in planta. We then determined whether overexpression of NtERF5 in tobacco lacking the N gene (nn tobacco) inhibited infection by potato virus X (PVX: genus Potexvirus). Transient overexpression of NtERF5 inhibited the accumulation of PVX without affecting virus spread and increased the transcript levels of NtPRB-1b and NtPR6, which are jasmonic acid/ethylene-signaling marker genes encoding pathogenesis-related (PR) proteins. Stable overexpression of NtERF5 in nn tobacco also resulted in decreased PVX accumulation and the induction of the expression of NtPRB-1b and NtPR6. Our results revealed that overexpression of NtERF5 limited successful infection and accumulation of PVX, suggesting the role of NtERF5 as a positive regulator of basal defense against virus infection. [ABSTRACT FROM AUTHOR]

In order to explore new drug molecules with higher antiviral activity against plant viruses, 12 fluorinated isoquinolinedione derivatives were synthesized by using cheaper raw materials and milder reaction conditions, and the anti-Potato virus Y (PVY) activity of the synthesized target compounds was determined by using the half-leaf necrosis method. The results showed that the fluorinated isoquinolinedione derivatives had good inhibitory activity against potato virus Y (PVY). Among them, the compound 3e showed good effects in the therapeutic activity (43.5%), protective activity (47.1%) and inactivate activity (51.9%), which was comparable to the positive control agricultural antiviral drug ribavirin. It was expected that the compounds with higher antiviral activity could be obtained by some structural modification on the basis of its structure. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the response of the grapevine variety 'Tribidrag' to virus infection over two vegetation seasons. Virus-free plants were greenhouse cultivated and green grafted with five different virus inocula composed of grapevine leafroll-associated virus 3 (GLRaV-3) singly or in coinfection with other most economically important grapevine viruses. Changes in nutrient status and photosynthesis-related parameters, along with symptom development, were measured. Using the quantitative PCR method, the relative concentration of five selected Vitis genes was determined. Cluster analysis and ANOVA revealed the reduction in phosphorus concentration (P) and photosynthesis-related parameters in infected plants in both seasons, even in the absence of symptom expression, indicating P and assimilation rate (Photo (A)) as stable markers of virus infection. Plants infected with inoculum Y composed of five different viruses provoked major significant changes in the first season while, in the second, fewer changes were measured. The sucrose synthase 3 gene was upregulated in infected plants confirming disturbed sugar metabolism related to virus-induced stress. This study showed that virus-induced changes in 'Tribidrag' plants even in the absence of symptoms are dependent on plant age, as well as on the composition of virus inocula. [ABSTRACT FROM AUTHOR]

The plant microbes are an integral part of the host and play fundamental roles in plant growth and health. There is evidence indicating that plants have the ability to attract beneficial microorganisms through their roots in order to defend against pathogens. However, the mechanisms of plant microbial community assembly from below- to aboveground compartments under pathogen infection remain unclear. In this study, we investigated the bacterial and fungal communities in bulk soil, rhizosphere soil, root, stem, and leaf of both healthy and infected (Potato virus Y disease, PVY) plants. The results indicated that bacterial and fungal communities showed different recruitment strategies in plant organs. The number and abundance of shared bacterial ASVs between bulk and rhizosphere soils decreased with ascending migration from below- to aboveground compartments, while the number and abundance of fungal ASVs showed no obvious changes. Field type, plant compartments, and PVY infection all affected the diversity and structures of microbial community, with stronger effects observed in the bacterial community than the fungal community. Furthermore, PVY infection, rhizosphere soil pH, and water content (WC) contributed more to the assembly of the bacterial community than the fungal community. The analysis of microbial networks revealed that the bacterial communities were more sensitive to PVY infection than the fungal communities, as evidenced by the lower network stability of the bacterial community, which was characterized by a higher proportion of positive edges. PVY infection further increased the bacterial network stability and decreased the fungal network stability. These findings advance our understanding of how microbes respond to pathogen infections and provide a rationale and theoretical basis for biocontrol technology in promoting sustainable agriculture. Key points: • Different recruitment strategies between plant bacterial and fungal communities. • Bacterial community was more sensitive to PVY infection than fungal community. • pH and WC drove the microbial community assembly under PVY infection. [ABSTRACT FROM AUTHOR]

Introduction: Potato (Solanum tuberosum L.), the fourth most important food crop in the world, is affected by several viral pathogens with potato virus Y (PVY) having the greatest economic impact. At least nine biologically distinct variants of PVY are known to infect potato. These include the relatively new recombinant types named PVY-NTN and PVYN-Wi, which induce tuber necrosis in susceptible cultivars. To date, the molecular plant-virus interactions underlying this pathogenicity have not been fully characterized. We hypothesized that this necrotic behavior is supported by transcriptional and functional signatures that are unique to PVY-NTN and PVYN-Wi. Methods: To test this hypothesis, transcriptional responses of cv. Russet Burbank, a PVY susceptible cultivar, to three PVY strains PVY-O, PVY-NTN, and PVYN-Wi were studied using mRNA-Seq. A haploid-resolved genome assembly for tetraploid potato was used for bioinformatics analysis. Results: The study revealed 36 GO terms and nine KEGG 24 pathways that overlapped across the three PVY strains, making them generic features of PVY susceptibility in potato. Ten GO terms and three KEGG pathways enriched for PVY-NTN and PVYN-Wi only, which made them candidate functional signatures associated with PVY-induced tuber necrosis in potato. In addition, five other pathways were enriched for PVYNTN or PVYN-Wi. One carbon pool by folate was enriched exclusively in response to PVY-NTN infection; PVYN-Wi infection specifically impacted cutin, suberine and wax biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and monoterpenoid biosynthesis. Discussion: Results suggest that PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVY-NTN. Our study provides a basis for understanding the mechanism underlying the development of PVYinduced tuber necrosis in potato. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) is one of the most dangerous agricultural pathogens that causes substantial harm to vegetative propagated crops, such as potatoes (Solanum tuberosum L.). A necessary condition for PVY infection is an interaction between the plant cap-binding translation initiation factors eIF4E and a viral protein VPg, which mimics the cap-structure. In this study, we identified the point mutations in potato eIF4E1 and eIF4E2 that disrupt VPg binding while preserving the functional activity. For the structural interpretation of the obtained results, molecular models of all the studied forms of eIF4E1 and eIF4E2 were constructed and analyzed via molecular dynamics. The results of molecular dynamics simulations corresponds to the biochemical results and suggests that the β1β2 loop plays a key role in the stabilization of both eIF4E–cap and eIF4E–VPg complexes. • S. tuberosum eIF4E1 and eIF4E2 are susceptible factors for the potato virus Y. • Conformation of eIF4E β1β2 loop defines an interaction with viral protein VPg. • Mutations that disrupt 4E-VPg binding but preserve factor functionality were found. [ABSTRACT FROM AUTHOR]

Potato virus Y is the most important potato virus worldwide, affecting tuber yield and quality. The resistance gene Rychc, derived from the potato wild relative Solanum chacoense, provides broad spectrum and durable resistance to the virus and has been used to develop resistant cultivars. Several DNA markers have been developed and have contributed to the efficient selection of resistant individuals. In this study, we developed Kompetitive Allele Specific PCR markers for Rychc using whole-genome resequencing data for a diverse set of 25 PVY susceptible cultivars and a Rychc-positive clone. Marker Ry_4099 targets two variants in the 3ʹ-UTR and was able to discriminate all five allele dosages in a tetraploid test population. Marker Ry_3331 targets two variants in Exon 4 and, although it only provides presence/absence information, it discriminates between the two known resistant alleles of Rychc. These markers will greatly contribute to efficient development of resistant cultivars. [ABSTRACT FROM AUTHOR]

Three potato cultivars, Payette Russet, Dark Red Norland, and Chieftain were challenged with four strains of potato virus Y (PVY), PVYO, PVYEu−N, PVYN−Wi, and PVYNTN. Cultivars Dark Red Norland and Chieftain exhibited strain-specific, hypersensitive resistance to PVYO and PVYNTN strains.. These same two cultivars, Dark Red Norland and Chieftain, appeared to have an additional resistance source in their genomes providing partial resistance against PVYN−Wi but were found fully susceptible to the non-recombinant PVYEu−N strain. Payette Russet was found immune to the same four strains of PVY; PVYO, PVYEu−N, PVYN−Wi, and PVYNTN, and was additionally challenged with the total of 18 isolates of PVY representing 12 genetic variants of the virus from potato and non-potato solanaceous hosts. None of the 18 isolates of the virus was found able to replicate in the inoculated or upper non-inoculated leaves of Payette Russet, confirming the broad specificity of the Rysto gene present in the Payette Russet genome. [ABSTRACT FROM AUTHOR]

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Introduction: Potatoes (Solanum tuberosum L.) can be infected by various viruses, but out of all of viruses, the potato virus Y (PVY) is the most detrimental. Research shows that the potato cultivar YouJin is especially vulnerable to PVY and displays severe symptoms, including leaf vein chlorosis, curled leaf margins, large necrotic spots on the leaf blades, and the growth of small new leaves. Methods: PVY infection in potato cultivar YouJin was confirmed through symptom observation, RT-PCR, and Western blot analysis. Transcriptome sequencing was used to analyze the genes associated with PVY pathogenesis in this cultivar. Result: Transcriptome analysis of differential genes was conducted in this study to examine the pathogenesis of PVY on YouJin. The results showed that 1,949 genes were differentially regulated, including 853 upregulated genes and 1,096 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that carbohydrate synthesis and metabolism pathways were suppressed, and electron transferase and hydrolase activities were reduced. Moreover, there were increased expression levels of protein kinase genes. By focusing on plant–pathogen interaction pathways, six core genes all upregulating the WARK family of transcription factors were obtained. Additionally, a constructed PPI network revealed the identification of key modular differential genes, such as downregulated photosynthesis-related protein genes and upregulated AP2/ ERF-ERF transcription factors. Functional network enrichment analysis revealed that PVY infection limited RNA metabolism, glutathionylation, and peroxiredoxin activity while triggering the expression of associated defense genes in YouJin. After analyzing the above, 26 DEGs were screened and 12 DEGs were confirmed via RT-qPCR. Conclusion: These results establish a hypothetical framework for clarifying the pathogenesis of PVY in the YouJin variety of potatoes, which will help design the disease resistance of YouJin. [ABSTRACT FROM AUTHOR]

Plant health statesmay influence the distribution of rhizospheremicroorganisms, which regulate plant growth and development. In this study, the response of rhizosphere bacteria and fungi of healthy and diseased plants compared to bulk microbes was analyzed using high-throughput sequencing. Plant adaptation strategies of plants under potato virus Y (PVY) infection have been studied from a microbial perspective. The diversity and community structure of bacteria and fungi varied between bulk and rhizosphere soils, but not between healthy and diseased rhizosphere soils. A LEfSe analysis revealed the significant differences between different treatments on bacterial and fungal community compositions and identified Roseiflexaceae, Sphingomonas, and Sphingobium as the bacterial biomarkers of bulk (BCK), healthy rhizosphere (BHS), and diseased rhizosphere (BIS) soils, respectively; Rhodotorula and Ascomycota_unidentified_1_1 were identified as the fungal biomarkers of bulk (FCK) and healthy rhizosphere (FHS) soils. Bacterial networks were found to be more complex and compact than fungal networks and revealed the roles of biomarkers as network keystone taxa. PVY infection further increased the connectedness among microbial taxa to improve rhizosphere microbial community stability and resistance to environmental stress. Additionally, water content (WC) played an apparent influence on bacterial community structure and diversity, and pH showed significant effects on fungal community diversity. WC and pH greatly affected the biomarkers of bacterial rhizosphere communities, whereas the biomarkers of bulk bacterial communities were significantly affected by soil nutrients, especially for Sphingobium. Overall, the rhizosphere microbial community enrichment processes were different between healthy and diseased plants by changing the community compositions and identifying different biomarkers. These findings provide insight into the assemblage of rhizosphere microbial communities and soil physicochemical properties, which contributes to a deeper understanding of the establishment of an artificial core root microbiota to facilitate plant growth and bolstering resistance mechanisms. This knowledge contributes to a deeper understanding of the establishment of an artificial core root microbiota, thereby facilitating plant growth and bolstering resistance mechanisms. [ABSTRACT FROM AUTHOR]

As the fourth most prevalent food crop, potato is very important in the global economy, but it is affected by numerous pests, and by many bacterial, viral and fungal diseases. Among these diseases, potato virus Y (PVY), which is transmitted from plant to plant by aphids, causes significant yield losses, but as far as we know, the economic impact of PVY in Europe has not been quantified. Our economic study covers a period of 13 years between 2004 and 2017 and is based on an analysis of statistical, economic and agronomic data, obtained from various stakeholders in the potato sector in Switzerland and the European Union, as well as from field experiments. In Switzerland, the economic loss due to PVY for seed and ware production was estimated at about 2000 and 200 CHF/ha, respectively. For the European Union, the annual losses were estimated at 187 M EUR, respectively 96 and 91 M EUR for seed and ware. These losses were due mainly to the cost of chemical treatments applied in seed potato production and the yield drop in ware potato production. However, based on literature, these significant losses are lower than those caused by potato late blight (Phytophthora infestans), which is considered to be the most economically damaging potato disease in Europe. [ABSTRACT FROM AUTHOR]

A series of novel thiazine derivatives featuring axial chirality in both (R) and (S) configurations were successfully synthesized by N‐heterocyclic carbene (NHC)‐catalyzed enantioselective [3 + 3] annulations, and their potential as anti‐plant virus agents against potato virus Y (PVY) was evaluated. Biological activity results demonstrated that most of these chiral thiazine derivatives exhibited significant activities against PVY. Notably, compound (S)‐3g displayed a remarkable 58% inactivation effect against PVY at a concentration of 500 μg/mL, slightly surpassing the effectiveness of Ningnanmycin (NNM) at 57%. Additionally, (S)‐3g exhibited curative activity of 57%, which is superior to NNM (53%). Molecular docking studies revealed preliminary insights into the distinct biological properties of the two different enantiomers, (R) or (S)‐3g against PVY, wherein single enantiomer (S)‐3g formed a more stable interaction with PVY‐CP, as indicated by its lower binding free energy (−41.18 kcal/mol) compared to (R)‐3g (−36.9 kcal/mol). The findings in this study with a new class of axially chiral thiazine derivatives shall inspire further development of chiral heterocycles as potential drug candidates for the protection of plant virus infections. [ABSTRACT FROM AUTHOR]

Tobacco (Nicotiana tabacum) is one of the major cash crops in China. Potato virus Y (PVY), a representative member of the genus Potyvirus, greatly reduces the quality and yield of tobacco leaves by inducing veinal necrosis. Mild strain-mediated cross-protection is an attractive method of controlling diseases caused by PVY. Currently, there is a lack of effective and stable attenuated PVY mutants. Potyviral helper component-protease (HC-Pro) is a likely target for the development of mild strains. Our previous studies showed that the residues lysine at positions 124 and 182 (K124 and K182) in HC-Pro were involved in PVY virulence, and the conserved KITC motif in HC-Pro was involved in aphid transmission. In this study, to improve the stability of PVY mild strains, K at position 50 (K50) in KITC motif, K124, and K182 were separately substituted with glutamic acid (E), leucine (L), and arginine (R), resulting in a triple-mutant PVY-HCELR. The mutant PVY-HCELR had attenuated virulence and did not induce leaf veinal necrosis symptoms in tobacco plants and could not be transmitted by Myzus persicae. Furthermore, PVY-HCELR mutant was genetically stable after six serial passages, and only caused mild mosaic symptoms in tobacco plants even at 90 days post inoculation. The tobacco plants cross-protected by PVY-HCELR mutant showed high resistance to the wild-type PVY. This study showed that PVY-HCELR mutant was a promising mild mutant for cross-protection to control PVY.

Viral disease is one of the major reasons leading to yield and quality reduction of potato production. To gain better knowledge about seed potato quality in China, the occurrences of six common viruses, including potato leafroll virus (PLRV) and potato viruses A (PVA), M (PVM), S (PVS), X (PVX) and Y (PVY), were investigated in two of China's four potato production zones (specifically, Zone I and Zone IV) from 2013 to 2016. A total of 1231 random tuber samples (Zone I, n = 571; Zone IV, n = 660) and 532 symptomatic leaf samples (Zone I, n = 375; Zone IV, n = 157) were collected in seed potato and commercial potato fields and tested for the viruses by reverse transcription (RT)-PCR (tuber samples) and/or enzyme-linked immunosorbent assay (ELISA; leaf samples). The results showed that virus-free tubers accounted for 79.7% and 52.0% in seed tuber samples from zones I and IV, respectively. All of the six viruses analysed were present in both zones I and IV, but occurred at different frequencies, with PVY and PVS being the predominant viruses in zones I and IV, respectively. Moreover, 44.0% and 39.8% of the virus-positive samples in zones I and IV, respectively, were found to be infected with more than one virus. Strain typing of PVS and PVY demonstrated the existence of similar strains of PVY (i.e. PVYO, PVYNTNb, PVYN:O, PVYN-Wi, PVY – (SYR-I and -II) and of PVS (i.e. PVSO and PVSA) in both zones. For PVY, recombinant strains were predominant, with SYR-II (27.7%) being the most abundant strain in Zone I and SYR-I (53.3%) being the predominant strain in Zone IV. PVSO was the predominant strain in Zone I whereas PVSA was the dominant strain in Zone IV. This study revealed not only the high incidence of viruses in both seed and commercial potatoes in China, but also the differential occurrence and strain composition of the viruses between two major production zones in China for the first time. In addition, the study suggests the need for different management strategies for different production zones to enhance the quality of seed potatoes in China. [ABSTRACT FROM AUTHOR]

The Root Zone Water Quality Model (RZWQM) is a one-dimensional process-based model used for simulating major physical, chemical, and biological processes in agricultural systems. To date, the model has not been applied to potato production systems for simulating nitrate leaching. In this study, 35 datasets collected between 2009 and 2016 at a field under a three-year potato (potato–barley–red clover) rotation in Prince Edward Island (PEI), Canada, have been employed for calibrating and validating the water, nitrogen (N) cycling, and plant growth routines of RZWQM and for subsequently estimating nitrate leaching. The model fitness, evaluated using univariate and bivariate indicators, was rated as high for most of the parameters tested. As a result of the combined influence of higher infiltration and reduced plant uptake, the model showed that the highest leaching at the rotation level occurred between September and December. A secondary leaching period occurred in spring, when residual soil nitrate was mobilized by increased percolation due to snowmelt. Most of the nitrate leaching occurred during the potato year (89.9 kg NO3–N ha−1 y−1), while leaching for barley and red clover years had comparable values (28.6 and 29.7 kg NO3–N ha−1 y−1, respectively). The low N use efficiency of the entire rotation (i.e., 30.2%), combined with the high NO3–N concentration in leachate (i.e., 34.9 mg NO3–N L−1 for potato and 16.3 mg NO3–N L−1 for the complete rotation), suggest that significant efforts are required for adapting management practices to ensure sustainability of potato production systems. [ABSTRACT FROM AUTHOR]

Potato virus Y (PVY) disease is a global problem that causes significant damage to crop quality and yield. As traditional chemical control methods are ineffective against PVY, it is crucial to explore new control strategies. MicroRNAs (miRNAs) play a crucial role in plant and animal defense responses to biotic and abiotic stresses. These endogenous miRNAs act as a link between antiviral gene pathways and host immunity. Several miRNAs target plant immune genes and are involved in the virus infection process. In this study, we conducted small RNA sequencing and transcriptome sequencing on healthy and PVY-infected N. benthamiana tissues (roots, stems, and leaves). Through bioinformatics analysis, we predicted potential targets of differentially expressed miRNAs using the N. benthamiana reference genome and the PVY genome. We then compared the identified differentially expressed mRNAs with the predicted target genes to uncover the complex relationships between miRNAs and their targets. This study successfully constructed a miRNA-mRNA network through the joint analysis of Small RNA sequencing and transcriptome sequencing, which unveiled potential miRNA targets and identified potential binding sites of miRNAs on the PVY genome. This miRNA-mRNA regulatory network suggests the involvement of miRNAs in the virus infection process. [ABSTRACT FROM AUTHOR]

The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context. Capsid proteins (CPs) of various icosahedral and rod-shaped viruses exhibit structural diversity and tunability as well as application in smart hybrid nanoparticles, however, the potential of CPs of filamentous plant viruses remains underexplored. Here, the authors exploit the structure-based design of CP from potato virus Y to tune the shape, size, RNA encapsidation ability, symmetry, stability, and surface functionalization of nanoparticles. [ABSTRACT FROM AUTHOR]

Background: Viral diseases continue to pose a major threat to the world's commercial crops. The in-depth exploration and efficient utilization of resistance proteins have become crucial strategies for their control. However, current delivery methods for introducing foreign DNA suffer from host range limitations, low transformation efficiencies, tissue damage, or unavoidable DNA integration into the host genome. The nanocarriers provides a convenient channel for the DNA delivery and functional utilization of disease-resistant proteins. Results: In this research, we identified a cysteine-rich venom protein (NbCRVP) in Nicotiana benthamiana for the first time. Virus-induced gene silencing and transient overexpression clarified that NbCRVP could inhibit the infection of tobacco mosaic virus, potato virus Y, and cucumber mosaic virus, making it a broad-spectrum antiviral protein. Yeast two-hybrid assay, co-immunoprecipitation, and bimolecular fluorescence complementation revealed that calcium-dependent lipid-binding (CaLB domain) family protein (NbCalB) interacted with NbCRVP to assist NbCRVP playing a stronger antiviral effect. Here, we demonstrated for the first time the efficient co-delivery of DNA expressing NbCRVP and NbCalB into plants using poly(amidoamine) (PAMAM) nanocarriers, achieving stronger broad-spectrum antiviral effects. Conclusions: Our work presents a tool for species-independent transfer of two interacting protein DNA into plant cells in a specific ratio for enhanced antiviral effect without transgenic integration, which further demonstrated new strategies for nanocarrier-mediated DNA delivery of disease-resistant proteins. [ABSTRACT FROM AUTHOR]

Plant viruses can modulate insect vector behaviour directly and/or indirectly by altering plant biochemistry. In many instances, such behavioural alterations increase the frequency of encounters between host and vector, leading to enhanced virus dispersal in ecosystems. In the current study using Cucumber mosaic virus (CMV), Capsicum annuum L. (Solanaceae), and Myzus persicae (Sulzer) (Hemiptera: Aphididae) as a pathosystem, we evaluated the direct and indirect effects of CMV on M. persicae biology and behavioural responses. Data showed that CMV indirectly modulates the aphid vector by providing fitness benefits to aphids, leading to enhanced aphid reproduction on CMV‐infected pepper plants in comparison with non‐infected C. annuum plants. Furthermore, CMV can also alter aphid behaviour directly by modulating the behavioural response of viruliferous aphids towards non‐infected plants. We demonstrate that CMV directly and indirectly modulates the insect vector thereby enhancing its transmission in agroecosystems. [ABSTRACT FROM AUTHOR]

Coat proteins (CP) of the potato virus A virions (PVA) contain partially disordered N-terminal domains, which are necessary for performing vital functions of the virus. Comparative analysis of the structures of coat proteins (CPs) in the intact PVA virions and in the virus particles lacking N-terminal 32 amino acids (PVAΔ32) was carried out in this work based on the tritium planigraphy data. Using atomic-resolution structure of the potato virus Y potyvirus (PVY) protein, which is a homolog of the CP PVA, the available CP surfaces in the PVY virion were calculated and the areas of intersubunit/interhelix contacts were determined. For this purpose, the approach of Lee and Richards [Lee, B., and Richards, F. M. (1971) J. Mol. Biol., 55, 379-400] was used. Comparison of incorporation profiles of the tritium label in the intact and trypsin-degraded PVA∆32 revealed position of the ΔN-peptide shielding the surface domain (a.a. 66-73, 141-146) and the interhelix zone (a.a. 161-175) of the PVA CP. Presence of the channels/cavities was found in the virion, which turned out to be partially permeable to tritium atoms. Upon removal of the ∆N-peptide, decrease in the label incorporation within the virion (a.a. 184-200) was also observed, indicating possible structural transition leading to the virion compactization. Based on the obtained data, we can conclude that part of the surface ∆N-peptide is inserted between the coils of the virion helix thus increasing the helix pitch and providing greater flexibility of the virion, which is important for intercellular transport of the viruses in the plants. [ABSTRACT FROM AUTHOR]

The paper reports the study which was carried out to investigate the genetic polymorphism of potato virus Y isolates using new marker sequences. The work was performed in 2022–2023. PVY isolates collected in 2017 from domestic and foreign varieties grown in different regions of the Russian Federation and preselected for serotype were used for analysis. Three loci were selected as potential markers with high phylogenetic information content, namely, the coat protein gene (Cp), the 5'-untranslated region of NTR, and the VPg protein gene, which covalently binds to the 5'-end of RNA and acts as a transcription regulator. Highest amplification efficiency (100% of the cDNA samples tested) was achieved using the NTR fragment. It was also the most phylogenetically informative: a comparative analysis of the studied sequences showed the presence of 23.8 and 15% variable and phylogenetically informative positions, respectively. The phylogenetic tree constructed on the basis of the comparative analysis of the NTR marker sequences included several clusters supported by high bootstrap values. The clusters encompassed the isolates from the following subgroups: PVYNTN—Red Scarlett (III), Red Scarlett (5-4), and Dunya (7-12); PVYN:O—Pomdor, Zagadka, and Nida; PVYO/C—Picasso, Favorit (III), CH991 131 (8-2), Floris (7-14), and Romano (5-3), and PVYWilga—Red Scarlett (6-10) and Kenza, as well as the type strains belonging to these subgroups, the marker sequences of which being deposited in the NCBI database. An isolate from the potato variety Zhukovsky rannii (5-2) showed an intermediate position between the necrotic and ordinal clusters, forming a separate branch and not grouping with any of the type strains on the phylogenetic tree based on the marker nucleotide sequences of the NTR locus. Sequencing analysis generally confirmed the initial serological identification of the tested samples demonstrating the predominance of the necrotic and recombinant groups of strains. [ABSTRACT FROM AUTHOR]