Major tomato viruses in the Mediterranean basin

Complete genome characterization of chilli veinal mottle virus associated with mosaic and mottling disease of tomato and development of LAMP assay for quick detection

Chilli veinal mottle virus (ChiVMV) is a potyvirus known to cause havoc in many solanaceous crops. Samples from tomato plants exhibiting typical mosaic and mottling symptoms in two locations from farmers' fields were collected and tested using DAC ELISA for the presence of ChiVMV and other viruses known to infect tomato. ChiVMV Gauribidanur isolate from infected tomato was mechanically inoculated to Datura metel, Nicotiana tabacum, Nicotiana benthamiana, Nicotiana glutinosa, chilli, and tomato plants which exhibited systemic mosaic and mottling symptoms 10 days post-inoculation. This results were further confirmed by RT-PCR and DAC ELISA using CP gene-specific primers and ChiVMV antisera, respectively. Transmission electron microscopy revealed the presence of long filamentous particles (800 × 11 nm) resembling viruses in the Potyviridae family. The complete genome of ChiVMV comprised 9716 nucleotides except for poly A tail, with a predicted open reading frame spanning 9270 nucleotides encoding polyproteins of 3089 amino acids. Comparative analysis revealed that ChiVMV-tomato isolates reported across the world shared maximum nucleotide identity (93-96.7%) with chilli isolates from India and Pakistan. These results were well supported by sequence demarcation analysis. Further, the Neibhor-Net network analysis of the complete genome of ChiVMV-tomato, along with other host isolates, formed a reticular network phylogenetic tree suggesting recombination events. Subsequently, RDP5 detected intra-specific recombination breakpoints at the positions 1656-5666 nucleotides with major parent ChiVMV (MN508960) Uravakonda and minor parent ChiVMV (MN508956) with a significant average p value of 1.905 × 10-22. The LAMP assay using ChiVMV-specific primers resulted in ladder-like amplified products on electrophoresed gel and a distinct red colour pattern with hydroxy naphthalene blue, indicating a positive reaction for the presence of ChiVMV in infected tomato samples. To validate LAMP-designed primers, RNA extracted from ChiVMV-infected tomato, chilli, datura, and tobacco samples were subjected to LAMP assay and it accurately detected the presence of ChiVMV in infected plant samples. Overall, this study provides holistic information of ChiVMV infecting tomato, spanning diagnosis, transmission, genetic characterization, and detection of recombination events, which collectively contribute to effective disease management, crop protection, and informed decision-making in agricultural practices.

Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection

Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.

Nanopore Technology Applied to Targeted Detection of Tomato Brown Rugose Fruit Virus Allows Sequencing of Related Viruses and the Diagnosis of Mixed Infections

Tomato (Solanum lycopersicum) plants from a commercial glasshouse were identified with symptoms compatible with a tomato brown rugose fruit virus (ToBRFV) infection. Reverse transcription-PCR and quantitative PCR confirmed the presence of ToBRFV. Subsequently, the same RNA sample and a second from tomato plants infected with a similar tobamovirus, tomato mottle mosaic virus (ToMMV), were extracted and processed for high-throughput sequencing with the Oxford Nanopore Technology (ONT). For the targeted detection of ToBRFV, the two libraries were synthesized by using six ToBRFV sequence-specific primers in the reverse transcription step. This innovative target enrichment technology enabled deep coverage sequencing of ToBRFV, with 30% of the total reads mapping to the target virus genome and 57% mapping to the host genome. The same set of primers applied to the ToMMV library generated 5% of the total reads mapping to the latter virus, indicating that sequencing of similar, non-target viral sequences was also allowed. Further, the complete genome of pepino mosaic virus (PepMV) was also sequenced from the ToBRFV library, thus suggesting that, even using multiple sequence-specific primers, a low rate of off-target sequencing can usefully provide additional information on unexpected viral species coinfecting the same samples in an individual assay. These results demonstrate that targeted nanopore sequencing can specifically identify viral agents and has sufficient sensitivity towards non-target organisms to provide evidence of mixed virus infections.

Overexpression of Pyrus sinkiangensis HAT5 enhances drought and salt tolerance, and low-temperature sensitivity in transgenic tomato

The homeodomain-leucine zipper protein HAT belongs to the homeodomain leucine zipper subfamily (HD-Zip) and is important for regulating plant growth and development and stress tolerance. To investigate the role of HAT5 in tolerance to drought, salt, and low temperature stress, we selected a HAT gene from Pyrus sinkiangensis Yü (Pyrus sinkiangensis T.T. Yu). The sequences were analyzed using ioinformatics, and the overexpressed tomato lines were obtained using molecular biology techniques. The phenotypes, physiological, and biochemical indexes of the wild-type and transgenic tomato lines were observed under different stress conditions. We found that the gene had the highest homology with PbrHAT5. Under drought and NaCl stress, osmotic regulatory substances (especially proline) were significantly accumulated, and antioxidant enzyme activities were enhanced. The malondialdehyde level and relative electrical conductivity of transgenic tomatoes under low temperature (freezing) stress were significantly higher than those of wild-type tomatoes. The reactive oxygen species scavenging system was unbalanced. This study found that PsHAT5 improved the tolerance of tomatoes to drought and salt stress by regulating proline metabolism and oxidative stress ability, reducing the production of reactive oxygen species, and maintaining normal cell metabolism. In conclusion, the PsHAT5 transcription factor has great potential in crop resistance breeding, which lays a theoretical foundation for future excavation of effective resistance genes of the HD-Zip family and experimental field studies.

Tomato brown rugose fruit virus: An emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide

Tomato brown rugose fruit virus (ToBRFV) is an emerging and rapidly spreading RNA virus that infects tomato and pepper, with tomato as the primary host. The virus causes severe crop losses and threatens tomato production worldwide. ToBRFV was discovered in greenhouse tomato plants grown in Jordan in spring 2015 and its first outbreak was traced back to 2014 in Israel. To date, the virus has been reported in at least 35 countries across four continents in the world. ToBRFV is transmitted mainly via contaminated seeds and mechanical contact (such as through standard horticultural practices). Given the global nature of the seed production and distribution chain, and ToBRFV's seed transmissibility, the extent of its spread is probably more severe than has been disclosed. ToBRFV can break down genetic resistance to tobamoviruses conferred by R genes Tm-1, Tm-2, and Tm-2² in tomato and L¹ and L² alleles in pepper. Currently, no commercial ToBRFV-resistant tomato cultivars are available. Integrated pest management-based measures such as rotation, eradication of infected plants, disinfection of seeds, and chemical treatment of contaminated greenhouses have achieved very limited success. The generation and application of attenuated variants may be a fast and effective approach to protect greenhouse tomato against ToBRFV. Long-term sustainable control will rely on the development of novel genetic resistance and resistant cultivars, which represents the most effective and environment-friendly strategy for pathogen control.

TAXONOMY

Tomato brown rugose fruit virus belongs to the genus Tobamovirus, in the family Virgaviridae. The genus also includes several economically important viruses such as Tobacco mosaic virus and Tomato mosaic virus.

GENOME AND VIRION

The ToBRFV genome is a single-stranded, positive-sense RNA of approximately 6.4 kb, encoding four open reading frames. The viral genomic RNA is encapsidated into virions that are rod-shaped and about 300 nm long and 18 nm in diameter. Tobamovirus virions are considered extremely stable and can survive in plant debris or on seed surfaces for long periods of time.

DISEASE SYMPTOMS

Leaves, particularly young leaves, of tomato plants infected by ToBRFV exhibit mild to severe mosaic symptoms with dark green bulges, narrowness, and deformation. The peduncles and calyces often become necrotic and fail to produce fruit. Yellow blotches, brown or black spots, and rugose wrinkles appear on tomato fruits. In pepper plants, ToBRFV infection results in puckering and yellow mottling on leaves with stunted growth of young seedlings and small yellow to brown rugose dots and necrotic blotches on fruits.

Chemical Cues From Honeydew and Cuticular Extracts of Trialeurodes Vaporariorum Serve as Kairomones for The Parasitoid Encarsia Formosa

Kairomones are semiochemicals that are emitted by an organism and which mediate interspecific interaction that is of benefit to an organism of another species that receives these chemical substances. Parasitoids find and recognize their hosts through eavesdropping on the kairomones emitted from the by-products or the body of the host. Hemipteran insect pests feed on plant sap and excrete the digested plant materials as honeydew. Honeydew serves as a nutritional food source for parasitoids and a medium for micro-organisms whose activity induces the release of volatiles exploited by parasitoids for host location. The parasitoid Encarsia formosa preferentially parasitizes its host, the greenhouse whitefly, Trialeurodes vaporariorum, on tomato Solanum lycopersicum, but little is known about the chemicals that mediate these interactions. We investigated the olfactory responses of the parasitoid E. formosa to odours from honeydew and nymphs of T. vaporariorum in a Y-tube olfactometer. Arrestment behaviour of the parasitoid to honeydew and nymph extracts, as well as to synthetic hydrocarbons, was also observed in Petri-dish bioassays. We found that T. vaporariorum honeydew volatiles attracted the parasitoid E. formosa but odours from the whitefly nymphs did not. We also found that the parasitoid spent more time searching on areas treated with extracts of honeydew and nymphs than on untreated areas. Gas-chromatography-mass spectrometric analysis revealed that the honeydew volatiles contained compounds such as (Z)-3-hexenol, δ-3-carene, 3-octanone, α-phellandrene, methyl salicylate, β-ocimene, β-myrcene, and (E)-β-caryophyllene which are known to be attractive to E. formosa. The cuticular extracts of the nymphs predominantly contained alkanes, alkenes, and esters. Among the alkanes, synthetic nonacosane arrested the parasitoid. Our findings are discussed in relation to how the parasitoid E. formosa uses these chemicals to locate its host, T. vaporariorum.

Hybrid Feature-Based Disease Detection in Plant Leaf Using Convolutional Neural Network, Bayesian Optimized SVM, and Random Forest Classifier

Plant diseases are unfavourable factors that cause a significant decrease in the quality and quantity of crops. Experienced biologists or farmers often observe plants with the naked eye for disease, but this method is often imprecise and can take a long time. In this study, we use artificial intelligence and computer vision techniques to achieve the goal of designing and developing an intelligent classification mechanism for leaf diseases. This paper follows two methodologies and their simulation outcomes are compared for performance evaluation. In the first part, data augmentation is performed on the PlantVillage data set images (for apple, corn, potato, tomato, and rice plants), and their deep features are extracted using convolutional neural network (CNN). These features are classified by a Bayesian optimized support vector machine classifier and the results attained in terms of precision, sensitivity, f-score, and accuracy. The above-said methodologies will enable farmers all over the world to take early action to prevent their crops from becoming irreversibly damaged, thereby saving the world and themselves from a potential economic crisis. The second part of the methodology starts with the preprocessing of data set images, and their texture and color features are extracted by histogram of oriented gradient (HoG), GLCM, and color moments. Here, the three types of features, that is, color, texture, and deep features, are combined to form hybrid features. The binary particle swarm optimization is applied for the selection of these hybrid features followed by the classification with random forest classifier to get the simulation results. Binary particle swarm optimization plays a crucial role in hybrid feature selection; the purpose of this Algorithm is to obtain the suitable output with the least features. The comparative analysis of both techniques is presented with the use of the above-mentioned evaluation parameters.

Strawberry Fungal Leaf Scorch Disease Identification in Real-Time Strawberry Field Using Deep Learning Architectures

Plant health is the basis of agricultural development. Plant diseases are a major factor for crop losses in agriculture. Plant diseases are difficult to diagnose correctly, and the manual disease diagnosis process is time consuming. For this reason, it is highly desirable to automatically identify the diseases in strawberry plants to prevent loss of crop quality. Deep learning (DL) has recently gained popularity in image classification and identification due to its high accuracy and fast learning. In this research, deep learning models were used to identify the leaf scorch disease in strawberry plants. Four convolutional neural networks (SqueezeNet, EfficientNet-B3, VGG-16 and AlexNet) CNN models were trained and tested for the classification of healthy and leaf scorch disease infected plants. The performance accuracy of EfficientNet-B3 and VGG-16 was higher for the initial and severe stage of leaf scorch disease identification as compared to AlexNet and SqueezeNet. It was also observed that the severe disease (leaf scorch) stage was correctly classified more often than the initial stage of the disease. All the trained CNN models were integrated with a machine vision system for real-time image acquisition under two different lighting situations (natural and controlled) and identification of leaf scorch disease in strawberry plants. The field experiment results with controlled lightening arrangements, showed that the model EfficientNet-B3 achieved the highest classification accuracy, with 0.80 and 0.86 for initial and severe disease stages, respectively, in real-time. AlexNet achieved slightly lower validation accuracy (0.72, 0.79) in comparison with VGGNet and EfficientNet-B3. Experimental results stated that trained CNN models could be used in conjunction with variable rate agrochemical spraying systems, which will help farmers to reduce agrochemical use, crop input costs and environmental contamination.

Terpenes from herbivore-induced tomato plant volatiles attract Nesidiocoris tenuis (Hemiptera: Miridae), a predator of major tomato pests

BACKGROUND

Biological control plays a key role in reducing crop damage by Tuta absoluta (Meyrick) and Trialeurodes vaporariorum (Westwood), which cause huge yield losses in tomato (Solanum lycopersicum L.). The mirid predator Nesidiocoris tenuis (Reuter) preys heavily on these pests, with satisfying control levels in tomato greenhouses. Although N. tenuis is known to be attracted to volatiles of tomato plants infested by T. absoluta and whitefly, little is known about the specific attractive compounds and the effect of prey density on the predator response.

RESULTS

Y-tube olfactometer bioassays revealed that the attraction of N. tenuis to tomato volatiles was positively correlated with the density of T. absoluta infestation, unlike T. vaporariorum infestation. The predator was also attracted to volatiles of T. absoluta larval frass, but not to T. vaporariorum honeydew or T. absoluta sex pheromone. Among the herbivore-induced plant volatiles (HIPVs) that characterised the attractive plants infested with 20 T. absoluta larvae, olfactometer bioassays revealed that N. tenuis is attracted to the monoterpenes α-pinene, α-phellandrene, 3-carene, β-phellandrene and β-ocimene, whereas (E)-β-caryophyllene was found to repel the predator. In dose-response bioassays, the five-component blend of the attractants elicited a relatively low attraction in the predator, and removal of β-phellandrene from the blend enhanced the attraction of the predator to the resulting four-component blend, suggesting synergism among four monoterpenes.

CONCLUSION

These findings suggest that a four-component blend of α-pinene, α-phellandrene, 3-carene and β-ocimene could be used as a kairomone-based lure to recruit the predator for the biological control of T. absoluta and T. vaporariorum.

Characterization of the detrimental effects of type IV glandular trichomes on the aphid Macrosiphum euphorbiae in tomato

BACKGROUND

Glandular trichomes are essential in plants' defence against pests however, the mechanisms of action are not completely understood. While there is considerable evidence of feeding and movement impairment by trichomes, the effect on other traits is less clear. We combined laboratory and greenhouse experiments with molecular analysis to understand how glandular trichomes affect the behavior, population growth, and the expression of biomarkers involved in detoxification, primary metabolism, and developmental pathways of the aphid Macrosiphum euphorbiae. We used two isogenic tomato lines that differ in the presence of type IV glandular trichomes and production of acylsucroses; i.e.,Solanum lycopersicum cv. 'Moneymaker' and an introgressed line from Solanum pimpinellifolium (with trichomes type IV).

RESULTS

Type IV glandular trichomes affected host selection and aphid proliferation with aphids avoiding, and showing impaired multiplication on the genotype with trichomes. The exposure to type IV glandular trichomes resulted in the overexpression of detoxication markers (i.e., Hsp70, Hsp17, Hsp10); the repression of the energetic metabolism (GAPDH), and the activation of the ecdysone pathway; all these, underlying the key adaptations and metabolic trade-offs in aphids exposed to glandular trichomes.

CONCLUSION

Our results demonstrate the detrimental effect of glandular trichomes (type IV) on the aphid and put forward their mode of action. Given the prevalence of glandular trichomes in wild and cultivated Solanaceae; and of the investigated molecular biomarkers in insects in general, our results provide relevant mechanisms to understand the effect of trichomes not only on herbivorous insects but also on other trophic levels.

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.

Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops

We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus species were identified, with pepino mosaic virus being the most abundant one. The dsRNA input provided better coverage and read depth but missed one virus species compared with the total RNA input. By performing in silico analyses, we determined a minimum sequencing depth per sample of 0.2 and 1.5 million reads for dsRNA and rRNA-depleted total RNA inputs, respectively, to detect even the less abundant viruses. Primers and TaqMan probes targeting conserved regions in the viral genomes were designed and/or used for virus detection; all viruses were detected by qRT-PCR/RT-PCR in individual samples, with all except one sample showing mixed infections. Three virus species (Olive latent virus 1, Lettuce ring necrosis virus and Tomato fruit blotch virus) are herein reported for the first time in tomato crops in Spain.

The Role of Trialeurodes vaporariorum-Infested Tomato Plant Volatiles in the Attraction of Encarsia formosa (Hymenoptera: Aphelinidae)

Natural enemies locate their herbivorous host and prey through kairomones emitted by host plants and herbivores. These kairomones could be exploited to attract and retain natural enemies in crop fields for insect pest control. The parasitoid Encarsia formosa preferentially parasitises its whitefly host, Trialeurodes vaporariorum, a major pest of tomato Solanum lycopersicum, thus offering an effective way to improve whitefly control. However, little is known about the chemical interactions that occur in E. formosa-T. vaporariorum-S. lycopersicum tritrophic system. Using behavioural assays and chemical analyses, we investigated the kairomones mediating attraction of the parasitoid to host-infested tomato plants. In Y-tube olfactometer bioassays, unlike volatiles of healthy tomato plants, those of T. vaporariorum-infested tomato plants attracted E. formosa, and this response varied with host infestation density. Coupled gas chromatography/mass spectrometric analyses revealed that host infestation densities induced varying qualitative and quantitative differences in volatile compositions between healthy and T. vaporariorum adult-infested tomato plants. Bioassays using synthetic chemicals revealed the attractiveness of 3-carene, β-ocimene, β-myrcene and α-phellandrene to the parasitoid, and the blend of the four compounds elicited the greatest attraction. Our results suggest that these terpenes could be used as an attractant lure to recruit the parasitoid E. formosa for the control of whiteflies in tomato crop fields.

Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area

Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.

Comparison of Convolutional Neural Network Architectures for Classification of Tomato Plant Diseases

Tomato plants are highly affected by diverse diseases. A timely and accurate diagnosis plays an important role to prevent the quality of crops. Recently, deep learning (DL), specifically convolutional neural networks (CNNs), have achieved extraordinary results in many applications, including the classification of plant diseases. This work focused on fine-tuning based on the comparison of the state-of-the-art architectures: AlexNet, GoogleNet, Inception V3, Residual Network (ResNet) 18, and ResNet 50. An evaluation of the comparison was finally performed. The dataset used for the experiments is contained by nine different classes of tomato diseases and a healthy class from PlantVillage. The models were evaluated through a multiclass statistical analysis based on accuracy, precision, sensitivity, specificity, F-Score, area under the curve (AUC), and receiving operating characteristic (ROC) curve. The results present significant values obtained by the GoogleNet technique, with 99.72% of AUC and 99.12% of sensitivity. It is possible to conclude that this significantly success rate makes the GoogleNet model a useful tool for farmers in helping to identify and protect tomatoes from the diseases mentioned.

Identification and Expression Analysis of Genes Induced in Response to Tomato chlorosis virus Infection in Tomato

Tomato (Solanum lycopersicum) is one of the most widely grown and economically important vegetable crops in the world. Tomato chlorosis virus (ToCV) is one of the recently emerged viruses of tomato distributed worldwide. ToCV-tomato interaction was investigated at the molecular level for determining changes in the expression of tomato genes in response to ToCV infection in this study. A cDNA library enriched with genes induced in response to ToCV infection were constructed and 240 cDNAs were sequenced from this library. The macroarray analysis of 108 cDNAs revealed that the expression of 92 non-redundant tomato genes was induced by 1.5-fold or greater in response to ToCV infection. The majority of ToCV-induced genes identified in this study were associated with a variety of cellular functions including transcription, defense and defense signaling, metabolism, energy, transport facilitation, protein synthesis and fate and cellular biogenesis. Twenty ToCV-induced genes from different functional groups were selected and induction of 19 of these genes in response to ToCV infection was validated by RT-qPCR assay. Finally, the expression of 6 selected genes was analyzed in different stages of ToCV infection from 0 to 45 dpi. While the expression of three of these genes was only induced by ToCV infection, others were induced both by ToCV infection and wounding. The result showed that ToCV induced the basic defense response and activated the defense signaling in tomato plants at different stages of the infection. Functions of these defense related genes and their potential roles in disease development and resistance to ToCV are also discussed.

A New Distinct Clade for Iranian Tomato spotted wilt virus Isolates Based on the Polymerase, Nucleocapsid, and Non-structural Genes

Tomato spotted wilt virus (TSWV; Genus Orthotospovirus: Family Tospoviridae) is one of the most destructive viruses affecting a wide range of horticultural crops on a worldwide basis. In 2015 and 2016, 171 leaf and fruit samples from tomato (Solanum lycopersicum) plants with viral symptoms were collected from the fields in various regions of Iran. ELISA test revealed that the samples were infected by TSWV. The results of RT-PCR showed that the expected DNA fragments of about 819 bp in length were amplified using a pair of universal primer corresponding to the RNA polymerase gene and DNA fragments of ca 777 bp and 724 bp in length were amplified using specific primers that have been designed based on the nucleocapsid (N) and non-structural (NSs) genes, respectively. The amplified fragments were cloned into pTG19-T and sequenced. Sequence comparisons with those available in the GenBank showed that the sequences belong to TSWV. The high nucleotide identity and similarities of new sequences based on the L, N, and NSs genes showed that minor evolutionary differences exist amongst the isolates. The phylogenetic tree grouped all isolates six clades based on N and NSs genes. Phylogenetic analysis showed that the Iranian isolates were composed a new distinct clade based on a part of polymerase, N and NSs genes. To our knowledge, this is the first detailed study on molecular characterization and genetic diversity of TSWV isolates from tomato in Iran that could be known as new clade of TSWV isolates.

Characterization of Begomoviruses Sampled during Severe Epidemics in Tomato Cultivars Carrying the Ty-1 Gene

Tomato yellow leaf curl virus (TYLCV, genus Begomovirus, family Geminiviridae) is a major species that causes a tomato disease for which resistant tomato hybrids (mainly carriers of the Ty-1/Ty-3 gene) are being used widely. We have characterized begomoviruses severely affecting resistant tomato crops in Southeast Spain. Circular DNA was prepared from samples by rolling circle amplification, and sequenced by massive sequencing (2015) or cloning and Sanger sequencing (2016). Thus, 23 complete sequences were determined, all belonging to the TYLCV Israel strain (TYLCV-IL). Massive sequencing also revealed the absence of other geminiviral and beta-satellite sequences. A phylogenetic analysis showed that the Spanish isolates belonged to two groups, one related to early TYLCV-IL isolates in the area (Group 1), and another (Group 2) closely related to El Jadida (Morocco) isolates, suggesting a recent introduction. The most parsimonious evolutionary scenario suggested that the TYLCV isolates of Group 2 are back recombinant isolates derived from TYLCV-IS76, a recombinant virus currently predominating in Moroccan epidemics. Thus, an infectious Group 2 clone (TYLCV-Mu15) was constructed and used in in planta competition assays against TYLCV-IS76. TYLCV-Mu15 predominated in single infections, whereas TYLCV-IS76 did so in mixed infections, providing credibility to a scenario of co-occurrence of both types of isolates.

Prospects for engineering and improvement of cross-protective virus strains

Mild strain cross-protection is currently an important method for the production of high quality plant products; despite challenge from severe virus isolates the initial protecting strain precludes symptom development. The mechanism of cross-protection is not yet resolved as RNA silencing does not sufficiently explain the phenomenon. Six requirements have been put forward to ensure long-lasting protection. We propose two additional requirements for effective and durable mild strain cross-protection; mild strains based on knowledge of the mechanism and consideration of impacts to consumers. Future research on predicting phenotype from genotype and understanding virus-plant and virus-vector interactions will enable improvement of cross-protective strains. Shared international databases of whole ecosystem interactions across a wide range of virus patho- and symbiotic-systems will form the basis for making step-change advances towards our collective ability to engineer and improve mild strain cross-protection.

Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing

RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.

Grafting on a Non-Transgenic Tolerant Tomato Variety Confers Resistance to the Infection of a Sw5-Breaking Strain of Tomato spotted wilt virus via RNA Silencing

RNA silencing controls endogenous gene expression and drives defensive reactions against invasive nucleic acids like viruses. In plants, it has been demonstrated that RNA silencing can be transmitted through grafting between scions and silenced rootstocks to attenuate virus and viroid accumulation in the scions. This has been obtained mostly using transgenic plants, which may be a drawback in current agriculture. In the present study, we examined the dynamics of infection of a resistance-breaking strain of Tomato spotted wilt virus (RB-TSWV) through the graft between an old Apulian (southern Italy) tomato variety, denoted Sl-Ma, used as a rootstock and commercial tomato varieties used as scions. In tests with non-grafted plants, Sl-Ma showed resistance to the RB-TSWV infection as viral RNA accumulated at low levels and plants recovered from disease symptoms by 21 days post inoculation. The resistance trait was transmitted to the otherwise highly susceptible tomato genotypes grafted onto Sl-Ma. The results from the analysis of small RNAs hallmark genes involved in RNA silencing and virus-induced gene silencing suggest that RNA silencing is involved in the resistance showed by Sl-Ma against RB-TSWV and in scions grafted on this rootstock. The results from self-grafted susceptible tomato varieties suggest also that RNA silencing is enhanced by the graft itself. We can foresee interesting practical implications of the approach described in this paper.

Torradoviruses

Torradoviruses are an example of a group of recently discovered plant viruses. The first description of Tomato torrado virus, now the type member of the newly established genus Torradovirus within the family Secoviridae, was published in 2007 and was quickly followed by findings of other torradoviruses, initially all on tomato. Their characterization led to the development of tools that allowed recognition of still other torradoviruses, only very recently found on non-tomato crops, which indicates these viruses have a much wider host range and diversity than previously believed. This review describes the characteristics of this newly emerged group of plant viruses. It looks in detail at taxonomic relationships and specific characteristics in their genomes and encoded proteins. Furthermore, it discusses their epidemiology, including host range, semipersistent transmission by whitefly vectors, and impact on diverse cropping systems.

Evolution and emergence of plant viruses

Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.