Assessment of the diversity and dynamics of Plum pox virus and aphid populations in transgenic European plums under Mediterranean conditions

Agrobacterium-Mediated Transformation of Russian Commercial Plum cv. "Startovaya" (Prunus domestica L.) With Virus-Derived Hairpin RNA Construct Confers Durable Resistance to PPV Infection in Mature Plants

In modern horticulture Plum pox virus (PPV) imposes serious threats to commercial plantations of a wide range of fruit species belonging to genera Prunus. Given the lack of natural genetic resources, which display reliable resistance to PPV infection, there has been considerable interest in using genetic engineering methods for targeted genome modification of stone fruit trees to control Sharka disease caused by PPV. Among the many virus defense mechanisms, RNA interference is shown to be the most promising transgenic disease-control strategy in plant biotechnology. The present study describes the production of transgenic PPV resistant European plum "Startovaya" (P. domestica L.) through the Agrobacterium-mediated transformation of in vitro leaf explants. Due to organogenesis from leaves, the established protocol allows the genetic engineering of the plum genome without losing clonal fidelity of original cultivar. Seven independent transgenic plum lines containing the self-complementary fragments of PPV-CP gene sequence separated by a PDK intron were generated using hpt as a selective gene and uidA as a reporter gene. The transformation was verified through the histochemical staining for β-glucuronidase activity, PCR amplification of appropriate vector products from isolated genomic DNA and Southern blot analysis of hairpin PPV-CP gene fragments. To clarify the virus resistance, plum buds infected by PPV-M strain were grafted onto 1-year-old transgenic plants, which further were grown into mature trees in the greenhouse. As evaluated by RT-PCR, DAS-ELISA, Western blot, ImmunoStrip test, and visual observations, GM plum trees remained uninfected over 9 years. Infected branches that developed from grafted buds displayed obvious symptoms of Sharka disease over the years and maintained the high level of virus accumulation, whereby host transgenic trees had been constantly challenged with the pathogen. Since the virus was unable to spread to transgenic tissues, the stable expression of PPV-derived gene construct encoding intron-spliced hairpin RNAs provided a highly effective protection of plum trees against permanent viral infection. At the same time, this observation indicates the lack of the systemic spread of resistance from GM tissues to an infected plum graft even after years of joint growth.

Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome

For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of any part of the transgene to an existing gene pool, have been raised. Here, we report no evidence of any undesirable impacts of genetically modified (GM) grapevine rootstock on its biotic environment. Using state of the art metagenomics, we analysed two compartments in depth, the targeted Grapevine fanleaf virus (GFLV) populations and nontargeted root-associated microbiota. Our results reveal no statistically significant differences in the genetic diversity of bacteria that can be linked to the GM trait. In addition, no novel virus or bacteria recombinants of biosafety concern can be associated with transgenic grapevine rootstocks cultivated in commercial vineyard soil under greenhouse conditions for over 6 years.

Surveys of Viruliferous Alate Aphid of Plum pox virus in Prunus mume Orchards in Japan

Plum pox virus (PPV) is transmitted by infected buds and aphids. It is important to analyze the outbreak trends and viruliferous rate of aphids in areas where the occurrence of PPV is reported, so as to develop strategies for disease control. Between April 2011 and December 2012, yellow insect-trapping adhesive plates were placed for 2 days at a time each week in an area where PPV is occurring in Japan. Outbreak trends were analyzed based on the trapped alate aphid samples, and up to 50 of them were tested per week to identify species and determine the rate of viruliferous specimens. Although the number of aphids varied according to survey year, three peaks were noticeable in each year. Based on the sequence data for the mitochondrial cytochrome c oxidase I region, approximately 40 different species of aphid were trapped in both years. Of the five dominant species of aphids identified during the 2 years, Aphis spiraecola was trapped in large numbers. PPV-positive aphids were higher in fall onward, when the total number of trapped aphids decreased, than in spring and summer, when a larger number of aphids was caught. PPV transmission tests using the most abundant species revealed that A. spiraecola, A. craccivora, A. gossypii, and Rhopalosiphum maidis were transmitters, although A. spiraecola is likely of epidemiological significance.

The influence of virus infections on antioxidant levels in the genetically modified plum variety "Honeysweet" (Prunus domestica L.)

It is well-known that polyphenolic compounds are found abundantly in fruit, but various kinds of diseases  lower these levels. This work measures total polyphenolic content, antioxidant activity and the levels of specific important antioxidants in fruits of the genetically modified (GM) plum variety HoneySweet, trees  which were previously inoculated with a range of different virus infections.  These were the Plum Pox virus (PPV), Prune Dwarf virus (PDV) and Apple Chlorotic Leaf-Spot virus (ACLSV). Uninoculated trees were used as controls. Antioxidant activity was measured using four different photometric  methods – DPPH (2,2-diphenyl-1-picrylhydrazyl), DMPD (N-dimethyl-p-phenylenediamine), ABTS (2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) and FRAP (Ferric reducing antioxidant power). Total polyphenol content was measured using the Folin–Ciocalteau method. The profiles of 10 specific antioxidant constituents in the fruits of the GM plum variety HoneySweet were detected and analyzed, since these are of interest for their role in human diets and could play a role in the resistance of plants to viruses. Detection was made using HPLC with UV-VIS detection.  They were: gallic acid, p-coumaric acid, 4-aminobenzoic acid, chlorogenic acid, caffeic acid, ferulic acid, vanillin, rutin and quercetin. The compound with the highest concentration was chlorogenic acid (587 mg/100 g), and that with the lowest was p-coumaric acid (0.95 mg/100 g). Of the four methods of antioxidant activity used, in three the lowest levels of antioxidant activity were seen where the PPV virus was combined with ACLSV, and in three the highest levels were seen in the un-inoculated control without any infection. The highest values of total polyphenols were seen in the control (65.3 mg/100 g), followed by infection of PPV, then treatment PPV, PDV and ACLSV, then treatment PPV and PDV and finally the lowest levels were seen in treatment PPV and ACLSV (44.2 mg/100 g), which was also that with the lowest antioxidant activity.

Control of pome and stone fruit virus diseases

Many different systemic pathogens, including viruses, affect pome and stone fruits causing diseases with adverse effects in orchards worldwide. The significance of diseases caused by these pathogens on tree health and fruit shape and quality has resulted in the imposition of control measures both nationally and internationally. Control measures depend on the identification of diseases and their etiological agents. Diagnosis is the most important aspect of controlling fruit plant viruses. Early detection of viruses in fruit trees or in the propagative material is a prerequisite for their control and to guarantee a sustainable agriculture. Many quarantine programs are in place to reduce spread of viruses among countries during international exchange of germplasm. All these phytosanitary measures are overseen by governments based on agreements produced by international organizations. Also certification schemes applied to fruit trees allow the production of planting material of known variety and plant health status for local growers by controlling the propagation of pathogen-tested mother plants. They ensure to obtain propagative material not only free of "quarantine" organisms under the national legislation but also of important "nonquarantine" pathogens. The control of insect vectors plays an important role in the systemic diseases management, but it must be used together with other control measures as eradication of infected plants and use of certified propagation material. Apart from the control of the virus vector and the use of virus-free material, the development of virus-resistant cultivars appears to be the most effective approach to achieve control of plant viruses, especially for perennial crops that are more exposed to infection during their long life span. The use of resistant or tolerant cultivars and/or rootstocks could be potentially the most important aspect of virus disease management, especially in areas in which virus infections are endemic. The conventional breeding for virus-tolerant or resistant fruit tree cultivars using available germplasm is a long-term strategy, and the development and production of these cultivars may take decades, if successful. Genetic engineering allows the introduction of specific DNA sequences offering the opportunity to obtain existing fruit tree cultivars improved for the desired resistance trait. Unfortunately, genetic transformation of pome and stone fruits is still limited to few commercial genotypes. Research carried out and the new emerging biotechnological approaches to obtain fruit tree plants resistant or tolerant to viruses are discussed.

Plum pox virus and sharka: a model potyvirus and a major disease

TAXONOMIC RELATIONSHIPS

Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains.

GEOGRAPHICAL DISTRIBUTION

First discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents.

GENOMIC STRUCTURE

Typical of potyviruses, the PPV genome is a positive-sense single-stranded RNA (ssRNA), with a protein linked to its 5' end and a 3'-terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N-PIPO is predicted to be produced by a translational frameshift.

PATHOGENICITY FEATURES

PPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner.

SOURCES OF RESISTANCE

A few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, 'HoneySweet', transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.

Non-coding RNAs in crop genetic modification: considerations and predictable environmental risk assessments (ERA)

Of late non-coding RNAs (ncRNAs)-mediated gene silencing is an influential tool deliberately deployed to negatively regulate the expression of targeted genes. In addition to the widely employed small interfering RNA (siRNA)-mediated gene silencing approach, other variants like artificial miRNA (amiRNA), miRNA mimics, and artificial transacting siRNAs (tasiRNAs) are being explored and successfully deployed in developing non-coding RNA-based genetically modified plants. The ncRNA-based gene manipulations are typified with mobile nature of silencing signals, interference from viral genome-derived suppressor proteins, and an obligation for meticulous computational analysis to prevaricate any inadvertent effects. In a broad sense, risk assessment inquiries for genetically modified plants based on the expression of ncRNAs are competently addressed by the environmental risk assessment (ERA) models, currently in vogue, designed for the first generation transgenic plants which are based on the expression of heterologous proteins. Nevertheless, transgenic plants functioning on the foundation of ncRNAs warrant due attention with respect to their unique attributes like off-target or non-target gene silencing effects, small RNAs (sRNAs) persistence, food and feed safety assessments, problems in detection and tracking of sRNAs in food, impact of ncRNAs in plant protection measures, effect of mutations etc. The role of recent developments in sequencing techniques like next generation sequencing (NGS) and the ERA paradigm of the different countries in vogue are also discussed in the context of ncRNA-based gene manipulations.

MicroRNA-mediated gene regulation: potential applications for plant genetic engineering

Food security is one of the most important issues challenging the world today. Any strategies to solve this problem must include increasing crop yields and quality. MicroRNA-based genetic modification technology (miRNA-based GM tech) can be one of the most promising solutions that contribute to agricultural productivity directly by developing superior crop cultivars with enhanced biotic and abiotic stress tolerance and increased biomass yields. Indirectly, the technology may increase usage of marginal soils and decrease pesticide use, among other benefits. This review highlights the most recent progress of transgenic studies utilizing various miRNAs and their targets for plant trait modifications, and analyzes the potential of miRNA-mediated gene regulation for use in crop improvement. Strategies for manipulating miRNAs and their targets in transgenic plants including constitutive, stress-induced, or tissue-specific expression of miRNAs or their targets, RNA interference, expressing miRNA-resistant target genes, artificial target mimic and artificial miRNAs were discussed. We also discussed potential risks of utilizing miRNA-based GM tech. In general, miRNAs and their targets not only provide an invaluable source of novel transgenes, but also inspire the development of several new GM strategies, allowing advances in breeding novel crop cultivars with agronomically useful characteristics.

Top 10 plant viruses in molecular plant pathology

Many scientists, if not all, feel that their particular plant virus should appear in any list of the most important plant viruses. However, to our knowledge, no such list exists. The aim of this review was to survey all plant virologists with an association with Molecular Plant Pathology and ask them to nominate which plant viruses they would place in a 'Top 10' based on scientific/economic importance. The survey generated more than 250 votes from the international community, and allowed the generation of a Top 10 plant virus list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Tobacco mosaic virus, (2) Tomato spotted wilt virus, (3) Tomato yellow leaf curl virus, (4) Cucumber mosaic virus, (5) Potato virus Y, (6) Cauliflower mosaic virus, (7) African cassava mosaic virus, (8) Plum pox virus, (9) Brome mosaic virus and (10) Potato virus X, with honourable mentions for viruses just missing out on the Top 10, including Citrus tristeza virus, Barley yellow dwarf virus, Potato leafroll virus and Tomato bushy stunt virus. This review article presents a short review on each virus of the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant virology community, as well as laying down a benchmark, as it will be interesting to see in future years how perceptions change and which viruses enter and leave the Top 10.

Antiviral strategies in plants based on RNA silencing

One of the challenges being faced in the twenty-first century is the biological control of plant viral infections. Among the different strategies to combat virus infections, those based on pathogen-derived resistance (PDR) are probably the most powerful approaches to confer virus resistance in plants. The application of the PDR concept not only revealed the existence of a previously unknown sequence-specific RNA-degradation mechanism in plants, but has also helped to design antiviral strategies to engineer viral resistant plants in the last 25 years. In this article, we review the different platforms related to RNA silencing that have been developed during this time to obtain plants resistant to viruses and illustrate examples of current applications of RNA silencing to protect crop plants against viral diseases of agronomic relevance. This article is part of a Special Issue entitled: MicroRNAs in viral gene regulation.

Genetically engineered virus-resistant plants in developing countries: current status and future prospects

Plant viruses cause severe crop losses worldwide. Conventional control strategies, such as cultural methods and biocide applications against arthropod, nematode, and plasmodiophorid vectors, have limited success at mitigating the impact of plant viruses. Planting resistant cultivars is the most effective and economical way to control plant virus diseases. Natural sources of resistance have been exploited extensively to develop virus-resistant plants by conventional breeding. Non-conventional methods have also been used successfully to confer virus resistance by transferring primarily virus-derived genes, including viral coat protein, replicase, movement protein, defective interfering RNA, non-coding RNA sequences, and protease, into susceptible plants. Non-viral genes (R genes, microRNAs, ribosome-inactivating proteins, protease inhibitors, dsRNAse, RNA modifying enzymes, and scFvs) have also been used successfully to engineer resistance to viruses in plants. Very few genetically engineered (GE) virus resistant (VR) crops have been released for cultivation and none is available yet in developing countries. However, a number of economically important GEVR crops, transformed with viral genes are of great interest in developing countries. The major issues confronting the production and deregulation of GEVR crops in developing countries are primarily socio-economic and related to intellectual property rights, biosafety regulatory frameworks, expenditure to generate GE crops and opposition by non-governmental activists. Suggestions for satisfactory resolution of these factors, presumably leading to field tests and deregulation of GEVR crops in developing countries, are given.