Biosafety considerations of RNAi-mediated virus resistance in fruit-tree cultivars and in rootstock

JrGA20ox1-transformed rootstocks deliver drought response signals to wild-type scions in grafted walnut

Targeted regulation using transgrafting technology has become a trend. However, the mechanisms of transgene-derived signal communication between rootstocks and scions remain unclear in woody plants. Here, we grafted wild-type (WT) walnut (Juglans regia L.) on WT (WT/WT), JrGA20ox1 (encodes a gibberellin 20-oxidase)-overexpressing (WT/OE), and JrGA20ox1-RNAi transformation (WT/RNAi) walnut in vitro. We aimed to elucidate the mechanisms of JrGA20ox1-derived signal communication under PEG-simulated drought stress between rootstocks and scions in walnut. We demonstrated that JrGA20ox1-OE and JrGA20ox1-RNAi rootstocks could transport active gibberellins (GAs) and JrGA20ox1-RNAi vector-produced sRNAs to WT scions under PEG-simulated drought stress, respectively. The movement of sRNAs further led to a successive decline in JrGA20ox1 expression and active GA content. Meanwhile, unknown mobile signals may move between rootstocks and scions. These mobile signals reduced the expression of a series of GA-responsive and GA-non-responsive genes, and induced ROS production in guard cells and an increase in ABA content, which may contribute to the drought tolerance of WT/RNAi, while the opposite occurred in WT/OE. The findings suggest that JrGA20ox1-derived rootstock-to-scion movement of signals is involved in drought tolerance of scions. Our research will provide a feasible approach for studying signal communication in woody plants.

Physiological, biochemical, and molecular aspects of grafting in fruit trees

Grafting is a widely used practice for asexual propagation of fruit trees. Many physiological, biochemical, and molecular changes occur upon grafting that can influence important horticultural traits. This technology has many advantages, including avoidance of juvenility, modifying the scion architecture, improving productivity, adapting scion cultivars to unfavourable environmental conditions, and developing traits in resistance to insect pests, bacterial and fungal diseases. A limitation of grafting is scion-rootstock incompatibility. It may be caused by many factors, including insufficient genetic proximity, physiological or biochemical factors, lignification at the graft union, poor graft architecture, insufficient cell recognition between union tissues, and metabolic differences in the scion and the rootstock. Plant hormones, like auxin, ethylene (ET), cytokinin (CK), gibberellin (GA), abscisic acid (ABA), and jasmonic acid (JA) orchestrate several crucial physiological and biochemical processes happening at the site of the graft union. Additionally, epigenetic changes at the union affect chromatin architecture by DNA methylation, histone modification, and the action of small RNA molecules. The mechanism triggering these effects likely is affected by hormonal crosstalk, protein and small molecules movement, nutrients uptake, and transport in the grafted trees. This review provides an overview of the basis of physiological, biochemical, and molecular aspects of fruit tree grafting between scion and rootstock.

Effect of Grafting on Viral Resistance of Non-transgenic Plum Scion Combined With Transgenic PPV-Resistant Rootstock

In stone fruit trees, resistance to Plum pox virus (PPV) can be achieved through the specific degradation of viral RNA by the mechanism of RNA interference (RNAi). Transgenic virus-resistant plants, however, raise serious biosafety concerns due to the insertion and expression of hairpin constructs that usually contain various selective foreign genes. Since a mature stone tree represents a combination of scion and rootstock, grafting commercial varieties onto transgenic virus-tolerant rootstocks is a possible approach to mitigate biosafety problems. The present study was aimed at answering the following question: To what extent are molecular RNAi silencing signals transmitted across graft junctions in transgrafted plum trees and how much does it affect PPV resistance in genetically modified (GM)/non-transgenic (NT) counterparts? Two combinations, NT:GM and GM:NT (scion:rootstock), were studied, with an emphasis on the first transgrafting scenario. Viral inoculation was carried out on either the scion or the rootstock. The interspecific rootstock "Elita" [(Prunus pumila L. × P. salicina Lindl.) × (P. cerasifera Ehrh.)] was combined with cv. "Startovaya" (Prunus domestica L.) as a scion. Transgenic plum lines of both cultivars were transformed with a PPV-coat protein (CP)-derived intron-separate hairpin-RNA construct and displayed substantial viral resistance. High-throughput sequence data of small RNA (sRNA) pools indicated that the accumulation of construct-specific small interfering RNA (siRNA) in transgenic plum rootstock reached over 2%. The elevated siRNA level enabled the resistance to PPV and blocked the movement of the virus through the GM tissues into the NT partner when the transgenic tissues were inoculated. At the same time, the mobile siRNA signal was not moved from the GM rootstock to the target NT tissue to a level sufficient to trigger silencing of PPV transcripts and provide reliable viral resistance. The lack of mobility of transgene-derived siRNA molecules was accompanied by the transfer of various endogenous rootstock-specific sRNAs into the NT scion, indicating the exceptional transitivity failure of the studied RNAi signal. The results presented here indicate that transgrafting in woody fruit trees remains an unpredictable practice and needs further in-depth examination to deliver molecular silencing signals.

Substantial Equivalence of a Transgenic Lemon Fruit Showing Postharvest Fungal Pathogens Resistance

The development of genetically modified (GM) crops speeds up the obtainment of novel varieties with improved agronomic characteristics. However, the risk evaluation of the use of GMs is mandatory before their release in the market. In this paper, an untargeted and comprehensive nuclear magnetic resonance-based metabolomic study was carried out on the peel and flesh of a transgenic lemon clone (E23) expressing the chit42 gene and exhibiting an increased tolerance to some pathogenic fungi and on its wild type. Results highlighted a substantial equivalence of the metabolomics profile of the transgenic clone compared to the wild type. In addition, an enhanced response of the E23 clone toward fungal pathogens affecting the postharvest management in lemon was evidenced. These results confirm the potential of genetic engineering for the punctual modification of specific agronomic traits without altering the whole pattern of metabolites and open new perspectives for a more sustainable and effective management of specific postharvest diseases in citrus.

The Rooting of Stem Cuttings and the Stability of uidA Gene Expression in Generative and Vegetative Progeny of Transgenic Pear Rootstock in the Field

Adventitious rooting plays an important role in the commercial vegetative propagation of trees. Adventitious root formation is a complex biological process, but knowledge of the possible unintended effects induced by both the integration/expression of transgenes and in vitro conditions on the rooting is limited. The long-term stability of transgene expression is important both for original transformants of woody plants and its progeny. In this study, we used field-grown pear rootstock GP217 trees transformed with the reporter ß-glucuronidase (uidA) genes with and without intron and re-transformed with the herbicide resistance bar gene as model systems. We assessed the unintended effects on rooting of pear semi-hardwood cuttings and evaluated the stability of transgene expression in progeny produced by generative (seedlings) and vegetative (grafting, cutting) means up to four years. Our investigation revealed that: (1) The single and repeated transformations of clonal pear rootstocks did not result in unintended effects on adventitious root formation in cuttings; (2) stability of the transgene expression was confirmed on both generative and vegetative progeny, and no silenced transgenic plants were detected; (3) yearly variation in the gene expressions was observed and expression levels were decreased in extremely hot and dry summer; (4) the intron enhanced the expression of uidA gene in pear plants approximately two-fold compared to gene without intron. The current study provides useful information on transgene expression in progeny of fruit trees under natural environmental conditions.

Factors Affecting the Regeneration, via Organogenesis, and the Selection of Transgenic Calli in the Peach Rootstock Hansen 536 (Prunus persica × Prunus amygdalus) to Express an RNAi Construct against PPV Virus

Prunus spp. is one of the most recalcitrant fruit tree species in terms of in vitro regeneration and transformation, mostly when mature tissues are used as explants. The present study describes the in vitro regeneration via indirect organogenesis, and Agrobacterium tumefaciens-mediated transformation of the peach rootstock Hansen 536 (Prunus persica × Prunus amygdalus) through the use of meristematic bulks (MBs) as starting explants. Efficient adventitious shoot regeneration was obtained when Hansen 536 MBs were cultured on an optimized medium consisting of modified McCown Woody Plant medium (WPM) enriched with 4.4 M 6-Benzyladenine (BA), 0.1 M 1-Naphthaleneacetic acid (NAA) and 6.0 g L-1 plant agar S1000 (B&V). MB slices were used later as starting explants for Agrobacterium-mediated transformation to introduce an RNAi construct "ihp35S-PPV194" against PPV virus. Transgenic events were identified by both green fluorescent protein (GFP) screening and kanamycin selection at different concentrations (0, 17 or 42 M). GFP-fluorescent proliferating callus lines were selected and confirmed to stably express the ihp35S-PPV194::eGFP gene construct by molecular analysis. Although shoot regeneration from these transgenic calli has not been obtained yet, this represents one of the few examples of successful attempts in peach genetic transformation from somatic tissues, and also serves as a useful in vitro system for future gene functional analysis in peach.

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.

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.

A plant regeneration platform to apply new breeding techniques for improving disease resistance in grapevine rootstocks and cultivars

Worldwide grapevine cultivation is based on the use of elite cultivars, in many cases strictly linked to local important wine brands. Most of Vitis viniferacultivars have high susceptibility to fungal and viral diseases therefore, new breeding techniques (e.g. Cisgenesis, RNAi and gene editing) offer the possibility to introduce new clones of the main cultivars with increased diseases resistance, in order to reduce environmental impact and improve quality in the intensive wine grape industry. This study is finalized to develop efficient in vitro regeneration and transformation protocols to extend the application of these technologies in wine grape cultivars and rootstocks. With this aim, in vitro regeneration protocols based on the production of meristematic bulks (Mezzetti et al., 2002) were optimized for different grapevine cultivars (Glera, Vermentino, Sangiovese, Thompson Seedless) and rootstocks (1103 Paulsen, and 110 Richter). The meristematic bulks were then used as explants for Agrobacteriummediated genetic transformation protocols, by comparing the use of NPTII and e-GFP as marker genes. Results confirmed the efficiency of meristematic bulks as the regenerating tissue to produce new modified plants in almost all the above genotypes. The highest regeneration efficiency in some genotypes allowed the selection of stable modified lines/calli with only the use of e-GFP marker gene. This protocol can be applied in the use of MYB marker gene for the production of cisgenic lines. Genotypes having the highest regeneration and transformation efficiency were also used for transformation experiments using a hairpin gene construct designed to silence the RNA-dependent RNA polymerase (RpRd) of the GFLV and GLRaV3, which would induce multiple virus resistances, and the Dicer-like protein 1 (Bc-DCL1) and Bc-DCL2 to control B. cinerea infection.

New Biotechnological Tools for the Genetic Improvement of Major Woody Fruit Species

The improvement of woody fruit species by traditional plant breeding techniques has several limitations mainly caused by their high degree of heterozygosity, the length of their juvenile phase and auto-incompatibility. The development of new biotechnological tools (NBTs), such as RNA interference (RNAi), trans-grafting, cisgenesis/intragenesis, and genome editing tools, like zinc-finger and CRISPR/Cas9, has introduced the possibility of more precise and faster genetic modifications of plants. This aspect is of particular importance for the introduction or modification of specific traits in woody fruit species while maintaining unchanged general characteristics of a selected cultivar. Moreover, some of these new tools give the possibility to obtain transgene-free modified fruit tree genomes, which should increase consumer's acceptance. Over the decades biotechnological tools have undergone rapid development and there is a continuous addition of new and valuable techniques for plant breeders. This makes it possible to create desirable woody fruit varieties in a fast and more efficient way to meet the demand for sustainable agricultural productivity. Although, NBTs have a common goal i.e., precise, fast, and efficient crop improvement, individually they are markedly different in approach and characteristics from each other. In this review we describe in detail their mechanisms and applications for the improvement of fruit trees and consider the relationship between these biotechnological tools and the EU biosafety regulations applied to the plants and products obtained through these techniques.

Marker-free PLRV resistant potato mediated by Cre-loxP excision and RNAi

An inverted repeat construct corresponding to a segment of the potato leaf roll virus coat protein gene was created under control of a constitutive promoter and transferred into a transformation vector with a heat inducible Cre-loxP system to excise the nptII antibiotic resistance marker gene. Fifty-eight transgenic events were evaluated for resistance to PLRV by greenhouse inoculations, which lead to the identification of 7 highly resistant events, of which 4 were extremely resistant. This resistance was also highly effective against accumulation in subsequent tuber generations from inoculated plants, which has not been reported before. Northern blot analysis showed correlation of PLRV specific siRNA accumulation with the level of PLRV resistance. Heat mediated excision of the nptII antibiotic resistance gene in PLRV resistant events was highly efficient in one event with full excision in 71 % of treated explants. On the other hand 8 out of 10 analyzed events showed truncated T-DNA insertions lacking one of the two loxP sites as determined by PCR and confirmed by sequencing flanking regions in 2 events, suggesting cryptic LB sites in the non-coding region between the nptII gene and the flanking loxP site. Accordingly, it is proposed to modify the Cre-loxP vector by reducing the 1 kb size of the region between nptII, loxP, and the LB.

Fighting Sharka in Peach: Current Limitations and Future Perspectives

Sharka, caused by Plum Pox Virus (PPV), is by far the most important infectious disease of peach [P. persica (L.) Batsch] and other Prunus species. The progressive spread of the virus in many important growing areas throughout Europe poses serious issues to the economic sustainability of stone fruit crops, peach in particular. The adoption of internationally agreed-upon rules for diagnostic tests, strain-specific monitoring schemes and spatial-temporal modeling of virus spread, are all essential for a more effective sharka containment. The EU regulations on nursery activity should be modified based on the zone delimitation of PPV presence, limiting open-field production of propagation materials only to virus-free areas. Increasing the efficiency of preventive measures should be augmented by the short-term development of resistant cultivars. Putative sources of resistance/tolerance have been recently identified in peach germplasm, although the majority of novel resistant sources to PPV-M have been found in almond. However, the complexity of introgression from related-species imposes the search for alternative strategies. The use of genetic engineering, particularly RNA interference (RNAi)-based approaches, appears as one of the most promising perspectives to introduce a durable resistance to PPV in peach germplasm, notwithstanding the well-known difficulties of in vitro plant regeneration in this species. In this regard, rootstock transformation to induce RNAi-mediated systemic resistance would avoid the transformation of numerous commercial cultivars, and may alleviate consumer resistance to the use of GM plants.

Unravelling rootstock×scion interactions to improve food security

While much recent science has focused on understanding and exploiting root traits as new opportunities for crop improvement, the use of rootstocks has enhanced productivity of woody perennial crops for centuries. Grafting of vegetable crops has developed very quickly in the last 50 years, mainly to induce shoot vigour and to overcome soil-borne diseases in solanaceous and cucurbitaceous crops. In most cases, such progress has largely been due to empirical interactions between farmers, gardeners, and botanists, with limited insights into the underlying physiological mechanisms. Only during the last 20 years has science realized the potential of this old activity and studied the physiological and molecular mechanisms involved in rootstock×scion interactions, thereby not only explaining old phenomena but also developing new tools for crop improvement. Rootstocks can contribute to food security by: (i) increasing the yield potential of elite varieties; (ii) closing the yield gap under suboptimal growing conditions; (iii) decreasing the amount of chemical (pesticides and fertilizers) contaminants in the soil; (iv) increasing the efficiency of use of natural (water and soil) resources; (v) generating new useful genotypic variability (via epigenetics); and (vi) creating new products with improved quality. The potential of grafting is as broad as the genetic variability able to cross a potential incompatibility barrier between the rootstock and the scion. Therefore, understanding the mechanisms underlying the phenotypic variability resulting from rootstock×scion×environment interactions will certainly contribute to developing and exploiting rootstocks for food security.

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.

Crop immunity against viruses: outcomes and future challenges

Viruses cause epidemics on all major cultures of agronomic importance, representing a serious threat to global food security. As strict intracellular pathogens, they cannot be controlled chemically and prophylactic measures consist mainly in the destruction of infected plants and excessive pesticide applications to limit the population of vector organisms. A powerful alternative frequently employed in agriculture relies on the use of crop genetic resistances, approach that depends on mechanisms governing plant-virus interactions. Hence, knowledge related to the molecular bases of viral infections and crop resistances is key to face viral attacks in fields. Over the past 80 years, great advances have been made on our understanding of plant immunity against viruses. Although most of the known natural resistance genes have long been dominant R genes (encoding NBS-LRR proteins), a vast number of crop recessive resistance genes were cloned in the last decade, emphasizing another evolutive strategy to block viruses. In addition, the discovery of RNA interference pathways highlighted a very efficient antiviral system targeting the infectious agent at the nucleic acid level. Insidiously, plant viruses evolve and often acquire the ability to overcome the resistances employed by breeders. The development of efficient and durable resistances able to withstand the extreme genetic plasticity of viruses therefore represents a major challenge for the coming years. This review aims at describing some of the most devastating diseases caused by viruses on crops and summarizes current knowledge about plant-virus interactions, focusing on resistance mechanisms that prevent or limit viral infection in plants. In addition, I will discuss the current outcomes of the actions employed to control viral diseases in fields and the future investigations that need to be undertaken to develop sustainable broad-spectrum crop resistances against viruses.