Project context and overall objectives
Tomato and cucurbits are affected by global emerging viruses such as ToLCNDV and ToBRFV, which reduce crop value. Their mitigation leads to increased production costs and environmental impacts. VIRTIGATION builds on increasing knowledge about the biology, pathways of entry and spread of plant viruses, and the development of new tools and plant materials to provide novel and sustainable tools to mitigate the negative impact of viral pandemics in tomato and cucurbits production in the EU and its partner countries. To meet this agenda, VIRTIGATION is managing a network of stakeholders following the multi-actor approach to help disseminate and implement novel solutions. To characterize the viral pathogens, diagnostics tools are being implemented to facilitate rapid identification and characterization of the plant virus diversity. These will provide plant health services with adapted tools and measures to predict and prevent future viral outbreaks arising from climate change.
The full genome approach is on its way to provide a comprehensive characterization of the virus diversity in Europe. The fundamental research focuses on the in-depth analysis of plant-virus-vector interactions and the role of alternative host plants (weeds) in disease perseverance and spread, as well as virus and host factors that contribute to the jump from old (tomato) to new (cucurbits) host plants leading to disease epidemics. This is key to select and introgress natural resistance in tomato and cucurbit varieties, and to develop a novel cross-protection strategy.
Work performed and main results reached
Internal guidelines were drafted for the project’s multi-actor approach. The most relevant actors for the VIRTIGATION network were identified and around 150 have already joined. The first multi-actor activities included a regional workshop with 30 stakeholders in Almería (Spain), and a questionnaire on whitefly control answered by 208 growers across the EU. To develop novel high-throughput sequencing approaches and analyse samples from growers across Europe, epidemiological descriptors for infected plant samples were combined in a questionnaire for correct annotation of the collected samples. Those descriptors were implemented in the Genome Detective Platform. To perform high-throughput sequencing of full viral genomes, a protocol using Oxford Nanopore Technology and a bioinformatic pipeline has been implemented. Similarly, a protocol for RNA viruses has been developed.
Clones of betasatellites co-occuring with begomoviruses were generated to understand interactions between plant viruses and their hosts. Several tomato lines remaining asymptomatic under inoculation of tomato leaf curl Bangalore virus (ToLCBV) were identified. Their resistance across other geminiviruses will help determine their potential for source of begomovirus resistance to improve varieties currently used in Europe. The near isogenic lines of tomatoes from Israel screened for resistance to Indian begomoviruses displayed varying levels of geminivirus resistances from highly symptomatic to no disease symptoms. However, the asymptomatic lines appeared to have some level of virus replication. Fine mapping of the major QTL associated with whitefly resistance in tomatoes has been performed and a region containing genes involved in trichome development and whitefly resistance has been identified. ToBRFV mutants were also generated and evaluated for symptom development. Mutant viruses are being validated for mild phenotypes before selection for cross-protection experiments. Several protocols including steaming of soil and substrate as well as solarization have been tested and optimized. Work on ToBRFV mutant viruses and survival of ToBRFV under soil conditions has led to increased knowledge about the disease caused by ToBRFV.
Progress beyond the state of the art and expected socio-economic & societal impacts
Cost-effective sequencing of full viral genomes has been established. This is a pioneering result, which will allow a more in-depth analysis of virus evolution and spread in natural and alternative hosts, as well as in crop plants with various levels of resistance. This will support in better characterizing the impact of virus resistance or susceptibility on virus evolution. New sources of full or partial virus resistances were identified and characterized. This will help building novel combination of natural resistances. Several natural molecules with activities against the virus vectors were identified to develop alternative methods for pest control and reduction of conventional pesticides. Updated procedures for hygiene protocols are also opening new perspectives to mitigate virus outbreaks.
Multi-actor tools and guidelines are being implemented to foster the bottom-up approach of the scientific impacts. Growers and the value chain are being provided with an integrated strategy for virus and vector management, and a toolbox to help eradicating viruses after infection, with focus on soil, substrates and plant materials. The screening activities will be complemented with molecular analysis to elucidate the regulatory pathways involved in plant responses to viral infections. This will help identify factors involved in the transmission and disease symptom development. It includes understanding the effects of climate change conditions by analysing plant transcription profiles, the role of seed-borne virus infection in disease spread and ways to control it. In-depth characterisation of natural plant responses to viruses and vectors will also contribute to new approaches for rapid screening of germplasms.
The focus on new biorational whitefly control strategies will also help implement multiprone approaches to mitigate virus outbreaks. A cross-protection strategy concept will be proven to control ToBRFV. The identification and characterization of natural virus resistance and the development and cultivation of ToBRFV-resistant tomato varieties and ToLCNDV-resistant tomato & cucurbit varieties will provide a long-term solution. The identification of natural molecules for biopesticide development will help reduce insecticide application and dosage, thereby improving the environment for growers and the society. Similarly, screening of the tomato and cucurbit germplasm and a better understanding of crop responses to the two viruses will identify novel sources of natural resistance that will be a basis for implementing IPM measures. VIRTIGATION’s diagnostics and the analysis of virus diversity combined with the online tool for sequencing data upload and analysis will provide details about virus diversity and movement across EU countries that can be used for other emerging viral diseases. Viral pandemics could be prevented by early detection of hyper-virulent isolates, thus limiting the occurrence of plant viral pandemics in vegetable and other crops. VIRTIGATION will contribute to other important pathosystems by developing virus analysis tools, and testing and implementing IPM approaches. Field assessment of IPM practices and exchange of best practices between participating countries will lead to a roadmap to reduce pesticide usage. As environmental conditions can impact vector and virus spread, the project will also develop preventive measures against emerging begomovirus and tobamovirus diseases in countries at risk of pandemics.