A transnational collaboration leads to the characterization of an emergent plant virus

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A transnational collaboration leads to the characterization of an emergent plant virus

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Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis

The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties

Innovation et développement dans les systèmes agricoles et alimentaires

L’innovation est souvent présentée comme l’un des principaux leviers pour promouvoir un développement plus durable et plus inclusif. Dans les domaines de l’agriculture et de l’alimentation, l’innovation est marquée par des spécificités liées à sa relation à la nature, mais aussi à la grande diversité d’acteurs concernés, depuis les agriculteurs jusqu’aux consommateurs, en passant par les services de recherche et de développement. L’innovation émerge des interactions entre ces acteurs, qui mobilisent des ressources et produisent des connaissances dans des dispositifs collaboratifs, afin de générer des changements. Elle recouvre des domaines aussi variés que les pratiques de production, l’organisation des marchés, ou les pratiques alimentaires. L’innovation est reliée aux grands enjeux de développement : innovation agro-écologique, innovation sociale, innovation territoriale, etc. Cet ouvrage porte un regard sur l’innovation dans les systèmes agricoles et alimentaires. Il met un accent particulier sur l’accompagnement de l’innovation, en interrogeant les méthodes et les organisations, et sur l’évaluation de l’innovation au regard de différents critères. Il s’appuie sur des réflexions portées par différentes disciplines scientifiques, sur des travaux de terrain conduits tant en France que dans de nombreux pays du Sud, et enfin sur les expériences acquises en accompagnant des acteurs qui innovent. Il combine des synthèses sur l’innovation et des études de cas emblématiques pour illustrer les propos. L’ouvrage est destiné aux enseignants, professionnels, étudiants et chercheurs

High Throughput sequencing technologies complemented by growers’ perceptions highlight the impact of tomato virome in diversified vegetable farms and a lack of awareness of emerging virus threats

peer reviewedThe number of small-scale diversified vegetable growers in industrialized countries has risen sharply over the last 10 years. The risks associated with plant viruses in these systems have been barely studied in Europe, yet dramatic virus emergence events, such as tomato brown fruit rugose virus (ToBRFV), sometimes occur. We developed a methodology that aimed to understand better the implications related to viruses for tomato production in Belgian’s vegetable farms by comparing growers’ perception and the presence of plant-viral-like symptoms (visual inspection) with non-targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS). Virus presence and impact were interpreted considering the farm’s typology and cultural practices, and the grower’s professional profiles. Overall, the data indicated that most growers have limited understanding of tomato viruses and are not concerned about them. Field observations were correlated to this perception as the prevalence of symptomatic plants was usually lower than 1%. However, important and potentially emergent viruses, mainly transmitted by insects, were detected in several farms. Notably, the presence of these viruses tended to be associated with the number of plant species grown per site (diversity) but not with a higher awareness of the growers regarding plant viral diseases, or a higher number of symptomatic plants. In addition, both HTS and perception analysis underlined the rising incidence and importance of an emergent virus: Physostegia chlorotic mottle virus. This study also revealed a notable lack of knowledge among producers regarding the highly contagious quarantine virus ToBRFV. Overall, the original methodology developed here, involving the integration of two separate fields of study (social science with phytopathology using HTS technologies), could be applied to other crops in other systems to identify emergent risks associated with plant viruses, and can highlight the communication needed with growers to mitigate epidemics. This exploratory investigation provides relevant insights, which, ideally, would be further tested on wider samples to allow finer statistical treatment to be performed

Plant neighbour-modulated susceptibility to pathogens in intraspecific mixtures

International audienceAs part of a trend towards diversifying cultivated areas, varietal mixtures are subject to renewed interest as a means to manage diseases. Besides the epidemiological effects of varietal mixtures on pathogen propagation, little is known about the effect of intraspecific plant–plant interactions and their impact on responses to disease. In this study, genotypes of rice (Oryza sativa) or durum wheat (Triticum turgidum) were grown with different conspecific neighbours and manually inoculated under conditions preventing pathogen propagation. Disease susceptibility was measured together with the expression of basal immunity genes as part of the response to intra-specific neighbours. The results showed that in many cases for both rice and wheat susceptibility to pathogens and immunity was modified by the presence of intraspecific neighbours. This phenomenon, which we term ‘neighbour-modulated susceptibility’ (NMS), could be caused by the production of below-ground signals and does not require the neighbours to be infected. Our results suggest that the mechanisms responsible for reducing disease in varietal mixtures in the field need to be re-examined