RIMBAUD Loup

Since 1st September 2018, I have been working as a Research Scientist in the team ‘Virology’ of the Plant Pathology Research Unit (INRAE, Avignon). My main research interest focus on the identification of efficient, cost-effective and durable strategies to manage plant diseases and especially those caused by viruses on vegetable crops.
 

RESEARCH ACTIVITIES

I use spatiotemporal simulation models, complemented with laboratory and glasshouse experiments, as well as statistical analyses of epidemiological data. These experiments and field data result in the acquisition of crucial knowledge on the biology of the interactions between host plants, pathogens and possibly their vectors. Indeed, these knowledge give the possibility to calibrate model parameters or test model predictions, and can be very helpful to identify promising control methods. Finally, it is crucial for me to identify strategies that match with farmers’ needs, and communicate them in such a way that my researches have an impact on the real world.

1. Modelling control strategies of epidemics

Simulation models are very useful to optimise management strategies of epidemics, and circumvent the ethical, legal, logistical and economic constraints associated with experiments at large spatiotemporal scales. My models simulate the epidemiological dynamics of pathogens in cultivated landscapes under disease management, and aim at optimising management strategies. However, pathogens have an extraordinary evolutionary potential that allow them to overcome control methods employed in the field. This is particularly the case with the deployment of plant resistance. Thus, because they include pathogen evolution, the demo-genetic models I use are of great interest, and enable the identification of strategies that are both efficient and durable to manage plant diseases.

In collaboration with the BioSP unit (Biostatistics and spatial processes, INRAE PACA Avignon), I contributed to the development of the R package landsepi (Landscape Epidemiology and Evolution), which can be downloaded following this link [https://cran.r-project.org/package=landsepi]. This package allows the simulation of a panel of resistance deployment strategies against plant pathogens, especially:

• rusts of wheat, caused by fungi of the genus Puccinia
• downy mildew of grapevine, caused by the oomycota Plasmopara viticola
• black sigatoka of banana, caused by the fungus Pseudocercospora fijiensis
• cucumber mosaic virus (CMV) and potato virus Y (PVY) on pepper

Diverse strategies can be compared with respect to their epidemiological (plant health), evolutionary (resistance durability) and economic (cost efficiency) performance. The package also includes a shiny web interface for pedagogical purpose.  

Resistance deployment strategies. A durable management of plant resistance includes the choice of the resistance source, and its wise spatiotemporal deployment at different nested scales, with the aim of mitigating pathogen evolution towards resistance breakdown.
Adapté from Rimbaud L., Fabre F., Papaïx J., Moury B., Lannou C., Barrett L. and Thrall P. (2021). Models of plant resistance deployment. Annu. Rev. Phytopathol. 59:125-152.

Example of simulation of an epidemic with landsepi. Right panel: colonization of a pathogen in an agricultural landscape composed of a susceptible cultivar (fields initially infected) and two resistant cultivar (hatched fields). Left panel: dynamics of disease prevalence, with time of resistance breakdown (blue vertical lines).
Adapté de de Rimbaud L, Papaïx J, Rey JF, Barrett LG and Thrall PH (2018). Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. PLoS Comput. Biol. 14:e1006067.

SEIR architecture of the model. Healthy hosts can be infected by propagules. Following a latent period, infectious hosts produce new propagules which may mutate and disperse across the landscape. At the end of the infectious period, infected hosts become epidemiologically inactive. A web pedagogical interface of SEIR models is available [https://loup.shinyapps.io/loup_demo_shiny/].
Adapté de Rimbaud L, Papaïx J, Barrett LG, Burdon JJ and Thrall PH (2018). Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? Evol. Appl. 11(10):1791-1810.

2. 2.    Understanding plant-virus-vector interactions via experiments

A fine understanding of the biology of interaction between pathogens, hosts and vectors is necessary to identify relevant control strategies.
It is crucial to identify the key factors of epidemic spread. It is the objective of my researches on the cucumber mosaic virus (Bromoviridae, Cucumovirus), which recently emerged on Espelette pepper crops, causing severe damages. based on field sampling, laboratory diagnostic tools (using serological and molecular methods) and statistical analyses, I explore the different dissemination pathways of CMV in the Basque Country (Southwestern France).

CMV impacts yield, size, form, colour and taste of Espelette pepper.

From Verdin E. & Rimbaud L. (2024). Biologie végétale : des cultures sous pression virale. La Recherche, Dossier « Les Virus », n°576:49-51 and adapted from Lepage E., Szadkowski M., Girardot G., Pascal M., Dumeaux P., Papaïx J., Moury B. and Rimbaud L. (2025). Cucumber mosaic virus degrades pepper fruit production, marketability and organoleptic quality, with isolate-specific effects. Plant Pathol. 74:1244-1255

Cucumber mosaic virus is a tri-partite virus composed of 3 particles, each of them containing a positive single stranded RNA. It infects a very wide range of host plants, among which pepper. It is transmitted by the seed of some host plants, and by more than 80 species of aphids in the non-persistant mode.

TRANSFER OF KNOWLEDGE

1. Teaching

I teach yearly: 

• on these three main themes:
  • bases of phytopathology
  • bases of biostatistics
  • mathematical approaches to assess resistance deployment strategies ;
• in these organisms::
  • Avignon Université : Sciences et Durabilité des Productions Végétales (SDPV, M1 & M2),  Ingénierie des Filières végétales (IFV, M1 & M2) 
  • Montpellier SupAgro : Protection des Plantes et Environnement (PPE, M2)

2. PhD supervision

• 2026 – 2029 : Alban Fesquet (INRAE, directeur) : Identification, par la modélisation, de stratégies de déploiement de la résistance variétale et des traitements phytosanitaires pour une gestion réactive, efficace, durable et rentable des maladies.
• 2022 - 2025 : Elise Lepage (AgroParisTech IPEF, co-directeur) : Emergences à l’interface agro-écologique : le rôle des réservoirs naturels sur les dynamiques épidémique et évolutive des agents pathogènes.

3. Post-doctorate supersivion

2021 - 2024 : Marta Zaffaroni (INRAE, co-encadrant) : Stratégies de diversification des gènes de résistance pour gérer les agents pathogènes dans les agro-écosystèmes : approches théoriques et application aux vignobles français.

4. Internship supervision

• 2026 : Guillaume Visomblain (M2 Institut Agro Rennes, encadrant principal) : Evaluation de la compétence de 5 adventices pour constituer un réservoir viral du CMV.
• 2024 : 
  • Alice Conilh (L2 Avignon Univ., 2024, encadrant principal) : Evaluation des différentes voies de transmission du CMV.
  • Lucas Gonzalez (L3 Avignon Univ., 2024, encadrant principal) : Evaluation des différentes voies de transmission du CMV.
• 2023 : Manon Couty (M2 INSA Lyon, co-encadrant) : Modélisation spatio-temporelle des épidémies : comment diversifier les paysages agricoles ?
• 2022 : Ulysse Caromel (L3 Avignon Univ., encadrant principal) : Analyse d’image pour mesurer la résistance du piment au PVY.
• 2021 :
  •  Elise Lepage (M2 AgroParisTech, encadrant principal) : Itinéraire d’un virus fluorescent : Etudier la résistance du piment au Potato virus Y.
  • Pauline Bouvet (2^nde Cité Scolaire du Diois, encadrant principal): Stage de découverte en milieu professionnel.
• 2020 : 
  • Pierre Mustin (M2 Agrocampus Ouest, encadrant principal) : Evaluation de la résistance des plantes à la transmission des virus.
  • Clarisse Vincent (M2 Montpelier SupAgro, co-encadrant) : Assurer la durabilité des résistances à la cercosporiose noire de nouvelles variétés de bananiers.
• 2019 : Jean-Loup Gaussen (M2 Avignon Univ., co-encadrant) : Développement d’outils spatiaux pour le package R landsepi.
• 2014 : Samuel Marchat (M1 Univ. de Montpellier, co-encadrant) : Développement d’un protocole de détection précoce du virus de la sharka dans des Prunus.