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Thématiques de recherche

Trois axes principaux

Depuis les dernières décennies, les enjeux de la protection des plantes ont évolué vers une volonté d’accroître la durabilité. En France, cette mutation s’est concrétisée récemment par la mise en place des plans Ecophyto en 2007 et Agroécologie en 2011, qui encouragent la substitution ou la complémentation des applications phytosanitaires par d’autres méthodes de lutte.

En tant que mécanisme évolutif, l’adaptation des champignons phytopathogènes aux produits de protection des plantes (ou « résistance ») remet largement en cause cette durabilité, du fait des pertes d’efficacité régulièrement constatées et de la portée du phénomène. Dans ce contexte de transition, il est donc fondamental d’améliorer nos connaissances sur les mécanismes et modalités de sélection des résistances, tant au niveau individuel que populationnel, pour viser à mieux raisonner les stratégies de lutte et ainsi répondre à l’enjeu actuel de durabilité des pratiques.

Ainsi, les travaux de recherche de l’équipe AMAR tendent à répondre aux questions suivantes déclinées dans les trois grands axes de l’équipe:                              

1 - Comment les champignons perçoivent-ils et répondent-ils aux antifongiques à l’échelle cellulaire ?

2 - Quels sont les processus adaptatifs et évolutifs aux fongicides à l’échelle de l’individu et des populations ?

3 - Quelles stratégies de gestion de la résistance aux antifongiques sont les plus durables dans le contexte Ecophyto 2018 ?


Axes de Recherches


Afin d’appréhender ces axes de recherche de manière intégrative, l’équipe AMAR fait appel à une approche pluridisciplinaire allant de la génétique moléculaire, la biochimie, la génétique des populations, l’agronomie et la modélisation. Les modèles biologiques concernés sont Botrytis cinerea, agent de la pourriture grise, et Mycosphaerella graminicola, agent de la septoriose du blé



With the objective to trace fungicide sensing and transduction, we have developed phosphoproteomics in Botrytis cinerea in collaboration with PAPPSO (Davanture et al, 2015). Even from limited quantitative data, we identified unsuspected links between signal-transduction pathways and new virulence factors in the grey mould agent (PhD J. Kilani, 2018).

illustration highlight MDR 1
illustration highlight MDR 2

Important progress has been made in the characterization of multi-drug-resistance MDR in Zymoseptoria tritici. This type of resistance has been neglected for a long time in plant pathogenic fungi. Due to active drug efflux MDR confers only moderate resistance levels that do not impact efficacy of full-rate treatments. However, MDR may become a major problem in wheat production in the case of dose-reductions that might specifically select this type of resistance. In collaboration with Arvalis and agrochemical companies we deciphered the molecular mechanism of MDR in Z. tritici (Omrane et al., 2015 &2017).

The evolution of fungicide resistance is an emblematic case of local adaptation to spatially heterogeneous and temporally variable selection pressures. We dissected the adaptation of Botrytis cinerea populations to several fungicides (Walker et al., 2017). We found that treatment with currently used fungicides reduced B. cinerea effective population size, leading to a significant decrease in genic diversity and allelic richness in treated vs. untreated plots. Most importantly, we used the population data to estimate the costs of fungicide resistance by modelling the decrease in the frequency of resistant mutations in the absence of treatment. These data provide important information to be considered for fungicide resistance management.


Maxime Garnault studied in his thesis the evolutions of previously-described resistances to fungicides occurring in French Zymoseptoria tritici populations. Using spatial, ANOVA and dynamic models, we statistically analysed the Performance trial network dataset (2004-2017; 70 locations in France yearly) and highlighted contrasted behaviours among phenotypes such as: (i) specific spatial distributions; (ii) colonization front structures; (iii) large diversity of national evolution speeds; (iv) differential growth rates among regions. These results (Garnault et al., submitted) are of great interest to anticipate the evolution and management of future resistances.

In order to investigate the durability of anti-resistance strategies, we developed a spatial model describing the evolution of resistance in crop pathogen populations in response to fungicide deployment at the landscape scale. This model was used to explore the consequences of heterogeneity of fungicide dose application and to highlight the impact of dose distribution in space, which showed that designing antifungal treatment at a scale larger than the parcel may help delay selection of resistance and thereby increase fungicide durability.

Botrytis book

The publication of a new edition of the “Botrytis-book” in 2016, 12 years after the previous one, resulted from a big community effort launched by Yigal Elad from the Volcani Institute (Israel) and Sabine Fillinger (INRA). The book serves as a source of general information for specialists in agriculture, but also for students and scientists.

logo R4P

Together with scientists of INRA, Anses and the Ministry of Agriculture (DGAL), AMAR scientists contribute to knowledge transfer through the actions of our network R4P (“Réseau de Réflexion et de Recherche sur la Résistance aux Pesticides”). R4P created a web-site harboring basic and close-to-field knowledge about pesticide resistance. In addition, R4P is responsible for the scientific management of a new research unit at Anses in Lyon, under joint contract with INRA.