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Our project takes advantage of the new synergies and broader research questions generated by the emergence of our new group. It aims to understand, anticipate and manage the adaptation of wheat pathogens in the context of agroecology. Our ambition is to achieve an integrated vision of (1) the different causes of adaptation (e.g. synthetic and biocontrol antifungals and cultivars) by studying their joint selection pressure and the related adaptive trade-off observed in populations. This holistic approach leads us to consider (2) the diversity of the patterns of adaptation (e.g. specific, generalist and/or pleiotropic) in fungi, and finally (3) to nest whenever possible the various scales relevant to assess adaptation (i.e. genome, individual, population and landscape; intra- and inter-epidemic periods).

Our biological models are Zymoseptoria tritici (causing Septoria leaf blotch) and Puccinia triticina (causing leaf rust), both wheat pathogens. However, depending on research questions, some alternative application models might be considered. Landscape epidemiology projects (see below) also includes multi-disease risk assessment.

 

Zymoseptoria tritici

 

Puccinia triticina

By considering together, and not independently, as traditionally explored, the selection pressure exerted by the main levers of disease protection, our work has primary applications for the sustainability of pathogen control. This global approach is more realistic from an operational point of view and offers the possibility to rethink the organization of disease management, while combining creatively the sources of selection heterogeneity, which is in accordance with the principles of agroecology.

The GAIA team relies on long-established collaborations with scientific but also field partners (in particular, for the access to ambitious experimental set-ups) and ensures a two-way flow between basic and applied science, to best serve the users of our research.

Our project is organized around 4 complementary questions, each enriching the next, from fundamental to more applied research.

TOPIC 1: What constraints do control methods exert on fungi? (#Selection)

Our objective in this topic is to understand the intimate interaction between antifungals (in particular to biocontrol antifungals, whose modes of action remain poorly explored) and fungi, at the molecular and cellular scales, leading to individual selection (on-going projects: PhD A. Le Ruyet on 4-PBA, coll. INRAE IJPB; Dyonisos project, coll. CEA & SATT Paris-Saclay). At larger scales, we take benefit of public databases and dedicated trials to describe quantitatively how the selection pressures are unevenly distributed over time and space on fungal population (coll. CST Ecophyto & project MP XRisks SESRisks). This topic links the applied selection pressure and the adaptation observed in the field (topic 2).
1.1 Molecular interaction of antifungals with the fungal cell: identifying (biocontrol) targets and modes of action
1.2 Distribution of selection pressure from antifungals and cultivars over time and space leading to the selection of adaptive variants in fungal populations.

TOPIC 2: Which are the processes underlying adaptation to cultivars and antifungals in fungi? (#Adaptation)

Topic 2 is historically associated to the key expertise and recognition of the previous AMAR team, that we want to extend to new boundaries. Our objective is to understand the genetic and genomic determinism of adaptation to antifungals in Z. tritici, while focusing on natural compounds and non-target site resistance (on-going PhDs of A. Le Ruyet & E. Neau; projects BASC MECADETOX, coll. INRAE Ecosys & INRAE SPE ANTIGUA, coll. CNRS ICSN & PARSADA ASAP, coll. R4P). The ANR AEROBIOMICS project will also help us, together with international colleagues, to develop a multiplex molecular tool useful to quantify resistant genotypes of Z. tritici in populations from different countries. At the population and landscape scales, we aim to understand how the joint selection from multiple control measures (as made possible from the revised “Performance network” set-up, including contrasting cultivars and fungicide treatments, starting in 2024 & project PARSADA ASAP) and the global fungal environment (e.g. space-time crop rotation or landscape features) impact the frequency of adapted variants and more generally of epidemics, over time and space (project PEPR MathVives).
2.1 Molecular mechanisms leading to the adaptation of pathogens to antifungals: new mechanisms selected by natural compounds and relevance of generalist mechanisms.
2.2 Genome-wide adaptation to antifungals: changes in genome integrity and variation in mutation rate.
2.3 Adaptive trajectories of fungal populations in response to joint selection: surveillance of adapted variants
2.4 Distribution of adapted variants in agricultural landscapes: hierarchizing multi-scale environmental effects on population dynamics (landscape epidemiology).

TOPIC 3: How to improve the sustainability of control measures in the context of agroecology? (#Sustainability)

Our aim for topic 3 is to improve the sustainability of control measures by predicting, through experimental evolution, the resistance mechanisms that may be selected by antifungal compounds (especially those not yet on the market, including biocontrol) and, by anticipating resistance evolution in populations, through modelling approaches. This will also enable us to test and validate in vitro and in silico smart strategies that promote the heterogeneity and diversity of selection pressure, using innovative combinations of control measures (cultivars, synthetic and natural antifungals) (projects PARSADA ASAP & PEPR SOLUBIOD, coll. CNRS CEBC) and are relevant for the mechanisms and status of adaptation in population established in topic 2.
3.1 Predicting and preventing adaptation: identifying variants to be selected from new antifungals, modelling  evolution in populations and designing preventive strategies
3.2 Mitigation of adaptation: assessing and designing sustainable strategies combining control measures.

TOPIC 4: How to implement adaptation management? (#Transfer)

In topic 4, we aim to promote the use of relevant strategies (topic 3) among farmers and advisors, while understanding the organisational and technical issues limiting their implementation, via the collaboration with our social sciences colleagues (projects PPR FAST, coll. INRAE SADAPT & Ecophyto PAPEETE). More generally, we promote knowledge about adaptation in agriculture to a general audience (e.g. via the activities and website of the R4P network or popularization papers and designing smart recommendations together with stakeholders) but also guide public policies (via expertise and contribution to the governance of relevant institutions).
4.1 Getting to know farmers' outlooks and constraints while encouraging them to anticipate adaptation: input from social and citizen sciences.
4.2 Educating about adaptation management: from popularization to guidance to public policies.