PhD position OT-22016

The demo-genetics of resistance overcoming


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INRAE presentation

The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.

Work environment, missions and activities

Working environment:

The thesis will be carried out in the ECPF (Ecologie des Champignons Pathogènes Forestiers) team of the UMR IAM (Interactions Arbres-Microorganismes) at the INRAE Grand Est center in Nancy, which studies emerging diseases in forests using population biology approaches. The PhD student will have strong interactions with teams from two other units, BIOGER (Palaiseau) and ISA (Sophia Antipolis), with expertise respectively in the study of molecular interactions between phytopathogenic fungi and their host plant (on the rapeseed phoma pathosystem) and in modeling dynamic systems. The thesis will be co-directed by Fabien HALKETT (IAM) and Isabelle FUDAL (BIOGER), and co-supervised by Suzanne Touzeau (ISA). Depending on the needs of the project, stays will be scheduled at BIOGER and ISA, and regular updates will be given to all supervisors.


Background and challenges:

The growing of genetically resistant plants is an environmentally-friendly and effective means of controlling pathogen populations. However, pathogens can quickly overcome plant resistance. So how can we ensure sustainable crop protection? This seemingly simple question has been the subject of decades of intense debate and research.

Based on a bibliometric analysis [1], we have shown that research on the durability of plant resistance is highly structured, with a clear split between molecular approaches and epidemiological studies. This gap obviously hampers scientific progress. We believe that using the tools and concepts of population genetics would make it possible to overcome this limitation, as this discipline makes it possible to integrate the study of genetic bases at the higher scales of host and pathogen populations.

This thesis will be carried out within the framework of the ANR Endurance project, which aims to better integrate population genetics studies (and in particular demogenetics) into studies on resistance durability. To achieve this, the Endurance project brings together a broad consortium with complementary disciplinary skills, enabling epidemiological modeling work to be closely associated with experimental characterization of the molecular mechanisms underlying the evolution of pathogen populations. The ultimate aim of the project is to propose innovative and relevant resistance management scenarios, grounded as they are in the biology of the pathosystems under study, and taking into account the feedback between epidemic dynamics and molecular evolution.


Thesis objectives:

We are proposing an intrinsically multidisciplinary project combining experiments in molecular plant pathology and demo-genetic modeling. We are basing this thesis project on the blackleg disease of oilseed rape, for which there is both a good knowledge of the molecular basis of interactions and temporal monitoring of pathogen populations [2]. Another original feature is that we will take into account the unconventional molecular interactions that have been described in this pathosystem [3].

The central objective of this thesis is to retrace the demographic and adaptive dynamics of Leptosphaeria maculans populations during successive plant resistance bypasses. These analyses will be based on several previous works by the Nancy host team [4-5], which have enabled us to infer the evolutionary scenario during a major resistance overcoming event. This thesis will combine population genetics modeling and experimental characterization using molecular biology tools, targeting both neutral and avirulence loci to explore and retrace the evolutionary trajectories of pathogen populations. The balance between modeling and experimentation can be adapted according to the skills and motivations of the PhD student. The PhD work will strengthen the Endurance project consortium and tie in with the other recruitments envisaged during the project.

The person recruited will thus have the opportunity to train at the interface between molecular characterization and analysis of evolutionary trajectories within a rich and dynamic consortium of researchers interested in the durability of plant resistances.



[1] Saubin, M., Louet, C., Bousset, L., Fabre, F., Frey, P., Fudal, I., Grognard, F., Hamelin, F., Mailleret, L., Stoeckel, S., Touzeau, S., Petre, B., & Halkett, F. (2023). Improving sustainable crop protection using population genetics concepts. Molecular Ecology, 32(10), 2461–2471.

[2] Balesdent, M.-H., Gautier, A., Plissonneau, C., Le Meur, L., Loiseau, A., Leflon, M., Carpezat, J., Pinochet, X., & Rouxel, T. (2022). Twenty Years of Leptosphaeria maculans Population Survey in France Suggests Pyramiding Rlm3 and Rlm7 in Rapeseed Is a Risky Resistance Management Strategy. Phytopathology®, 112(10), 2126–2137.

[3] Lazar, N., Mesarich, C. H., Petit-Houdenot, Y., Talbi, N., Sierra-Gallay, I. L. de la, Zélie, E., Blondeau, K., Gracy, J., Ollivier, B., Blaise, F., Rouxel, T., Balesdent, M.-H., Idnurm, A., Tilbeurgh, H. van, & Fudal, I. (2022). A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins. PLOS Pathogens, 18(7), e1010664.

[4] Louet, C., Saubin, M., Andrieux, A., Persoons, A., Gorse, M., Pétrowski, J., Fabre, B., De Mita, S., Duplessis, S., Frey, P., & Halkett, F. (2023). A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown. Molecular Ecology, 32(10), 2472–2483.

[5] Saubin, M., Tellier, A., Stoeckel, S., Andrieux, A., & Halkett, F. (2023). Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population. Molecular Ecology, mec.16965.

Medium-term stays in project partners, in particular BIOGER and ISA teams. 

Training and skills

Master's degree/Engineering degree

We are looking for a student with a solid initial training in genetics, population genetics and biostatistics, for example from a Biology, Ecology and Evolution course. Ideally, this person will have a taste for modeling and conceptual approaches. Experience in plant pathology would be a plus, but is not mandatory. Scientific curiosity and good interpersonal skills are required to successfully complete this multi-disciplinary projects.
An advanced level of English is required: you can speak the language in a complex, spontaneous way and on a variety of subjects. Good writing skills. 


INRAE's life quality

By joining our teams, you benefit from (depending on the type of contract and its duration):

- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
parenting support: CESU childcare, leisure services;
- skills development systems: trainingcareer advise;
social support: advice and listening, social assistance and loans;
holiday and leisure services: holiday vouchers, accommodation at preferential rates;
sports and cultural activities;
- collective catering.

How to apply

Your application must include: (1) a detailed CV, (2) a letter of motivation, (3) Master's grades or equivalent and a copy of the diploma if available, (4) two letters of recommendation, if possible from the Master's supervisor and the tutor of your Master's internship. If available, please also send us your research internship dissertation.
Applications should be sent by e-mail to Fabien Halkett ( and Isabelle Fudal ( The deadline for applications is July 1, 2024. 


Offer reference

  • Contract: PhD position
  • Duration: 3 years
  • Beginning: 01/09/2024
  • Remuneration: 2 100 € gross per month
  • Reference: OT-22016
  • Deadline: 01/07/2024


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