Postdoctoral position of 10 months Epidemiological modelling of plant disease

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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

SCIENTIFIC CONTEXT : 

Cultivated plants possess resistance genes that protect them from pathogen infections. However, pathogens adapt: resistance is often either overcome or eroded, leading to an increase in the proportion of virulent individuals able to infect resistant varieties. Some varietal deployment strategies can slow down this adaptive process. These strategies rely on diversifying host populations at different spatiotemporal scales: over time through crop rotations or in space, either at the field scale (varietal mixtures; Borg et al., 2018) or at the landscape scale (mosaics of varieties; Rimbaud et al., 2021). The demo-genetic model Landsepi (Rimbaud et al., 2018a) was design to compare the performance of deployment strategies for qualitative or quantitative resistances and study the effect of landscape, epidemiological, and evolutionary parameters on disease control.
OBJECTIVES OF THE POSTDOCTORAL PROJECT :

This postdoctoral project is part of the ANR COMBINE project. One objective is to evaluate multi-scale varietal diversification scenarios that enable effective and sustainable control of septoria leaf blotch caused by the fungus Zymoseptoria tritici. Previous results show that varietal mixtures enhance the durability of resistance through various demographic and genetic processes (Orellana-Torrejon et al., 2022).

The Landsepi model, initially applied to cereal rusts (Rimbaud et al., 2018a & 2018b), was adapted for grapevine downy mildew, caused by the oomycete Plasmopara viticola, by integrating a module that simulates the sexual phase of the pathogen’s life cycle (Zaffaroni et al., 2024a,b). A first parameterization of the model for Z. tritici, which also alternates between asexual and sexual reproduction phases, was carried out during a Master’s internship (Sesia, 2024). You will first continue this parameterization using here key life-history traits of the pathogen and data available in the team then you will use Landsepi to simulate the effects of: (i) landscapes sensu lato composed of different resistant wheat varieties, and (ii) the introduction of varietal mixtures, themselves composed of resistant varieties, within these landscapes, on the evolution of epidemic intensity and the frequency of virulent strains in fungal populations.

You will test the hypothesis that the genetic diversity of wheat populations (number, frequencies, effects, and combinations of resistance genes) effectively contributes to disease reduction over multiple years. You will develop and evaluate scenarios in two contexts studied experimentally by the team: (i) in the French context, considering mixtures of wheat varieties possessing different resistance genes, based on ongoing micro-plot trials (Suffert et al., 2024); in the Tunisian context, considering wheat landrace populations that experience low disease incidence despite high pathogen pressure, based on an ongoing study aimed at characterizing the genetic architecture of resistance.

References: 

Borg J, Kiær LP, et al. (2018). Unfolding the potential of wheat cultivar mixtures: A meta-analysis perspective
and identification of knowledge gaps. Field Crops Research, 221: 298-313.
Orellana-Torrejon C, Vidal T, et al. (2022). Annual dynamics of Zymoseptoria tritici populations in wheat
cultivar mixtures: A compromise between the efficacy and durability of a recently broken-down resistance
gene? Plant Pathol. 71(2): 289-303.
Rimbaud, L, Papaïx J, et al. (2018a). Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy
to deploy major gene resistance? Evolutionary Applications 11(10): 1791-1810.
Rimbaud L, Papaïx J, et al. (2018b). Assessing the durability and efficiency of landscape-based strategies to
deploy plant resistance to pathogens. PLoS Computational Biology 14(4): e1006067.
Rimbaud L, Fabre F, et al. (2021). Models of plant resistance deployment. Annu. Rev. Phytopathol. 59: 6.1-
6.28.
Sesia M (2024) Première application du modèle Landsepi sur la septoriose du blé causé par Zymoseptoria
tritici afin de comparer les stratégies de déploiement variétaux à une échelle paysagère. Rapport de stage de
Master1 Biodiversité, Ecologie, Evolution.
Suffert F, Papin C, et al. (2024). Impact des mélanges sur l’évolution des populations de Zymoseptoria
tritici. Phytoma 779-780: 26-30.
Zaffaroni M, Papaïx J, et al. (2024a). Combining single-gene-resistant and pyramided cultivars of perennial
crops in agricultural landscapes compromises pyramiding benefits in most production situations.
Phytopathol. 114: 2310–2321.
Zaffaroni M, Rimbaud L, et al. (2024b). Effects of pathogen reproduction system on the evolutionary and
epidemiological control provided by deployment strategies for two major resistance genes in agricultural
landscapes. Evolutionary Applications 17: e13627.

 

Training and skills

 Recommended training: PhD in modelling for plant disease epidemiology.
 Knowledge required: Strong knowledge in epidemiology, mathematics and modelling. The candidate
should have programming skills (at least R) and knowledge of data processing. An interest for applied
question in agronomy.
 Skills sought: Proven skills in writing scientific publications, enthusiasm and team player attitude

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: training, career 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

I send my CV and my motivation letter