PhD Student in Statistical Genetics: Modeling the Genetic Contribution to the Emergence of Group-Level Resilience, a Cross-Perspective between Animals and Plants

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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

You will be welcomed in the GenPhySE and GQE Le Moulon joint research units. The scientific activities of GenPhySE, located near Toulouse, are focused on characterizing and understanding the complex mechanisms underlying animals' ability to adapt to changing environments. The UMR GQE Le Moulon, located near Paris, focuses on generating knowledge about the genetics and evolution of quantitative traits, primarily in crop populations.

Improving resilience is a major challenge for agriculture in the context of climate change and agroecological transition. Resilience can be considered at different scales: the individual (animal or plant), the group (herd or plot), or the system (farm). Phenotypic diversity (different species) has been identified as a key element for increasing the resilience of systems, but it imposes constraints that are poorly accepted by farmers and breeders. As a result, genetic diversity—within a single-breed herd or within a plot of varietal mixtures—has been proposed as a more feasible alternative. However, the genetic foundations of this diversification have rarely been addressed.

The objective of this thesis is to develop new modeling approaches to assess the link between genetic diversity and group/plot resilience, and to propose methods for leveraging genetic diversity to ensure resilience in group or plot performance.

Group resilience can be an emergent property resulting, for example, from phenotypic diversity, interactions between individuals, or collective responses to environmental disturbances. The most classical genetic approach to modeling individual phenotypes in groups is the social genetic effects model where the genotypes of conspecifics influence the phenotype of the target individual. This model does not account for genetic proximity between individuals and assumes a linear relationship between the observed phenotype of the target individual and the phenotypes of conspecifics. Thus, it does not allow us to determine whether there is a link between genetic diversity within the group and resilience, nor to assess whether nonlinearity is the emergent factor.

Therefore, it is necessary to develop new modeling approaches that overcome these limitations to study the emergent properties of resilience at the group level—particularly genetic ones—and to propose new strategies for the genetic evaluation and management of groups.

You will be in charge of:

• Exploring and proposing different models that explain—or do not explain—the link between diversity and group resilience, and/or the nonlinear relationship between phenotypes and group resilience.
• Evaluating for each proposed model the type and volume of data required to ensure the practical identifiability of their parameters.
• Testing, using the proposed models, the various hypotheses explaining the emergence of plot resilience on a varietal mixture dataset.
• Providing recommendations, based on the results obtained, for group composition and/or breeding schemes that ensure the best group resilience.

The PhD student may carry out the entirety of their thesis at one of the two research units (GenPhySE or GQE-Le Moulon) or change locations during the course of the thesis.

Training and skills

Recommended training: Genetics, Ecology and Evolution or Applied Mathematics 

Knowledge required: Statistics

Appreciated experience: Python, fortran or R language

Skills sought: strong writing and oral presentations 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: 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