DOCTORAL CONTRACT: Modelling Selection Plans for Resilience in Laying Hens

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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 under joint supervision by two INRAE research units: 

• Primary host research unit: Physiology, Environment and Genetics for Animals and Livestock Systems joint research unit (UMR PEGASE), located in Brittany, about 10 km from Rennes. The unit brings together INRAE and Institut Agro staff conducting research and teaching in animal biology and livestock systems. Within PEGASE, the Avian Genetics and Genomics team (GGA) works on innovative genetic‑improvement strategies to increase the multi‑performance and longevity of laying hens, thereby contributing to more resilient farming systems. 
• Co‑supervising research unit: the Research Unit Genetic Animal and Integrative Biology (UMR GABI), based near Paris. The team “Genetics Useful for Fish and Insects in Agro‑ecology” (GUPPIE) conducts work on modelling selection plans for species raised in large groups. Regular stays in Jouy‑en‑Josas will be required, with a longer immersion stay of a few months recommended.

The PhD project is set in the context of the agro‑ecological transition, as the phased ban on cage‑based laying systems across Europe creates new challenges. Alternative systems (free‑range, organic) expose hens to greater climatic, sanitary and social stressors (e.g. pecking, large‑group dynamics). The overall aim is to design multi‑objective selection strategies that boost animal resilience to these disturbances while extending the productive lifespan of the hens. 

➥ The central objective of your thesis will be to develop and evaluate, through stochastic modelling, selection strategies that promote resilience at different scales (population, system, and group). Your work will be divided into three main phases.

• Real‑world data analysis: Use commercial data supplied by the breeding company Novogen (covering > 7 000 hens) to assess how social interactions (pecking, nest‑box use recorded by electronic nests) affect production traits and egg quality under different housing systems. 
• Group‑level social‑interaction modelling: Propose innovative selection strategies that limit competition and promote cooperation among hens kept in very large groups (several thousand individuals). Individual‑based simulation approaches will be used to evaluate the impact of environmental fluctuations. 
• Population‑level multi‑criteria modelling: Develop models and selection strategies that preserve genetic diversity and maintain overall line adaptability.

The PhD project is co‑funded by the INRAE Animal Genetics division and the Brittany Region, and relies on a public‑private partnership between INRAE and Novogen (Plédran, France). The candidate will be jointly supervised by Nicolas Bédère (UMR PEGASE) and Florence Phocas (UMR GABI), with co‑supervision by Sophie Allais (UMR PEGASE). Frequent meetings with Novogen’s R&D team are planned. The PhD will be registered at Institut Agro Rennes‑Angers and at the “Ecology, Geosciences, Agronomy, Food” (EGAAL) doctoral school of the University of Rennes 1. 

Training and skills

➥ Recommended training: Master 2 (or equivalent) with a specialisation in quantitative genetics, biostatistics or mathematical modelling. 

➥ Knowledge required: advanced proficiency with statistical tools and programming; experience in stochastic simulations is a strong asset.

➥ Appreciated experience: a Master's-level internship with research activities in quantitative genetics

➥ Skills sought: scientific rigor, curiosity about agro‑ecological transitions, autonomy, strong communication skills for interaction with industrial and academic partners, and technical English for international dissemination.

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