PhD Contract: Modeling Selection Plans for Resilience in Laying Hens

INRAE Presentation

The National Institute for Agricultural, Food and Environmental Research (INRAE) is a public research establishment bringing together a workforce of 12,000 people, with 272 research, service, and experimental units, located in 18 centers across France. INRAE is among the world's leading institutions in agricultural and food sciences, plant and animal sciences. Its research aims to develop solutions for multi-performant agriculture, high-quality food, and sustainable management of resources and ecosystems.

Work Environment, Missions, and Activities ➥ You will be hosted in co-supervision between two INRAE research units:

Your primary assignment will be within the mixed research unit Physiology, Environment and Genetics for Animal and Farming Systems (UMR PEGASE), located in Brittany, 10 km from Rennes. INRAE and Agro Rennes-Angers Institute agents conduct research and teach in animal biology and farming systems. Within the unit, the Avian Genetics and Genomics team (GGA) studies, among other things, the optimization of innovative genetic improvement strategies to increase the multi-performance and longevity of laying hens, thus promoting more resilient farming systems. This thesis is co-supervised by researchers from the mixed research unit Animal Genetics and Integrative Biology (UMR GABI), located in the Paris region. INRAE agents conduct research within their team Genetic Useful for Fish and Insects in Agroecology (GUPPIE) on modeling selection plans for species raised in large groups. As part of this co-supervision, regular stays at Jouy-en-Josas are expected, with a few months of immersion being desirable.

This thesis project is part of an agroecological transition context where the planned end of cage farming in Europe imposes new challenges. Alternative systems (outdoor, organic) expose hens to greater climatic, sanitary, and negative social interactions such as pecking, with animals evolving in large groups. The objective of the thesis is to design multi-criteria selection strategies to increase the resilience of animals to these perturbations, while extending the career duration of hens.

➥ You will be primarily responsible for:

The Central Objective of Your Thesis Will Be To Develop And Evaluate, Through Stochastic Modeling, Selection Strategies Favorable To Resilience At Different Scales (Population, System, And Group). Your Activities Will Be Divided Into Three Main Phases

• Data analysis: You will use commercial data from the Novogen selector (covering more than 7000 hens) to evaluate the impact of social interactions (pecking, laying behavior via electronic nests) on production and egg quality characteristics according to the farming system.
• Modeling social interactions at the group scale: You will propose innovative selection strategies to limit competition and promote cooperation among hens raised in large groups (several thousand individuals), using individual-centered approaches to simulate the impact of environmental hazards.
• Multi-criteria modeling at the population scale: You will develop models and selection strategies to preserve genetic diversity and maintain the overall adaptability of the line.

**This thesis is co-funded by INRAE's Animal Genetics department and the Brittany region. It is based on a public-private partnership between INRAE and NOVOGEN, a laying hen selector (Plédran, France).

During the thesis, the doctoral student will be jointly supervised by Nicolas Bédère (UMR PEGASE) and Florence Phocas (UMR GABI), and co-supervised by Sophie Allais (UMR PEGASE). Frequent meetings with Novogen's R&D team will take place. The doctoral student will enroll in a thesis at the Agro Rennes-Angers Institute and the EGAAL doctoral school of the University of Rennes 1.**

Required Education and Skills

Master's/Engineer (Bac+5) ➥ Recommended education:

Master 2 (or equivalent) with a specialization in quantitative genetics, biostatistics, or mathematical modeling ➥ Desired knowledge: Advanced mastery of statistical tools and programming. Basic knowledge in stochastic simulations would be a major asset ➥ Appreciated experience: an internship at the Master's level with research activities in quantitative genetics ➥ Desired skills: Scientific rigor, curiosity for the challenges of the agroecological transition, autonomy, and communication skills to interact with industrial and academic partners. Technical English proficiency is necessary for the international valorization of your work

Start date: October 1 or November 1.

Your Quality of Life at INRAE

By joining INRAE, you benefit (depending on the type and duration of the contract):

• up to 30 days of vacation + 15 RTT per year (for full-time)
• parental support: CESU childcare, leisure allowances;
• skill development: training, career counseling;
• social support: counseling and listening, social aids and loans;
• vacation and leisure benefits: vacation vouchers, preferential accommodation;
• sports and cultural activities;
• collective dining.
• Application Procedures
• Submit your CV and cover letter

*Individuals hired at INRAE, a public research establishment, are subject to the provisions of the Civil Service Code, particularly regarding the obligation of neutrality and the respect of the principle of laïcité. In the exercise of their functions, whether or not they are in contact with the public, they must not manifest their convictions, by their behavior or appearance, whether they are religious, philosophical, or political. Learn more: site* *civil service.gouv.fr*