DOCTORAL CONTRACT: Selection criteria for hens to improve their resilience to environmental variations

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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 unit Physiology, Environment and Genetics for Animals and Livestock Systems joint research unit (UMR PEGASE), located in Brittany, 10 km from Rennes. INRAE and Institut Agro staff conduct research and provide training in animal biology and breeding systems. 

Within the unit, the Avian Genetics and Genomics team (GGA) studies, among other things, the genetic determinism of laying hen adaptation to innovative and sustainable rearing environments. 

Cage rearing of laying hens is disappearing in Europe, in favor of alternative systems that offer living conditions more respectful of animal welfare. In 2020, 52% of laying hens in the European Union were raised in alternative systems to cages. An end to cage farming in the European Union is even planned in the short term, following the End the Cage Age citizens' initiative.

In these alternative systems, animals are more exposed to hazards that disrupt their living environment, such as a heatwave or the emergence of a virus. It is therefore crucial to select animals that are resilient, i.e. less sensitive to these disturbances.

Thanks to new high-throughput phenotyping tools, such as an electronic nest, we have access to information enabling us to study animal responses to hazards, such as changes in egg-laying rhythms, from which indicators of resilience can be derived.

The aim of this thesis will be to propose selection criteria for improving animal resilience based on these longitudinal phenotyping data. 

• First, it will be necessary to explore several indicators of resilience (logarithm of variance of deviations, reaction norm coefficient, curve modeling and parameters, UpDown method parameters, GAMs method parameters...) and to determine their genetic parameters (heritabilities and genetic correlations, including with other selection criteria). 
• The genetic determinism of these traits will then be studied by QTL detection. 
• Finally, simulations will be used to assess the impact of selection on resilience, according to scenarios that differ in terms of frequency and intensity of climatic and sanitary disturbances. 

Special conditions of activity: This thesis is based on a public-private partnership between INRAE and NOVOGEN, a breeder of laying hens (Plédran, France). 

The request for funding for this thesis will be submitted to the Conventions industrielles de formation par la recherche (Cifre; https://www.anrt.asso.fr/fr/le-dispositif-cifre-7844) scheme. This scheme enables a company to benefit from financial assistance to recruit a doctoral student whose research, supervised by a public research laboratory, will lead to the defense of a thesis. It is necessary to have already identified a candidate who will submit a CIFRE application.

During his/her thesis, the PhD student will be supervised by Nicolas Bédère (UMR PEGASE), and under the co-direction of Ingrid David (UMR GenPhySE) and Nicolas Friggens (UMR PEGASE). As part of the co-direction, visits to Castanet-Tolosan (UMR GenPhySE) will be scheduled as and when required. At Novogen, the PhD student will be supervised by Thierry Burlot (R&D manager) and Lorry Bécot (geneticist), and will meet frequently with other members of the R&D team. The doctoral student will be enrolled in a thesis at the Institut Agro Rennes-Angers and in the Ecologie, Géosciences, Agronomie, Alimentation (EGAAL) graduate school at the University of Rennes 1.

Training and skills

 

Recommended training: Master 2 (or equivalent) with a specialization in quantitative genetics, biostatistics, or mathematical modeling.

Knowledge required: Advanced mastery of statistical tools and programming. A background in longitudinal analysis would be a major asset.

Appreciated experience: A Master's-level internship with research activities in quantitative genetics or equivalent (linear mixed model, random regressions...).

Skills sought: Scientific rigor, curiosity about agroecological transition issues, autonomy, and communication skills to interact with industrial and academic partners. Proficiency in technical English is required for the international valorization of your work.

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