Context

The National Institute for Agricultural Research (INRAE) is a world‑class research institution in Europe. Within the UMR Pegase (Physiology, Environment and Genetics for the Animal and Farm Systems) in Saint‑Gilles (near Rennes, Bretagne) the  GGA (Avian Genetics & Genomics) team is investigating the genetic mechanisms that enable laying hens to thrive in innovative and sustainable production systems. Inside the UMR BOA (Bird Physiology & Aviculture) in Nouzilly (near Tours, Centre France) the Genuts (Genetics, Nutrition and Farm System Studies) team studies the genetic, nutritional and environmental bases for improving poultry productivity, health and welfare.

The HEN-CARE (Hen Emotional Needs - Comprehensive Assessment and Resilience Enhancement), EU project Eupawh (European Partnership on Animal Health and Welfare) brings together Newcastle (UK), KU Leuven (Belgium), Bern (CH) and the commercial breeding company Hendrix Genetics (NL).  Its objective is to enhance hen welfare by uncovering the links between stress recovery, long‑term emotional states (mood), and their genetic basis. In this context, Nicolas Bédère, an expert in the genetics of chicken adaptation within the GGA team, collaborates with Julie Collet and Justine Chartrain, an expert in the genetics of behavior and social networks within the Genuts team, to :

• Estimate heritabilities of resilience indicators (both behavioural and physiological recovery after stress).
• Identify genomic loci affecting these traits through GWAS.
• Analyse genetic correlations between resilience, mood, health (e.g., keel‑bone fractures, immune response) and production (e.g., laying behaviour).

Your main mission will be to perform GWAS analyses on the genomic and phenotypic data collected in the project.

To carry out this mission, you will have access to genotyping, genealogy, and phenotyping data for 2,200 F1 hens resulting from the crossing of pure lines, as well as genotyping data for their parents. Additionally, 1,200 hens have physiological, behavioral, and neurophysiological phenotypic data.

Tasks

In this internship you will work under the guidance of Nicolas Bédère (GGA) and Justine Chartrain (Genuts) with Julie Collet (Genuts):

Data Pre‑processing

• Select fixed effects for mixed‑model analyses (e.g. R lme4).
• Perform SNP quality control (e.g. PLINK).

GWAS

• Run association tests (e.g. GCTA).
• Interpret Manhattan plots and extract significant SNPs.

Functional Annotation

• Explore functionnal annotations and identify positional candidate genes (using Ensembl, NCBI Gene).
• Explore enriched biological pathways (e.g. biomaRt, MAGMA).

Reporting

• Draft a scientific report and an article for submission to the “Avian Research Days” (JRA, that will take place a year after the internship in march 2028).
• Present results in GGA/Genuts team meetings and the consortium.
   

Required profile

Training :

• Equivalent of Master II with specialization in bioinformatics, biostatistics or genetics.
• Experiences with genetic or genomic studies (bonus).
• Familiarity with linear mixed models, R programming, Linux (bonus)

Skills :

• Autonomous and rigorous.
• Team-player.
• International collaboration mindset

Conditions

• Duration: 6 months (start possible January 2027, subject to university calendar).
• Location: INRAE UMR Pegase, 35590 Saint-Gilles (10 km west of Rennes, Brittany).
• Public transport from Rennes (available).
• Possible subsidised meals at INRAE restaurant.
• Bonus ≈ 656 €/month (or 31.50 €/day of work)

To apply for this position, send your application letter, your CV and the contact details of a lecturer for recommendation to Nicolas Bédère (nicolas.bedere[at]inrae.fr).