Genomics for young rabbit health

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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 based at GenPhySE (Genetics, Physiology and Breeding Systems), an INRAE-Université de Toulouse-ENVT Joint Research Unit (UMR) located south of Toulouse. GenPhySE brings together over 150 people working on livestock species (pigs, sheep, goats, rabbits, quail, bees). You will be part of the MAGE (Animal multiperformance and genetics) team.

Context. Improving the health of farm animals is a major challenge to reduce dependence on antibiotics, limit economic losses due to disease, and preserve animal welfare. In rabbit production, young rabbits are particularly vulnerable: before weaning, their survival depends largely on maternal effects, in particular the quality and composition of milk; after weaning, their survival depends on their resistance to digestive and infectious disorders caused by multiple pathogens. Genetic selection of breeding animals that passes on better health traits is therefore a promising lever for sustainably improving the resilience of the rabbit farming industry.

Objective. Exploring the genetic determinism of health and survival in young rabbits, before and after weaning.

Available data. The internship will be based on an original dataset from a rabbit line comprising:

•    health records (mortality and morbidity related to digestive and infectious disorders) for 17,000 young rabbits

•    milk composition measurements (IgA, IgG, proteins, lactose, lipids, oligosaccharides) at four stages of lactation (D3, D10, D17 and D25) on 120 does

•    the genotypes of 960 breeding rabbits (Affymetrix 200,000 SNP marker chip)

•    Complete DNA sequences of 22 founding males of the line.

Internship schedule:

1.    Genomic imputation: use of dedicated software (FImpute or equivalent) to impute SNP genotypes at the sequence level, based on sequenced founders. This step will fill in missing information for genotyped rabbits and obtain a complete DNA sequence for these animals.

2.    Genome-wide association studies (GWAS): detection of regions of the genome associated with different health and milk quality traits

This internship will serve as an introduction to a thesis project (subject to funding) focused on the genomics of health and survival in young rabbits.

Publication related to the subject:

J. Bouza. Genomics for non-specific disease resistance in rabbits. 2025. ⟨hal-05224546⟩

Mélanie Gunia, Julien Ruesche, Patrick Aymard, Emilie Gillet, Caroline Herbert, et al. Breeding for general disease resistance: a selection experiment in rabbits. WCGALP 2022. https://hal.inrae.fr/hal-03766847

¡ You will be responsible for :

- Assessing the quality of genotyping data from high-density SNPs chips to generate a reliable dataset for subsequent analyses

- Identification of genome regions associated with disease resistance (PLINK and GEMMA software)

- Study of selection footprints (HAPFLK software)

- Writing a scientific article

The internship will take place on the INRAE Occitanie-Toulouse campus in Auzeville, south of Toulouse. The campus is accessible from Toulouse by public transport (Tisseo L6). It is close to the Canal du Midi, providing excellent access by bicycle.

Training and skills

Final-year Master’s student or equivalent (e.g., engineering school)

Desired skills: knowledge of quantitative and molecular genetics

Experience appreciated: data analysis

Desired skills : an aptitude for analysing data sets, scientific rigour, and strong writing and summarising 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