PhD position OT-11566

Transcriptionnal and epigenetic responses of blood leukocytes in pigs: toward new indicators of health and welfare

35590 Saint-Gilles

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INRAE presentation

The French National Research Institute for Agriculture, Food, and the Environment (INRAE) is a public research establishment. It is a community of 12,000 people with more than 200 research units and 42 experimental units located throughout France. The institute is among the world leaders in agricultural and food sciences, in plant and animal sciences, and is 11th in the world in ecology and environment. INRAE’s main goal is to be a key player in the transitions necessary to address major global challenges. In the face of the increase in population, climate change, scarcity of resources and decline in biodiversity, the institute develops solutions for multiperformance agriculture, high quality food and sustainable management of resources and ecosystems.

Work environment, missions and activities

You will be hosted in the UMR PEGASE (Physiology, Environment and Genetics for Animals and Livestock Systems), INRAE, Agro-Agrocampus Ouest Institute, located near Rennes (35).

Your doctoral thesis topic will concern the evaluation of animal welfare. Today, biologists know how to use behavioral, endocrine or immune indicators to measure the transient responses of animals to brief negative situations (=stress), but know much less well how to evaluate the responses related to positive emotions or mental states established over the long term. Inspired by results obtained in humans and other animal species, this project will investigate, in pigs, whether variations in the transcriptome and epigenome of blood immune cells can be indicative of stable states of well-being or malaise, and whether these signatures could be used as a tool for assessing animal well-being. The project will study the impact of differently enriched or unenriched living environments on the welfare of sows and on their blood immune cells.

More specifically, you will be in charge of:

1.            Analyze methylome and transcriptome data of blood immune cells from sows reared in contrasting environments (one conventional, the other on straw bedding). You will implement the required bioinformatics and biostatistical methods with the objective of identifying differentially regulated genes and biological functions, or differentially methylated regions in the genomic DNA of sows raised in the two environments.

2.            Set up and carry on an experiment where the sow environment will be enriched by other means than in the first study (other sensory or cognitive stimuli). You will produce and analyze biochemical and molecular biological data selected according to the results of the first study, including the study of DNA methylation by a specific sequence approach and the expression of specific genes by quantitative PCR.

3.            Integrate the results of both experiments, and identify potential molecular markers of animal welfare. You will write your thesis manuscript and valorize your work through scientific articles, conference presentations and participate in the dissemination of the results to professional actors and society.

Training and skills

Master's degree/Engineering degree

- Recommended training: Master's degree in molecular and cellular biology or agri/agro engineer, validated by the end of 2021

- Desired knowledge: animal physiology, molecular and cellular biology, bioinformatics, English; notions of ethology would be appreciated.

- Desired skills: interest in animal experimentation (trial monitoring) and enjoy working in the bench (molecular biology techniques) and in silico (functional analysis of gene networks and DNA methylation data, statistical analysis with R software), organizational skills, critical thinking, teamwork skills, oral and written communication 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: trainingcareer 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

 For more information on this offer, contact Elodie Merlot ( or Hélène Jammes (

The detailed project is available on the website of the doctorate school of Bretagne Loire EGAAL : > PEGASE

Applications must be  submitted on this digital platform. Information on the procedure to follow is available at the following address:

Application deadline : July 15, 2021

Offer reference

  • Contract: PhD position
  • Duration: 36 months
  • Beginning: 01/11/2021
  • Remuneration: 1874 € gross per month
  • Reference: OT-11566
  • Dealine: 15/07/2021