PhD position OT-11670

A transcriptomic approach for improving the understanding of the mechanisms of heat adaptation and developing plasma biomarkers of heat tolerance in pigs

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 at the PEGASE unit (Physiology, Environment and Genetics for Animals and Livestock Systems), INRAE, L'Institut Agro-Agrocampus Ouest, located near Rennes (35) and at the GenPhySE unit (Genetics, Physiology and Livestock Systems) located near Toulouse

Socio-economic and scientific context: Heat is a major constraint for pig production in tropical regions (Brazil, South East Asia, etc.) but also in temperate regions during the summer especially when summer heat waves occur. The frequency and the severity of such extreme events are planned to increase 2050 due to global warming. Coping with thermal heat stress is therefore a major concern for maintaining the competitiveness of the pork industry. Within a pig population, there is great phenotypic individual variability in responses to heat. While some of this variability is genetic, adaptation to heat probably involves a large number of genes that interact with each other with environmental factors. The biological mechanisms involved in the individual variability of heat sensitivity are still poorly understood in pigs. The first objective of this thesis work is to improve knowledge of these mechanisms by using gene expression data measured in different tissues in different experiments that used very contrasting experimental modalities or large cohorts of animals. The second objective of this project is to identify and validate biomarkers to classify animals according to their sensitivity to heat. These biomarkers could be used to improve breeding practices (precision breeding) and / or select animals with a low susceptibility to climatic perturbations.

This work was based on the hypothesis of using DNA microarrays to measure the expression levels of large numbers of genes simultaneously in various tissues and in several pig genotypes with the aim to provide a significant and comprehensive view of heat acclimation in pigs. Moreover, analysis of the blood transcriptome can contribute to identify HS response specific signatures (overexpressed or under-expressed transcripts) which might be translated into useful molecular biomarkers for differential HS susceptibility. Ultimately these biomarkers or patterns of markers could help to improve animal selection programs or feeding managements.

 Main steps of the thesis: The thesis will be based on analyses of gene expression data from DNA microarrays and obtained within the framework of a general project aimed at characterizing the pigs responses to heat exposure. Initially, gene expression data obtained from the two first studies will be used to describe how genes expression changes in different tissues in response to heat exposure of pigs and to test whether there is a relationship between these molecular changes and the animal thermoregulatory and production responses. One of the original features of this program will be to be able to assess the kinetics of gene expression profiles as a function of the duration of heat acclimation (steps 1 and 2). Thereafter, one objective is to investigate whether genome-wide transcriptional data in blood can lead to the identification of candidate biomarkers associated with variations of heat tolerance in pigs (step 3). Finally, the ability of its biomarkers to predict the physiological status of an animal subjected to acute or chronic heat stress will be evaluated using data from the third study obtained on a large cohort of animals (step 4).

Supervised and unsupervised bio statistical approaches will be used to cluster genes that are differentially expressed and / or co-expressed according to climatic conditions or the duration of exposure to heat. Specific methods will be used to explore the relationships that may exist between the expression data and other phenotypes measured on the same set of individuals.

Training and skills

Master's degree/Engineering degree

Recommended training: Master's degree in bioinformatics and bio-statistics or in animal physiology (but in this case the candidate will have a strong interest in bioinformatics and bio-statistics).

Skills sought: a strong interest for data analysis and an ability to use statistical tools and computer languages such as R or Python are required. Skills in animal physiology, molecular and cellular biology or bioinformatics will be appreciated in the evaluation of the candidate.

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

I send my CV and my motivation letter

Offer reference

  • Contract: PhD position
  • Duration: 36 mois
  • Beginning: 01/10/2021
  • Remuneration: 1874€
  • Reference: OT-11670
  • Dealine: 09/07/2021
Centre Brittany-Normandy

UMR PEGASE/UMR GenPhySe 35590 Saint Gilles Website