Internship position

Context of the internship

The French National Research Institute for Agriculture, Food and the Environment (INRAE) is a world leader in agricultural and food sciences, plant and animal sciences. Its research aims to build solutions for multiperforming agriculture, quality food and sustainable management of resources and ecosystems. The joint research unit Physiology, Environment and Genetics for Animals and Livestock Systems (UMR Pegase) is located in Brittany, 10 km from Rennes, in Saint-Gilles. INRAE and Institut Agro agents carry out research and provide training in animal biology and breeding systems. Within the unit, researchers from the Genetics and Genomics team study the genetic background of the adaptation of laying hens to innovative and sustainable rearing environments.
Aarhus University (AU) ranks among the top 25 universities in the EU, and is located in Aarhus, Denmark. Center for Quantitative Genetics and Genomics (QGG) is an international research center at AU, where both basic and applied research on the genetic basis of complex traits in plants, animals, model organisms, and in humans is carried out. The core research process in QGG is the development and implementation of advanced statistical and bioinformatic methods and tools for the analysis of complex genetic and genomic data.

A few breeding companies are supplying farmers with laying hens all over the world. Purebred birds of the nuclei of these breeding companies are housed in cages to ensure pedigree and performance monitoring. Although most of the egg production is produced in cage systems, there is a large diversity in farming systems. Some alternative systems to cage are expanding, for instance in 2020, 52% of laying hens are raised in cage-free systems in E.U. (barn, free-range, and organic; European Commission, 2021). In all these systems, breeding goals include the number of eggs produced, egg qualities (regarding the albumen, yolk, and shell), feed efficiency, behaviour, fertility and disease resistance. In the current situation, birds are selected in the nuclei based on performance in cage system. Some studies indicate that some major traits such as egg production traits may be under the influence of genotype-by-environment interactions (G×E), which can affect the ranking of selection candidates. The magnitude of G×E would be due to the fact that different sets of genes build the phenotype in each environment. The objectives of the present MSc thesis are:

• to evaluate G×E in a population laying hens in contrasting systems,
• to identify regions on the genome associated with these G×E.

In order to produce knowledge on this problem, we propose an internship for original analyses of the data collected in an exploratory project named “TRADE'OUT - Trade-off between immunocompetence, behaviour and production in laying hens raised with an outdoor access” (https://eng-sanba.hub.inrae.fr/verticalheadings/our-actions/ exploratory-projects/trade-out-exploratory-project-2022-2023 ). This project is funded by an INRAE program named “Sanba - Health and Welfare of Farmed Livestock”.

Assignments

The student's mission will be :

• to estimate genetic parameters of major traits of the breeding goal (such as the body weight of the hens) in two contrasting environment: the nucleus of the collaborating breeding company (Novogen, Plédran, France) and an experimental set-up with outdoor access on an INRAE experimental farm (PEAT, Nouzilly, France). The genetic parameters will be the heritability in each environment and the genetic correlation for the same phenotype between the two environments,
• to detect regions of the genome associated with the covariance using a genome-wide association study method developed by Aarhus University.

This internship is an opportunity to discover research in animal genetics with impact (partnership with the egg industry), in two different institutes (Aarhus University and INRAE), and to learn the scientific approach by: identifying the question to be addressed, conducting bibliographic research, data analysis (e.g. R), and genetic calculations, writing a scientific report and participating in the research team daily life.

Profile and skills required

• Interest in genetic improvement of adaptive capacities of farm animals.
• Interest in data analysis.
• Agricultural engineer or Master's degree. Internship possible.
• Possibility to do this internship in English.

Reception and contact details.

• Internship allowance: approximately 586€ per month (according to the effective minimum hourly rate in January 2024).
• Place of the training course: INRAE, UMR Pegase, 35590 Saint-Gilles, France.
• Lunch is available at the INRAE restaurant at a subsidized rate.
• Possible access by public transport from Rennes, France.
• Duration / period desired: 6 months, ideally starting from January 2024.
• First contact by email only to both nicolas.bedere[at]inrae.fr AND helene.rome[at]qgg.au.dk with CV and cover letter.