Doctoral position in quantitative genetics - Benefits of genotype diversification for the resilience of trout farms

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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 welcomed in the joint research unit GABI at the INRAE ​​site in Jouy-en-Josas (78), located 20 km southwest of Paris. You will join the GUPPIE team that conducts research on the genetic improvement of fish and bees. Your work will be part of the broader ‘CoBreeding’ project, led by the team and funded by the ANR under the ‘Agroecology and Digital Technology’ PEPR (Priority Research and Equipment Programme). The PhD project aims to lay the practical foundations for an innovative approach to designing multi-criteria selection schemes—integrating genetic diversity and social interactions—in order to propose strategies that ensure the resilience of fish farming operations against environmental fluctuations and thereby foster the agroecological transition.

 In agroecology, a central hypothesis is that diversifying genotypes enhances the resilience of production systems. This involves combining a variety of species—or, within a single species, diverse genetic profiles—in the same system. However, this strategy of leveraging animal genetic heterogeneity has not yet gained acceptance among the vast majority of livestock farmers surveyed, regardless of the species involved. Farmers view genetic heterogeneity as a constraint on herd management and an obstacle to commercial value, as markets prefer purchasing batches of animals that are phenotypically uniform. Consequently, geneticists and animal scientists need to provide experimental evidence demonstrating the genuine benefits of assembling genetically heterogeneous animal groups in terms of herd resilience against environmental stressors (such as climate and pathogens). Yet, experimental evidence supporting this benefit in livestock farming remains very limited.

This PhD project focuses on rainbow trout farming and aims to demonstrate, through experimentation, the benefits of genotype diversification for enhancing the resilience and multi-performance of stocks facing environmental stressors. The objective is to explore the mechanisms underlying collective resilience, particularly in response to social stressors and environmental disturbances in a farming context. To this end, the large-scale experiment planned under the ANR PEPR CoBreeding project—featuring 11 cohabitation scenarios involving isogenic lines (where all individuals within a line share the same genotype) and a synthetic line (characterized by high genetic diversity)—offers a unique opportunity to analyze the impact of social interactions and genetic diversity on growth trajectories, feeding behavior, chronic stress levels, and the trout microbiome. The thesis will rely primarily on the analysis of longitudinal data from this experiment (specifically, near-monthly growth measurements, three photographic assessments of fish welfare, feeding behavior, and health monitoring over a nine-month period) to derive resilience indicators—first for each genotype individually, and subsequently by factoring in inter-genotype interactions at the group level. The availability of isogenic line sequences and genotype data for the 1,500 individuals in the synthetic line will enable the identification of genomic regions associated with the observed performance variations. This experiment is expected to provide a robust foundation for revisiting concepts of multi-performance and resilience in aquaculture, as well as for paving the way for innovative breeding strategies that incorporate social effects and optimize within-stock genetic diversity to enhance the resilience of fish farming systems.

 

Your mission will be divided into three phases corresponding to answer three main research questions:

1)            Comparing performance across the 11 experimental conditions will address the question: What are the performance differences (mean and variability at both individual and group levels) among animals raised in groups of a single genotype versus groups comprising two or four distinct genotypes?

2)            Analyzing longitudinal data will allow for the definition of theoretical trajectories for each genotype and resilience indicators to address the question: Which rearing conditions foster greater herd resilience regarding growth and welfare (stress limitation) in the face of environmental stressors?

3)            Genome-Wide Association Studies (GWAS) will aim to identify, as precisely as possible, the genomic regions (QTL– Quantitative Trait Loci) involved in trout resilience.

The student will register for the PhD program at the doctoral school ABIES at Université Paris-Saclay.

Training and skills

Recommended training: Master’s degree (or equivalent) specializing in quantitative genetics or biostatistics

Desired knowledge: : Animal biology, analysis of longitudinal and/or genomic data

Appreciated experience: : Master’s-level internship involving research in quantitative genetics or aquaculture

Skills: Scientific rigor, scientific curiosity, ability to work independently, and strong oral and written communication skills. Proficiency in English is required for disseminating your work.

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