Postdoctoral position OT-23427
Studying trade-offs between resilience, health and production using top-down and bottom-up approaches
78350 JOUY EN JOSAS
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 multidisciplinary unit UMR GABI (Animal Genetics & Integrative Biology), INRAE, 78350 Jouy-en-Josas (FRANCE) with research stays at UMR PEGASE, INRAE, 35590 St Gilles
Background:
In the framework of the European Partnership on Animal Health and Welfare (EUPAHW, www.eupahw.eu), our research project (2024-2026, 16 partners) has for objective to identify resilience indicators and their relation (trade-offs) with health, welfare and production traits so that we could integrate novel resilience traits in selective breeding.
The issue of trade-offs, for example between health and production traits, is an increasing issue in livestock farming and even more so in an agroecological transition vision. It is a truly complex research question, which requires ambitious, multidisciplinary and across-scales research.
Your mission will be to explore trade-offs between resilience, health and production in chicken and small ruminants using two complimentary approaches: multivariate data analyses and mechanistic modelling, in two phases:
Phase 1: Deciphering the molecular mechanisms of trade-offs between health and efficiency in chicken by analysis of RNAseq transcriptomic data.
In two experimental INRAE chicken lines (selected for a vaccine response and its control line), we showed, from a phenotypic point of view, trade-offs between vaccine response and body weight gain. Blood and muscle samples were taken sequentially after vaccination. The postdoc will be in charge of analysing this comprehensive set of original phenotypic and transcriptomic data on the question of trade-offs between immunocompetence and growth by performing:
- Differential expression analysis with R/Bioconductor package edgeR …
- Functional enrichment analysis with available online tools and databases (String, Ingenuity Pathway Analysis, ClueGo etc)
- Expression clusters of highly correlated genes will be identify using WGCNA
- Interpretation of the results: differential expression, functional enrichment, co-expression clusters.
The postdoc will be able to bring new knowledge, contributing to the deciphering of the molecular mechanisms underlying trade-offs among life history traits. The results, when combined with other omics information, will pave the way to design sustainable genomic breeding programme taking into account trade-offs between immune and efficiency traits.
Phase 2: Simulation of the trade-offs between resilience and performance in contrasted environments
The broader context of trade-offs, and in particular the trade-off between resilience production traits, will be studied using mechanistic models. Resilience has a cost as it relies on a complex of underlying physiological and behavioural mechanisms. This can create trade-offs with other resource demanding traits but the expression of these trade-offs is affected by the environment.
We have state-of-the-art models that simulate the lifetime performance of animals according to their capacities to acquire and allocate energy resources. These mechanistic models allow simulation of the dynamic interplay between resilience and other performance traits in differing environmental scenarios, and thus allow evaluation of the consequences of selecting on resilience in differing environments. The work envisaged will:
- Integrate resilience mechanisms (response/recovery) into the existing mechanistic model, extending it to include individual animal variability in resilience, and its consequences on other life functions.
- Using existing date on lifetime performance and resilience, calibrate and evaluate the impact of this resilience on lifetime performance and longevity.
- Develop environmental scenarios with differing types of perturbation
- Simulate the impact of environmental variability and harshness on lifetime performance
- Quantify the trade-offs between resilience and performance from these simulations
- The postdoc will thereby contribute significantly to ascribing a biotechnical and economic value for the trait resilience in different environments and farm management scenarios.
Training and skills
Recommended training: Doctorate (or equivalent) in genetics/genomics or computational biology
Desired knowledge: Biostatistical approaches for the integration of heterogeneous data and experience in simulation models
Appreciated experience: Hands-on experience in bioinformatics, RNA sequencing, gene expression networking or other NGS workflows, as well as in Python and SQL
Skills: Interest and knowledge in animal health or immunology would be a strong asset
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
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