Postdoctoral position (M/F) — Epidemiogenetics of resistance to coccidiosis in chicken

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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 unit "Animal Genetics and Integrative Biology" (GABI, 130 permanent staff, GA "Animal Genetics" department) at the INRAE site in Jouy-en-Josas (78), near Paris. Within GABI, you will be part of the GeMS team: "Genetics, Microbiota, Health." The team studies the combined impact of genetics, the gut microbiota and immunity, as well as their interactions, on the health of pigs and chickens. It analyses the genetic determinism of resistance to specific pathogens and develops integrative biology approaches to identify predictive biomarkers or good-health signatures that can be used in livestock farming and/or for selection.

Your mission will be part of the European partnership EUPAHW (European Partnership on Animal Health and Welfare), within activity SOA23 dedicated to epidemiogenetic approaches to animal health. Improving the resistance of livestock to infectious diseases is a major lever for the agroecological transition, animal welfare and the reduction of inputs. Avian coccidiosis, which is endemic and costly, is a good illustration of this challenge: the growing resistance of Eimeria to anticoccidials and the cost of vaccines make it necessary to turn to alternative strategies, among which is genetic selection. However, classical quantitative genetics models predict poorly the effect of selection on the prevalence of an infectious disease, because they ignore host-host interactions and transmission dynamics within groups. Epidemiogenetics combines epidemiology and genetics to guide selection towards traits that promote animal health in the face of infectious diseases, not only at the individual scale but also within the group.

The position will draw on data from the EPIDGENCO experiment, which has already been carried out and whose design constitutes a rare resource on an international scale. Two contrasting chicken lines — the Fayoumi breed, known to be resistant to coccidiosis, and a commercial broiler line — were reared in small groups within which a single animal was inoculated with Eimeria acervulina, allowing the natural spread of the parasite to its naïve group-mates to be monitored. Each animal was subject to daily individual monitoring for one month, combining measurement of oocyst excretion and body-weight measurement, supplemented by feed-intake data, a lesion score and biological samples. This design opens the possibility of jointly estimating several key host-response traits that have never been quantified simultaneously in this species: susceptibility, infectivity, duration of infection, tolerance and compensatory growth. Their estimation and comparison between breeds is precisely the object of this postdoctoral position, together with the use of its results for simulation and modelling studies.

You will be more specifically in charge of making the most of this dataset and to link it to an epidemiogenetic modelling framework, around three areas :

1. Analysis of experimental data — estimating and comparing the epidemiological and production parameters of the two breeds from the excretion and growth curves, drawing on SIR-type infection dynamics models. This work extends and confronts against real data the simulation model developed in Ithurbide et al. 2026 (doi.org/10.1371/journal.pone.0343712).
2. Modelling and simulation — using the phenotypic contrast observed between breeds as an upper bound on the genetic variability that can be mobilised, in order to define a range of plausible genetic parameters for the five traits studied. Coupled with the epidemiological model, these parameters will make it possible to simulate coccidiosis epidemics in a large number of situations and virtual farms incorporating genetic variability between animals. These simulations will serve to identify the trade-off between phenotyping effort (nature, frequency and resolution of measurements of infection status) and the precision of genetic evaluation, including for socially modulated traits such as susceptibility and infectivity.
3. Dissemination — writing scientific articles, presenting results at EUPAHW consortium meetings and international conferences.

No special conditions

Training and skills

Recommended training : phd in animal genetics, epidemiology, biostatistics, computational biology or a related discipline. 

Desired knowledge : proficiency in statistical programming (e.g. R and/or Python) and in handling complex datasets; knowledge of epidemiological modelling (compartmental models) and/or quantitative genetics.

Appreciated experience : experience in infectious disease modelling and/or quantitative genetics will be particularly appreciated.

Skills : rigour, organisation, ability to work independently.

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