Application and evaluation of a model for predicting neonatal maturity in pigs

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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

A major concern in pig production is the substantial increase in piglet mortality before weaning, which raises ethical issues regarding animal welfare and causes economic losses. The perinatal period—the first 24 hours after birth—is the most critical. We previously developed a predictive molecular signature of maturity at birth based on 14 metabolites quantified by ¹H-NMR identified as potential biomarkers of stunted growth on 300 piglets of three different genotypes (Maigné et al., hal-04239517). This signature predicts a maturity status (mature or immature) as well as the stability of the prediction (high or low confidence). The objective of the internship is to confirm the role of these 14 metabolites as biomarkers in another dataset.

We propose to study a set of 500 piglets with different genetic backgrounds (e.g. LW lines divergent for residual feed intake, Duroc, Meishan, and also LW, LR, LWxLR piglets from commercial maternities) at different time points before or after the first consumption of colostrum. Several piglet phenotypes were already registered as birth weight, crown-rump length, shoulder width, thorax circumference, survival status, and rectal temperature (critical for thermoregulation at birth), along with vitality score and respiratory ability. For some piglets, infrared thermography data are available to assess thermoregulation abilities (Schmitt et al., 2021). For all piglets, plasma and serum were already collected within the first 24 hours after birth and were already analyzed by metabolomics (1H-NMR spectra, Nuclear Magnetic Resonance). 

The objective of the work will be to analyze the 14 metabolites, the predicted maturity status, and to link them with the piglet phenotypes.

Therefore, the work will mainly consist in performing biostatistics under the free software R. The student will evaluate the relevance of these molecules with an integrative analysis with the available biometric traits. 

The mission will be to develop a Shiny application to apply the predictive signature on new data.

To perform an integrative analysis:

- to evaluate the relevance of the prediction across genotypes, breeding systems, time of samples collection (before or after colostrum taken), serum or plasma,

- to help for interpretation of the biological meaning of the metabolic signature and its relevance for health and genetics.

Training and skills

master 2 biostatistics, master 2 bioinformatics 

systems biology, biostatistics, Shiny application development

statistics, R (R markdown)

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