PhD position - Epigenetic clocks for ruminant species

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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 join the EFISA team at the UMR GABI, based at the INRAE centre in Jouy-en-Josas (Yvelines). The aim of the PhD is to assess the potential role of epigenetic clocks in improving the sustainability of livestock farming, and in particular the functional longevity of dairy ruminants. An ‘epigenetic clock’ is an algorithm that takes localised epigenetic markers (such as DNA methylation) as input and produces an epigenetic age, or physiological age, that is closely correlated with the chronological age of the sample. The difference between epigenetic age and chronological age is a potential biomarker of accelerated or, conversely, slowed ageing. You will have access to DNA methylation datasets, derived either from a bovine methylation chip or from RRBS (reduced representation bisulphite sequencing) for training machine learning algorithms (glmnet, random forest, gradient boosting, etc.) that will suited to the application datasets. Two applications will be available: one on the milk production performance of Holstein cows on the farm, and one on two branches of a divergent genetic selection experiment on functional longevity in goats.

◼ You will be in charge of:

• training and validating epigenetic clocks in cattle and goats, comparing different types of algorithms (penalised regression, random forest, gradient descent, etc.)
• analysing a possible correlation between the epigenetic clock and the maintenance of lactation performance throughout a cow’s career
• investigating the potential impact of genetic selection for functional longevity on ‘epigenetic ageing’ during a lactation cycle in goats
• the estimation of a possible genetic determinism of ‘epigenetic ageing’ as measured by an epigenetic clock in cattle.

 

 

Special conditions of activity :  

This PhD research is funded by the PEPR Agroecology and Digital Technology programme via the ADAAPT scheme. It will be co-supervised by a researcher from the EFISA team at UMR GABI and a researcher from the DREAM team at UMR BREED.

Training and skills

◼ Recommended training :  Agronomy, bio-informatics, genetics, genomics, veterinary sciences

◼ Knowledge required : data sciences and statistics for genomic studies

◼ Appreciated experience : R language, machine learning, analysis of DNA methylation data

◼ Skills sought : strong writing and presentation skills 

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