PhD Opportunity in Plant Epigenetics – Characterization of Inter-Individual Epigenetic Variability
Institution: INRAE (French National Research Institute for Agriculture, Food and Environment)
Location: Versailles, France
Start Date: October 2025
Funding: Fully funded via the Concours de l’ED SEVE (GS-BIOSPHERA)
Duration: 3 years
Supervisor: Dr. Vincent Coustham, VarEpi Team, IJPB
Project Overview
A fully funded PhD position is available to investigate inter-individual epigenetic variability in the model plant Arabidopsis thaliana. This project aims to explore variable DNA methylation regions (VMRs) and their potential role in phenotypic plasticity, particularly under changing environmental conditions.
In animals and humans, numerous epigenomic regions exhibit individual-specific methylation patterns, often influencing developmental and environmental response genes. However, the impact of such epigenetic diversity within genetically identical plant populations remains understudied.
This PhD project will address this gap by characterizing VMRs in Arabidopsis, assessing their environmental responsiveness, transcriptional effects, and potential for epigenetic inheritance.
Research Objectives
- Identify and map Variable Methylation Regions (VMRs) in Arabidopsis using Oxford Nanopore sequencing.
- Evaluate the influence of temperature stress during embryonic development on VMR patterns.
- Analyze the association between VMRs and gene regulation, including proximity to regulatory elements and polymorphisms.
- Examine transcriptomic changes related to temperature-sensitive VMRs using RNA-seq and RT-qPCR.
- Study the epigenetic response of VMRs to additional abiotic stresses.
- Investigate whether VMRs are reset or inherited across generations.
Methodology
- Generate clonal populations of Arabidopsis from Col-0 seeds exposed to controlled temperature conditions (18–20°C and 24–26°C).
- Sequence DNA methylation profiles from rosette leaves and primary roots using Oxford Nanopore long-read sequencing.
- Apply validated statistical models to identify VMRs and analyze their distribution and functional relevance.
- Integrate data with existing epigenomic resources, including epiRILs and accession methylomes.
- Explore translational potential by extending findings to tomato (Solanum lycopersicum) in parallel lab research.
Candidate Profile
Required Qualifications:
- Master’s degree (Master 2 or equivalent) in Molecular Biology, Epigenetics, or related fields.
- Strong foundation in statistics and experimental plant biology.
- Basic experience or interest in bioinformatics and genomic data analysis is an asset.
How to Apply
Interested applicants should submit the following documents:
- A summary of qualifications and research interests
- A detailed cover letter
- If available, attach your previous research internship or traineeship report
Send applications to:
📧 Dr. Vincent Coustham
📨 vincent.coustham@inrae.fr