PhD position OT-21912

PhD (M/F) in Bioinformatics: Investigating the Role of Regulatory Elements in Crop Domestication

38000 GRENOBLE

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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

About Us: Join the dynamic research group Floral Regulators (Flo_Re) at the Laboratoire de Physiologie Cellulaire et Végétale (LPCV), located at CEA Grenoble, France. The Flo_Re team specializes in studying the developmental program leading to flower formation, with a specific focus on the function and evolutionary history of key regulators of gene expression, predominantly transcription factors (TFs).

PhD Journey: Embark on a captivating PhD journey to unveil the genetic determinants of crop domestication. During the domestication process, humans have selected plants based on agronomically advantageous traits. These traits are often related to flower development, such as the size of tomatoes or the number of grains in rice. These traits are underlined by genetic mutations, which increasing evidence suggests are linked to regulatory elements that govern gene expression. The goal of this project is to exploit the team's expertise on regulatory elements and flower development to accurately identify mutations that led to the formation of cauliflower and broccoli.

Research Approach: The successful candidate will identify genetic variants from whole genome short reads sequence data available for hundreds of cauliflower, broccoli, cabbages, and wild-type morphotypes of Brassica oleracea. You will develop a machine learning model for statistical association between sequence variation and morphotypes. The model will take into account the predicted functional effect of the variant, in particular those affecting the binding affinity of transcription factors to DNA in promoter of flower developmental genes. Ultimately candidates sequence variants will be functionally validated in planta.

Collaborative Opportunities: The successful candidate will have the opportunity to collaborate with machine learning experts both in Grenoble and Kyoto.

Training and skills

Master's degree/Engineering degree
  • Proficiency in general bioinformatics and statistics for biology.
  • Programming skills in bash, Python, or R.
  • Prior experience with machine learning packages like caret or scikit-learn would be a valuable asset.
  • A strong Master's degree in a relevant field (bioinformatics, computer science, or related subjects).
  • Knowledge or a strong interest in plant science and gene expression regulation.
  • Excellent proficiency in English (both oral and written).
  • Strong writing 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: trainingcareer 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

Offer reference

  • Contract: PhD position
  • Duration: 36 months
  • Beginning: 01/10/2024
  • Remuneration: about 2 130,00 € gross monthly
  • Reference: OT-21912
  • Deadline: 24/05/2024
Centre Lyon-Grenoble Auvergne-Rhône-Alpes

Laboratoire Physiologie Cellulaire & Végétale - UMR 5168 CEA-CNRS-UNIV. GRENOBLE ALPES – UMR 1417 INRAE 38000 GRENOBLE Website

Contact

BLANC-MATHIEU Romain
romain.blancmathieu@cea.fr
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