Mots-Clés

Plants, Brassica, Transcription factors, DNA-binding, DNA variant, association study

Description

Fully-Funded PhD Opportunity in Bioinformatics: Investigating the Role of Regulatory Elements in Crop Domestication (Grenoble, France)

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.

Candidate Profile:

• 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.

Application Details: We will consider applications until end of April for a start on October 1, 2024.

Practical Information:

• The PhD position comes with a 36-months contract, offering a gross salary of approximately 2200 euros.
• You will be supervised by:
  • Romain BLANC-MATHIEU (CEA Researcher-Engineer)
  • François PARCY (CNRS Research Director and Head of the Flo_Re team)

For informal inquiries and application submissions, please contact Romain Blanc-Mathieu at romain.blancmathieu@cea.fr.

Bibliography ( * our team’s production):

1.            Lai, X. et al. (2019) Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants. Mol. Plant 12, 743–763*

5.            Azpeitia, E. et al. (2021) Cauliflower fractal forms arise from perturbations of floral gene networks. Science 373, 192–197*

6.            Li, X. et al. (2024) Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea. Nat. Genet. DOI: 10.1038/s41588-024-01655-4