2D GWAS in Beech Trees – CEFE Collaboration

In collaboration with the Centre d’Écologie Fonctionnelle et Évolutive (CEFE)

BionomeeX is leading the development and implementation of high-resolution 2D GWAS pipelines to investigate the genetic architecture of key phenotypic traits in beech trees.

The project aims to uncover complex interactions between genetic variants that influence traits critical for forest adaptation, growth, and resilience.

Project Goals

• 🔍 Identify epistatic interactions underlying 5 key phenotypic traits measured in beech trees

• 🌿 Expand the analysis to 20 additional traits, providing a comprehensive view of the genetic determinants of forest phenotypes

• 🖥️ Develop tools that allow researchers to explore and visualize billions of 2D GWAS signals in an interactive and interpretable way

BionomeeX’s Contributions

• ⚙️ In-house 2D GWAS analysis pipeline tailored to large tree datasets (up to 300 individuals, 450,000 SNPs), ensuring data security and high computational performance

• 📊 Processing and delivery of 2D GWAS results for the 5 main traits (~1 TB per phenotype), allowing CEFE researchers to access high-resolution interaction maps

• 💻 Development of a customized LuXioL visualization interface for tree 2D GWAS, including license and training, enabling interactive exploration of complex genetic interaction networks

• 🛠️ Technical support and online interfaces for running rapid 1D GWAS and requesting 2D GWAS analyses via a user-friendly platform, facilitating continuous research workflows

Toward Advanced Forest Genomics

By combining AI, high-performance computing, and advanced visualization, this collaboration allows CEFE to quantitatively dissect the genetic basis of phenotypic variation in beech trees.

It provides insights that can inform forest management, conservation, and adaptation strategies in a changing environment.