GFP2 team

Functional Genomics, Population Genomics and Prediction Team

Objectives

For trees, wood is a vital tissue that provides mechanical support, sap conduction and reserve storage. For humans, it is a very important renewable resource, an alternative to fossil carbon, enabling carbon sequestration and providing biomaterials, energy and biomolecules. Roots are important for anchoring trees in the soil and for water and mineral nutrition. The team is developing complementary approaches in functional genomics and quantitative and population genetics to (1) understand some developmental processes involved in physiological functions characteristic of trees - wood formation, root development - that are important for their adaptation to a fluctuating environment, and (2) predict some complex traits, related to the adaptation and production of trees.

The team is developing genomics approaches mainly on poplar model species, with 1)  the production of transgenic or CRISPR-Cas9-edited poplars for genes of interest (chosen from functional or genetic studies), 2) the detailed analysis of transcriptomic and phenotypic changes in wood and roots produced by these poplars, 3) the identification of polymorphisms and characterisation of gene diversity, 4) the integration of experimental endo-phenotypic data into dynamic biological networks to understand and predict phenotypes.

The team aims to answer the following questions:

  • What are the molecular mechanisms underlying wood formation and its properties?
  • What are the main genetic regulators of root architecture and development, and what are their genetic targets?
  • What genome-wide variations explain the distribution, structure and dynamics of populations?
  • How can variation in endo-phenotypes explain and help to predict traits of interest in terms of adaptation and production within populations?

The team's research can rely locally on the PHENOBOIS platform and the LICA, and nationally on the network of comparative plantations (GEN4X).

Species

Poplars are the main studied species. Functional genomics studies are being carried out on INRA clone 717-1B4 (P. tremula x P. alba), which is amenable for genetic engineering and genome editing. Diversity studies are being carried out on a large collection of natural populations of P. nigra. Some studies are also performed on larch, Douglas fir and black locust.

Keywords

Gene networks, modelling, microphenotyping, single cell, multi-omics

Team leaders

Annabelle DEJARDIN and Véronique JORGE

Members

Research scientists: Christian BRETON (CRHC),  Annabelle DEJARDIN (DR2, HDR), Harold DURUFLÉ (CRCN), Jean-Charles GAUDIN (CRCN), Véronique JORGE (CRHC), Leopoldo SANCHEZ (DR2, HDR),  Gilles PILATE (DR1, HDR)

Engineers and technicians : Nassim BELMOKTHAR (IECN), Vanina BENOIT (IECN),  Nathalie BOIZOT (IECN), Corinne BURET (TREX), Justine CORRET (AI), Françoise LAURANS (IR1), Odile ROGIER (IEHC)

Non-permanent staff : Xabi CAZENAVE (Post-doc, funded by DIVEDIT), Alexandre DUPLAN (PhD student, funded by the Centre Val de Loire Region 2022-2025), Yiyi TAN (PhD student, funded by the Centre Val de Loire Region 2022-2025), Laura VIMENET (PhD student, funded by INRAE- Centre Val de Loire Region 2022-2025), Orlane TOUZET (Fixed-term contract, FuturoChêne Project)

  • Alexandre DUPLAN studies the pan-genomic prediction of complex phenotypes using an integrative multi-omics approach in black poplar.
  • Yiyi TAN studies the dynamics of secondary wood fibre wall formation in poplar using a single cell approach.
  • Laura VIMENET studies the impact of lignin acylation on tree development, wood formation and biomass energy conversion.

Current projects

European projects

FORGENIUS (Improving access to FORest GENetic Resources Information and Services for End-USers) - 2021-2025

National projects (ANR, PEPR)

ANR AAPG21 DEOX (Puzzling out the role of plant and fungal laccases with auxiliary enzymes during depolymerization and polymerization of lignin in a polysaccharide environment) - 2022-2026

PEPR Advanced Plant Breeding TYPEX (Toward highlY Predictable Editing of the plant genome leXicon) - 2023-2028

PEPR Advanced Plant Breeding DIVEDIT (Promoting agrobioDIVersity through genome EDITing) - 2023-2028

Regional projects

APR - IR WoodProActif (Bioactive mulches for soil sanitation and crop protection) - 2020 - 2024

APR-IA MycoPop (Mycorrhization of poplars to preserve water resources) - 2024 - 2025

APR-IR Futurochêne (Chemical and sensory characterisation of the oak of the future) - 2023-2025

Publications

Modification date : 12 March 2024 | Publication date : 05 January 2024 | Redactor : BV