Our research unit benefits of many research contracts, either international (EU, bilateral collaborations etc.) or national (ANR, Aquitaine Region, INRA...).
Ongoing Research Projects
(non exhaustive list)
European research Projects
2012-2016 Project FORGER supported by the European Union (FP7, N°289119) « Towards the Sustainable Management of forest genetic resources » Coordinated by Koen Kramer (Alterra, Wageningen, Hollande). 9 partners from 8 countries.
The FORGER project aims at integrating and extending existing knowledge to provide science-based recommendations on the management and sustainable use of FGR for EU-policy makers, national stakeholders, forest managers, and managers of natural areas. The project will galvanize around five interconnected objectives: 1) synthesize and further develop knowledge from European FGR inventories by linking and extending existing databases to provide the knowledge base to sustain FGR at the pan-European level for stakeholders; 2) deliver a general monitoring system of forest genetic diversity that can be efficiently and economically applied by all EU Member States; 3) assess current and future distribution of genetic diversity under a number of forest management scenarios and climate change; 4) provide an overview of past and current transfer of forest reproductive material across Europe and its consequences for local adaptation; 5) formulate guidelines and recommendations to sustain forest genetic resources in both gene conservation units and production forests to meet the challenge of a changing environment and societal needs."
2010-2011 Coordination and Support Action FORESTTRAC supported by the European Commission (FP7, # 244096) “Forest ecosystem genomics Research : supporTing Transatlantic Cooperation” Coordinator: Antoine Kremer (INRA, UMR Biogeco). 11 partners from 7 countries http://www.foresttrac.eu/
The main aim of the coordination action is to prepare future coordinated research plans between Europe and North America regarding adaptation of forest trees to climate changes, linking different disciplines: ecology, genetics, genomics and evolution. The Coordination Action will deliver a mapping of current research capacity and state of the art research in forest ecosystem genomics, a validated research roadmap regarding adaptation to climate change, a set of joint science plan, a collection of genomic resources preparing future whole genome sequencing of ecologically and economically important tree species. All project outcomes will be validated during the project by a wide group of stakeholders from Europe and North America and will be disseminated widely via the project website and key dissemination
2009-2013 Project MOTIVE supported by the European Commission (FP7, # 226544) « Models for Adaptive Forest management». Coordinator : Mark Hanewinkel (Forest Research Institute of Baden-Wuerttemberg, Germany). 20 partners from 14 countries. http://motive-project.net/
Which trees can adapt best to climate change – this is one of the key questions which the newly started project is trying to answer. MOTIVE investigates adaptive management strategies that address climate and land use change. It also examines the impacts of these changes with respect to a broad range of forest goods and services. The project focuses on a wide range of European forest types under different intensities of forest management. Specific attention will be given to uncertainties and risks and how they can be considered in improved decision support tools.
2006-2010 Network of Excellence EVOLTREE supported by the European Commission (FP6, # 016322) « Evolution of trees as drivers of terrestrial biodiversity ». Coordinator : Antoine Kremer (INRA, UMR Biogeco). 25 partners from 15 countries. http://www.evoltree.eu/.
This project aims to associate four complementary disciplines – ecology, evolution, genomics and genetics – in order to predict how species and communities will respond to environmental changes. The research carried out by network will centre around the diversity of woodyn species and their evolution in response to climate change, and the effects of this evolution on the biodiversity of forest ecosystems. Indeed, the intensity of predicted climate changes raises questions as to the response of long-living species. The adaptive capacities of trees are linked to the functional genetic diversity existing within current stands. One of the aims of this project is to determine the degree and distribution of gene diversity involved in adaptation to the environment: drought-resistance, length of growing season, etc. Particular emphasis is laid on trees and their diversity, but other associated organisms such as insects and fungi are also being studied
National Research Projects
2011-2015 Project GENOAK supported by ANR « Sequencing of the oak genome and Identification of genes that matter for forest tree adaptation » Coordinated by Christophe Plomion (INRA, Biogeco). 5 partners (INRA Biogeco, Genoscope, INRA Urgi, INRA Gdec, INRA Iam)
The objectives of GENOAK are three fold: 1/to obtain a reference sequence for the pedunculate oak (Quercus robur) genome. Sequencing of a genome like oak (740Mb/C) is indeed becoming possible at a substantially reduced cost due to breakthroughs in sequencing technologies and advances in bioinformatics, 2/annotate the genome and make the data and results available to the scientific community through interoperable databases, and 3/identify genes that matter for forest tree adaptation through the analysis of adaptive divergence (incipient ecological speciation) at the transcriptome and genome-wide levels by respectively i) identifying differentially expressed genes between four interfertile white oak species (sessile, pedunculate, pubescent and pyrenean oaks) adapted to different edapho-climatic environments, and ii) analyzing the size, distribution and nature of genomic islands of divergence maintained in the face of gene flow of the same four sympatric species. The project is a joint initiative of 4 INRA labs and Genoscope.
2010-2013 Project PHYLOSPACE supported by ANR «Integrating cophylogenies, area shifts and paleomaps for inferring history of associations under climate change». Coordinator : Alain Franc (INRA-UMR Biogeco). 5 partners https://w3.pierroton.inra.fr/phylospace/index.php
The question addressed in the project is to better elucidate the connections between climatic oscillations and loss or gains in biodiversity. This is a key issue, as we are facing a challenge of both rapid climatic change and biodiversity loss as consequences of anthropogenic causes. The project consists in (i) developing a new method for taking into account geographical information within the phylogenetics inference process, (ii) including construction of series of paleoclimatic and paleoenvironmental maps throughout the time periods where speciation and migration will be inferred, (iii) reconstructing the interplay between long distance migration and speciation as an adaptation to climatic changes, (iv) deriving some possible consequences on associations between species, especially trees and phytophagous insects, and (v) testing it on various systems. A second expected outcome is that learning the lessons from the past may lead to a better understanding of the problems at present or in the future. A specific attention will be paid to PETM (Paleocene / Eocene Thermal Maximum) which is a well documented Cenozoic event (55.8 My ago) where temperatures raised by several degrees within a very short time period (of the order of centuries).
2009-2011 Project METAQTL supported by ANR « Methods and bioinformatics tools for QTL meta-analysis and integration of meta-QTL, physical maps and genome sequence » Coordinator : Johann Joets (INRA-Moulon). 7 partners.
METAQTL is a project dealing with methods and bioinformatics tools for QTL meta-analysis and integration of meta-QTL, physical maps and genome sequence. Integrative QTL meta-analysis methods are developed to take full advantage of existing results to more accurately predict the most probable location of QTL. Methods are also devised to build consensus map by integrating genetic map and QTL map positions and making it easier to search for co-localization between genes and QTL. These methods are implemented into the BioMercator software thanks to the previous support of Génoplante and The Generation Challenge program. This tool is widely used by the community but suffers from a number of limitations, that will be addressed in this proposal..In particular, a new and urgent requirement is to be able to project meta-QTL onto a physical map or genome sequence. This will allow a user to integrate QTL mapping results with genome annotation usually provided by genome browsers that become central tool for research as soon as genomic resources are made available. This project brings together a large panel of public and private researchers working on several crop and forestry species (maize, wheat, peach, apricot, oak, poplar), who will contribute to the definition of the specifications and test of an improved version of BioMercator and GnpIS
Regional Research Projects
2010-2013 Project PHENOLOGY supported by the Aquitaine Region «Phenolgy and adaptational strategies of populations to climate change ». Coordinator: Sylvain Delzon (INRA-UMR Biogeco). 5 partners
The project aims has three major objectives (1) provide an assessment of biodiversity in different ecosystems of South West of France, (2) identify key mechanisms that drive the evolution of biological diversity, (3) estimate the capacities of natural populations to adapt to climatic changes. The project focuses on biological rhythms of natural populations, as being important components of their adaptive value, by addressing three different issues:
- Variation of phenological traits as indicators of global changes
- Ecological and genetic drivers of phenological variations
- Changes of phenological synchronization in communties