The « Quantitative genetics and evolution » Research Unit has international recognition in plant quantitative genetics and molecular diversity, from fundamental aspects including genome evolution to pioneer application in breeding. Our main species of interest is maize, and the UMR is recognized as the main public structure for maize genetics in France, with a total of 54 permanent scientists and technicians. Our expertise covers a large spectrum of aspects including characterization of genetic and genome structure diversity and their impact on phenotype, mapping and recombination, development of new genetic materials and designs for quantitative genetics, application to the analysis of adaptive traits (flowering time, adaptation to water deficit, nitrogen use efficiency). The capacity to explore all these aspects relies on large facilities for material development and phenotyping (approx. 10 ha per year), advanced generic developments in Bioinformatics (meta-analysis, sequence annotation, database development), modeling of metabolic fluxes and recombination, and quantitative proteomics. The UMR has also developed international connections that are directly related to the current project: coordination of the “CornFed” cooperative program, participation to the “DROPS” EU program, participation to the “Integrated Breeding Platform” funded by the Bill and Melinda Gates foundation, coordination of “CNV-Maize” (Coll. with Pat Schnable) and participation to several scientific comities.
UMR Laboratoire d’écophysiologie des plantes sous stress environnementaux (Inra – Montpellier Sup Agro)UMR LEPSE
LEPSE has internationally recognised experience in genetic analysis and modelling of development, growth and transpiration of plants in response to environmental conditions. It has been one of the first groups to develop phenotyping platforms (Phenodyn and Phenopsis which measures growth and development of hundreds of plants of cereals and Arabisopsis respectively under controlled conditions and robotised handling with short (mn) temporal definition), from 2 000 onwards, and the conceptual framework to use them in combination with modelling and with genetic analyses. It is currently building a new platform, PhenoArch with 1 650 plants specialised in plant architecture and growth and their plasticity. It participates as coordinator or as WP leader in major projects associating geneticists, modellers, crop physiologists and breeding groups (ANR Waterless, Dromadair, Generation CP, FP7 DROPS). Publications in major journals involve quantitative genetics, modelling and whole-plant physiology.
UMR Amélioration génétique et adaptation des plantes tropicales et méditerranéennes (Inra – Montpellier Sup Agro – CIRAD - INRIA)UMR AGAP
The maize laboratory of UMR “diversity and adaptation of cultivated plants” (DIAPC) at Montpellier works on maize genetic resources and studies their diversity and adaptation. The laboratory is in charge of the conservation and management of the maize INRA – PROMAIS population collection for France. The team had been the coordinator of a European project on maize genetic resources (RESGEN88) grouping 8 European institutes. Expertise comprises studies on maize genetic resources: genetic structuration, methodology of use, and core collection sampling with software largely used over world. Recently, research of sources of drought tolerance is being studied among temperate and subtropical accessions.
UMR Stress abiotiques et différenciation des végétaux cultivés (Inra – Université Lille 1)UMR SADV
UMR SADV is in charge of several projects dedicated to the study of the physiological and genetic basis of crop responses to abiotic stresses (mainly nitrogen and cold stresses). It has competences in quantitative genetics, genomics and (eco)physiology. The group has a strong expertise on phenotyping under low temperature stress in field conditions as well as in controlled conditions.
The field of expertise of the team “Nitrogen Use Efficiency and Plant Productivity” is to better understand and improve nitrogen use efficiency (NUE: Nitrogen Use Efficiency) in cereal crops. The team has made significant progress in understanding the mechanisms of assimilation and recycling of nitrogen during vegetative growth and during the grain filling period. A multidisciplinary approach combining molecular physiology and agronomy has been developed to study in an integrated manner the regulation of plant nitrogen management. This includes the absorption of nitrogen before and after flowering and its remobilization to the grain after pollination. The group has also developed a quantitative genetics approach to identify key genes involved in the regulation of nitrogen management and to exploit the genetic variability for selecting new varieties with improved NUE. The team is currently searching for other structural and regulatory candidate genes involved in the control of NUE in maize and wheat by combining transcriptome, proteome and whole plant physiology approaches.
The Bordeaux Metabolome Fluxome Platform (BMFP), a French pioneer in the plant metabolomics field since 2001, became an open facility in 2003 and gained an IBiSA label in 2008. In 2009, it contributed to 65 projects (including 6 European projects), acquired about 14 000 spectra or chromatograms yielding about 200 000 data and participated in 23 articles and two book chapters. It is implemented with state-of-the-art equipments and techniques in metabolomics, now involving 19 permanent people (5.9 full time equivalents). Substantial investments (about 3 M€ for 2001-2010) have been implemented in analytic tools such as NMR and mass spectrometers, as well as a nearly unique robotic facilty dedicated to high throughput metabolic phenotyping (Hit-Me). BMFP provides a world-class facility staffed by experts in metabolomics, working closely with leaders in the fields of plant functional genomics, plant genetics and breeding, plant-pathogen/pest relationships and plant ecophysiology, who can provide training, sample analysis and collaboration on experimental design and data handling. BMFP has contributed to 49 projects in 2009 including several European projects and is in close contact with most of the major European plant metabolomics platforms.
Members of partner UMR MIA are all statisticians with a strong experience in molecular biology applications. The “Statistic and Genome” team of the unit AgroParisTech / INRA 518 belongs to the Statistics for Systems Biology (SSB) group (www.ssbgroup.fr/), which is probably the most ancient French statistical group in that field, since it started in the early 90s. Its members have an expertise on linear models, mixture models, segmentation models, model selection, multivariate analysis and variational inference.
MIA-Jouy develops research in mathematics (statistics, system analysis, image analysis) applied to biological and agricultural sciences, for the assessment of health, epidemiological and environmental risks (MathRisq team), and for the analysis of biological systems at the cell and tissue level (MathCell team). The main methodological research topics include: selection of models, branching processes, semi-Markovian processes, experimental design, identification of dynamical systems. The data analysed are very diverse: georeferenced data, enquiry databases, genomic or proteomic databases, time series, digital images in microscopy. MIA-Jouy has a long and strong experience in multidisciplinary research projects involving applied mathematics and genetics, epidemiology or ecology. It offers to such projects a rare combination of competences on theoretical and applied statistics and on dynamic system modelling. MIA-Jouy has collaborated for many years with INRA Le Moulon (partner 1). Recently, both teams have started joint research on bayesian approaches to the modelling of genotype-environment interaction.
The Laboratory of Plant-Microbe Interactions (LIPM), created in 1981, is a combined INRA-CNRS Research Unit, attached to the CNRS Institutes of Biological Sciences (INSB) and Ecology & Environment (INEE), as well as to the INRA Departments of Plant Health & Environment (SPE) and Genetics & Plant Breeding (GAP).
From the outset, the LIPM has focused its research on the interactions between plants and either symbiotic or pathogenic microbes, co-ordinating studies on both plant and microbial partners. This research is performed using a small number of model species (Arabidopsis thaliana, Medicago truncatula), and more recently model plants of agronomic importance such as sunflower and tomato.
These studies allow us to address key biological questions concerning the determinants which control pathogenic/symbiotic associations, the mechanisms of host infection, inter- and intra-organism signaling, developmental programs, regulation of gene expression and finally the mechanisms of metabolic adaptation. Bacterial and plant genome organization is also a theme that we are actively studying using both bioinformatic and genomic approaches.
INRA URGI is a bioinformatics laboratory dedicated to plant and crops parasites genomics. The URGI research activity studies, through “omics” data integration, genome dynamics from functional and evolutionary perspectives. The URGI hosts a major international bioinformatics platform in plant sciences. It has been recognized as an IBISA platform and considered by INRA as “Strategic Platform” (label CNOC from INRA). It also belongs to ReNaBi, the national network of bioinformatic platforms. Services offered by URGI platform cover database design, software engineering, software hosting, data integration, genomics annotation support and support to bioinformatics analysis. The URGI platform develops and maintains a modular and interoperable Information System for plant and pest genomics called GnpIS (URL: http://urgi.versailles.inra.fr/gnpis). It is a powerful multispecies centralized information system with 7 linked relational databases (GnpMap, GnpSnp, GnpArray, GnpSnp, Siregal, GnpSeq, GnpGenome and Ephesis). It is designed to bridge genetic and genomic data, allowing researchers to cross genetic information (i.e QTL, markers, SNPs, germplasms, genotypes, phenotypes) with genomic data (i.e. physical maps, genome annotation, expression data) for species of agronomical interest. The system is used as an international repository for INRA data, Genoplante program data, grapevine data produced by the grape international genome consortium, wheat physical maps and first wheat sequences.
US Etude du polymorphisme des génomes végétaux (Inra)US EPGV
The INRA EPGV, located at the site of the CEA/ Institut de Génomique (IG)/ Centre National de Génotypage (CNG) in Evry i) make available to different groups high-throughput SNP (single nucleotide polymorphism) genotyping tools necessary to respond to diverse questions concerning the plant species studied at the INRA; ii) participate and coordinate the network of genotyping platforms of the plant breeding domain of the INRA; and iii) in collaboration with bio-informaticians, to put in place a system of management for SNP data and the necessary analysis tools.
In 2010, the CEA/IG/CNG is in possession of re-sequencing tools for extremely high capacity sequencing (Sanger sequencing on ABI3730, Roche 454, Illumina Solexa). Direct access to sequencing and genotyping tools of the CEA/IG/CNG by the INRA EPGV group, offers the possibility to INRA groups, in turn, to have an access to tools adequate for their needs during the different steps of their scientific projects.
The “Seed Development” team is part of the “Plant Reproduction and Development” laboratory at the ENS-Lyon, which is internationally recognized for its excellent contributions to our present knowledge in the fields of flower and seed development, both in the model species Arabidopsis and in crop (maize) or ornamental species (rose, petunia). Using functional genomics, the Seed Development team defined and characterized a novel endosperm domain in maize before focusing on a series of transcription factors governing embryo and endosperm development in maize. In 2008 it implemented a maize transformation platform, which has been opened in 2010 for outside collaborations.
The GAEL Research Unit – the Grenoble Applied Economic Laboratory- is a laboratory associated to the INRA and the University Pierre Mendès France. The vocation of this laboratory is to undertake research applied to agricultural biotechnology, consumption behavior and environmental economics. The discipline of reference of the GAEL unit is the economy, and in particular the industrial organization economics, the experimental economics and the environmental economics. The laboratory includes fifteen permanent researchers and professors and many PhD students and post-doctorates. GAEL research programs are articulated around three main topics:
- Innovation and technological changes: research analyzes the economic conditions of the development of biotechnologies, like their impact on the agricultural, food dies and of health.
- Consumption behavior relates more particularly to the analysis of the behavior of food consumption starting from the experimental method.
- The environmental and the natural resources research analyzes the negative and positive externalities generated by the agricultural activities and the exploitation of natural resources.
GEVES (Group for study and control of varieties and seeds) is a partnership of INRA, Ministry for Food, Agriculture and Fisheries, and French Association for seeds and seedlings. It has in charge the evaluation of new plant varieties, quality control and seed conformity, granted by the Ministry in charge of Agriculture. Each year, GEVES studies and controls 2500 plant varieties and 50 000 seed lots. GEVES is involved in research in the field of genetic markers, plant diversity, seed physiology and pathology, improvement of experimental methodology, varietal identification, and seed quality control.