UMR de Génétique Végétale

The Plant Genetics Unit  (PGU) has international recognition in Genetics, Genomics & Evolution of Complex traits (multifactorial genetics). Our projects favor integration across levels, from genome organization and gene/metabolic networks to populations and crop varieties. We have four main related objectives:

• Increasing knowledge in fundamental multifactorial genetics, in the fields of QTL detection and identification, modeling quantitative variation, systems biology, dynamic management of genetic resources and evolution of complex traits.
• Increasing knowledge on processes driving the organizational and functional evolution of plant genomes, in order to detect genomic features and mechanisms responsible for adaptation and phenotypic innovations.
• Conceiving pioneer breeding methods, by combining genomics and exploitation of genetic resources, with special attention to traits related to growth, development and adaptation.
• Providing genetic materials meeting requirement for sustainable agriculture.

We primarily work on crops (maize, wheat, Brassica), but model species are also used to address specific questions regarding recombination modeling, network functioning, experimental evolution or long term evolution (Arabidopsis, yeast, E. coli, early-diverging eudicots).
The Plant Genetic Unit is supervised by INRA (UMR 320), University Paris-Sud and CNRS (UMR 8120), and includes people from these institutions and from AgroParisTech, an agronomical University. There are 80 permanent and temporary people, including PhD students and postdocs. The Plant Genetics Unit is one of the four Units of the Federative Research Institute The plant and its environment (IFR 87, CNRS-INRA-University Paris-Sud-AgroParisTech-ENGREF), and is member of a Research Federation of the CNRS (IDEV, FR3284).

Research teams

Fundamental Quantitative Genetics (GQF). Head: Christine Dillmann, University Paris Sud.
Modelling of quantitative variation, integrating the genetic, molecular, genomic, physiological (using the theory of metabolic control) and environmental levels.  

Quantitative Proteomics and Molecular Genetics (GQMP). Head: Michel Zivy CNRS.

Molecular and physiological characterization of QTL involved in the responses of maize to drought stress using a “candidate gene and protein” approach. This strategy is based on a quantitative analysis of the variability of protein expression.

Evolutionary Genetics: Adaptation and Redundancy (GEAR). Head: Catherine Damerval, CNRS.

Study of evolutionary mechanisms responsible for phenotypic diversity, with a particular interest in the role of genetic redundancy. The topics include the evolution of duplicated genes, domestication, polyploidy and floral symmetry.

Quantitative Genetics and Plant Breeding Methodology (GQMS). Head: Alain Charcosset, INRA.

Study of genetic bases of complex traits and mechanisms of response to selection, from the analysis of diversity in collections and experimental populations. Optimizing genetic resource management and selection process using the results of these studies and theoretical approaches.

Diversity, Evolution and Adaptation of Populations (DEAP). Head: Isabelle Goldringer, INRA.

Using wheat as the experimental model, study of the dynamic management of crop biodiversity and its exploitation through sustainable and innovative agro-ecosystems.

Proteomic platform and other facilities

Our objectives imply methodological developments in modeling, bioinformatics, system biology, population & quantitative genetics/genomics and proteomics. We have created a recognized platform and two facilities to implement technological approaches required for large-scale genetics and genomics projects, and we have access to an experimental field facility:

• PAPPSO, the IBiSA-labelled proteomics platform of Paris South-West (http://pappso.inra.fr) is the largest in Paris area. It includes 9 scientists and technicians. It is located on two close sites, one in the Plant Genetics Unit and the other in INRA at Jouy. It includes all equipment for proteomics based on protein separation (2D-gels, scanners, image analysis, robot for spot picking) and for proteomics based on peptide separation, i.e. digestion of complex mixtures of proteins followed by LC and MS/MS.
• The bioinformatics and informatics facility (ABI, Atelier Bioinformatique et Informatique) provides bioinformatics expertise and IT support. The staff includes 6 experts in system administration, software development or bio-analysis, and develops databases and softwares for proteomics, genetics and genomics. ABI offers hardware resources, scientific programming and consulting for DNA, RNA and protein sequence analysis up to genome-wide scale. ABI works in tight collaboration with the Bioinformatics facilities of University Paris-Sud and INRA, and contributes to the future French Bioinformatics Institute.
• The molecular biology facility (ACEP, Atelier Cartographie, Expression et Polymorphisme) includes 4 engineers and technicians, and offers expertise, technological watch, training and support for the projects of the laboratory. It is oriented towards (i) molecular markers, (ii) sequence polymorphism analysis and (iii) gene expression studies. This facility is organized to analyze large numbers of plant samples over short periods of time, due to the seasonal constraints of marker-assisted breeding.
• We have a privileged access to a local experimental field facility (92 ha) managed by INRA, which is equipped with all standard and specialized agricultural machinery. This facility is used for the in-field experiments of breeding and dynamic management of genetic resources, for displaying collections of genetic material and for educational experiments for the students of the University Paris Sud and AgroParisTech.

National and international scientific contracts

Currently, partner GVM is involved in 23 research contracts:

• 10 ANR contracts (total 1.637 M€), 5 of them led by scientists of partner GVM.
• 9 non-ANR contracts (total 732 k€), 7 of them led by scientists of partner GVM.
• 3 European contracts (total 1.060 M€), 1 of them led by a scientist of partner GVM.
• 1 international contract funded by Generation Challenge Program and the Bill and Melinda Gates Foundation: Integrated breeding platform, oriented towards developing countries (157 k€; leaded by CIMMYT and involving 10 partners including Mexico, China, Philippines and Africa).

Major results
In the recent years, the Plant Genetics Unit has obtained major results in various fields:

• Tool and method developments: genetic mapping of hundreds candidate genes in maize, development of software’s and databases (see below), development of multiparental and intermated genetic material for QTL detection, that have proven instrumental to reveal allelic series and epistatic effects.
• Modeling: analysis of robustness and evolvability in gene networks, heuristic modeling of metabolic networks and new approaches for modeling recombination and interference.
• Genetics and genomics: exploitation of maize genetic resources using association genetics (relationship between flowering precocity and Dwarf8 polymorphism, and major role of Vgt1); importance of epistasis between O2 transcription factor and its target CyPPDK for seed quality; relationship between FT and VRN-1 polymorphism and flowering precocity and local adaptation to climate in wheat; validating the role of protein ZmASR1 for the adaptation of maize to drought; diversity of life-history strategies in yeast, rapid alteration of protein expression in Brassica in response to allopolyploidisation.