Fundamental Quantitative Genetics team (GQF)

Members of the team

Christine DILLMANN	Professor Univ. Paris Sud
Dominique de VIENNE	Professor Univ. Paris Sud
Olivier MARTIN	Professor Univ. Paris Sud
Adrienne RESSAYRE	Junior researcher INRA
Delphine SICARD	Assistant Professor Univ. Paris Sud
Aurélie BOURGAIS	technician CNRS
Warren ALBERTIN	postdoc ANR
Tibault NIDELET	postdoc ANR
Eleonore DURAND	PhD student
Victor SABARLY	PhD student
Aymé SPOR	PhD student

Genome dynamics

Genetic and evolution of biological network

Genetic basis of adaptation

Research topics

The research projects of team GQF aim at modelling the relationship between genetic polymorphism and phenotypic variation, in order to understand the adaptation of populations to new environments. Adaptation is defined as the increase of individual’s fitnesses as a response to environmental changes, which occurs thanks to phenotypics changes for life history traits. Those changes can be plastic, genetic or epigenetic. In order to understand the nature of phenotypic variations, as well as their evolutionary potential, we need to take into account (1) the multiplicity of the sources of genetic and phenotypic variations (Genome dynamics); (2) the effects of genetic variations on phenotypic variation at different integrated levels. In particular, fluxes through metabolic networks are considered as model quantitative traits, which variation depend on the polymorphism of the genes that control the enzymes of the network (Genetics and evolution of biological networks ; Quantitative variations); (3) The consequences of selection and other evolutionary pressures on phenotypic diversity, but also on genetic polymorphism and on the distribution of genetic polymorphism throughout the genome (evolutionary Forces). We develop population genetics and quantitative genetics models. Different model organisms are used to test the predictions of the models (Saccharomyces cerevisiae, Zea mays ssp. mays, genus Helianthus), with different approaches, from statistical modelling to experimental evolution.

Futur prospect: Part of our approach aims at linking the diversity of cell functioning to phenotypic variation. To do this, we wish now to develop a genetics and evolution of biological systems relying on experimental approaches on two microorganisms, S. cerevisiae and E. coli . Both projects aim at characterizing the extant of within species metabolic variation, relating metabolic variation to phenotypic variation possibly submitted to selection (life-history traits, heterosis), and building-up models for the evolution of biological networks. Beside, it seemed to us necessary to develop knowledge on the mechanisms of phenotypic innovation, i.e. the appearance within a population of a new phenotypic trait susceptible to invade the population and the forces that may constraint its success. To understand constraints on genomic innovation, we develop statistical methods to characterize the spatial organization of the genome on the one hand, and on the other hand, we try to understand the genetic basis of recombination in plants. In parallel, we also develop population genetics models to understand the success self-incompatibility in plants (which appear to be a recurrent phenotypic innovation). Finally, we perform experimental evolution experiments in two model species, yeast S. cerevisiae and maize, in order to find the genes that were involved in the adaptation of the evolved populations.

Actual fundings:

COPATH (ANR Blanche): Unraveling crossover pathways with Arabidopsis thaliana and crop relatives. Coord: C. Mézard
METACOLI (ANR SYSCOM): Data integration and modelling of the metabolic diversity of commensal and virulent Escherichia coli strains. Coord: C. Dillmann
HETEROS YEAST (ANR ALIA): Exploitation of the heterosis phenomenon for wine improvement. Coord: D. de Vienne

Collaborations

Metabolic diversity in E. coli :
Claudine Medigue, Pierre-Yves Bourguignon, David Vallenet, Gilles Vieira, Genoscope, Evry, France ; Odile Bouvet, Eric Denamur, Bichat, Paris, France
Metabolism, adaptation and heterosis in yeast :
Monique Bollotin-Fukuhara, Université Paris XI, France ; Michel Aigle, Université Lyon 1, France ; Marina Bely et Isabelle Masneuf-Pomarède, Université Bordeaux 2, France; Philippe Marullo, Entreprise SARCO, France; Sylvie Huet et Christophe Giraud, Mathématiques et Informatiques appliquées, INRA Jouy-en-Josas, France.
Recombinaison :
Raphael Mercier et Christine Mezard, INRA, Versailles, France ; Denise Zickler, Universite Paris-Sud, Orsay, France ; Pierre Sourdille et Cyril Saintenac, INRA, Clermont-Ferrand, France ; Lorinda Anderson, Colorado State University, USA
Reproduction :
Sophie Nadot et Béatrice Albert, ESE, Université Paris XI, France; Pierre-Henri Gouyon et Emmanuelle Porcher, MNHN, Paris, France; Sylvain Billiard, Université de Lilles, France
Robustness and biological network :
Andreas Wagner, University of Zürich, Suisse.
Selective sweep and adaptation in H. paradoxus :
Loren Rieseberg, University of Brittish Columbia, Vancouver, Canada; Sophie Karrenberg, University of Zürich, Suisse

Teaching at the University Paris XI Orsay

Licence 1

PCEM Statistics and Population genetics
UE Discovering biology via current problems (for students in physics)
UE Initiation to research on plants
UE Diversity and evolution of the living world
UE Methodolgy

Licence 2

UE The mathematics of modeling II (for students in biology)

Licence 3

UE Quantitative and population genetics
UE Molecular Biology and Biochemistry
UE Mathematics and Biology

Master 1

UE Biostatistics
UE Parasitism, symbiosis and mutualism in plants
UE Human genetics
UE Evolutionary Ecology
UE Quantitative genomics

Master 2

UE Multifactorial genetics
UE Plant metabolism, metabolomics and proteomics
UE Quantitative genetics and plant breeding
UE The determinants of the variation of complex traits
UE Physics and biological systems
UE Molecular Population Genomics

Graduate school

European Erasmus Course Mathematics and Biology
UE Statistical modelling and analysis of biological data

Former members of the team

(since 3 years)

C. Edelist (PhD)
L. Grima (undergraduate student)
F. Hospital (Senior researcher INRA)
E. Porcher (postdoc)
J. Simon (undergraduate student)
G. Talbot (undergraduate student)
S. Wang (Postdoc)

Selected publications

Martin O.C., Wagner A. (2009). Effects of Recombination on Complex Regulatory Circuits. Genetics, in press
Santure A., Ewen J., Sicard D., Roff D., Møller A.P. (2009). Population structure in the barn swallow, Hirundo rustica: a comparison between neutral DNA markers and quantitative traits. Proc. R. Soc. B. In press
Albert B., Gouyon P.-H., Ressayre A. (2009). Microsporogenesis variation in codiaeum producing inaperturate pollen grain. C R Biol, 332(6), 507–516.
Albertin W., Marullo P., Aigle M., Bourgais A., Bely M., Dillmann C., de Vienne D. and Sicard D. 2009. Evidence for autotetraploidy associated with reproductive isolation in Saccharomyces cerevisiae: towards a new domesticated species. J. Evol. Biol. 10.1371/journal.pgen.1000530
Edelist C., Raffoux X., Falque M., Dillmann C., Sicard D., Rieseberg L. H., Karrenberg S. (2009) Differential expression of candidate salt-tolerance genes in the halophyte Helianthus paradoxus and its glycophyte progenitors H. annuus and H. petiolaris (Asteraceae). Am. J. Bot. 96 1830–1838.
Johannes F., Porcher E., Teixeira F. K., Saliba-Colombani V., Simon M., Agier N., Bulski A., Albuisson J., Heredia F., Audigier P., Bouchez D., Dillmann C., Guerche P., Hospital F., Colot V. (2009). Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet, 5(6), e1000530.
Marullo P., Mansour C., Dufour M., Albertin W., Sicard D., Bely M., Dubourdieu D. (2009). Genetic improvement of thermo-tolerance in wine saccharomyces cerevisiae strains by a backcross approach. FEMS Yeast Res. DOI : 10.1111/j.1567-1364.2009.00550.x
Saintenac C., Falque M., Martin O. C., Paux E., Feuillet C., Sourdille P. (2009). Detailed recombination studies along chromosome 3b provide new insights on crossover distribution in wheat (triticum aestivum l.). Genetics, 181(2), 393–403.
Martin O.C. and Wagner A. 2008. Multifunctionality and robustness tradeoffs in model genetic circuits, Biophysical Journal 94, 2927-2937.
Spor A., Wang S., Dillmann C., de Vienne D. and Sicard D. 2008. “Ant” and “Grasshopper” Life-History Strategies in Saccharomyces cerevisiae. PLoS ONE 3(2): e1579. doi:10.1371/journal.pone.0001579
Kuang H., Van Eck H., Sicard D.,Michelmore R.W., and Nevo E. 2008. Evolution and Genetic Population Structure of Prickly Lettuce (Lactuca serriola) and Its RGC2 Resistance Gene Cluster. Genetics 178, 1547-1558.
Nadot S., Furness C.A., Sannier J., Penet L., Triki-Teurtroy S., Albert B. and Ressayre A 2008. Phylogenetic comparative analysis of microsporogenesis in angiosperms with a focus on monocots. Am. J. Bot. 95, 1426-1436.
Ciliberti S., Martin O.C. and Wagner A. 2007a. Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology, PLoS Comput Biol 3(2): e15.
Ciliberti S. , Martin O.C. and Wagner A. 2007b. Innovation and robustness in complex regulatory gene networks, PNAS 104, 13591-6.
Drouaud J., Mercier R, Chelysheva, L., Bérard A., Falque M., Martin O., Zanni V., Brunel, D. and Mézard C. 2007. Sex-specific crossover distribution and variations in interference level along Arabidopsis thaliana chromosome 4. PLoS Genet 3(6): e106
Falque M., Mercier R., Mézard C., de Vienne D., and O.C. Martin.2007. Patterns of recombination rate along chromosomes : importance of interference and obligate chiasma, Genetics 176, 1453-1467.
Manicacci D., Falque M., Le Guillou S., Piégu B., Henry A.M., Le Guillou M., Damerval C. and de Vienne D. 2007. Maize Sh2 gene is constrained by natural selection but escaped domestication. Journal of Evolutionary Biology 20, 503–516.
Sicard D., Pennings P.S., Grandclément C., Acosta J., Kaltz O. and Shykoff, J.A.> 2007. Specialization and local adaptation of a fungal parasite on two host species as revealed by two fitness traits. Evolution 61, 27-41.
Edelist C, Lexer C., Dillmann C., Sicard D. , and Rieseberg L.H. 2006. Microsatellite signature of ecological selection for salt tolerance in a wild sunflower hybrid species, Helianthus paradoxus. Molecular Ecology, 15, 4623-4634.
Fievet J., Dillmann C., Curien G., and de Vienne D. 2006. Simplified modelling of metabolic pathways for flux prediction and optimization : lessons from an in vitro reconstruction of the upper part of glycolysis. iochem. J. 396: 17-26.
Karrenberg S., Edelist C., Lexer C., Rieseberg L.H. 2006. Response to salinity in the homoploid hybrid species Helianthus paradoxus and its progenitors H. annuus and H. petiolaris. New Phytol. 170, 615-29.
Martin, O.C., Hospital, F. 2006 Two and three-locus tests for linkage analysis using recombinant inbred lines. Genetics 173: 451-459.
Penet L, Nadot S, Ressayre A, Forchioni A., Dreyer L., Gouyon P.H 2005 Multiple developmental pathways leading to a single morph: monosulcate pollen (examples from the Asparagales).Ann Bot (Lond). 2005 Jan;95(2):331-43
Ressayre A., Dreyer L., Triky-Teurtroy S., Forchioni S. and Nadot S. 2005. Post-meiotic cytokinesis and pollen aperture ontogeny : comparison of development in for species differing in aperture pattern. Am. J. Bot. 92, 576-583
Fiévet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, de Vienne D. 2004. Assessing factors for reliable quantitative proteomics based on two-dimensional electrophoresis. Proteomics, 4, 1939-1949.
Lion S, Gabriel F, Bost B, Fievet J, Dillmann C, de Vienne D. 2004. An extension to the metabolic control theory taking into account correlations between enzyme concentrations. Eur. J. Biochem, 271, 1-17.
Ressayre A, Godelle B, Raquin C, Gouyon PH. (2002). Aperture pattern ontogeny in angiosperms. J Exp Zool. 294:122-35.
Bost B., de Vienne D., Moreau L., Hospital F., and Dillmann C. (2001). Genetic and non genetic bases for the L-shaped distribution of QTL effects. Genetics 157: 1773-1787.

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