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Génétique Quantitative et Évolution - Le Moulon

BASE - Biology and Adaptation, Systems in Evolution

BASE team members TO REDO

We combine experimental approaches and mathematical modeling to investigate the complexity of genotype-phenotype relationships and their evolutionary consequences at different scales, and to understand how a population can adapt to a changing environment.


Illustration of our research themes

The environment includes abiotic (resources, climate) and biotic (conspecifics, other species) factors which interact with the organism along its whole life cycle. Phenotypes can be declined at different integration levels: life history traits, development, growth and morphology, but also molecular phenotypes and cellular-scale metabolism. We develop mathematical models in quantitative genetics, epidemiology, and systems biology, to understand how the phenotype is buiilt from the genome and its interactions with the environment at these different levels of integration. Our favorite study models are Maize (Zea mays) and the budding yeast (Saccharomyces cerevisiae).

Roles of evolutionary pressures on the dynamics of adaptation

  • Experimental evolution

    • The Saclay Divergent Selection Experiments: since 1996, four Maize populations are being selected for flowering date on the Saclay plateau. Each population descends from a seed lot of an inbred line (F252 or MBS847) and was selected for earlyness of lateness of its flowering date. The original genetic material produced allows to investigate the target traits of selection, to study the dynamics of the response to selection, and to generate inbred lines descending from the same genetic background but differing for their flowering date.
      Collaborators: INRAE experimental units in Saint-Martin de Hinx and Mons-Picardie.

    • Recurrent selection for meiotic recombination rate in budding yeast: using original tools developed in the team for high-throughput phenotyping of recombination rate and interference (Raffoux et al., 2018), our objective is to better understand the evolutionary nature of recombination rate within a species, and the link between recombination and adaptation to stress.
      Collaborators: G. Litti.

    • Selection for resistance to starvation in E. coli: in the frame of a teaching module of the Biology licence of University Paris-Saclay, we introduce Evolution to the students by making them participating to an experimental evolution experiment.
      Each year, we compare the proteome of ancestor and evolved strains thanks to a collaboration with the PAPPSO platform.

  • Models for population genetics and quantitative genetics

    • Dynamics of response to selection: we have demonstrated the interest of introducing hyper-recombinant progenitors in genomic selecion programs (Tourrette et al., 2020). Elsewhere, mathematical modeling of the response to selection in the Saclay Divergent Selection experiments on Maize allowed us to unveil the combined roles of drift and selection for a quick adaptation to a new environment (PhD A. Desbiez-Piat).

Projets : Itemaize. ANR Evolrec (submitted)

Phenotypic plasticity, genotype-phenotype relationship, and variation of life-history traits

Life-history traits and phenotypes of interest have a complex heredity that emerges from the organisation in gene network and metabolism along development, and their complex interplay with the environment leading to phenotypic plasticity. We are particularly interested in genetic variations of phenotypic plasticity, also called genotype by environment interactions. Our favorite models are :

  • drought tolerance and flowering time in Maize
  • plant/herbivorous insects interactions in Maize
  • molecular bases of heterosis and inbreeding depression

and we use and develop therefore different approaches, including:

  • taking into account climatic variables
  • genetic mapping
  • integrative biology
  • analysis of the regulation of protein abundances

Projets : Amaizing; Warm Rules; projet GNIS Phenophore; ANR HeteroYeast.

Genomes dynamics

Some traits like recombination rate, gene structure, and the mode of reproduction, are submitted to selection at the level of the species and determine the level of intra-specific genetic diversity. We use comparative genomic approaches combined with population genetics models to understand the dynamics of genomes.

Main collaborators: S. Glémin (structure of genes), R. Mercier (meiotic recombination), J. Enjalbert, X. Veckemans (modes of reproduction).


BASE is attached to the LabEx BASC, Biodiversité, Agroécosystèmes, Société, Climat.

Members

  • Romain Benoist Postdoctoral fellow (INRAE)
  • Willy Vincent Bienvenut Junior Investigator (CNRS), 50% BASE, 50% PAPPSO
  • Mélisande Blein-Nicolas Engineer (INRAE), 50% BASE, 50% PAPPSO
  • Charlotte Coton PhD student (Université Paris-Saclay)
  • Dominique de Vienne Professor (Université Paris-Saclay)
  • Arnaud Desbiez-Piat PhD student (Université Paris-Saclay), 50% ACEP, 50% BASE
  • Christine Dillmann Professor (Université Paris-Saclay, Faculté des Sciences)
  • Yacine Djabali PhD student (Université Paris-Saclay)
  • Matthieu Falque Research Engineer (INRAE), 50% ACEP, 50% BASE
  • Nathalie Galic Technician (INRAE)
  • Judith Legrand Assistant professor (Université Paris-Saclay)
  • Élodie Marchadier Assistant Professor (Université Paris-Saclay)
  • Xavier Raffoux Technician (INRAE), 50% ACEP, 50% BASE
  • Adrienne Ressayre Research scientist (INRAE)
  • Inoussa Sanané PhD student (Université Paris-Saclay)
  • Elise Tourrette M2, doctorante et postdoctorante (INRAE)
  • Adrien Vidal Ingénieur d'études, CDD (INRAE)
  • Michel Zivy Senior Investigator (CNRS), 50% BASE, 50% PAPPSO

Former members

Edith Garot Postdoc (2020), Olivier Martin Senior Investigator (2010-2019), Marianyela Petrizzelli PhD student (2015-2019), Dorian Collot PhD student (2015-2018), Dephine Sicard (2007-2015), Johan Ramsayer (2008-2015), Thelma da Silva PhD student (2011-2014), Timeri Atuhahiva PhD student (2015-2014), Eleonore Durand PhD student (2008-2011), Thibault Nidelet Post-doctoral fellow (2011-2010)

Publications

  • Blein-Nicolas M. , Negro SS., Balliau T., Welcker C., Cabrera-Bosquet L., Nicolas SD., Charcosset A., Zivy M. . (2020) A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize. Genome Res., 11 (30) 1593-1604
  • Carrillo-Perdomo E., Vidal A. , Kreplak J., Duborjal H., Leveugle M., Duarte J., Desmetz C., Deulvot C., Raffiot B., Marget P., Tayeh N., Pichon JP., Falque M. , Martin OC., Burstin J., Aubert G.. (2020) Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map. Sci Rep, 1 (10) 6790
  • Falque M. , Jebreen K., Paux E., Knaak C., Mezmouk S., Martin OC.. (2020) CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data. Genetics, 3 (214) 561-576
  • Hanemian M., Vasseur F., Marchadier É. , Gilbault E., Bresson J., Gy I., Violle C., Loudet O.. (2020) Natural variation at FLM splicing has pleiotropic effects modulating ecological strategies in Arabidopsis thaliana. Nat Commun, 1 (11) 4140
  • Harlé O., Legrand J. , Tesnière C., Pradal M., Mouret JR., Nidelet T., Ohya Y.. (2020) Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions. PLoS ONE, 5 (15) e0233285
  • Henry V., Saïs F., Inizan O., Marchadier É. , Dibie J., Goelzer A., Fromion V.. (2020) BiPOm: a rule-based ontology to represent and infer molecule knowledge from a biological process-centered viewpoint. BMC Bioinformatics, 1 (21) 327
  • Sanane I., 20 octobre 2020, Composantes de la dynamique de l’interaction entre le maïs et les insectes lépidoptères foreurs de tige
  • de Vienne D. , Fiévet JB.. (2020) The Pitfalls of Heterosis Coefficients. Plants, 7 (9) 875
  • Bienvenut W. V. , 2 décembre 2019, Des débuts de la protéomique à l'acétylation N-terminale des protéines chez les plantes
  • Jebreen K., Petrizzelli M., Martin OC.. (2019) Probabilities of Multilocus Genotypes in SIB Recombinant Inbred Lines. Front. Genet., (10) 833
  • Petrizzelli M., de Vienne D. , Dillmann C. . (2019) Decoupling the Variances of Heterosis and Inbreeding Effects Is Evidenced in Yeast's Life-History and Proteomic Traits. Genetics, 2 (211) 741-756
  • Petrizzelli M., 8 juillet 2019, Mathematical modelling and integration of complex biological data: analysis of the heterosis phenomenon in yeas
  • Srisuwan S., Sihachakr D., Martin J., Valles J., Ressayre A. , Brown SC., Siljak-Yakovlev S.. (2019) Change in nuclear DNA content and pollen size with polyploidisation in the sweet potato (Ipomoea batatas, Convolvulaceae) complex. Plant Biol (Stuttg), 2 (21) 237-247
  • Termolino P., Falque M. , Aiese Cigliano R., Cremona G., Paparo R., Ederveen A., Martin OC., Consiglio FM., Conicella C.. (2019) Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. Plant J, 6 (100) 1163-1175
  • Tourrette E. , Bernardo R., Falque M. , Martin OC.. (2019) Assessing by Modeling the Consequences of Increased Recombination in Recurrent Selection of Oryza sativa and Brassica rapa. G3, 12 (9) 4169-4181
  • Tourrette E. , 25 novembre 2019, Unleashing genetic diversity in breeding by increasing recombination: an in silico study
  • Urien C., Legrand J. , Montalent P., Casaregola S., Sicard D.. (2019) Fungal Species Diversity in French Bread Sourdoughs Made of Organic Wheat Flour. Front. Microbiol., (10) 201
  • Vasseur F., Fouqueau L., de Vienne D. , Nidelet T., Violle C., Weigel D.. (2019) Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana. PLoS Biol, 4 (17) e3000214
  • Albert B., Ressayre A. , Dillmann C. , Carlson AL., Swanson RJ., Gouyon PH., Dobritsa AA.. (2018) Effect of aperture number on pollen germination, survival and reproductive success in Arabidopsis thaliana. Ann. Bot., 4 (121) 733-740
  • Carbonetto B., Ramsayer J., Nidelet T., Legrand J. , Sicard D.. (2018) Bakery yeasts, a new model for studies in ecology and evolution. Yeast, 11 (35) 591-603
  • Collot D., Nidelet T., Ramsayer J., Martin OC., Meleard S., Dillmann C. , Sicard D., Legrand J. . (2018) Feedback between environment and traits under selection in a seasonal environment: consequences for experimental evolution. Proceedings. Biological sciences, 1876 (285)
  • Fiévet JB., Nidelet T., Dillmann C. , de Vienne D. . (2018) Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From in Vitro Genetics and Computer Simulations. Front. Genet., (9)
  • Raffoux X. , 2018-06-11 06/11/18, Diversité et déterminisme génétique de la recombinaison méiotique chez Saccharomyces cerevisiae
  • Raffoux X. , Bourge M., Dumas F., Martin OC., Falque M. . (2018) High-throughput measurement of recombination rates and genetic interference in Saccharomyces cerevisiae. Yeast, 6 (35) 431-442
  • Raffoux X. , Bourge M., Dumas F., Martin OC., Falque M. . (2018) Role of Cis, Trans, and Inbreeding Effects on Meiotic Recombination in Saccharomyces cerevisiae. Genetics, 4 (210) 1213-1226
  • Tenaillon MI., Sedikki K., Mollion M., Guilloux ML., Marchadier É. , Ressayre A. , Dillmann C. . (2018) Transcriptomic response to divergent selection for flowering time in maize reveals convergence and key players of the underlying gene regulatory network. bioRxiv, 461947
  • Giraud H., Bauland C., Falque M. , Madur D., Combes V., Jamin P., Monteil C., Laborde J., Palaffre C., Gaillard A., Blanchard P., Charcosset A., Moreau L.. (2017) Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.). G3: Genes, Genomes, Genetics, g3.300121.2017
  • Henry VJ., Saïs F., Marchadier É. , Dibie J., Goelzer A., Fromion V.. (2017) BiPOm: Biological interlocked Process Ontology for metabolism. How to infer molecule knowledge from biological process?. , np
  • Pelé A., Falque M. , Trotoux G., Eber F., Nègre S., Gilet M., Huteau V., Lodé M., Jousseaume T., Dechaumet S., Morice J., Poncet C., Coriton O., Martin OC., Rousseau-Gueutin M., Chèvre AM.. (2017) Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas. PLoS Genet, 5 (13)
  • Sabarly V., Aubron C., Glodt J., Balliau T., Langella O., Chevret D., Rigal O., Bourgais A., Picard B., de Vienne D. , Denamur E., Bouvet O., Dillmann C. . (2016) Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates. Environmental microbiology, 1 (18) 100-17
  • Blein-Nicolas M. , Albertin W., da Silva T., Valot B., Balliau T., Masneuf-Pomarède I., Bely M., Marullo P., Sicard D., Dillmann C. , de Vienne D. , Zivy M. . (2015) A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast. Mol. Cell Proteomics, 8 (14) 2056-2071
  • Durand E., Tenaillon MI., Raffoux X. , Thépot S., Falque M. , Jamin P., Bourgais A., Ressayre A. , Dillmann C. . (2015) Dearth of polymorphism associated with a sustained response to selection for flowering time in maize. BMC Evol Biol, 1 (15) 103
  • Falque M. , 2015-10-15 15/10/15, Sur les traces de la recombinaison méiotique, source de biodiversité et outil génétique
  • Sidhu GK., Fang C., Olson MA., Falque M. , Martin OC., Pawlowski WP.. (2015) Recombination patterns in maize reveal limits to crossover homeostasis. PNAS, 52 (112) 15982-15987
  • da Silva T., Albertin W., Dillmann C. , Bely M., la Guerche S., Giraud C., Huet S., Sicard D., Masneuf-Pomarede I., de Vienne D. , Marullo P.. (2015) Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions. PloS one, 5 (10) e0123834
  • Anderson LK., Lohmiller LD., Tang X., Hammond DB., Javernick L., Shearer L., Basu-Roy S., Martin OC., Falque M. . (2014) Combined fluorescent and electron microscopic imaging unveils the specific properties of two classes of meiotic crossovers. Proceedings of the National Academy of Sciences of the United States of America, 37 (111) 13415-20
  • Jahns MT., Vezon D., Chambon A., Pereira L., Falque M. , Martin OC., Chelysheva L., Grelon M.. (2014) Crossover localisation is regulated by the neddylation posttranslational regulatory pathway. PLoS biology, 8 (12) e1001930
  • Roy S., 2014-03-31 31/03/14, Models of meiotic crossover formation, heterogeneity and inter-pathway cross-talks
  • Spor A., Kvitek DJ., Nidelet T., Martin J., Legrand J. , Dillmann C. , Bourgais A., de Vienne D. , Sherlock G., Sicard D.. (2014) Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast. Evolution; international journal of organic evolution, 3 (68) 772-90
  • Suay L., Zhang DS., Eber F., Jouy H., Lode M., Huteau V., Coriton O., Szadkowski E., Leflon M., Martin OC., Falque M. , Jenczewski E., Paillard S., Chevre AM.. (2014) Crossover rate between homologous chromosomes and interference are regulated by the addition of specific unpaired chromosomes in Brassica. The New phytologist, 2 (201) 645-656
  • Albertin W., Marullo P., Bely M., Aigle M., Bourgais A., Langella O., Balliau T., Chevret D., Valot B., da Silva T., Dillmann C. , de Vienne D. , Sicard D.. (2013) Linking post-translational modifications and variation of phenotypic traits. Molecular & cellular proteomics : MCP, 3 (12) 720-35
  • Albertin W., da Silva T., Rigoulet M., Salin B., Masneuf-Pomarede I., de Vienne D. , Sicard D., Bely M., Marullo P.. (2013) The mitochondrial genome impacts respiration but not fermentation in interspecific Saccharomyces hybrids. PloS one, 9 (8) e75121
  • Basu-Roy S., Gauthier F., Giraut L., Mezard C., Falque M. , Martin OC.. (2013) Hot Regions of Noninterfering Crossovers Coexist with a Nonuniformly Interfering Pathway in Arabidopsis thaliana. Genetics, 3 (195) 769-79
  • Bauer E., Falque M. , Walter H., Bauland C., Camisan C., Campo L., Meyer N., Ranc N., Rincent R., Schipprack W., Altmann T., Flament P., Melchinger AE., Menz M., Moreno-Gonzalez J., Ouzunova M., Revilla P., Charcosset A., Martin OC., Schon CC.. (2013) Intraspecific variation of recombination rate in maize. Genome biology, 9 (14) R103
  • Blein-Nicolas M. , Albertin W., Valot B., Marullo P., Sicard D., Giraud C., Huet S., Bourgais A., Dillmann C. , de Vienne D. , Zivy M. . (2013) Yeast proteome variations reveal different adaptive responses to grape must fermentation. Molecular biology and evolution, 6 (30) 1368-83
  • Drouaud J., Khademian H., Giraut L., Zanni V., Bellalou S., Henderson IR., Falque M. , Mezard C.. (2013) Contrasted Patterns of Crossover and Non-crossover at Arabidopsis thaliana Meiotic Recombination Hotspots. PLoS genetics, 11 (9) e1003922
  • Blein-Nicolas M. , Xu H., de Vienne D. , Giraud C., Huet S., Zivy M. . (2012) Including shared peptides for estimating protein abundances: a significant improvement for quantitative proteomics. Proteomics, 18 (12) 2797-801
  • Durand E., Bouchet S., Bertin P., Ressayre A. , Jamin P., Charcosset A., Dillmann C. , Tenaillon MI.. (2012) Flowering time in maize: linkage and epistasis at a major effect locus. Genetics, 4 (190) 1547-62
  • Albertin W., Marullo P., Aigle M., Dillmann C. , de Vienne D. , Bely M., Sicard D.. (2011) Population size drives industrial Saccharomyces cerevisiae alcoholic fermentation and is under genetic control. Applied and environmental microbiology, 8 (77) 2772-84
  • Fiévet JB., Gallais A., de Vienne D. , Prioul JL., Thévenot C., Molnar T., Mike Burrel .. (2011) Heterosis, inbreeding depression and hybrid varieties. , 67-87
  • Gauthier F., Martin O., Falque M. . (2011) CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes. BMC Bioinformatics, 1 (12) 27
  • Giraut L., Falque M. , Drouaud J., Pereira L., Martin OC., Mezard C.. (2011) Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS genetics, 11 (7) e1002354
  • Sabarly V., Bouvet O., Glodt J., Clermont O., Skurnik D., Diancourt L., de Vienne D. , Denamur E., Dillmann C. . (2011) The decoupling between genetic structure and metabolic phenotypes in Escherichia coli leads to continuous phenotypic diversity. Journal of evolutionary biology, 7 (24) 1559-71
  • Wang S., Spor A., Nidelet T., Montalent P., Dillmann C. , de Vienne D. , Sicard D.. (2011) Switch between life history strategies due to changes in glycolytic enzyme gene dosage in Saccharomyces cerevisiae. Applied and environmental microbiology, 2 (77) 452-9