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Génétique Quantitative et Évolution - Le Moulon

Timothée FLUTRE

Timothée FLUTRE

Research scientist, INRAE

Quantitative genetics of crop mixtures adapted to agroecological practices


+33 (0)1 69 15 61 33


  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • 12 route 128
  • 91190 Gif-sur-Yvette

To prospective students, do not hesitate to contact me if you are interested in combining genetics, field work and modeling for agroecology!

Positions and education

  • 2019-present: research scientist at UMR GQE-Le Moulon, team DEAP
  • 2014-2018: research scientist at UMR AGAP, team DAAV
  • 2011-2013: postdoctoral fellow at the University of Chicago with M. Stephens
  • 2007-2010: Ph.D. at URGI with H. Quesneville and C. Feuillet (UMR GDEC), in graduate school FIRE (ex-FDV)
  • 2003-2007: engineering school AgroParisTech (ex-INA P-G); M. Sc. AIRE (ex-AIV).

Research interests

Current research

I am interested in understanding the functioning and evolution of heterogeneous stands of cultivated plants for adaptation to agro-ecological practices. I conduct research on the growth dynamics and resource allocation of plants interacting with each other, notably to study the genetic basis of their phenotypic plasticity. In terms of applications, I work with intra-specific mixtures of bread-wheat cultivars and with wheat-pea inter-specific mixtures. My approach combines both modeling and field experiments; it is mainly grounded in quantitative genetics, but also draws knowledge from ecophysiology, statistics, ecology and agronomy thanks to inter-disciplinary collaborations, and it largely benefits from farmers’ know-how.

See this brief description (in French but with pictures!) about the PhD thesis of M. Gawinowski.

Past work

Before 2019, at the INRA in Montpellier, I developed research on the genetic architecture of traits of interest for breeding in grapevine, and genomic selection in perennial fruit species in general and grapevine in particular. My approach was based on linear mixed models and high-dimensional regression for variable selection and prediction. I still have collaborations on these topics, notably in terms of multivariate statistical modeling for genome-wide association studies and genomic prediction. Before that, during my postdoc at UChicago, I worked on the genetic regulation of gene transcription. To detect eQTLs jointly in multiple human tissues, I developed a multivariate hierarchical Bayesian model. During my PhD, I studied the dynamics of transposable elements (TE) and their impact on genome evolution. To annotate the repeat content of whole genomes, I developed a suite of bioinformatics tools. See selected publications on this previous topic

Selected publications

(More below as well as on ORCID and HAL)

Quantitative genetics of plant mixtures

  • Haug B, Messmer MM, Enjalbert J, Goldringer I, Flutre T, Mary-Huard T, Hohmann P. (2023) New insights towards breeding for mixed cropping of spring pea and barley to increase yield and yield stability. Field Crops Research. 297:108923. https:://doi.org/10.1016/j.fcr.2023.108923

  • Montazeaud G, Flutre T, Ballini E, Morel J, David J, Girodolle J, Rocher A, Ducasse A, Violle C, Fort F, et al. (2022) From cultivar mixtures to allelic mixtures: opposite effects of allelic richness between genotypes and genotype richness in wheat. New Phytologist.:nph.17915. https://doi.org/10.1111/nph.17915

  • Haug B, Messmer M, Enjalbert J, Goldringer I, Forst E, Flutre T, Mary-Huard T, Hohmann P. (2021) Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.620400

Association genetics and genomic prediction of perennial fruit crops

  • Flutre T, Berger G, Bertrand Y, Fodor A, Launay A, Romieu C, Beccavin I, Bouckenooghe V, Roques M, Cheynier V, Bacilieri R, Boursiquot J-M, Lacombe T, Laucou V, This P, Le Cunff L, Péros J-P, Doligez A. (2022) Genome-wide association and predictionstudy of a diverse grapevine panel uncovers the genetic architecture of numerous traits of interest. G3 Genes|Genomes|Genetics jkac103. https://doi.org/10.1093/g3journal/jkac103

  • Brault C, Doligez A, Le Cunff L, Coupel-Ledru A, Simonneau T, Chiquet J, This P, Flutre T. (2021) Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine. G3 Genes|Genomes|Genetics 11: jkab248. https://doi.org/10.1093/g3journal/jkab248

Genetic regulation of gene expression

Comparative genomics of transposable elements’ dynamics

PhD students

  • V. Freitas (2023-2026): co-supervision with J. Enjalbert and J.-M. Gilliot; doctoral school SEVE
  • J. Salomon (2023-2026): co-supervision with J. Enjalbert; doctoral school SEVE
  • M. Gawinowski (2019-2023): co-supervision with P.-H. Cournède (CentraleSupélec); doctoral school FIRE
  • C. Brault (2018-2021): co-supervision with P. This, A. Doligez and L. Le Cunff (UMR AGAP); doctoral school GAIA
  • C. Bouffartigue (2016-2020): co-supervision with L. Hazard and N. Couix (UMR AGIR); doctoral school ABIES

Selected projects and funding

  • 2023-2025: coordinator of the PrediMix project with J.-M. Gilliot and funded by AgroParisTech
    • Methodology for prediction and selection of cereal-legume mixtures allowing an agroecological nitrogen management thanks to modeling and high-throughput phenotyping by drone
  • 2023-2027: task leader in the CoBreeding project coordinated by F. Phocas, C. Dillmann and A. Charcosset and funded by the ANR
    • Co-design of animal and plant breeding schemes with multi-performance objectives (economic, social and environmental) to develop agroecological production
    • Task: “High-throughput, UAV-based phenotyping of cereale-legume intercrops”, with J.-M. Gilliot
  • 2021-2026: workpackage leader in the MoBiDiv project coordinated by J. Enjalbert and A. Fugeray-Scarbel and funded by the ANR
    • Mobilizing and breeding intra ad inter-specific crop diversity for a systemic change towards pesticide-free agriculture
    • WP: “Methodology to assemble, select and evaluate mixtures”
  • 2021-2025: workpackage co-leader (with A. Gauffreteau) in the BLADE2025 project coordinated by B. Rolland and J. Le Gouis and funded by INRAE
    • BLés pour une Agriculture Durable et Ecologique
  • 2020-2023: member of the STABLE project coordinated by A. Gauffreteau and funded by the CASDAR
    • Assess the stability of winter wheat cultivars grown in pure and in mixtures
  • 2022: coordinator of the intercropRNAseq suported by the Biosphera graduate school of the Université Paris-Saclay
    • Pilot study of gene expression profiles underlying plant-plant interactions in intercrop mixtures with field trials of wheat-pea and maize-bean
  • 2020-2022: member of the TUHR-DRONAé project coordinated by J.-M. Gilliot and funded by AgroParisTech
    • Ultra-high-resolution remote sensing by drone for adaptation to agroecological practices
  • 2020-2021: coordinator of the PerfoMix project funded by INRAE (BAP department)
    • Performance of intra-species mixtures: explaining cultivar proportions at harvest
  • 2020-2024: member of the G2WAS project coordinated by L. Torregrosa and funded by the ANR
    • Genetic architecture of the tolerance to water deficit in a perennial fruit species (V. vinifera)
  • 2016-2020: member of the SIGNE project coordinated by L. Le Cunff and funded by the CASDAR
    • Spectroscopy, a tool for the traceability and management of intra-cultivar variability in grapevine
  • 2014-2018: coordinator of the genomic prediction for the EDGARR project coordinated by L. Le Cunff and funded by the CASDAR
    • Exploitation of genomic selection in order to accelerate the creation of resistant and qualitative cultivars for the rosé wine industry
  • 2015-2016: coordinator of the FruitSelGen project funded by the INRA (Selgen meta-program), in addition to the SelVi project funded by the INRA (BAP department)
    • Assessment of genotyping by sequencing and genomic selection for perenial fruit crops
  • 2011-2013: post-doctoral fellowship funded by the INRA (ASC)
  • 2007-2010: PhD fellowship funded by the INRA (ASC)


  • One-day course on “Quantitative genetics and genomic prediction” with L. Moreau
    • master M2 EvoGEM of the master BEE, Université Paris-Saclay and other institutions
  • Half-day course on “Managing genetic diversity for the agro-ecological transition” with J. Enjalbert
    • master M2 Plant Sciences, Université Paris-Saclay and other institutions
  • One-hour presentation on “Decomposition of biodiversity–ecosystem functioning” in the half-day course on “Biodiversity and functioning of agroecosystems” by J. Enjalbert
    • master M2 FEE of the master BEE, Université Paris-Saclay and other institutions
  • Half-day visit of field trials on “Intra-plot diversification for agroecology” with J. Enjalbert
  • app on the breeder’s equation
  • app on yield stability (in French)
  • tutorial on statistical contrasts in R
  • workshop on reproducible research (in French)
  • serious game on plant breeding and genomic selection
  • workshop on genomic prediction (in French)
  • tutorial on multiple testing (in French)
  • tutorial on reproducible research.

Research management

  • 2023-ongoing: leader of the DEAP team
  • 2020-2023: nominated at the scientific council of the SEVE graduate school (Univ. Paris-Saclay) with D. Manicacci as substitute
  • 2019-2023: active member of the working group of the experimental unit Versailles-Saclay
  • 2015-2020: elected at the scientific council of the BAP department (INRAE) as substitute of J. Ronfort (UMR AGAP)
  • 2014-2019: elected at the council of the UMR AGAP
  • 2009: co-organization of the Paris Interdisciplinary PhD symposium “From sparse entities to crowded environment: numbers in living systems”

Selected software

(More on GitHub and SourceSup; many contributions to free and open-source software)

  • rutilstimflutre: R package with numerous functions useful in quantitative genetics and bioinformatics
  • gbs.py: call and filter SNP genotypes from raw sequencing reads
  • demultiplex.py: demultiplex raw reads from different samples sequenced together
  • PlantBreedGame: serious game on plant breeding
  • eQtlBma: detect eQTLs jointly in multiple subgroups via Bayesian model averaging
  • REPET: detect, annotate and analyze repeats in genomic sequences, specifically designed for transposable elements.


  • Brault C., Segura V., Roques M., Lamblin P., Bouckenooghe V., Pouzalgues N., Cunty C., Breil M., Frouin M., Garcin L., Camps L., Ducasse MA., Romieu C., Masson G., Julliard S., Flutre T. , Le Cunff L., Wisser R.. (2024) Enhancing grapevine breeding efficiency through genomic prediction and selection index. G3: Genes, Genomes, Genetics, jkae038
  • Coupel‐Ledru A., Westgeest AJ., Albasha R., Millan M., Pallas B., Doligez A., Flutre T. , Segura V., This P., Torregrosa L., Simonneau T., Pantin F.. (2024) Clusters of grapevine genes for a burning world. New Phytologist, 1 (242) 10-18
  • Gawinowski M., Enjalbert J., Cournède PH., Flutre T. . (2024) Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance. Field Crops Research, (310) 109368
  • Blanc E., Enjalbert J., Flutre T. , Barbillon P., Lunn J.. (2023) Efficient Bayesian automatic calibration of a functional–structural wheat model using an adaptive design and a metamodelling approach. Journal of Experimental Botany, erad339
  • Gawinowski M., 11/01/2023, Importance des interactions plante-plante dans les mélanges de variétés de blé tendre : étude de la compétition pour la lumière avec une approche interdisciplinaire entre expérimentation au champ et modélisation mécaniste, PhD, Université Paris-Saclay
  • Haug B., Messmer MM., Enjalbert J., Goldringer I., Flutre T. , Mary-Huard T., Hohmann P.. (2023) New insights towards breeding for mixed cropping of spring pea and barley to increase yield and yield stability. Field Crops Research, (297) 108923
  • Brault C., Segura V., This P., Le Cunff L., Flutre T. , François P., Pons T., Péros JP., Doligez A.. (2022) Across-population genomic prediction in grapevine opens up promising prospects for breeding. Horticulture Research, (9) uhac041
  • Flutre T. , Le Cunff L., Fodor A., Launay A., Romieu C., Berger G., Bertrand Y., Terrier N., Beccavin I., Bouckenooghe V., Roques M., Pinasseau L., Verbaere A., Sommerer N., Cheynier V., Bacilieri R., Boursiquot JM., Lacombe T., Laucou V., This P., Péros JP., Doligez A., Paterson A.. (2022) A genome-wide association and prediction study in grapevine deciphers the genetic architecture of multiple traits and identifies genes under many new QTLs. G3 Genes|Genomes|Genetics, 7 (12) jkac103
  • Gawinowski M., Enjalbert J., Cournède PH., Flutre T. . (2022) Contrasted reaction norms of wheat yield in pure vs mixed stands explained by tillering plasticities and shade avoidance. Plant Biology,
  • Montazeaud G., Flutre T. , Ballini E., Morel JB., David J., Girodolle J., Rocher A., Ducasse A., Violle C., Fort F., Fréville H.. (2022) From cultivar mixtures to allelic mixtures: opposite effects of allelic richness between genotypes and genotype richness in wheat. New Phytologist, 6 (233) 2573-2584
  • Brault C., Doligez A., Cunff L., Coupel-Ledru A., Simonneau T., Chiquet J., This P., Flutre T. , Jannink JL.. (2021) Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine. G3 Genes|Genomes|Genetics, 9 (11) jkab248
  • Haug B., Messmer MM., Enjalbert J., Goldringer I., Forst E., Flutre T. , Mary-Huard T., Hohmann P.. (2021) Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept. Front. Plant Sci., (11) 620400
  • R2D2 Consortium, Fugeray-Scarbel A., Bastien C., Dupont-Nivet M., Lemarié S.. (2021) Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience. Front. Genet., (12) 629737
  • Badouin H., Velt A., Gindraud F., Flutre T. , Dumas V., Vautrin S., Marande W., Corbi J., Sallet E., Ganofsky J., Santoni S., Guyot D., Ricciardelli E., Jepsen K., Käfer J., Berges H., Duchêne E., Picard F., Hugueney P., Tavares R., Bacilieri R., Rustenholz C., Marais GAB.. (2020) The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication. Genome Biol, 1 (21) 223
  • Bouffartigue C., Debille S., Fabreguettes O., Cabrer AR., Pereira-Lorenzo S., Flutre T. , Harvengt L.. (2020) Two main genetic clusters with high admixture between forest and cultivated chestnut (Castanea sativa Mill.) in France. Annals of Forest Science, 3 (77) 74
  • Nsibi M., Gouble B., Bureau S., Flutre T. , Sauvage C., Audergon JM., Regnard JL.. (2020) Adoption and Optimization of Genomic Selection To Sustain Breeding for Apricot Fruit Quality. G3, g3.401452.2020
  • Tello J., Torres-Pérez R., Flutre T. , Grimplet J., Ibáñez J.. (2020) VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine. Genes, 6 (11) 598
  • Flutre T. , Bacilieri R., Bécavin I., Berger G., Bertrand Y., Boursiquot JM., Fodor A., Lacombe T., Laucou V., Launay A., Le Cunff L., Romieu C., This P., Péros JP., Doligez A.. (2019) Genome-wide association study of a diverse grapevine panel: example of berry weight. Acta Hortic., 1248 227-234
  • Flutre T. , Diot J., David J.. (2019) PlantBreedGame: A Serious Game that Puts Students in the Breeder’s Seat. Crop Science, 0 (52) 1-2
  • Tello J., Roux C., Chouiki H., Laucou V., Sarah G., Weber A., Santoni S., Flutre T. , Pons T., This P., Péros JP., Doligez A.. (2019) A novel high-density grapevine (Vitis vinifera L.) integrated linkage map using GBS in a half-diallel population. Theor Appl Genet, 8 (132) 2237-2252
  • Moisy C., Berger G., Flutre T. , Le Cunff L., Péros JP.. (2017) Quantitative assessment of grapevine wood colonization by the dieback fungus Eutypa lata. Journal of Fungi, 2 (3) 21
  • Andújar B., Campderrós G., García M., Marino M., Mas M., Narbona L., Pérez L., Rodrigo P., Velásquez A., Vilà J., Laguna D., Flutre T. , Bonnefond M., Sescousse G., Riboli-Sasco L.. (2015) Twenty Tips for High-School Students Engaging in Research with Scientists. Frontiers for Young Minds, (3)
  • Fagny M., Patin E., MacIsaac JL., Rotival M., Flutre T. , Jones MJ., Siddle KJ., Quach H., Harmant C., McEwen LM., Froment A., Heyer E., Gessain A., Betsem E., Mouguiama-Daouda P., Hombert JM., Perry GH., Barreiro LB., Kobor MS., Quintana-Murci L.. (2015) The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nature Communications, (6)
  • The GTEx Consortium, Ardlie K., Deluca D., Segrè A., Sullivan T., Young T., Gelfand E., Trowbridge C., Maller J., Tukiainen T., Lek M., Ward L., Kheradpour P., Iriarte B., Meng Y., Palmer C., Esko T., Winckler W., Hirschhorn J., Kellis M., MacArthur D., Getz G., Shabalin A., Li G., Zhou YH., Nobel A., Rusyn I., Wright F., Lappalainen T., Ferreira P., Ongen H., Rivas M., Battle A., Mostafavi S., Monlong J., Sammeth M., Mele M., Reverter F., Goldmann J., Koller D., Guigó R., McCarthy M., Dermitzakis E., Gamazon E., Im H., Konkashbaev A., Nicolae D., Cox N., Flutre T. , Wen X., Stephens M., Pritchard J., Tu Z., Zhang B., Huang T., Long Q., Lin L., Yang J., Zhu J., Liu J., Brown A., Mestichelli B., Tidwell D., Lo E., Salvatore M., Shad S., Thomas J., Lonsdale J., Moser M., Gillard B., Karasik E., Ramsey K., Choi C., Foster B., Syron J., Fleming J., Magazine H., Hasz R., Walters G., Bridge J., Miklos M., Sullivan S., Barker L., Traino H., Mosavel M., Siminoff L., Valley D., Rohrer D., Jewell S., Branton P., Sobin L., Barcus M., Qi L., McLean J., Hariharan P., Um K., Wu S., Tabor D., Shive C., Smith A., Buia S., Undale A., Robinson K., Roche N., Valentino K., Britton A., Burges R., Bradbury D., Hambright K., Seleski J., Korzeniewski G., Erickson K., Marcus Y., Tejada J., Taherian M., Lu C., Basile M., Mash D., Volpi S., Struewing J., Temple G., Boyer J., Colantuoni D., Little R., Koester S., Carithers L., Moore H., Guan P., Compton C., Sawyer S., Demchok J., Vaught J., Rabiner C., Lockhart N., Ardlie K., Getz G., Wright F., Kellis M., Volpi S., Dermitzakis E.. (2015) Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans.. Science, 6235 (348) 648-660
  • Flutre T. , Wen X., Pritchard J., Stephens M.. (2013) A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genetics, 5 (9) e1003486
  • Bigot Y., Permal E., Flutre T. , Quesneville H.. (2012) Roadmap for annotating transposable elements in eukaryote genomes. , (859) 53-68
  • Flutre T. , Permal E., Quesneville H., Grandbastien MA., Casacuberta J.. (2012) Transposable element annotation in completely sequenced eukaryote genomes. , (24) 17-39
  • Leroy P., Guilhot N., Sakai H., Bernard A., Choulet F., Theil S., Reboux S., Amano N., Flutre T. , Pelegrin C., Ohyanagi H., Seidel M., Giacomoni F., Reichstadt M., Alaux M., Gicquello E., Legeai F., Cerutti L., Numa H., Tanaka T., Mayer K., Itoh T., Quesneville H., Feuillet C.. (2012) TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.. Frontiers in Plant Science, (3)
  • Ségurel L., Thompson E., Flutre T. , Lovstad J., Venkat A., Margulis S., Moyse J., Ross S., Gamble K., Sella G., Ober C., Przeworski M.. (2012) The ABO blood group is a trans-species polymorphism in primates. Proceedings of the National Academy of Sciences, 45 (109) 18493-18498
  • Flutre T. , Duprat E., Feuillet C., Quesneville H.. (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One, 1 (6) e16526
  • Flutre T. , Permal E., Quesneville H.. (2011) In search of lost trajectories: recovering the diversification of transposable elements. Mobile Genetic Elements, 2 (1)
  • Flutre T. , Julou T., Riboli-Sasco L., Ribrault C.. (2011) Pilot scheme for misconduct database. Nature, 37 (478) 37-37
  • Flutre T. , octobre 28, 2010, L'annotation des éléments transposables par la compréhension de leur diversification, , Université Paris VII - Denis Diderot
  • Flutre T. , Julou T., Riboli-Sasco L., Ribrault C.. (2010) Scientific Red Cards: a collaborative website for better communication between scientists and institutions about misconduct. European Science Editing, 2 (36) 51-52
  • d'Alençon E., Sezutsu H., Legeai F., Permal E., Bernard-Samain S., Gimenez S., Gagneur C., Cousserans F., Shimomura M., Brun-Barale A., Flutre T. , Couloux A., East P., Gordon K., Mita K., Quesneville H., Fournier P., Feyereisen R.. (2010) Extensive synteny conservation of holocentric chromosomes in {L}epidoptera despite high rates of local genome rearrangements. Proceedings of the National Academy of Sciences, 17 (107) 7680-7685
  • Abad P., Gouzy J., Aury JM., Castagnone-Sereno P., Danchin E., Deleury E., Perfus-Barbeoch L., Anthouard V., Artiguenave F., Blok V., Caillaud MC., Coutinho P., Dasilva C., De Luca F., Deau F., Esquibet M., Flutre T. , Goldstone J., Hamamouch N., Hewezi T., Jaillon O., Jubin C., Leonetti P., Magliano M., Maier T., Markov G., McVeigh P., Pesole G., Poulain J., Robinson-Rechavi M., Sallet E., Ségurens B., Steinbach D., Tytgat T., Ugarte E., van Ghelder C., Veronico P., Baum T., Blaxter M., Bleve-Zacheo T., Davis E., Ewbank J., Favery B., Grenier E., Henrissat B., Jones J., Laudet V., Maule A., Quesneville H., Rosso MN., Schiex T., Smant G., Weissenbach J., Wincker P.. (2008) Genome sequence of the metazoan plant-parasitic nematode \emph{{M}eloidogyne incognita}. Nature Biotechnology, 8 (26) 909-915