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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

timothee.flutre@inrae.fr

+33 (0)1 69 15 61 33

orcid.org/0000-0003-4489-4782

Publications

  • Génétique Quantitative et Évolution - Le Moulon
  • Université Paris-Saclay, INRAE, CNRS, AgroParisTech
  • Ferme du Moulon
  • F-91190 Gif-sur-Yvette

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 populations 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 mostly with intra-specific mixtures of bread-wheat cultivars but also 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, and it largely benefits from farmers’ know-how.

See this brief description (in French but with pictures!) about one of my current projects.

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, 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 on ORCID and HAL)

Quantitative genetics of plant mixtures

  • Haug B, Messmer M, Enjalbert J, Goldringer I, Forst E, Flutre T, Mary-Huard T, Hohmann P. Advances in Breeding for Mixed Cropping – Incomplete Factorials and the Producer/Associate Concept. Frontiers in Plant Science (2021). 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. Genome-wide association and predictionstudy of a diverse grapevine panel uncovers the genetic architecture of numerous traits of interest. In prep.
  • Brault C, Doligez A, Le Cunff L, Coupel-Ledru A, Simonneau T, Chiquet J, This P, Flutre Tet al. Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine. G3 Genes|Genomes|Genetics (2021) 11: jkab248. https://doi.org/10.1093/g3journal/jkab248

Genetic regulation of gene expression

  • Flutre T, Wen X, Pritchard J, and Stephens M. (2013) A statistical framework for joint eQTL analysis in multiple tissues. PLoS Genetics, 9 e1003486.

Comparative genomics of transposable elements’ dynamics

  • Flutre T, Duprat E, Feuillet C, and Quesneville H. (2011) Considering transposable element diversification in de novo annotation approaches. PLoS One, 6 e16526.

PhD students

  • M. Gawinowski (2019-ongoing): co-supervision with P.-H. Cournède (CentraleSupélec); doctoral school FIRE
  • C. Brault (2018-ongoing): collaboration with her supervisors 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

Teaching

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.

Selected projects and funding

  • 2021-2026: workpackage co-leader (with J. David) 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
  • 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
  • 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)

Research management

  • 2020-ongoing: nominated at the scientific council of the SEVE graduate school (Univ. Paris-Saclay) with D. Manicacci as substitute
  • 2019-ongoing: 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”

Publications

  • 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
  • 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