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portrait de Timothée Flutre, 2018Timothée FLUTRE

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Quantitative genetics of wheat heterogeneous populations adapted to agroecological practices

Génétique Quantitative et Évolution – Le Moulon
INRA, Université Paris-Sud, CNRS, AgroParisTech
Ferme du Moulon
91190 Gif sur Yvette, France
Email: timothee.flutre[AT]inra.fr
Tel: +33 (1) 69 15 61 33
ORCID

 

> 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; 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 plan to conduct research on the growth dynamics and resource allocation of plants interacting with each other, with varietal mixtures of bread wheat as application. My modeling approach will depend on field experiments and farmers’ know-how, and draw on knowledge mainly from quantitative genetics, ecophysiology and statistics, but also ecology and agronomy.

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.

 

> Selected publications

(More on ORCID and ProdInra)

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.

- Launay A, Denancé C, Muranty H, Audergon J-M, Confolent C, Lambert P, Quilot-Turion B, Bert P-F, Marguerit E, Campoy J, Dirlewanger E, Quero Garcia J, Decroocq S, Decroocq V, Butterlin G, Duchêne E, Costes E, Kelner J-J, Pallas B, Mournet P, Flutre T. Combining genotyping by sequencing and genomic prediction within bi-parental crosses to speed-up the selection of perennial fruit crops. In prep.

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. PLoSOne, 6 e16526.

 

> Teachings

 

> Selected software

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

  • 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

  • 2015-2016: coordinator of the FruitSelGen project, INRA (Selgen meta-program)
  • 2007-2010: PhD fellowship, INRA (ASC).