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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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Brachi Benjamin

Researcher in ecological genomics and evolutionary ecology.

Brachi Benjamin
My research is focused on understanding selective and ecological processes maintaining variation within populations. In particular I want to understand why oak populations display so much within population diversity and what is the influence of this within species variation on the insect and microbial communities. My model traits are leaf specialized metabolites. In general, the natural variation of these traits is genetically tractable thanks to simple genetics and high heritabilities. They are also know to influence plant resistance to insect herbivores and pathogens, and to contribute to the extended phenotype of plants and trees in particular. My overall working hypothesis is that biotic environment contributes to maintaining within population phenotypic variation by processes analogous to those contributing to maintaining species diversity tropical forests. Investigating this question necessarily involves investigating the ecological function of within species phenotypic variation, in a manner analogous to ecological studies investigating the effect of species diversity on herbivores and pest. Understanding the functional role of within species variation in the forest ecosystem is likely key for long-term success of forest management strategies in the context of global change. Keywords: evolution, natural selection, adaptation, defense, herbivores, pathogens, oak, genomics,metabolomics, association mapping

I did my PhD work (2007-2010) on ecological genomics in Arabidopsis thaliana at the University of Lille 1 under the direction of Fabrice Roux and Joël Cuguen. During this time I contributed in seminal genome-wide association studies (GWAs) and environmental association in A. thaliana and established collaboration which led me to a postdoc at the university of Chicago, in Joy Bergelson's lab (2011-2016). During the five years spent in Chicago, I participated and led projects in ecological genomics using field experiments, genomics, metabolomics and metabarcoding to investigate the genetics of local adaptation, but also the role of biotic interactions in shaping natural variation. In 2016 I joined the UMR BIOGECO as a postdoc for two years and stayed as a researcher from 2018. 

In BIOGECO I started studying natural variation of leaf specialized metabolites in oaks. Many of these compounds turned out to be highly heritable (genetically determined) and very variable within populations. In particular, many compounds appear to display bimodal distributions in 9 out of 9 distant European provenances of Q. petraea within populations, suggesting that different phenotypic "classes" coexist. We also know from the literature and our own observations that they are correlated with leaf damage by herbivores and quantitative resistance to pathogens. From there emerged the hypothesis that oak variable phenotypes within populations were the results of selective processes maintaining variation likely involving biotic interactions.

My current work now attacks these topics from multiple angles.

First we are continuing to follow-up on the genetic bases of leaf specialized variation in oaks. This part is now part of the PhD work of Domitille Coq-Etchegaray. Her work will contribute to exploring the genetics of leaf specialized metabolites natural variation in oak populations. The idea is to use low-depth short-read sequencing to generate genome-wide genotypic data and perform genome-wide association mapping and selection scans.

Second, in parallel and to help better interpret the results of mapping, we are in the process of annotating the many specialized metabolites highlighted by QTL analysis and variation in provenances. Indeed, phenotyping was performed using a specially optimized high throughput protocol for untargeted metabolomics (using LC-MS). Now we are in the process of annotating the compounds displaying particularly strong association with genetic variation and those displaying high levels of polymorphisms in oak provenances.

Third, we are exploring the effect of leaf specialized metabolite variation on the microbial community of leaves and investigating if this variation impacts leaf decomposition. This project is lead in collaboration with Virgil Fievet (BIOGECO), Bastien Castagneyrol (BIOGECO, INRAE) and Nicolas Fanin (ISPA, INRAE), and is funded in as a emergent subject by the department "Science de l'environnement" of the university of Bordeaux.

In addition to on-going work, my ambition is to quantify the selective pressures acting on specialized metabolite variation within oak populations and genetic bases of this variation at multiple life stages. This is topic of my ANR pre-proposal, which is currently being evaluated.

Finally, I am now contributing and coordinating the contribution of BIOGECO to a collaborative effort to study oak dieback in the Chantilly forest. Specifically I propose to quantify the genetic component of oak dieback within the populations, investigate if this genetic component is related to regions of the genomes associated with climate variation or displaying signatures of local adaptation in European provenances. 

I'm also co-heading the group E4E in BIOGECO with Marta Benito-Garzon. 

See also

Scientific production

  • Atwell, Susanna, Yu S. Huang, Bjarni J. Vilhjálmsson, Glenda Willems, Matthew Horton, Yan Li, Dazhe Meng, et al. “Genome-Wide Association Study of 107 Phenotypes in Arabidopsis Thaliana Inbred Lines.” Nature 465, no. 7298 (June 2010): 627–31.
  • Bartholomé, Jérôme, Benjamin Brachi, Benoit Marçais, Amira Mougou‐Hamdane, Catherine Bodénès, Christophe Plomion, Cécile Robin, and Marie-Laure Desprez‐Loustau. “The Genetics of Exapted Resistance to Two Exotic Pathogens in Pedunculate Oak.” New Phytologist 226, no. 4 (2020): 1088–1103.
  • Beilsmith, Kathleen, Manus P.M. Thoen, Benjamin Brachi, Andrew D. Gloss, Mohammad H. Khan, and Joy Bergelson. “Genome-Wide Association Studies on the Phyllosphere Microbiome: Embracing Complexity in Host-Microbe Interactions.” The Plant Journal, 2018, 164–81.
  • Brachi, Benjamin, Carla Aimé, Cédric Glorieux, Joel Cuguen, and Fabrice Roux. “Adaptive Value of Phenological Traits in Stressful Environments: Predictions Based on Seed Production and Laboratory Natural Selection.” PLoS ONE 7, no. 3 (January 2012): e32069.
  • Brachi, Benjamin, Nathalie Faure, Joy Bergelson, Joël Cuguen, and Fabrice Roux. “Genome-Wide Association Mapping of Flowering Time in Arabidopsis Thaliana in Nature: Genetics for Underlying Components and Reaction Norms across Two Successive Years.” Acta Botanica Gallica 160, no. 3–4 (December 2013): 205–19.
  • Brachi, Benjamin, Nathalie Faure, Matt Horton, Emilie Flahauw, Adeline Vazquez, Magnus Nordborg, Joy Bergelson, Joel Cuguen, and Fabrice Roux. “Linkage and Association Mapping of Arabidopsis Thaliana Flowering Time in Nature.” PLoS Genetics 6, no. 5 (May 2010): e1000940.
  • Brachi, Benjamin, Daniele Filiault, Paul Darme, Marine Le Mentec, Envel Kerdaffrec, Fernando Rabanal, Alison Anastasio, et al. “Plant Genes Influence Microbial Hubs That Shape Beneficial Leaf Communities.” BioRxiv, 2017.
  • ———. “Plant Genes Influence Microbial Hubs That Shape Beneficial Leaf Communities.” BioRxiv, August 29, 2017, 181198.
  • Brachi, Benjamin, Christopher G. Meyer, Romain Villoutreix, Alexander Platt, Timothy C. Morton, Fabrice Roux, and Joy Bergelson. “Coselected Genes Determine Adaptive Variation in Herbivore Resistance throughout the Native Range of Arabidopsis Thaliana.” Proceedings of the National Academy of Sciences 112, no. 13 (March 2015): 4032–37.
  • Brachi, Benjamin, Geoffrey P Morris, and Justin O Borevitz. “Genome-Wide Association Studies in Plants: The Missing Heritability Is in the Field.” Genome Biology 12, no. 10 (2011): 232.
  • Brachi, Benjamin, Romain Villoutreix, Nathalie Faure, Nina Hautekèete, Yves Piquot, Maxime Pauwels, Dominique Roby, Joël Cuguen, Joy Bergelson, and Fabrice Roux. “Investigation of the Geographical Scale of Adaptive Phenological Variation and Its Underlying Genetics in Arabidopsis Thaliana.” Molecular Ecology 22, no. 16 (August 2013): 4222–40.
  • Chen, Jia-hui, Yuan Huang, Benjamin Brachi, Quan-zheng Yun, Wei Zhang, Wei Lu, Hong-na Li, et al. “Genome-Wide Analysis of Cushion Willow Provides Insights into Alpine Plant Divergence in a Biodiversity Hotspot.” Nature Communications 10, no. 1 (November 19, 2019): 1–12.
  • Damestoy, Thomas, Benjamin Brachi, Xoaquín Moreira, Hervé Jactel, Christophe Plomion, and Bastien Castagneyrol. “Oak Genotype and Phenolic Compounds Differently Affect the Performance of Two Insect Herbivores with Contrasting Diet Breadth.” Edited by Jörg-Peter Schnitzler. Tree Physiology, no. iii (January 2019): 1–13.
  • Dufaÿ, Mathilde, Emna Lahiani, and Benjamin Brachi. “Gender Variation and Inbreeding Depression in Gynodioecious-Gynomonoecious Silene Nutans(Caryophyllaceae).” International Journal of Plant Sciences 171, no. 1 (2010): 53–62.
  • Exposito-Alonso, Moises, Claude Becker, Verena J Schuenemann, Ella Reiter, Claudia Setzer, Radka Slovak, Benjamin Brachi, et al. “The Rate and Potential Relevance of New Mutations in a Colonizing Plant Lineage.” PLOS Genetics 14, no. 2 (2018): 1–21.
  • Garraud, C, Benjamin Brachi, M Dufay, P Touzet, and J a Shykoff. “Genetic Determination of Male Sterility in Gynodioecious Silene Nutans.” Heredity 106, no. 5 (May 2011): 757–64.
  • Gloss, Andrew D, Benjamin Brachi, Mitchell J Feldmann, Simon C Groen, Claudia Bartoli, Jerome Gouzy, Erika R LaPlante, et al. “Genetic Variants Affecting Plant Size and Chemical Defenses Jointly Shape Herbivory in Arabidopsis.” BioRxiv, January 2017, 156299.
  • Hancock, Angela M, Benjamin Brachi, Nathalie Faure, Matthew W Horton, Lucien B Jarymowycz, F Gianluca Sperone, Christopher Toomajian, Fabrice Roux, and Joy Bergelson. “Adaptation to Climate across the Arabidopsis Thaliana Genome.” Science 334, no. 6052 (2011): 83–86.
  • Plomion, Christophe, Jean-Marc Aury, Joëlle Amselem, Thibault Leroy, Florent Murat, Sébastien Duplessis, Sébastien Faye, et al. “Oak Genome Reveals Facets of Long Lifespan.” Nature Plants 4, no. 7 (July 2018): 440–52.
  • Van Rossum, Fabienne, Hélène Martin, Solenn Le Cadre, Benjamin Brachi, Maarten J.M. Christenhusz, and Pascal Touzet. “Phylogeography of a Widely Distributed Species Reveals a Cryptic Assemblage of Distinct Genetic Lineages Needing Separate Conservation Strategies.” Perspectives in Plant Ecology, Evolution and Systematics 35, no. April (December 2018): 44–51.