Development and Plasticity of the Root System

Group leader : Benjamin Péret
CNRS Research Director
Website :



Plants show a strong level of developmental plasticity that is controlled by a complex combination of perception, integration and response. Root system is a fantastic tool to study this plasticity since the number and position of lateral roots is deeply altered by the environment. We are trying to understand the fundamental mechanisms governing lateral root development and its control by the environment. Our research focuses on two main biological systems: the model plant Arabidopsis thaliana and white lupin (Lupinus albus).


Cluster root initiation

In the context of the ERC “Starting grant” LUPIN ROOTS project, we are trying to unravel cluster root development in white lupin. These structures are root adaptations to phosphate deficiency; they are made of numerous rootlets that have a highly specialized development, anatomy and physiology dedicated towards efficient phosphate acquisition. We will develop genetic and molecular tools to make white lupin a model plant (genome sequencing, transcriptomics datasets and screening a mutagenized population but also new growth chambers). This will help us understanding how this plant can perceive its environment to produce cluster roots (Benjamin Péret and Fanchon Divol).


Rootlets determinate growth

In parallel, we are interested in the specific mode of development of white lupin rootlets. Interestingly, they have a determinate mode of development. This behaviour is associated with the local exhaustion of phosphate and the need for the plant to produce new cluster roots further away to find phosphate. We want to identify the molecular mechanisms controling the switch from indeterminate to determinate development (Patrick Doumas and Laurence Marquès).




Team members
Main results


  • White lupin genome sequence. We produced a high quality assembly of white lupin genome with a N50 of 17Mb and a total number of 89 contigs for 2n=50. This resource is now available to the community :
  • Mutant identification. We have a collection of mutants that constitutively produce cluster roots, screened from an EMS mutagenized population.
  • Transcriptomics. We have generated several transcriptomics datasets describing the various stages of cluster root development.
Significant publications


Hufnagel B✉, Soriano A, Taylor J, Divol F, Kroc M, Sanders H, Yeheyis L, Nelson M, Péret B✉ (2020) Pangenome of white lupin provides insights into the diversity of the species. bioRxiv,

Leonhardt N, Divol F, Chiarenza S, Deschamps S, Renaud J, Giacalone C, Nussaume L, Berthomé R, Péret B✉ (2020) Tissue-specific inactivation by cytosine deaminase/uracil phosphoribosyl transferase as a tool to study plant biology. Plant J., 101(3):731-741

Hufnagel B, Marques A, Soriano A, Marquès L, Divol F, Doumas P, Sallet E, Mancinotti D, Carrere S, Marande W, Arribat S, Keller J, Huneau C, Blein T, Aimé D, Laguerre M, Taylor J, Schubert V, Nelson M, Geu-Flores F, Crespi M, Gallardo-Guerrero K, Delaux P-M, Salse J, Bergès H, Guyot R, Gouzy J, Péret B✉ (2020) High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nat. Commun., 11:492

Gallardo C*, Hufnagel B*, Casset C, Alcon C, Garcia F, Divol F, Marquès L, Doumas P, Péret B✉ (2019) Anatomical and hormonal description of rootlet primordium development along white lupin cluster root. Physiol. Plantarum, 165(1):4-16

Porco S*, Larrieu A*, Du Y, Gaudinier A, Goh T, Swarup K, Swarup R, Kuempers B, Bishopp A, Lavenus J, Casimiro I, Hill K, Benková E, Fukaki H, Brady SM, Scheres B, Péret B✉, Bennett MJ✉ (2016) Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulating auxin influx carrier LAX3. Development, 143(18):3340-3349

Péret B✉, Desnos T, Jost R, Kanno S, Berkowitz O, Nussaume L (2014) Root architecture responses: in search of phosphate. Plant Physiol., 166(4):1713-1723

Péret B, Middleton AM, French AP, Larrieu A, Bishopp A, Njo M, Wells DM, Porco S, Mellor N, Band LR, Casimiro I, Kleine-Vehn J, Vanneste S, Sairanen I, Mallet R, Sandberg G, Ljung K, Beeckman T, Benková E, Friml J, Kramer E, King JR, De Smet I, Pridmore TP, Owen MR, Bennett MJ✉ (2013) Sequential induction of auxin efflux and influx carriers regulates lateral root emergence. Mol. Syst. Biol., 9(1):699

Péret B*, Li G*, Zhao J*, Band LR*, Voß U, Postaire O, Luu D-T, Da Ines O, Casimiro I, Lucas M, Wells DM, Lazzerini L, Nacry P, King JR, Jensen OE, Schäffner AR✉, Maurel C✉, Bennett MJ✉ (2012) Auxin regulates aquaporin function to facilitate lateral root emergence. Nat. Cell Biol., 14(10):991-998

Péret B, Swarup K, Ferguson A, Seth M, Yang Y, Dhondt S, James N, Casimiro I, Perry P, Syed A, Yang H, Reemmer J, Venison E, Howells C, Perez-Amador MA, Yun J, Alonso J, Beemster GTS, Laplaze L, Murphy AS, Bennett MJ, Nielsen E, Swarup R✉ (2012) AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. Plant Cell, 24(7):2874-2885

Péret B✉, Clément M, Nussaume L, Desnos T (2011) Root developmental adaptation to phosphate starvation: better safe than sorry. Trends Plant Sci., 16(8):442-450

Péret B✉, Larrieu A, Bennett MJ (2009) Lateral root emergence: a difficult birth. J. Exp. Bot., 60(13):3637-3643

Péret B*✉, De Rybel B*, Casimiro I, Benková E, Swarup R, Laplaze L, Beeckman T, Bennett MJ (2009) Arabidopsis lateral root development: an emerging story. Trends Plant Sci., 14(7):399-408

  • Genome sequencing
    Jérôme Gouzy and Erika Sallet – LIPM Toulouse France
    Hélène Bergès and William Marande – CNRGV Toulouse France
  • Plant systems biology
    Malcolm Bennett – CPIB Nottingham UK
    Laurent Laplaze – IRD Montpellier
  • Small RNA
    Martin Crespi and Thomas Blein – IPS2 Saclay
  • Auxin transport and response
    Tatsuaki Goh – NAIST Japan
    Hidehiro Fukaki – University of Kobe Japan
    Stéphanie Robert – UPSC Umeå Sweden

  • 2014 The LUPIN ROOTS project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 637420 – Starting grant).


  • 2017 Projet Exploratoire Labex Agro – ROOT4EVER
  • 2017 Projet Soutien Ponctuel Labex Agro – Lateral Root workshop
  • 2018 Projet Exploration Japon – Ambassade de France au Japon
  • 2018 Projet INUPRAG – Fondation Kempe Sweden
  • 2018 ERC Implementing arrangement – CONFAP Brazil
Jobs / Trainings

Job offers will be available throughout the ERC project and applications for fellowships and internships are welcome. Please contact the PI for more information.

Former team members

IBIP seminar: Inge Verstraeten

March 24, 2022 – Role of LRR-RLKs in root development

Thesis defended by Tamara Le Thanh

December 16, 2021 – Research of molecular players involved in the determinate growth of rootlets of white lupin cluster roots

White lupin: The genome of this legume has finally been sequenced

White lupin has a root system that is highly adapted for poor soils thanks to its proteoid or cluster roots, which allow it to extract phosphate from the soil very effectively. The mapping of its genome represents a major step toward understanding this mechanism.

Thesis defended by Cécilia Gallardo

Dec 6, 2019 – Study of the development of proteoid roots in white lupins

IBIP seminar – André Marques

Apr. 19, 2018 – Estimating the repetitive DNA profile of white lupin (Lupinus albus) genome: a cytogenomic approach

Lateral Root Workshop

Oct 26-27, 2017 – The meeting was jointly organized by Benjamin PERET (CNRS, UMR BPMP) and Laurent LAPLAZE (IRD, UMR DIADE)