Systemic control of root developmental plasticity
Plants continuously adjust their root system architecture to fluctuations in nutrient availability. Our team studies the molecular and cellular mechanisms underlying this plasticity, with an emphasis on long-distance signaling between shoots and roots.
A major line of work focuses on the AoDev/AoN systemic pathways controlling developmental responses to phosphate and nitrogen availability. We recently identified the leucine-rich repeat receptor kinase LalbCCR1 as a key component of this systemic regulation in white lupin, linking nutrient perception to the coordinated formation of cluster roots and nodules (Marquès et al., 2025).
This work provides a mechanistic framework to understand how nutritional status is translated into large-scale developmental reprogramming of the root system.
Cluster roots as a model for adaptive organogenesis
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White lupin develops dense clusters of short lateral roots (cluster roots) under phosphate deficiency, representing one of the most striking examples of adaptive root organogenesis in plants.
We use this system to dissect:
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the genetic control of cluster root initiation and patterning,
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systemic versus local regulation of root developmental programs,
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coordination between root development and symbiotic nodulation
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the physiological consequences for nutrient acquisition in low-input agroecosystems.
Cell wall remodeling and root morphogenesis
Root organogenesis requires precise control of tissue mechanics and cell wall composition. Our group develops integrative approaches combining:
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single-nucleus transcriptomics,
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quantitative imaging of cell wall polysaccharides,
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gene family analyses of wall remodeling enzymes,
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and developmental modeling.
This work has led to the formulation of a “push-and-yield” conceptual model linking gene expression dynamics to changes in cell wall composition and mechanical properties during lateral root formation.
Comparative and evolutionary perspectives
To understand how developmental strategies vary across plant lineages, we adopt comparative approaches between:
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dicots with type I cell walls (e.g. white lupin),
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monocots with type II cell walls (Brachypodium, cereals).
This axis is currently developed through the Marie Skłodowska-Curie postdoctoral project of Kevin Bellande, combining transcriptomics and cell wall biology in Brachypodium.
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Genomic resources for white lupin
​​To support functional and comparative studies, our team has contributed to the development of large-scale genomic resources for white lupin.
We participated in the production and analysis of:
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the first high-quality reference genome sequence of Lupinus albus,
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cultivated and wild accessions.a species-wide pangenome capturing structural variation and gene content diversity across
These resources now constitute the genomic foundation for genetic, evolutionary and breeding-oriented studies in this species and are available on the White Lupin Genome portal at www.whitelupin.fr
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PULSAR – systemic regulation and genetic dissection of root traits
​​Within the ANR France 2030 PULSAR project, our team investigates the genetic and developmental bases of root system adaptation to nutrient limitation in white lupin. We lead the analysis of root system architecture and cluster root traits using large-scale phenotyping combined with genome-wide association studies (GWAS) on diverse germplasm. Candidate genes identified through GWAS and systemic signaling studies are then functionally validated using a dedicated TILLING / FIND-IT reverse-genetics platform currently being developed in the project. This strategy directly connects systemic developmental mechanisms with natural genetic variation and provides actionable targets for future breeding of nutrient-efficient lupin varieties.
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PULSAR brings together a multidisciplinary consortium combining plant developmental biology, genetics, agronomy and food science, including academic partners (CNRS, INRAE, ESA) and private stakeholders involved in lupin breeding and valorisation. This integrated framework enables close interactions between fundamental research, genetic resource development and applied crop improvement.
Root phenotyping platforms and imaging infrastructures
​​Understanding root system plasticity requires quantitative and reproducible phenotyping across developmental scales.
Our team has developed and operates several experimental platforms dedicated to root phenotyping, including:
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controlled growth systems for cluster root induction under nutrient deficiency,
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imaging pipelines for whole root system architecture
and a new high-throughput root phenotyping facility developed within the PULSAR project, specifically designed to quantify root architectural responses to nutrient availability in large germplasm panels.
This platform enables standardized, multi-scale analysis of root development, from organ-level architecture down to cellular organization and gene expression patterns.
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COLLABORATIONS
PULSAR Project
​Coordinator Joëlle Fustec - Ecole Supérieure d'Agricultures (ESA) Angers FR
INRAE Partners
IPSiM Montpellier, Agroécologie Dijon, STLO Rennes, IRHS Angers, BIA Nantes
Private partners
Cérience - Poitiers FR
Kédelaï - Paris FR
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Cell wall and cluster root development
Joop Vermeer - Université de Neuchâtel - Switzerland