Periodic Reporting for period 1 - LUMIROOT (Probing the role of miRNAs in cluster root development in white lupin)
Période du rapport: 2023-07-01 au 2025-06-30
Context and Overall Objectives
Phosphorus is one of the most important nutrients for plant growth, yet it is often scarce in agricultural soils. To compensate, farmers rely on large amounts of chemical fertilizers, which are expensive, environmentally harmful, and unsustainable in the long term. At the same time, the global demand for food continues to increase, making it urgent to find alternative strategies for nutrient-efficient and climate-resilient agriculture.
White lupin (Lupinus albus), a legume crop, has developed a remarkable natural strategy to thrive in nutrient-poor soils. It produces specialized “cluster roots,” which enhance its ability to capture phosphorus from the environment. Understanding the molecular processes behind this adaptation could open new pathways to improve crop resilience and reduce fertilizer dependency.
Recent discoveries have shown that small molecules called microRNAs, along with other non-coding RNAs, play key roles in regulating plant development and stress responses. However, their role in cluster root formation and nutrient uptake is still poorly understood. Traditional genetic approaches to study these molecules are slow and rely on transgenic plants, which face limitations in terms of technical feasibility, regulatory acceptance, and scalability.
The LUMIROOT project seeks to overcome these barriers by combining advanced molecular biology, bioinformatics, and innovative nanotechnological approaches to deliver RNA into plants without genetic modification. This strategy will help unravel how plants sense and respond to phosphorus limitation, and how root systems can be tuned to improve nutrient use efficiency.
The project’s objectives are to:
Clarify the regulatory functions of microRNAs in cluster root formation under phosphorus-deficient conditions.
Develop RNA-based nanotechnology as a safe and non-transgenic tool for gene function analysis in crops.
Build systems-level models linking microRNAs with the key genes that control root architecture.
Share findings with the agricultural sector, breeders, and rural communities, to translate scientific knowledge into sustainable practices.
By generating new insights into plant adaptation to nutrient limitation, LUMIROOT contributes to the EU’s goals of reducing dependence on fertilizers, preserving soil health, and supporting a transition towards greener and more resilient agriculture.
Phosphorus is one of the most important nutrients for plant growth, yet it is often scarce in agricultural soils. To compensate, farmers rely on large amounts of chemical fertilizers, which are expensive, environmentally harmful, and unsustainable in the long term. At the same time, the global demand for food continues to increase, making it urgent to find alternative strategies for nutrient-efficient and climate-resilient agriculture.
White lupin (Lupinus albus), a legume crop, has developed a remarkable natural strategy to thrive in nutrient-poor soils. It produces specialized “cluster roots,” which enhance its ability to capture phosphorus from the environment. Understanding the molecular processes behind this adaptation could open new pathways to improve crop resilience and reduce fertilizer dependency.
Recent discoveries have shown that small molecules called microRNAs, along with other non-coding RNAs, play key roles in regulating plant development and stress responses. However, their role in cluster root formation and nutrient uptake is still poorly understood. Traditional genetic approaches to study these molecules are slow and rely on transgenic plants, which face limitations in terms of technical feasibility, regulatory acceptance, and scalability.
The LUMIROOT project seeks to overcome these barriers by combining advanced molecular biology, bioinformatics, and innovative nanotechnological approaches to deliver RNA into plants without genetic modification. This strategy will help unravel how plants sense and respond to phosphorus limitation, and how root systems can be tuned to improve nutrient use efficiency.
The project’s objectives are to:
Clarify the regulatory functions of microRNAs in cluster root formation under phosphorus-deficient conditions.
Develop RNA-based nanotechnology as a safe and non-transgenic tool for gene function analysis in crops.
Build systems-level models linking microRNAs with the key genes that control root architecture.
Share findings with the agricultural sector, breeders, and rural communities, to translate scientific knowledge into sustainable practices.
By generating new insights into plant adaptation to nutrient limitation, LUMIROOT contributes to the EU’s goals of reducing dependence on fertilizers, preserving soil health, and supporting a transition towards greener and more resilient agriculture.
The LUMIROOT project has advanced our understanding of the molecular basis of root adaptation to phosphorus (P) deficiency, with a special focus on the formation of cluster roots (CRs) in white lupin. Over the course of the project, several complementary approaches were undertaken:
Identification of key miRNAs involved in CR development
Using high-throughput sequencing and bioinformatics analyses, we generated comprehensive profiles of small RNAs expressed in lupin roots under phosphorus-limited conditions. Several candidate miRNAs were identified as potential regulators of CR initiation and development.
Main achievement: A catalogue of P-responsive miRNAs in white lupin roots was established, providing an essential resource for functional studies in legumes and other crops.
Functional validation of candidate miRNAs using RNA delivery technologies
To overcome the limitations of traditional transgenic approaches, we developed and optimized nanoparticle-mediated delivery of small RNAs and double-stranded RNAs into lupin roots. This strategy enabled the transient modulation of candidate miRNAs in planta without generating genetically modified organisms.
Main achievement: Proof-of-concept experiments demonstrated the feasibility of RNA-based delivery systems to study gene function in crops, opening a sustainable alternative to genetic modification.
Regulatory network modelling
Integration of transcriptomic and small RNA datasets allowed us to generate predictive gene regulatory networks linking specific miRNAs with transcription factors and target genes controlling root development.
Main achievement: Novel connections between miRNA activity and root developmental plasticity under nutrient stress were revealed, supporting the central role of non-coding RNAs in adaptive responses.
Knowledge advancement for sustainable agriculture
By elucidating how non-coding RNAs regulate plant nutrient acquisition, the project generated insights that can be translated into sustainable practices aimed at reducing fertilizer use. Preliminary results highlight the potential of RNA-based technologies to be applied in crops of agronomic interest beyond lupin.
Main achievement: The project delivered both fundamental knowledge and innovative methodologies that can inform the development of eco-friendly strategies to enhance nutrient use efficiency in agriculture.
Identification of key miRNAs involved in CR development
Using high-throughput sequencing and bioinformatics analyses, we generated comprehensive profiles of small RNAs expressed in lupin roots under phosphorus-limited conditions. Several candidate miRNAs were identified as potential regulators of CR initiation and development.
Main achievement: A catalogue of P-responsive miRNAs in white lupin roots was established, providing an essential resource for functional studies in legumes and other crops.
Functional validation of candidate miRNAs using RNA delivery technologies
To overcome the limitations of traditional transgenic approaches, we developed and optimized nanoparticle-mediated delivery of small RNAs and double-stranded RNAs into lupin roots. This strategy enabled the transient modulation of candidate miRNAs in planta without generating genetically modified organisms.
Main achievement: Proof-of-concept experiments demonstrated the feasibility of RNA-based delivery systems to study gene function in crops, opening a sustainable alternative to genetic modification.
Regulatory network modelling
Integration of transcriptomic and small RNA datasets allowed us to generate predictive gene regulatory networks linking specific miRNAs with transcription factors and target genes controlling root development.
Main achievement: Novel connections between miRNA activity and root developmental plasticity under nutrient stress were revealed, supporting the central role of non-coding RNAs in adaptive responses.
Knowledge advancement for sustainable agriculture
By elucidating how non-coding RNAs regulate plant nutrient acquisition, the project generated insights that can be translated into sustainable practices aimed at reducing fertilizer use. Preliminary results highlight the potential of RNA-based technologies to be applied in crops of agronomic interest beyond lupin.
Main achievement: The project delivered both fundamental knowledge and innovative methodologies that can inform the development of eco-friendly strategies to enhance nutrient use efficiency in agriculture.
The LUMIROOT project has generated results that go significantly beyond the current state of the art in the field of plant adaptation to nutrient stress and RNA-based technologies:
Novel insights into the role of miRNAs in cluster root formation
While previous studies had suggested a regulatory role for miRNAs in root system architecture, LUMIROOT provided the first in-depth catalogue of phosphorus-responsive miRNAs in white lupin, a model species for studying cluster root development. This constitutes an unprecedented resource for the legume community and for researchers interested in nutrient acquisition strategies.
Impact: Establishes the foundation for a new research avenue on non-coding RNAs as central regulators of root developmental plasticity under nutrient stress.
Development of innovative RNA delivery technologies in non-model crops
The use of nanoparticle-mediated RNA delivery represents a technological leap forward. Most functional studies in plants rely on genetically modified organisms or model species with efficient transformation systems. By demonstrating transient RNA delivery and functional validation in lupin, the project showcases a non-transgenic, flexible, and rapid approach applicable to diverse crops.
Impact: Positions RNA-based sprays and nanoparticle delivery as promising tools for both basic research and agricultural innovation.
Integration of regulatory networks for adaptive responses
The modelling of gene regulatory networks combining small RNAs, transcription factors, and downstream targets enabled the identification of novel hubs of control in root development. This integrative perspective goes beyond descriptive studies, offering predictive frameworks that can guide targeted interventions in crops.
Impact: Opens the way for precision design of RNA-based strategies to modulate nutrient acquisition traits.
Proof-of-concept for sustainable crop improvement
By linking RNA-based regulation to phosphorus acquisition, the project connects fundamental molecular biology to urgent agricultural needs. Fertilizer overuse represents a major environmental and economic challenge. LUMIROOT results highlight the possibility of reducing fertilizer dependency by harnessing RNA regulation to enhance natural plant adaptive traits.
Impact: Contributes to EU strategies for sustainable agriculture, food security, and environmental protection.
Novel insights into the role of miRNAs in cluster root formation
While previous studies had suggested a regulatory role for miRNAs in root system architecture, LUMIROOT provided the first in-depth catalogue of phosphorus-responsive miRNAs in white lupin, a model species for studying cluster root development. This constitutes an unprecedented resource for the legume community and for researchers interested in nutrient acquisition strategies.
Impact: Establishes the foundation for a new research avenue on non-coding RNAs as central regulators of root developmental plasticity under nutrient stress.
Development of innovative RNA delivery technologies in non-model crops
The use of nanoparticle-mediated RNA delivery represents a technological leap forward. Most functional studies in plants rely on genetically modified organisms or model species with efficient transformation systems. By demonstrating transient RNA delivery and functional validation in lupin, the project showcases a non-transgenic, flexible, and rapid approach applicable to diverse crops.
Impact: Positions RNA-based sprays and nanoparticle delivery as promising tools for both basic research and agricultural innovation.
Integration of regulatory networks for adaptive responses
The modelling of gene regulatory networks combining small RNAs, transcription factors, and downstream targets enabled the identification of novel hubs of control in root development. This integrative perspective goes beyond descriptive studies, offering predictive frameworks that can guide targeted interventions in crops.
Impact: Opens the way for precision design of RNA-based strategies to modulate nutrient acquisition traits.
Proof-of-concept for sustainable crop improvement
By linking RNA-based regulation to phosphorus acquisition, the project connects fundamental molecular biology to urgent agricultural needs. Fertilizer overuse represents a major environmental and economic challenge. LUMIROOT results highlight the possibility of reducing fertilizer dependency by harnessing RNA regulation to enhance natural plant adaptive traits.
Impact: Contributes to EU strategies for sustainable agriculture, food security, and environmental protection.