High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings

Fernandez Romain, Crabos Amandine, Maillard Morgan, Nacry Philippe, Pradal Christophe. 2022. High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings. Plant Methods, 18:127, 19 p.

Url - autres données associées : https://github.com/Rocsg/RootSystemTracker / Url - autres données associées : https://imagej.net/plugins/rootsystemtracker

Résumé : Background: High-throughput phenotyping is crucial for the genetic and molecular understanding of adaptive root system development. In recent years, imaging automata have been developed to acquire the root system architecture of many genotypes grown in Petri dishes to explore the Genetic x Environment (GxE) interaction. There is now an increasing interest in understanding the dynamics of the adaptive responses, such as the organ apparition or the growth rate. However, due to the increasing complexity of root architectures in development, the accurate description of the topology, geometry, and dynamics of a growing root system remains a challenge. Results: We designed a high-throughput phenotyping method, combining an imaging device and an automatic analysis pipeline based on registration and topological tracking, capable of accurately describing the topology and geometry of observed root systems in 2D + t. The method was tested on a challenging Arabidopsis seedling dataset, including numerous root occlusions and crossovers. Static phenes are estimated with high accuracy (R2=0.996 and 0.923 for primary and second-order roots length, respectively). These performances are similar to state-of-the-art results obtained on root systems of equal or lower complexity. In addition, our pipeline estimates dynamic phenes accurately between two successive observations (R2=0.938 for lateral root growth). Conclusions: We designed a novel method of root tracking that accurately and automatically measures both static and dynamic parameters of the root system architecture from a novel high-throughput root phenotyping platform. It has been used to characterise developing patterns of root systems grown under various environmental conditions. It provides a solid basis to explore the GxE interaction controlling the dynamics of root system architecture adaptive responses. In future work, our approach will be adapted to a wider range of imaging configurations and species.

Mots-clés Agrovoc : système racinaire, phénotype, racine, Arabidopsis thaliana, analyse d'image, imagerie

Mots-clés libres : High-throughput phenotyping, Time-lapse imaging, Root system architecture

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement européennes : European Commission

Agences de financement hors UE : Agropolis Fondation, Thomas Jefferson Fund

Programme de financement européen : H2020

Projets sur financement : (FRA) Rhizopolis a federal project on the root system of plants, (EU) Enhancing resource Uptake from Roots under stress in cereal crops, (EU) Pre-breeding strategies for obtaining new resilient and added value berries

Auteurs et affiliations

• Fernandez Romain, CIRAD-BIOS-UMR AGAP (FRA)
• Crabos Amandine, INRAE (FRA)
• Maillard Morgan, Université de Montpellier (FRA)
• Nacry Philippe, INRAE (FRA) - auteur correspondant
• Pradal Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-2555-761X - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/603069/)

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