Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

CRootBox: A structural-functional modelling framework for root systems

Andrea Schnepf, Daniel Leitner, Magdalena Landl, Guillaume Lobet, Trung Hieu Mai, Shehan Morandage, Cheng Sheng, Mirjam Zörner, Jan Vanderborght, Harry Vereecken
doi: https://doi.org/10.1101/139980
Andrea Schnepf
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Daniel Leitner
2Simulationswerkstatt, Ortmayrstrasse 20, A-4060 Leonding, Austria; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: daniel.leitner@simwerk.at
Magdalena Landl
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Guillaume Lobet
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Trung Hieu Mai
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Shehan Morandage
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Cheng Sheng
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Mirjam Zörner
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Jan Vanderborght
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
Harry Vereecken
1Institut für Bio- und Geowissenschaften: Agrosphäre (IBG-3), Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; Email:
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: a.schnepf@fz-juelich.de
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Background and Aims Root architecture development determines the sites in soil where roots provide input of carbon and take up water and solutes. However, root architecture is difficult to determine experimentally when grown in opaque soil. Thus, root architectural models have been widely used and been further developed into functional-structural models that simulate the fate of water and solutes in the soil-root system. We present a root architectural model, CRootBox, as a flexible framework to model architecture and its interactions with static and dynamic soil environments.

Methods CRootBox is a C++ -based root architecture model with Python binding, so that CRootBox can be included via a shared library into any Python code. Output formats include VTP, DGF, RSML and CSV. We further created a database of published root architectural parameters. The capabilities of CRootBox for the unconfined growth of single root systems, as well as the different parameter sets, are highlighted into a freely available web application.

Key results We demonstrate the use of CRootBox for 5 different cases (1) free growth of individual root systems (2) growth of root systems in containers as a way to mimic experimental setups, (3), field scale simulation, (4) root growth as affected by heterogeneous, static soil conditions, and (5) coupling CRootBox with Soil Physics with Python code to dynamically compute water flow in soil, root water uptake, and water flow inside roots.

Conclusions In conclusion, we present a fast and flexible functional-structural root model which is based on state-of-the-art computational science methods. Its aim is to facilitate modelling of root responses to environmental conditions as well as the impact of root on soil. In the future, we plan to extend this approach to the aboveground part of the plant.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted May 19, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
CRootBox: A structural-functional modelling framework for root systems
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
CRootBox: A structural-functional modelling framework for root systems
Andrea Schnepf, Daniel Leitner, Magdalena Landl, Guillaume Lobet, Trung Hieu Mai, Shehan Morandage, Cheng Sheng, Mirjam Zörner, Jan Vanderborght, Harry Vereecken
bioRxiv 139980; doi: https://doi.org/10.1101/139980
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
CRootBox: A structural-functional modelling framework for root systems
Andrea Schnepf, Daniel Leitner, Magdalena Landl, Guillaume Lobet, Trung Hieu Mai, Shehan Morandage, Cheng Sheng, Mirjam Zörner, Jan Vanderborght, Harry Vereecken
bioRxiv 139980; doi: https://doi.org/10.1101/139980

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Plant Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3477)
  • Biochemistry (7316)
  • Bioengineering (5294)
  • Bioinformatics (20188)
  • Biophysics (9972)
  • Cancer Biology (7697)
  • Cell Biology (11243)
  • Clinical Trials (138)
  • Developmental Biology (6415)
  • Ecology (9911)
  • Epidemiology (2065)
  • Evolutionary Biology (13270)
  • Genetics (9347)
  • Genomics (12544)
  • Immunology (7667)
  • Microbiology (18928)
  • Molecular Biology (7415)
  • Neuroscience (40868)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2125)
  • Physiology (3138)
  • Plant Biology (6836)
  • Scientific Communication and Education (1268)
  • Synthetic Biology (1891)
  • Systems Biology (5295)
  • Zoology (1083)