Calibration and evaluation of ArchiSimple, a simple model of root system architecture

Pagès, Loïc; Bécel, Carole; Boukcim, Hassan; Moreau, Delphine; Nguyen, Christophe; Voisin, Anne‐Sophie

doi:10.1016/j.ecolmodel.2013.11.014

Cited by 93 publications

(84 citation statements)

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“…The relationships between diameter, length and branching density and their hierarchical connections are discussed below. The positive correlation between daughter root diameter and mother root diameter has been already noted and quantified for several species (Bouma et al, 2001;Lecompte et al, 2005;Bécel et al, 2012;Pagès et al, 2013Pagès et al, , 2014. However, in these studies the sampling methods and definitions of daughter root and bearing root diameter were mostly different from those used here.…”

Section: Discussionmentioning

confidence: 53%

“…However, in these studies the sampling methods and definitions of daughter root and bearing root diameter were mostly different from those used here. The earlier studies normally linked the median apical diameter of the daughter roots in a whole or a distal bearing root to the apical or average diameter of the bearing root for various dicotyledonous and monocotyledonous species (Lecompte et al, 2005;Bécel et al, 2012;Pagès et al, 2013Pagès et al, , 2014. To account for the change in diameter along the bearing roots, which were not considered in previous studies, we linked the median basal diameters of daughter roots in successive bearing root segments to the diameters of these segments for axile roots and higher-order LRs (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Pagès

2016

Ann Bot

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Background and Aims Root diameter, especially apical diameter, plays an important role in root development and function. The variation in diameter between roots, and along roots, affects root structure and thus the root system's overall foraging performance. However, the effect of diameter variation on root elongation, branching and topological connections has not been examined systematically in a population of high-order roots, nor along the roots, especially for mature plants grown in the field.Methods A method combining both excavation and analysis was applied to extract and quantify root architectural traits of adult, field-grown maize plants. The relationships between root diameter and other root architectural characteristics are analysed for two maize cultivars.Key Results The basal diameter of the lateral roots (orders 1-3) was highly variable. Basal diameter was partly determined by the diameter of the bearing segment. Basal diameter defined a potential root length, but the lengths of most roots fell far short of this. This was explained partly by differences in the pattern of diameter change along roots. Diameter tended to decrease along most roots, with the steepness of the gradient of decrease depending on basal diameter. The longest roots were those that maintained (or sometimes increased) their diameters during elongation. The branching density (cm -1 ) of laterals was also determined by the diameter of the bearing segment. However, the location of this bearing segment along the mother root was also involved -intermediate positions were associated with higher densities of laterals.Conclusions The method used here allows us to obtain very detailed records of the geometry and topology of a complex root system. Basal diameter and the pattern of diameter change along a root were associated with its final length. These relationships are especially useful in simulations of root elongation and branching in source-sink models.

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Section: Discussionmentioning

confidence: 53%

Section: Discussionmentioning

confidence: 99%

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Pagès

2016

Ann Bot

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“…growth rates, branching rates). At the population and plant scales, root development models [39,104] offer the possibility to convert root pattern properties into predicted root structures. While root anatomical patterns can be automatically characterized by image analysis tools such as PHIVRootCell [22] , no root anatomy development model exists at that scale.…”

Section: Discussion and Perspectivesmentioning

confidence: 99%

“…Root architecture models, such as SimRoot [37] , RootBox [38] , RootTyp [39] , ArchiSimple [40] , OpenSimRoot [41] or CRootBox [42] , are designed to simulate root systems from a limited number of traits, given as input parameters. The major interest of root architectural models is to generate a large number of contrasted root system architectures.…”

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Connecting the dots between computational tools to analyse soil-root water relations

Passot

Couvreur

Meunier

et al. 2018

Preprint

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In the recent years, many computational tools, such as image analysis, data management, processbased simulation and upscaling tools, were developed to help quantify and understand water flow in the soilroot system, at multiple scales (tissue, organ, plant and population). Several of these tools work together or, at least, are compatible. However, for the uninformed researcher, they might seem disconnected, forming a unclear and disorganised succession of tools.In this article, we present how different pieces of work can be further developed by connecting them to analyse soilrootwater relations in a comprehensive and structured network. This "explicit network of soilroot computational tools" informs the reader about existing tools and help them understand how their data (past and future) might fit within the network. We also demonstrate the novel possibilities of scaleconsistent parameterizations made possible by the network with a set of case studies from the literature. Finally, we discuss existing gaps in the network and how we can move forward to fill them.. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/312918 doi: bioRxiv preprint first posted online May. 9, 2018; Passot, Couvreur, Meunier et al. 2018 Tools for the analysis of water relations Preprint HighlightsMany computational tools exist to quantify water flow in the soilroot system. These tools can be arranged in a comprehensive network that can be leveraged to better interpret experimental data. KeywordsComputational tools, image analysis, simulation, network, root, soil, water was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/312918 doi: bioRxiv preprint first posted online May. 9, 2018; Passot, Couvreur, Meunier et al. 2018 Tools for the analysis of water relations Preprint Glossary TermDefinition Reference Standard Uptake FractionRelative distribution of root water uptake between root segments when water is equally available in space (units: %)[1]High pressure flow meter Device designed to measure the root system conductance by perfusing pressurized water into a root system opposite from the natural direction of the transpiration stream[2]Root pressure probe Device designed to measure the hydraulic conductance of a single root through variations of water pressure and flow at the cut end of a root [3] Cell pressure probe Device designed to measure the hydraulic conductivity of the membranes of a single plant cell by observing the relaxation time of water pressure pulses applied to the cell Upscaled property System property that is an output of the model, at a higher scale than the input parameters. For instance, the root radial conductivity is an upscaled property of models of root organ water f...

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“…At the time of writing, RSML support has been implemented into the following imaging or modeling suites: ArchiSimple (Pagès et al, 2014), OpenAlea (Pradal et al, 2008), RhizoBox (Leitner et al, 2010), RhizoScan (Diener et al, 2013), RootNav (Pound et al, 2013), RooTrak (Mairhofer et al, 2012(Mairhofer et al, , 2013, RootSystemAnalyser (Leitner et al, 2014), R-SWMS (Javaux et al, 2008), and SmartRoot (Lobet et al, 2011).…”

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confidence: 99%

Root System Markup Language: Toward a Unified Root Architecture Description Language

et al. 2015

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Calibration and evaluation of ArchiSimple, a simple model of root system architecture

Cited by 93 publications

References 32 publications

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Relationships between root diameter, root length and root branching along lateral roots in adult, field-grown maize

Connecting the dots between computational tools to analyse soil-root water relations

Root System Markup Language: Toward a Unified Root Architecture Description Language

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