DigR: a generic model and its open source simulation software to mimic three-dimensional root-system architecture diversity

Barczi, Jean‐François; Rey, Hervé; Griffon, Sébastien; Jourdan, Christophe

doi:10.1093/aob/mcy018

Cited by 30 publications

(24 citation statements)

References 54 publications

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“…The root anatomy is the result of a generative algorithm and is fixed in time. One possible improvement to GRANAR would be to include a developmental module within the model, similar to the current root architectural models (Postma et al, 2017;Barczi et al, 2018;Schnepf et al, 2018). This would allow the model to create root anatomies for different root ages in one simulation, enabling the estimation of the evolution of the root conductivity with the root maturation.…”

Section: Discussionmentioning

confidence: 99%

GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy

et al. 2019

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Root hydraulic conductivity is a limiting factor along the water pathways between the soil and the leaf, and root radial conductivity is itself defined by cell-scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex time-consuming experimental procedures. We present an open-source computational tool, the Generator of Root Anatomy in R (GRANAR; http://granar.github.io), that can be used to rapidly generate digital versions of contrasted monocotyledon root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties. We used GRANAR to reanalyze large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA (model of explicit cross-section hydraulic architecture). Our simulations highlight the large importance of the width of the stele and the cortex. GRANAR is a computational tool that generates root anatomical networks from experimental data. It enables the quantification of the effect of individual anatomical features on the root radial conductivity.

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Section: Discussionmentioning

confidence: 99%

GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy

et al. 2019

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“…Mommer et al, 2016), FSP modelling of roots and soils has been gaining momentum. In this issue, new root modelling frameworks are presented that allow for easy simulation of root growth and development over time for a range of root architectures (Barczi et al, 2018;Schnepf et al, 2018). Particular attention is given in these studies to the ability to couple simulation of root growth to simulations of other relevant components, allowing for, for example, analysis of the effects of below-ground interactions on wholeplant performance.…”

Section: Extending Models Of Plant Architecturementioning

confidence: 99%

Computational botany: advancing plant science through functional–structural plant modelling

et al. 2018

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The need to integrate the ever-expanding body of knowledge in the plant sciences has led to the development of sophisticated modelling approaches. This special issue focuses on functional-structural plant (FSP) models, which are the result of cross-fertilization between the domains of plant science, computer science and mathematics. FSP models simulate growth and morphology of individual plants that interact with their environment, from which complex plant community properties emerge. FSP models can be used for a broad range of research questions across disciplines related to plant science. This special issue presents the latest developments in FSP modelling, including the novel incorporation of plant ecophysiological concepts and the application of FSP models to address new scientific questions. Additionally, it illustrates the breadth of model evaluation approaches that are performed. FSP modelling is a very active domain of plant research which brings together a wide range of scientific disciplines. It offers the opportunity to address questions in complex plant systems that cannot be addressed by empirical approaches alone, including questions on fundamental concepts related to plant development such as regulation of morphogenesis, as well as on applied concepts such as the relationship between crop performance and plant competition for resources.

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“…We found that bio-organic fertilizer (BIO) significantly increased the number, length and density of lateral roots of pear trees, and reduced inter-branching distance ( Fig 3A -C and F), supporting the first hypothesis proposed in this paper. Different orders of lateral roots have different functions; lateral roots less than 2 mm in diameter are the most activate part of the root system [37], playing a key role in absorbing soil nutrients and water [9,27]. We found that while the diameter of 2 nd order and above lateral roots of trees grown in all media was 2 mm or less (Fig 4), the number and length of lateral roots in BIO-CF boxes was significantly higher than that of CF-CF boxes, indicating that the bio-organic/chemical fertilizer combination was particularly conducive to allowing pear roots to occupy a large soil space and thereby improve nutrient absorption efficiency.…”

Section: Bio-cf Had a Significant Synergistic Effect On The Growth Ofmentioning

confidence: 99%

A split supply of bio-organic and chemical fertilizer synergistically affects root system architecture and improves above-ground growth in pear tree (Pyrus pyrifolia Nakai)

Kang¹,

An²,

Ma³

et al. 2020

Preprint

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Background: Root system architecture (RSA) is highly plastic, responding to nutrient availability and the heterogeneity of the soil environment. However, the linkage of root morphology to anatomy and root nutrient, and its implication for root function at the heterogeneous application of bio-organic and chemical fertilizer have not yet been defined, especially for pear trees.Results: In this study, a split-root experiment was conducted using 1-year old ‘Cuiguan’ trees. No fertilizer (NF), chemical fertilizer (CF), and bio-organic fertilizer (BIO) were paired to test six combinations: NF-NF, NF-CF, NF-BIO, CF-CF, BIO-BIO, and BIO-CF. Root morphological, anatomical traits and root nutrient concentrations, and their relationships were determined. Trees receiving BIO had significantly higher lateral root numbers, activity, total lateral root length, and specific root length than trees receiving no BIO, while the effects on root tissue density were the direct opposite. Compared with CF-CF treatment, root xylem thickness, stele diameter, vessel diameter, and number of vessels all increased in response to BIO-CF treatment. Root growth was synergistically promoted in BIO-CF, with increased special root length and root nitrogen concentration, but root tissue density and the carbon:nitrogen ratio were reduced. Intriguingly, the synergistic effect resulted in greater trunk girth without sacrificing height, compared to trees receiving CF or BIO alone.Conclusions: The combination of BIO and CF improves root traits and tree growth, suggesting that using bio-organic fertilizer as a supplement to reduce the application rate of chemical fertilizer is beneficial to orchard ecosystems.

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DigR: a generic model and its open source simulation software to mimic three-dimensional root-system architecture diversity

Cited by 30 publications

References 54 publications

GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy

GRANAR, a Computational Tool to Better Understand the Functional Importance of Monocotyledon Root Anatomy

Computational botany: advancing plant science through functional–structural plant modelling

A split supply of bio-organic and chemical fertilizer synergistically affects root system architecture and improves above-ground growth in pear tree (Pyrus pyrifolia Nakai)

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