Advances in root architectural modeling

Postma, Johannes; Black, Christopher K.

doi:10.19103/as.2020.0075.02

Cited by 5 publications

(4 citation statements)

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“…Several functional-structural models of root architecture including Archisimple, RootTyp, OpenSimRoot (and its forerunner SimRoot)(Fig. 19), ROOTMAP, SPACSYS, R-SWMS, RootBox, CRoot-Box have been used to study various aspects of rootsoil interactions (Pages et al 2004(Pages et al , 2014Wu et al 2007;Javaux et al 2008;Postma et al 2017;Leitner et al 2010;Schnepf et al 2018;Lynch et al 1997;Diggle 1988;Moraes et al 2019b, a;Dunbabin et al 2013a, b;Postma and Black 2021). Root models have been successfully used to evaluate various architectural and anatomical phenotypes for nitrogen capture (Postma et al 2014;Rangarajan et al 2018;Rangarajan et al 2022;Saengwilai et al 2021;Perkins and Lynch 2021;Ajmera et al 2022;Postma and Lynch 2011a, b;Schneider et al 2017a, b;Schneider et al 2020a, b), to identify optimal root architectures for nitrogen and water uptake (Dunbabin et al 2003;Renton and Poot 2014;Ho et al 2005, Rangarajan et al 2022, Ajmera et al 2022, inter-and intraspecific root competition (Postma and Lynch 2012;Dunbabin 2007;Hoffland et al 1990), kinetics of nitrogen uptake (York et al 2016a, b), and nitrogen capture under different soil physical scenarios (Strock et al 2022a, b).…”

Section: Exploring the Fitness Landscape Of The Root Phenome In Silicomentioning

confidence: 99%

“…The integration of root models with robust models of shoots, soil, microbes and agroecologies will comprise increasingly powerful tools towards developing crops and cropping systems, a requirement to sustainably provide for an increasing population in a degrading environment (Benes et al 2020). Modeling and integrating processes across scales that are on different biological, temporal and computational scales however is a challenge (Baldazzi et al 2012;Band et al 2012;Postma and Black 2021). Recent studies have explored different methods to integrate models in efforts to fulfill inadequacies in model integration and multi-scale modeling (Mai et al 2018;Lobet et al 2014;Fang et al 2019;Lang 2019;Ajmera et al 2022;Seidel et al 2022a, b;Wu et al 2007;Marshall-Colon et al 2017;Benes et al 2020).…”

Section: Exploring the Fitness Landscape Of The Root Phenome In Silicomentioning

confidence: 99%

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Root phenotypes for improved nitrogen capture

Lynch,

Galindo-Castañeda,

Schneider

et al. 2023

Plant Soil

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Background Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer. Scope Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes. Conclusions Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

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Section: Exploring the Fitness Landscape Of The Root Phenome In Silicomentioning

confidence: 99%

Section: Exploring the Fitness Landscape Of The Root Phenome In Silicomentioning

confidence: 99%

Root phenotypes for improved nitrogen capture

Lynch,

Galindo-Castañeda,

Schneider

et al. 2023

Plant Soil

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“…The FSPM explicitly describes the development of the 3D architecture of plants over time as governed by physiological processes which, in turn, depend on environmental factors (Vos et al 2010). Thus, they provide insight into key processes underlying plant growth, notably the allocation of resources (Postma and Black 2021). Recently benchmarking of root-focused FSPM models showed the ability of several codes to solve challenging scenarios (Schnepf et al 2023).…”

Section: Introductionmentioning

confidence: 99%

Modeling cassava root system architecture and the underlying dynamics in shoot-root carbon allocation

Nattharat,

Thaiprsit,

Kalapanulak

et al. 2023

Preprint

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· Background and Aims: Plants store carbohydrates for later use during, e.g., night, drought, and recovery after stress. Carbon allocation presents the plant with tradeoffs, notably between growth and storage. We asked how this tradeoff works for cassava (Manihot esculenta)pre- and post-storage root (SR) formation and if manipulation of the number of storage organs and leaf growth rate might increase yield. · Methods: We developed a functional-structural plant model, called MeOSR, to simulate carbon partitioning underlying cassava growth and SR formation in conjunction with the root system's three-dimensional (3D) architecture (RSA). We validated the model against experimental data and simulated phenotypes varying in the number of SR and leaf growth rate. · Results: The simulated 3D RSA and the root mass closely represented those of field-grown plants. The model simulated root growth and associated carbon allocation across development stages. Substantial accumulation of non-structural carbohydrates (NSC) preceded SR formation, suggesting sink-limited growth. SR mass and canopy photosynthesis might be increased by both increasing the number of SR and the leaf growth rate. · Conclusion: MeOSR offers a valuable tool for simulating plant growth, its associated carbon economy, and 3D RSA over time. In the first month, the specific root length increased due to root branching, but in the third month, it decreased due to secondary root growth. The accumulation of NSC might initiate SR development in cassava. Cassava growth is relatively slow during the first 3 months, and a faster crop establishment combined with a greater SR growth might increase yield.

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“…To address questions surrounding the interface between soil structure and soil foraging strategies, functional–structural plant models that combine 3-D representations of plant architecture with physiological models can provide useful insights into such systems, which are challenging to study empirically ( Vos et al , 2010 ; Dunbabin et al , 2013 ). Plant growth models have historically used very simple representations of soil structure because of uncertainties about how to represent the complexity of the soil matrix, but recent developments in soil modelling have relaxed this limitation and are now ready to be adopted by plant growth models ( Postma and Black, 2021 ). ‘OpenSimRoot’ is an open-source, functional–structural model of root growth and is one of the most comprehensive root architectural models developed to date ( Postma et al , 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture

et al. 2021

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Background and Aims Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. Methods We utilize the functional-structural plant model OpenSimRoot to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with 1) uniform bulk density, 2) plow pans, and 3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. Key Results Soils with plow pans and bulk density gradients affected overall size, distribution, and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of N and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. Conclusions While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.

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Advances in root architectural modeling

Cited by 5 publications

References 105 publications

Root phenotypes for improved nitrogen capture

Root phenotypes for improved nitrogen capture

Modeling cassava root system architecture and the underlying dynamics in shoot-root carbon allocation

Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture

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