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Poupard M, Gallo A, Boulord R, Guillem P, Rolland G, Simonneau T, Christophe A, Pallas B. Source-sink manipulations through shading, crop load and water deficit affect plant morphogenesis and carbon sink priorities leading to contrasted plant carbon status in grapevine. ANNALS OF BOTANY 2024:mcae203. [PMID: 39656901 DOI: 10.1093/aob/mcae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Indexed: 12/17/2024]
Abstract
BACKGROUNDS AND AIMS Shading, water deficit, and crop load shape plant development in a very plastic way. They directly influence the plant's carbon supply and demand to and from the different organs via metabolic, hydraulic and hormonal mechanisms. However, how the multiple environmental factors combine through these mechanisms and how they interplay with carbon status, vegetative and reproductive development and carbon assimilation of the plant needs to be investigated in the context of current climatic and technological constraints. METHODS With this aim, two experiments were conducted on potted grapevines, subjected to ten combinations of treatments. Axis organogenesis, berry characteristics at harvest (weight, number and total soluble content) and a series of leaf traits (gas exchanges, non-structural carbohydrate contents, water potential and SPAD values) were measured. KEY RESULTS Grapevine development showed different responses corresponding to different sink priorities: under shade, vegetative development was maintained at the expense of berries, whereas under high crop load and water deficit, berry growth was the priority sink. These responses were accompanied by changes in the specific leaf area in agreement with the shade avoidance syndrome. These different strategies affected the plant carbon status as estimated through the starch content in leaves. Leaf starch content was not affected by shade, while it decreased under water deficit and crop load conditions. Carbon assimilation was decreased under water deficit, low crop load and shading conditions. Hydraulic properties and leaf nitrogen content correlated withthis decrease while plant carbon status has a very low impact. Finally, no major interaction between the different types of constraints were observed both on morphological and functional variables. CONCLUSIONS Depending on the type of abiotic constraints, grapevine exhibits specific morphogenetic responses at plant and leaf levels. The absence of interaction between the different constraints showed that grapevine is able to exhibit independent responses to shade and water deficit. This result is of major importance to further design new agricultural systems facing multiple abiotic constraints, such as those in agroforestery and agrivolatic system.
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Affiliation(s)
- Magali Poupard
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Agustina Gallo
- EEA Mendoza, INTA, San Martin 3853, Luján de Cuyo, Mendoza, Argentina
- CONICET, Av. Rivadavia 1917, ciudad Autónoma de Buenos Aires, C1033AAJ, Argentina
| | - Romain Boulord
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Pablo Guillem
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Gaëlle Rolland
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Thierry Simonneau
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Angélique Christophe
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
| | - Benoît Pallas
- Université de Montpellier, INRAE, UMR LEPSE, 2 Place Viala 34060 Montpellier, France
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2
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de Vries J, Fior S, Pålsson A, Widmer A, Alexander JM. Unravelling drivers of local adaptation through evolutionary functional-structural plant modelling. THE NEW PHYTOLOGIST 2024; 244:1101-1113. [PMID: 39256946 DOI: 10.1111/nph.20098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 08/01/2024] [Indexed: 09/12/2024]
Abstract
Local adaptation to contrasting environmental conditions along environmental gradients is a widespread phenomenon in plant populations, yet we lack a mechanistic understanding of how individual agents of selection contribute to this evolutionary process. Here, we developed a novel evolutionary functional-structural plant (E-FSP) model that recreates local adaptation of virtual plants along an environmental gradient. First, we validate the model by testing if it can reproduce two elevational ecotypes of Dianthus carthusianorum occurring in the Swiss Alps. Second, we use the E-FSP model to disentangle the relative contribution of abiotic (temperature) and biotic (competition and pollination) selection pressures to elevational adaptation in D. carthusianorum. Our results suggest that elevational adaptation in D. carthusianorum is predominantly driven by the abiotic environment. The model reproduced the qualitative differences between the elevational ecotypes in two phenological (germination and flowering time) and one morphological trait (stalk height), as well as qualitative differences in four performance variables that emerge from G × E interactions (flowering time, number of stalks, rosette area and seed production). Our approach shows how E-FSP models incorporating physiological, ecological and evolutionary mechanisms can be used in combination with experiments to examine hypotheses about patterns of adaptation observed in the field.
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Affiliation(s)
- Jorad de Vries
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
- Department Environmental Sciences, Wageningen University, 6708 PB, Wageningen, the Netherlands
| | - Simone Fior
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Aksel Pålsson
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Jake M Alexander
- Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
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3
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Nauber T, Hodač L, Wäldchen J, Mäder P. Parametrization of biological assumptions to simulate growth of tree branching architectures. TREE PHYSIOLOGY 2024; 44:tpae045. [PMID: 38696364 PMCID: PMC11128038 DOI: 10.1093/treephys/tpae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/22/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Modeling and simulating the growth of the branching of tree species remains a challenge. With existing approaches, we can reconstruct or rebuild the branching architectures of real tree species, but the simulation of the growth process remains unresolved. First, we present a tree growth model to generate branching architectures that resemble real tree species. Secondly, we use a quantitative morphometric approach to infer the shape similarity of the generated simulations and real tree species. Within a functional-structural plant model, we implement a set of biological parameters that affect the branching architecture of trees. By modifying the parameter values, we aim to generate basic shapes of spruce, pine, oak and poplar. Tree shapes are compared using geometric morphometrics of landmarks that capture crown and stem outline shapes. Five biological parameters, namely xylem flow, shedding rate, proprioception, gravitysense and lightsense, most influenced the generated tree branching patterns. Adjusting these five parameters resulted in the different tree shapes of spruce, pine, oak, and poplar. The largest effect was attributed to gravity, as phenotypic responses to this effect resulted in different growth directions of gymnosperm and angiosperm branching architectures. Since we were able to obtain branching architectures that resemble real tree species by adjusting only a few biological parameters, our model is extendable to other tree species. Furthermore, the model will also allow the simulation of structural tree-environment interactions. Our simplifying approach to shape comparison between tree species, landmark geometric morphometrics, showed that even the crown-trunk outlines capture species differences based on their contrasting branching architectures.
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Affiliation(s)
- Tristan Nauber
- Data-intensive Systems and Visualization Group, Technische Universität Ilmenau, Ehrenbergstraße 29, Ilmenau 98693, Germany
| | - Ladislav Hodač
- Department Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena 07745, Germany
| | - Jana Wäldchen
- Department Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, Jena 07745, Germany
- German Centre for Integrative Biodiversity Research, iDiv (Halle-Jena-Leipzig), Puschstraße 4, Leipzig 04103, Germany
| | - Patrick Mäder
- Data-intensive Systems and Visualization Group, Technische Universität Ilmenau, Ehrenbergstraße 29, Ilmenau 98693, Germany
- German Centre for Integrative Biodiversity Research, iDiv (Halle-Jena-Leipzig), Puschstraße 4, Leipzig 04103, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Fürstengraben 1, Jena 07737, Germany
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4
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Wu Y, Wen W, Gu S, Huang G, Wang C, Lu X, Xiao P, Guo X, Huang L. Three-Dimensional Modeling of Maize Canopies Based on Computational Intelligence. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0160. [PMID: 38510827 PMCID: PMC10950926 DOI: 10.34133/plantphenomics.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
The 3-dimensional (3D) modeling of crop canopies is fundamental for studying functional-structural plant models. Existing studies often fail to capture the structural characteristics of crop canopies, such as organ overlapping and resource competition. To address this issue, we propose a 3D maize modeling method based on computational intelligence. An initial 3D maize canopy is created using the t-distribution method to reflect characteristics of the plant architecture. The subsequent model considers the 3D phytomers of maize as intelligent agents. The aim is to maximize the ratio of sunlit leaf area, and by iteratively modifying the azimuth angle of the 3D phytomers, a 3D maize canopy model that maximizes light resource interception can be constructed. Additionally, the method incorporates a reflective approach to optimize the canopy and utilizes a mesh deformation technique for detecting and responding to leaf collisions within the canopy. Six canopy models of 2 varieties plus 3 planting densities was constructed for validation. The average R2 of the difference in azimuth angle between adjacent leaves is 0.71, with a canopy coverage error range of 7% to 17%. Another 3D maize canopy model constructed using 12 distinct density gradients demonstrates the proportion of leaves perpendicular to the row direction increases along with the density. The proportion of these leaves steadily increased after 9 × 104 plants ha-1. This study presents a 3D modeling method for the maize canopy. It is a beneficial exploration of swarm intelligence on crops and generates a new way for exploring efficient resources utilization of crop canopies.
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Affiliation(s)
- Yandong Wu
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application,
Anhui University, Hefei 230601, China
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Weiliang Wen
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Nongxin Science & Technology (Beijing) Co., Ltd, Beijing 100097, China
| | - Shenghao Gu
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
| | - Guanmin Huang
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Nongxin Science & Technology (Beijing) Co., Ltd, Beijing 100097, China
| | - Chuanyu Wang
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
| | - Xianju Lu
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
- Nongxin Science & Technology (Beijing) Co., Ltd, Beijing 100097, China
| | - Pengliang Xiao
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application,
Anhui University, Hefei 230601, China
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xinyu Guo
- Information Technology Research Center,
Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Beijing 100097, China
| | - Linsheng Huang
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application,
Anhui University, Hefei 230601, China
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5
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Blanc E, Enjalbert J, Flutre T, Barbillon P. Efficient Bayesian automatic calibration of a functional-structural wheat model using an adaptive design and a metamodelling approach. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6722-6734. [PMID: 37632355 DOI: 10.1093/jxb/erad339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/25/2023] [Indexed: 08/28/2023]
Abstract
Functional-structural plant models are increasingly being used by plant scientists to address a wide variety of questions. However, the calibration of these complex models is often challenging, mainly because of their high computational cost, and, as a result, error propagation is usually ignored. Here we applied an automatic method to the calibration of WALTer: a functional-structural wheat model that simulates the plasticity of tillering in response to competition for light. We used a Bayesian calibration method to jointly estimate the values of five parameters and quantify their uncertainty by fitting the model outputs to tillering dynamics data. We made recourse to Gaussian process metamodels in order to alleviate the computational cost of WALTer. These metamodels are built from an adaptive design that consists of successive runs of WALTer chosen by an efficient global optimization algorithm specifically adapted to this particular calibration task. The method presented here performed well on both synthetic and experimental data. It is an efficient approach for the calibration of WALTer and should be of interest for the calibration of other functional-structural plant models.
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Affiliation(s)
- Emmanuelle Blanc
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Timothée Flutre
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, 91190, Gif-sur-Yvette, France
| | - Pierre Barbillon
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
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6
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Zhang P, Huang J, Ma Y, Wang X, Kang M, Song Y. Crop/Plant Modeling Supports Plant Breeding: II. Guidance of Functional Plant Phenotyping for Trait Discovery. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0091. [PMID: 37780969 PMCID: PMC10538623 DOI: 10.34133/plantphenomics.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/26/2023] [Indexed: 10/03/2023]
Abstract
Observable morphological traits are widely employed in plant phenotyping for breeding use, which are often the external phenotypes driven by a chain of functional actions in plants. Identifying and phenotyping inherently functional traits for crop improvement toward high yields or adaptation to harsh environments remains a major challenge. Prediction of whole-plant performance in functional-structural plant models (FSPMs) is driven by plant growth algorithms based on organ scale wrapped up with micro-environments. In particular, the models are flexible for scaling down or up through specific functions at the organ nexus, allowing the prediction of crop system behaviors from the genome to the field. As such, by virtue of FSPMs, model parameters that determine organogenesis, development, biomass production, allocation, and morphogenesis from a molecular to the whole plant level can be profiled systematically and made readily available for phenotyping. FSPMs can provide rich functional traits representing biological regulatory mechanisms at various scales in a dynamic system, e.g., Rubisco carboxylation rate, mesophyll conductance, specific leaf nitrogen, radiation use efficiency, and source-sink ratio apart from morphological traits. High-throughput phenotyping such traits is also discussed, which provides an unprecedented opportunity to evolve FSPMs. This will accelerate the co-evolution of FSPMs and plant phenomics, and thus improving breeding efficiency. To expand the great promise of FSPMs in crop science, FSPMs still need more effort in multiscale, mechanistic, reproductive organ, and root system modeling. In summary, this study demonstrates that FSPMs are invaluable tools in guiding functional trait phenotyping at various scales and can thus provide abundant functional targets for phenotyping toward crop improvement.
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Affiliation(s)
- Pengpeng Zhang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Jingyao Huang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing 100094, China
| | - Xiujuan Wang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Mengzhen Kang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
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7
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Triki HEM, Ribeyre F, Pinard F, Jaeger M. Coupling Plant Growth Models and Pest and Disease Models: An Interaction Structure Proposal, MIMIC. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0077. [PMID: 37545839 PMCID: PMC10403158 DOI: 10.34133/plantphenomics.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/10/2023] [Indexed: 08/08/2023]
Abstract
Coupling plant growth model with pests and diseases (P&D) models, with consideration for the long-term feedback that occurs after the interaction, is still a challenging task nowadays. While a number of studies have examined various methodologies, none of them provides a generic frame able to host existing models and their codes without updating deeply their architecture. We developed MIMIC (Mediation Interface for Model Inner Coupling), an open-access framework/tool for this objective. MIMIC allows to couple plant growth and P&D models in a variety of ways. Users can experiment with various interaction configurations, ranging from a weak coupling that is mediated by the direct exchange of inputs and outputs between models to an advanced coupling that utilizes a third-party tool if the models' data or operating cycles do not align. The users decide how the interactions operate, and the platform offers powerful tools to design key features of the interactions, mobilizing metaprogramming techniques. The proposed framework is demonstrated, implementing coffee berry borers' attacks on Coffea arabica fruits. Observations conducted in a field in Sumatra (Indonesia) assess the coupled interaction model. Finally, we highlight the user-centric implementation characteristics of MIMIC, as a practical and convenient tool that requires minimal coding knowledge to use.
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Affiliation(s)
- Houssem E. M. Triki
- CIRAD, UMR AMAP, F-34398 Montpellier, France
- AMAP, University of Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- CIRAD, UMR PHIM, F-34398 Montpellier, France
- PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Fabienne Ribeyre
- CIRAD, UMR PHIM, F-34398 Montpellier, France
- PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Fabrice Pinard
- PHIM, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, 00100 Nairobi, Kenya
| | - Marc Jaeger
- CIRAD, UMR AMAP, F-34398 Montpellier, France
- AMAP, University of Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
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8
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Shu Q, Ludwig F. A circuit analogy based girth growth model for living architecture design. J R Soc Interface 2023; 20:20230168. [PMID: 37221863 PMCID: PMC10206466 DOI: 10.1098/rsif.2023.0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023] Open
Abstract
Architecture with and from living trees (Baubotanik) is a promising approach to sustainable, climate-adapted construction. Shaping and grafting allows one to create resilient structures that combine the ecological performance and aesthetics of trees with the functions of buildings. In order to design and engineer such living structures, it is necessary to predict the growth of different tree segments, especially when trunks, branches or roots are bent and jointed into a complex inosculated network. To address this, we have developed a tool to forecast the relative girth growth of different segments in such structures based on topological skeletons, the pipe model theory and circuit analogy. We have validated our results with a set of (scaled) photographs of inosculated tree structures of the so-called 'Tree Circus', covering over 80 years of their growth. Our model has proven to predict the relative girth growth with sufficient accuracy for conceptual design purposes. So far, it does not allow the simulation of absolute growth in circumference over the course of time that is necessary to predict quantitative technical aspects, such as mechanical performance at a given time. We conclude by briefly outlining how this could be addressed in future research.
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Affiliation(s)
- Qiguan Shu
- Green Technologies in Landscape Architecture, School of Engineering and Design, Technical University of Munich, Arcisstr. 21, 80333 Munich, Germany
| | - Ferdinand Ludwig
- Green Technologies in Landscape Architecture, School of Engineering and Design, Technical University of Munich, Arcisstr. 21, 80333 Munich, Germany
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9
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Horvath DP, Clay SA, Swanton CJ, Anderson JV, Chao WS. Weed-induced crop yield loss: a new paradigm and new challenges. TRENDS IN PLANT SCIENCE 2023; 28:567-582. [PMID: 36610818 DOI: 10.1016/j.tplants.2022.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 05/22/2023]
Abstract
Direct competition for resources is generally considered the primary mechanism for weed-induced yield loss. A re-evaluation of physiological evidence suggests weeds initially impact crop growth and development through resource-independent interference. We suggest weed perception by crops induce a shift in crop development, before resources become limited, which ultimately reduce crop yield, even if weeds are subsequently removed. We present the mechanisms by which crops perceive and respond to weeds and discuss the technologies used to identify these mechanisms. These data lead to a fundamental paradigm shift in our understanding of how weeds reduce crop yield and suggest new research directions and opportunities to manipulate or engineer crops and cropping systems to reduce weed-induced yield losses.
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Affiliation(s)
- David P Horvath
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA.
| | | | | | - James V Anderson
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
| | - Wun S Chao
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
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10
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Dickman LT, Jonko AK, Linn RR, Altintas I, Atchley AL, Bär A, Collins AD, Dupuy J, Gallagher MR, Hiers JK, Hoffman CM, Hood SM, Hurteau MD, Jolly WM, Josephson A, Loudermilk EL, Ma W, Michaletz ST, Nolan RH, O'Brien JJ, Parsons RA, Partelli‐Feltrin R, Pimont F, Resco de Dios V, Restaino J, Robbins ZJ, Sartor KA, Schultz‐Fellenz E, Serbin SP, Sevanto S, Shuman JK, Sieg CH, Skowronski NS, Weise DR, Wright M, Xu C, Yebra M, Younes N. Integrating plant physiology into simulation of fire behavior and effects. THE NEW PHYTOLOGIST 2023; 238:952-970. [PMID: 36694296 PMCID: PMC10952334 DOI: 10.1111/nph.18770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Wildfires are a global crisis, but current fire models fail to capture vegetation response to changing climate. With drought and elevated temperature increasing the importance of vegetation dynamics to fire behavior, and the advent of next generation models capable of capturing increasingly complex physical processes, we provide a renewed focus on representation of woody vegetation in fire models. Currently, the most advanced representations of fire behavior and biophysical fire effects are found in distinct classes of fine-scale models and do not capture variation in live fuel (i.e. living plant) properties. We demonstrate that plant water and carbon dynamics, which influence combustion and heat transfer into the plant and often dictate plant survival, provide the mechanistic linkage between fire behavior and effects. Our conceptual framework linking remotely sensed estimates of plant water and carbon to fine-scale models of fire behavior and effects could be a critical first step toward improving the fidelity of the coarse scale models that are now relied upon for global fire forecasting. This process-based approach will be essential to capturing the influence of physiological responses to drought and warming on live fuel conditions, strengthening the science needed to guide fire managers in an uncertain future.
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Affiliation(s)
- L. Turin Dickman
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Alexandra K. Jonko
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Rodman R. Linn
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Ilkay Altintas
- San Diego Supercomputer Center and Halicioglu Data Science InstituteUniversity of California San DiegoLa JollaCA92093USA
| | - Adam L. Atchley
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Andreas Bär
- Department of BotanyUniversity of Innsbruck6020InnsbruckAustria
| | - Adam D. Collins
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Jean‐Luc Dupuy
- Ecologie des Forêts Méditerranéennes (URFM)INRAe84914AvignonFrance
| | | | | | - Chad M. Hoffman
- Department of Forest and Rangeland StewardshipColorado State UniversityFort CollinsCO80523USA
| | - Sharon M. Hood
- Rocky Mountain Research StationUSDA Forest ServiceMissoulaMT59801USA
| | | | - W. Matt Jolly
- Rocky Mountain Research StationUSDA Forest ServiceMissoulaMT59801USA
| | - Alexander Josephson
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | | | - Wu Ma
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Sean T. Michaletz
- Department of Botany and Biodiversity Research CentreThe University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Rachael H. Nolan
- Hawkesbury Institute for the EnvironmentWestern Sydney UniversityPenrithNSW2753Australia
- NSW Bushfire Risk Management Research HubWollongongNSW2522Australia
| | | | | | - Raquel Partelli‐Feltrin
- Department of Botany and Biodiversity Research CentreThe University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - François Pimont
- Ecologie des Forêts Méditerranéennes (URFM)INRAe84914AvignonFrance
| | - Víctor Resco de Dios
- School of Life Sciences and EngineeringSouthwest University of Science and TechnologyMianyang621010China
- Department of Crop and Forest Sciences and JRU CTFC‐AGROTECNIOUniversitat de LleidaLleida25198Spain
| | - Joseph Restaino
- Fire and Resource Assessment ProgramCalifornia Department of Forestry and Fire ProtectionSouth Lake TahoeCA96155USA
| | - Zachary J. Robbins
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Karla A. Sartor
- Environmental Protection and Compliance DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Emily Schultz‐Fellenz
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Shawn P. Serbin
- Environmental and Climate Sciences DepartmentBrookhaven National LaboratoryUptonNY11973USA
| | - Sanna Sevanto
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Jacquelyn K. Shuman
- Climate and Global Dynamics Laboratory, Terrestrial Sciences SectionNational Center for Atmospheric ResearchBoulderCO80305USA
| | - Carolyn H. Sieg
- Rocky Mountain Research StationUSDA Forest ServiceFlagstaffAZ86001USA
| | | | - David R. Weise
- Pacific Southwest Research StationUSDA Forest ServiceRiversideCA92507USA
| | - Molly Wright
- Cibola National ForestUSDA Forest ServiceAlbuquerqueNM87113USA
| | - Chonggang Xu
- Earth & Environmental Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
| | - Marta Yebra
- Fenner School of Environment and SocietyAustralian National UniversityCanberraACT2601Australia
- School of EngineeringAustralian National UniversityCanberraACT2601Australia
| | - Nicolas Younes
- Fenner School of Environment and SocietyAustralian National UniversityCanberraACT2601Australia
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11
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van der Meer M, Lee H, de Visser PHB, Heuvelink E, Marcelis LFM. Consequences of interplant trait variation for canopy light absorption and photosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1012718. [PMID: 36743508 PMCID: PMC9895853 DOI: 10.3389/fpls.2023.1012718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Plant-to-plant variation (interplant variation) may play an important role in determining individual plant and whole canopy performance, where interplant variation in architecture and photosynthesis traits has direct effects on light absorption and photosynthesis. We aimed to quantify the importance of observed interplant variation on both whole-plant and canopy light absorption and photosynthesis. Plant architecture was measured in two experiments with fruiting tomato crops (Solanum lycopersicum) grown in glasshouses in the Netherlands, in week 16 (Exp. 1) or week 19 (Exp. 2) after transplanting. Experiment 1 included four cultivars grown under three supplementary lighting treatments, and Experiment 2 included two different row orientations. Measured interplant variations of the architectural traits, namely, internode length, leaf area, petiole angle, and leaflet angle, as well as literature data on the interplant variation of the photosynthesis traits alpha, J max28, and V cmax28, were incorporated in a static functional-structural plant model (FSPM). The FSPM was used to analyze light absorption and net photosynthesis of whole plants in response to interplant variation in architectural and photosynthesis traits. Depending on the trait, introducing interplant variation in architecture and photosynthesis traits in a functional-structural plant model did not affect or negatively affected canopy light absorption and net photosynthesis compared with the reference model without interplant variation. Introducing interplant variation of architectural and photosynthesis traits in FSPM results in a more realistic simulation of variation of plants within a canopy. Furthermore, it can improve the accuracy of simulation of canopy light interception and photosynthesis although these effects at the canopy level are relatively small (<4% for light absorption and<7% for net photosynthesis).
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Affiliation(s)
- Maarten van der Meer
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
| | - Hyeran Lee
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
| | | | - Ep Heuvelink
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
| | - Leo F. M. Marcelis
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
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12
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Ciurans C, Guerrero JM, Martínez-Mongue I, Dussap CG, Marin de Mas I, Gòdia F. Enhancing control systems of higher plant culture chambers via multilevel structural mechanistic modelling. FRONTIERS IN PLANT SCIENCE 2022; 13:970410. [PMID: 36340344 PMCID: PMC9632494 DOI: 10.3389/fpls.2022.970410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Modelling higher plant growth is of strategic interest for modern agriculture as well as for the development of bioregenerative life support systems for space applications, where crop growth is expected to play an essential role. The capability of constraint-based metabolic models to cope the diel dynamics of plants growth is integrated into a multilevel modelling approach including mass and energy transfer and enzyme kinetics. Lactuca sativa is used as an exemplary crop to validate, with experimental data, the approach presented as well as to design a novel model-based predictive control strategy embedding metabolic information. The proposed modelling strategy predicts with high accuracy the dynamics of gas exchange and the distribution of fluxes in the metabolic network whereas the control architecture presented can be useful to manage higher plants chambers and open new ways of merging metabolome and control algorithms.
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Affiliation(s)
- Carles Ciurans
- Micro-Ecological Life Support System Alternative (MELiSSA) Pilot Plant-Claude Chipaux Laboratory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep M. Guerrero
- Centre for Research on Microgrids (CROM), Aalborg University, Aalborg, Denmark
| | | | - Claude G. Dussap
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Igor Marin de Mas
- AAU Energy, Novo Nordisk Foundation Center for Sustainability, Lyngby, Denmark
| | - Francesc Gòdia
- Micro-Ecological Life Support System Alternative (MELiSSA) Pilot Plant-Claude Chipaux Laboratory, Universitat Autònoma de Barcelona, Barcelona, Spain
- Centre for Space Studies and Research - Universitat Autònoma de Barcelona (CERES-UAB), Institut d’Estudis Espacials de Catalunya, Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Kattenborn T, Richter R, Guimarães‐Steinicke C, Feilhauer H, Wirth C. AngleCam
: Predicting the temporal variation of leaf angle distributions from image series with deep learning. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Teja Kattenborn
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Ronny Richter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
- Systematic Botany and Functional Biodiversity Institute of Biology Leipzig University Leipzig Germany
| | - Claudia Guimarães‐Steinicke
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Hannes Feilhauer
- Remote Sensing Centre for Earth System Research (RSC4Earth) Leipzig University Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Germany
- Systematic Botany and Functional Biodiversity Institute of Biology Leipzig University Leipzig Germany
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14
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Lin Y, Hyyppä J. Towards 3D basic theories of plant forms. Commun Biol 2022; 5:703. [PMID: 35835949 PMCID: PMC9283379 DOI: 10.1038/s42003-022-03652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 06/29/2022] [Indexed: 11/25/2022] Open
Abstract
Allometric, metabolic, and biomechanical theories are the critical foundations for scientifically deciphering plant forms. Their concrete laws, however, are found to deviate for plenty of plant specimens. This phenomenon has not been extensively studied, due to technical restrictions. This bottleneck now can be overcome by the state-of-the-art three-dimensional (3D) mapping technologies, such as fine-scale terrestrial laser scanning. On these grounds, we proposed to reexamine the basic theories regarding plant forms, and then, we case validated the feasibility of upgrading them into 3D modes. As an in-time enlightening of 3D revolutionizing the related basic subject, our theoretical prospect further sorted out the potential challenges as the cutting points for advancing its future exploration, which may enable 3D reconstruction of the basic theories of plant forms and even boost life science. In this Perspective, the authors discuss how state-of-the-art three-dimensional mapping technologies such as fine-scale terrestrial laser scanning can help us understand the theories of plant forms.
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Affiliation(s)
- Yi Lin
- School of Earth and Space Sciences, Peking University, Beijing, 100871, China.
| | - Juha Hyyppä
- Finnish Geospatial Research Institute, FI-02430, Masala, Finland
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15
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Ajmera I, Henry A, Radanielson AM, Klein SP, Ianevski A, Bennett MJ, Band LR, Lynch JP. Integrated root phenotypes for improved rice performance under low nitrogen availability. PLANT, CELL & ENVIRONMENT 2022; 45:805-822. [PMID: 35141925 PMCID: PMC9303783 DOI: 10.1111/pce.14284] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 05/06/2023]
Abstract
Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional-structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L-type and S-type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct-seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct-seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.
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Affiliation(s)
- Ishan Ajmera
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Amelia Henry
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
| | - Ando M. Radanielson
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
- Centre for Sustainable Agricultural Systems, Institute for Life Sciences and the Environment, Toowoomba CampusUniversity of Southern QueenslandToowoombaQueenslandAustralia
| | - Stephanie P. Klein
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Malcolm J. Bennett
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Leah R. Band
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Centre for Mathematical Medicine and Biology, School of Mathematical SciencesUniversity of NottinghamNottinghamUK
| | - Jonathan P. Lynch
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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16
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Zhang Y, Henke M, Li Y, Xu D, Liu A, Liu X, Li T. Analyzing the Impact of Greenhouse Planting Strategy and Plant Architecture on Tomato Plant Physiology and Estimated Dry Matter. FRONTIERS IN PLANT SCIENCE 2022; 13:828252. [PMID: 35242156 PMCID: PMC8885523 DOI: 10.3389/fpls.2022.828252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/13/2022] [Indexed: 05/17/2023]
Abstract
Determine the level of significance of planting strategy and plant architecture and how they affect plant physiology and dry matter accumulation within greenhouses is essential to actual greenhouse plant management and breeding. We thus analyzed four planting strategies (plant spacing, furrow distance, row orientation, planting pattern) and eight different plant architectural traits (internode length, leaf azimuth angle, leaf elevation angle, leaf length, leaflet curve, leaflet elevation, leaflet number/area ratio, leaflet length/width ratio) with the same plant leaf area using a formerly developed functional-structural model for a Chinese Liaoshen-solar greenhouse and tomato plant, which used to simulate the plant physiology of light interception, temperature, stomatal conductance, photosynthesis, and dry matter. Our study led to the conclusion that the planting strategies have a more significant impact overall on plant radiation, temperature, photosynthesis, and dry matter compared to plant architecture changes. According to our findings, increasing the plant spacing will have the most significant impact to increase light interception. E-W orientation has better total light interception but yet weaker light uniformity. Changes in planting patterns have limited influence on the overall canopy physiology. Increasing the plant leaflet area by leaflet N/A ratio from what we could observe for a rose the total dry matter by 6.6%, which is significantly better than all the other plant architecture traits. An ideal tomato plant architecture which combined all the above optimal architectural traits was also designed to provide guidance on phenotypic traits selection of breeding process. The combined analysis approach described herein established the causal relationship between investigated traits, which could directly apply to provide management and breeding insights on other plant species with different solar greenhouse structures.
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Affiliation(s)
- Yue Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
| | - Michael Henke
- Plant Sciences Core Facility, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Yiming Li
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
- College of Engineering, Shenyang Agricultural University, Shenyang, China
| | - Demin Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
| | - Anhua Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
| | - Xingan Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China
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17
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Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
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Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
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18
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Soualiou S, Wang Z, Sun W, de Reffye P, Collins B, Louarn G, Song Y. Functional-Structural Plant Models Mission in Advancing Crop Science: Opportunities and Prospects. FRONTIERS IN PLANT SCIENCE 2021; 12:747142. [PMID: 35003151 PMCID: PMC8733959 DOI: 10.3389/fpls.2021.747142] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/22/2021] [Indexed: 06/02/2023]
Abstract
Functional-structural plant models (FSPMs) have been evolving for over 2 decades and their future development, to some extent, depends on the value of potential applications in crop science. To date, stabilizing crop production by identifying valuable traits for novel cultivars adapted to adverse environments is topical in crop science. Thus, this study will examine how FSPMs are able to address new challenges in crop science for sustainable crop production. FSPMs developed to simulate organogenesis, morphogenesis, and physiological activities under various environments and are amenable to downscale to the tissue, cellular, and molecular level or upscale to the whole plant and ecological level. In a modeling framework with independent and interactive modules, advanced algorithms provide morphophysiological details at various scales. FSPMs are shown to be able to: (i) provide crop ideotypes efficiently for optimizing the resource distribution and use for greater productivity and less disease risk, (ii) guide molecular design breeding via linking molecular basis to plant phenotypes as well as enrich crop models with an additional architectural dimension to assist breeding, and (iii) interact with plant phenotyping for molecular breeding in embracing three-dimensional (3D) architectural traits. This study illustrates that FSPMs have great prospects in speeding up precision breeding for specific environments due to the capacity for guiding and integrating ideotypes, phenotyping, molecular design, and linking molecular basis to target phenotypes. Consequently, the promising great applications of FSPMs in crop science will, in turn, accelerate their evolution and vice versa.
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Affiliation(s)
| | - Zhiwei Wang
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Weiwei Sun
- School of Agronomy, Anhui Agricultural University, Hefei, China
| | - Philippe de Reffye
- The French Agricultural Research and International Cooperation Organization, Montpellier, France
| | - Brian Collins
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | | | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, China
- Centre for Crop Science, The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD, Australia
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19
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van Delden SH, SharathKumar M, Butturini M, Graamans LJA, Heuvelink E, Kacira M, Kaiser E, Klamer RS, Klerkx L, Kootstra G, Loeber A, Schouten RE, Stanghellini C, van Ieperen W, Verdonk JC, Vialet-Chabrand S, Woltering EJ, van de Zedde R, Zhang Y, Marcelis LFM. Current status and future challenges in implementing and upscaling vertical farming systems. NATURE FOOD 2021; 2:944-956. [PMID: 37118238 DOI: 10.1038/s43016-021-00402-w] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/05/2021] [Indexed: 04/30/2023]
Abstract
Vertical farming can produce food in a climate-resilient manner, potentially emitting zero pesticides and fertilizers, and with lower land and water use than conventional agriculture. Vertical farming systems (VFS) can meet daily consumer demands for nutritious fresh products, forming a part of resilient food systems-particularly in and around densely populated areas. VFS currently produce a limited range of crops including fruits, vegetables and herbs, but successful implementation of vertical farming as part of mainstream agriculture will require improvements in profitability, energy efficiency, public policy and consumer acceptance. Here we discuss VFS as multi-layer indoor crop cultivation systems, exploring state-of-the-art vertical farming and future challenges in the fields of plant growth, product quality, automation, robotics, system control and environmental sustainability and how research and development, socio-economic and policy-related institutions must work together to ensure successful upscaling of VFS to future food systems.
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Affiliation(s)
- S H van Delden
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands.
| | - M SharathKumar
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - M Butturini
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - L J A Graamans
- Greenhouse Horticulture and Flower Bulbs, Wageningen University & Research, Wageningen, the Netherlands
| | - E Heuvelink
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - M Kacira
- Biosystems Engineering, University of Arizona, Tucson, AZ, USA
| | - E Kaiser
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - R S Klamer
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - L Klerkx
- Knowledge, Technology and Innovation Group, Wageningen University, Wageningen, the Netherlands
| | - G Kootstra
- Farm Technology, Wageningen University, Wageningen, the Netherlands
| | - A Loeber
- Faculty of Science, Athena Institute, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - R E Schouten
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - C Stanghellini
- Greenhouse Horticulture and Flower Bulbs, Wageningen University & Research, Wageningen, the Netherlands
| | - W van Ieperen
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - J C Verdonk
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - S Vialet-Chabrand
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
| | - E J Woltering
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands
- Wageningen Food & Biobased Research, Wageningen, the Netherlands
| | - R van de Zedde
- Wageningen University & Research, Wageningen, the Netherlands
| | - Y Zhang
- Agricultural and Biological Engineering, University of Florida, Gainesville, FL, USA
| | - L F M Marcelis
- Horticulture and Product Physiology, Wageningen University, Wageningen, the Netherlands.
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20
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O’Sullivan H, Raumonen P, Kaitaniemi P, Perttunen J, Sievänen R. Integrating terrestrial laser scanning with functional-structural plant models to investigate ecological and evolutionary processes of forest communities. ANNALS OF BOTANY 2021; 128:663-684. [PMID: 34610091 PMCID: PMC8557364 DOI: 10.1093/aob/mcab120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Woody plants (trees and shrubs) play an important role in terrestrial ecosystems, but their size and longevity make them difficult subjects for traditional experiments. In the last 20 years functional-structural plant models (FSPMs) have evolved: they consider the interplay between plant modular structure, the immediate environment and internal functioning. However, computational constraints and data deficiency have long been limiting factors in a broader application of FSPMs, particularly at the scale of forest communities. Recently, terrestrial laser scanning (TLS), has emerged as an invaluable tool for capturing the 3-D structure of forest communities, thus opening up exciting opportunities to explore and predict forest dynamics with FSPMs. SCOPE The potential synergies between TLS-derived data and FSPMs have yet to be fully explored. Here, we summarize recent developments in FSPM and TLS research, with a specific focus on woody plants. We then evaluate the emerging opportunities for applying FSPMs in an ecological and evolutionary context, in light of TLS-derived data, with particular consideration of the challenges posed by scaling up from individual trees to whole forests. Finally, we propose guidelines for incorporating TLS data into the FSPM workflow to encourage overlap of practice amongst researchers. CONCLUSIONS We conclude that TLS is a feasible tool to help shift FSPMs from an individual-level modelling technique to a community-level one. The ability to scan multiple trees, of multiple species, in a short amount of time, is paramount to gathering the detailed structural information required for parameterizing FSPMs for forest communities. Conventional techniques, such as repeated manual forest surveys, have their limitations in explaining the driving mechanisms behind observed patterns in 3-D forest structure and dynamics. Therefore, other techniques are valuable to explore how forests might respond to environmental change. A robust synthesis between TLS and FSPMs provides the opportunity to virtually explore the spatial and temporal dynamics of forest communities.
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Affiliation(s)
- Hannah O’Sullivan
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, Berkshire, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Pasi Raumonen
- Mathematics, Tampere University, Korkeakoulunkatu 7, FI-33720 Tampere, Finland
| | - Pekka Kaitaniemi
- Hyytiälä Forestry Field Station, Faculty of Agriculture and Forestry, University of Helsinki, Hyytiäläntie 124, FI-35500 Korkeakoski, Finland
| | - Jari Perttunen
- Natural Resources Institute Finland, Latokartanontie 9, 00790 Helsinki, Finland
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21
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Bahr C, Schmidt D, Kahlen K. Missing Links in Predicting Berry Sunburn in Future Vineyards. FRONTIERS IN PLANT SCIENCE 2021; 12:715906. [PMID: 34712249 PMCID: PMC8545822 DOI: 10.3389/fpls.2021.715906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Sunburn in grapevine berries is known as a recurring disorder causing severe yield losses and a decline in berry quality. The transition from healthy to sunburnt along a temporal trajectory is not fully understood. It is driven by light-boosted local heat impact and modulated by, e.g., past environments of the berry and its developmental state. Events of berry sunburn are often associated with heatwaves, indicating a link to climate change. In addition, the sensitivity of grapevine architecture to changing environmental condition indicates an urgent need to investigate and adapt mitigation strategies of berry sunburn in future vineyards. In this perspective, we want to identify missing links in predicting berry sunburn in vineyards and propose a modeling framework that may help us to investigate berry sunburn in future vineyards. For this, we propose to address open issues in both developing a model of berry sunburn and considering dynamic canopy growth, and canopy interaction with the environment and plant management such as shoot positioning or leaf removal. Because local environmental conditions drive sunburn, we aim at showing that identifying sunburn-reducing strategies in a vineyard under future environmental conditions can be supported by a modeling approach that integrates effects of management practices over time and takes grapevine architecture explicitly into account. We argue that functional-structural plant models may address such complex tasks. Once open issues are solved, they might be a promising tool to advance our knowledge on reducing risks of berry sunburn in silico.
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Wen W, Wang Y, Wu S, Liu K, Gu S, Guo X. 3D phytomer-based geometric modelling method for plants-the case of maize. AOB PLANTS 2021; 13:plab055. [PMID: 34603653 PMCID: PMC8482417 DOI: 10.1093/aobpla/plab055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Geometric plant modelling is crucial in in silico plants. Existing geometric modelling methods have focused on the topological structure and basic organ profiles, simplifying the morphological features. However, the models cannot effectively differentiate cultivars, limiting FSPM application in crop breeding and management. This study proposes a 3D phytomer-based geometric modelling method with maize (Zea Mays) as the representative plant. Specifically, conversion methods between skeleton and mesh models of 3D phytomer are specified. This study describes the geometric modelling of maize shoots and populations by assembling 3D phytomers. Results show that the method can quickly and efficiently construct 3D models of maize plants and populations, with the ability to show morphological, structural and functional differences among four representative cultivars. The method takes into account both the geometric modelling efficiency and 3D detail features to achieve automatic operation of geometric modelling through the standardized description of 3D phytomers. Therefore, this study provides a theoretical and technical basis for the research and application of in silico plants.
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Affiliation(s)
- Weiliang Wen
- Beijing Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Yongjian Wang
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Sheng Wu
- Beijing Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Kai Liu
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Shenghao Gu
- Beijing Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Xinyu Guo
- Beijing Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, National Engineering Research Center for Information Technology in Agriculture, Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
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23
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Blanc E, Barbillon P, Fournier C, Lecarpentier C, Pradal C, Enjalbert J. Functional-Structural Plant Modeling Highlights How Diversity in Leaf Dimensions and Tillering Capability Could Promote the Efficiency of Wheat Cultivar Mixtures. FRONTIERS IN PLANT SCIENCE 2021; 12:734056. [PMID: 34659301 PMCID: PMC8511389 DOI: 10.3389/fpls.2021.734056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/30/2021] [Indexed: 06/02/2023]
Abstract
Increasing the cultivated diversity has been identified as a major leverage for the agroecological transition as it can help improve the resilience of low input cropping systems. For wheat, which is the most cultivated crop worldwide in terms of harvested area, the use of cultivar mixtures is spreading in several countries, but studies have seldom focused on establishing mixing rules based on plant architecture. Yet, the aerial architecture of plants and the overall canopy structure are critical for field performance as they greatly influence light interception, plant interactions and yield. The very high number of trait combinations in wheat mixtures makes it difficult to conduct experimentations on this issue, which is why a modeling approach appears to be an appropriate solution. In this study, we used WALTer, a functional structural plant model (FSPM), to simulate wheat cultivar mixtures and try to better understand how differences between cultivars in key traits of the aerial architecture influence mixture performance. We simulated balanced binary mixtures of cultivars differing for different critical plant traits: final height, leaf dimensions, leaf insertion angle and tillering capability. Our study highlights the impact of the leaf dimensions and the tillering capability on the performance of the simulated mixtures, which suggests that traits impacting the plants' leaf area index (LAI) have more influence on the performance of the stand than traits impacting the arrangement of the leaves. Our results show that the performance of mixtures is very variable depending on the values of the explored architectural traits. In particular, the best performances were achieved by mixing cultivars with different leaf dimensions and different tillering capability, which is in agreement with numerous studies linking the diversity of functional traits in plant communities to their productivity. However, some of the worst performances were also achieved by mixing varieties differing in their aerial architecture, which suggests that diversity is not a sufficient criterion to design efficient mixtures. Overall, these results highlight the importance of simulation-based explorations for establishing assembly rules to design efficient mixtures.
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Affiliation(s)
- Emmanuelle Blanc
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
| | - Pierre Barbillon
- Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, 75005, Paris, France
| | | | | | - Christophe Pradal
- CIRAD, UMR AGAP Institut, Montpellier, France
- INRIA and LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE—Le Moulon, Gif-sur-Yvette, France
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Miao T, Wen W, Li Y, Wu S, Zhu C, Guo X. Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots. Gigascience 2021; 10:giab031. [PMID: 33963385 PMCID: PMC8105162 DOI: 10.1093/gigascience/giab031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 03/10/2021] [Accepted: 04/12/2021] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The 3D point cloud is the most direct and effective data form for studying plant structure and morphology. In point cloud studies, the point cloud segmentation of individual plants to organs directly determines the accuracy of organ-level phenotype estimation and the reliability of the 3D plant reconstruction. However, highly accurate, automatic, and robust point cloud segmentation approaches for plants are unavailable. Thus, the high-throughput segmentation of many shoots is challenging. Although deep learning can feasibly solve this issue, software tools for 3D point cloud annotation to construct the training dataset are lacking. RESULTS We propose a top-to-down point cloud segmentation algorithm using optimal transportation distance for maize shoots. We apply our point cloud annotation toolkit for maize shoots, Label3DMaize, to achieve semi-automatic point cloud segmentation and annotation of maize shoots at different growth stages, through a series of operations, including stem segmentation, coarse segmentation, fine segmentation, and sample-based segmentation. The toolkit takes ∼4-10 minutes to segment a maize shoot and consumes 10-20% of the total time if only coarse segmentation is required. Fine segmentation is more detailed than coarse segmentation, especially at the organ connection regions. The accuracy of coarse segmentation can reach 97.2% that of fine segmentation. CONCLUSION Label3DMaize integrates point cloud segmentation algorithms and manual interactive operations, realizing semi-automatic point cloud segmentation of maize shoots at different growth stages. The toolkit provides a practical data annotation tool for further online segmentation research based on deep learning and is expected to promote automatic point cloud processing of various plants.
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Affiliation(s)
- Teng Miao
- College of Information and Electrical Engineering, Shenyang Agricultural University, Dongling Road, Shenhe District, Liaoning Province, Shenyang 110161, China
| | - Weiliang Wen
- Beijing Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- National Engineering Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Yinglun Li
- National Engineering Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Sheng Wu
- Beijing Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- National Engineering Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
| | - Chao Zhu
- College of Information and Electrical Engineering, Shenyang Agricultural University, Dongling Road, Shenhe District, Liaoning Province, Shenyang 110161, China
| | - Xinyu Guo
- Beijing Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- National Engineering Research Center for Information Technology in Agriculture, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
- Beijing Key Lab of Digital Plant, 11#Shuguang Huayuan Middle Road, Haidian District, Beijing 100097, China
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25
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Abstract
Plants and animals are both important for studies in evolutionary developmental biology (EvoDevo). Plant morphology as a valuable discipline of EvoDevo is set for a paradigm shift. Process thinking and the continuum approach in plant morphology allow us to perceive and interpret growing plants as combinations of developmental processes rather than as assemblages of structural units (“organs”) such as roots, stems, leaves, and flowers. These dynamic philosophical perspectives were already favored by botanists and philosophers such as Agnes Arber (1879–1960) and Rolf Sattler (*1936). The acceptance of growing plants as dynamic continua inspires EvoDevo scientists such as developmental geneticists and evolutionary biologists to move towards a more holistic understanding of plants in time and space. This review will appeal to many young scientists in the plant development research fields. It covers a wide range of relevant publications from the past to present.
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