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Zhang Y, Gu S, Du J, Huang G, Shi J, Lu X, Wang J, Yang W, Guo X, Zhao C. Plant microphenotype: from innovative imaging to computational analysis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:802-818. [PMID: 38217351 PMCID: PMC10955502 DOI: 10.1111/pbi.14244] [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: 03/10/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/15/2024]
Abstract
The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shenghao Gu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guanmin Huang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiawei Shi
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianju Lu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Guo
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Sukhova EM, Vodeneev VA, Sukhov VS. Mathematical Modeling of Photosynthesis and Analysis of Plant Productivity. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2021. [DOI: 10.1134/s1990747821010062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Patterns of presence-absence variants in Upland cotton. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1600-1603. [PMID: 32279283 DOI: 10.1007/s11427-019-1602-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 10/24/2022]
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Kang M, Hua J, Wang X, de Reffye P, Jaeger M, Akaffou S. Estimating Sink Parameters of Stochastic Functional-Structural Plant Models Using Organic Series-Continuous and Rhythmic Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1688. [PMID: 30555494 PMCID: PMC6284058 DOI: 10.3389/fpls.2018.01688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/31/2018] [Indexed: 05/28/2023]
Abstract
Functional-structural plant models (FSPMs) generally simulate plant development and growth at the level of individual organs (leaves, flowers, internodes, etc.). Parameters that are not directly measurable, such as the sink strength of organs, can be estimated inversely by fitting the weights of organs along an axis (organic series) with the corresponding model output. To accommodate intracanopy variability among individual plants, stochastic FSPMs have been built by introducing the randomness in plant development; this presents a challenge in comparing model output and experimental data in parameter estimation since the plant axis contains individual organs with different amounts and weights. To achieve model calibration, the interaction between plant development and growth is disentangled by first computing the occurrence probabilities of each potential site of phytomer, as defined in the developmental model (potential structure). On this basis, the mean organic series is computed analytically to fit the organ-level target data. This process is applied for plants with continuous and rhythmic development simulated with different development parameter sets. The results are verified by Monte-Carlo simulation. Calibration tests are performed both in silico and on real plants. The analytical organic series are obtained for both continuous and rhythmic cases, and they match well with the results from Monte-Carlo simulation, and vice versa. This fitting process works well for both the simulated and real data sets; thus, the proposed method can solve the source-sink functions of stochastic plant architectures through a simplified approach to plant sampling. This work presents a generic method for estimating the sink parameters of a stochastic FSPM using statistical organ-level data, and it provides a method for sampling stems. The current work breaks a bottleneck in the application of FSPMs to real plants, creating the opportunity for broad applications.
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Affiliation(s)
- Mengzhen Kang
- The State Key Laboratory of Management and Control for Complex Systems, LIAMA, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Innovation Center for Parallel Agriculture, Qingdao Academy of Intelligent Industries, Qingdao, China
| | - Jing Hua
- The State Key Laboratory of Management and Control for Complex Systems, LIAMA, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Innovation Center for Parallel Agriculture, Qingdao Academy of Intelligent Industries, Qingdao, China
| | - Xiujuan Wang
- The State Key Laboratory of Management and Control for Complex Systems, LIAMA, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Beijing Engineering Research Center of Intelligent Systems and Technology, Beijing, China
| | - Philippe de Reffye
- CIRAD, Amap Unit, Univ. Montpellier, CNRS, INRA, IRD, Montpellier, France
| | - Marc Jaeger
- CIRAD, Amap Unit, Univ. Montpellier, CNRS, INRA, IRD, Montpellier, France
| | - Sélastique Akaffou
- Department of Seeds and Seedlings Production, University Jean Lorougnon Guédé, Daloa, Ivory Coast
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Evers JB, Letort V, Renton M, Kang M. Computational botany: advancing plant science through functional–structural plant modelling. ANNALS OF BOTANY 2018; 121. [PMCID: PMC5906916 DOI: 10.1093/aob/mcy050] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
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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Affiliation(s)
- Jochem B Evers
- Centre for Crop Systems Analysis, Wageningen University, Wageningen, The Netherlands
- For correspondence. E-mail:
| | - Veronique Letort
- Mathématiques et Informatique pour la Complexité et les Systèmes, CentraleSupélec, Université Paris-Saclay, Gif-Sur-Yvette, France
| | - Michael Renton
- Schools of Biological Sciences, Agriculture and Environment, University of Western Australia, Perth, Australia
| | - Mengzhen Kang
- State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Qingdao Academy of Intelligent Industries, Qingdao, China
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