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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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2
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Hostetler AN, Morais de Sousa Tinoco S, Sparks EE. Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:553-562. [PMID: 37798135 DOI: 10.1093/jxb/erad390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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3
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Lescano MR, Macagno J, Berli CLA. Model-Based Analysis of Lactuca sativa Root Growth under the Action of Herbicides in Milli-Channel Arrays with In Situ Imaging. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13255-13262. [PMID: 37651710 DOI: 10.1021/acs.jafc.3c04105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Extracting practical information from the large amounts of data gathered during the live imaging analysis of plant organs is a challenging issue. The present work investigates the use of the logistic growth model to analyze experimental data from root elongation assays performed in milli-fluidic devices with in situ imaging. Lactuca sativa was used as a bioindicator and was subjected to wide concentration ranges of four different herbicides: 2,4-D, atrazine, glyphosate, and paraquat. The model parameters were directly connected to standard indicators of toxicity and plant development, such as the LD50 and the absolute growth rate, respectively. In addition, it was found that realistic predictions of the maximum root length can be achieved about 60 h before the bioassay end point, which could significantly shorten the turnaround time. The combination of milli-fluidic devices, real-time imaging, and model-based data analysis becomes a powerful tool for environmental studies and ecotoxicity testing.
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Affiliation(s)
- Maia R Lescano
- INTEC (Universidad Nacional del Litoral-CONICET), Predio CCT CONICET Santa Fe, RN 168, Santa Fe 3000, Argentina
| | - Joana Macagno
- INTEC (Universidad Nacional del Litoral-CONICET), Predio CCT CONICET Santa Fe, RN 168, Santa Fe 3000, Argentina
| | - Claudio L A Berli
- INTEC (Universidad Nacional del Litoral-CONICET), Predio CCT CONICET Santa Fe, RN 168, Santa Fe 3000, Argentina
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4
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Kaiser CF, Perilli A, Grossmann G, Meroz Y. Studying root-environment interactions in structured microdevices. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad122. [PMID: 37042515 PMCID: PMC10353529 DOI: 10.1093/jxb/erad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 06/19/2023]
Abstract
In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.
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Affiliation(s)
- Christian-Frederic Kaiser
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alessia Perilli
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Yasmine Meroz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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5
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Ma L, Chai C, Wu W, Qi P, Liu X, Hao J. Hydrogels as the plant culture substrates: A review. Carbohydr Polym 2023; 305:120544. [PMID: 36737215 DOI: 10.1016/j.carbpol.2023.120544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/20/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023]
Abstract
A class of hydrophilic polymers known as "hydrogels" have extensive water content and three-dimensional crosslinked networks. Since the old period, they have been utilized as plant culture substrates to get around the drawbacks of hydroponics and soil. Numerous hydrogels, particularly polysaccharides with exceptional stability, high clarity, and low cost can be employed as plant substrates. Although numerous novel and functionalized hydrogels might assist in overcoming the drawbacks of conventional media and giving them more functions, the existing hydrogel-based plant growth substrates rarely benefit from the developments of gels in the previous few decades. Prospects include the development of new conduction techniques, the creation of potential new hydrogels, and the functionalization of the hydrogel as plant culture substrates.
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Affiliation(s)
- Lin Ma
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China
| | - Chunxiao Chai
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China
| | - Wenna Wu
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China
| | - Ping Qi
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China
| | - Xingcen Liu
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry (Shandong University), Ministry of Education, Jinan 250100, PR China.
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6
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Cui Y, Zhang X, Li X, Lin J. Multiscale microscopy to decipher plant cell structure and dynamics. THE NEW PHYTOLOGIST 2023; 237:1980-1997. [PMID: 36477856 DOI: 10.1111/nph.18641] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
New imaging methodologies with high contrast and molecular specificity allow researchers to analyze dynamic processes in plant cells at multiple scales, from single protein and RNA molecules to organelles and cells, to whole organs and tissues. These techniques produce informative images and quantitative data on molecular dynamics to address questions that cannot be answered by conventional biochemical assays. Here, we review selected microscopy techniques, focusing on their basic principles and applications in plant science, discussing the pros and cons of each technique, and introducing methods for quantitative analysis. This review thus provides guidance for plant scientists in selecting the most appropriate techniques to decipher structures and dynamic processes at different levels, from protein dynamics to morphogenesis.
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Affiliation(s)
- Yaning Cui
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xi Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, 100083, China
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 100083, China
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7
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Hsiao AS, Huang JY. Bioimaging tools move plant physiology studies forward. FRONTIERS IN PLANT SCIENCE 2022; 13:976627. [PMID: 36204075 PMCID: PMC9530904 DOI: 10.3389/fpls.2022.976627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Affiliation(s)
- An-Shan Hsiao
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ji-Ying Huang
- Cell Biology Core Lab, Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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8
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Allan C, Morris RJ, Meisrimler CN. Encoding, transmission, decoding, and specificity of calcium signals in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3372-3385. [PMID: 35298633 PMCID: PMC9162177 DOI: 10.1093/jxb/erac105] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Calcium acts as a signal and transmits information in all eukaryotes. Encoding machinery consisting of calcium channels, stores, buffers, and pumps can generate a variety of calcium transients in response to external stimuli, thus shaping the calcium signature. Mechanisms for the transmission of calcium signals have been described, and a large repertoire of calcium binding proteins exist that can decode calcium signatures into specific responses. Whilst straightforward as a concept, mysteries remain as to exactly how such information processing is biochemically implemented. Novel developments in imaging technology and genetically encoded sensors (such as calcium indicators), in particular for multi-signal detection, are delivering exciting new insights into intra- and intercellular calcium signaling. Here, we review recent advances in characterizing the encoding, transmission, and decoding mechanisms, with a focus on long-distance calcium signaling. We present technological advances and computational frameworks for studying the specificity of calcium signaling, highlight current gaps in our understanding and propose techniques and approaches for unravelling the underlying mechanisms.
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Affiliation(s)
- Claudia Allan
- University of Canterbury, School of Biological Science, Christchurch, New Zealand
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich, UK
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9
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Hostetler AN, Erndwein L, Reneau JW, Stager A, Tanner HG, Cook D, Sparks EE. Multiple brace root phenotypes promote anchorage and limit root lodging in maize. PLANT, CELL & ENVIRONMENT 2022; 45:1573-1583. [PMID: 35141927 DOI: 10.1111/pce.14289] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/20/2021] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Plant mechanical failure (lodging) causes global yield losses of 7%-66% in cereal crops. We have previously shown that the above-ground nodal roots (brace roots) in maize are critical for anchorage. However, it is unknown how brace root phenotypes vary across genotypes and the functional consequence of this variation. This study quantifies the contribution of brace roots to anchorage, brace root traits, plant height, and root lodging susceptibility in 52 maize inbred lines. We show that the contribution of brace roots to anchorage and root lodging susceptibility varies among genotypes and this contribution can be explained by plant architectural variation. Additionally, supervised machine learning models were developed and show that multiple plant architectural phenotypes can predict the contribution of brace roots to anchorage and root lodging susceptibility. Together these data define the plant architectures that are important in lodging resistance and show that the contribution of brace roots to anchorage is a good proxy for root lodging susceptibility.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Lindsay Erndwein
- Department of Plant and Soil Sciences, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Jonathan W Reneau
- Department of Plant and Soil Sciences, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Adam Stager
- Department of Plant and Soil Sciences, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Herbert G Tanner
- Department of Mechanical Engineering, University of Delaware, Newark, Delaware, USA
| | - Douglas Cook
- Department of Mechanical Engineering, Brigham Young University, Provo, Utah, USA
| | - Erin E Sparks
- Department of Plant and Soil Sciences, The Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
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10
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Colin L, Martin-Arevalillo R, Bovio S, Bauer A, Vernoux T, Caillaud MC, Landrein B, Jaillais Y. Imaging the living plant cell: From probes to quantification. THE PLANT CELL 2022; 34:247-272. [PMID: 34586412 PMCID: PMC8774089 DOI: 10.1093/plcell/koab237] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 05/20/2023]
Abstract
At the center of cell biology is our ability to image the cell and its various components, either in isolation or within an organism. Given its importance, biological imaging has emerged as a field of its own, which is inherently highly interdisciplinary. Indeed, biologists rely on physicists and engineers to build new microscopes and imaging techniques, chemists to develop better imaging probes, and mathematicians and computer scientists for image analysis and quantification. Live imaging collectively involves all the techniques aimed at imaging live samples. It is a rapidly evolving field, with countless new techniques, probes, and dyes being continuously developed. Some of these new methods or reagents are readily amenable to image plant samples, while others are not and require specific modifications for the plant field. Here, we review some recent advances in live imaging of plant cells. In particular, we discuss the solutions that plant biologists use to live image membrane-bound organelles, cytoskeleton components, hormones, and the mechanical properties of cells or tissues. We not only consider the imaging techniques per se, but also how the construction of new fluorescent probes and analysis pipelines are driving the field of plant cell biology.
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Affiliation(s)
- Leia Colin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Simone Bovio
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
- LYMIC-PLATIM imaging and microscopy core facility, Univ Lyon, SFR Biosciences, ENS de Lyon, Inserm US8, CNRS UMS3444, UCBL-50 Avenue Tony Garnier, 69007 Lyon, France
| | - Amélie Bauer
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Marie-Cecile Caillaud
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
| | - Benoit Landrein
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, CNRS, INRAE, 69342 Lyon, France
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11
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Yanagisawa N, Kozgunova E, Grossmann G, Geitmann A, Higashiyama T. Microfluidics-Based Bioassays and Imaging of Plant Cells. PLANT & CELL PHYSIOLOGY 2021; 62:1239-1250. [PMID: 34027549 PMCID: PMC8579190 DOI: 10.1093/pcp/pcab067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/13/2021] [Accepted: 05/23/2021] [Indexed: 05/03/2023]
Abstract
Many plant processes occur in the context of and in interaction with a surrounding matrix such as soil (e.g. root growth and root-microbe interactions) or surrounding tissues (e.g. pollen tube growth through the pistil), making it difficult to study them with high-resolution optical microscopy. Over the past decade, microfabrication techniques have been developed to produce experimental systems that allow researchers to examine cell behavior in microstructured environments that mimic geometrical, physical and/or chemical aspects of the natural growth matrices and that cannot be generated using traditional agar plate assays. These microfabricated environments offer considerable design flexibility as well as the transparency required for high-resolution, light-based microscopy. In addition, microfluidic platforms have been used for various types of bioassays, including cellular force assays, chemoattraction assays and electrotropism assays. Here, we review the recent use of microfluidic devices to study plant cells and organs, including plant roots, root hairs, moss protonemata and pollen tubes. The increasing adoption of microfabrication techniques by the plant science community may transform our approaches to investigating how individual plant cells sense and respond to changes in the physical and chemical environment.
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Affiliation(s)
- Naoki Yanagisawa
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Elena Kozgunova
- Department of Plant Biotechnology, Faculty of Biology, University of Freiburg, Freiburg, Schänzlestr. 1, Freiburg, Baden-Württemberg 79104, Germany
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Baden-Württemberg 69120, Germany
| | - Anja Geitmann
- Department of Plant Science, Faculty of Agricultural and Environmental Sciences, McGill University, Québec H9X 3V9, Canada
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Nagoya Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-0033, Japan
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12
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Higashiyama T, Maizel A, Simon R. Seeing is Believing: Advances in Plant Imaging Technologies. PLANT & CELL PHYSIOLOGY 2021; 62:1217-1220. [PMID: 34510209 DOI: 10.1093/pcp/pcab133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/28/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Rüdiger Simon
- Cluster of Excellence on Plant Sciences, Heinrich Heine University, Universitätsstraße 1, Düsseldorf 40225, Germany
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13
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Van den Broeck L, Spurney RJ, Fisher AP, Schwartz M, Clark NM, Nguyen TT, Madison I, Gobble M, Long T, Sozzani R. A hybrid model connecting regulatory interactions with stem cell divisions in the root. QUANTITATIVE PLANT BIOLOGY 2021; 2:e2. [PMID: 37077208 PMCID: PMC10095808 DOI: 10.1017/qpb.2021.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Stem cells give rise to the entirety of cells within an organ. Maintaining stem cell identity and coordinately regulating stem cell divisions is crucial for proper development. In plants, mobile proteins, such as WUSCHEL-RELATED HOMEOBOX 5 (WOX5) and SHORTROOT (SHR), regulate divisions in the root stem cell niche. However, how these proteins coordinately function to establish systemic behaviour is not well understood. We propose a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identify a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions. Here, we show with a multi-scale hybrid model integrating ordinary differential equations (ODEs) and agent-based modeling that quiescent center (QC) and CEI divisions have different dynamics. Specifically, by combining continuous models to describe regulatory networks and agent-based rules, we model systemic behaviour, which led us to predict cell-type-specific expression dynamics of SHR, SCARECROW, WOX5, AN3 and CYCLIND6;1, and experimentally validate CEI cell divisions. Conclusively, our results show an interdependency between CEI and QC divisions.
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Affiliation(s)
- Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Ryan J. Spurney
- Electrical and Computer Engineering Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Adam P. Fisher
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael Schwartz
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Natalie M. Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, Iowa 50010, USA
| | - Thomas T. Nguyen
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Imani Madison
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Mariah Gobble
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Terri Long
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, North Carolina, USA
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14
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Zhang X, Man Y, Zhuang X, Shen J, Zhang Y, Cui Y, Yu M, Xing J, Wang G, Lian N, Hu Z, Ma L, Shen W, Yang S, Xu H, Bian J, Jing Y, Li X, Li R, Mao T, Jiao Y, Sodmergen, Ren H, Lin J. Plant multiscale networks: charting plant connectivity by multi-level analysis and imaging techniques. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1392-1422. [PMID: 33974222 DOI: 10.1007/s11427-020-1910-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022]
Abstract
In multicellular and even single-celled organisms, individual components are interconnected at multiscale levels to produce enormously complex biological networks that help these systems maintain homeostasis for development and environmental adaptation. Systems biology studies initially adopted network analysis to explore how relationships between individual components give rise to complex biological processes. Network analysis has been applied to dissect the complex connectivity of mammalian brains across different scales in time and space in The Human Brain Project. In plant science, network analysis has similarly been applied to study the connectivity of plant components at the molecular, subcellular, cellular, organic, and organism levels. Analysis of these multiscale networks contributes to our understanding of how genotype determines phenotype. In this review, we summarized the theoretical framework of plant multiscale networks and introduced studies investigating plant networks by various experimental and computational modalities. We next discussed the currently available analytic methodologies and multi-level imaging techniques used to map multiscale networks in plants. Finally, we highlighted some of the technical challenges and key questions remaining to be addressed in this emerging field.
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Affiliation(s)
- Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaohong Zhuang
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Jinbo Shen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Yaning Cui
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Meng Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Jingjing Xing
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 457004, China
| | - Guangchao Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Na Lian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Lingyu Ma
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Weiwei Shen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Shunyao Yang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiahui Bian
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yanping Jing
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Ruili Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China.,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, Department of Plant Sciences, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing, 100101, China
| | - Sodmergen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Haiyun Ren
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Science, Beijing Normal University, Beijing, 100875, China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083, China. .,College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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15
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Strable J. Developmental genetics of maize vegetative shoot architecture. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:19. [PMID: 37309417 PMCID: PMC10236122 DOI: 10.1007/s11032-021-01208-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/25/2021] [Indexed: 06/13/2023]
Abstract
More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01208-1.
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Affiliation(s)
- Josh Strable
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853 USA
- Present Address: Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 USA
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16
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Reneau JW, Khangura RS, Stager A, Erndwein L, Weldekidan T, Cook DD, Dilkes BP, Sparks EE. Maize brace roots provide stalk anchorage. PLANT DIRECT 2020; 4:e00284. [PMID: 33204937 PMCID: PMC7649601 DOI: 10.1002/pld3.284] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/19/2020] [Accepted: 10/08/2020] [Indexed: 05/16/2023]
Abstract
Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we use a non-destructive field-based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal. Previous studies demonstrated that the number of nodes that produce brace roots is correlated with flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauer's Tusón tropical population was analyzed. Despite significant variation in flowering time and anchorage, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize and that the contribution of brace roots to anchorage was not linearly related to flowering time.
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Affiliation(s)
- Jonathan W. Reneau
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | | | - Adam Stager
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Lindsay Erndwein
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Teclemariam Weldekidan
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
| | - Douglas D. Cook
- Department of Mechanical EngineeringBrigham Young UniversityProvoUTUSA
| | - Brian P. Dilkes
- Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Erin E. Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology InstituteUniversity of DelawareNewarkDEUSA
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17
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Zhang X, Hu Z, Guo Y, Shan X, Li X, Lin J. High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants. PLANT METHODS 2020; 16:100. [PMID: 32742298 PMCID: PMC7390866 DOI: 10.1186/s13007-020-00642-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/20/2020] [Indexed: 05/30/2023]
Abstract
BACKGROUND The increasing number of novel approaches for large-scale, multi-dimensional imaging of cells has created an unprecedented opportunity to analyze plant morphogenesis. However, complex image processing, including identifying specific cells and quantitating parameters, and high running cost of some image analysis softwares remains challenging. Therefore, it is essential to develop an efficient method for identifying plant complex multicellularity in raw micrographs in plants. RESULTS Here, we developed a high-efficiency procedure to characterize, segment, and quantify plant multicellularity in various raw images using the open-source software packages ImageJ and SR-Tesseler. This procedure allows for the rapid, accurate, automatic quantification of cell patterns and organization at different scales, from large tissues down to the cellular level. We validated our method using different images captured from Arabidopsis thaliana roots and seeds and Populus tremula stems, including fluorescently labeled images, Micro-CT scans, and dyed sections. Finally, we determined the area, centroid coordinate, perimeter, and Feret's diameter of the cells and harvested the cell distribution patterns from Voronoï diagrams by setting the threshold at localization density, mean distance, or area. CONCLUSIONS This procedure can be used to determine the character and organization of multicellular plant tissues at high efficiency, including precise parameter identification and polygon-based segmentation of plant cells.
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Affiliation(s)
- Xi Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Zijian Hu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Yayu Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Xiaoyi Shan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Xiaojuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083 China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 10083 China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 10083 China
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18
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Guichard M, Bertran Garcia de Olalla E, Stanley CE, Grossmann G. Microfluidic systems for plant root imaging. Methods Cell Biol 2020; 160:381-404. [PMID: 32896330 DOI: 10.1016/bs.mcb.2020.03.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Plant roots adapt their development and metabolism to changing environmental conditions. In order to understand the response mechanisms of roots to the dynamic availability of water or nutrients, to biotic and abiotic stress conditions or to mechanical stimuli, microfluidic platforms have been developed that offer microscopic access and novel experimental means. Here, we describe the design, fabrication and use of microfluidic devices suitable for imaging growing Arabidopsis roots over several days under controlled perfusion. We present a detailed protocol for the use of our exemplar platform-the RootChip-8S-and offer a guide for troubleshooting, which is also largely applicable to related device designs. We further discuss considerations regarding the design of custom-made plant microdevices, the choice of suitable materials and technologies as well as the handling of the specimen.
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Affiliation(s)
- Marjorie Guichard
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | | | | | - Guido Grossmann
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany,; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany,.
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