1
|
Cunha Neto IL, Hall BT, Lanba AR, Blosenski JD, Onyenedum JG. Laser ablation tomography (LATscan) as a new tool for anatomical studies of woody plants. THE NEW PHYTOLOGIST 2023; 239:429-444. [PMID: 36811411 DOI: 10.1111/nph.18831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/09/2023] [Indexed: 06/02/2023]
Abstract
Traditionally, botanists study plant anatomy by carefully sectioning samples, histological staining to highlight tissues of interests, then imaging slides under light microscopy. This approach generates significant details; however, this workflow is laborious, particularly in woody vines (lianas) with heterogeneous anatomies, and ultimately yields two-dimensional (2D) images. Laser ablation tomography (LATscan) is a high-throughput imaging system that yields hundreds of images per minute. This method has proven useful for studying the structure of delicate plant tissues; however, its utility in understanding the structure of woody tissues is underexplored. We report LATscan-derived anatomical data from several stems of lianas (c. 20 mm) of seven species and compare these results with those obtained through traditional anatomical techniques. LATscan successfully allows the description of tissue composition by differentiating cell type, size, and shape, but also permits the recognition of distinct cell wall composition (e.g. lignin, suberin, cellulose) based on differential fluorescent signals on unstained samples. LATscan generate high-quality 2D images and 3D reconstructions of woody plant samples; therefore, this new technology is useful for both qualitative and quantitative analyses. This high-throughput imaging technology has the potential to bolster phenotyping of vegetative and reproductive anatomy, wood anatomy, and other biological systems.
Collapse
Affiliation(s)
- Israel L Cunha Neto
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, NY, 14853, Ithaca, USA
| | - Benjamin T Hall
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
| | - Asheesh R Lanba
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
- Department of Engineering, University of Southern Maine, 37 College Ave., Gorham, ME, 04038, USA
| | - Joshua D Blosenski
- Laser for Innovative Solutions (L4iS), Suite 261, 200 Innovation Boulevard, State College, PA, 16803, USA
| | - Joyce G Onyenedum
- School of Integrative Plant Sciences and L. H. Bailey Hortorium, Cornell University, NY, 14853, Ithaca, USA
| |
Collapse
|
2
|
Legland D, Le TDQ, Alvarado C, Girousse C, Chateigner-Boutin AL. New Growth-Related Features of Wheat Grain Pericarp Revealed by Synchrotron-Based X-ray Micro-Tomography and 3D Reconstruction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1038. [PMID: 36903900 PMCID: PMC10005608 DOI: 10.3390/plants12051038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops as it provides 20% of calories and proteins to the human population. To overcome the increasing demand in wheat grain production, there is a need for a higher grain yield, and this can be achieved in particular through an increase in the grain weight. Moreover, grain shape is an important trait regarding the milling performance. Both the final grain weight and shape would benefit from a comprehensive knowledge of the morphological and anatomical determinism of wheat grain growth. Synchrotron-based phase-contrast X-ray microtomography (X-ray µCT) was used to study the 3D anatomy of the growing wheat grain during the first developmental stages. Coupled with 3D reconstruction, this method revealed changes in the grain shape and new cellular features. The study focused on a particular tissue, the pericarp, which has been hypothesized to be involved in the control of grain development. We showed considerable spatio-temporal diversity in cell shape and orientations, and in tissue porosity associated with stomata detection. These results highlight the growth-related features rarely studied in cereal grains, which may contribute significantly to the final grain weight and shape.
Collapse
Affiliation(s)
- David Legland
- INRAE, UR BIA, 44316 Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44316 Nantes, France
| | - Thang Duong Quoc Le
- INRAE, UR BIA, 44316 Nantes, France
- INRAE, PROBE Research Infrastructure, BIBS Facility, 44316 Nantes, France
| | | | - Christine Girousse
- INRAE, Université Clermont-Auvergne, UMR GDEC, 63000 Clermont-Ferrand, France
| | | |
Collapse
|
3
|
Legland D, Guillon F, Devaux MF. Parametric mapping of cellular morphology in plant tissue sections by gray level granulometry. PLANT METHODS 2020; 16:63. [PMID: 32391070 PMCID: PMC7201695 DOI: 10.1186/s13007-020-00603-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 04/21/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND The cellular morphology of plant organs is strongly related to other physical properties such as shape, size, growth, mechanical properties or chemical composition. Cell morphology often vary depending on the type of tissue, or on the distance to a specific tissue. A common challenge in quantitative plant histology is to quantify not only the cellular morphology, but also its variations within the image or the organ. Image texture analysis is a fundamental tool in many areas of image analysis, that was proven efficient for plant histology, but at the scale of the whole image. RESULTS This work presents a method that generates a parametric mapping of cellular morphology within images of plant tissues. It is based on gray level granulometry from mathematical morphology for extracting image texture features, and on Centroidal Voronoi Diagram for generating a partition of the image. Resulting granulometric curves can be interpreted either through multivariate data analysis or by using summary features corresponding to the local average cell size. The resulting parametric maps describe the variations of cellular morphology within the organ. CONCLUSIONS We propose a methodology for the quantification of cellular morphology and of its variations within images of tissue sections. The results should help understanding how the cellular morphology is related to genotypic and / or environmental variations, and clarify the relationships between cellular morphology and chemical composition of cell walls.
Collapse
Affiliation(s)
- David Legland
- UR1268 Biopolymères, Interactions et Assemblages, INRAE, Nantes, France
| | - Fabienne Guillon
- UR1268 Biopolymères, Interactions et Assemblages, INRAE, Nantes, France
| | | |
Collapse
|
4
|
Mironova V, Xu J. A single-cell view of tissue regeneration in plants. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:149-154. [PMID: 31655397 DOI: 10.1016/j.pbi.2019.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
With the development of advanced molecular-genetic and computational technologies it becomes possible to tackle individual cells within a regenerating tissue, to define morphogenetic and cellular changes in space and time by live imaging, to acquire transcriptome status with single-cell RNA sequencing (ScRNA-seq), and to delineate the candidate mechanisms by iterative computational and experimental approaches. Here, we review recent findings and current knowledge on tissue regeneration in plants, focusing on four evolutionarily conserved scenarios that a cell may embark on to facilitate the regeneration of a plant tissue structure lost by injury, namely cell death, division, dedifferentiation, and transdifferentiation. Understanding of these scenarios at single-cell resolution, singularly and in combination, could provide an unprecedented view of tissue regeneration in plants.
Collapse
Affiliation(s)
- Victoria Mironova
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia; Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia.
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands; Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, 117543, Singapore.
| |
Collapse
|
5
|
Le TDQ, Alvarado C, Girousse C, Legland D, Chateigner-Boutin AL. Use of X-ray micro computed tomography imaging to analyze the morphology of wheat grain through its development. PLANT METHODS 2019; 15:84. [PMID: 31384289 PMCID: PMC6668075 DOI: 10.1186/s13007-019-0468-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Wheat is one of the most important staple source in the world for human consumption, animal feed and industrial raw materials. To deal with the global and increasing population demand, enhancing crop yield by increasing the final weight of individual grain is considered as a feasible solution. Morphometric analysis of wheat grain plays an important role in tracking and understanding developmental processes by assessing potential impacts on grains properties, size and shape that are major determinants of final grain weight. X-ray micro computed tomography (μCT) is a very powerful non-invasive imaging tool that is able to acquire 3D images of an individual grain, enabling to assess the morphology of wheat grain and of its different compartments. Our objective is to quantify changes of morphology during growth stages of wheat grain from 3D μCT images. METHODS 3D μCT images of wheat grains were acquired at various development stages ranging from 60 to 310 degree days after anthesis. We developed robust methods for the identification of outer and inner tissues within the grains, and the extraction of morphometric features using 3D μCT images. We also developed a specific workflow for the quantification of the shape of the grain crease. RESULTS The different compartments of the grain could be semi-automatically segmented. Variations of volumes of the compartments adequately describe the different stages of grain developments. The evolution of voids within wheat grain reflects lysis of outer tissues and growth of inner tissues. The crease shape could be quantified for each grain and averaged for each stage of development, helping us understand the genesis of the grain shape. CONCLUSION This work shows that μCT acquisitions and image processing methodologies are powerful tools to extract morphometric parameters of developing wheat grain. The results of quantitative analysis revealed remarkable features of wheat grain growth. Further work will focus on building a computational model of wheat grain growth based on real 3D imaging data.
Collapse
Affiliation(s)
| | | | - Christine Girousse
- UMR GDEC, INRA, Université Clermont-Auvergne, 63000 Clermont-Ferrand, France
| | | | | |
Collapse
|
6
|
Raines C, Ingram J. JXB at SEB Florence 2018. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3797-3799. [PMID: 29905802 PMCID: PMC6054182 DOI: 10.1093/jxb/ery218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- Christine Raines
- Department of Biological Sciences, University of Essex, Colchester, UK
| | | |
Collapse
|
7
|
Mathers AW, Hepworth C, Baillie AL, Sloan J, Jones H, Lundgren M, Fleming AJ, Mooney SJ, Sturrock CJ. Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography. PLANT METHODS 2018; 14:99. [PMID: 30455724 PMCID: PMC6231253 DOI: 10.1186/s13007-018-0367-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/03/2018] [Indexed: 05/18/2023]
Abstract
BACKGROUND Leaf cellular architecture plays an important role in setting limits for carbon assimilation and, thus, photosynthetic performance. However, the low density, fine structure, and sensitivity to desiccation of plant tissue has presented challenges to its quantification. Classical methods of tissue fixation and embedding prior to 2D microscopy of sections is both laborious and susceptible to artefacts that can skew the values obtained. Here we report an image analysis pipeline that provides quantitative descriptors of plant leaf intercellular airspace using lab-based X-ray computed tomography (microCT). We demonstrate successful visualisation and quantification of differences in leaf intercellular airspace in 3D for a range of species (including both dicots and monocots) and provide a comparison with a standard 2D analysis of leaf sections. RESULTS We used the microCT image pipeline to obtain estimates of leaf porosity and mesophyll exposed surface area (Smes) for three dicot species (Arabidopsis, tomato and pea) and three monocot grasses (barley, oat and rice). The imaging pipeline consisted of (1) a masking operation to remove the background airspace surrounding the leaf, (2) segmentation by an automated threshold in ImageJ and then (3) quantification of the extracted pores using the ImageJ 'Analyze Particles' tool. Arabidopsis had the highest porosity and lowest Smes for the dicot species whereas barley had the highest porosity and the highest Smes for the grass species. Comparison of porosity and Smes estimates from 3D microCT analysis and 2D analysis of sections indicates that both methods provide a comparable estimate of porosity but the 2D method may underestimate Smes by almost 50%. A deeper study of porosity revealed similarities and differences in the asymmetric distribution of airspace between the species analysed. CONCLUSIONS Our results demonstrate the utility of high resolution imaging of leaf intercellular airspace networks by lab-based microCT and provide quantitative data on descriptors of leaf cellular architecture. They indicate there is a range of porosity and Smes values in different species and that there is not a simple relationship between these parameters, suggesting the importance of cell size, shape and packing in the determination of cellular parameters proposed to influence leaf photosynthetic performance.
Collapse
Affiliation(s)
- Andrew W. Mathers
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Christopher Hepworth
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Alice L. Baillie
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Jen Sloan
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Hannah Jones
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Marjorie Lundgren
- Lancaster Environment Centre, Lancaster University, LEC 2 Yellow Zone B43, Lancaster, LA1 4YQ UK
| | - Andrew J. Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN UK
| | - Sacha J. Mooney
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Craig J. Sturrock
- Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| |
Collapse
|