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Li M, Frank MH, Coneva V, Mio W, Chitwood DH, Topp CN. The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology. PLANT PHYSIOLOGY 2018; 177:1382-1395. [PMID: 29871979 PMCID: PMC6084663 DOI: 10.1104/pp.18.00104] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/21/2018] [Indexed: 05/21/2023]
Abstract
Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (Solanum pennellii). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | | | - Washington Mio
- Department of Mathematics, Florida State University, Tallahassee, Florida 32306
| | - Daniel H Chitwood
- Independent Scientist, Santa Rosa, California 95409
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824
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Alves VM, Hernández MIM. Morphometric Modifications in Canthon quinquemaculatus Castelnau 1840 (Coleoptera: Scarabaeinae): Sublethal Effects of Transgenic Maize? INSECTS 2017; 8:insects8040115. [PMID: 29065452 PMCID: PMC5746798 DOI: 10.3390/insects8040115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/27/2017] [Accepted: 10/18/2017] [Indexed: 11/16/2022]
Abstract
The effects of transgenic compounds on non-target organisms remain poorly understood, especially in native insect species. Morphological changes (e.g., changes in body size and shape) may reflect possible responses to environmental stressors, like transgenic toxins. The dung beetle Canthon quinquemaculatus (Coleoptera: Scarabaeinae) is a non-target species found in transgenic crops. We evaluated whether C. quinquemaculatus individuals inhabiting corn fields cultivated with different seed types (conventional, creole and transgenic) present modifications in body shape compared to individuals inhabiting adjacent native forest fragments. We collected C. quinquemaculatus specimens across an agricultural landscape in southern Brazil, during the summer of 2015. Six populations were sampled: three maize crop populations each under a different seed type, and three populations of adjacent forests. After sampling, specimens were subjected to morphometric analyses to discover differences in body shape. We chose fifteen landmarks to describe body shape, and morphometric data were tested with Procrustes ANOVA and Discriminant Analysis. We found that body shape did not differ between individuals collected in conventional and creole crops with their respective adjacent forests (p > 0.05); however, transgenic crop populations differed significantly from those collected in adjacent forests (p < 0.05). Insects in transgenic maize are more oval and have a retraction in the abdominal region, compared with the respective adjacent forest, this result shows the possible effect of transgenic crops on non-target species. This may have implications for the ecosystem service of organic matter removal, carried out by these organisms.
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Affiliation(s)
- Victor Michelon Alves
- Programa de Pós Graduação em Ecologia, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brasil.
| | - Malva Isabel Medina Hernández
- Programa de Pós Graduação em Ecologia, Departamento de Ecologia e Zoologia, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brasil.
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Abstract
The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, following an idea of Darwin's, the various movements in a renewed and observation-based perspective of the plant development. With this perspective, the different movements fit together logically, and in particular we point out that the mature reversible movements, such as the sensitive or circadian movements, are just partial regressions of the developmental ones.
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Affiliation(s)
- Mathieu Rivière
- Laboratoire Matière & Systèmes Complexes UMR 7057, Université Paris Diderot, Sorbonne Paris Cité, CNRS, F-75205 Paris Cedex 13, France
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Abstract
Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.
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Affiliation(s)
- Karen Alim
- Max Planck Institute for Dynamics and Self-Organization, D-37077 Göttingen, Germany
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From Sponges to Nanotubes: A Change of Nanocrystal Morphology for Acute-Angle Bent-Core Molecules. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604915] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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From Sponges to Nanotubes: A Change of Nanocrystal Morphology for Acute-Angle Bent-Core Molecules. Angew Chem Int Ed Engl 2016; 55:12238-42. [DOI: 10.1002/anie.201604915] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 07/18/2016] [Indexed: 11/07/2022]
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Fraas S, Lüthen H. Novel imaging-based phenotyping strategies for dissecting crosstalk in plant development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4947-4955. [PMID: 26041318 DOI: 10.1093/jxb/erv265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In an era of genomics, proteomics, and metabolomics a large number of mutants are available. The discovery of their phenotypes is fast becoming the bottleneck of molecular plant physiology. This crisis can be overcome by imaging-based phenotyping, an emerging, rapidly developing and innovative approach integrating plant and computer science. A tremendous amount of digital image data are automatically analysed using techniques of 'machine vision'. This minireview will shed light on the available imaging strategies and discuss standard methods for the automated analysis of images to give the non-bioinformatic reader an idea how the new technology works. A number of successful platforms will be described and the prospects that image-based phenomics may offer for elucidating hormonal cross-talk and molecular growth physiology will be discussed.
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Affiliation(s)
- Simon Fraas
- Biozentrum Hamburg der Universität, Physiology, Ohnhorststr. 18, D-22609 Hamburg, Germany
| | - Hartwig Lüthen
- Biozentrum Hamburg der Universität, Physiology, Ohnhorststr. 18, D-22609 Hamburg, Germany
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Thérien-Aubin H, Moshe M, Sharon E, Kumacheva E. Shape transformations of soft matter governed by bi-axial stresses. SOFT MATTER 2015; 11:4600-5. [PMID: 25978294 DOI: 10.1039/c5sm00561b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Rational design of the programmable soft matter requires understanding of the effect of a complex metric on shape transformations of thin non-Euclidean sheets. In the present work, we explored experimentally and using simulations how simultaneous or consecutive application of two orthogonal perturbations to thin patterned stimuli-responsive hydrogel sheets affects their three-dimensional shape transformations. The final shape of the sheet is governed by the metric, but not the order, in which the perturbations are applied to the system, and is determined by the competition of small-scale bidirectional stresses. In addition, a new, unexpected transition from a planar state to an equilibrium helical shape of the hydrogel sheet is observed via a mechanism that is yet to be explained.
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Affiliation(s)
- Héloïse Thérien-Aubin
- University of Toronto, Department of Chemistry, 80 Saint George street, Toronto, Ontario M5S 3H6, Canada.
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Abstract
The development of plant leaves follows a common basic program that is flexible and is adjusted according to species, developmental stage and environmental circumstances. Leaves initiate from the flanks of the shoot apical meristem and develop into flat structures of variable sizes and forms. This process is regulated by plant hormones, transcriptional regulators and mechanical properties of the tissue. Here, we review recent advances in the understanding of how these factors modulate leaf development to yield a substantial diversity of leaf forms. We discuss these issues in the context of leaf initiation, the balance between morphogenesis and differentiation, and patterning of the leaf margin.
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Affiliation(s)
- Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
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Amir A, van Teeffelen S. Getting into shape: How do rod-like bacteria control their geometry? SYSTEMS AND SYNTHETIC BIOLOGY 2014; 8:227-35. [PMID: 25136385 DOI: 10.1007/s11693-014-9143-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 03/26/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Abstract
Rod-like bacteria maintain their cylindrical shapes with remarkable precision during growth. However, they are also capable to adapt their shapes to external forces and constraints, for example by growing into narrow or curved confinements. Despite being one of the simplest morphologies, we are still far from a full understanding of how shape is robustly regulated, and how bacteria obtain their near-perfect cylindrical shapes with excellent precision. However, recent experimental and theoretical findings suggest that cell-wall geometry and mechanical stress play important roles in regulating cell shape in rod-like bacteria. We review our current understanding of the cell wall architecture and the growth dynamics, and discuss possible candidates for regulatory cues of shape regulation in the absence or presence of external constraints. Finally, we suggest further future experimental and theoretical directions which may help to shed light on this fundamental problem.
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Affiliation(s)
- Ariel Amir
- Department of Physics, Harvard University, Cambridge, MA 02138 USA
| | - Sven van Teeffelen
- Groupe Croissance et Morphogénése Microbienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
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