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Morphological plant modeling: Unleashing geometric and topological potential within the plant sciences

Alexander Bucksch, Acheampong Atta-Boateng, Akomian Fortuné Azihou, Mathilde Balduzzi, Dorjsuren Battogtokh, Aly Baumgartner, Brad M. Binder, Siobhan A. Braybrook, Cynthia Chang, Viktoiriya Coneva, Thomas J. DeWitt, Alexander G. Fletcher, Malia A. Gehan, Diego Hernan Diaz Martinez, Lilan Hong, Anjali S. Iyer-Pascuzzi, Laura L. Klein, Samuel Leiboff, Mao Li, Jonathan P. Lynch, Alexis Maizel, Julin N. Maloof, R.J. Cody Markelz, Ciera C. Martinez, Laura A. Miller, Washington Mio, Wojtek Palubicki, Hendrik Poorter, Christophe Pradal, Charles A. Price, Eetu Puttonen, John Reese, Rubén Rellán-Álvarez, Edgar P. Spalding, Erin E. Sparks, Christopher N. Topp, Joseph Williams, Daniel H. Chitwood
doi: https://doi.org/10.1101/078832
Alexander Bucksch
1Department of Plant Biology, University of Georgia, Athens, GA USA
2Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA USA
3Institute of Bioinformatics, University of Georgia, Athens, GA USA
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  • For correspondence: dhchitwood@gmail.com bucksch@uga.edu
Acheampong Atta-Boateng
4School of Forestry and Environmental Studies, Yale University, New Haven, CT USA
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Akomian Fortuné Azihou
5Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 Cotonou, Benin
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Mathilde Balduzzi
6VirtualPlants, Inria, Montpellier, France
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Dorjsuren Battogtokh
7Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA USA
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Aly Baumgartner
8Department of Geosciences, Baylor University, Waco, TX USA
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Brad M. Binder
9Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN USA
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Siobhan A. Braybrook
10The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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Cynthia Chang
11Division of Biology, University of Washington, Bothell, WA USA
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Viktoiriya Coneva
12Donald Danforth Plant Science Center, St. Louis, MO USA
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Thomas J. DeWitt
13Department of Wildlife & Fisheries Sciences and Department of Plant Pathology & Microbiology, Texas A & M; University, College Station, TX USA
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Alexander G. Fletcher
14School of Mathematics & Statistics and Bateson Centre, University of Sheffield, Sheffield,UK
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Malia A. Gehan
12Donald Danforth Plant Science Center, St. Louis, MO USA
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Diego Hernan Diaz Martinez
15Department of Mathematics, Florida State University, Tallahassee, FLUSA
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Lilan Hong
16Weill Institute for Cell and Molecular Biology and Section of Plant Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA
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Anjali S. Iyer-Pascuzzi
17Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN USA
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Laura L. Klein
18Department of Biology, Saint Louis University, St. Louis, MO USA
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Samuel Leiboff
19School of Integrative Plant Science, Cornell University, Ithaca, NY USA
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Mao Li
15Department of Mathematics, Florida State University, Tallahassee, FLUSA
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Jonathan P. Lynch
20Department of Plant Science, The Pennsylvania State University, University Park, PA USA
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Alexis Maizel
21Center for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Julin N. Maloof
22Department of Plant Biology, University of California, Davis, CA USA
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R.J. Cody Markelz
22Department of Plant Biology, University of California, Davis, CA USA
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Ciera C. Martinez
23Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
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Laura A. Miller
24Program in Bioinformatics and Computational Biology, The University of North Carolina, Chapel Hill, NC USA
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Washington Mio
15Department of Mathematics, Florida State University, Tallahassee, FLUSA
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Wojtek Palubicki
10The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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Hendrik Poorter
25Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, Jülich, Germany
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Christophe Pradal
26CIRAD, UMR AGAP and Inria, VirtualPlants, Montpellier, France
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Charles A. Price
27National Institute for Mathematical and Biological Synthesis, University of Tennessee,Knoxville, TN USA
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Eetu Puttonen
28Finnish Geospatial Research Institute and Centre of Excellence in Laser Scanning Research, National Land Survey of Finland, Masala, Finland
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John Reese
29Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
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Rubén Rellán-Álvarez
30Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, CINVESTAV, Irapuato, México
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Edgar P. Spalding
31Department of Botany, University of Wisconsin, Madison, WI USA
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Erin E. Sparks
32Department of Biology, Duke University, Durham, NC USA
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Christopher N. Topp
12Donald Danforth Plant Science Center, St. Louis, MO USA
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Joseph Williams
29Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN USA
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Daniel H. Chitwood
12Donald Danforth Plant Science Center, St. Louis, MO USA
33 Current address: Independent Researcher, St Louis, MO USA
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  • For correspondence: dhchitwood@gmail.com bucksch@uga.edu
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Abstract

Plant morphology is inherently mathematical in that morphology describes plant form and architecture with geometrical and topological descriptors. The geometries and topologies of leaves, flowers, roots, shoots and their spatial arrangements have fascinated plant biologists and mathematicians alike. Beyond providing aesthetic inspiration, quantifying plant morphology has become pressing in an era of climate change and a growing human population. Modifying plant morphology, through molecular biology and breeding, aided by a mathematical perspective, is critical to improving agriculture, and the monitoring of ecosystems with fewer natural resources. In this white paper, we begin with an overview of the mathematical models applied to quantify patterning in plants. We then explore fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the movement of leafs in air streams. We end with a discussion concerning the incorporation of plant morphology into educational programs. This strategy focuses on synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. This white paper arose from bringing mathematicians and biologists together at the National Institute for Mathematical and Biological Synthesis (NIMBioS) workshop titled “Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences” held at the University of Tennessee, Knoxville in September, 2015. Never has the need to quantify plant morphology been more imperative. Unleashing the potential of geometric and topological approaches in the plant sciences promises to transform our understanding of both plants and mathematics.

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Posted February 08, 2017.
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Morphological plant modeling: Unleashing geometric and topological potential within the plant sciences
Alexander Bucksch, Acheampong Atta-Boateng, Akomian Fortuné Azihou, Mathilde Balduzzi, Dorjsuren Battogtokh, Aly Baumgartner, Brad M. Binder, Siobhan A. Braybrook, Cynthia Chang, Viktoiriya Coneva, Thomas J. DeWitt, Alexander G. Fletcher, Malia A. Gehan, Diego Hernan Diaz Martinez, Lilan Hong, Anjali S. Iyer-Pascuzzi, Laura L. Klein, Samuel Leiboff, Mao Li, Jonathan P. Lynch, Alexis Maizel, Julin N. Maloof, R.J. Cody Markelz, Ciera C. Martinez, Laura A. Miller, Washington Mio, Wojtek Palubicki, Hendrik Poorter, Christophe Pradal, Charles A. Price, Eetu Puttonen, John Reese, Rubén Rellán-Álvarez, Edgar P. Spalding, Erin E. Sparks, Christopher N. Topp, Joseph Williams, Daniel H. Chitwood
bioRxiv 078832; doi: https://doi.org/10.1101/078832
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Morphological plant modeling: Unleashing geometric and topological potential within the plant sciences
Alexander Bucksch, Acheampong Atta-Boateng, Akomian Fortuné Azihou, Mathilde Balduzzi, Dorjsuren Battogtokh, Aly Baumgartner, Brad M. Binder, Siobhan A. Braybrook, Cynthia Chang, Viktoiriya Coneva, Thomas J. DeWitt, Alexander G. Fletcher, Malia A. Gehan, Diego Hernan Diaz Martinez, Lilan Hong, Anjali S. Iyer-Pascuzzi, Laura L. Klein, Samuel Leiboff, Mao Li, Jonathan P. Lynch, Alexis Maizel, Julin N. Maloof, R.J. Cody Markelz, Ciera C. Martinez, Laura A. Miller, Washington Mio, Wojtek Palubicki, Hendrik Poorter, Christophe Pradal, Charles A. Price, Eetu Puttonen, John Reese, Rubén Rellán-Álvarez, Edgar P. Spalding, Erin E. Sparks, Christopher N. Topp, Joseph Williams, Daniel H. Chitwood
bioRxiv 078832; doi: https://doi.org/10.1101/078832

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