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Morphological plant modeling: Unleashing geometric and topologic 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, Viktoirya 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: dchitwood@danforthcenter.org 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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Viktoirya 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, FL USA
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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, FL USA
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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, FL USA
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Wojtek Palubicki
10The Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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Hendrik Poorter
25Forschungszentrum Jülich, 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
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  • For correspondence: dchitwood@danforthcenter.org bucksch@uga.edu
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Abstract

Plant morphology is inherently mathematical. The geometries of leaves and flowers and intricate topologies of the root have fascinated plant biologists and mathematicians alike. Beyond providing aesthetic inspiration, understanding plant morphology has become pressing in an era of climate change and a growing population. Gaining an understanding of how to modify plant architecture through molecular biology and breeding is critical to improving agriculture, and the monitoring of ecosystems and global vegetation is vital to modeling a future with fewer natural resources. In this white paper, we begin by summarizing the rich history and state of the art in quantifying the form of plants, mathematical models of patterning in plants, and how plant morphology manifests dynamically across disparate scales of biological organization. We then explore the fundamental challenges that remain unanswered concerning plant morphology, from the barriers preventing the prediction of phenotype from genotype to modeling the fluttering of leaves in a light breeze. We end with a discussion concerning the education of plant morphology synthesizing biological and mathematical approaches and ways to facilitate research advances through outreach, cross-disciplinary training, and open science. Never has the need to model 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 October 04, 2016.
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Morphological plant modeling: Unleashing geometric and topologic 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, Viktoirya 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 topologic 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, Viktoirya 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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