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Persistent homology: a tool to universally measure plant morphologies across organs and scales

Mao Li, Margaret H. Frank, Viktoriya Coneva, Washington Mio, View ORCID ProfileChristopher N. Topp, View ORCID ProfileDaniel H. Chitwood
doi: https://doi.org/10.1101/104141
Mao Li
1Donald Danforth Plant Science Center, St. Louis, MO USA
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Margaret H. Frank
1Donald Danforth Plant Science Center, St. Louis, MO USA
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Viktoriya Coneva
1Donald Danforth Plant Science Center, St. Louis, MO USA
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Washington Mio
2Department of Mathematics, Florida State University, Tallahassee, FL, USA
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Christopher N. Topp
1Donald Danforth Plant Science Center, St. Louis, MO USA
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Daniel H. Chitwood
3Independent Researcher, St. Louis, MO USA
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Abstract

Genetic contributions to plant morphology are not partitioned between shoots and roots. Yet, shoot and root architectures are rarely measured in the same plants. Even if shoot and root architectures are both studied, the application of mathematical methods flexible enough to accommodate the disparate topologies and shapes within a plant, and across scales, are lacking. Here, we advocate the use of persistent homology, a mathematical method robust to noise, invariant with respect to orientation, capable of application across diverse scales, and importantly, compatible with diverse functions to quantify disparate plant morphologies, architectures, and textures. To demonstrate the usefulness of this method, we apply persistent homology approaches to the shape of leaves, serrations, and root architecture as measured in the same plants of a domesticated tomato Solanum pennellii near-isogenic introgression line population under field conditions. We find that genetic contributions to morphology affect the plant in a concerted fashion, affecting both the shoot and root, revealing a pleiotropic basis to natural variation in tomato.

Footnotes

  • Author Contributions: ML, MHF, VC, WM, CNT, DHC conceived and designed research; ML and WM carried out analysis and developed novel tools; MHF and VC collected data; CNT and DHC oversaw research; ML, MHF, VC, WM, CNT, and DHC wrote the paper.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 03, 2017.
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Persistent homology: a tool to universally measure plant morphologies across organs and scales
Mao Li, Margaret H. Frank, Viktoriya Coneva, Washington Mio, Christopher N. Topp, Daniel H. Chitwood
bioRxiv 104141; doi: https://doi.org/10.1101/104141
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Persistent homology: a tool to universally measure plant morphologies across organs and scales
Mao Li, Margaret H. Frank, Viktoriya Coneva, Washington Mio, Christopher N. Topp, Daniel H. Chitwood
bioRxiv 104141; doi: https://doi.org/10.1101/104141

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