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Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Abigail E. Bryson, Maya Wilson Brown, Joey Mullins, Wei Dong, Keivan Bahmani, Nolan Bornowski, Christina Chiu, Philip Engelgau, Bethany Gettings, Fabio Gomezcano, Luke M. Gregory, Anna C. Haber, Donghee Hoh, Emily E. Jennings, Zhongjie Ji, Prabhjot Kaur, Sunil K. Kenchanmane Raju, Yunfei Long, Serena G. Lotreck, Davis T. Mathieu, Thilanka Ranaweera, Eleanore J. Ritter, Rie Sadohara, Robert Z. Shrote, Kaila E. Smith, Scott J. Teresi, Julian Venegas, Hao Wang, McKena L. Wilson, Alyssa R. Tarrant, Margaret H. Frank, Zoë Migicovsky, Jyothi Kumar, Robert VanBuren, Jason P. Londo, Daniel H. Chitwood
doi: https://doi.org/10.1101/2020.06.22.163899
Abigail E. Bryson
1Genetics Program, Michigan State University, East Lansing, Michigan 48824 USA
2Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Maya Wilson Brown
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Joey Mullins
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Wei Dong
2Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Keivan Bahmani
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Nolan Bornowski
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Christina Chiu
5Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824 USA
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Philip Engelgau
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Bethany Gettings
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Fabio Gomezcano
2Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Luke M. Gregory
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Anna C. Haber
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Donghee Hoh
6Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan 48824 USA
7MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824 USA
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Emily E. Jennings
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
8Molecular Plant Sciences Program, Michigan State University, East Lansing, Michigan 48824 USA
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Zhongjie Ji
5Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824 USA
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Prabhjot Kaur
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
9Plant Breeding, Genetics, and Biotechnology, Michigan State University, East Lansing, Michigan 48824 USA
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Sunil K. Kenchanmane Raju
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Yunfei Long
10Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 USA
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Serena G. Lotreck
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Davis T. Mathieu
1Genetics Program, Michigan State University, East Lansing, Michigan 48824 USA
2Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Thilanka Ranaweera
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Eleanore J. Ritter
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Rie Sadohara
5Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824 USA
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Robert Z. Shrote
5Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824 USA
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Kaila E. Smith
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Scott J. Teresi
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Julian Venegas
11Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan 48824 USA
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Hao Wang
11Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan 48824 USA
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McKena L. Wilson
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Alyssa R. Tarrant
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Margaret H. Frank
12School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, New York 14850 USA
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Zoë Migicovsky
13Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia B2N 5E3 Canada
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Jyothi Kumar
3Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 USA
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Robert VanBuren
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
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Jason P. Londo
14Grape Genetics Research Unit, USDA ARS, Geneva, New York 14456 USA
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Daniel H. Chitwood
4Department of Horticulture, Michigan State University, East Lansing, Michigan 48824 USA
11Department of Computational Mathematics, Science & Engineering, Michigan State University, East Lansing, Michigan 48824 USA
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  • For correspondence: chitwoo9@msu.edu
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ABSTRACT

Premise of study Leaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite “shape of shapes” can better capture variation and predict species identity compared to individual leaves.

Methods Using homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies.

Results We found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping.

Discussion Observations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape—an assemblage of modeled leaf snapshots across the shoot—is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/DanChitwood/grapevine_shoots

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves
Abigail E. Bryson, Maya Wilson Brown, Joey Mullins, Wei Dong, Keivan Bahmani, Nolan Bornowski, Christina Chiu, Philip Engelgau, Bethany Gettings, Fabio Gomezcano, Luke M. Gregory, Anna C. Haber, Donghee Hoh, Emily E. Jennings, Zhongjie Ji, Prabhjot Kaur, Sunil K. Kenchanmane Raju, Yunfei Long, Serena G. Lotreck, Davis T. Mathieu, Thilanka Ranaweera, Eleanore J. Ritter, Rie Sadohara, Robert Z. Shrote, Kaila E. Smith, Scott J. Teresi, Julian Venegas, Hao Wang, McKena L. Wilson, Alyssa R. Tarrant, Margaret H. Frank, Zoë Migicovsky, Jyothi Kumar, Robert VanBuren, Jason P. Londo, Daniel H. Chitwood
bioRxiv 2020.06.22.163899; doi: https://doi.org/10.1101/2020.06.22.163899
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Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves
Abigail E. Bryson, Maya Wilson Brown, Joey Mullins, Wei Dong, Keivan Bahmani, Nolan Bornowski, Christina Chiu, Philip Engelgau, Bethany Gettings, Fabio Gomezcano, Luke M. Gregory, Anna C. Haber, Donghee Hoh, Emily E. Jennings, Zhongjie Ji, Prabhjot Kaur, Sunil K. Kenchanmane Raju, Yunfei Long, Serena G. Lotreck, Davis T. Mathieu, Thilanka Ranaweera, Eleanore J. Ritter, Rie Sadohara, Robert Z. Shrote, Kaila E. Smith, Scott J. Teresi, Julian Venegas, Hao Wang, McKena L. Wilson, Alyssa R. Tarrant, Margaret H. Frank, Zoë Migicovsky, Jyothi Kumar, Robert VanBuren, Jason P. Londo, Daniel H. Chitwood
bioRxiv 2020.06.22.163899; doi: https://doi.org/10.1101/2020.06.22.163899

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