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Voxel Carving Based 3D Reconstruction of Sorghum Identifies Genetic Determinants of Radiation Interception Efficiency

Mathieu Gaillard, View ORCID ProfileChenyong Miao, View ORCID ProfileJames C. Schnable, View ORCID ProfileBedrich Benes
doi: https://doi.org/10.1101/2020.04.06.028605
Mathieu Gaillard
1Department of Computer Graphics Technology, Purdue University, USA
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Chenyong Miao
2Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, USA
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James C. Schnable
2Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, USA
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Bedrich Benes
1Department of Computer Graphics Technology, Purdue University, USA
3Department of Computer Science, Purdue University, USA
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  • For correspondence: bbenes@purdue.edu
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Abstract

Changes in canopy architecture traits have been shown to contribute to yield increases. Optimizing both light interception and radiation use efficiency of agricultural crop canopies will be essential to meeting growing needs for food. Canopy architecture is inherently 3D, but many approaches to measuring canopy architecture component traits treat the canopy as a two dimensional structure in order to make large scale measurement, selective breeding, and gene identification logistically feasible. We develop a high throughput voxel carving strategy to reconstruct three dimensional representations of maize and sorghum from a small number of RGB photos. This approach was employed to generate three dimensional reconstructions of a sorghum association population at the late vegetative stage of development. Light interception parameters estimated from these reconstructions enabled the identification of both known and previously unreported loci controlling light interception efficiency in sorghum. The approach described here is generalizable and scalable and it enables 3D reconstructions from existing plant high throughput phenotyping datasets. For future datasets we propose a set of best practices to increase the accuracy of three dimensional reconstructions.

Footnotes

  • Funding information, Research reported in the publication was supported by the Foundation for Food and Agriculture Research under award number – Grant ID: 602757. The content of this publication is solely the responsibility of the authors and does not necessarily represent the official views of the foundation for Food and Agriculture Research. Research reported in the publication was supported in part by National Science Foundation grant #10001387.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted April 07, 2020.
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Voxel Carving Based 3D Reconstruction of Sorghum Identifies Genetic Determinants of Radiation Interception Efficiency
Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes
bioRxiv 2020.04.06.028605; doi: https://doi.org/10.1101/2020.04.06.028605
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Voxel Carving Based 3D Reconstruction of Sorghum Identifies Genetic Determinants of Radiation Interception Efficiency
Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes
bioRxiv 2020.04.06.028605; doi: https://doi.org/10.1101/2020.04.06.028605

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