Rhizovision crown: An integrated hardware and software platform for root crown phenotyping

Anand Seethepalli; Haichao Guo; Xiuwei Liu; Marcus Griffiths; Hussien Almtarfi; Zenglu Li; Shuyu Liu; Alina Zare; Felix B. Fritschi; Elison B. Blancaflor; Xue Feng Ma; Larry M. York

doi:10.34133/2020/3074916

Rhizovision crown: An integrated hardware and software platform for root crown phenotyping

Anand Seethepalli, Haichao Guo, Xiuwei Liu, Marcus Griffiths, Hussien Almtarfi, Zenglu Li, Shuyu Liu, Alina Zare, Felix B. Fritschi, Elison B. Blancaflor, Xue Feng Ma, Larry M. York

Research output: Contribution to journal › Article › peer-review

71 Scopus citations

Abstract

Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a backlight and a monochrome machine vision camera to capture root crown silhouettes. The RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. The RhizoVision Analyzer was physically validated using copper wire, and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating that differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns and sets a standard by which open plant phenotyping platforms can be benchmarked.

Original language	English
Article number	3074916
Journal	Plant Phenomics
Volume	2020
DOIs	https://doi.org/10.34133/2020/3074916
State	Published - 2020
Externally published	Yes

Funding

We thank Frank Maulana, Bryce Walker, Wangqi Wang, Tadele Kumssa, Jarron Peoples, Franco Guadarrama, Willie Hart, Matt Hogan, Erika Phillips, Cheng Lin Chai, and Erica Judd for root excavation, washing, and imaging of the wheat population. The work was funded by the Noble Research Institute, LLC; the USDA NIFA EAGER program (2017-67007-26953); the Department of Energy ARPA-E ROOTS program (DE-AR0000822); and the United Soybean Board (1420-532-5613).

Funders	Funder number
Department of Energy ARPA-E	DE-AR0000822
USDA NIFA	2017-67007-26953
United Soybean Board	1420-532-5613
Noble Research Institute

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title = "Rhizovision crown: An integrated hardware and software platform for root crown phenotyping",

abstract = "Root crown phenotyping measures the top portion of crop root systems and can be used for marker-assisted breeding, genetic mapping, and understanding how roots influence soil resource acquisition. Several imaging protocols and image analysis programs exist, but they are not optimized for high-throughput, repeatable, and robust root crown phenotyping. The RhizoVision Crown platform integrates an imaging unit, image capture software, and image analysis software that are optimized for reliable extraction of measurements from large numbers of root crowns. The hardware platform utilizes a backlight and a monochrome machine vision camera to capture root crown silhouettes. The RhizoVision Imager and RhizoVision Analyzer are free, open-source software that streamline image capture and image analysis with intuitive graphical user interfaces. The RhizoVision Analyzer was physically validated using copper wire, and features were extensively validated using 10,464 ground-truth simulated images of dicot and monocot root systems. This platform was then used to phenotype soybean and wheat root crowns. A total of 2,799 soybean (Glycine max) root crowns of 187 lines and 1,753 wheat (Triticum aestivum) root crowns of 186 lines were phenotyped. Principal component analysis indicated similar correlations among features in both species. The maximum heritability was 0.74 in soybean and 0.22 in wheat, indicating that differences in species and populations need to be considered. The integrated RhizoVision Crown platform facilitates high-throughput phenotyping of crop root crowns and sets a standard by which open plant phenotyping platforms can be benchmarked.",

author = "Anand Seethepalli and Haichao Guo and Xiuwei Liu and Marcus Griffiths and Hussien Almtarfi and Zenglu Li and Shuyu Liu and Alina Zare and Fritschi, {Felix B.} and Blancaflor, {Elison B.} and Ma, {Xue Feng} and York, {Larry M.}",

note = "Publisher Copyright: Copyright {\textcopyright} 2020 Anand Seethepalli et al. Exclusive Licensee Nanjing Agricultural University. Distributed under a Creative Commons Attribution License (CC BY 4.0).",

year = "2020",

doi = "10.34133/2020/3074916",

language = "English",

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AU - Guo, Haichao

AU - Liu, Xiuwei

AU - Griffiths, Marcus

AU - Almtarfi, Hussien

AU - Li, Zenglu

AU - Liu, Shuyu

AU - Zare, Alina

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AU - Blancaflor, Elison B.

AU - Ma, Xue Feng

AU - York, Larry M.

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Rhizovision crown: An integrated hardware and software platform for root crown phenotyping

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