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dc.contributor.author
Pfeifer, Johannes
dc.contributor.author
Kirchgessner, Norbert
dc.contributor.author
Colombi, Tino
dc.contributor.author
Walter, Achim
dc.date.accessioned
2019-04-17T10:04:47Z
dc.date.available
2017-06-11T19:11:24Z
dc.date.available
2019-04-17T10:04:47Z
dc.date.issued
2015-08-28
dc.identifier.issn
1746-4811
dc.identifier.other
10.1186/s13007-015-0084-4
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/103905
dc.identifier.doi
10.3929/ethz-b-000103905
dc.description.abstract
Background X-ray computed tomography (CT) has become a powerful tool for root phenotyping. Compared to rather classical, destructive methods, CT encompasses various advantages. In pot experiments the growth and development of the same individual root can be followed over time and in addition the unaltered configuration of the 3D root system architecture (RSA) interacting with a real field soil matrix can be studied. Yet, the throughput, which is essential for a more widespread application of CT for basic research or breeding programs, suffers from the bottleneck of rapid and standardized segmentation methods to extract root structures. Using available methods, root segmentation is done to a large extent manually, as it requires a lot of interactive parameter optimization and interpretation and therefore needs a lot of time. Results Based on commercially available software, this paper presents a protocol that is faster, more standardized and more versatile compared to existing segmentation methods, particularly if used to analyse field samples collected in situ. To the knowledge of the authors this is the first study approaching to develop a comprehensive segmentation method suitable for comparatively large columns sampled in situ which contain complex, not necessarily connected root systems from multiple plants grown in undisturbed field soil. Root systems from several crops were sampled in situ and CT-volumes determined with the presented method were compared to root dry matter of washed root samples. A highly significant (P < 0.01) and strong correlation (R2 = 0.84) was found, demonstrating the value of the presented method in the context of field research. Subsequent to segmentation, a method for the measurement of root thickness distribution has been used. Root thickness is a central RSA trait for various physiological research questions such as root growth in compacted soil or under oxygen deficient soil conditions, but hardly assessable in high throughput until today, due to a lack of available protocols. Conclusions Application of the presented protocol helps to overcome the segmentation bottleneck and can be considered a step forward to high throughput root phenotyping facilitating appropriate sample sizes desired by science and breeding.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Field soil
en_US
dc.subject
High throughput
en_US
dc.subject
Image analysis
en_US
dc.subject
Non-destructive root phenotyping
en_US
dc.subject
Root growth dynamics
en_US
dc.subject
Root system architecture (RSA)
en_US
dc.subject
Root thickness
en_US
dc.subject
X-ray computed tomography (CT)
en_US
dc.title
Rapid phenotyping of crop root systems in undisturbed field soils using X-ray computed tomography
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
Plant Methods
ethz.journal.volume
11
en_US
ethz.journal.abbreviated
Plant methods
ethz.pages.start
41
en_US
ethz.size
8 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.scopus
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03894 - Walter, Achim / Walter, Achim
en_US
ethz.leitzahl.certified
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02350 - Dep. Umweltsystemwissenschaften / Dep. of Environmental Systems Science::02703 - Institut für Agrarwissenschaften / Institute of Agricultural Sciences::03894 - Walter, Achim / Walter, Achim
ethz.date.deposited
2017-06-11T19:12:07Z
ethz.source
ECIT
ethz.identifier.importid
imp593653721a81530839
ethz.ecitpid
pub:162446
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2017-07-26T19:11:06Z
ethz.rosetta.lastUpdated
2019-04-17T10:05:11Z
ethz.rosetta.exportRequired
true
ethz.rosetta.versionExported
true
ethz.COinS
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