Abstract
BACKGROUND: X-ray computed tomography (CT) allows us to visualize root system architecture (RSA) beneath the soil, non-destructively and in a three-dimensional (3-D) form. However, CT scanning, reconstruction processes, and root isolation from X-ray CT volumes, take considerable time. For genetic analyses, such as quantitative trait locus mapping, which require a large population size, a high-throughput RSA visualization method is required. RESULTS: ) RSA (consisting of radicle and crown roots), using X-ray CT. The process flow includes use of a uniform particle size, calcined clay to reduce the possibility of visualizing non-root segments, use of a higher tube voltage and current in the X-ray CT scanning to increase root-to-soil contrast, and use of a 3-D median filter and edge detection algorithm to isolate root segments. Using high-performance computing technology, this analysis flow requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing, to visualize rice RSA. This reduced time allowed us to conduct the genetic analysis associated with 3-D RSA phenotyping. In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively. The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth. Using the developed process flow, we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over 3 weeks. CONCLUSIONS: We developed a high-throughput process flow for 3-D rice RSA visualization by X-ray CT. The X-ray dose assay on plant growth has shown that this methodology could be applicable for 4-D RSA phenotyping. We named the RSA visualization method 'RSAvis3D' and are confident that it represents a potentially efficient application for 3-D RSA phenotyping of various plant species.
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Claims 8
Claim · model-written summary
The workflow took 10 min for CT scanning and reconstruction.
- Taxon
- rice
Oryza sativae1 - Outcome
- CT scanning and reconstructione0
- Value
- 10 mine0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“requires only 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction”
e1“to visualize rice RSA.”
Claim · model-written summary
A rough image could be produced in 33 s.
- Taxon
- riceOryza sativae1
- Outcome
- rough imagee0
- Value
- 33 se0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“33 s, if a rough image is acceptable”
e1“to visualize rice RSA.”
Claim · model-written summary
Image processing took 2 min.
- Taxon
- riceOryza sativae0
- Outcome
- image processinge0
- Value
- 2 mine0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“2 min for image processing, to visualize rice RSA”
Claim · model-written summary
At two weeks, 85% of radicle roots were detected in 16 cm pots.
- Taxon
- riceOryza sativae1
- Organ / stage
- radiclee0
- Outcome
- radicle and crown roots were detectede0
- Value
- 85%e0
- Qualifier
- 16 cme0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively.”
e1“to visualize rice RSA.”
Claim · model-written summary
At two weeks, 100% of crown roots were detected in 20 cm pots.
- Taxon
- riceOryza sativae1
- Organ / stage
- crown rootse0
- Outcome
- radicle and crown roots were detectede0
- Value
- 100%e0
- Qualifier
- 20 cme0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In 2-week-old seedlings, 85% and 100% of radicle and crown roots were detected, when 16 cm and 20 cm diameter pots were used, respectively.”
e1“to visualize rice RSA.”
Claim · model-written summary
The scan X-ray dose was below 0.09 Gy.
- Taxon
- riceOryza sativae0
- Outcome
- X-ray dose per scane0
- Value
- < 0.09 Gye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth.”
Claim · model-written summary
The X-ray dose did not impede rice growth.
- Taxon
- riceOryza sativae0
- Treatment
- X-ray dose per scane0
- Outcome
- rice growthe0
- Direction
- did not impedee0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The X-ray dose per scan was estimated at < 0.09 Gy, which did not impede rice growth.”
Claim · model-written summary
The workflow enabled daily 4D imaging of an upland rice variety for more than three weeks.
- Taxon
- riceOryza sativae0
- Material
- upland rice varietye0
- Outcome
- daily RSA developmente0
- Value
- 3 weekse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we were able to follow daily RSA development, i.e., 4-D RSA development, of an upland rice variety, over 3 weeks”
The same questions in other papers
radiation · growth · Oryza sativa (rice)Results differ
61 papers in the same direction as this paper · 22 in the opposite direction
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