High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography
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 ge...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | Plant Methods |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13007-020-00612-6 |
| _version_ | 1828407793448648704 |
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| author | Shota Teramoto Satoko Takayasu Yuka Kitomi Yumiko Arai-Sanoh Takanari Tanabata Yusaku Uga |
| author_facet | Shota Teramoto Satoko Takayasu Yuka Kitomi Yumiko Arai-Sanoh Takanari Tanabata Yusaku Uga |
| author_sort | Shota Teramoto |
| collection | DOAJ |
| description | 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 We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) 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. |
| first_indexed | 2024-12-10T11:30:40Z |
| format | Article |
| id | doaj.art-3c6ff861c1ec4d83b3a6ee9b684a8324 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-12-10T11:30:40Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-3c6ff861c1ec4d83b3a6ee9b684a83242022-12-22T01:50:36ZengBMCPlant Methods1746-48112020-05-0116111410.1186/s13007-020-00612-6High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomographyShota Teramoto0Satoko Takayasu1Yuka Kitomi2Yumiko Arai-Sanoh3Takanari Tanabata4Yusaku Uga5Institute of Crop Science, National Agriculture and Food Research OrganizationInstitute of Crop Science, National Agriculture and Food Research OrganizationInstitute of Crop Science, National Agriculture and Food Research OrganizationInstitute of Crop Science, National Agriculture and Food Research OrganizationKazusa DNA Research InstituteInstitute of Crop Science, National Agriculture and Food Research OrganizationAbstract 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 We have developed a high-throughput process flow for the 3-D visualization of rice (Oryza sativa) 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.http://link.springer.com/article/10.1186/s13007-020-00612-6Image processingOryza sativaPlant rootRoot plasticityRSAvis3DX-ray CT |
| spellingShingle | Shota Teramoto Satoko Takayasu Yuka Kitomi Yumiko Arai-Sanoh Takanari Tanabata Yusaku Uga High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography Plant Methods Image processing Oryza sativa Plant root Root plasticity RSAvis3D X-ray CT |
| title | High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography |
| title_full | High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography |
| title_fullStr | High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography |
| title_full_unstemmed | High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography |
| title_short | High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography |
| title_sort | high throughput three dimensional visualization of root system architecture of rice using x ray computed tomography |
| topic | Image processing Oryza sativa Plant root Root plasticity RSAvis3D X-ray CT |
| url | http://link.springer.com/article/10.1186/s13007-020-00612-6 |
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