Phenotyping of plant root systems

Phenotyping of plant root systems

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  Advances and limitationsof a non-invasive methods for the phenotyping of plant root systems Słota Michał Department of Genetics, University of Silesia Phot.M.Slota
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  Słota M., 2015INTRODUCTION Slotaet al. 2015 (in review)
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  Słota M., 2015 Fioraniet al. 2012 RGB imaging NIR imaging INTRODUCTION Thermal imaging 1 2 3
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  Słota M., 2015 Techniquesfor non-invasive imaging of plants in soil Phenotypic data can be obtained by detecting reflected, transmitted or emitted electromagnetic radiation, or magnetic resonance properties of nuclei. 3D structural as well as physiological traits can be acquired non-invasively by positron emission tomography (PET), magnetic resonance imaging (MRI) and Micro Computed Tomography (MicroCT). Method Description Resolution Application Studies MRI (Magnetic Resonance Imaging) Water (1H) mapping 200-500 µm 1-600 s Morphometric parameters in 3D, water content B. vulgaris, H. spontaneum, bean, sugar beet PET (Positron Emission Tomography) Radiotracer mapping 1-2 mm, 10 s, 20 min Transport partitioning, flow velocty H. spontaneum, B. vulgaris MicroCT (Micro Computed Tomography) X-ray digital radiography <100 µm hours Morphometric parameters in 3D, grain quality O. sativa, T. aestivum INTRODUCTION (Li et al. 2014)
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  Słota M., 2015 MagneticResonance Imaging (MRI)/ Nuclear Magnetic Resonance (NMR) ▪ imaging technique used in radiology to investigate the anatomy and physiology of the living organisms, ▪ MRI scanner is actually a long coil of superconducting wire (magnet) and RF (Radio frequency) transmitters that create localized electromagnetic fields, which push some of these protons out of alignment. When the radio transmitters are turned off the displaced protons flip back into alignment, generating a radio signal that is picked up. IMAGING TECHNIQUES An image from Damadian's MRI Patent (1974). 1) The magnetic field is used to align hydrogen protons in the body. 2) Radio frequency waves are absorbed by the protons and then emitted as a signal. 3) A radio frequency coil (transceiver) picks up the signal and transmits it to the computer. The computer processes the data and an image is generated. [http://www.bangscience.org/]
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  Słota M., 2015 x-rayTomography/ Micro–Computed Tomography (microCT) ▪ non-destructive imaging technique that uses x-rays to provide three- dimensional images of the internal structure of an object, ▪ There are two types of imaging setups: 1) X-ray source and detector can be stationary during the scan while the sample/animal rotates. 2) clinical CT scanner, where the sample is stationary in space while the X-ray tube and detector rotate around. ▪ The gray levels in a CT slice image correspond to X-ray attenuation, which reflects the proportion of X-rays scattered or absorbed as they pass through each voxel (volume element). IMAGING TECHNIQUES [www.mayo.edu/] « Schematic diagram of a micro-CT scanner. The specimen is mounted on a rotating stage and is illuminated by a X-ray beam.
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  Słota M., 2015 PositronEmission Tomography (PET) ▪ functional imaging technique that produces a 3D image of functional processes in the living organism, ▪ the system detects pairs of gamma rays emitted indirectly by a positron- emitting radionuclide (tracer), ▪ tracer with a short-lived positron-emitting radionuclide of carbon, oxygen, nitrogen, or fluorine is injected into the living organism. The activity of such a compound is measured throughout the target organs by detectors. IMAGING TECHNIQUES [www.medchem.web.ne.kr/] « Schematic illustration of an annihilation reaction (A) and the subsequent coincidence detection (B).
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  Słota M., 2015 PositronEmission Tomography (PET) IMAGING TECHNIQUES (Hubeau and Steppe 2015) Overview of the most commonly used short-lived positron-emitting radionuclides in biological research. a- Half-life of the radionuclides. b- Distance which the emitted positron travels on average in water before annihilating with an electron. This is an important factor in determining the resolution of PET. Radio- nuclide t1/2 (min)a Mean travel distance in water (mm)b 11C 20.4 1.1 13N 9.96 1.5 15O 2.03 2.5 18F 109.8 0.6
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  Słota M., 2015 (a)NMR image of a Hordeum vulgare plant grown in a pot with a volume of 1.3 L for 44 days. Roots in the inner 50% of the soil volume are colour-coded yellow, roots in the outer 50% blue (b) Idem for a Beta vulgaris plant 48 days after sowing. The developing storage root is colour-coded red. (Poorter et al. 2012) APPLICATION IN RESEARCH NMR: ’Pot size matters’ NMR image
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  Słota M., 2015 (Pietruschkael al. 2012) APPLICATION IN RESEARCH Combining MRI and PET data Coregistration of MRI and PET data workflow.
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  Słota M., 2015APPLICATIONIN RESEARCH Combining the NMR and PET data Roots of a maize plant growing in soil visualized by co-registered MRI–PET images consecutively obtained on days 16 and 17 after sowing, respectively [b-c]. Data for a second maize plant growing in sand [d-g]. Temporal profiles of 11C radioactivity of the tip of root in ROIs shown in (d) and (g) [f-h]. (Jahnke et al. 2009)
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  Słota M., 2015 Wheatcv. Gregory with even supply of phosphate (left) compared with a patch of phosphate applied at 8 μM between the blue beads (right). » (Flavel et al. 2012) Values followed by the same superscript letter within a column are not significantly different (P > 0.05). LSD, least significant difference. APPLICATION IN RESEARCH MICROCT: P metabolism
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  Słota M., 2015 Ptreatment Root length [mm] Micro-CT (diameter ∼250 μm) WinRhizo (diameter >280 μm) Control 2860a 3120a Diffuse 2960a 4230a,b Banded 3580a 4570b LSD 1067 1152 Comparison of root-length measurements of wheat plants obtained using micro-CT and WinRhizo.» Comparison of root-length measurements of wheat plants obtained using micro-CT and WinRhizo. (Flavel et al. 2012) Values followed by the same superscript letter within a column are not significantly different (P > 0.05). LSD, least significant difference. APPLICATION IN RESEARCH MICROCT: P metabolism »
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  Słota M., 2015APPLICATIONIN RESEARCH MICROCT: hydropatterning of root development MicroCT-generated images of maize seed- lings grown through a macropore of air (I and K) or a continuous volume of soil (J). Root tissue is false-colored in white, and soil is false-colored in brown. (Bao et al. 2014)
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  Słota M., 2015 MRIand CT images of a bean root system in a medium soil filled pot. The root system segmented from the same CT image (b) as in on a voxel size of 56 × 56 × 56 μm3. Shows the same root system imaged one day later with MRI (c) and a voxel size of 333 × 333 × 1000 μm3 with the last value representing the vertical dimension. » Root traits calculated from CT and MRI root images of the volumes. Small pots (I.D. 34 mm) Medium pots (I.D. 56) Large pots (I.D. 81) Measurement modality CT MRI Win- RHIZO CT MRI Win- RHIZO CT MRI Total root length [mm] 2775 2910 4012 2787 4602 4855 6632 10496 Percent root length of WinRHIZO [%] 69 73 57 95 APPLICATION IN RESEARCH MICROCT and MRI comparison »
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  ▪ High costs($$$). ▪ Low throughput. ▪ Labour-intensive (data analysis). ▪ It requires to establishspecialized facilities Słota M., 2015SUMMARY What are the pros and cons? ▪ High precision (up to <10µm). ▪ Acquiring a 3D root architecture of a soil-grown plant. ▪ Wide range of applications. (2-Tesla MRI at Forschungszentrum Jülich)
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  Słota M., 2015 (Downieet al. 2014) SUMMARY What are the other applications? Applicability of imaging techniques to root:rhizosphere interactions (x, low usage to xxx, highly suitable) Current research topics: ▪ Impact of compaction on roots. ▪ Visualization of water distribution in bulk and rhizosphere soils. ▪ Root interaction with fertilizer granules. ▪ Effect of intercroping on root system architectures.
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  Słota M., 2015 (Nagelel al. 2012, FZJ Jülich) SUMMARY Non-invasive imaging – is there a proxy? Correlation of visible root length with root biomass.
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  Słota M., 2015SUMMARY Non-invasiveimaging – is there a proxy? VS. VolumeGraphics rendering WinRHIZO Volume [mm2] 102,01 121,5 Area [mm2] 1148,67 1320,65 Convex Hull Volume [mm3] 45759,4 - Depth [mm] 79,38 - Width [mm] 50,1811 -
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  Slota M., 2015 LITERATURE Bao,Y., Aggarwal, P., Robbins, N. E., Sturrock, C. J., Thompson, M. C., Tan, H. Q., & Dinneny, J. R. (2014). Plant roots use a patterning mechanism to position lateral root branches toward available water. Proceedings of the National Academy of Sciences, 111(25), 9319-9324. Fiorani, F., Rascher, U., Jahnke, S., & Schurr, U. (2012). Imaging plants dynamics in heterogenic environments. Current opinion in biotechnology, 23(2), 227-235. Flavel, R. J., Guppy, C. N., Tighe, M., Watt, M., McNeill, A., & Young, I. M. (2012). Non- destructive quantification of cereal roots in soil using high-resolution X-ray tomography. Journal of Experimental Botany, err421. Jahnke, S., Menzel, M. I., Van Dusschoten, D., Roeb, G. W., Bühler, J., Minwuyelet, S., & Schurr, U. (2009). Combined MRI–PET dissects dynamic changes in plant structures and functions. The Plant Journal, 59(4), 634-644. Hubeau, M., & Steppe, K. (2015). Plant-PET Scans: In Vivo Mapping of Xylem and Phloem Functioning. Trends in plant science, 20(10), 676-685 Li, L., Zhang, Q., & Huang, D. (2014). A review of imaging techniques for plant phenotyping. Sensors, 14(11), 20078-20111 Nagel KA Putz A Gilmer F et al . 2012. GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons. Functional Plant Biology 39, 891–904. Poorter, H., Bühler, J., van Dusschoten, D., Climent, J., & Postma, J. A. (2012). Pot size matters: a meta-analysis of the effects of rooting volume on plant growth. Functional Plant Biology, 39(11), 839-850.