Skip to main content

3D Quantification of Plant Root Architecture In Situ

  • Chapter
  • First Online:
Book cover Measuring Roots

Abstract

Root systems play important roles in plant nutrient and water uptake. The spatial distribution and structure of root systems can affect many physiological functions, carbon distribution, and plant anchorage. The accurate measurement of root systems is necessary for better understanding of plant growth and responses to biotic and abiotic stress. Due to their underground growth habitat, root systems are usually excavated from the soil before root measurements are taken. This process can destroy the root system architecture and result in the lose of fine root structures, and consequently, many devices and technologies have been developed to nondestructively capture and measure root systems in situ in 2D or 3D, such as WinRhizo, minirhizotrons, X-ray computed tomography, and magnetic resonance imaging.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abramoff M, Magelhaes P, Ram S (2004) Image processing with image. J Biophotonics Int 11:36–42

    Google Scholar 

  • Al-Ghazi Y, Muller B, Pinloche S, Tranbarger TJ, Nacry P, Rossignol M, Tardieu F, Doumas P (2003) Temporal responses of Arabidopsis root architecture to phosphate starvation: evidence for the involvement of auxin signaling. Plant Cell Environ 26:1053–1066

    Article  CAS  Google Scholar 

  • Ao J, Fu J, Tian J, Yan XL, Liao H (2010) Genetic variability for root morph-architecture traits and root growth dynamics as related to phosphorus efficiency in soybean. Funct Plant Biol 37:304–312

    Article  Google Scholar 

  • Armengaud P, Zambaux K, Hills A, Sulpice R, Pattison JR, Blatt RM, Amtmann A (2009) EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture. Plant J 57:945–956

    Article  PubMed  CAS  Google Scholar 

  • Arsenault JL, Pouleur S, Messier C, Guay R (1995) WinRHIZ O, a root-measuring system with a unique overlap correction method. Hort Sci 30:906

    Google Scholar 

  • Atger C, Edelin C (1994) Premières données sur l’architecture comparée des systèmes racinaires et caulinaires. Can J Bot 72:963–975

    Article  Google Scholar 

  • Bailey PHJ, Currey JD, Fitter AH (2002) The role of root system architecture and root hairs in promoting anchorage against uprooting forces in Allium cepa and root mutants of Arabidopsis thaliana. J Exp Bot 53:333–340

    Article  PubMed  CAS  Google Scholar 

  • Barber SA (1995) Soil nutrient bioavailability: a mechanistic approach. Wiley-Interscience, New York

    Google Scholar 

  • Barthelemy D, Caraglio Y (2007) Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny. Ann Bot 99:375–407

    Article  PubMed  Google Scholar 

  • Barton CVM, Montagu KD (2004) Detection of tree roots and determination of root diameter by ground penetrating radar under optimal conditions. Tree Physiol 24:1323–1331

    Article  PubMed  Google Scholar 

  • Bates GH (1937) A device for the observation of root growth in the soil. Nature 139:966–967

    Article  Google Scholar 

  • Bidel LPR, Pages L, Riviere LM, Pelloux G, Lorendeau JY (2000) MassFlowDyn I: A carbon transport and partitioning model for root system architecture. Ann Bot 85:869–886

    Article  CAS  Google Scholar 

  • Bonser AM, Lynch JP, Snapp S (1996) Effect of phosphorus deficiency on growth angle of basal roots of Phaseolus vulgaris L. New Phytol 132:281–288

    Article  PubMed  CAS  Google Scholar 

  • Bowman DC, Devitt DA, Engelke MC, Rufty TW (1998) Root architecture affects nitrate leaching from bentgrass turf. Crop Sci 38:1633–1639

    Article  Google Scholar 

  • Butnor JR, Doolittle JA, Kress L, Cohen S, Johnsen KH (2001) Use of ground-penetrating radar to study tree roots in the southeastern United States. Tree Physiol 21:1269–1278

    Article  PubMed  CAS  Google Scholar 

  • Cermak J, Hruska J, Martinkova M, Prax A (2000) City tree roots and survival near houses analyzed using sap flow and ground penetrating radar technique. Plant Soil 219:103–116

    Article  CAS  Google Scholar 

  • Cho ZH, Son YD, Kim HK, Kim KN, Oh SH, Han JY, Kim YB (2008) A fusion PET–MRI system with high-resolution research tomograph-PET and ultra-high field 7.0T-MRI for the molecular-genetic imaging of the brain. Proteomics 8:1302–1323

    Article  PubMed  CAS  Google Scholar 

  • Cichy KA, Snapp SS, Kirk WW (2007) Fusarium root rot incidence and root system architecture in grafted common bean lines. Plant Soil 300:233–244

    Article  CAS  Google Scholar 

  • Coll L, Potvin C, Messier C, Delagrange S (2008) Root architecture and allocation patterns of eight native tropical species with different successional status used in open-grown mixed plantations in Panama. Trees Struct Funct 22:585–596

    Article  Google Scholar 

  • Cox KD, Scherm H, Serman N (2005) Ground-penetrating radar to detect and quantify residual root fragments following peach orchard cleaning. Hort Technol 15:600–607

    Google Scholar 

  • Danjon F, Reubens B (2008) Assessing and analyzing 3D architecture of woody root systems, a review of methods and applications in tree and soil stability, resource acquisition and allocation. Plant Soil 303:1–34

    Article  CAS  Google Scholar 

  • Danjon F, Bert D, Godin C, Trichet P (1999a) Structural root architecture of 5-year-old Pinus pinaster measured by 3D digitizing and analyzed with AMAPmod. Plant Soil 217:49–63

    Article  Google Scholar 

  • Danjon F, Sinoquet H, Godin C, Colin F, Drexhage M (1999b) Characterization of structural tree root architecture using 3D digitizing and AMAPmod software. Plant Soil 211:241–258

    Article  CAS  Google Scholar 

  • Danjon F, Fourcaud T, Bert D (2005) Root architecture and windfirmness of mature Pinus pinaster. New Phytol 168:387–400

    Article  PubMed  Google Scholar 

  • Danjon F, Barker DH, Drexhage M, Stokes A (2008) Using three-dimensional plant root architecture in models of shallow-slope stability. Ann Bot 101:1281–1293

    Article  PubMed  Google Scholar 

  • Dannoura M, Hirano Y, Igarashi T, Ishii M, Aono K, Yamase K, Kanazawa Y (2008) Detection of cryptomeria japonica roots with ground penetrating radar. plant biosystems – an international journal dealing with all aspects of plant biology. Official J Soc Bot Ital 142:375–380

    Google Scholar 

  • de Reffye P (1979) Modélisation de l’architecture des arbres par des processus stochastiques. Simulation spatiale des modèles tropicaux sous l’effet de la pesanteur. Application au Coffea robusta. Thèse de doctorat d’Etat. Université de Paris-Sud Orsay, pp 194

    Google Scholar 

  • Di Iorio A, Lasserre B, Scippa GS, Chiatante D (2005) Root system architecture of Quercus pubescens trees growing on different sloping conditions. Ann Bot 95:351–361

    Article  PubMed  Google Scholar 

  • Doi K (2006) Diagnostic imaging over the last 50 years: research and development in medical imaging science and technology. Phys Med Biol 51:5–27

    Article  Google Scholar 

  • Doolittle JA (1987) Using ground-penetrating radar to increase the quality and efficiency of soil surveys. In: Reybold WU, Peterson GW (eds) Soil survey techniques, SSSA special publication No. 20. Soil Science Society of America, Madison, WI

    Google Scholar 

  • Doussan C, Pages L, Vercambre G (1998) Modelling of the hydraulic architecture of root systems: an integrated approach to water absorption – model description. Ann Bot 81:213–223

    Article  Google Scholar 

  • Drexhage M, Chauvière M, Colin F, Nielsen CNN (1999) Development of structural root architecture and allometry of Quercus petraea. Can J For Res 29:600–608

    Article  Google Scholar 

  • Evers JB, Vos J, Fournier C, et al (2005) Towards a generic architectural model of tillering in Gramineae, as exemplified by spring wheat (Triticum aestivum). New Phytologist 166(3):801–812

    Article  PubMed  Google Scholar 

  • Fang S, Yan X, Liao H (2009) 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research. Plant J 60:1096–1108

    Article  PubMed  CAS  Google Scholar 

  • Fisher JB, Honda H (1979) Branch geometry and effective leaf area: a study of Terminalia branching pattern. 2 Survey of real trees. Am J Bot 66:645–655

    Article  Google Scholar 

  • Fitter AH (1991) Characteristics and functions of root systems. In: Wisel Y, Eshel A, and Kafkafi U (eds) Plant roots: The Hidden Half. Marcel Dekker, Inc, New York, Basel, Hongkong, pp 3–24

    Google Scholar 

  • Fitter AH, Stickland TR (1991) Architectural analysis of plant-root systems 2. Influence of nutrient supply on architecture in contrasting plant-species. New Phytol 118:383–389

    Article  Google Scholar 

  • Fitter AH, Stickland TR, Harvey ML, Wilson GW (1991) Architectural analysis of plant-root systems 1. Architectural correlates of exploitation efficiency. New Phytol 118:375–382

    Article  Google Scholar 

  • Fitter AH, Self GK, Brown TK, Bogie DS, Graves JD, Benham D, Ineson P (1999) Root production and turnover in an upland grassland subjected to artificial soil warming respond to radiation flux and nutrients, not temperature. Oecologia 120:575–581

    Article  Google Scholar 

  • French A, Ubeda-Tomas S, Holman TJ, Bennett MJ, Pridmore T (2009) High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol 150:1784–1795

    Article  PubMed  CAS  Google Scholar 

  • Gärtner H, Denier C (2006) Application of a 3D Laser scanning device to acquire the structure of whole root systems- A pilot study. In: Heinrich I, Gärtner H, Monbaron M, Schleser G (eds) TRACE – tree rings in archaeology. Climatology and Ecology Association for Tree-Ring Research, Tervuren, pp 288–294

    Google Scholar 

  • Gärtner H, Wagner B, Heinrich I, Denier C (2009) 3D laser scanning-a new methodology to analyze coarse tree root systems. For Snow Landsc Res 82:95–106

    Google Scholar 

  • Godin C (2000) Representing and encoding plant architecture: a review. Ann For Sci 57:413–438

    Article  Google Scholar 

  • Godin C, Costes E, Sinoquet H (1999) A method for describing plant architecture which integrates topology and geometry. Ann Bot 84:343–357

    Article  Google Scholar 

  • Godin C, Costes E, Sinoquet H (2005) Plant architecture modelling: virtual plants and complex systems. In: Turnbull CGN (ed) Plant architecture and its manipulation. Blackwell, Oxford, pp 238–287

    Google Scholar 

  • Gregory PJ (2006) Plant roots: growth, activity and interaction with soils. Blackwell, Oxford

    Google Scholar 

  • Gregory PJ, Hutchison DJ, Read DB, Jenneson PM, Gilboy WB, Morton EJ (2003) Non-invasive imaging of roots with high resolution X-ray micro-tomography. Plant Soil 255:351–359

    Article  CAS  Google Scholar 

  • Guo D, Mitchell R, Hendricks J (2004) Fine root branch orders respond differentially to carbon source-sink manipulations in a longleaf pine forest. Oecologia 140:450–457

    Article  PubMed  Google Scholar 

  • Guo D, Li H, Mitchell RJ, Han W, Hendricks JJ, Fahey TJ, Hendrick RL (2008) Fine root heterogeneity by branch order: exploring the discrepancy in root turnover estimates between minirhizotron and carbon isotopic methods. New Phytol 177:443–456

    Article  PubMed  Google Scholar 

  • Hagrey SA (2007) Geophysical imaging of root-zone, trunk, and moisture heterogeneity. J Exp Bot 58:839–854

    Article  Google Scholar 

  • Hallé F, Oldemann RAA (1970) Essai sur l’architecture et la dynamique de croissance des arbres tropicaux. Masson, Paris, p 178

    Google Scholar 

  • Heeraman DA, Hopmans JW, Clausnitzer V (1997) Three dimensional imaging of plant roots in situ with X-ray computed tomography. Plant Soil 189:167–179

    CAS  Google Scholar 

  • Hendrick RL, Pregitzer KS (1993) Patterns of fine root mortality in two sugar maple forests. Nature 361:59–61

    Article  Google Scholar 

  • Hendrick RL, Pregitzer KS (1996) Temporal and depth-related patters of fine root dynamics in northern hardwood forests. J Ecol 84:167–176

    Article  Google Scholar 

  • Hruska J, Cermak J, Sustek S (1999) Mapping of tree root systems by means of the ground penetrating radar. Tree Physiol 19:125–130

    Article  PubMed  Google Scholar 

  • Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Benfey PN (2010) Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol 152:1148–1157

    Article  PubMed  CAS  Google Scholar 

  • Jahnke S, Menzel MI, Van Dusschoten D, Roeb GW, Bühler J, Minwuyelet S, Blümler P, Temperton VM, Hombach T, Streun M (2009) Combined MRI–PET dissects dynamic changes in plant structures and functions. Plant J 59:634–644

    Article  PubMed  CAS  Google Scholar 

  • Johnson MG, Tingey DT, Phillips DL, Storm MJ (2001) Advancing fine root research with minirhizotrons. Environ Exp Bot 45:263–289

    Article  PubMed  Google Scholar 

  • Joslin JD, Wolfe MH (1999) Disturbances during minirhizotron installation can affect root observation data. Soil Sci Soc Am J 63:218–221

    Article  CAS  Google Scholar 

  • Kaestner A, Schneebeli M, Graf F (2006) Visualizing three dimensional root networks using computed tomography. Geoderma 136:459–469

    Article  Google Scholar 

  • Köckenberger W, De Panfilis C, Santoro D, Dahiya P, Rawsthorne S (2004) High resolution NMR microscopy of plants and fungi. J Microsc 214:182–189

    Article  PubMed  Google Scholar 

  • Kosola KR, Eissenstat DM, Grahm JH (1995) Root demography of mature citrus trees: the influence of Phytophthora nicotianae. Plant Soil 171:283–288

    Article  CAS  Google Scholar 

  • Lambers H, Shane MW, Cramer MD, Pearse SJ, Veneklaas EJ (2006) Root structure and functioning for efficient acquisition of phosphorus: matching morphological and physiological traits. Ann Bot 98:693–713

    Article  PubMed  Google Scholar 

  • Lang ARG (1973) Leaf orientation of a cotton plant. Agric Meteorol 11:37–51

    Article  Google Scholar 

  • Liao H, Ge Z, Yan XL (2001) Ideal root architecture for phosphorus acquisition of plants under water and phosphorus coupled stresses: from simulation to application. Chin Sci Bull 46:1346–1351

    Article  CAS  Google Scholar 

  • Lontoc-Roy M, Dutilleul P, Prasher SO, Han LW, Brouillet T, Smith DL (2006) Advances in the acquisition and analysis of CT scan data to isolate a crop root system from the soil medium and quantify root system complexity in 3-D space. Geoderma 137:231–241

    Article  Google Scholar 

  • Lynch J (1995) Root architecture and plant productivity. Plant Physiol 109:7–13

    PubMed  CAS  Google Scholar 

  • MacFall JS, Johnson GA (1996) Plants, seeds and roots as applications for magnetic resonance imaging. In: Grant DM, Harris RK (eds) Encyclopedia of nuclear magnetic resonance. Wiley, London, pp 3633–3640

    Google Scholar 

  • MacFall JS (1997) Visualization of root growth and development through magnetic resonance imaging. In: Flores HE, Lynch JP, Eissenstat D (eds) Radical Biology: Advances and Perspectives on the Function of Plant Roots. American Society of Plant Physiologists, Rockville, MD, pp 57–80

    Google Scholar 

  • Mahesh M (2002) The AAPM/RSNA physics tutorial for residents: search for isotropic resolution in CT from conventional through multiple-row detector. RadioGraphics 22:949–962

    PubMed  Google Scholar 

  • Matusik W, Buehler C, Raskar R (2000) Image-based visual hulls. Sig-Graph, New Orleans, LA, pp 369–374

    Google Scholar 

  • Miller DE (1986) Root systems in relation to stress tolerance. Hortscience 21:963–970

    Google Scholar 

  • Miller TW, Hendrickx JMH, Borchers B (2004) Radar detection of buried landmines in field soils. Vod Zone J 3:1116–1127

    Google Scholar 

  • Oppelt AL, Kurth W, Dzierzon H, Jentschke G, Godbold DL (2000) Structure and fractal dimensions of root systems of four co-occurring fruit tree species from Botswana. Ann For Sci 57:463–475

    Article  Google Scholar 

  • Perret JS, Al-Belushi ME, Deadman M (2007) Non-destructive visualization and quantification of roots using computed tomography. Soil Biol Biochem 39:391–399

    Article  CAS  Google Scholar 

  • Petzold B, Reiss P, Stössel W (1999) Laser scanning surveying and mapping agencies are using a new technique for the derivation of digital terrain models. ISPRS J Photogramm Remote Sens 54:95–104

    Article  Google Scholar 

  • Phillips DL, Johnson MG, Tingey DT, Biggart C, Nowak RS, Newsom JC (2000) Minirhizotron installation in sandy, rocky soils with minimal soil disturbance. Soil Sci Soc Am J 64:761–764

    Article  CAS  Google Scholar 

  • Pierret A, Capowiez Y, Belzunces L, Moran CJ (2002) 3D reconstruction and quantification of macropores using X-ray computed tomography and image analysis. Geoderma 106:247–271

    Article  Google Scholar 

  • Rakocevic M, Sinoquet H, Christophe A, et al (2000) Assessing the geometric structure of a white clover (Trifolium repens L.) canopy using 3-D digitising. Annals of Botany 86(3):519–526

    Google Scholar 

  • Reubens B, Poesen J, Danjon F, Geudens G, Muys B (2007) The role of fine and coarse roots in shallow slope stability and soil erosion control with a focus on root system architecture: a review. Trees 21:385–402

    Article  Google Scholar 

  • Reynolds JF, Virginia RA, Kemp PR, De Soyza AG, Tremmel DC (1999) Impact of drought on desert shrubs: effects of seasonality and degree of resource island development. Ecol Monogr 69:69–106

    Article  Google Scholar 

  • Samson BK, Sinclair TR (1994) Soil core and minirhizotron comparison for the determination of root length density. Plant Soil 161:225–232

    Article  Google Scholar 

  • Seitz SM, Dyer CR (1995) Complete scene structure from four point correspondences. In: IEEE (ed) Proceedings of the fifth international conference on computer vision. IEEE Computer Society Press, Cambridge, pp 330–337

    Google Scholar 

  • Sinoquet H, Rivet P (1997) Measurement and visualization of the architecture of an adult tree based on a three-dimensional digitising device. Trees Struct Funct 11:265–270

    Article  Google Scholar 

  • Sinoquet H, Rivet P, Godin C (1997) Assessment of the three-dimensional architecture of walnut trees using digitising. Silva Fenn 31:265–273

    Google Scholar 

  • Skaggs TH, Shouse PJ (2008) Roots and root function: introduction. Vadose Zone J 7:1008–1009

    Article  Google Scholar 

  • Snapp S, Kirk W, Roman-Aviles B, Kelly J (2003) Root traits play a role in integrated management of Fusarium root rot in snap beans. Hortscience 38:187–191

    Google Scholar 

  • Stokes A, Fourcaud T, Hruska J, Cermak J, Nadyezdhina N, Nadyezhdin V, Praus L (2002) An evaluation of different methods to investigate root system architecture of urban trees in situ: 1. Ground-penetrating radar. J Arboric 28:2–10

    Google Scholar 

  • Strand AE, Pritchard SG, McCormack ML, Davis MA, Oren R (2008) Irreconcilable differences: fine-root life spans and soil carbon persistence. Science 319:456–458

    Article  PubMed  CAS  Google Scholar 

  • Sustek S, Hruska J, Druckmuller M, Michalek T (1999) Root surfaces in the large oak tree estimated by image analysis of the map obtained by the ground penetrating radar. J For Sci 45:139–143

    Google Scholar 

  • Tingey DT, McVeety BD, Waschmann R, Johnson MG, Phillips DL, Rygiewicz PT, Olszyk DM (1996) A versatile sun-lit controlled-environment facility for studying plant and soil processes. J Environ Qual 25:614–625

    Article  CAS  Google Scholar 

  • Tracy SR, Roberts JA, Black CR, McNeill A, Davidson R, Mooney SJ (2010) The X-factor: visualizing undisturbed root architecture in soils using X-ray computed tomography. J Exp Bot 61:311–313

    Article  PubMed  CAS  Google Scholar 

  • van der Heijden GWAM, de Visser PHB, Heuvelink E (2007) Measurements for functional-structural plant models. In: Vos J, Marcelis LFM, de Visser PHB, Struik PC, Evers JB (eds) Functional-structural plant modeling in crop production, vol 22, Wageningen UR Frontis Series. Springer, Berlin, pp 13–25

    Chapter  Google Scholar 

  • van der Weerd L, Claessens MM, Ruttink T, Vergeldt FJ, Schaafsma TJ, Van As H (2001) Quantitative NMR microscopy of osmotic stress responses in maize and pearl millet. J Exp Bot 52:2333–2343

    Article  PubMed  Google Scholar 

  • van Noordwijk M, de Jager A, Floris J (1985) A new dimension to observations in minirhizotrons: a stereoscopic view on root photographs. Plant Soil 86:447–453

    Article  Google Scholar 

  • Wagner B, Gärtner H, Ingensand H, Santini S (2010) Incorporating 2D tree-ring data in 3D laser scans of coarse-root systems. Plant Soil 334:175–187

    Article  CAS  Google Scholar 

  • Watanabe T, Hanan JS, Room PM, Hasegawa T, Nakagawa H, Takahashi W (2005) Rice morphogenesis and plant architecture: measurement, specification and the reconstruction of structural development by 3D architectural modeling. Ann Bot 95:1131–1143

    Article  PubMed  Google Scholar 

  • Wells CE, Eissenstat DM (2001) Marked differences in survivorship among apple roots of different diameters. Ecology 82:882–892

    Article  Google Scholar 

  • Zhou XC, Luo XW (2009) Advances in Non-Destructive Measurement and 3D Visualization Methods for Plant Root Based on Machine Vision. In Proceedings of the 2nd International Conference on BioMedical Engineering and Informatics. Tianjin, BMEI’09, pp 1–5

    Google Scholar 

  • Zhu XX (2000) Free curves and surfaces modeling technology (in Chinese). Science Press, Beijing, pp 138–169

    Google Scholar 

  • Zhu TL, Fang SQ, Li ZY, Yan X (2005) A generalized Hough transform template and its applications in computer vision. J Comput Inform Syst 1:601–607

    Google Scholar 

  • Zhu TL, Fang SQ, Li ZY, Liu Y, Liao H, Yan X (2006) Quantitative analysis of 3-dimensional root architecture based on image reconstruction and its application to research on phosphorus uptake in soybean. Chin Sci Bull 51:2351–2361

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hong Liao .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Fang, S., Clark, R., Liao, H. (2012). 3D Quantification of Plant Root Architecture In Situ. In: Mancuso, S. (eds) Measuring Roots. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-22067-8_9

Download citation

Publish with us

Policies and ethics