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Phenotyping for Root Traits

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Phenomics in Crop Plants: Trends, Options and Limitations

Abstract

Root system architecture determines crop capacity to acquire water and nutrients in the dynamic and variable soil environment. Increasing attention is paid to searching for optimal root traits to improve resource uptake efficiency and adaptation to heterogeneous soil conditions. This chapter summarises genetic variability and plasticity in root traits relevant to increased efficiency of soil resource acquisition. Approaches available for high-throughput phenotyping of root architecture traits at both laboratory and field scales are critically assessed. The advent of several novel imaging technologies such as X-ray computed tomography coupled with image-analysing software packages offers a great opportunity to non-invasively assess root architecture and its interactions with soil environments. The use of three-dimensional structure–function simulation root models is complementary to phenotyping methods, providing assistance in the crop breeding programmes. We also discuss applications and limitations of these novel visualisation technologies in characterising root growth and the root–soil interactions.

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References

  • Achat DL, Trichet P, Bakker MR (2008) Rooting patterns and fine root biomass of Pinus pinaster assessed by trench wall and core methods. J For Res 13:165–175

    Google Scholar 

  • Ao J, Yan X, Liao H, Fu J, Tian J (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

    Google Scholar 

  • Araki H, Iijima M (1998) Rooting nodes of deep roots in rice and maize grown in a long tube. Plant Prod Sci 1:242–247

    Google Scholar 

  • Araki H, Hirayama M, Hirasawa H, Iijima M (2000) Which roots penetrate the deepest in rice and maize root systems? Plant Prod Sci 3:281–288

    Google Scholar 

  • Aravena JE, Berli M, Menon M, Ghezzehei TA, Mandava AK, Regentova EE, Pillai NS, Steude J, Young MH, Nico PS, Tyler SW (2013) Synchrotron X–ray microtomography – new means to quantify root induced changes of rhizosphere physical properties. In: Anderson SH, Hopmans JW (eds) Soil–water–root processes: advances in tomography and imaging, pp 39–67

    Google Scholar 

  • Armengaud P (2009) EZ–Rhizo software. Plant Signal Behav 4:139–141

    PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Arsenault JL, Poulcur S, Messier C, Guay R (1995) WinRHIZOâ„¢, a root–measuring system with a unique overlap correction method. HortSci 30:906–906

    Google Scholar 

  • Asseng S, Aylmore LAG, MacFall JS, Hopmans JW, Gregory PJ (2000) Computer–assisted tomography and magnetic resonance imaging. In: Smit AL, Bengough AG, Engels C, van Noordwijk M, Pellerin S, van de Geijn SC (eds) Root methods: a handbook. Springer, Berlin/Heidelberg, pp 343–363

    Google Scholar 

  • Baddeley JA, Bingham IJ, Hoad SP (2007) Development of cereal root systems for sustainable agriculture. In: ØstergÃ¥rd H, Backes G, Kovács G (eds) Varietal characteristics of cereals in different growing systems with special emphasis on below ground traits. Velence, Hungary, pp 9–13

    Google Scholar 

  • Basu P, Pal A (2012) A new tool for analysis of root growth in the spatio–temporal continuum. New Phytol 195:264–274

    PubMed  Google Scholar 

  • Basu P, PalA LJP, Brown KM (2007) A novel image–analysis technique for kinematic study of growth and curvature. Plant Physiol 145:305–316

    PubMed Central  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Beebe SE, Rojas–Pierce M, Yan X, Blair MW, Pedraza F, Muñoz F, Tohme J, Lynch JP (2006) Quantitative trait loci for root architecture traits correlated with phosphorus acquisition in common bean. Crop Sci 46:413–423

    CAS  Google Scholar 

  • Bengough AG, Gordon DC, Al-Menaie H, Ellis RP, Allan D, Keith R, Thomas WTB, Forster BP (2004) Gel observation chamber for rapid screening of root traits in cereal seedlings. Plant Soil 262:63–70

    CAS  Google Scholar 

  • Bingham IJ, Wu L (2011) Simulation of wheat growth using the 3D root architecture model SPACSYS: validation and sensitivity analysis. Europ J Agron 34:181–189

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Carminati A, Vetterlein D, Weller U, Vogel HJ, Oswald SE (2009) When roots lose contact. Vadose Zone J 8:805–809

    Google Scholar 

  • Carvalho IS, Ricardo CP, Chaves M (2004) Quality and distribution of assimilates within the whole plant of lupines (L. albus and L. mutabilis) influenced by water stress. J Agron Crop Sci 190:205–210

    Google Scholar 

  • Chen YL, Dunbabin VM, Diggle AJ, Siddique KHM, Rengel Z (2011a) Development of a novel semi-hydroponic phenotyping system for studying root architecture. Funct Plant Biol 38:355–363

    Google Scholar 

  • Chen YL, Dunbabin VM, Postma J, Diggle AJ, Palta JA, Lynch JP, Siddique KHM, Rengel Z (2011b) Phenotypic variability and modelling of root structure of wild Lupinus angustifolius genotypes. Plant Soil 348:345–364

    CAS  Google Scholar 

  • Chen YL, Dunbabin VM, Diggle AJ, Siddique KHM, Rengel Z (2012) Assessing variability in root parameters of wild Lupinus angustifolius germplasm: basis for modelling root system structure. Plant Soil 354:141–155

    CAS  Google Scholar 

  • Chen YL, Dunbabin VM, Diggle AJ, Siddique KHM, Rengel Z (2013a) Phosphorus starvation boosts carboxylate secretion in P-deficient genotypes of Lupinus angustifolius with contrasting root structure. Crop Pasture Sci 64:588–599

    CAS  Google Scholar 

  • Chen YL, Dunbabin VM, Postma JA, Diggle AJ, Siddique KHM, Rengel Z (2013b) Modelling root plasticity and response of narrow-leafed lupin to heterogeneous phosphorus supply. Plant Soil 372:319–337

    CAS  Google Scholar 

  • Chen YL, Palta J, Clements J, Buirchell B, Siddique KHM, Rengel Z (2014) Root architecture alteration of narrow-leafed lupin and wheat in response to soil compaction. Field Crops Res 165:61–70

    Google Scholar 

  • Clark LJ, Whalley WR, Leigh RA, Dexter AR, Barraclough PB (1999) Evaluation of agar and agarose gels for studying mechanical impedance in rice roots. Plant Soil 207:37–43

    Google Scholar 

  • Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV (2011) Three–dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 156:455–465

    PubMed Central  CAS  PubMed  Google Scholar 

  • Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, Mccouch SR, Aneshansley DJ, Kochian LV (2013) High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ 36:454–466

    CAS  PubMed  Google Scholar 

  • De Dorlodot S, Forster B, Pages L, Price A, Tuberosa R, Draye X (2007) Root system architecture: opportunities and constraints for genetic improvement of crops. Trends Plant Sci 12:474–481

    PubMed  Google Scholar 

  • Diggle AJ (1988a) ROOTMAP – a model in three–dimensional coordinates of the growth and structure of fibrous root systems. Plant Soil 105:169–178

    Google Scholar 

  • Diggle AJ (1988b) ROOTMAP: a root growth model. Maths Comp Simul 30:175–180

    Google Scholar 

  • Doussan C, Pages L, Pierret A (2003) Soil exploration and resource acquisition by plant roots: an architectural and modelling point of view. Agronomie 23:419–431

    Google Scholar 

  • Dubrovsky JG, Gambetta GA, Hernández-Barrera A, Shishkova S, González I (2006) Lateral root initiation in Arabidopsis: developmental window, spatial patterning, density and predictability. Ann Bot 97:903–915

    PubMed Central  CAS  PubMed  Google Scholar 

  • Dunbabin V, Rengel Z, Diggle A (2001a) Lupinus angustifolius has a plastic uptake response to heterogeneously supplied nitrate while Lupinus pilosus does not. Aust J Agr Res 52:505–512

    CAS  Google Scholar 

  • Dunbabin V, Rengel Z, Diggle A (2001b) The root growth response to heterogeneous nitrate supply differs for Lupinus angustifolius and Lupinus pilosus. Aust J Agr Res 52:495–503

    CAS  Google Scholar 

  • Dunbabin V, Rengel Z, Diggle A (2002a) Simulation of field data by a basic three–dimensional model of interactive root growth. Plant Soil 239:39–54

    CAS  Google Scholar 

  • Dunbabin V, Rengel Z, Diggle A, van Hugten R (2002b) Modelling the interactions between water and nutrient uptake and root growth. Plant Soil 239:19–38

    CAS  Google Scholar 

  • Dunbabin VM, McDermott S, Bengough AG (2006) Upscaling from rhizosphere to whole root system: modelling the effects of phospholipid surfactants on water and nutrient uptake. Plant Soil 283:57–72

    CAS  Google Scholar 

  • Dunbabin VM, Postma JA, Schnepf A, Pagès L, Javaux M, Wu L, Leitner D, Chen YL, Rengel Z, Diggle AJ (2013) Modelling root–soil interactions using three–dimensional models of root growth, architecture and function. Plant Soil 372:93–124

    CAS  Google Scholar 

  • Eshel A, Beeckman T (2013) Plant roots: the hidden half. CRC Press, New York

    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

    CAS  PubMed  Google Scholar 

  • Fiorani F, Schurr U (2013) Future scenarios for plant phenotyping. Ann Rev Plant Biol 64:267–291

    CAS  Google Scholar 

  • Fitter A, Williamson L, Linkohr B, Leyser O (2002) Root system architecture determines fitness in an Arabidopsis mutant in competition for immobile phosphate ions but not for nitrate ions. Proc Roy Soc B–BiolSci 269:2017–2022

    CAS  Google Scholar 

  • Flavel RJ, GuppyCN TM, Watt M, McNeill A, Young IM (2012) Non–destructive quantification of cereal roots in soil using high–resolution X–ray tomography. J Exp Bot 63:2503–2511

    CAS  PubMed  Google Scholar 

  • French A, Ubeda-Tomás 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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Futsaether CM, Oxaal U (2002) A growth chamber for idealized studies of seedling root growth dynamics and structure. Plant Soil 246:221–230

    CAS  Google Scholar 

  • Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, ToppCN I-PAS, Zurek PR, Fang S, Harer J, Benfey PN, Weitz JS (2012) GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol 12:116

    PubMed Central  PubMed  Google Scholar 

  • Garbout A, Munkholm LJ, HansenSB PBM, Munk OL, Pajor R (2012) The use of PET/CT scanning technique for 3D visualization and quantification of real–time soil/plant interactions. Plant Soil 352:113–127

    CAS  Google Scholar 

  • Gregory PJ (2008) Plant roots: growth, activity and interactions with the soil. Wiley, 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

    CAS  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

    CAS  Google Scholar 

  • Gregory PJ, Bengough AG, Grinev D, Schmidt S, Thomas WTB, Wojciechowski T, Young M (2009) Root phenomics of crops: opportunities and challenges. Funct Plant Bioly 36:922–929

    Google Scholar 

  • Hall DJM, Jones HR, Crabtree WL, Daniels TL (2010) Claying and deep ripping can increase crop yields and profits on water repellent sands with marginal fertility in southern Western Australia. Soil Res 48:178–187

    Google Scholar 

  • Hammond JP, Broadley MR, White PJ, King GJ, Bowen HC, Hayden R, Meacham MC, Mead A, Overs T, Spracklen WP, Greenwood DJ (2009) Shoot yield drives phosphorus use efficiency in Brassica oleracea and correlates with root architecture traits. J Exp Bot 60:1953–1968

    CAS  PubMed  Google Scholar 

  • Hargreaves CE, Gregory PJ, Bengough AG (2009) Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and X–ray microtomography. Plant Soil 316:285–297

    CAS  Google Scholar 

  • Hendrick RL, Pregitzer KS (1992) Spatial variation in tree root distribution and growth associated with minirhizotrons. Plant Soil 143:283–288

    Google Scholar 

  • Hinsinger P, Brauman A, DevauN GF, Jourdan C, Laclau JP, Le Cadre E, Jaillard B, Plassard C (2011) Acquisition of phosphorus and other poorly mobile nutrients by roots: where do plant nutrition models fail? Plant Soil 348:29–61

    CAS  Google Scholar 

  • Ho MD, McCannon BC, Lynch JP (2004) Optimization modeling of plant root architecture for water and phosphorus acquisition. J Theo Biol 226:331–340

    CAS  Google Scholar 

  • Ho MD, Rosas JC, Brown KM, Lynch JP (2005) Root architectural tradeoffs for water and phosphorus acquisition. Funct Plant Biol 32:737–748

    CAS  Google Scholar 

  • Hodge A (2004) The plastic plant: root responses to heterogeneous supplies of nutrients. New Phytol 162:9–24

    Google Scholar 

  • Huang CY, Kuchel H, Edwards J, Hall S, Parent B, Eckermann P, Herdina HDM, Langridge P, McKay AC (2013) A DNA–based method for studying root responses to drought in field–grown wheat genotypes. SciRep3. doi:10.1038/srep03194

    Google Scholar 

  • Hund A, Ruta N, Liedgens M (2009a) Rooting depth and water use efficiency of tropical maize inbred lines, differing in drought tolerance. Plant Soil 318:311–325

    CAS  Google Scholar 

  • Hund A, Trachsel S, Stamp P (2009b) Growth of axile and lateral roots of maize: I. Development of a phenotyping platform. Plant Soil 325:335–349

    CAS  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

    PubMed Central  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Juraniec M, Lequeux H, Hermans C, Willems G, Nordborg M, Schneeberger K, Salis P, Vromant M, Lutts S, Verbruggen N (2014) Towards the discovery of novel genetic component involved in stress resistance in Arabidopsis thaliana. New Phytol 201:810–824

    CAS  PubMed  Google Scholar 

  • Kamoshita A, Wade LJ, Yamauchi A (2000) Genotypic variation in response of rainfed lowland rice to drought and rewatering. III. Water extraction during the drought period. Plant Prod Sci 3:189–196

    Google Scholar 

  • Keyes SD, Daly KR, Gostling NJ, Jones DL, Talboys P, Pinzer BR, Boardman R, Sinclair I, Marchant A, Roose T (2013) High resolution synchrotron imaging of wheat root hairs growing in soil and image based modelling of phosphate uptake. New Phytol 198:1023–1029

    CAS  PubMed  Google Scholar 

  • Kimura K, Kikuchi S, Yamasaki SI (1999) Accurate root length measurement by image analysis. Plant Soil 216(1–2):117–127

    CAS  Google Scholar 

  • Kondo M, Murty MV, Aragones DV, Okada K, Winn T, Kwak KS (1999) Characteristics of the root system and water uptake in upland rice. In: Ito O, O’Toole J, Hardy B (eds) Genetic improvement of rice for water limited environments. International Rice Research Institute, Makati City, pp 117–131

    Google Scholar 

  • Lambers H, Brundrett MC, Raven JA, Hopper SD (2011) Plant mineral nutrition in ancient landscapes: high plant species diversity on infertile soils is linked to functional diversity for nutritional strategies. Plant Soil 348:7–27

    CAS  Google Scholar 

  • Landi P, Giuliani MM, Sanguineti MC, Albrecht B (1998) Seedling characteristics in hydroponic culture and field performance of maize genotypes with different resistance to root lodging. Maydica 43:111–116

    Google Scholar 

  • Le Bot J, Serra V, Fabre J, Draye X, Adamowicz S, Pagès L (2010) DART: a software to analyse root system architecture and development from captured images. Plant Soil 326:261–273

    Google Scholar 

  • Leitner D, Klepsch S, Knieß A, Schnepf A (2010) The algorithmic beauty of plant roots – an L-system model for dynamic root growth simulation. Math Comp Model Dyn 16:575–587

    Google Scholar 

  • Leitner D, Felderer B, Vontobel P, Schnepf A (2014) Recovering root system traits using image analysis exemplified by two–dimensional neutron radiography images of lupine. Plant Physiol 164:24–35

    PubMed Central  CAS  PubMed  Google Scholar 

  • Liao H, Yan XL, Rubio G, Beebe SE, Blair MW, Lynch JP (2004) Genetic mapping of basal root gravitropism and phosphorus acquisition efficiency in common bean. Funct Plant Biol 31:959–970

    CAS  Google Scholar 

  • Liu X, Zhang S, Shan L, Yang X, Wu A (2007) The heterosis of water uptake by single root of maize. Acta Agron Sin 33:1625–1629

    Google Scholar 

  • Lobet G, Pagès L, Draye X (2011) A novel image–analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiol 157:29–39

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lobet G, Draye X, Périlleux C (2013) An online database for plant image analysis software tools. Plant Methods 9:38

    PubMed Central  PubMed  Google Scholar 

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

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lynch JP (2007) Roots of the second green revolution. Aus J Bot 55:493–512

    Google Scholar 

  • Lynch JP, Brown KM (2012) New roots for agriculture: exploiting the root phenome. Philos Trans R Soc B 367:1598–1604

    Google Scholar 

  • Lynch JP, Brown KM (2001) Topsoil foraging – an architectural adaptation of plants to low phosphorus availability. Plant Soil 237:225–237

    CAS  Google Scholar 

  • Lynch JP, Ho MD (2005) Rhizoeconomics: carbon costs of phosphorus acquisition. Plant Soil 269:45–56

    CAS  Google Scholar 

  • Lynch JP, Nielsen KL, Davis RD, Jablokow AG (1997) SimRoot: modelling and visualization of root systems. Plant Soil 188:139–151

    CAS  Google Scholar 

  • Mairhofer S, Zappala S, Tracy SR, Sturrock C, Bennett M, Mooney SJ, Pridmore T (2012) RooTrak: automated recovery of three–dimensional plant root architecture in soil from X–ray microcomputed tomography images using visual tracking. Plant Physiol 158:561–569

    PubMed Central  CAS  PubMed  Google Scholar 

  • Malamy JE (2005) Intrinsic and environmental response pathways that regulate root system architecture. Plant Cell Environ 28:67–77

    CAS  PubMed  Google Scholar 

  • Manschadi AM, Manske GGB (2013) Root architecture and resource acquisition: wheat as a model plant. In: Eshel A, Beeckman T (eds) Plant roots–the hidden half, 4th edn. CRC Press, London

    Google Scholar 

  • Manschadi AM, Christopher J, Voil PD, Hammer GL (2006) The role of root architectural traits in adaptation of wheat to water–limited environments. Funct Plant Biol 33:823–837

    CAS  Google Scholar 

  • Manschadi AM, Hammer GL, Christopher JT, deVoil P (2008) Genotypic variation in seedling root architectural traits and implications for drought adaptation in wheat (Triticum aestivum L.). Plant Soil 303:115–129

    CAS  Google Scholar 

  • Manschadi AM, Christopher JT, Hammer GL, Devoil P (2010) Experimental and modelling studies of drought–adaptive root architectural traits in wheat (Triticum aestivum L.). Plant Biosyst 144:458–462

    Google Scholar 

  • Mian MAR, Nafziger ED, Kolb FL, Teyker RH (1994) Root size and distribution of fieldgrown wheat genotypes. Crop Sci 34:810–812

    Google Scholar 

  • Mooney SJ, Pridmore TP, Helliwell J, Bennett MJ (2012) Developing X–ray Computed Tomography to non–invasively image 3–D root systems architecture in soil. Plant Soil 352:1–22

    CAS  Google Scholar 

  • Nagel KA, Kastenholz B, Jahnke S, Van Dusschoten D, Aach T, Mühlich M, TruhnD Scharr H, Terjung S, Walter A, Schurr U (2009) Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping. Funct Plant Biol 36:947–959

    CAS  Google Scholar 

  • Nielsen KL, Lynch JP, Jablokow AG, Curtis PS (1994) Carbon cost of root systems: an architectural approach. Plant Soil 165:161–169

    CAS  Google Scholar 

  • Nielsen KL, Lynch JP, Weiss HN (1997) Fractal geometry of bean root systems: correlations between spatial and fractal dimension. Am J Bot 84:26–33

    CAS  PubMed  Google Scholar 

  • Nielsen KL, Miller CR, Beck D, Lynch JP (1998) Fractal geometry of root systems: field observations of contrasting genotypes of common bean (Phaseolus vulgaris L.) grown under different phosphorus regimes. Plant Soil 206:1998–1999

    Google Scholar 

  • Nielsen KL, Eshel A, Lynch JP (2001) The effect of phosphorus availability on the carbon economy of contrasting common bean (Phaseolus vulgaris L.) genotypes. J Exp Bot 52:329–339

    CAS  PubMed  Google Scholar 

  • Ober ES, Clark CJ, Bloa ML, Smith CH (2005) Root growth, soil water extraction and drought tolerance in sugar beet. Aspects Appl Biol 73:213–220

    Google Scholar 

  • Oswald S, Menon M, Carminati A, Vontobel P, Lehmann E, Schulin R (2008) Quantitative imaging of infiltration, root growth, and root water uptake via neutron radiography. Vadose Zone J 7:1035–1047

    Google Scholar 

  • Pagès L, Vercambre G, Drouet JL, Lecompte F, Collet C, Le Bot J (2004) Root Typ: a generic model to depict and analyse the root system architecture. Plant Soil 258:103–119

    Google Scholar 

  • Paterson E, Sim A, Standing D, Dorward M, McDonald AJS (2006) Root exudation from Hordeum vulgare in response to localized nitrate supply. J Exp Bot 57:2413–2420

    CAS  PubMed  Google Scholar 

  • Pearse SJ, Veneklaas EJ, Cawthray GR, Bolland MD, Lambers H (2006) Carboxylate release of wheat, canola and 11 grain legume species as affected by phosphorus status. Plant Soil 288:127–139

    CAS  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

    CAS  Google Scholar 

  • Pierret A, Doussan C, Pages L (2006) Spatio–temporal variations in axial conductance of primary and first–order lateral roots of a maize crop as predicted by a model of the hydraulic architecture of root systems. Plant Soil 282:117–126

    CAS  Google Scholar 

  • Pierret A, Gonkhamdee S, Jourdan C, Maeght JL (2013) IJ_Rhizo: an open–source software to measure scanned images of root samples. Plant Soil 373:531–539

    CAS  Google Scholar 

  • Postma JA, Lynch JP (2011) Root cortical aerenchyma enhances the growth of maize on soils with suboptimal availability of nitrogen, phosphorus, and potassium. Plant Physiol 156:1190–1201

    PubMed Central  CAS  PubMed  Google Scholar 

  • Pound MP, French AP, AtkinsonJA WDM, Bennett MJ, Pridmore T (2013) RootNav: navigating images of complex root architectures. Plant Physiol 162:1802–1814

    PubMed Central  CAS  PubMed  Google Scholar 

  • Rascher U, BlossfeldS FF, Jahnke S, Jansen M, Kuhn AJ, Matsubara S, Märtin LLA, Merchant A, Metzner R, Müller-Linow M, Nagel KA, Pieruschka R, Pinto F, Schreiber CM, Temperton VM, Thorpe MR, van Dusschoten D, van Volkenburgh E, Windt CW, Schurr U (2011) Non–invasive approaches for phenotyping of enhanced performance traits in bean. Funct Plant Biol 38:968–983

    CAS  Google Scholar 

  • Rengel Z (2005) Breeding crops for adaptation to environments with low nutrient availability. In: Ashraf M, Harris PJC (eds) Abiotic stresses: plant resistance through breeding and molecular approaches. The Haworth Press, New York, pp 239–276

    Google Scholar 

  • Rengel Z (2013) Improving water and nutrient-use efficiency in food production systems. Wiley-Blackwell, Ames

    Google Scholar 

  • Richards RA (1996) Defining selection criteria to improve yield under drought. Plant Growth Regul 20:157–166

    CAS  Google Scholar 

  • Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM (2013) RootScape: a landmark–based system for rapid screening of root architecture in Arabidopsis. Plant Physiol 161:1086–1096

    PubMed Central  CAS  PubMed  Google Scholar 

  • Sanguineti MC, Duvick DN, Smith S, Landi P, Tuberosa R (2006) Effects of long–term selection on seedling traits and ABA accumulation in commercial maize hybrids. Maydica 51:329–338

    Google Scholar 

  • Shaff J, Schultz B, Craft E, Clark R, Kochian L (2009) GEOCHEM–EZ: a chemical speciation program with greater power and flexibility. Plant Soil 303:207–214

    Google Scholar 

  • Shi L, Shi T, Broadley MR, White PJ, Long Y, Meng J, Xu F, Hammond JP (2013) High–throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities. Ann Bot 112:381–389

    PubMed Central  CAS  PubMed  Google Scholar 

  • Singh D, Dikshit HK, Singh R (2013) A new phenotyping technique for screening for drought tolerance in lentil (Lens culinaris Medik.). Plant Breed 132:185–190

    Google Scholar 

  • Smit AL, Bengough AG, Engels C, van Noordwijk M, Pellerin S, van de Geijn SC (2000) Root methods: a handbook. Springer, Berlin

    Google Scholar 

  • Smith S, De Smet I (2012) Root system architecture: insights from Arabidopsis and cereal crops. Phil Trans Royal Society B: Biol Sci 367:1441–1452

    CAS  Google Scholar 

  • Somma F, Clausnitzer V, Hopmans JW (1997) An algorithm for three–dimensional, simultaneous modeling of root growth, transient soil water flow, and solute transport and uptake. Version 2.1. Paper No. 100034. Dept of Land, Air, and Water Resources, University of California

    Google Scholar 

  • Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker–assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Gen 112:208–221

    CAS  Google Scholar 

  • Stingaciu L, Schulz H, Pohlmeier A, Behnke S, Zilken H, Javaux M, Vereecken H (2013) In situ root system architecture extraction from magnetic resonance imaging for application to water uptake modeling. Vadose Zone J 12:1–9

    Google Scholar 

  • Stover DB, Drake BG, Butnor JR, Day FP (2007) Effect of elevated CO2 on coarse–root biomass in Florida scrub detected by ground–penetrating radar. Ecology 88:1328–1334

    PubMed  Google Scholar 

  • Struik PC, Yin X (2007) Combined model and QTL analysis of crop physiological traits in barley. In: ØstergÃ¥rd H, Backes G, Kovács G (eds) Varietal characteristics of cereals in different growing systems with special emphasis on below ground traits. Velence, Hungary, pp 25–30

    Google Scholar 

  • Tajima R, Kato Y (2011) Comparison of threshold algorithms for automatic image processing of rice roots using freeware. Image J Field Crops Res 121:460–463

    Google Scholar 

  • Topp CN, Iyer–Pascuzzi AS, Anderson JT, Lee CR, Zurek PR, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore BT, Harer J, Edelsbrunner H, Mitchell-Olds T, Weitz JS, Benfey PN (2013) 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture. PNAS 110:E1695–E1704

    PubMed Central  CAS  PubMed  Google Scholar 

  • Trachsel S, Kaeppler S, Brown K, Lynch J (2011) Shovelomics: high throughput phenotyping of maize (Zea mays L.) root architecture in the field. Plant Soil 341:75–87

    CAS  Google Scholar 

  • Trachsel S, Kaeppler SM, Brown KM, Lynch JP (2013) Maize root growth angles become steeper under low N conditions. Field Crop Res 140:18–31

    Google Scholar 

  • Tracy SR, Roberts JA, BlackCR MNA, 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

    CAS  PubMed  Google Scholar 

  • Tuberosa R, Salvi S, Sanguineti MC, Landi P, Maccaferri M, Conti S (2002a) Mapping QTLs regulating morpho-physiological traits and yield: case studies, shortcomings and perspectives in drought-stressed maize. Ann Bot 89:941–963

    PubMed Central  CAS  PubMed  Google Scholar 

  • Tuberosa R, Sanguineti MC, Landi P, Giuliani MM, Salvi S, Conti S (2002b) Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes. Plant Mol Biol 48:697–712

    CAS  PubMed  Google Scholar 

  • Valizadeh GR, Rengel Z, Rate AW (2003) Response of wheat genotypes efficient in P utilisation and genotypes responsive to P fertilisation to different P banding depths and watering regimes. Aust J Agric Res 54:59–65

    Google Scholar 

  • Vamerali T, Ganis A, Bona S, Mosca G (1999) An approach to minirhizotron root image analysis. Plant Soil 217:183–193

    Google Scholar 

  • van der Weele CM, Jiang HS, Palaniappan KK, Ivanov VB, Palaniappan K, Baskin TI (2003) A new algorithm for computational image analysis of deformable motion at high spatial and temporal resolution applied to root growth. Roughly uniform elongation in the meristem and also, after an abrupt acceleration, in the elongation zone. Plant Physiol 132:1138–1148

    PubMed Central  PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Wang E, Smith CJ (2004) Modelling the growth and water uptake function of plant root systems: a review. Aust J Agric Res 55:501–523

    Google Scholar 

  • Watt M, Rebetzke GJ, Kirkegaard JA (2005) A wheat genotype developed for rapid leaf growth copes well with the physical and biological constraints of unploughed soil. Funct Plant Biol 32:695–706

    Google Scholar 

  • Watt M, Silk WK, Passioura JB (2006) Rates of root and organism growth, soil conditions, and temporal and spatial development of the rhizosphere. Ann Bot (Lond) 97:839–855

    Google Scholar 

  • Watt M, Magee LJ, McCully ME (2008) Types, structure and potential for axial water flow in the deepest roots of field–grown cereals. New Phytol 178:135–146

    PubMed  Google Scholar 

  • Wiese AH, Riemenschneider DE, Zalesny RS (2005) An inexpensive rhizotron design for two–dimensional, horizontal root growth measurements. Tree Planters Notes 51:40

    Google Scholar 

  • Wong MTF, Asseng S (2006) Determining the causes of spatial and temporal variability of wheat yields at sub–field scale using a new method of upscaling a crop model. Plant Soil 283:203–215

    CAS  Google Scholar 

  • Wu L, McGechan MB, Watson CA, Baddeley JA (2005) Developing existing plant root system architecture models to meet future agricultural challenges. Adv Agron 85:181–219

    Google Scholar 

  • Wu L, McGechan MB, McRoberts N, Baddeley JA, Watson CA (2007) SPACSYS: integration of a 3D root architecture component to carbon, nitrogen and water cycling – Model description. Ecol Model 200:343–359

    Google Scholar 

  • Wulfsohn D, Nyengaard JR, Gundersen HJG, Cutler AJ, Squires TM (1999) Non–destructive, stereological estimation of plant root lengths, branching pattern and diameter distribution. Plant Soil 214:15–26

    CAS  Google Scholar 

  • Zeng G, Birchfield ST, Wells CE (2008) Rapid automated detection of roots in minirhizotron images. Mach Vis Appl 21:309–317

    Google Scholar 

  • Zhu JM, Brown KM, Lynch JP (2010) Root cortical aerenchyma improves the drought tolerance of maize (Zea mays L.). Plant Cell Environ 33:740–749

    PubMed  Google Scholar 

  • Zhu J, Ingram AP, Benfey NP, Elich T (2011) From lab to field, new approaches to phenotyping root system architecture. Cur Opin Plant Biol 14:310–317

    Google Scholar 

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Acknowledgements

This work was supported by the Australian Research Council (DP130104825) and the National Natural Science Foundation of China (31471946).

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Correspondence to Zed Rengel .

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Chen, Y.L., Djalovic, I., Rengel, Z. (2015). Phenotyping for Root Traits. In: Kumar, J., Pratap, A., Kumar, S. (eds) Phenomics in Crop Plants: Trends, Options and Limitations. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2226-2_8

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