Rhizoslides: paper-based growth system for non-destructive, high throughput phenotyping of root development by means of image analysis

Plant Methods

Andreas Hund¹  Achim Walter¹  Daniela Marschall¹  Norbert Kirchgessner¹  Chantal Le Marié¹ 

[1] Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland

关键词: Agriculture;    Breeding;    Rhizoslide;    Imaging;    High-throughput;    Maize;    Root system architecture;   

Others  :  1151866
DOI  :  10.1186/1746-4811-10-13

 received in 2014-02-10, accepted in 2014-05-13,  发布年份 2014

【 摘 要 】

Background

A quantitative characterization of root system architecture is currently being attempted for various reasons. Non-destructive, rapid analyses of root system architecture are difficult to perform due to the hidden nature of the root. Hence, improved methods to measure root architecture are necessary to support knowledge-based plant breeding and to analyse root growth responses to environmental changes. Here, we report on the development of a novel method to reveal growth and architecture of maize root systems.

Results

The method is based on the cultivation of different root types within several layers of two-dimensional, large (50 × 60 cm) plates (rhizoslides). A central plexiglass screen stabilizes the system and is covered on both sides with germination paper providing water and nutrients for the developing root, followed by a transparent cover foil to prevent the roots from falling dry and to stabilize the system. The embryonic roots grow hidden between a Plexiglas surface and paper, whereas crown roots grow visible between paper and the transparent cover. Long cultivation with good image quality up to 20 days (four fully developed leaves) was enhanced by suppressing fungi with a fungicide. Based on hyperspectral microscopy imaging, the quality of different germination papers was tested and three provided sufficient contrast to distinguish between roots and background (segmentation). Illumination, image acquisition and segmentation were optimised to facilitate efficient root image analysis. Several software packages were evaluated with regard to their precision and the time investment needed to measure root system architecture. The software 'Smart Root’ allowed precise evaluation of root development but needed substantial user interference. 'GiaRoots’ provided the best segmentation method for batch processing in combination with a good analysis of global root characteristics but overestimated root length due to thinning artefacts. 'WhinRhizo’ offered the most rapid and precise evaluation of root lengths in diameter classes, but had weaknesses with respect to image segmentation and analysis of root system architecture.

Conclusion

A new technique has been established for non-destructive root growth studies and quantification of architectural traits beyond seedlings stages. However, automation of the scanning process and appropriate software remains the bottleneck for high throughput analysis.

【 授权许可】

   
2014 Le Marié et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Lynch JP: Turner Review No. 14 Roots of the second green revolution. Aust J Bot 2007, 55:493-512.
• [2]Springer: High-Throughput Phenotyping in Plants. Heidelberg: Humana Press; 2012.
• [3]Rafalski JA: Association genetics in crop improvement. Curr Opin Plant Biol 2010, 13:174-180.
• [4]Hochholdinger F, Park WJ, Sauer M, Woll K: From weeds to crops: genetic analysis of root development in cereals. Trends Plant Sci 2004, 9:42-48.
• [5]Hund A, Reimer R, Messmer R: A consensus map of QTLs controlling the root length of maize. Plant Soil 2011, 344:143-158.
• [6]Singh V, van Oosterom EJ, Jordan DR, Messina CD, Cooper M, Hammer GL: Morphological and architectural development of root systems in sorghum and maize. Plant Soil 2010, 333:287-299.
• [7]Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV: High‒throughput 2D root system phenotyping platform facilitates genetic analysis of root growth and development. Plant Cell Environ 2013, 36:454-466.
• [8]Babé A, Lavigne T, Séverin JP, Nagel KA, Walter A, Chaumont F, Batoko H, Beeckman T, Draye X: Repression of early lateral root initiation events by transient water deficit in barley and maize. Philos Trans R Soc Lond B Biol Sci 2012, 367:1534-1541.
• [9]Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T: High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability. Philos Trans R Soc Lond B Biol Sci 2012, 367:1559-1569.
• [10]Hund A, Trachsel S, Stamp P: Growth of axile and lateral roots of maize: I development of a phenotying platform. Plant Soil 2009, 325:335-349.
• [11]Smith S, De Smet I: Root system architecture: insights from Arabidopsis and cereal crops. Philos Trans R Soc Lond B Biol Sci 2012, 367:1441-1452.
• [12]Hochholdinger F, Woll K, Sauer M, Dembinsky D: Genetic dissection of root formation in maize (Zea mays) reveals root‒type specific developmental programmes. Ann Bot-London 2004, 93:359-368.
• [13]Smit AL, Groenwold J: Root characteristics of selected field crops: data from the Wageningen Rhizolab (1990–2002). Plant Soil 2005, 272:365-384.
• [14]Kuchenbuch RO, Ingram KT, Buczko U: Effects of decreasing soil water content on seminal and lateral roots of young maize plants. Journal of Plant Nutrition and Soil Science-Zeitschrift Fur Pflanzenernahrung Und Bodenkunde 2006, 169:841-848.
• [15]Mooney SJ, Pridmore TP, Helliwell J, Bennett MJ: Developing X-ray computed tomography to non-invasively image 3-D root systems architecture in soil. Plant Soil 2012, 352:1-22.
• [16]Jahnke S, Menzel MI, van Dusschoten D, Roeb GW, Buhler J, Minwuyelet S, Blumler P, Temperton VM, Hombach T, Streun M, Jahnke S, Menzel MI, van Dusschoten D, Roeb GW, Buhler J, Minwuyelet S, Blumler P, Temperton VM, Hombach T, Streun M, Beer S, Khodaverdi M, Ziemons K, Coenen HH, Schurr U: Combined MRI-PET dissects dynamic changes in plant structures and functions. Plant J 2009, 59:634-644.
• [17]Nagel KA, Putz A, Gilmer F, Heinz K, Fischbach A, Pfeifer J, Faget M, Blossfeld S, Ernst M, Dimaki C: GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons. Funct Plant Biol 2012, 39:891-904.
• [18]Famoso AN, Clark RT, Shaff JE, Craft E, McCouch SR, Kochian LV: Development of a novel aluminum tolerance phenotyping platform used for comparisons of cereal aluminum tolerance and investigations into rice aluminum tolerance mechanisms. Plant Physiol 2010, 153:1678-1691.
• [19]Nagel KA, Kastenholz B, Jahnke S, Van Dusschoten D, Aach T, Muehlich M, Truhn D, Scharr H, Terjung S, Walter A, Schurr U: Temperature responses of roots: impact on growth, root system architecture and implications for phenotyping. Funct Plant Biol 2009, 36:947-959.
• [20]Hund A, Reimer R, Stamp P, Walter A: Can we improve heterosis for root growth of maize by selecting parental inbred lines with different temperature behaviour? Philos Trans R Soc Lond B Biol Sci 2012, 367:1580-1588.
• [21]Chen YL, Dunbabin VM, Diggle AJ, Siddique KHM, Rengel Z: Development of a novel semi-hydroponic phenotyping system for studying root architecture. Funct Plant Biol 2011, 38:355-363.
• [22]Planchamp C, Balmer D, Hund A, Mauch-Mani B: A soil-free root observation system for the study of root-microorganism interactions in maize. Plant Soil 2013, 367:605-614.
• [23]Reimer R, Stich B, Melchinger AE, Schrag TA, Sørensen AP, Stamp P, Hund A: Root response to temperature extremes: association mapping of temperate maize (Zea mays L). Maydica 2013, 58:156-168.
• [24]Ruta N, Liedgens M, Fracheboud Y, Stamp P, Hund A: QTLs for the elongation of axile and lateral roots of maize in response to low water potential. Theor Appl Genet 2009, 120:621-631.
• [25]Ruta N, Stamp P, Liedgens M, Fracheboud Y, Hund A: Collocations of QTLs for seedling traits and yield components of tropical maize under water stress conditions. Crop Sci 2010, 50:1385-1392.
• [26]Liao H, Rubio G, Yan X, Cao A, Brown KM, Lynch JP: Effect of phosphorus availability on basal root shallowness in common bean. Plant Soil 2001, 232:69-79.
• [27]Zhu J, Kaeppler SM, Lynch JP: Mapping of QTLs for lateral root branching and length in maize (Zea mays L.) under differential phosphorus supply. Theor Appl Genet 2005, 111:688-695.
• [28]Trachsel S, Stamp P, Hund A: Effect of high temperatures, drought and aluminum toxicity on root growth of tropical maize (Zea Mays L.) seedlings. Maydica 2010, 55:249-260.
• [29]Flint LH: Light and the elongation of the mesocotyl in corn. Plant Physiol 1944, 19:537-543.
• [30]Zobel RW: Hardware and software efficacy in assessment of fine root diameter distributions. Comput Electron Agr 2008, 60:178-189.
• [31]Yang C, Everitt JH, Fernandez CJ: Comparison of airborne multispectral and hyperspectral imagery for mapping cotton root rot. Biosyst Eng 2010, 107:131-139.
• [32]Nakaji T, Noguchi K, Oguma H: Classification of rhizosphere components using visible–near infrared spectral images. Plant Soil 2008, 310:245-261.
• [33]Armengaud P, Zambaux K, Hills A, Sulpice R, Pattison RJ, Blatt MR, Amtmann A: EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture. Plant J 2009, 57:945-956.
• [34]Burton AL, Williams M, Lynch JP, Brown KM: RS: Software for high-throughput analysis of root anatomical traits. Plant Soil 2012, 357:189-203.
• [35]Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV: Three-dimensional root phenotyping with a novel imaging and software platform. Plant Physiol 2011, 156:455-465.
• [36]French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T: High-throughput quantification of root growth using a novel image-analysis tool. Plant Physiol 2009, 150:1784-1795.
• [37]Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price C, Topp C, Iyer-Pascuzzi A, Zurek P, Fang S: GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol 2012, 12:116.
• [38]Regent Instruments Inc: WinRhizo. Canada: Regent Instruments Inc; 2009.
• [39]Le Bot J, Serra V, Fabre J, Draye X, Adamowicz S, Pages L: DART: a software to analyse root system architecture and development from captured images. Plant Soil 2010, 326:261-273.
• [40]Lobet G, Pages L, Draye X: A novel image-analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiol 2011, 157:29-39.
• [41]Mairhofer S, Zappala S, Tracy SR, Sturrock C, Bennett M, Mooney SJ, Pridmore T: RooTrak: automated recovery of three-dimensional plant root architecture in soil from X-ray microcomputed tomography images using visual tracking. Plant Physiol 2012, 158:561-569.
• [42]Naeem A, French AP, Wells DM, Pridmore TP: High-throughput feature counting and measurement of roots. Bioinformatics 2011, 27:1337-1338.
• [43]Pierret A, Gonkhamdee S, Jourdan C, Maeght J-L: IJ_Rhizo: an open-source software to measure scanned images of root samples. Plant Soil 2013, 373:531-539.
• [44]Pound MP, French AP, Atkinson J, Wells DM, Bennett MJ, Pridmore TP: RootNav: navigating images of complex root architectures. Plant Physiol 2013, 162:1802-1814.
• [45]Stefanelli D, Fridman Y, Perry RL: DigiRoot (TM): new software for root studies. Eur J Hortic Sci 2009, 74:169-174.
• [46]Lobet G, Draye X, Périlleux C: An online database for plant image analysis software tools. Plant Methods 2013, 9:38.
• [47]Clark RT, Shaff J, Aneshansley DJ, Kochian L: Advances to Whole Root System Quantification Tools and Techniques. In The Proceedings of the International Plant Nutrition Colloquium XVI. UC Davis: Department of Plant Sciences; 2009. Retrieved from: http://www.escholarship.org/uc/item/40v4x53m webcite
• [48]Stefanelli D, Fridman Y, Perry RL: DigiRoot (TM): new software for root studies. European Journal of Horticultural Science 2009, 74:169-174.
• [49]Yu P, Li X, Yuan L, Li C: A novel morphological response of maize (Zea mays) adult roots to heterogeneous nitrate supply revealed by a split‒root experiment. Physiol Plantarum 2014, 150:133-144.
• [50]Pfeifer J, Faget M, Walter A, Blossfeld S, Fiorani F, Schurr U, Nagel K: Spring barley shows dynamic compensatory root and shoot growth responses when exposed to localized soil compaction and fertilization. Funct Plant Biol 2014, 41:581-597.
• [51]Drew M, Saker L: Nutrient supply and the growth of the seminal root system in barley II. localized, compensatory increases in lateral root growth and rates of nitrate uptake when nitrate supply is restricted to only part of the root system. J Exp Bot 1975, 26:79-90.
• [52]Walter A, Silk WK, Schurr U: Environmental effects on spatial and temporal patterns of leaf and root growth. Annu Rev Plant Biol 2009, 60:279-304.
• [53]Zhu J, Kaeppler SM, Lynch JP: Mapping of QTL controlling root hair length in maize (Zea mays L.) under phosphorus deficiency. Plant Soil 2005, 270:299-310.
• [54]Mollier A, Pellerin S: Maize root system growth and development as influenced by phosphorus deficiency. J Exp Bot 1999, 50:487.
• [55]Liu J, Li J, Chen F, Zhang F, Ren T, Zhuang Z, Mi G: Mapping QTLs for root traits under different nitrate levels at the seedling stage in maize (Zea mays L.). Plant Soil 2008, 305:253-265.
• [56]Watt M, Moosavi S, Cunningham SC, Kirkegaard JA, Rebetzke GJ, Richards RA: A rapid, controlled-environment seedling root screen for wheat correlates well with rooting depths at vegetative, but not reproductive, stages at two field sites. Ann Bot-London 2013, 112:447-455.
• [57]Rahnama A, Munns R, Poustini K, Watt M: A screening method to identify genetic variation in root growth response to a salinity gradient. J Exp Bot 2011, 62:69-77.
• [58]Almgren I, Gustafsson M, AS F, ält , Lindgren H, Liljeroth E: Interaction between root and leaf disease development in barley cultivars after inoculation with different isolates of Bipolaris sorokiniana. J Phytopathol 1999, 147:331-337.
• [59]Bonser AM, Lynch J, Snapp S: Effect of phosphorus deficiency on growth angle of basal roots in Phaseolus vulgaris. New Phytol 1996, 132:281-288.
• [60]Blossfeld S, Schreiber CM, Liebsch G, Kuhn AJ, Hinsinger P: Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes. Ann Bot-London 2013, 112:267-276.
• [61]Björn L, Suzuki Y, Nilsson J: Influence of wavelength on the light response of excised wheat roots. Physiol Plantarum 1963, 16:132-141.
• [62]Feldman LJ, Briggs WR: Light-regulated gravitropism in seedling roots of maize. Plant Physiol 1987, 83:241.
• [63]Walter A, Silk WK, Schurr U: Effect of soil pH on growth and cation deposition in the root tip of Zea mays L. J Plant Growth Regul 2000, 19:65-76.
• [64]Ruts T, Matsubara S, Wiese-Klinkenberg A, Walter A: Diel patterns of leaf and root growth: endogenous rhythmicity or environmental response? J Exp Bot 2012, 63:3339-3351.
• [65]Hund A, Fracheboud Y, Soldati A, Frascaroli E, Salvi S, Stamp P: QTL controlling root and shoot traits of maize seedlings under cold stress. Theor Appl Genet 2004, 109:618-629.
• [66]Trachsel S, Messmer R, Stamp P, Hund A: Mapping of QTLs for lateral and axile root growth of tropical maize. Theor Appl Genet 2009, 119:1413-1424.
• [67]Ruta N, Liedgens M, Fracheboud Y, Stamp P, Hund A: QTLs for the elongation of axile and lateral roots of maize in response to low water potential. Theor Appl Genet 2010, 120:621-631.
• [68]Sorgonà A, Abenavoli M, Gringeri P, Lupini A, Cacco G: Root architecture plasticity of citrus rootstocks in response to nitrate availability. J Plant Nutr 2007, 30:1921-1932.
• [69]Sorgonà A, Abenavoli MR, Cacco G: A comparative study between two citrus rootstocks: effect of nitrate on the root morpho-topology and net nitrate uptake. Plant Soil 2005, 270:257-267.
• [70]Liao M, Fillery IRP, Palta JA: Early vigorous growth is a major factor influencing nitrogen uptake in wheat. Funct Plant Biol 2004, 31:121-129.
• [71]Trachsel S, Stamp P, Hund A: Growth of axile and lateral roots of maize: response to desiccation stress induced by polyethylene glycol 8000. Maydica 2010, 55:101-109.
• [72]Freund H: Sterilisieren der fertigen Ampullen. In Die Ampullenfabrikation. Berlin Heidelberg: Springer; 1916:61-72.
• [73]Bohn M, Novais J, Fonseca R, Tuberosa R, Grift T: Genetic evaluation of root complexity in maize. Acta Agronomica Hungarica 2006, 54:291-303.
• [74]Butler D: asreml: asreml() fits the linear mixed model. R package version 3.0. 2009. http://www.vsni.co.uk webcite