Root system markup language: Toward a unified root architecture description language

Plant Physiology

Volumn 167, Issue 3, 2015, Pages 617-627

  Lobet, Guillaume ^a   Pound, Michael P ^b   Diener, Julien ^c   Pradal, Christophe ^c,d   Draye, Xavier ^e   Godin, Christophe ^c   Javaux, Mathieu ^e,f   Leitner, Daniel ^g   Meunier, Félicien ^e   Nacry, Philippe ^h   Pridmore, Tony P ^b   Schnepf, Andrea ^f  

^a UNIVERSITY OF LIÈGE   (Belgium)

^b UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^c INRIA   (France)

^d LIRMM   (France)

^e UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^f FORSCHUNGSZENTRUM JÜLICH   (Germany)

^g UNIVERSITY OF VIENNA   (Austria)

^h CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANATOMY AND HISTOLOGY; BIOLOGICAL MODEL; COMPUTER LANGUAGE; GROWTH, DEVELOPMENT AND AGING; PHYSIOLOGY; PLANT ROOT; SOFTWARE; THREE DIMENSIONAL IMAGING; WORKFLOW;

IMAGING, THREE-DIMENSIONAL; MODELS, BIOLOGICAL; PLANT ROOTS; PROGRAMMING LANGUAGES; SOFTWARE; WORKFLOW;

EID: 84923649159     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.114.253625     Document Type: Article

References (54)

1. 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 signalling. Plant Cell Environ 26: 1053-1066.
2. 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.
3. Avraham S, Tung CW, Ilic K, Jaiswal P, Kellogg EA, McCouch S, Pujar A, Reiser L, Rhee SY, Sachs MM, et al (2008) The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Res (Suppl 1) 36: D449-D454.
4. Barthélémy D, Caraglio Y (2007) Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny. Ann Bot (Lond) 9: 375-407.
5. Boudon F, Pradal C, Cokelaer T, Prusinkiewicz P, Godin C (2012) L-py: an L-system simulation framework for modeling plant architecture development based on a dynamic language. Front Plant Sci 3: 76.
6. Bucksch A, Burridge J, York LM,Das A,Nord E, Weitz JS, Lynch JP (2014) Image-based high-throughput field phenotyping of crop roots. Plant Physiol 166: 470-486.
7. 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.
8. 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.
9. Comas LH, Becker SR, Cruz VM, Byrne PF, Dierig DA (2013) Root traits contributing to plant productivity under drought. Front Plant Sci 4: 442.
10. Danjon F, Khuder H, Stokes A (2013) Deep phenotyping of coarse root architecture in R. pseudoacacia reveals that tree root system plasticity is confined within its architectural model. PLoS ONE 8: e83548.
11. Danjon F, Reubens B (2007) 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.
12. Danjon F, Sinoquet H, Godin C, Colin F, Drexhage M (1999) Characterisation of structural tree root architecture using 3D digitising and AMAPmod software. Plant Soil 211: 241-258.
13. Diener J, Nacry P, Périn C, Dievart A, Draye X, Boudon F, Gaujon A, Godin C (2013) An automated image-processing pipeline for highthroughput analysis of root architecture in OpenAlea. In R Sievanen, E Nikinmaa, C Godin, A Lintunen, and P Nygren, eds, 7th International Conference on Functional-Structural Plant Models. Saariselka, Finland, pp 85-87.
14. Draye X, Kim Y, Lobet G, Javaux M (2010) Model-assisted integration of physiological and environmental constraints affecting the dynamic and spatial patterns of root water uptake from soils. J Exp Bot 61: 2145-2155.
15. 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.
16. Fournier C, Pradal C, Louarn G, Combes D, Soulié JC, Luquet D, Boudon F, Chelle M (2010) Building modular FSPM under OpenAlea: concepts and applications. In T DeJong, D Da Silva, 6th International Workshop on Functional-Structural Plant Models. Davis, CA, pp 109-112.
17. French A, Ubeda-Tomás S, Holman TJ, Bennett MJ, Pridmore T (2009) High-throughput quantification of root growth using a novel imageanalysis tool. Plant Physiol 150: 1784-1795.
18. Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S, et al (2012) GiA Roots: software for the high throughput analysis of plant root system architecture. BMC Plant Biol 12: 116.
19. Garin G, Fournier C, Andrieu B, Houlès V, Robert C, Pradal C (2014) A modelling framework to simulate foliar fungal epidemics using functionalstructural plant models. Ann Bot (Lond) 114: 795-812.
20. Godin C, Caraglio Y (1998) A multiscale model of plant topological structures. J Theor Biol 191: 1-46.
21. Godin C, Costes E, Sinoquet H (1999) A method for describing plant architecture which integrates topology and geometry. Ann Bot (Lond) 84: 343-357.
22. Godin C, Costes E, Sinoquet H (2005). Plant architecture modelling. In CGN Turnbull, ed, Plant Architecture and Its Manipulation. Wiley- Blackwell, Oxford, pp 238-288.
23. Godin C, Sinoquet H (2005) Functional-structural plant modelling. New Phytol 166: 705-708.
24. Griffon S, de Coligny F (2014) AMAPstudio: an editing and simulation software suite for plants architecture modelling. Ecol Modell 290: 3-10.
25. Gruber BD, Giehl RFH, Friedel S, von Wirén N (2013) Plasticity of the Arabidopsis root system under nutrient deficiencies. Plant Physiol 163: 161-179.
26. Guédon Y, Barthélémy D, Caraglio Y, Costes E (2001) Pattern analysis in branching and axillary flowering sequences. J Theor Biol 212: 481-520.
27. Hammer G, Dong Z, McLean G, Doherty A, Messina C, Schussler J, Zinselmeier C, Paszkiewicz S, Cooper M (2009) Can changes in canopy and/or root system architecture explain historical maize yield trends in the U.S. Corn Belt? Crop Sci 49: 299-312.
28. 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.
29. Javaux M, Schroeder T, Vanderborght J, Vereecken H (2008) Use of a three-dimensional detailed modeling approach for predicting root water uptake. Vadose Zone J 7: 1079-1088.
30. Kellermeier F, Armengaud P, Seditas TJ, Danku J, Salt DE, Amtmann A (2014) Analysis of the root system architecture of Arabidopsis provides a quantitative readout of crosstalk between nutritional signals. Plant Cell 26: 1480-1496.
31. 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.
32. 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.
33. Leitner D, Klepsch S, Bodner G, Schnepf A (2010) A dynamic root system growth model based on L-systems. Plant Soil 332: 117-192.
34. Lobet G, Couvreur V, Meunier F, Javaux M, Draye X (2014) Plant water uptake in drying soils. Plant Physiol 164: 1619-1627.
35. Lobet G, Draye X, Périlleux C (2013) An online database for plant image analysis software tools. Plant Methods 9: 38.
36. Lobet G, Pagès L, Draye X (2011) A novel image-analysis toolbox enabling quantitative analysis of root system architecture. Plant Physiol 157: 29-39.
37. Lynch J (1995) Root architecture and plant productivity. Plant Physiol 109: 7-13.
38. Lynch JP (2007) Roots of the second green revolution. Aust J Bot 55: 493- 512.
39. Mairhofer S, Zappala S, Tracy S, Sturrock C, Bennett MJ, Mooney SJ, Pridmore TP (2013) Recovering complete plant root system architectures from soil via x-ray μ-computed tomography. Plant Methods 9: 8.
40. 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.
41. 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.
42. Mündermann L, Erasmus Y, Lane B, Coen E, Prusinkiewicz P (2005) Quantitative modeling of Arabidopsis development. Plant Physiol 139: 960-968.
43. Negrón C, Contador L (2013) Systematic analysis of branching patterns of three almond cultivars with different tree architectures. J Am Soc Hortic Sci 138: 407-415.
44. Pace J, Lee N, Naik HS, Ganapathysubramanian B, Lübberstedt T (2014) Analysis of maize (Zea mays L.) seedling roots with the high-throughput image analysis tool ARIA (Automatic Root Image Analysis). PLoS ONE 9: e108255.
45. Pagès L, Bécel C, Boukcim H, Moreau D, Nguyen C, Voisin AS (2014) Calibration and evaluation of ArchiSimple, a simple model of root system architecture. Ecol Modell 290: 76-84.
46. Parekh R, Ascoli GA (2013) Neuronal morphology goes digital: a research hub for cellular and system neuroscience. Neuron 77: 1017-1038.
47. Péret B, Li G, Zhao J, Band LR, Voß U, Postaire O, Luu DT, Da Ines O, Casimiro I, Lucas M, et al (2012) Auxin regulates aquaporin function to facilitate lateral root emergence. Nat Cell Biol 14: 991-998.
48. Plant Ontology Consortium (2002) The Plant Ontology Consortium and plant ontologies. Comp Funct Genomics 3: 137-142.
49. 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.
50. Pound MP, French AP, Atkinson JA, Wells DM, Bennett MJ, Pridmore T (2013) RootNav: navigating images of complex root architectures. Plant Physiol 162: 1802-1814.
51. Pradal C, Dufour-Kowalski S, Boudon F, Fournier C, Godin C (2008) OpenAlea: a visual programming and component-based software platform for plant modelling. Funct Plant Biol 35: 751-760.
52. Pradal C, Boudon F, Nouguier C, Chopard J, Godin C (2009) PlantGL: a Python-based geometric library for 3D plant modelling at different scales. Graph Models 71: 1-21.
53. R Core Team (2008) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna.
54. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, et al (2013) ArrayExpress update: trends in database growth and links to data analysis tools. Nucleic Acids Res 41: D987-D990.