F. Aiteanu and R. Klein, Hybrid tree reconstruction from inhomogeneous point clouds, The Visual Computer, vol.15, issue.1, pp.763-771, 2014.
DOI : 10.1007/s00371-014-0977-7

V. Baldazzi, N. Bertin, D. Jong, H. Génard, and M. , Towards multiscale plant models: integrating cellular networks, Trends in Plant Science, vol.17, issue.12, pp.728-736, 2012.
DOI : 10.1016/j.tplants.2012.06.012
URL : https://hal.archives-ouvertes.fr/hal-00762615

L. R. Band, J. A. Fozard, C. Godin, O. E. Jensen, T. Pridmore et al., Multiscale Systems Analysis of Root Growth and Development: Modeling Beyond the Network and Cellular Scales, The Plant Cell, vol.24, issue.10, pp.3892-3906, 2012.
DOI : 10.1105/tpc.112.101550
URL : https://hal.archives-ouvertes.fr/hal-00828879

L. R. Band and J. R. King, Multiscale modelling of auxin transport in the plant-root elongation zone, Journal of Mathematical Biology, vol.12, issue.4, pp.743-785, 2012.
DOI : 10.1007/s00285-011-0472-y

Y. Bao, P. Aggarwal, N. E. Robbins, C. J. Sturrock, M. C. Thompson et al., Plant roots use a patterning mechanism to position lateral root branches toward available water, Proceedings of the National Academy of Sciences, vol.26, issue.3, pp.9319-9324, 2014.
DOI : 10.1105/tpc.113.119495
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4078807

D. Barthélémy, C. , Y. D. , T. , and J. J. , Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure, and ontogeny A bistable switch mechanism for stem cell domain nucleation in the shoot apical meristem, Ann. Bot. Front. Plant Sci, vol.99, issue.7, pp.375-407674, 2007.

P. N. Benfey and T. Mitchell-olds, From Genotype to Phenotype: Systems Biology Meets Natural Variation, Science, vol.13, issue.21, pp.495-497, 2008.
DOI : 10.1016/j.cub.2003.10.001
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2727942

G. P. Bernasconi, Reaction-diffusion model for phyllotaxis, Physica D: Nonlinear Phenomena, vol.70, issue.1-2, pp.90-99, 1994.
DOI : 10.1016/0167-2789(94)90058-2

F. L. Bookstein, Morphometric Tools for Landmark Data: Geometry and Biology, 1997.
DOI : 10.1017/CBO9780511573064

A. D. Bradshaw, Evolutionary Significance of Phenotypic Plasticity in Plants, Adv. Genet, vol.13, issue.08, pp.115-155, 1965.
DOI : 10.1016/S0065-2660(08)60048-6

S. A. Braybrook and H. Jönsson, Shifting foundations: the mechanical cell wall and development, Current Opinion in Plant Biology, vol.29, 2016.
DOI : 10.1016/j.pbi.2015.12.009
URL : http://doi.org/10.1016/j.pbi.2015.12.009

T. L. Brooks, N. D. Miller, and E. P. Spalding, Plasticity of Arabidopsis Root Gravitropism throughout a Multidimensional Condition Space Quantified by Automated Image Analysis, PLANT PHYSIOLOGY, vol.152, issue.1, pp.206-216, 2010.
DOI : 10.1104/pp.109.145292

A. Bucksch, A Practical Introduction to Skeletons for the Plant Sciences, Applications in Plant Sciences, vol.2, issue.8, 2014.
DOI : 10.3732/apps.1400005.s2

A. Bucksch, A. Das, H. Schneider, N. Merchant, and J. S. Weitz, Overcoming the Law of the Hidden in Cyberinfrastructures, Trends in Plant Science, vol.22, issue.2, pp.117-123, 2017.
DOI : 10.1016/j.tplants.2016.11.014

A. Bucksch and S. Fleck, Automated Detection of Branch Dimensions in Woody Skeletons of Fruit Tree Canopies, Photogrammetric Engineering & Remote Sensing, vol.77, issue.3, 2011.
DOI : 10.14358/PERS.77.3.229

A. Bucksch, R. Lindenbergh, and M. Menenti, SkelTre, The Visual Computer, vol.14, issue.7, pp.1283-1300, 2010.
DOI : 10.1007/s00371-010-0520-4

A. Bucksch, G. Turk, and J. S. Weitz, The Fiber Walk: A Model of Tip-Driven Growth with Lateral Expansion, PLoS ONE, vol.9, issue.1, 2014.
DOI : 10.1371/journal.pone.0085585.s008

J. G. Chimungu, M. F. Maliro, P. C. Nalivata, G. Kanyama-phiri, K. M. Brown et al., Utility of root cortical aerenchyma under water limited conditions in tropical maize (Zea mays L.). Field Crops Res, pp.86-98, 2015.

D. H. Chitwood, L. R. Headland, A. Ranjan, C. C. Martinez, S. A. Braybrook et al., Leaf Asymmetry as a Developmental Constraint Imposed by Auxin-Dependent Phyllotactic Patterning, The Plant Cell, vol.24, issue.6, pp.2318-2327, 2012.
DOI : 10.1105/tpc.112.098798
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406905

D. H. Chitwood, R. Kumar, L. R. Headland, A. Ranjan, M. F. Covington et al., A Quantitative Genetic Basis for Leaf Morphology in a Set of Precisely Defined Tomato Introgression Lines, The Plant Cell, vol.25, issue.7, pp.2465-2481, 2013.
DOI : 10.1105/tpc.113.112391

D. H. Chitwood, A. Ranjan, R. Kumar, Y. Ichihashi, K. Zumstein et al., Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context, The Plant Cell, vol.26, issue.9, pp.3616-3629, 2014.
DOI : 10.1105/tpc.114.130112

D. H. Chitwood, A. Ranjan, C. C. Martinez, L. R. Headland, T. Thiem et al., A Modern Ampelography: A Genetic Basis for Leaf Shape and Venation Patterning in Grape, PLANT PHYSIOLOGY, vol.164, issue.1, pp.259-272, 2014.
DOI : 10.1104/pp.113.229708

D. H. Chitwood, S. M. Rundell, D. Y. Li, Q. L. Woodford, T. Y. Tommy et al., Climate and developmental plasticity: interannual variability in grapevine leaf morphology, Plant Physiol, vol.170, pp.1480-1491, 2016.
DOI : 10.1101/030957

D. H. Chitwood and C. N. Topp, Revealing plant cryptotypes: defining meaningful phenotypes among infinite traits, Current Opinion in Plant Biology, vol.24, 2015.
DOI : 10.1016/j.pbi.2015.01.009

R. M. Clark, T. N. Wagler, P. Quijada, and J. Doebley, A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture, Nature Genetics, vol.134, issue.5, pp.594-597, 1038.
DOI : 10.1111/j.1365-313X.2004.02285.x

R. T. Clark, R. B. Maccurdy, J. K. Jung, J. E. Shaff, S. R. Mccouch et al., Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform, PLANT PHYSIOLOGY, vol.156, issue.2, pp.455-465, 2011.
DOI : 10.1104/pp.110.169102
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3177249

J. Clausen, D. D. Keck, and W. M. Hiesey, Regional Differentiation in Plant Species, The American Naturalist, vol.75, issue.758, pp.231-250, 1941.
DOI : 10.1086/280955

J. E. Cohen, Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better, PLoS Biology, vol.88, issue.12, 2004.
DOI : 10.1371/journal.pbio.0020439.t001
URL : http://doi.org/10.1371/journal.pbio.0020439

S. Cohen-boulakia, K. Belhajjame, O. Collin, J. Chopard, C. Froidevaux et al., Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems, 2017.
DOI : 10.1016/j.future.2017.01.012
URL : https://hal.archives-ouvertes.fr/hal-01516082

S. Cordell, G. Goldstein, D. Mueller-dombois, D. Webb, and P. M. Vitousek, Physiological and morphological variation in Metrosideros polymorpha , a dominant Hawaiian tree species, along an altitudinal gradient: the role of phenotypic plasticity, Oecologia, vol.113, issue.2, pp.188-196, 1007.
DOI : 10.1007/s004420050367

D. Corney, J. Y. Clark, H. L. Tang, and P. Wilkin, Automatic extraction of leaf characters from herbarium specimens, Taxon, vol.61, pp.231-244, 2012.

F. Danjon, D. Bert, C. Godin, and P. Trichet, Structural root architecture of 5-year-old Pinus pinaster measured by 3D digitising and analysed with AMAPmod, Plant Soil, vol.217, pp.49-63, 1999.
DOI : 10.1007/978-94-017-3469-1_6

A. Das, H. Schneider, J. Burridge, A. K. Ascanio, T. Wojciechowski et al., Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics, Plant Methods, vol.44, issue.11, p.51, 2015.
DOI : 10.1186/s13007-015-0093-3

D. Gupta, M. Nath, and U. , Divergence in patterns of leaf growth polarity is associated with the expression divergence of miR396, Plant Cell, vol.27, pp.2785-2799, 2015.

T. J. Dewitt, Expanding the phenotypic plasticity paradigm to broader views of trait space and ecological function, Current Zoology, vol.62, issue.5, pp.463-473, 2016.
DOI : 10.1093/cz/zow085

T. J. Dewitt and S. M. Scheiner, Phenotypic Plasticity: Functional and Conceptual Approaches, 2004.

S. Díaz, J. Kattge, J. H. Cornelissen, I. J. Wright, S. Lavorel et al., The global spectrum of plant form and function, Nature, vol.81, issue.7585, pp.167-171, 1038.
DOI : 10.1038/nature16489

J. Doebley, The Genetics of Maize Evolution, Annual Review of Genetics, vol.38, issue.1, pp.37-59, 2004.
DOI : 10.1146/annurev.genet.38.072902.092425

S. Douady, C. , and Y. , Phyllotaxis as a Dynamical Self Organizing Process Part I: The Spiral Modes Resulting from Time-Periodic Iterations, Journal of Theoretical Biology, vol.178, issue.3, pp.255-273, 1996.
DOI : 10.1006/jtbi.1996.0024

M. C. Drew, COMPARISON OF THE EFFECTS OF A LOCALISED SUPPLY OF PHOSPHATE, NITRATE, AMMONIUM AND POTASSIUM ON THE GROWTH OF THE SEMINAL ROOT SYSTEM, AND THE SHOOT, IN BARLEY, New Phytologist, vol.3, issue.3, pp.479-490, 1975.
DOI : 10.1007/BF01373498

V. M. Dunbabin, J. A. Postma, A. Schnepf, L. Pagès, M. Javaux et al., Modelling root?soil interactions using three?dimensional models of root growth, architecture and function, Plant and Soil, vol.192, issue.3, pp.93-124, 2013.
DOI : 10.1007/s11104-013-1769-y

H. Edelsbrunner and J. Harer, Computational Topology: An Introduction, 2010.
DOI : 10.1090/mbk/069

A. R. Ennos, Wind as an ecological factor, Trends in Ecology & Evolution, vol.12, issue.3, pp.108-111, 1997.
DOI : 10.1016/S0169-5347(96)10066-5

K. Esau, Anatomy of Seed Plants, Soil Science, vol.90, issue.2, 1960.
DOI : 10.1097/00010694-196008000-00031

S. A. Etnier and S. Vogel, Reorientation of Daffodil (Narcissus: Amaryllidaceae) Flowers in Wind: Drag Reduction and Torsional Flexibility, American Journal of Botany, vol.87, issue.1, pp.29-32, 2000.
DOI : 10.2307/2656682

T. Feng, P. J. Bradbury, P. J. Brown, H. Hung, Q. Sun et al., Genome-wide association study of leaf architecture in the maize nested association mapping population, Nat. Genet, vol.43, pp.159-162, 2011.

Z. Feng, Y. Chen, T. Hakala, and J. Hyyppä, Range calibration of airborne profiling radar used in forest inventory, 2016 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), 2016.
DOI : 10.1109/IGARSS.2016.7730742

F. Fiorani, U. Rascher, S. Jahnke, and U. Schurr, Imaging plants dynamics in heterogenic environments, Current Opinion in Biotechnology, vol.23, issue.2, 2012.
DOI : 10.1016/j.copbio.2011.12.010

A. H. Fitter, AN ARCHITECTURAL APPROACH TO THE COMPARATIVE ECOLOGY OF PLANT ROOT SYSTEMS, New Phytologist, vol.39, pp.61-77, 1987.
DOI : 10.1111/j.1469-8137.1987.tb04683.x

A. Frary, T. C. Nesbitt, A. Frary, S. Grandillo, E. Van-der-knaap et al., fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size, Science, vol.289, issue.5476, pp.85-88, 2000.
DOI : 10.1126/science.289.5476.85

W. E. Friedman and P. K. Diggle, Charles Darwin and the Origins of Plant Evolutionary Developmental Biology, The Plant Cell, vol.23, issue.4, pp.1194-1207, 2011.
DOI : 10.1105/tpc.111.084244

H. Fujita, K. Toyokura, K. Okada, and M. Kawaguchi, Reaction-Diffusion Pattern in Shoot Apical Meristem of Plants, PLoS ONE, vol.16, issue.3, 2011.
DOI : 10.1371/journal.pone.0018243.s024

T. Galkovskyi, Y. Mileyko, A. Bucksch, B. Moore, O. Symonova et al., GiA Roots: software for the high throughput analysis of plant root system architecture, BMC Plant Biology, vol.12, issue.1, pp.116-126, 2012.
DOI : 10.1186/1471-2229-8-82

C. Godin, E. Costes, and H. Sinoquet, A Method for Describing Plant Architecture which Integrates Topology and Geometry, Annals of Botany, vol.84, issue.3, pp.343-357, 1999.
DOI : 10.1006/anbo.1999.0923
URL : https://hal.archives-ouvertes.fr/hal-00827477

C. Godin and P. Ferraro, Quantifying the Degree of Self-Nestedness of Trees: Application to the Structural Analysis of Plants, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.4, pp.688-70329, 2009.
DOI : 10.1109/TCBB.2009.29
URL : https://hal.archives-ouvertes.fr/inria-00353645

C. Godin and H. Sinoquet, Functional-structural plant modelling, New Phytologist, vol.166, issue.3, pp.705-708, 2005.
DOI : 10.1111/j.1469-8137.2005.01445.x
URL : https://hal.archives-ouvertes.fr/hal-00830073

J. W. Goethe, Versuch die Metamorphose der Pflanzen zu erklaren, 1790.
DOI : 10.5962/bhl.title.127448

S. A. Goff, M. Vaughn, S. Mckay, E. Lyons, A. E. Stapleton et al., The iPlant Collaborative: Cyberinfrastructure for Plant Biology, Frontiers in Plant Science, vol.2, 2011.
DOI : 10.3389/fpls.2011.00034
URL : http://doi.org/10.3389/fpls.2011.00034

R. H. Grant and P. B. Green, The scaling of flow in vegetative structures Expression of pattern in plants: combining molecular and calculus-based biophysical paradigms, Boundary Layer Meteorol. Am. J. Bot, vol.27, issue.86, pp.171-184, 1983.

R. N. Gutenkunst, J. J. Waterfall, F. P. Casey, K. S. Brown, C. R. Myers et al., Universally sloppy parameter sensitivities in systems biology models, PLoS Comput. Biol, 2007.
DOI : 10.1371/journal.pcbi.0030189.eor
URL : http://doi.org/10.1371/journal.pcbi.0030189.eor

F. Hallé, Architecture and Growth of Tropical Trees Exemplified by the Euphorbiaceae, Biotropica, vol.3, issue.1, pp.56-62, 1971.
DOI : 10.2307/2989706

F. Hallé, Modular Growth in Seed Plants, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.313, issue.1159, p.26, 1986.
DOI : 10.1098/rstb.1986.0026

O. Hamant, M. G. Heisler, H. Jönsson, P. Krupinski, M. Uyttewaal et al., Developmental Patterning by Mechanical Signals in Arabidopsis, Science, vol.5, issue.12, pp.1650-1655, 2008.
DOI : 10.1105/tpc.5.12.1725
URL : https://hal.archives-ouvertes.fr/hal-00412612

H. Hofhuis, D. Moulton, T. Lessinnes, A. L. Routier-kierzkowska, R. J. Bomphrey et al., Morphomechanical Innovation Drives Explosive Seed Dispersal, Cell, vol.166, issue.1, pp.222-233, 2016.
DOI : 10.1016/j.cell.2016.05.002
URL : http://doi.org/10.1016/j.cell.2016.05.002

T. Hohm, E. Zitzler, and R. Simon, A Dynamic Model for Stem Cell Homeostasis and Patterning in Arabidopsis Meristems, PLoS ONE, vol.5, issue.2, 2010.
DOI : 10.1371/journal.pone.0009189.s011

H. S. Horn, The Adaptive Geometry of Trees, 1971.

O. E. Jensen and J. A. Fozard, Multiscale Models in the Biomechanics of Plant Growth, Physiology, vol.30, issue.2, 2015.
DOI : 10.1152/physiol.00030.2014

H. Jönsson, M. Heisler, G. V. Reddy, V. Agrawal, V. Gor et al., Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem Combining lidar and synthetic aperture radar data to estimate forest biomass: status and prospects, Bioinformatics, vol.213390, issue.6, pp.232-240, 2005.

D. R. Kaplan, The Science of Plant Morphology: Definition, History, and Role in Modern Biology, American Journal of Botany, vol.88, issue.10, pp.1711-1741, 2001.
DOI : 10.2307/3558347

D. G. Kendall, Shape Manifolds, Procrustean Metrics, and Complex Projective Spaces, Bulletin of the London Mathematical Society, vol.16, issue.2, pp.81-121, 1984.
DOI : 10.1112/blms/16.2.81
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.452.9838

K. Kenis and J. Keulemans, Study of tree architecture of apple (Malus?????domestica Borkh.) by QTL analysis of growth traits, Molecular Breeding, vol.92, issue.3, pp.193-208, 2007.
DOI : 10.1007/s11032-006-9022-5

S. Kimura, D. Koenig, J. Kang, F. Y. Yoong, and N. Sinha, Natural Variation in Leaf Morphology Results from Mutation of a Novel KNOX Gene, Current Biology, vol.18, issue.9, pp.672-677, 2008.
DOI : 10.1016/j.cub.2008.04.008

M. S. Kitazawa and K. Fujimoto, A Dynamical Phyllotaxis Model to Determine Floral Organ Number, PLOS Computational Biology, vol.96, issue.545, 2015.
DOI : 10.1371/journal.pcbi.1004145.s008

L. X. Ku, W. M. Zhao, J. Zhang, L. C. Wu, C. L. Wang et al., Quantitative trait loci mapping of leaf angle and leaf orientation value in maize (Zea mays L.), Theoretical and Applied Genetics, vol.32, issue.9, pp.951-959, 2010.
DOI : 10.1007/s00122-010-1364-z

F. P. Kuhl and C. R. Giardina, Elliptic Fourier features of a closed contour, Computer Graphics and Image Processing, vol.18, issue.3, pp.236-258, 1982.
DOI : 10.1016/0146-664X(82)90034-X

F. Kumi, M. Hanping, H. Jianping, and I. Ullah, Review of applying X-ray computed tomography for imaging soil-root physical and biological processes, Int. J. Agric. Biol. Eng, vol.8, pp.1-14, 2015.

W. Kurth, Growth Grammar Interpreter Grogra 2.4-A Software Tool for the 3-Dimensional Interpretation of Stochastic, Sensitive Growth Grammars in the Context of Plant Modelling, 1994.

K. Kvilekval, D. Fedorov, B. Obara, A. Singh, B. S. Manjunath et al., Bisque: a platform for bioimage analysis and management Landmark-free statistical analysis of the shape of plant leaves, Bioinformatics J. Theor. Biol, vol.26, issue.363, pp.544-552, 2010.

N. B. Langlade, X. Feng, T. Dransfield, L. Copsey, A. I. Hanna et al., Evolution through genetically controlled allometry space, Proceedings of the National Academy of Sciences, vol.307, issue.5708, pp.10221-10226, 2005.
DOI : 10.1126/science.1105201
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1177394

S. Leiboff, X. Li, H. C. Hu, N. Todt, J. Yang et al., Genetic control of morphometric diversity in the maize shoot apical meristem, Nature Communications, vol.40, 2015.
DOI : 10.1038/ncomms9974

M. Li, K. Duncan, C. N. Topp, and D. H. Chitwood, Persistent homology and the branching topologies of plants, American Journal of Botany, vol.104, issue.3, pp.349-353, 2017.
DOI : 10.3732/ajb.1700046

G. Lobet, L. Pagès, and X. Draye, A Novel Image-Analysis Toolbox Enabling Quantitative Analysis of Root System Architecture, Plant Physiology, vol.157, issue.1, pp.29-39, 2011.
DOI : 10.1104/pp.111.179895

G. Lobet, M. P. Pound, J. Diener, C. Pradal, X. Draye et al., Root System Markup Language: Toward a Unified Root Architecture Description Language, Plant Physiology, vol.167, issue.3, pp.617-627, 2015.
DOI : 10.1104/pp.114.253625
URL : https://hal.archives-ouvertes.fr/hal-01113767

J. P. Lynch, J. P. Lynch, and K. M. Brown, Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems New roots for agriculture: exploiting the root phenome, Ann. Bot. Philos. Trans. R. Soc. B, vol.112, issue.367, pp.347-357, 2012.

R. Macpherson and B. Schweinhart, Measuring shape with topology, Journal of Mathematical Physics, vol.53, issue.7, 2012.
DOI : 10.1007/s00454-004-1146-y

C. C. Martinez, D. H. Chitwood, R. S. Smith, and N. R. Sinha, Left-right leaf asymmetry in decussate and distichous phyllotactic systems, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.37, p.20150412, 2016.
DOI : 10.1101/043869
URL : http://pubman.mpdl.mpg.de/pubman/item/escidoc:2326725/component/escidoc:2377691/martinez_phil_trans_B_2016_OA.pdf

E. Mayr, Biological Classification: Toward a Synthesis of Opposing Methodologies, Science, vol.214, issue.4520, pp.510-516, 1981.
DOI : 10.1126/science.214.4520.510

H. Meinhardt, Morphogenesis of lines and nets, 1976.

H. Meinhardt, Out-of-phase oscillations and traveling waves with unusual properties: the use of three-component systems in biology, Physica D: Nonlinear Phenomena, vol.199, issue.1-2, 2004.
DOI : 10.1016/j.physd.2004.08.018

H. Meinhardt and A. Gierer, Applications of a theory of biological pattern formation based on lateral inhibition, J. Cell Sci, vol.15, pp.321-346, 1974.

L. A. Miller, A. Santhanakrishnan, S. Jones, C. Hamlet, K. Mertens et al., Reconfiguration and the reduction of vortex-induced vibrations in broad leaves, Journal of Experimental Biology, vol.215, issue.15, pp.2716-2727, 2012.
DOI : 10.1242/jeb.064501

N. D. Miller, B. M. Parks, and E. P. Spalding, Computer-vision analysis of seedling responses to light and gravity, The Plant Journal, vol.142, issue.2, 2007.
DOI : 10.1111/j.1365-313X.2007.03237.x

J. W. Milnor, Morse Theory Das gesetz des minimums und das gesetz des abnehmenden bodenertrages, Landw. Jahrb, vol.38, pp.537-552, 1909.

A. J. Monforte, A. I. Diaz, A. Caño-delgado, E. Van-der-knaap, B. Moulia et al., The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon The power and control of gravitropic movements in plants: a biomechanical and systems biology view Plant phenotypic plasticity in a changing climate, J. Exp. Bot. J. Exp. Bot. Trends Plant Sci, vol.65, issue.15, pp.4625-4637, 2009.

K. L. Nielsen, J. P. Lynch, A. G. Jablokow, C. , P. S. Niklas et al., Carbon cost of root systems: an architectural approach, Plant and Soil, vol.151, issue.6, pp.161-169, 1992.
DOI : 10.1007/BF00009972

K. J. Niklas, Plant Allometry: The Scaling of form and Process, 1994.

K. J. Niklas, The Evolutionary Biology of Plants, 1997.

S. V. Nikolaev, A. V. Penenko, V. V. Lavreha, E. D. Mjolsness, and N. A. Kolchanov, A model study of the role of proteins CLV1, CLV2, CLV3, and WUS in regulation of the structure of the shoot apical meristem, Russian Journal of Developmental Biology, vol.38, issue.6, pp.383-388, 2007.
DOI : 10.1134/S1062360407060069

K. Palacio-lópez, B. Beckage, S. Scheiner, and J. Molofsky, The ubiquity of phenotypic plasticity in plants: a synthesis, Ecology and Evolution, vol.167, issue.16, pp.3389-3400, 2015.
DOI : 10.1002/ece3.1603

W. Palubicki, A Computational Study of Tree Architecture, 2013.

W. Palubicki, K. Horel, S. Longay, A. Runions, B. Lane et al., Self-organizing tree models for image synthesis, ACM Trans. Graph, vol.28, pp.58-68, 2009.
DOI : 10.1145/1576246.1531364
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.324.1531

I. Paran and E. Van-der-knaap, Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper, Journal of Experimental Botany, vol.58, issue.14, pp.3841-3852, 2007.
DOI : 10.1093/jxb/erm257

A. Peaucelle, S. A. Braybrook, L. Guillou, L. Bron, E. Kuhlemeier et al., Pectin-Induced Changes in Cell Wall Mechanics Underlie Organ Initiation in Arabidopsis, Current Biology, vol.21, issue.20, pp.1720-1726, 2011.
DOI : 10.1016/j.cub.2011.08.057
URL : http://doi.org/10.1016/j.cub.2011.08.057

H. Poorter, Ü. Niinemets, A. Walter, F. Fiorani, and U. Schurr, A method to construct dose?response curves for a wide range of environmental factors and plant traits by means of a meta-analysis of phenotypic data Root cortical aerenchyma enhances the growth of maize on soils with suboptimal availability of nitrogen, phosphorus, and potassium, J. Exp. Bot. Plant Physiol, vol.61, issue.156, pp.2043-2055, 1104.

C. Pradal, S. Artzet, J. Chopard, D. Dupuis, C. Fournier et al., InfraPhenoGrid: A scientific workflow infrastructure for plant phenomics on the Grid, Future Generation Computer Systems, vol.67, pp.341-353, 2017.
DOI : 10.1016/j.future.2016.06.002
URL : https://hal.archives-ouvertes.fr/hal-01336655

C. Pradal, S. Dufour-kowalski, F. Boudon, C. Fournier, and C. Godin, OpenAlea: a visual programming and component-based software platform for plant modelling, Functional Plant Biology, vol.35, issue.10, pp.751-760, 1071.
DOI : 10.1071/FP08084
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.513.3232

C. Pradal, C. Fournier, P. Valduriez, and S. Cohen-boulakia, OpenAlea, Proceedings of the 27th International Conference on Scientific and Statistical Database Management, SSDBM '15, 2015.
DOI : 10.1145/2791347.2791365
URL : https://hal.archives-ouvertes.fr/hal-00831785

C. Pradal, G. Varoquaux, and H. P. Langtangen, Publishing scientific software matters, Thinking in Patterns: Fractals and Related Phenomena in Nature, pp.311-312, 2004.
DOI : 10.1016/j.jocs.2013.08.001
URL : https://hal.archives-ouvertes.fr/hal-00858663

P. Prusinkiewicz, P. B. De-reuille, and A. Lindenmayer, Constraints of space in plant development, Journal of Experimental Botany, vol.61, issue.8, pp.2117-2129, 1990.
DOI : 10.1093/jxb/erq081

P. Prusinkiewicz, L. Mündermann, R. Karwowski, L. , and B. , The use of positional information in the modeling of plants, Proceedings of the 28th annual conference on Computer graphics and interactive techniques , SIGGRAPH '01, pp.289-300, 2001.
DOI : 10.1145/383259.383291

P. Prusinkiewicz, A. Runions, P. Raumonen, M. Kaasalainen, M. Åkerblom et al., Computational models of plant development and form Fast automatic precision tree models from terrestrial laser scanner data. Remote Sens, New Phytol, vol.1933390, issue.5, pp.549-569, 2012.

K. A. Razak, A. Bucksch, M. Damen, C. Van-westen, M. Straatsma et al., Characterizing Tree Growth Anomaly Induced by Landslides Using LiDAR, Landslide Science and Practice: Landslide Inventory, Susceptibility and Hazard Zoning, pp.235-241, 2013.
DOI : 10.1007/978-3-642-31325-7_31

R. Rellán-Álvarez, G. Lobet, and J. R. Dinneny, Environmental Control of Root System Biology, Annual Review of Plant Biology, vol.67, issue.1, pp.619-642, 2016.
DOI : 10.1146/annurev-arplant-043015-111848

R. Rellán-Álvarez, G. Lobet, H. Lindner, P. L. Pradier, J. Sebastian et al., GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems, 2015.

L. Remmler and A. G. Rolland-lagan, Computational Method for Quantifying Growth Patterns at the Adaxial Leaf Surface in Three Dimensions, PLANT PHYSIOLOGY, vol.159, issue.1, pp.27-39, 2012.
DOI : 10.1104/pp.112.194662

M. Reuter, S. Biasotti, D. Giorgi, G. Patanè, and M. Spagnuolo, Discrete Laplace?Beltrami operators for shape analysis and segmentation, Computers & Graphics, vol.33, issue.3, pp.381-390, 2009.
DOI : 10.1016/j.cag.2009.03.005
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.157.757

N. E. Robbins and J. R. Dinneny, The divining root: moisture-driven responses of roots at the micro- and macro-scale, Journal of Experimental Botany, vol.66, issue.8, pp.2145-2154, 2015.
DOI : 10.1093/jxb/eru496

J. S. Roden, R. W. Pearcy, A. G. Rolland-lagan, J. A. Bangham, C. et al., Effect of leaf flutter on the light environment of poplars, Oecologia, vol.25, issue.2, pp.201-207, 1038.
DOI : 10.1007/BF00317672

M. Ron, M. W. Dorrity, M. De-lucas, T. Toal, R. I. Hernandez et al., Identification of Novel Loci Regulating Interspecific Variation in Root Morphology and Cellular Development in Tomato, PLANT PHYSIOLOGY, vol.162, issue.2, pp.755-768, 2013.
DOI : 10.1104/pp.113.217802

D. L. Royer, L. A. Meyerson, K. M. Robertson, A. , and J. M. , Phenotypic Plasticity of Leaf Shape along a Temperature Gradient in Acer rubrum, PLoS ONE, vol.83, issue.10, 2009.
DOI : 10.1371/journal.pone.0007653.s001

A. Runions, B. Lane, P. Prusinkiewicz, S. Ebert, and . Merillou, Modeling trees with a space colonization algorithm, Proceedings of the 2007 Eurographics Workshop on Natural Phenomena, pp.63-70, 2007.

D. Ryan, The Global Plants Initiative Celebrates its Achievements and Plans for the Future, Taxon, vol.62, issue.2, pp.417-418, 2013.
DOI : 10.12705/622.26

V. Segura, C. E. Durel, C. , and E. , Dissecting apple tree architecture into genetic, ontogenetic and environmental effects: QTL mapping, Tree Genetics & Genomes, vol.166, issue.1, pp.165-179, 2009.
DOI : 10.1007/s11295-008-0181-x

D. Seidel, P. Schall, M. Gille, and C. Ammer, Relationship between tree growth and physical dimensions of Fagus sylvatica crowns assessed from terrestrial laser scanning, iForest - Biogeosciences and Forestry, vol.8, issue.6, pp.735-742, 2015.
DOI : 10.3832/ifor1566-008
URL : http://ir.library.oregonstate.edu/xmlui/bitstream/1957/58021/1/SeidelDominikForestEcosystSocRelationshipBetweenTree.pdf

G. F. Smith, Y. Steenkamp, R. R. Klopper, S. J. Siebert, A. et al., The price of collecting life, Nature, vol.7, issue.6930, pp.375-376, 2003.
DOI : 10.1038/417017a

E. P. Spalding and N. D. Miller, Image analysis is driving a renaissance in growth measurement, Current Opinion in Plant Biology, vol.16, issue.1, 2013.
DOI : 10.1016/j.pbi.2013.01.001
URL : http://doi.org/10.1016/j.pbi.2013.01.001

T. A. Steeves and I. M. Sussex, Patterns in Plant Development, 1989.
DOI : 10.1017/CBO9780511626227

O. Symonova, C. N. Topp, and H. Edelsbrunner, DynamicRoots: A Software Platform for the Reconstruction and Analysis of Growing Plant Roots, PLOS ONE, vol.81, issue.3, 2015.
DOI : 10.1371/journal.pone.0127657.s001

M. Tester and P. Langridge, Breeding Technologies to Increase Crop Production in a Changing World, Science, vol.325, issue.5941, pp.818-822, 2010.
DOI : 10.1126/science.1174320

A. S. Thom, The exchange of momentum, mass, and heat between an artificial leaf and the airflow in a wind-tunnel, Quarterly Journal of the Royal Meteorological Society, vol.84, issue.399, pp.44-55, 1968.
DOI : 10.1002/qj.49709439906

A. M. Thompson, J. Yu, M. C. Timmermans, P. Schnable, J. C. Crants et al., Diversity of Maize Shoot Apical Meristem Architecture and Its Relationship to Plant Morphology, G3: Genes|Genomes|Genetics, vol.5, issue.5, pp.819-827, 2015.
DOI : 10.1534/g3.115.017541

F. Tian, P. J. Bradbury, P. J. Brown, H. Hung, Q. Sun et al., Genome-wide association study of leaf architecture in the maize nested association mapping population, Nature Genetics, vol.26, issue.2, pp.159-162, 2011.
DOI : 10.1126/science.1178534

S. Tisné, M. Reymond, D. Vile, J. Fabre, M. Dauzat et al., Combined Genetic and Modeling Approaches Reveal That Epidermal Cell Area and Number in Leaves Are Controlled by Leaf and Plant Developmental Processes in Arabidopsis, PLANT PHYSIOLOGY, vol.148, issue.2, pp.1117-1127, 2008.
DOI : 10.1104/pp.108.124271

C. N. Topp, A. S. Iyer-pascuzzi, J. T. Anderson, C. R. Lee, P. R. Zurek et al., 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture, Proceedings of the National Academy of Sciences, vol.84, issue.1595, pp.1695-1704, 2013.
DOI : 10.1098/rstb.2011.0291

S. K. Truong, R. F. Mccormick, W. L. Rooney, and J. E. Mullet, Harnessing Genetic Variation in Leaf Angle to Increase Productivity of Sorghum bicolor, Genetics, vol.201, issue.3, pp.1229-1238, 2015.
DOI : 10.1534/genetics.115.178608

A. M. Turing, The chemical basis of morphogenesis, Philos. Trans. R. Soc. B, vol.237, 1952.

A. M. Turing, Collected Works of AM Turing. Morphogenesis, P.T. Saunders, 1992.

Y. Uga, K. Sugimoto, S. Ogawa, J. Rane, M. Ishitani et al., Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions, Nature Genetics, vol.36, issue.9, pp.1097-1102, 2013.
DOI : 10.1007/s10681-007-9605-1

D. Van-dusschoten, R. Metzner, J. Kochs, J. A. Postma, D. Pflugfelder et al., Quantitative 3D Analysis of Plant Roots growing in Soil using Magnetic Resonance Imaging, Plant Physiology, vol.170, pp.1176-1188, 2016.
DOI : 10.1104/pp.15.01388

S. Vogel, Drag and Reconfiguration of Broad Leaves in High Winds, Journal of Experimental Botany, vol.40, issue.8, pp.941-948, 1989.
DOI : 10.1093/jxb/40.8.941

S. Vogel, Drag reduction by leaf aquaplaning in Hexastylis (Aristolochiaceae) and other plant species in floods, Journal of the North American Benthological Society, vol.25, issue.1, pp.2-8, 2006.
DOI : 10.1899/0887-3593(2006)25[2:DRBLAI]2.0.CO;2

S. Vogel, The Life of a Leaf Airborne and Terrestrial Laser Scanning, 2010.

T. Watanabe, J. S. Hanan, P. M. Room, T. Hasegawa, H. Nakagawa et al., Rice Morphogenesis and Plant Architecture: Measurement, Specification and the Reconstruction of Structural Development by 3D Architectural Modelling, Annals of Botany, vol.95, issue.7, pp.1131-1143, 2005.
DOI : 10.1093/aob/mci136

J. J. Wiens, Coding morphological variation within species and higher taxa for phylogenetic analysis, Phylogenetic Analysis of Morphological Data, pp.115-145, 2000.

P. Wilf, S. Zhang, S. Chikkerur, S. A. Little, S. L. Wing et al., Computer vision cracks the leaf code, Proceedings of the National Academy of Sciences, vol.46, issue.1-2, pp.3305-3310, 2016.
DOI : 10.1109/TPAMI.2010.161
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4812720

L. Willis, Y. Refahi, R. Wightman, B. Landrein, J. Teles et al., apical stem cell niche, Proceedings of the National Academy of Sciences, vol.29, issue.7572, pp.8238-8246, 2016.
DOI : 10.1038/nmeth.1472

R. Woltereck, Weitere experimentelle untersuchungen über artveränderung, speziel über das wesen quantitativer artunterschiede bei Daphniden. (Further investigations of type variation, specifically concerning the nature of quantitative differences between varieties of Daphnia), Verh. Deutsch. Zool. Ges, vol.19, pp.110-173, 1909.

W. Yang, Z. Guo, C. Huang, L. Duan, G. Chen et al., Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice, Nature Communications, vol.5, 2014.
DOI : 10.1073/pnas.1007431107
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214417

J. Zhang, L. X. Ku, Z. P. Han, S. L. Guo, H. J. Liu et al., The ZmCLA4 gene in the qLA4-1 QTL controls leaf angle in maize, 2014.

J. Zhu, K. M. Brown, and J. P. Lynch, Root cortical aerenchyma improves the drought tolerance of maize (Zea mays L.). Plant Cell Environ, pp.740-749, 2010.

J. Zhu, S. M. Kaeppler, and J. P. Lynch, Mapping of QTLs for lateral root branching and length in maize (Zea mays L.) under differential phosphorus supply, Theoretical and Applied Genetics, vol.21, issue.4, pp.688-695, 2005.
DOI : 10.1007/s00122-005-2051-3

P. R. Zurek, C. N. Topp, and P. N. Benfey, Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture, Plant Physiology, vol.167, issue.4, pp.1487-1496, 2015.
DOI : 10.1104/pp.114.251751

. Pascuzzi, . Klein, . Leiboff, . Li, . Lynch et al., This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited