J. L. Araus and J. E. Cairns, Field high-throughput phenotyping : the new crop breeding frontier, vol.19, 2014.

C. Baey, A. Mathieu, A. Jullien, S. Trevezas, and P. Cournède, Mixed-effects estimation in dynamic models of plant growth for the assessment of inter-individual variability, Journal of Agricultural, Biological and Environmental Statistics, vol.23, issue.2, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01766698

P. Bancal and F. Soltani, Source-sink partitioning. do we need Münch ?, Journal of Experimental Botany, vol.53, issue.376, 2002.

D. Barthélémy and Y. Caraglio, Plant architecture : a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny, Annals of botany, vol.99, issue.3, 2007.

N. Bertin, P. Martre, M. Génard, B. Quilot, and C. Salon, Under what circumstances can process-based simulation models link genotype to phenotype for complex traits ? case-study of fruit and grain quality traits, Journal of Experimental Botany, vol.61, issue.4, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01189446

B. Bouman, H. Van-keulen, H. Van-laar, and R. Rabbinge, The 'school of de wit'crop growth simulation models : a pedigree and historical overview, Agricultural systems, vol.52, issue.2-3, 1996.

N. Brisson, B. Mary, D. Ripoche, M. H. Jeuffroy, F. Ruget et al., STICS : a generic model for the simulation of crops and their water and nitrogen balances. I. Theory and parameterization applied to wheat and corn, vol.18, pp.5-6, 1998.
URL : https://hal.archives-ouvertes.fr/hal-00885888

Y. Chen and P. Cournède, Data assimilation to reduce uncertainty of crop model prediction with convolution particle filtering, Ecological Modelling, vol.290, pp.165-177, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00997728

P. Cournède, M. Kang, A. Mathieu, J. Barczi, H. Yan et al., Reffye. Structural factorization of plants to compute their functional and architectural growth, Simulation, vol.82, issue.7, 2006.

P. Cournède, V. Letort, A. Mathieu, M. Z. Kang, S. Lemaire et al., Some parameter estimation issues in functional-structural plant modelling, Mathematical Modelling of Natural Phenomena, vol.6, issue.2, 2011.

P. Cournède, Y. Chen, Q. Wu, C. Baey, and B. Bayol, Development and evaluation of plant growth models : Methodology and implementation in the pygmalion platform, Mathematical Modelling of Natural Phenomena, vol.8, issue.4, 2013.

S. De-dorlodot, B. Forster, L. Pagès, A. Price, R. Tuberosa et al., Root system architecture : opportunities and constraints for genetic improvement of crops, Trends in plant science, vol.12, issue.10, 2007.

B. De-reffye and . Hu, Relevant qualitative and quantitative choices for building an efficient dynamic plant growth model : Greenlab case, International Symposium on Plant Growth Modeling, Simulation, Visualization and their Applications-PMA'03, 2003.
URL : https://hal.archives-ouvertes.fr/inria-00126213

P. De-reffye, C. Edelin, J. Françon, M. Jaeger, and C. Puech, Plant models faithful to botanical structure and development, Proceedings of the 15th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH '88, 1988.

P. De-reffye, T. Fourcaud, F. Blaise, D. Barthélémy, and F. Houllier, A functional model of tree growth and tree architecture, Silva Fennica, vol.31, issue.3, 1997.

C. De-wit, H. Van-laar, and H. Van-keulen, Physiological potential of crop production, Plant breeding perspectives. Pudoc, 1979.

L. Dupuy, P. J. Gregory, and A. G. Bengough, Root growth models : towards a new generation of continuous approaches, Journal of experimental botany, issue.8, p.61, 2010.

G. Farquhar and S. V. Caemmerer, Modelling of photosynthetic response to environmental conditions, Physiological plant ecology II, pp.549-587, 1982.

C. Fournier and B. Andrieu, A 3d architectural and process-based model of maize development, Annals of botany, vol.81, issue.2, 1998.

M. Génard, N. Bertin, C. Borel, P. Bussières, H. Gautier et al., Towards a virtual fruit focusing on quality : modelling features and potential uses, Journal of Experimental Botany, vol.58, issue.5, pp.917-928, 2007.

F. Hallé and R. Oldeman, Essai sur l'architecture et la dynamique de croissance des arbres tropicaux, 1970.

C. A. Jones, J. R. Kiniry, and P. Dyke, CERES-Maize : A simulation model of maize growth and development, 1986.

M. Kang, P. Cournède, P. De-reffye, D. Auclair, and B. Hu, Analytical study of a stochastic plant growth model : application to the greenlab model, Mathematics and Computers in Simulation, vol.78, issue.1, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00306691

M. Launay and M. Guerif, Assimilating remote sensing data into a crop model to improve predictive performance for spatial applications. Agriculture, ecosystems & environment, vol.111, 2005.

J. Lecoeur, R. Poiré-lassus, A. Christophe, B. Pallas, P. Casadebaig et al., Quantifying physiological determinants of genetic variation for yield potential in sunflower. SUNFLO : a model-based analysis, Functional plant biology, vol.38, issue.3, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00964303

S. Lemaire, F. Maupas, P. Cournède, and P. De-reffye, A morphogenetic crop model for sugar-beet (beta vulgaris l.). In Crop Modeling and Decision Support, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00336415

V. Letort, P. Cournède, A. Mathieu, P. De-reffye, and T. Constant, Parametric identification of a functional-structural tree growth model and application to beech trees (Fagus sylvatica), Functional Plant Biology, vol.35, issue.10, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00529461

V. Letort, P. Mahe, P. Cournède, P. De-reffye, and B. Courtois, Quantitative genetics and functional-structural plant growth models : simulation of quantitative trait loci detection for model parameters and application to potential yield optimization, Annals of Botany, vol.101, issue.8, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00288538

C. Loi and P. H. Cournède, Generating Functions of Stochastic L-Systems and Application to Models of Plant Development, Discrete Mathematics & Theoretical Computer Science, DMTCS Proceedings, vol.AI, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01194661

A. Mathieu, P. Cournède, V. Letort, D. Barthélémy, and P. De-reffye, A dynamic model of plant growth with interactions between development and functional mechanisms to study plant structural plasticity related to trophic competition, Annals of Botany, vol.103, issue.8, 2009.
URL : https://hal.archives-ouvertes.fr/halsde-00418643

R. Mccown, G. Hammer, J. Hargreaves, D. Holzworth, and D. Freebairn, Apsim : a novel software system for model development, model testing and simulation in agricultural systems research, Agricultural systems, vol.50, issue.3, 1996.

P. Minchin and M. Thorpe, What determines carbon partitioning between competing sinks, Journal of Experimental Botany, vol.47, 1996.

J. L. Monteith and C. Moss, Climate and the efficiency of crop production in britain, Philosophical Transactions of the Royal Society of London. B, vol.281, 1977.

L. Pagès, G. Vercambre, J. Drouet, F. Lecompte, C. Collet et al., Root typ : a generic model to depict and analyse the root system architecture, Plant and Soil, vol.258, issue.1, 2004.

P. Prusinkiewicz and A. Lindenmayer, The algorithmic beauty of plants, 1990.

P. Prusinkiewicz, A. Lindenmayer, and J. Hanan, Development models of herbaceous plants for computer imagery purposes, Proceedings of the 15th Annual Conference on Computer Graphics and Interactive Techniques, SIGGRAPH '88, 1988.

D. D. Pury and G. Farquhar, Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models, Plant, Cell & Environment, vol.20, issue.5, 1997.

H. Scholten, A. Kassahun, J. C. Refsgaard, T. Kargas, C. Gavardinas et al., A methodology to support multidisciplinary model-based water management, Environmental Modelling & Software, vol.22, 2007.

R. Sievänen, E. Nikinmaa, and J. Perttunen, Evaluation of importance of sapwood senescence on tree growth using the model lignum, Silva Fennica, vol.31, issue.3, 1997.

A. R. Smith, Plants, fractals, and formal languages, ACM SIGGRAPH Computer Graphics, vol.18, issue.3, 1984.

K. A. Sorrensen-cothern, E. D. Ford, and D. G. Sprugel, A model of competition incorporating plasticity through modular foliage and crown development, Ecological Monographs, vol.63, issue.3, 1993.

F. Tardieu, Virtual plants : modelling as a tool for the genomics of tolerance to water deficit, Trends in plant Science, vol.8, issue.1, 2003.

S. Tisne, Y. Serrand, L. Bach, E. Gilbault, R. Ben-ameur et al., Phenoscope : an automated large-scale phenotyping platform offering high spatial homogeneity, The Plant Journal, vol.74, issue.3, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01004455

S. Trevezas and P. Cournède, A sequential monte carlo approach for mle in a plant growth model, Journal of Agricultural, Biological, and Environmental Statistics, vol.18, issue.2, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00796154

F. Varenne, La simulation informatique faceà la «méthode des modèles». Le cas de la croissance des plantes, Nature Sciences Sociétés, vol.11, issue.1, 2003.

G. Viaud, O. Loudet, and P. Cournède, Leaf segmentation and tracking in arabidopsis thaliana combined to an organ-scale plant model for genotypic differentiation, Frontiers in plant science, vol.7, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01602596

Q. Wu, P. Cournède, and A. Mathieu, An efficient computational method for global sensitivity analysis and its application to tree growth modelling, Reliability Engineering & System Safety, p.107, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00639539