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references.bib
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@article{dauzatSimulationLeafTranspiration2001,
title = {Simulation of leaf transpiration and sap flow in virtual plants: model description and application to a coffee plantation in {Costa} {Rica}},
volume = {109},
issn = {0168-1923},
doi = {http://dx.doi.org/10.1016/S0168-1923(01)00236-2},
abstract = {Computer representations of plants (virtual plants) are used as the basis for a model simulating leaf transpiration and sap flow. The virtual plants provide a detailed description of plant geometry and topology and, once positioned in a scene, enable a highly realistic reconstruction of a portion of the canopy. Stomatal conductance as well as energy balance are simulated by the model at the level of individual leaves in order to calculate their transpiration. Leaf transpiration is then cumulated to get the sap flow throughout the plant. Owing to its structure, the model can take into account feedbacks such as the effect of the temperature of a leaf on its stomatal conductance, transpiration and water potential, and in return, the effect of water potential of a leaf on its stomatal conductance. The model has been validated on a coffee tree stand in Costa Rica. The geometry (i.e. 3D position, area and diameter of organs) of six adult coffee trees in a row was measured in the field in order to generate a computer scene. Stomatal conductance, sap flow, water potential and wood hydraulic conductivity were measured for model parameterisation and validation. Analysis of model outputs lead to a correction of leaf boundary layer thickness. After calibration, the model exhibited correct values of transpiration and water potential in different microclimatic conditions.},
number = {2},
journal = {Agricultural and Forest Meteorology},
author = {Dauzat, Jean and Rapidel, Bruno and Berger, André},
year = {2001},
keywords = {Coffea arabica, Leaf transpiration, Plant architecture, Sap flow, Simulation model, Virtual plant},
pages = {143--160},
file = {Dauzat et al_2001_Simulation of leaf transpiration and sap flow in virtual plants.pdf:D\:\\OneDrive\\Documents\\zotero\\Dauzat et al_2001_Simulation of leaf transpiration and sap flow in virtual plants2.pdf:application/pdf}
}
@article{perezDesigningOilPalm2017,
title = {Designing oil palm architectural ideotypes for optimal light interception and carbon assimilation through a sensitivity analysis of leaf traits},
volume = {121},
issn = {0305-7364},
doi = {10.1093/aob/mcx161},
abstract = {Background and Aims: Enhancement of light harvesting in annual crops has successfully led to yield increases since the green revolution. Such an improvement has mainly been achieved by selecting plants with optimal canopy architecture for specific agronomic practices. For perennials such as oil palm, breeding programmes were focused more on fruit yield, but now aim at exploring more complex traits. The aim of the present study is to investigate potential improvements in light interception and carbon assimilation in the study case of oil palm, by manipulating leaf traits and proposing architectural ideotypes. Methods: Sensitivity analyses (Morris method and metamodel) were performed on a functional–structural plant model recently developed for oil palm which takes into account genetic variability, in order to virtually assess the impact of plant architecture on light interception efficiency and potential carbon acquisition. Key Results: The most sensitive parameters found over plant development were those related to leaf area (rachis length, number of leaflets, leaflet morphology), although fine attributes related to leaf geometry showed increasing influence when the canopy became closed. In adult stands, optimized carbon assimilation was estimated on plants with a leaf area index between 3.2 and 5.5 m2 m−2 (corresponding to usual agronomic conditions), with erect leaves, short rachis and petiole, and high number of leaflets on the rachis. Four architectural ideotypes for carbon assimilation are proposed based on specific combinations of organ dimensions and arrangement that limit mutual shading and optimize light distribution within the plant crown. Conclusions: A rapid set-up of leaf area is critical at young age to optimize light interception and subsequently carbon acquisition. At the adult stage, optimization of carbon assimilation could be achieved through specific combinations of architectural traits. The proposition of multiple morphotypes with comparable level of carbon assimilation opens the way to further investigate ideotypes carrying an optimal trade-off between carbon assimilation, plant transpiration and biomass partitioning.},
language = {eng \%J Annals of Botany},
number = {5},
urldate = {2018-03-15},
journal = {Annals of Botany},
author = {Perez, Raphael P.A. and Dauzat, Jean and Pallas, Benoit and Lamour, Julien and Verley, Philippe and Caliman, Jean-Pierre and Costes, Evelyne and Faivre, Robert},
year = {2017},
keywords = {tree structure, tree architecure, Carbon, Elaeis guineensis, evapotranspiration, leaf, plant nutrition, photosynthesis},
pages = {909--926},
file = {Perez et al_2017_Designing oil palm architectural ideotypes for optimal light interception and.pdf:D\:\\OneDrive\\Documents\\zotero\\Perez et al_2017_Designing oil palm architectural ideotypes for optimal light interception and.pdf:application/pdf}
}
@article{perez3DPlantModel2018,
title = {{3D} plant model assessed by terrestrial {LiDAR} and hemispherical photographs: {A} useful tool for comparing light interception among oil palm progenies},
volume = {249},
issn = {0168-1923},
shorttitle = {{3D} plant model assessed by terrestrial {LiDAR} and hemispherical photographs},
url = {http://www.sciencedirect.com/science/article/pii/S0168192317303817},
doi = {10.1016/j.agrformet.2017.11.008},
abstract = {The paradigm of functional-structural models (FSPM) assumes that studying the detailed organisation of plant structure allows a better understanding of functional processes; in particular the way plants capture light for performing photosynthesis. However, much attention must be paid toward the consistency between virtual plants and plants in the field in terms of size and geometry to accurately evaluate light interception. This paper thus aimed at i) assessing the capacity of a 3D architectural model based on oil palms (Elaeis guineensis) to accurately represent plants structural characteristics at both the scale of the individual plant and the cultivated plot and ii) employing the validated 3D mock-ups to investigate how light interception efficiency varies among progenies that exhibit different architectures. Innovative indicators related to plant geometry and topology were derived from terrestrial LiDAR scanners (TLS) and hemispherical photographs (HP) in order to assess a 3D plant model. Indicators such as plant height, width and volume, gap fractions and solid angle projections were established from field measurements and were compared to equivalent indicators that had been extracted from virtual TLS (VTLS) and virtual HP (VHP) simulated on 3D mock-ups. Indicators were then evaluated for their significance in terms of light interception. Progeny effect on light interception efficiency was finally evaluated for five progenies. The structural indicators estimated from VTLS and VHP were significantly correlated with equivalent indicators estimated from TLS and HP, respectively, and with simulated outputs related to light interception. Light interception efficiencies estimated from validated 3D mock-ups differed significantly among the five progenies under study, most notably along plant development. Our results highlight the relevance of combining TLS- and HP-derived indicators to evaluate the reliability of virtual 3D reconstruction of plants in relation to light capture, at both the plant and plot scales. The study paves the way for further investigations aiming at unravelling the relationships between oil palm architecture and the physiological processes driving its production.},
language = {en},
urldate = {2020-01-24},
journal = {Agricultural and Forest Meteorology},
author = {Perez, Raphael P. A. and Costes, Evelyne and Theveny, Frederic and Griffon, Sebastien and Caliman, Jean-Pierre and Dauzat, Jean},
month = feb,
year = {2018},
keywords = {3D mock-up, Genetic variability, Light interception, Terrestrial LiDAR, Validation},
pages = {250--263},
file = {Perez et al_2018_3D plant model assessed by terrestrial LiDAR and hemispherical photographs.pdf:D\:\\OneDrive\\Documents\\zotero\\Perez et al_2018_3D plant model assessed by terrestrial LiDAR and hemispherical photographs.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\vezy\\Zotero\\storage\\7DGNVYVL\\S0168192317303817.html:text/html}
}
@article{perezIntegratingMixedeffectModels2016,
title = {Integrating mixed-effect models into an architectural plant model to simulate inter- and intra-progeny variability: a case study on oil palm (Elaeis guineensis Jacq.)},
volume = {67},
issn = {0022-0957, 1460-2431},
shorttitle = {Integrating mixed-effect models into an architectural plant model to simulate inter- and intra-progeny variability},
url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/erw203},
doi = {10.1093/jxb/erw203},
abstract = {Three-dimensional (3D) reconstruction of plants is time-consuming and involves considerable levels of data acquisition. This is possibly one reason why the integration of genetic variability into 3D architectural models has so far been largely overlooked. In this study, an allometry-based approach was developed to account for architectural variability in 3D architectural models of oil palm (Elaeis guineensis Jacq.) as a case study. Allometric relationships were used to model architectural traits from individual leaflets to the entire crown while accounting for ontogenetic and morphogenetic gradients. Inter- and intra-progeny variabilities were evaluated for each trait and mixed-effect models were used to estimate the mean and variance parameters required for complete 3D virtual plants. Significant differences in leaf geometry (petiole length, density of leaflets, and rachis curvature) and leaflet morphology (gradients of leaflet length and width) were detected between and within progenies and were modelled in order to generate populations of plants that were consistent with the observed populations. The application of mixed-effect models on allometric relationships highlighted an interesting trade-off between model accuracy and ease of defining parameters for the 3D reconstruction of plants while at the same time integrating their observed variability. Future research will be dedicated to sensitivity analyses coupling the structural model presented here with a radiative balance model in order to identify the key architectural traits involved in light interception efficiency.},
language = {en},
number = {15},
urldate = {2020-02-11},
journal = {Journal of Experimental Botany},
author = {Perez, Raphael P.A. and Pallas, Benoît and Le Moguedec, Gilles and Rey, Herve and Griffon, Sébastien and Caliman, Jean-Pierre and Costes, Evelyne and Dauzat, Jean},
month = aug,
year = {2016},
pages = {4507--4521},
file = {Perez et al. - 2016 - Integrating mixed-effect models into an architectu.pdf:C\:\\Users\\vezy\\Zotero\\storage\\WXPG3BUV\\Perez et al. - 2016 - Integrating mixed-effect models into an architectu.pdf:application/pdf}
}
@inproceedings{vezyLightExchangesDiscrete2020,
address = {Online},
title = {Light exchanges in discrete directions as an alternative to raytracing and radiosity},
url = {https://www.researchgate.net/publication/344340475_Light_exchanges_in_discrete_directions_as_an_alternative_to_raytracing_and_radiosity},
doi = {10.13140/RG.2.2.13421.20968/1},
abstract = {Introduction
Light modelling at the scale of organs is essential to account accurately for the complex interactions between biophysical processes such as photosynthesis, stomatal conductance and energy balance. Yet, the calculation of radiative exchanges at fine scales is computationally-intensive and it remains a hindrance to a widespread use of FSPMs despite advances in light modelling using either radiosity (Chelle and Andrieu, 1998) or raytracing (Bailey, 2018). This study shows that simplifications based on the discretization of radiative fluxes allow processing radiative exchanges in a natural environment while maintaining good accuracy on the simulation of biophysical processes such as carbon assimilation.
Material and Methods
The present study is based on biophysical simulations performed using the ARCHIMED model. Incident radiation is depicted as a set of specular fluxes (i.e. parallel rays) in discrete directions using the sun direction for direct radiation and predefined “turtle” directions for the diffuse radiation. The “turtle” directions are obtained by splitting the sky hemisphere into sectors of equal solid angle (Dauzat et al, 2001). Optionally, direct radiation can be distributed in neighboring "turtle" sectors (turtle only). For each direction, the scene is projected on an image plane and the interception of incident light is deduced from rasterized pixel projections. Additionally, Z-Buffering gives the overlay of scene objects and, in this regard, pixels can be viewed as rays traced from outside down to the ground level. Light scattering can thus be processed similarly to raytracing. In the case of Lambertian objects, we further assume that all rays scattered by an object carry the same energy whatever the “turtle” direction. Net assimilation (An) is calculated with Farquhar’s model (Farquhar et al. 1980), stomatal conductance with Medlyn’s model (Medlyn et al. 2011) and the leaf temperature is found by solving the energy balance of the system. Simulations are run on a dense three-dimensional scene including two palms (Elaeis guineensis) with the following configuration: latitude= 15°, Day of year 71, time steps of 30mn, clearness index Kt= 0.5. A “toricity” option is used to generate a virtually infinite canopy. The number of “turtle” directions is set to 6, 16, 46 or 136. The sun position is either integrated into the turtle or separately computed. The pixel density ranges from 341 to 6821 pixels m-2. The reference outputs are obtained with the highest number of directions and pixels.
* Scene metrics: plot= 15.9m*9.2m, meshes= 24 863, triangles= 571 934, LAI= 3.2, leaflets= 24 493
Results and Discussions
Figure 1 (left, see poster) illustrates the effect of the number of discrete light directions on the estimation of biophysical processes in comparison with the reference of 136 directions. Sampling the sun direction provides best results since direct radiation largely contributes to the PAR irradiance, the energy load of leaflets and, finally, their assimilation. Bias remain low when the sun direction is not sampled except when the number of “turtle” directions is decreased to six. The dispersion of residuals remains quite limited for 46 directions, meaning that reliable values can be obtained at leaflet scale for such configuration. Figure 1 (right) shows that a low pixel density (682 pixels m-2, i.e. 50 000 pixels) is sufficient to get a relatively unbiased estimation of carbon assimilation at plot level, but a higher density is necessary to get reliable estimation at leaflet scale. The reference configuration in the left pane of Fig. 1 generates 68.5M rays for each time step and, since several hits are recorded per ray (6 on average) this generates about 5 sub-rays that are used for the calculation of light scattering. Running the complete simulation with the reference configuration from the right pane of Fig. 1 lasts {\textasciitilde}3.4 min for each time step (23M rays). This time can be decreased to only 2 seconds per step by storing partial scene illumination for each direction, but this preliminary step can be time-consuming, mainly during the multiple scattering for the PAR and NIR ranges. A considerable shortening is expected by treating light exchanges using directional form factors between pairs of objects instead of propagating scattered light by individual rays.
Conclusion
Using discrete ordinates allows performing accurate and unbiased simulations of light interception. Biases arise when decreasing the number of directions but with limited consequences on carbon assimilation. Larger biases occur when pixel density is too low to sample correctly individual leaflets. A configuration with 46 turtle directions for depicting both direct and diffuse radiation and a pixel density of 682 pixels m-2 allows fast computations while providing sufficient information to get precise light budget at fine scales.
References
Bailey, 2018, Ecological Modelling. 368:233-245, doi: 10.1016/j.ecolmodel.2017.11.022. Chelle and Andrieu, 1998, Ecological Modelling 111:75-91, doi: 10.1016/S0304-3800(98)00100-8 Dauzat et al., 2001, Agric. \& Forest Met. 109(2)143-160, doi: 10.1016/S0168-1923(01)00236-2 Farquhar et al., 1980, Planta. 149:78-90, doi: 10.1007/BF00386231 Medlyn et al., 2011, Global Change Biology. 17:2134-2144, doi: 10.1111/j.1365-2486.2010.02375.x},
author = {Vezy, Remi and Perez, Raphael P.A. and Grand, Francois and Dauzat, Jean},
year = {2020},
file = {Vezy et al_2020_Light exchanges in discrete directions as an alternative to raytracing and.pdf:D\:\\OneDrive\\Documents\\zotero\\Vezy et al_2020_Light exchanges in discrete directions as an alternative to raytracing and.pdf:application/pdf}
}
@inproceedings{perezFunctionalstructuralModelOil2020,
address = {Online},
title = {Toward a functional-structural model of oil palm accounting for architectural plasticity in response to planting density},
abstract = {Functional-structural plant modelling approaches (FSPM) open the way for exploring the relationships between the 3D structure and the physiological functioning of plants in relation to environmental conditions. FSPMs can be particularly interesting when dealing with perennial crops like oil palm, for which research on innovative management practices requires long and expensive agronomic trials. The present study is part of the PalmStudio project, which aims at developing a FSPM for oil palm capable of producing virtual experiments to test the relevance of innovative management practices and/or design ideotypes.
We propose a methodological framework which integrates architectural responses to planting density in an existing oil palm FSPM (Perez et al. 2018a b). Combining standard field phenotyping with Lidar-based derived measurements, we manage to evaluate the phenotypic plasticity of the main parameters required for the calibration of the 3D plant model. Density-based allometries of leaf geometry and biomass are then derived from the observed variations in phenotypic traits and integrated into the FSPM.
Our results illustrate the accuracy and the efficiency of Lidar-based phenotyping of leaf geometrical traits. In average, we find less than 3\% error in leaf dimensions (i.e. rachis length) in comparison with traditional manual field measurements. The fast and efficient measurements of usually labour-intensive traits such as leaf curvature allowed to estimate the plasticity of leaf geometry in response to density. We find that the main traits affected by density were leaf dimensions (up to 15\% and 25\% of increase in rachis length and petiole length respectively) and curvature (15\% of increase in leaf erectness-related parameter), whereas other structural traits like the number of leaflets per leaf remained unchanged. Simple density-based allometric relationships were then modelled and combined with the existing allometric-based 3D oil palm model Vpalm (Perez et al. 2018a). These data also enable the development and the integration in Vpalm of a biomechanical model simulating leaf curvature.
The methodology presented in this study paves the way for a rapid integration of phenotypic plasticity in FSPMs. Our FSPM is now able to estimate how planting density affect not only plant architecture but also functional processes such as carbon assimilation and transpiration using VPalm to build 3D mock-ups and ARCHIMED to simulate the biophysical processes. Ongoing research aims at coupling the current FSPM with a carbon allocation model (Pallas et al. 2013) to simulate the retroactions of functioning processes on plant architecture together with environmental and agronomic conditions.},
author = {Perez, Raphael P.A. and Vezy, Remi and Brancheriau, Loic and Boudon, Frederic and Grand, Francois and Artanto Raharjo, Doni and Caliman, Jean-Pierre and Dauzat, Jean},
year = {2020}
}
@Article{abdulaiCocoaAgroforestryLess2017,
title = {Cocoa Agroforestry Is Less Resilient to Sub-optimal and Extreme Climate than Cocoa in Full Sun},
author = {Issaka Abdulai and Philippe Vaast and Munir P. Hoffmann and Richard Asare and Laurence Jassogne and Piet {Van Asten} and Reimund P. R{\"o}tter and Sophie Graefe},
year = {2017},
issn = {1365-2486},
journal = {Global Change Biology},
}