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International audience; BackgroundTree above ground biomass (AGB) is currently estimated by tree-level allometrical models that take into account, tree volume estimated from proxy variables of tree size (DBH) and species average wood specific gravity (WSG). These methods are common and realistic from a practical point of view. However, they do not take into account deviance from fixed allometrical trajectories and species or tree level WSG variations. Here, we present Xtrawood software that allows computation of tree AGB according to structure and WSG variations.MethodXtrawood reconstructs tree structure and integrates WSG variations by merging tree structure and WSG data measured at different position in trees, leading to the computation of global AGB and visualization of WSG variation along tree structure. Tree structure is measured according to stem dimensions (length, diameter) and positions within tree, and encoded in Multiscale Tree Graph format (MTG). WSG data is made of radial WSG profiles (1 measure each 0,5 cm from pith to bark) sampled at different heights within whole tree. Xtrawood output are illustrated using a dataset collected on an Amazonian forest ‘biomass dominant species’, Dicorynia guianensis Amsh., also known to exhibit substantial WSG gradients along both radial and vertical axis. 9 trees ranging from 15 to 60 cm DBH were measured by climbers. Each tree was felled and samples were collected at different positions (3 in trunk, 1 to 5 in crown) to record WSG radial profiles.ResultsXtrawood allows computation of tree volume, but also visualization of WSG variations in tree as well as inference of WSG radial profiles at different heights. Output variables are decomposed according to different tree scale and locations (axis, trunk/crown) and easy to extract. Xtrawood results will be compared to those of standard estimation method and can be used to identify positions in trees where WSG value leads to the better estimate of tree AGB.Conclusion/perspectiveXtrawood produces AGB estimate with data from intensive measurements practices. The sampling protocol, used here, remains destructive and time-consuming because Xtrawood is not directly dedicated to forest managers, but to help calibration of realistic sampling strategies. Moreover, Xtrawood offers a way to understand relationships between tree development, WSG variations within tree structure and biomass accumulation in the context of natural forests or plantations. A software demo is available at coffee break.

Climate change is very likely to impact on oi l palm productivity and raise new questions on how to tackle these changes. The development of new strategies to find more sustainable and productive systems is a major challenge to cope with ceaseless increasing demands of palm oil. Agronomic practices or the selection of genetic material better adapted to future climate could be an option to maintain the high productivity of oil palm. The evaluation of plant and system performances related to climate change is nevertheless difficult to implement, particularly with perennial plants. Functional-structural plant mode ls (FSPM) have been developed to explore the relationships between plant structure, plant functioning and environmental conditions. FSPM are thus practical tools to set up virtual experiments and test hypotheses concerning processes that could otherwise take years in actual field conditions. The main assumption underlying this project is the possibility to enhance potential crop production optimizing plant architecture in relation to radiation us e efficiency. In this way, the present study proposes the basis of an oil palm FSPM, focusing on modelling oil palm architecture and light interception. A modelling approach has thus been developed to reconstruct oil palm architecture from simple field measurements while integrating the genetic variability observed on 5 progenies with contrasting genetic origins. The AMAPstudio software (Griffon & de Coligny, 2014) was used to generate 3D mock- ups and estimate light interception efficiency on virtual plants for each progeny. Model evaluation was performed using terrestrial laser scan (TLS) and hemispherical photographs (HPs) to compare the quality of 3D reconstruction respectively at the individual and stand scale. Significant differences in leaf geometry (petiole length, density of leaflets and rachis curvature) and leaflets morphology (gradients of leaflets length and width) were detected between and within progenies, and were accurately simulated by the modelling approach. The comparison of plant area obtained from TLS and virtual TLS highlight the capacity of the model to generate realistic 3D mock-ups. The architectural variabilities observed at plot scale were satisfactory simulated, as the gap fractions estimated from HP were compliant to the gap fractions estimated from virtual HPs. Finally, simulations revealed distinct light interception efficiency for the different progenies, from plant to stand scale. (Texte intégral)

International audience; Over the past decade, much attention has been devoted to the development of forest biomass estimation methods at a stand scale, leading to the establishment of allometric models (Chave et al., 2014). These allometric equations use a unique wood specific gravity value (WSG) per species, but neglect the within tree variations of WSG found by others (Wiemann & Williamson, 1989).The main objectives of this study are (1) to illustrate the diversity of radial (from pith to bark) and longitudinal (from bottom to top) patterns of WSG variation within and between species, (2) to highlight different trends of WSG radial variations and the possible misinterpretations of these trends due to the effect of heartwood and (3) to link these variations and patterns to the successional status of the species (from pioneer to sciaphilic species).We sampled 33 small trees (10

This study aimed to analyze the berry location and maturing within the plant architecture for two planting densities combined with two planting patterns in a first production year. Non destructive measurements of coffee plant architecture (cv. IAPAR 59) were performed on plants grown in two plant densities (6,000 and 10,000 plants ha-1) and planting patterns (square – Q or rectangular - R). The number of phytomers and length of the plagiotropic axes were linearly related to their rank on the trunk. In rectangular PP, the competition between plants in the row promoted the apical dominance more than in square PP. In first production year, the berries were situated close to the trunk in horizontal directions, and in lower layers in the vertical plant profile. Our results of total berry production per ha-1 argue in favor of very dense plantation with a square planting pattern. However, further observations are needed to check that canopy closure during the following years, and Arabica coffee biennial production will not reverse the observed trends.

La simulation de l'architecture du palmier dattier est basée sur la simulation fine de l'architecture de ses palmes ainsi leur mise en place sur le stipe au cours de son développement (phytomètre). Le présent travail vise à simuler t visualiser l'architecture de quatre cultivars : 'Boufegouss', 'Asian', 'Rochdi' et 'Barhi' d'origine marocaine et tunisienne, deux à deux respectivement. Les éléments botaniques pris en considération ainsi que leurs caractéristiques métriques et géométriques ont été mesurés sur le terrain en faisant appel au protocole du réseau Principes. La simulation a été effectuée par le software Xplo développé à UMR-AMAP-CIRAD, simulateur de l'architecture et la croissance des plantes, qui héberge le modèle Principes de palmiers. Les résultats obtenus indiquent bien que Xplo a reconstruit fidèlement la structure 3D des 4 cultivars étudiés dans leurs conditions réelles. Ces résultats ouvrent des perspectives sur la possibilité d'application dans les domaines d'agronomie, de biologie et de recherche, tout en associant la structure à sa fonction (photosynthèse, transpiration…).

Plants architecture modelling results in building complex models. Turning them into simulators requires strong interaction between scientists and software developers. The AMAPstudio project adapts a methodology that has been successfully conducted in the forestry modelling field for 12 years. It focuses on a long-term supported software environment and a strong customized technical backing to help modellers integrate their simulators in highly 3D interactive software.

Two Coffea arabica cultivars, IAPAR59 (drought tolerant) and RUBI (drought susceptible), were grown for two years with/without irrigation during the dry seasons. In addition to eco-physiological, anatomical and molecular biology observations, complete descriptions of plant architecture were performed. All architectural data were analysed owing to the AMAPstudio-XPlo software. The methodology for analysing data and the main results are presented here. A first general effect of drought was a decrease of the growth rate (i.e. an increase of the phyllochron) during the dry season. This effect, higher for Rubi than for Iapar59, concerned similarly the main stem and the branches of different ramification orders. Another important response concerned the setting of secondary and tertiary branches on the second year. Globally the treatments had effects on all studied variables but no architectural trait appeared as specifically responsive to temporary droughts. Aside the analyses of cultivars plasticity, the data collected in this study provided matchless information that is currently used for building a functional structural coffee model coupling architectural rules and ecophysiological processes such as the carbon acquisition. The outlines of this so-called Functional Structural Plant Modelling approach are presented as well as its interest for deriving the very primary mechanisms of phenotypic plasticity.

Several data sets are being gathered to build a functional-structural model for Coffea arabica. The one pitfall in this integration process is the difficulty of calibrating a large number of parameters. A step by step procedure is thus necessary to validate the sub-models. The focus is put here on the backward reconstruction of the plant structure from its description at a given times as a way to decrease the degrees of freedom of the model before addressing the carbon acquisition and allocation.

Improving our knowledge on plant architecture and development will help to answer remaining questions in ecology, agronomy and forestry, i.e. regarding plant acclimation and adaptation to changing environments or optimization of plant products. For this purpose, computational plants are becoming more and more popular and a lot of effort is made to build structural and functional models at the organ level in order to simulate plant growth and structure [1]. In this context, scientists need software to measure, analyse and model plant architectures. The Xplo project has been developed in UMR AMAP since 2008 aiming at edition, visualization, exploration and simulation of plant architecture in a userfriendly manner. The software gives interactive tools to handle the plant structure topology (i.e. organ addition/ deletion), geometry (i.e. 3D selection, edition, rotation) and dynamic (i.e. time line, scenarios). It has been used for various types of plant architecture studies (i.e Sunflower [2], Fir Sapling[3], Cecropia, Palm trees [4]). Xplo is fully compatible with the multi-scale tree graphs (MTGs) data structure, which is commonly used to represent plant topology [5]. Users can explore this data structure to find or to improve hypotheses on plant development. Specific data can be extracted with combination of criteria and be visualised in tables and graphs. Simple analysies functions can be launched or data can be exported to external tools, i.e. AMAPMod, R or any other statistical computing environment, for more can integrate their own plant simulation model to the platform and get benefit of its functionalities to test their hypothesis. Different scenarios can be computed for a growth model by interactively modifying model parameters or plant structure (i.e. by pruning) at defined time steps. A plant geometry builder is integrated to Xplo. It allows a 3D plant mockup to be computed according to available geometrical data in the tree graph. If geometrical information is missing, standard default algorithms are provided to compute the missing data and to make 3D rendering available. Xplo is an expandable software built around the stable Capsis kernel [6]. Independent simulation models are integrated in Xplo under the form of separated modules, and various tools can be plugged at any time using flexible extensions. This generic software can be run either in an interactive context with a multi-language graphical user interface or in script mode (Groovy/Python). Xplo is a free opensource software (LGPL) and is available on almost every OS. (Texte intégral)

[Departement_IRSTEA]Eaux [TR1_IRSTEA]GEUSI; International audience; Process Based Models (PBM) are used to compute crop yield, they treat a field as a homogenous medium, total production is computed accurately, but there is little information on individual variability of plants, and number and size of organs. Functional Structural Plant Models (FSPM) simulate individual plant development and growth, they build plant architecture on the basis of biomass production and partitioning according to botanical rules, but generally lack the ability to upscale to the field level to address crop production. In the present study we combined crop biomass production of maize estimated by the PBM PILOTE with biomass partitioning and individual plant architecture generated by the FSPM GreenLab, in order to benefit from the field-level accuracy of the former and from the heterogeneity of individual architecture of the latter.

Realistic visualization of crops, forest, peri/urban, natural scenes raises high interest under the environmental pressure and social demand. Unfortunately, despite the capabilities of the Internet and graphic boards, virtual landscapes and scenes are still restricted to small-scale user communities, with low dynamics, low aestheticism, low respect for biophysical laws. Web large-scale VR vegetation scenes are a challenging topic, due to the complex geometry and its rendering; and due to the lack of efficient modeling method and dynamics understanding. Moreover, VR must involve close objects that can interact easily with contextual background objects as to settle applications. However, specific solutions exist, and some of them can be used for WebVR display: light weighted static plant models, paged land scape map geometry, procedural vegetation generation on the fly. Reconstructions from photos, mixture of real and synthetic images in augmented reality are also of interest for this topic. On the study case "the Ecological project of Chinese ChongMing Island", new techniques are shown: Plant billboards and hybrid models, VRML classical scenes of historical farms, and guided maps with 3D web flash panoramic spot views. Perspectives are finally exposed from new developments: rule based geometry generation Web browsing, fast reconstruction from image models, high-level simulator output, with a background of new Web and graphical hardware approaches.

International audience

Over the past decade, much attention has been devoted to the development of forest biomass estimation methods at a stand scale, leading to the establishment of allometric models (Chave, et al. 2014). These allometric equations use a unique wood specific gravity value (WSG) per species, but neglect the within tree variations of WSG found by others (Wiemann & Williamson, 1989). The main objectives of this study are to (1) illustrate the diversity of radial and vertical patterns of WSG variation within tree trunks belonging to different ecological groups (from pioneer to sciaphilic species) and to (2) develop an estimation method of trunk biomass taking into account WSG variations. We sampled 33 young trees (10

Background: Tree above ground biomass (AGB) is currently estimated by tree-level allometrical models that take into account, tree volume estimated from proxy variables of tree size (DBH) and species average wood specific gravity (WSG). These methods are common and realistic from a practical point of view. However, they do not take into account deviance from fixed allometrical trajectories and spe-cies or tree level WSG variations. Here, we present Xtrawood software that allows computation of tree AGB according to structure and WSG variations. Method: Xtrawood reconstructs tree structure and integrates WSG variations by merging tree structure and WSG data measured at different position in trees, leading to the computation of global AGB and visualization of WSG variation along tree structure. Tree structure is measured according to stem dimensions (length, diameter) and positions within tree, and encoded in Multiscale Tree Graph format (MTG). WSG data is made of radial WSG profiles (1 measure each 0,5 cm from pith to bark) sampled at different heights within whole tree. Xtrawood output are illustrated using a dataset collected on an Amazonian forest "biomass dominant species", Dicorynia guianensis Amsh., also known to exhibit substantial WSG gradients along both radial and vertical axis. 9 trees ranging from 15 to 60 cm DBH were measured by climbers. Each tree was felled and samples were collected at different positions (3 in trunk, 1 to 5 in crown) to record WSG radial profiles. Results: Xtrawood allows computation of tree volume, but also visualization of WSG variations in tree as well as inference of WSG radial profiles at different heights. Output variables are decomposed according to different tree scale and locations (axis, trunk/crown) and easy to extract. Xtrawood results will be compared to those of standard estimation method and can be used to identify positions in trees where WSG value leads to the better estimate of tree AGB. Conclusion: Xtrawood produces AGB estimate with data from intensive measurements practices. The sampling protocol, used here, remains destructive and time-consuming because Xtrawood is not directly dedicated to forest managers, but to help calibration of realistic sampling strategies. Moreover, Xtrawood offers a way to understand relationships between tree development, WSG variations within tree structure and biomass accumulation in the context of natural forests or plantations. A software demo is available at coffe break. (Texte intégral)