DigR: a generic model and its open source simulation software to mimic three-dimensional root-system architecture diversity.

Background and Aims: Many studies exist in the literature dealing with mathematical representations of root systems, categorized, for example, as pure structure description, partial derivative equations or functional-structural plant models. However, in these studies, root architecture modelling has seldom been carried out at the organ level with the inclusion of environmental influences that can be integrated into a whole plant characterization. Methods: We have conducted a multidisciplinary study on root systems including field observations, architectural analysis, and formal and mathematical modelling. This integrative and coherent approach leads to a generic model (DigR) and its software simulator. Architecture analysis applied to root systems helps at root type classification and architectural unit design for each species. Roots belonging to a particular type share dynamic and morphological characteristics which consist of topological and geometric features. The DigR simulator is integrated into the Xplo environment, with a user interface to input parameter values and make output ready for dynamic 3-D visualization, statistical analysis and saving to standard formats. DigR is simulated in a quasi-parallel computing algorithm and may be used either as a standalone tool or integrated into other simulation platforms. The software is open-source and free to download at http://amapstudio.cirad.fr/soft/xplo/download. Key Results: DigR is based on three key points: (1) a root-system architectural analysis, (2) root type classification and modelling and (3) a restricted set of 23 root type parameters with flexible values indexed in terms of root position. Genericity and botanical accuracy of the model is demonstrated for growth, branching, mortality and reiteration processes, and for different root architectures. Plugin examples demonstrate the model's versatility at simulating plastic responses to environmental constraints. Outputs of the model include diverse root system structures such as tap-root, fasciculate, tuberous, nodulated and clustered root systems. Conclusions: DigR is based on plant architecture analysis which leads to specific root type classification and organization that are directly linked to field measurements. The open source simulator of the model has been included within a friendly user environment. DigR accuracy and versatility are demonstrated for growth simulations of complex root systems for both annual and perennial plants.

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.).

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.

Shifts in soil and plant functional diversity along an altitudinal gradient in the French Alps.

OBJECTIVES: Altitude integrates changes in environmental conditions that determine shifts in vegetation, including temperature, precipitation, solar radiation and edaphogenetic processes. In turn, vegetation alters soil biophysical properties through litter input, root growth, microbial and macrofaunal interactions. The belowground traits of plant communities modify soil processes in different ways, but it is not known how root traits influence soil biota at the community level. We collected data to investigate how elevation affects belowground community traits and soil microbial and faunal communities. This dataset comprises data from a temperate climate in France and a twin study was performed in a tropical zone in Mexico. DATA DESCRIPTION: The paper describes soil physical and chemical properties, climatic variables, plant community composition and species abundance, plant community traits, soil microbial functional diversity and macrofaunal abundance and diversity. Data are provided for six elevations (1400-2400 m) ranging from montane forest to alpine prairie. We focused on soil biophysical properties beneath three dominant plant species that structure local vegetation. These data are useful for understanding how shifts in vegetation communities affect belowground processes, such as water infiltration, soil aggregation and carbon storage. Data will also help researchers understand how plant communities adjust to a changing climate/environment.

Using a 3-D virtual sunflower to simulate light capture at organ, plant and plot levels: contribution of organ interception, impact of heliotropism and analysis of genotypic differences.

BACKGROUND AND AIMS: Light interception is a critical factor in the production of biomass. The study presented here describes a method used to take account of architectural changes over time in sunflower and to estimate absorbed light at the organ level. METHODS: The amount of photosynthetically active radiation absorbed by a plant is estimated on a daily or hourly basis through precise characterization of the light environment and three-dimensional virtual plants built using AMAP software. Several treatments are performed over four experiments and on two genotypes to test the model, quantify the contribution of different organs to light interception and evaluate the impact of heliotropism. KEY RESULTS: This approach is used to simulate the amount of light absorbed at organ and plant scales from crop emergence to maturity. Blades and capitula were the major contributors to light interception, whereas that by petioles and stem was negligible. Light regimen simulations showed that heliotropism decreased the cumulated light intercepted at the plant scale by close to 2.2% over one day. CONCLUSIONS: The approach is useful in characterizing the light environment of organs and the whole plant, especially for studies on heterogeneous canopies or for quantifying genotypic or environmental impacts on plant architecture, where conventional approaches are ineffective. This model paves the way to analyses of genotype-environment interactions and could help establish new selection criteria based on architectural improvement, enhancing plant light interception.

AmapSim: a structural whole-plant simulator based on botanical knowledge and designed to host external functional models.

BACKGROUND AND AIMS: AmapSim is a tool that implements a structural plant growth model based on a botanical theory and simulates plant morphogenesis to produce accurate, complex and detailed plant architectures. This software is the result of more than a decade of research and development devoted to plant architecture. New advances in the software development have yielded plug-in external functions that open up the simulator to functional processes. METHODS: The simulation of plant topology is based on the growth of a set of virtual buds whose activity is modelled using stochastic processes. The geometry of the resulting axes is modelled by simple descriptive functions. The potential growth of each bud is represented by means of a numerical value called physiological age, which controls the value for each parameter in the model. The set of possible values for physiological ages is called the reference axis. In order to mimic morphological and architectural metamorphosis, the value allocated for the physiological age of buds evolves along this reference axis according to an oriented finite state automaton whose occupation and transition law follows a semi-Markovian function. KEY RESULTS: Simulations were performed on tomato plants to demonstrate how the AmapSim simulator can interface external modules, e.g. a GREENLAB growth model and a radiosity model. CONCLUSIONS: The algorithmic ability provided by AmapSim, e.g. the reference axis, enables unified control to be exercised over plant development parameter values, depending on the biological process target: how to affect the local pertinent process, i.e. the pertinent parameter(s), while keeping the rest unchanged. This opening up to external functions also offers a broadened field of applications and thus allows feedback between plant growth and the physical environment.

Estimation of light interception in research environments: a joint approach using directional light sensors and 3D virtual plants applied to sunflower (Helianthus annuus) and Arabidopsis thaliana in natural and artificial conditions.

Light interception is a major factor influencing plant development and biomass production. Several methods have been proposed to determine this variable, but its calculation remains difficult in artificial environments with heterogeneous light. We propose a method that uses 3D virtual plant modelling and directional light characterisation to estimate light interception in highly heterogeneous light environments such as growth chambers and glasshouses. Intercepted light was estimated by coupling an architectural model and a light model for different genotypes of the rosette species Arabidopsis thaliana (L.) Heynh and a sunflower crop. The model was applied to plants of contrasting architectures, cultivated in isolation or in canopy, in natural or artificial environments, and under contrasting light conditions. The model gave satisfactory results when compared with observed data and enabled calculation of light interception in situations where direct measurements or classical methods were inefficient, such as young crops, isolated plants or artificial conditions. Furthermore, the model revealed that A. thaliana increased its light interception efficiency when shaded. To conclude, the method can be used to calculate intercepted light at organ, plant and plot levels, in natural and artificial environments, and should be useful in the investigation of genotype-environment interactions for plant architecture and light interception efficiency.

Integrated responses of rosette organogenesis, morphogenesis and architecture to reduced incident light in Arabidopsis thaliana results in higher efficiency of light interception.

Plants have a high phenotypic plasticity in response to light. We investigated changes in plant architecture in response to decreased incident light levels in Arabidopsis thaliana (L.) Heynh, focusing on organogenesis and morphogenesis, and on consequences for the efficiency of light interception of the rosette. A. thaliana ecotype Columbia plants were grown under various levels of incident photosynthetically active radiation (PAR), with blue light (BL) intensity proportional to incident PAR intensity and with a high and stable red to far-red light ratio. We estimated the PAR absorbed by the plant, using data from precise characterisation of the light environment and 3-dimensional simulations of virtual plants generated with AMAPsim software. Decreases in incident PAR modified rosette architecture; leaf area decreased, leaf blades tended to be more circular and petioles were longer and thinner. However, the efficiency of light interception by the rosette was slightly higher in plants subjected to lower PAR intensities, despite the reduction in leaf area. Decreased incident PAR delayed leaf initiation and slowed down relative leaf expansion rate, but increased the duration of leaf expansion. The leaf initiation rate and the relative expansion rate during the first third of leaf development were related to the amount of PAR absorbed. The duration of leaf expansion was related to PAR intensity. The relationships identified could be used to analyse the phenotypic plasticity of various genotypes of Arabidopsis. Overall, decreases in incident PAR result in an increase in the efficiency of light interception.

A whole-plant analysis of the dynamics of expansion of individual leaves of two sunflower hybrids.

Common features in the time-course of expansion of leaves which considerably differed in final area, due to phytomer position, growing conditions and genotype, were identified. Leaf development consisted of two phases of exponential growth, followed by a third phase of continuous decrease of the relative expansion rate. The rate and the duration of the first exponential phase were common to all phytomers, growing conditions and genotypes. Leaves differed in the rate and the duration of the second exponential phase. The decrease of the relative expansion rate during the third phase depended on neither genotype nor growing conditions. It was phytomer-dependent and was deduced from the rate of the second phase via a parameter common to all cases studied. Differences in final leaf area among growing conditions were linked to different expansion rates during the second exponential phase. The duration of the phases at any given phytomer position was the same for the two hybrids in different growing conditions. The dates of developmental events (initiation, end of the two exponential phases, full expansion), and the rate of the second exponential phase, were related to phytomer position, defining a strict pattern of leaf development at the whole plant level. Using this framework simplified the analysis of the response of leaf expansion to genotype and environment.