Simulating rhizodeposition as a function of shoot and root interactions within a new 3D Functional-Structural Plant Model

Introduction - Rhizodeposition, i.e. the release of organic materials by roots, represents a significant portion of plant's carbon (C) budget, ranging from 5% to 15% of net photosynthesized C (Pausch and Kuzyakov, 2018). Various rhizodeposits can be released by roots, e.g. soluble exudates, secreted mucilage, sloughed cells, or volatile organic compounds. Despite their short lifetime, some of these products have been shown to favor plant growth, e.g. by increasing water and nutrient uptake. Among rhizodeposition processes, exudation has been suggested to depend on the concentration of carbohydrates inside the roots (Personeni et al., 2007). However, rhizodeposition not only depends on the availability of C in the roots, but also on the architecture of the root system, and many have shown that rhizodeposits are more concentrated in specific areas, such as root tips. Consequently, a Functional-Structural Plant Model (FSPM) would theoretically represent the best framework for simulating the spatial and temporal dynamics of rhizodeposition, as it can describe the evolution of both the metabolism and the architecture of the plant. The objective of this work is to create such a framework by coupling a whole-plant FSPM, a 3D root architectural model, and a new model simulating rhizodeposition. Modelling approach - Our strategy has been to combine the FSPM CN-Wheat (Barillot et al., 2016), which describes the main processes of C and nitrogen (N) acquisition and transformation by an individual wheat plant and the 3D growth and development of its aerial organs, with the model ArchiSimple (Pagès et al., 2014) that simulates the development of the 3D root architecture for a range of plant species, and the new model RhizoDep, which calculates a full C balance in each part of a root system in order to simulate local rhizodeposition fluxes. The complementarity of the three models is illustrated in Figure 1: i) CN-Wheat is used to calculate the amount of C allocated from the shoots to the roots, ii) ArchiSimple provides the 3D structure of the root system, and iii) RhizoDep distributes the C provided by the shoots within the 3D root system and simulates the actual growth, respiration and rhizodeposition of each root element based on C availability. The major link between the three models lies in the exchange of C between aboveground and belowground tissues, which is driven by gradients of sucrose concentration in the different compartments of the plant. Preliminary results & short-term perspectives - The coupling of the three models has been started using the OpenAlea platform and its Multiscale Tree Graph formalism (Pradal et al., 2008). First simulations were done using the allocation of C to the roots simulated by CN-Wheat as an input to the root model based on the effective coupling of ArchiSimple and RhizoDep. These simulations show how rhizodeposition is intrinsically dependent on the architecture of the root system and on the total amount of available C. For completing the coupling, several issues still need to be tackled, e.g. how N uptake and metabolism should be spatialized in a 3D root system, how it may be regulated by local C and N availability, and how rhizodeposition can modify soil N availability. However, this modelling approach has already led to a first prototype able to simulate rhizodeposition processes on a dynamic, 3D root system that is fully integrated within the functioning of the whole plant. Its refinement will offer unique opportunities to study the possible link between rhizodeposition and the environmental factors affecting plant growth, e.g. atmospheric CO2 concentration or soil N availability

What determines the complex kinetics of stomatal conductance under blueless PAR in Festuca arundinacea? Subsequent effects on leaf transpiration

Light quality and, in particular, its content of blue light is involved in plant functioning and morphogenesis. Blue light variation frequently occurs within a stand as shaded zones are characterized by a simultaneous decrease of PAR and blue light levels which both affect plant functioning, for example, gas exchange. However, little is known about the effects of low blue light itself on gas exchange. The aims of the present study were (i) to characterize stomatal behaviour in Festuca arundinacea leaves through leaf gas exchange measurements in response to a sudden reduction in blue light, and (ii) to test the putative role of Ci on blue light gas exchange responses. An infrared gas analyser (IRGA) was used with light transmission filters to study stomatal conductance (gs), transpiration (Tr), assimilation (A), and intercellular concentration of CO2 (Ci) responses to blueless PAR (1.80 μmol m−2 s−1). The results were compared with those obtained under a neutral filter supplying a similar photosynthetic efficiency to the blueless PAR filter. It was shown that the reduction of blue light triggered a drastic and instantaneous decrease of gs by 43.2% and of Tr by 40.0%, but a gradual stomatal reopening began 20 min after the start of the low blue light treatment, thus leading to new steady-states. This new stomatal equilibrium was supposed to be related to Ci. The results were confirmed in more developed plants although they exhibited delayed and less marked responses. It is concluded that stomatal responses to blue light could play a key role in photomorphogenetic mechanisms through their effect on transpiration

Modélisation du partage de la lumière dans l'association de cultures blé - pois (<em>Triticum aestivum</em> L. -<em> Pisum sativum</em> L.): Une approche de type plante virtuelle

Cereal-legume intercropping systems are assumed to provide efficient and sustainable agrosystems. However, the proportion of each species in the stand, as well as their productivity, are highly related to the trade-off between the interspecific competition and their complementarity. Light partitioning between the cereal and the legume is therefore a determinant of the mixture functioning. The physical structure of the canopy, which drives light interception, emerges from the above-ground architecture of the individuals growing within the stand. In order to assess the relationships between plant architecture and light partitioning in wheat-pea mixtures (Triticum aestivum L.-Pisum sativum L), a 3D model of the above-ground morphogenesis of pea, so called L-Pea, was built up based on the virtual plant approach. Experiments were conducted in order to i) characterize the morphogenesis of contrasting pea genotypes grown under different conditions (greenhouse/field, pure/mixture), and ii) to model the above-ground architecture of pea. A tripartite simulator, integrating the L-Pea model, ADEL-Wheat an (architectural model of wheat) and CARIBU (a radiative transfer model), was then built up in order to study the architectural determinism of light partitioning in wheat-pea mixtures. This simulator furthermore demonstrates that architectural parameters (e.g. branches, internodes) are able to significantly and dynamically affect light partitioning and thus the mixture development. The present thesis contributes i) to demonstrate the pertinence of the virtual plant approach for accounting of light partitioning in mixtures and ii) to the selection/building of cultivars/ideotypes suited for multispecific stands.Les associations de cultures céréales-légumineuses participent au développement d’agrosystèmes performants et durables. La proportion de chaque espèce dans le couvert ainsi que leur productivité sont cependant fortement dépendantes de l’équilibre entre compétition et complémentarité interspécifique. Le partage de la lumière entre la céréale et la légumineuse est donc déterminant dans le fonctionnement des associations. La structuration physique de la canopée, qui conditionne l’interception du rayonnement lumineux, résulte de la mise en place de l’architecture aérienne des individus composant le peuplement. Afin d’appréhender les relations entre architecture et partage du rayonnement dans les associations blé–pois (Triticum aestivum L.-Pisum sativum L.), un modèle 3D de la morphogénèse aérienne du pois, baptisé L-Pea, a été développé sur la base de l’approche plante virtuelle. Des expérimentations ont été conduites afin i) de caractériser la morphogénèse de génotypes de pois contrastés cultivés sous différentes conditions (serre/champ, pur/associé), et ii) de modéliser l’architecture aérienne du pois. Un simulateur tripartite, intégrant les modèles L-Pea, ADEL-Blé (modèle architecturé de blé) ainsi que CARIBU (modèle de transferts radiatifs), a ensuite été construit afin de créer une association virtuelle. Cette approche de type plante virtuelle s’est révélée pertinente dans l’optique d’étudier le déterminisme architectural du partage de la lumière dans les associations blé–pois. Ce simulateur a par ailleurs montré que des paramètres architecturaux (e.g. ramifications, entrenoeuds) peuvent affecter de manière significative et dynamique le partage de la lumière et donc le développement de l’association. Cette thèse se propose i) de démontrer la pertinence de l’approche plante virtuelle pour appréhender le partage du rayonnement dans les associations et ii) de contribuer à la sélection/construction de variétés/idéotypes adaptés aux couverts plurispécifiques

Modélisation du partage de la lumière dans l'association de cultures blé - pois (Triticum aestivum L. Pisum sativum L.). Une approche de type plante virtuelle.

Cereal-legume intercropping systems are assumed to provide efficient and sustainable agrosystems. However, the proportion of each species in the stand, as well as their productivity, are highly related to the trade-off between the interspecific competition and their complementarity. Light partitioning between the cereal and the legume is therefore a determinant of the mixture functioning. The physical structure of the canopy, which drives light interception, emerges from the above-ground architecture of the individuals growing within the stand. In order to assess the relationships between plant architecture and light partitioning in wheat-pea mixtures (Triticum aestivum L.-Pisum sativum L), a 3D model of the above-ground morphogenesis of pea, so called L-Pea, was built up based on the virtual plant approach. Experiments were conducted in order to i) characterize the morphogenesis of contrasting pea genotypes grown under different conditions (greenhouse/field, pure/mixture), and ii) to model the above-ground architecture of pea. A tripartite simulator, integrating the L-Pea model, ADEL-Wheat an (architectural model of wheat) and CARIBU (a radiative transfer model), was then built up in order to study the architectural determinism of light partitioning in wheat-pea mixtures. This simulator furthermore demonstrates that architectural parameters (e.g. branches, internodes) are able to significantly and dynamically affect light partitioning and thus the mixture development. The present thesis contributes i) to demonstrate the pertinence of the virtual plant approach for accounting of light partitioning in mixtures and ii) to the selection/building of cultivars/ideotypes suited for multispecific stands.Les associations de cultures céréales-légumineuses participent au développement d'agrosystèmes performants et durables. La proportion de chaque espèce dans le couvert ainsi que leur productivité sont cependant fortement dépendantes de l'équilibre entre compétition et complémentarité interspécifique. Le partage de la lumière entre la céréale et la légumineuse est donc déterminant dans le fonctionnement des associations. La structuration physique de la canopée, qui conditionne l'interception du rayonnement lumineux, résulte de la mise en place de l'architecture aérienne des individus composant le peuplement. Afin d'appréhender les relations entre architecture et partage du rayonnement dans les associations blé-pois (Triticum aestivum L.-Pisum sativum L.), un modèle 3D de la morphogénèse aérienne du pois, baptisé L-Pea, a été développé sur la base de l'approche plante virtuelle. Des expérimentations ont été conduites afin i) de caractériser la morphogénèse de génotypes de pois contrastés cultivés sous différentes conditions (serre/champ, pur/associé), et ii) de modéliser l'architecture aérienne du pois. Un simulateur tripartite, intégrant les modèles L-Pea, ADEL-Blé (modèle architecturé de blé) ainsi que CARIBU (modèle de transferts radiatifs), a ensuite été construit afin de créer une association virtuelle. Cette approche de type plante virtuelle s'est révélée pertinente dans l'optique d'étudier le déterminisme architectural du partage de la lumière dans les associations blé-pois. Ce simulateur a par ailleurs montré que des paramètres architecturaux (e.g. ramifications, entrenoeuds) peuvent affecter de manière significative et dynamique le partage de la lumière et donc le développement de l'association. Cette thèse se propose i) de démontrer la pertinence de l'approche plante virtuelle pour appréhender le partage du rayonnement dans les associations et ii) de contribuer à la sélection/construction de variétés/idéotypes adaptés aux couverts plurispécifiques

Modélisation du partage de la lumière dans l'association de cultures blé - pois (Triticum aestivum L. Pisum sativum L.) (une approche de type plante virtuelle)

Les associations de cultures céréales-légumineuses participent au développement d'agrosystèmes performants et durables. La proportion de chaque espèce dans le couvert ainsi que leur productivité sont cependant fortement dépendantes de l'équilibre entre compétition et complémentarité interspécifique. Le partage de la lumière entre la céréale et la légumineuse est donc déterminant dans le fonctionnement des associations. La structuration physique de la canopée, qui conditionne l'interception du rayonnement lumineux, résulte de la mise en place de l'architecture aérienne des individus composant le peuplement. Afin d'appréhender les relations entre architecture et partage du rayonnement dans les associations blé-pois (Triticum aestivum L.-Pisum sativum L.), un modèle 3D de la morphogénèse aérienne du pois, baptisé L-Pea, a été développé sur la base de l'approche plante virtuelle. Des expérimentations ont été conduites afin i) de caractériser la morphogénèse de génotypes de pois contrastés cultivés sous différentes conditions (serre/champ, pur/associé), et ii) de modéliser l'architecture aérienne du pois. Un simulateur tripartite, intégrant les modèles L-Pea, ADEL-Blé (modèle architecturé de blé) ainsi que CARIBU (modèle de transferts radiatifs), a ensuite été construit afin de créer une association virtuelle. Cette approche de type plante virtuelle s'est révélée pertinente dans l'optique d'étudier le déterminisme architectural du partage de la lumière dans les associations blé-pois. Ce simulateur a par ailleurs montré que des paramètres architecturaux (e.g. ramifications, entrenoeuds) peuvent affecter de manière significative et dynamique le partage de la lumière et donc le développement de l'association. Cette thèse se propose i) de démontrer la pertinence de l'approche plante virtuelle pour appréhender le partage du rayonnement dans les associations et ii) de contribuer à la sélection/construction de variétés/idéotypes adaptés aux couverts plurispécifiques.Cereal-legume intercropping systems are assumed to provide efficient and sustainable agrosystems. However, the proportion of each species in the stand, as well as their productivity, are highly related to the trade-off between the interspecific competition and their complementarity. Light partitioning between the cereal and the legume is therefore a determinant of the mixture functioning. The physical structure of the canopy, which drives light interception, emerges from the above-ground architecture of the individuals growing within the stand. In order to assess the relationships between plant architecture and light partitioning in wheat-pea mixtures (Triticum aestivum L.-Pisum sativum L), a 3D model of the above-ground morphogenesis of pea, so called L-Pea, was built up based on the virtual plant approach. Experiments were conducted in order to i) characterize the morphogenesis of contrasting pea genotypes grown under different conditions (greenhouse/field, pure/mixture), and ii) to model the above-ground architecture of pea. A tripartite simulator, integrating the L-Pea model, ADEL-Wheat an (architectural model of wheat) and CARIBU (a radiative transfer model), was then built up in order to study the architectural determinism of light partitioning in wheat-pea mixtures. This simulator furthermore demonstrates that architectural parameters (e.g. branches, internodes) are able to significantly and dynamically affect light partitioning and thus the mixture development. The present thesis contributes i) to demonstrate the pertinence of the virtual plant approach for accounting of light partitioning in mixtures and ii) to the selection/building of cultivars/ideotypes suited for multispecific stands.ANGERS-BU Lettres et Sciences (490072106) / SudocSudocFranceF

CN-wheat: a mechanistic structural-functional model for carbon and nitrogen metabolism in wheat

In a context of global change, it is necessary to identify new practices and plant characteristics determining crop production and that can be potential targets for plant breeding. This could be achieved by numerical simulation, using mechanistic and integrative models that provide a holistic view of plant functioning. However, a central difficulty lies in building a coherent view of the involved processes and how to integrate them at plant and crop level. The model proposed here, called CN-Wheat, represents a significant progress to address these issues by using a fully mechanistic approach for integration of Carbon (C) and Nitrogen (N) metabolisms within wheat plants after anthesis. CN-Wheat is defined at culm scale; the crop is represented as a population of individual culms that compete for light and soil N. Culm structure is composed of a root compartment, a set of photosynthetic organs and the grains. Each module includes structural, storage and mobile materials. Fluxes of C-N among modules take place through a common pool and/or through the transpiration flow. The modelled physiological activities are the acquisition of C and N, the synthesis and degradation of primary metabolites (sucrose, fructans, starch, amino acids, proteins and nitrates), C respiration, C-N exudation and tissue death. A central role is given to metabolite concentrations as drivers of (i) physiological activities and (ii) transfers between organs. Thus, the integration within the plant results from that all processes act in parallel on interconnected metabolite pools, which is represented as a set of differential equations, solved numerically. Model behavior was evaluated against a field experimentation with three levels of N fertilization applied at anthesis. For each N treatment, CN-Wheat accurately predicted the post-anthesis kinetics of (i) C-N distribution among organs, (ii) green areas of laminae and (iii) dry mass and N content of grains. In our simulations, when soil N was non-limiting, N in grains was ultimately determined by the availability of C for root activity. Dry matter accumulation in grains was mostly affected by photosynthetic organ lifespan which was regulated by protein turn-over and C-regulated root activity. Whereas the use of response functions to metabolite concentration is accepted for each of the processes described in the model, here we show that it can be used for an integrative modelling of the whole plant. Besides, CN-Wheat provides insights into the interplay of C-N metabolism which is expected to improve our knowledge on the regulation of plant functioning. This approach also enables to identify potential targets for plant breeding in order to improve crop production and N efficiency as well as crop adaptation to climate changes and low N agronomical practices

Ideotype construction from an architectural model of pea

There is an increasing need for growing legume species in Europe in order to reduce dependency onimported vegetable proteins. Currently, pea (Pisum sativum) is the principle source of vegetableproteins. However, the productivity rate of pea crop is still under its potential mainly due to fungalfoliar diseases. The most damaging ones are caused by Ascochyta pisi, Mycosphaerella pinodes andPhoma medicaginis.Dynamics of such diseases have been shown to depend on plant architecture e.g. Leaf Area Index(LAI), plant height, internode length (Le May et al., 2009). Virtual models of canopy architecturetherefore appear as suitable tools for studying and modelling plant–pathogen interactions and diseasesdispersal.We have developed a 3D architectural model of pea growth based on the L-system formalism anddeveloped on the L-Py platform (Boudon et al., 2010). Initial parameters were based on data from afield-grown crop of winter pea cv Lucy. The above ground architecture is represented as a successionof phytomers emitted by main stems and branches. Phytomers are considered as a collection of organsencoded as modules that support their state i.e. age, length, topology and geometry. The rate ofphytomer emission was set for main stems and branches. The number of branches and their time ofemergence are attributes of each node of stems.Coupled with epidemiologic models, this simulator can be used as a conceptual framework forstudying the effects of pea architectural parameters on disease development and dispersal. Indeed, thepresent model is able to build contrasted canopies of ideotypes with regard to LAI and its spatialdistribution (plant density, phytomer number, branching ability, axis orientation, leaf growth), plantheight (internode growth), foliage orientation (leaf geometry) and dynamics of growth (rate ofphytomers and branch emission, organ growth kinetics). Moreover, the formalism chosen in thepresent study also allows to assess the benefits of intercropping systems, comprising pea-wheatmixtures, towards disease pressure such as the wheat/Septoria tritici pathosystem (Robert et al., 2008)

A 3D wheat model to study competition for light via the prediction of tillering dynamics

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