Using numerical plant models and phenotypic correlation space to design achievable ideotypes

Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi-objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process-based crop model of sunflower and a functional-structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, ranging from the most feasible to the most efficient. The present study thus provides successful proof of concept for this enhanced modeling approach, which identified paths for desirable trait modification, including direction and intensity.Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environmen

Influence of the variation of geometrical and topological traits on light interception efficiency of apple trees: sensitivity analysis and metamodelling for ideotype definition

Background and AimsThe impact of a fruit tree's architecture on its performance is still under debate, especially with regard to the definition of varietal ideotypes and the selection of architectural traits in breeding programmes. This study aimed at providing proof that a modelling approach can contribute to this debate, by using in silico exploration of different combinations of traits and their consequences on light interception, here considered as one of the key parameters to optimize fruit tree production.MethodsThe variability of organ geometrical traits, previously described in a bi-parental population, was used to simulate 1- to 5-year-old apple trees (Malus × domestica). Branching sequences along trunks observed during the first year of growth of the same hybrid trees were used to initiate the simulations, and hidden semi-Markov chains previously parameterized were used in subsequent years. Tree total leaf area (TLA) and silhouette to total area ratio (STAR) values were estimated, and a sensitivity analysis was performed, based on a metamodelling approach and a generalized additive model (GAM), to analyse the relative impact of organ geometry and lateral shoot types on STAR.Keys ResultsA larger increase over years in TLA mean and variance was generated by varying branching along trunks than by varying organ geometry, whereas the inverse was observed for STAR, where mean values stabilized from year 3 to year 5. The internode length and leaf area had the highest impact on STAR, whereas long sylleptic shoots had a more significant effect than proleptic shoots. Although the GAM did not account for interactions, the additive effects of the geometrical factors explained >90% of STAR variation, but much less in the case of branching factors.ConclusionsThis study demonstrates that the proposed modelling approach could contribute to screening architectural traits and their relative impact on tree performance, here viewed through light interception. Even though trait combinations and antagonism will need further investigation, the approach opens up new perspectives for breeding and genetic selection to be assisted by varietal ideotype definition

Competition-based Model of Pruning: Applications to Apple Trees

International audienceno abstrac

Linking carbon economy and architectural development of peach trees by integrating markovian models into L-PEACH

International audienceno abstrac

Effects of pruning on the apple tree: from tree architecture to modeling

International audienceArboricultural practices such as pruning, artificial bending or fruit thinning are crucial interventions in orchard management and are used for controlling tree size, penetration of light into the canopy and the equilibrium between vegetative and reproductive growth. The aim of this project is to explore the possibility of integrating such practices in a model of apple tree development. To this end we designed field experiments to study the effects of pruning (thinning or heading cuts) on two apple cultivars with contrasted architecture, ?Fuji? and ?Braeburn?. The results of these first experiments showed that the studied cultivars had significantly different reactions to pruning: ?Braeburn? trees were penalized more than ?Fuji? trees in terms of the total number of internodes despite the fact that a greater number of internodes had developed. Thinning cuts of laterals tended to be compensated by an increase in lateral branching. Results also indicated that trees which had been pruned tended to develop trunks with similar number of internodes than control trees (which were not pruned). These experiments constitute a first step for assessing the rules underlying tree responses to pruning, which will be further integrated in a model of growth

Exploring plant topological structure with the AMAPmod software: an outline.

In the last decades, architectural analysis has been used to understand and to model plant development. These studies have lead us to reconsider the problem of measuring plants while taking into account their topological structure at several scales of detail. A computational platform, called AMAPmod, was created to work on such plant representations. This paper outlines the general methodology used in AMAPmod to represent plant topological structures and to explore these special types of databases. Plant structures are first encoded in order to build corresponding formal representations. Then, a dedicated language, AML, enables the user to extract various types of information from the plant databases and provides appropriate analyzing tools

MAppleT: simulation of apple tree development using mixed stochastic and biomechanical models

International audienceConstruction of architectural databases over years is time consuming and cannot easily capture the event dynamics, especially when both tr ee topology and geometry are considered. The present project aimed to bring together models of topology and geometry in a single simulation such that the architecture of an apple t ree may emerge from process interactions. This integration was performed using L-systems. A m ixed approach was developed based on stochastic models to simulate plant topology and me chanistic model for the geometry. The succession of growth units (GUs) along axes and the ir branching structure were jointly modeled by a hierarchical hidden Markov model. A bi omechanical model, derived from previous studies, was used to calculate stem form a t the metamer scale, taking into account the intra-year dynamics of primary, secondary and f ruit growth. Outputs consist of 3D mock- ups geometric models representing the progression o f tree form over time. To asses these models, a sensitivity analysis was performed and de scriptors were compared between simulated and digitized trees, including the total number of GUs in the entire tree, descriptors of shoot geometry (basal diameter, length), and des criptors of axis geometry (inclination, curvature). In conclusion, in spite of some limitat ions MAppleT constitutes a useful tool for simulating development of apple trees in interactio n with gravity