Quantitative Genetics and Functional-Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

Background and Aims: Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype x environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional-structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods: The GreenLab model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions: By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits - such as cob weight - and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GreenLab maize model. The paper discusses the potentials of GreenLab to represent environment x genotype interactions, in particular through its main state variable, the ratio of biomass supply over demand

SUNLAB: a Functional-Structral Model for Genotypic and Phenotypic Characterization of the Sunflower Crop

International audienceA new functional-structural model SUNLAB for the crop sunflower (Helianthus annuus L.) is developed. It is dedicated to simulate the organogenesis, morphogenesis, biomass accumulation and biomass partitioning to organs in sunflower growth. It is adapted to model phenotypic response to diverse environment factors including temperature stress and water deficiency, and adapted to different genotypic variants. The model is confronted to experimental data and estimated parameter values of two genotypes "Melody" and "Prodisol" are presented. SUNLAB parameters seem to show genotypic variability, which potentially makes the model an interesting intermediate to discriminate between genotypes. Statistical tests on estimated parameter values suggest that some parameters are common between genotypes and others are genotypic specific. Since SUNLAB simulate individual leaf area and biomass as two state variables, an interesting corollary is that it also simulates dynamically the specific leaf area (SLA) variable. Further studies are performed to evaluate model performances with more genotypes and more discriminating environments to test and expand model's adaptability and usabilit

Source-sink relationships vary with age in Chinese pine (Pinus tabulaeformis Carr.): analysis using the GreenLab model

International audienceTree growth and development rely on the underlying dynamics of their source-sink balance. Given the difficulty of collecting experimental data on adult trees, models can be used as tools to disentangle the complex processes that drive biomass production and allocation. This paper investigates the variations of parameters with age driving the source-sink balance of individual trees through the functional-structural plant model GreenLab. Six Chinese pine (Pinus tabulaeformis Carr.) trees were destructively sampled and were divided into three groups based on ages: 5-year old, 10-year old and 18-year old. Firstly, the effects of age on organ dimensions and on organ relative mass were analyzed based on direct experimental measurement. Secondly, the hidden parameters of the GreenLab model were estimated using the data of total tree biomass for needle and wood compartment independently and then for the six trees in parallel. The statistical tests showed that there were significant differences between the tip attributes on first-, second-, and third-order branches of the three age stages for internode diameter, internode sink and needle sink. Preliminary fitting results showed that the sink of layers and the parameter of biomass production efficiency 1/r decrease with age

Optimizing plant growth model parameters for genetic selection based on QTL mapping

International audienceAn increasing interest is given to the potential benefits of introducing ecophysiological knowledge in breeding programs. Indeed, crop models provide powerful tools to predict phenotypic traits from new genotypes under untested environmental conditions. But, until now, few attempts have been undertaken to bridge the gap from genes to phenotype with a chain of functional processes. In this paper, we propose a framework for simulating plant growth from its genotype. Thus the genetic correlations between the parameters can be taken into consideration when optimization processes are used to define ideotypes based on model parameters. The example of virtual maize growing under constant environmental conditions is presented using the functional-structural model GreenLab

Parametric identification of a functional-structural tree growth model and application to beech trees (Fagus sylvatica)

International audienceFunctional-structural models provide detailed representations of tree growth and their application to forestry seems full of prospects. However, owing to the complexity of tree architecture, parametric identification of such models remains a critical issue. We present the GreenLab approach for modelling tree growth. It simulates tree growth plasticity in response to changes of their internal level of trophic competition, especially topological development and cambial growth. The model includes a simplified representation of tree architecture, based on a species-specific description of branching patterns. We study whether those simplifications allow enough flexibility to reproduce with the same set of parameters the growth of two observed understorey beech trees (Fagus sylvatica L.) of different ages in different environmental conditions. The parametric identification of the model is global, i.e. all parameters are estimated simultaneously, potentially providing a better description of interactions between sub-processes. As a result, the source-sink dynamics throughout tree development is retrieved. Simulated and measured trees were compared for their trunk profiles (fresh masses and dimensions of every growth units, ring diameters at different heights) and compartment masses of their order 2 branches. Possible improvements of this method by including topological criteria are discussed

Analysing the effects of local environment on the source-sink balance of Cecropia sciadophylla: a methodological approach based on model inversion

International audienceContext : Functional - structural models (FSM) of tree growth have great potential in forestry, but their development, calibration and validation are hampered by the difficulty of collecting experimental data at organ scale for adult trees. Due to their simple architecture and morphological properties, " model plants " such as Cecropia sciadophylla are of great interest to validate new models and methodologies, since exhaustive descriptions of their plant structure and mass partitioning can be gathered. * Aims : Our objective was to develop a model-based approach to analysing the influence of environmental conditions on the dynamics of trophic competition within C. sciadophylla trees. * Methods : We defined an integrated environmental factor that includes meteorological medium-frequency variations and a relative index representing the local site conditions for each plant. This index is estimated based on model inversion of the GreenLab FSM using data from 11 trees for model calibration and 7 trees for model evaluation. * Results : The resulting model explained the dynamics of biomass allocation to different organs during the plant growth, according to the environmental pressure they experienced. * Perspectives : By linking the integrated environmental factor to a competition index, an extension of the model to the population level could be considered

Oscillations in Functional Structural Plant Growth Models

International audienceThe dynamic model of plant growth GreenLab describes plant architecture and functional growth at the level of individual organs. Structural development is controlled by formal grammars and empirical equations compute the amount of biomass produced by the plant, and its partitioning among the growing organs, such as leaves, stems and fruits. The number of organs initiated at each time step depends on the trophic state of the plant, which is evaluated by the ratio of biomass available in plant to the demand of all the organs. The control of the plant organogenesis by this variable induces oscillations in the simulated plant behaviour. The mathematical framework of the GreenLab model allows to compute the conditions for the generation of oscillations and the value of the period according to the set of parameters. Two case-studies are presented, corresponding to emergence of oscillations associated to fructification and branching. Similar alternating patterns are commonly reported by botanists. In this article, two examples were selected: alternate patterns of fruits in cucumber plants and alternate appearances of branches in Cecropia trees. The model was calibrated from experimental data collected on these plants. It shows that a simple feedback hypothesis of trophic control on plant structure allows the emergence of cyclic patterns corresponding to the observed ones

Effect of topological and phenological changes on biomass partitioning in Arabidopsis thaliana inflorescence: a preliminary model-based study

International audienceAlthough the existence of phenological impact on biomass partitioning in the plant is known for many species, it is difficult to quantify this effect and to unravel it from the complex functional processes that interact during plant growth. This work explores the variations of biomass allocated to fruits according to simple changes in the topological and phenological development of Arabidopsis thaliana plants. Four plants of the same genotype (ecotype Columbia) were grown in controlled conditions in growth chamber. Their topological differences were studied using the functional-structural model GreenLab. It showed that when fitting the four plants with a single set of parameters, but each plant being given its own topological structure, half of the biomass variability can be reproduced

Growth and development simulation based on functional-structural model GreenLab for poplar (Salicaceae)

International audiencePoplar (salicaceae) is one of the widest planted fast-growing trees in the world. It is not only used for timber, but also used as windbreak and ecological protection of forest widely. The architecture of poplar has direct impact on poplar's growth and applications, but poplar's architecture still has not been discussed deeply in previous poplar models because of the difficulties raised by measurement, data processing and parameterization. This paper aimed to collect the biomass and architecture data of poplars of different ages, and construct the functional-structural model of poplar based on GreenLab. The selected poplar variety was poplar 107 (Populus × euramericana cv. Neva). The biomass and architecture data were collected from four trees with 3, 4, 5 and 6 years old, respectively. The architecture was simplified by classifying the branches into several types (physiological age) according to the length and size. Based on GreenLab model, some parameters were obtained and some strong correlation coefficients were got. The comparison between the measured and simulated results was given for the trunk data of all trees. The topological structures of poplar at different tree ages were reconstructed. This paper was a exploration of poplar growth simulation based on GreenLab model, and was a good reference in the Functional-Structural model construction of complex trees

Adaptation of the GreenLab model for analyzing sink-source relationships in Chinese Pine saplings

International audienceSince the 1990s, a new generation of models has emerged to simulate tree growth with consideration of both tree structure and functional processes. However, calibration of these functional-structural models (FSMs) often remains an open problem due to the topological complexity of trees and to the heavy measurements required. In this paper, we explore a possible way for dealing with the fitting problem, based on the GreenLab model approach. Detailed organ-level data including topological and geometrical measurements were collected on eight Chinese Pine saplings (Pinus tabulaeformis carr.) grown near Beijing. Adaptation of GreenLab to introduce a flexible modeling for biomass allocation to ring growth is presented. The main assumptions, such as allometry rules and sink relationships, were investigated. The problem of calibration of a complex branching structure was solved by defining an average tree. The results were interpreted with particular focus on the ones concerning the hidden mechanisms of secondary growth