Philippe De Reffye

Cirad - La recherche agronomique pour le développement | CIRAD · Unité Mixte de Recherche Botanique et Bio-Informatique de l’Architecture des Plantes (AMAP)

Recent advances in human-in-the-loop or human-centric research have sparked a new wave of scientific exploration. These studies have enhanced the understanding of complex social systems and contributed to more sustainable artificial intelligence (AI) ecosystems. However, the incorporation of human or social factors increases system complexity, maki...

The architectural plasticity forms observed in trees is a result of meristem functioning, which generates new organs and branches, and adjusts growth processes in response to heterogeneous climatic adaptations that affect biomass allocation. Analyzing this plasticity should enable the selection of adapted individuals for optimizing successful cropp...

It is crucial to assess the impact of climate change on crop productivity and sustainability for the development of effective adaptation measures. Crop models are essential for quantifying this impact on crop yields. To better express crops’ intrinsic growth and development patterns and their plasticity under different environmental conditions, the...

La déforestation menace fortement l’environnement et la biodiversité dans le monde et particulièrement en Côte d’Ivoire. Il paraît nécessaire de développer des stratégies de restauration, de conservation et de gestion durable d’espèces pionnières issues des écosystèmes dégradés. L’étude vise à optimiser la culture de trois espèces forestières in...

Getting to grips with the botanical automaton (GLOUPS) (FSPM apprenticeship) and understanding the stochastic processes that govern the development of cultivated plants.

Les formes plastiques d'architecture observées chez les arbres résultent du fonctionnement des méristèmes, qui produisent de nouveaux organes et branches, et de l'ajustement des processus de croissance en réponse à des adaptations climatiques hétérogènes affectant l'allocation de la biomasse. L'analyse de cette plasticité devrait permettre de sélec...

Seed size is a critical factor that can impact the regeneration process of plant populations. The objective of this study is to identify optimal seeds for the cultivation of two overexploited native forest species in Côte d’Ivoire, namely Khaya senegalensis (Desr.) A.Juss., 1830 and Parkia biglobosa (Jacq.) R.BR. ex G. Don, 1830. A total of 1080 se...

Agricultural metaverse (AgriVerse) aims to optimize the production chain by saving costs, increasing efficiencies, and breaking information silos, in order to achieve sustainable agriculture. While AgriVerse is featured by the virtual-real interaction of the agriculture-related processes based on heterogeneous data, knowledge, and models, the link...

Briefing: The demand for food is tremendously increasing with the growth of the world population, which necessitates the development of sustainable agriculture under the impact of various factors, such as climate change. To fulfill this challenge, we are developing Metaverses for agriculture, referred to as AgriVerse, under our Decentralized Comple...

Plants exhibit plasticity in response to various external conditions, characterized by changes in physiological and morphological features. Although being non-negligible, compared to the other environmental factors, the effect of wind on plant growth is less extensively studied, either experimentally or computationally. This study aims to propose a...

Seed size is a key factor that can affect the regeneration process of plant populations. This study aims to identify efficient seeds that can optimise the cultivation of two overexploited native forest species in Côte d'Ivoire, namely Khaya senegalensis and Parkia bliglobosa . Sets of 1080 seeds per species were tested for their germination and see...

La modélisation de la croissance et de l’architecture des plantes (modélisation structure-fonction des plantes ou FSPM) s’inscrit logiquement dans le cadre d’une discipline récente, dénommée « biologie intégrative ». Selon Gilbert Chauvet (1993) : « La biologie intégrative est une nouvelle science, dont le développement pose des difficultés théoriq...

Architecture and structure-function modelling of native agroforestry species of Côte d'Ivoire

Functional–structural plant models (FSPMs) have been evolving for over 2 decades and their future development, to some extent, depends on the value of potential applications in crop science. To date, stabilizing crop production by identifying valuable traits for novel cultivars adapted to adverse environments is topical in crop science. Thus, this...

Key message The determination by non-destructive measurement of biomass and leaf area is of great interest to avoid any plant degradation. These data are necessary for biomass allocation and estimation of carbon distribution in trees using functional and structural growth models such as GREENLAB. Abstract Organ biomass and leaf area are important...

In Côte d'Ivoire, biodiversity is threatened by deforestation, which has spread to the savannah areas. Reforestation and agroforestry based on local species are the two solutions chosen by Côte d'Ivoire to cushion and mitigate the negative consequences of this phenomenon. Khaya senegalensis, Pterocarpus erinaceus and Parkia biglobosa are three indi...

Seed size and the growth environment are important variables that influence seed germination, growth and biomass of seedlings and future tree harvest and should thus be taken into account in agroforestry and reforestation programmes for endangered species like Pterocarpus erinaceus. In the present study, to assess seedling germination and vigour in...

Seed size and the growth environment are important variables that influence seed germination, growth and biomass of seedlings and future tree harvest and should thus be taken into account in agroforestry and reforestation programmes for endangered species like Pterocarpus erinaceus. In the present study, to assess seedling germination and vigour in...

Generally, the relation between quantitative trait loci (QTLs) and yield is empirical, and their roles in source-sink dynamics are unclear. A tomato introgression line (IL) population (S. pennellii ILs) was applied to analyze the effect of chromosome segment from wild cultivar on numerous yield-related phenotypes, including plant yield, the weight...

Background: With up to two hundred published contributions, the GreenLab mathematical model of plant growth developed since 2000 under Sino-French cooperation for agronomic applications, is descended from the structural models developed in the AMAP unit (de Reffye, 1988) that characterize the development of plants and encompass them in a conceptua...

Background and aims: Using internal trophic pressure as a regulating variable to model the complex interaction loops between organogenesis, production of assimilates and partitioning in functional-structural models of plant growth has attracted increasing interest in recent years. However, this approach is hampered by the fact that internal trophi...

To elucidate the mechanisms underlying the differences in yield formation among two parents (P1 and P2) and their F1 hybrid of cucumber, biomass production and whole source–sink dynamics were analyzed using a functional–structural plant model (FSPM) that simulates both the number and size of individual organs. Observations of plant development and...

油菜(Brassica napus L.)具有复杂的分枝结构, 其分枝为向顶式发生(出现)、向基式扩展, 这种独特的生长模式使得油菜个体植株间的构型存在很大的差异. 本研究利用与位置有关的生长延迟函数, 计算各分枝从发生到扩展的时间间隔, 来模拟油菜分枝这种独特的生长模式. 此外, 利用随机概率模型来模拟油菜植株间分枝数、主干和分枝的叶元数等. 通过实际测量的四个油菜品种(ZY18, ZY50, ZS72和ZS11)的数据, 采用最小二乘法对该模型的参数进行校准. 结果表明, 该随机模型能够模拟油菜植株拓扑结构, 并根据参数估计的结果分析不同品种的拓扑结构差异性. 本研究提出了新的简化方法模拟油菜分枝的生长模式, 该模型可与油菜生长模型相结合, 从而模拟油菜的动态生长过程.

Functional-structural plant models (FSPMs) generally simulate plant development and growth at the level of individual organs (leaves, flowers, internodes, etc.). Parameters that are not directly measurable, such as the sink strength of organs, can be estimated inversely by fitting the weights of organs along an axis (organic series) with the corres...

In the past decade, with the power of graphical boards, visualization of virtual natural scene become popular in multimedia applications. It usually relies on degraded virtual single plant geometrical representations and massive use of textures. Such scenes show however poor variability in terms of the number of species and individual plasticity. T...

FSPM are getting popular, open to a wide range of application and implemented in numerous simulation software or platforms. However, those seldom cover the field calibration aspects. We propose here a simple tool, StemGL, limited to single-stemmed plants, covering both calibration and simulation aspects of biomass production and allocation. Based o...

The complex interaction loops between organogenesis, assimilate production and partitioning are a crucial core component of most functional-structural plant growth model; yet these three processes are seldom fully coupled and there is no consensus on how it should be done. In this context, the use of the internal trophic pressure as a regulating va...

The coffee tree is an important economic plant for several developing countries. Stem and leaf dry biomass, which are key traits of plant production, are used in functional-structural plant models to simulate plant growth and predict yield. These values are difficult to obtain since they classically rely on time-consuming protocols and require dest...

Background and aims: For a given genotype, the observed variability of tree forms results from the stochasticity of meristem functioning and from changing and heterogeneous environmental factors affecting biomass formation and allocation. In response to climate change, trees adapt their architecture by adjusting growth processes such as pre- and n...

The number of organs produced by a plant varies among the individuals of a population. Taking these variations into account is an important step in understanding phenotypic variability. The aim of this study was to simulate stochastic development and growth in response to environmental change using GreenLab, an organ level functional-structural mod...

FSPM Plant and crop models are popular in the research community and there is increasing interest in their applications, from yield prediction to crop management optimization. A wide range of approaches and their software implementation can be found in the literature, with a large diversity in modelling scale (from plant organ to plot levels) and s...

Plant architectures generally display structural variations among individuals. Stochastic FSPMs have been developed to capture such feature, but calibrating such models is a challenging issue. For GreenLab model, parameter identification has been achieved on several crops and trees, but the estimation of functional parameters is mostly limited to p...

Significance Plants respond to environmental change by triggering biochemical and developmental networks across multiple scales. Multiscale models that link genetic input to the whole-plant scale and beyond might therefore improve biological understanding and yield prediction. We report a modular approach to build such models, validated by a framew...

Se réfère à la notice suivante : http://prodinra.inra.fr/record/256421

In winter oilseed rape (WOSR), only a subset of ovules can develop into seeds in the majority of pods. Any difficulty during the process of seed production may result in seed or pod abortion. This study aimed to reproduce the process of seed development in WOSR based on a limited number of parameters. As a result of the complexity of the developmen...

Individual variability generally exists in crop fields. It increases with an increase in plant population density, water or nutrient deficiency, or spatio-temporal irregularity, and often results in a reduction in yield. As individual variability exists in a community but is expressed through individuals, we studied it by applying two models, one a...

Highlights: Present study has introduced a comprehensive theoretical architecture to note probability of phytomer occurrence to describe wheat structural development. This provided an intermediary to compute the overall level of growth functions. The model then was calibrated on observation of variform individuals.

Plant architecture development and growth mathematical modeling shows nowadays increasing interests in multiples areas ranging from agronomy to multimedia topics. Plant architecture results from meristems activities, developing axis establishing the plant structure, and from the various organ compartment source-sink relations, regulating their mutu...

The 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 num...

Tree 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...

Understanding the mechanisms of plant adaptation to their habitat can help developing relevant conservation politics, which is a crucial issue for several Coffea species. This comes through an understanding of the links between genetic diversity and architectural plasticity. In this study, we investigated the biomass production and allocation strat...

• Context 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 ar...

Mongolian Scots pine (Pinus sylvestris var. mongolica) is one of the principal tree species in the network of Three-North Shelterbelt for windbreak and sand stabilisation in China. The functions of shelterbelts are highly correlated with the architecture and eco-physiological processes of individual tree. Thus, model-assisted analysis of canopy arc...

Description of the adapted GreenLab model. (DOCX)

• Plants respond to environmental change through alterations in organ size, number and biomass. However, different phenotypes are rarely integrated in a single model, and the prediction of plant responses to environmental conditions is challenging. The aim of this study was to simulate and predict plant phenotypic plasticity in development and grow...

An optimal control methodology is proposed for plant growth. This methodology is demonstrated by solving a water supply problem for optimal sunflower fruit filling. The functional–structural sunflower growth is described by a dynamical system given soil water conditions. Numerical solutions are obtained through an iterative optimization procedure,...

Tree crown architecture affects light interception, biomass production and mechanical stability. Crown architecture is largely determined by the topological development of the plant due to meristem activity. Modeling approaches can provide new insights into the dynamics of plant topology, but they are often hampered by experimental difficulties in...

We present briefly a general mathematical model that simulates tree development and growth based on a flexible time scale. Two sub-models are coupled with each other: one simulates tree organogenesis in each year, another computes the biomass production and allocation into individual organs. Each year is divided into discrete time steps, namely Com...