David Da Silva - Academia.edu (original) (raw)
Papers by David Da Silva
HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific ... more HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Horticulture, Environment, and Biotechnology, 2016
Storage of carbohydrate is essential for perennial plants survival, but its modeling is often uns... more Storage of carbohydrate is essential for perennial plants survival, but its modeling is often unsatisfactory. We studied the dynamics of reserve storage and mobilization in Peach trees and introduced a modeling approach that consider storage as an active sink rather than a passive buffer as frequently done in carbon-based models of tree growth.
Summary There is a current trend towards managing forests with multiple objectives, in particular... more Summary There is a current trend towards managing forests with multiple objectives, in particular to preserve or increase biodiversity and sustainab ility. There is renewed in terest in understorey vegetation as a way both to in crease the number of species a nd, indirectly, to favour fauna, including game, or improve soil quality. However, this stratum of herbaceous or shrubby species can also compete with young tree seedli ng and jeopardise tree regeneration. Hence a compromise has to be found among the different management objectives fo r the forest and in particular the understorey. Light is one of the main environmental factor s controlling ecological and biological processes in forests. For example, light quantity and light quality control the success of seed germination and the establishment and growth of tree seedlings in the understorey. Light also promotes the development of the floor vegetati on, the composition of which varies with site conditions in addition to light. M...
Warming winters due to climate change may critically affect temperate tree species. Insufficientl... more Warming winters due to climate change may critically affect temperate tree species. Insufficiently cold winters are thought to result in fewer viable flower buds and the subsequent development of fewer fruits or nuts, decreasing the yield of an orchard or fecundity of a species. The best existing approximation for a threshold of sufficient cold accumulation, the “chilling requirement” of a species or variety, has been quantified by manipulating or modeling the conditions that result in dormant bud breaking. However, the physiological processes that affect budbreak are not the same as those that determine yield. This study sought to test whether budbreak-based chilling thresholds can reasonably approximate the thresholds that affect yield, particularly regarding the potential impacts of climate change on temperate tree crop yields. County-wide yield records for almond (Prunus dulcis), pistachio (Pistacia vera), and walnut (Juglans regia) in the Central Valley of California were compa...
IX International Symposium on Modelling in Fruit Research and Orchard Management, 2015
The efficiency of light interception is a driving factor for plant transpiration and photosynthes... more The efficiency of light interception is a driving factor for plant transpiration and photosynthesis, and contributes greatly to plant growth. For a fruit tree, the efficiency of light interception is also a key factor to improve yield quality. Such efficiency is highly dependent on the tree geometrical and topological organisation which may vary between genotypes, or as a result of agronomic practices such as pruning. The purpose of this study was to use a functional-structural plant model, in order to find out the major geometrical traits that influence the efficiency of light interception in apple trees. MAppleT, an architectural model of apple tree, and VPlants, a software library that includes functionalities to simulate light environment, provided the basis for this work. The STAR, namely the silhouette to total area ratio of leaves, was used to evaluate the light interception efficiency. The general methodology contained three steps: (1) manipulation of a set of geometrical parameters in MAppleT, such as those related to internode elongation, leaf area expansion, and branching angle; (2) integration of the resulting tree architecture within the simulated light environment for calculation of STAR values at the whole tree scale; (3) analysis of the influence of the variation of each geometrical trait on the variance of STAR outputs. As expected, leaf area manipulation had the highest impact on STAR values. Interactions between input parameters were also found, and are illustrated in the case of leaf area versus internode length. This suggests that optimal combination(s) of the corresponding traits could be found, setting a target for genetic improvement, as well as physiological studies on real apple trees.
Plant, cell & environment, Jan 18, 2017
Numerical plant models can predict the outcome of plant traits modifications resulting from genet... more 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 ...
Annals of botany, Aug 8, 2016
Plant growth depends on carbon availability and allocation among organs. QualiTree has been desig... more Plant growth depends on carbon availability and allocation among organs. QualiTree has been designed to simulate carbon allocation and partitioning in the peach tree (Prunus persica), whereas MappleT is dedicated to the simulation of apple tree (Malus × domestica) architecture. The objective of this study was to couple both models and adapt QualiTree to apple trees to simulate organ growth traits and their within-tree variability. MappleT was used to generate architectures corresponding to the 'Fuji' cultivar, accounting for the variability within and among individuals. These architectures were input into QualiTree to simulate shoot and fruit growth during a growth cycle. We modified QualiTree to account for the observed shoot polymorphism in apple trees, i.e. different classes (long, medium and short) that were characterized by different growth function parameters. Model outputs were compared with observed 3D tree geometries, considering shoot and final fruit size and growt...
There is a current trend towards managing forests with multiple objectives, in particular to pres... more There is a current trend towards managing forests with multiple objectives, in particular to preserve or increase biodiversity and sustainability. There is renewed interest in understorey vegetation as a way both to increase the number of species and, indirectly, to favour fauna, including game, or improve soil quality. However, this stratum of herbaceous or shrubby species can also compete with young tree seedling and jeopardise tree regeneration. Hence a compromise has to be found among the different management objectives for the forest and in particular the understorey. Light is one of the main environmental factors controlling ecological and biological processes in forests. For example, light quantity and light quality control the success of seed germination and the establishment and growth of tree seedlings in the understorey. Light also promotes the development of the floor vegetation, the composition of which varies with site conditions in addition to light. Modifying light a...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012
HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific ... more HAL is a multi-disciplinary open access archive for the deposit and dissemination of sci-entific research documents, whether they are pub-lished or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et a ̀ la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
Horticulture, Environment, and Biotechnology, 2016
Storage of carbohydrate is essential for perennial plants survival, but its modeling is often uns... more Storage of carbohydrate is essential for perennial plants survival, but its modeling is often unsatisfactory. We studied the dynamics of reserve storage and mobilization in Peach trees and introduced a modeling approach that consider storage as an active sink rather than a passive buffer as frequently done in carbon-based models of tree growth.
Summary There is a current trend towards managing forests with multiple objectives, in particular... more Summary There is a current trend towards managing forests with multiple objectives, in particular to preserve or increase biodiversity and sustainab ility. There is renewed in terest in understorey vegetation as a way both to in crease the number of species a nd, indirectly, to favour fauna, including game, or improve soil quality. However, this stratum of herbaceous or shrubby species can also compete with young tree seedli ng and jeopardise tree regeneration. Hence a compromise has to be found among the different management objectives fo r the forest and in particular the understorey. Light is one of the main environmental factor s controlling ecological and biological processes in forests. For example, light quantity and light quality control the success of seed germination and the establishment and growth of tree seedlings in the understorey. Light also promotes the development of the floor vegetati on, the composition of which varies with site conditions in addition to light. M...
Warming winters due to climate change may critically affect temperate tree species. Insufficientl... more Warming winters due to climate change may critically affect temperate tree species. Insufficiently cold winters are thought to result in fewer viable flower buds and the subsequent development of fewer fruits or nuts, decreasing the yield of an orchard or fecundity of a species. The best existing approximation for a threshold of sufficient cold accumulation, the “chilling requirement” of a species or variety, has been quantified by manipulating or modeling the conditions that result in dormant bud breaking. However, the physiological processes that affect budbreak are not the same as those that determine yield. This study sought to test whether budbreak-based chilling thresholds can reasonably approximate the thresholds that affect yield, particularly regarding the potential impacts of climate change on temperate tree crop yields. County-wide yield records for almond (Prunus dulcis), pistachio (Pistacia vera), and walnut (Juglans regia) in the Central Valley of California were compa...
IX International Symposium on Modelling in Fruit Research and Orchard Management, 2015
The efficiency of light interception is a driving factor for plant transpiration and photosynthes... more The efficiency of light interception is a driving factor for plant transpiration and photosynthesis, and contributes greatly to plant growth. For a fruit tree, the efficiency of light interception is also a key factor to improve yield quality. Such efficiency is highly dependent on the tree geometrical and topological organisation which may vary between genotypes, or as a result of agronomic practices such as pruning. The purpose of this study was to use a functional-structural plant model, in order to find out the major geometrical traits that influence the efficiency of light interception in apple trees. MAppleT, an architectural model of apple tree, and VPlants, a software library that includes functionalities to simulate light environment, provided the basis for this work. The STAR, namely the silhouette to total area ratio of leaves, was used to evaluate the light interception efficiency. The general methodology contained three steps: (1) manipulation of a set of geometrical parameters in MAppleT, such as those related to internode elongation, leaf area expansion, and branching angle; (2) integration of the resulting tree architecture within the simulated light environment for calculation of STAR values at the whole tree scale; (3) analysis of the influence of the variation of each geometrical trait on the variance of STAR outputs. As expected, leaf area manipulation had the highest impact on STAR values. Interactions between input parameters were also found, and are illustrated in the case of leaf area versus internode length. This suggests that optimal combination(s) of the corresponding traits could be found, setting a target for genetic improvement, as well as physiological studies on real apple trees.
Plant, cell & environment, Jan 18, 2017
Numerical plant models can predict the outcome of plant traits modifications resulting from genet... more 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 ...
Annals of botany, Aug 8, 2016
Plant growth depends on carbon availability and allocation among organs. QualiTree has been desig... more Plant growth depends on carbon availability and allocation among organs. QualiTree has been designed to simulate carbon allocation and partitioning in the peach tree (Prunus persica), whereas MappleT is dedicated to the simulation of apple tree (Malus × domestica) architecture. The objective of this study was to couple both models and adapt QualiTree to apple trees to simulate organ growth traits and their within-tree variability. MappleT was used to generate architectures corresponding to the 'Fuji' cultivar, accounting for the variability within and among individuals. These architectures were input into QualiTree to simulate shoot and fruit growth during a growth cycle. We modified QualiTree to account for the observed shoot polymorphism in apple trees, i.e. different classes (long, medium and short) that were characterized by different growth function parameters. Model outputs were compared with observed 3D tree geometries, considering shoot and final fruit size and growt...
There is a current trend towards managing forests with multiple objectives, in particular to pres... more There is a current trend towards managing forests with multiple objectives, in particular to preserve or increase biodiversity and sustainability. There is renewed interest in understorey vegetation as a way both to increase the number of species and, indirectly, to favour fauna, including game, or improve soil quality. However, this stratum of herbaceous or shrubby species can also compete with young tree seedling and jeopardise tree regeneration. Hence a compromise has to be found among the different management objectives for the forest and in particular the understorey. Light is one of the main environmental factors controlling ecological and biological processes in forests. For example, light quantity and light quality control the success of seed germination and the establishment and growth of tree seedlings in the understorey. Light also promotes the development of the floor vegetation, the composition of which varies with site conditions in addition to light. Modifying light a...
2012 IEEE 4th International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications, 2012