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

A Modified Ant Colony Algorithm for Traveling Salesman Problem

Ant colony algorithms such as Ant Colony Optimization (ACO) havebeen effectively applied to solve the Traveling Salesman problem (TSP). However,traditional ACO algorithm has some issues such as long iterative length and prone tolocal convergence. To this end, we propose we embed ACO into Cultural Algorithm(CA) framework by leveraging the dual inheritance mechanism. Best solutions areevolved in both population space and belief space, and the communication betweenthem is achieved by accept and influence operations. Besides, we employ multiplepopulation spaces for parallel execution. Experiments show that the performance ofour proposed algorithm is greatly improved

Investigating the Influence of Geometrical Traits on Light Interception Efficiency of Apple Trees: a Modelling Study with MAppleT

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresInternational audienceMAppleT is an in silico functional-structural plant model that has been built for simulating architectural development of apple trees. It has the capability of representing tree growth within a virtual space where the development of individual organs depends on geometrical traits. The purpose of this research is to investigate the influence of apple trees x architectural variability on their light interception efficiency. The STAR, namely the silhouette to total area ratio, of leaves, was chosen to evaluate the level of such efficiency. The strategy is to integrate MAppleT with the light interception model provided by the fractalysis module of the VPlants software library. Target values of four major traits (internode length, leaf area, branching angle and top shoot diameter), are varied in range previously observed in a segregating population of apple hybrids. A sensitivity analysis based on polynomial and generalised additive models was performed for highlighting the most influential trait on light interception and suggesting the optimal combination(s) of traits leading to the highest STAR. The contribution of stochastic processes that pilot tree topology in MAppleT is also investigated in the sensitivity analysis. This study not only provides a time- and resource-saving alternative for data collection, but also sets a methodology for ideotype definition and further genetic improvement of apple trees

Extremely powerful and frequency-tunable terahertz pulses from a table-top laser-plasma wiggler

The production of broadband, terawatt terahertz (THz) pulses has been demonstrated by irradiating relativistic lasers on solid targets. However, the generation of extremely powerful, narrow-band, and frequency-Tunable THz pulses remains a challenge. Here, we present a novel approach for such THz pulses, in which a plasma wiggler is elaborated by a tabletop laser and a near-critical density plasma. In such a wiggler, the laser-Accelerated electrons emit THz radiations with a period closely related to the plasma thickness. Theoretical model and numerical simulations predict a THz pulse with a laser-THz energy conversion over 2.0%, an ultra-strong field exceeding 80 GV/m, a divergence angle approximately 20?, and a center-frequency tunable from 4.4 to 1.5 THz, can be generated from a laser of 430 mJ. Furthermore, we demonstrate that this method can work across a wide range of laser and plasma parameters, offering potential for future applications with extremely powerful THz pulse. © 2023 Authors. All rights reserved.11Nsciescopu

Orchard level simulation of fruit tree light interception

Several functional-structural plant models have been built for studying fruit trees, most of which focus on single trees. Simulating an entire orchard has been a difficulty due to two challenges: one is in computing, limited by processor capability and memory capacity, as well as the sequential nature of conventional approaches; the other is the modelling of plant-plant and plant-environmental interactions. The purpose of this work is to address the first challenge using high-performance computing to simulate an orchard with fine-scale growth details and efficient implementation. A cluster of “thin” computing nodes with multiple processing cores are responsible for simulating individual trees in parallel. Then a “fat” computing node, with many more cores and larger memory capacity, is used to integrate the individual trees into an orchard. The time consumed by this orchard-level simulation is similar to that of a single tree, which significantly improves the efficiency of virtual-experiment implementation. Our first application of the orchard-level simulation is to investigate the optimal interval between neighboring trees for light interception efficiency. A 4×4 orchard with evenly distributed trees is simulated for this investigation, suggesting that 2 m might be an optimal tree interval. In future work, the orchard-level simulation will also allow evaluation of the impact on light interception efficiency of other factors, such as pruning, row orientation, cross planting, and unusual terrains, setting ideal targets for genetic, physiological and orchard-management studies

Orchard level simulation of fruit tree light interception

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitièresSeveral functional-structural plant models have been built for studying fruit trees, most of which focus on single trees. Simulating an entire orchard has been a difficulty due to two challenges: one is in computing, limited by processor capability and memory capacity, as well as the sequential nature of conventional approaches; the other is the modelling of plant-plant and plant-environmental interactions. The purpose of this work is to address the first challenge using high-performance computing to simulate an orchard with fine-scale growth details and efficient implementation. A cluster of “thin” computing nodes with multiple processing cores are responsible for simulating individual trees in parallel. Then a “fat” computing node, with many more cores and larger memory capacity, is used to integrate the individual trees into an orchard. The time consumed by this orchard-level simulation is similar to that of a single tree, which significantly improves the efficiency of virtual-experiment implementation. Our first application of the orchard-level simulation is to investigate the optimal interval between neighboring trees for light interception efficiency. A 4×4 orchard with evenly distributed trees is simulated for this investigation, suggesting that 2 m might be an optimal tree interval. In future work, the orchard-level simulation will also allow evaluation of the impact on light interception efficiency of other factors, such as pruning, row orientation, cross planting, and unusual terrains, setting ideal targets for genetic, physiological and orchard-management studies

Virtual soybean—a computational model for studying autoregulation of nodulation

Nitrogen fixation by legumes is the product of a symbiosis of legume plants and a group of bacteria known as rhizobia (Carroll, et al., 1985; Kinkema, et al., 2006). It has been hypothesised that when rhizobia receive flavonoid signals from the host plants, production of a chemical nodulation factor is induced. The perception of nodulation factor by legume roots then activates a signal cascade leading to division of cortical cells for nodule formation. The activated cells produce a translocatable signal (Q), sent through a root-shoot pathway to the leaves and then detected by a leucine-rich repeat receptor kinase encoded by the NARK gene (Searle, et al., 2003). The detection of this root-shoot signal further induces the production of a shoot-derived signal (SDI) transported to the root, which inhibits development of new nodules. These signals, operating in a growing structure of root and shoot, compose a regulatory network known as autoregulation of nodulation (AON). The overall purpose of this study is to develop a greater understanding of this system through multi-scale modelling of processes including intra- and inter-cellular signalling, long-distance signalling and phenotypic development regulated by internal control mechanisms. The first step is to build a structural framework capable of simulating soybean growth driven by empirical results and hypothetical patterns, incorporating control mechanisms modelling Q and SDI

Light interception efficiency of apple trees: A multi-scale computational study based on MAppleT model

4. International Symposium on Models for Plant Growth, Environmental Control and Farm Management in Protected Cultivation, Nanjing, China,1 November 2012 The light interception efficiency of a fruit tree plays a key role in its transpiration and photosynthesis, therefore has a strong impact on its growth and yield. Previous research has indicated that manipulations of tree architecture, either through genetics or by agronomic practices, can help in improving light interception efficiency. However, the complexity of fruit tree structure as well as their long growth period makes it difficult to use real trees for exploring the link between architecture and light interception throughout tree development. In order to save time, resource and labour, this study relies on MAppleT, an architectural model of apple tree, and MμSLIM, a multi-scale light interception model part of the Vplants software library, to implement in silico experiments. The influence of apple trees’ architecture on their light interception was analysed at four scales: leaves, shoots branches and whole tree. At each scale either the actual position of the radiative components or a turbid medium hypothesis was used to estimate light interception. The STAR, namely the silhouette to total area ratio, was used to evaluate the level of interception efficiency. These investigations aim at comparing light interception estimation on simulated apple trees with bibliographic data and at highlighting STAR variations depending on the underlying assumption, i.e. turbid medium vs. actual position. The results are interpreted in relation with the spatial organisation of components and shoot types within the tree, and its impact on light interception estimation, focusing on deviance from turbid medium assumption