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FSPM-P： towards a general functional-structural plant model for robust and comprehensive model development

Frontiers of Computer Science 2016年第6期10卷 1103-1117页

作者： Michael HENKE Winfried KURTH Gerhard H. BUCK-SORLIN Department of Ecoinformatics Biometrics and Forest Growth University of Gottingen Gottingen 37077 Germany UMR1345 Institut de Recherche en Horticulture et Semences (irhs) AGROCAMPUS OUEST Centre d'Angers Angers 49045 France

In the last decade, functional-structural plant modelling （FSPM） has become a more widely accepted paradigm in crop and tree production, as 3D models for the most important crops have been proposed. Given the wider portfolio of available models, it is now appropriate to enter the next level in FSPM development, by introducing more efficient methods for model development. This includes the consideration of model reuse （by modularisafion）, combination and comparison, and the enhancement of existing mod- els. To facilitate this process, standards for design and communication need to be defined and established. We present a first step towards an efficient and general, i.e., not speciesspecific FSPM, presently restricted to annual or bi-annual plants, but with the potential for extension and further generalization. Model structure is hierarchical and object-oriented, with plant organs being the base-level objects and plant individual and canopy the higher-level objects. Modules for the majority of physiological processes are incorporated, more than in other platforms that have a similar aim （e.g., photosynthesis, organ formation and growth）. Simulation runs with several general parameter sets adopted from the literature show that the present prototype was able to reproduce a plausible output range for different crops （rapeseed, barley, etc.） in terms of both the dynamics and final values （at harvest time） of model state variables such as assimilate production, organ biomass, leaf area and architecture.

关键词： functional-structural plant model prototyping,modelling standards teaching / learning FSPM GroIMP

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Effects of flight parameters for plant protection UAV on droplets deposition rate based on a 3D simulation approach

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International Journal of Agricultural and Biological Engineering 2023年第1期16卷 66-72页

作者： Lifeng Xu Zhongzhu Yang Zusheng Huang Weilong Ding Gerhard Buck-Sorlin College of Computer Science&Technology Zhejiang University of TechnologyHangzhou 310026China irhs INRAEAGROCAMPUS OUESTUniversite d’AngersSFR 4207 QUASAV42 rue Georges Morel49071 BeaucouzécedexFrance

With the development of aviation agricultural technology,the number of farmers adopting the use of drones in daily agricultural activities is growing rapidly in recent *** these,a large portion constitutes agricultural drones being used in pest control and crop protection practices,*** spraying of *** pesticides with drones have proven to be faster than other traditional *** the downside,flight time and range of Unmanned Aerial Vehicles(UAV)are often ***,a proper arrangement of flight height and velocity will greatly improve spraying efficiency.A new strategy to optimize the flight parameters,*** height and flight velocity,for fixed-wing UAV with a 3D simulation-based approach together with an automatic optimization algorithm was proposed in this *** find the optimal parameters for a UAV to fly and spray under certain environmental conditions,a three-dimensional model of the target crop was established first,followed by a detailed simulation of droplet *** a demonstration case,a grass model was developed and used as the target plant,and a physics-based method was used to simulate realistically the movement of the droplets in the air as well as the interaction between the droplets and the plant to obtain the droplet deposition rate under the specified operating ***,the standard Particle Swarm Optimization(PSO)algorithm was used to optimize the UAV operating parameters to obtain the best operating *** results indicate that using the standard PSO algorithm to optimize the operating parameters of the drone could significantly improve the deposition rate and find the best operating parameters.

关键词： unmanned aerial vehicle droplet deposition 3D simulation particle swarm optimization algorithm

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GenoDrawing:An Autoencoder Framework for Image Prediction from SNP Markers

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Plant Phenomics 2023年第4期5卷 816-824页

作者： Federico Jurado-Ruiz David Rousseau Juan A.Botía Maria José Aranzana Center for Research in Agricultural Genomics(CRAG) 08193 BarcelonaCerdanyolaSpain Universitéd'Angers LARISINRAe UMR IRHS49000 AngersFrance Department of Information and Communication Engineering University of Murcia30071 MurciaSpain IRTA(Institut de Recerca i Tecnologia Agroalimentàries) BarcelonaSpain

Advancements in genome sequencing have facilitated whole-genome characterization of numerous plant species,providing an abundance of genotypic data for genomic *** selection and neural networks(NNs),particularly deep learning,have been developed to predict complex traits from dense genotypic ***,an NN model to extract features from images in an unsupervised manner,has proven to be useful for plant *** study introduces an autoencoder framework,GenoDrawing,for predicting and retrieving apple images from a low-depth single-nucleotide polymorphism(SNP)array,potentially useful in predicting traits that are difficult to *** demonstrates proficiency in its task using a small dataset of shape-related *** indicate that the use of SNPs associated with visual traits has substantial impact on the generated images,consistent with biological *** using substantial SNPs is crucial,incorporating additional,unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important *** proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping,particularly beneficial for small to medium breeding companies to predict economically substantial heritable *** GenoDrawing has limitations,it sets the groundwork for future research in image prediction from genomic *** studies should focus on using stronger models for image reproduction,SNP information extraction,and dataset balance in terms of phenotypes for more precise outcomes.

关键词： Auto Drawing prediction

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Physics-based algorithm to simulate tree dynamics under wind load

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International Journal of Agricultural and Biological Engineering 2020年第2期13卷 26-32页

作者： Lifeng Xu Zhongzhu Yang Weilong Ding Gerhard Buck-Sorlin College of Computer Science&Technology Zhejiang University of TechnologyHangzhou 310026China irhs INRAEAGROCAMPUS OUESTUniversitéd'AngersSFR 4207 QUASAV42 rue Georges Morel49071 BeaucouzécedexFrance

Rapid development in the different computer science fields during the recent decades has facilitated the creation of new applications in the area of dynamic simulation of plant *** these new applications,simulation of trees swaying in the wind is of great importance,as those computer graphics related areas,e.g.,computer games,tree cultivation and forest management simulations,help a lot in revealing the mechanisms of tree dynamics under wind ***,it is a big challenge to balance the effect of visualization in real time and calculation efficiency for any simulation algorithm.A physics-based algorithm to simulate tree dynamics under wind load was proposed in this study.A mechanistic model simulating the bending of a cantilever beam was used within the algorithm to simulate deformation of stems,and the algorithm was integrated with a landscape model in which different types of trees were constructed with an L-system-based *** results show that realistic dynamic effects can be achieved with reasonably high computational efficiency.

关键词： physics-based algorithm tree model L-system Cantilever beam

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Morphological studies of rose prickles provide new in sights

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Horticulture Research 2021年第1期8卷 2849-2860页

作者： Ningning Zhou Fabienne Simonneau Tatiana Thouroude Laurence Hibrand-Saint Oyant Fabrice Foucher Univ Angers Institut AgroINRAEIRHSSFR QUASAVF-49000 AngersFrance National Engineering Research Center for Ornamental Horticulture Flower Research Institute(FRI)Yunnan Academy of Agricultural SciencesKunming 650231China Univ Angers INRAESFR QUASAVF-49000 AngersFrance

Prickles are common structures in plants that play a key role in defense against *** the Rosa genus,prickles are widely present with great diversity in terms of form and *** cut rose production,prickles represent an important issue,as they can damage the flower and injure *** objectives were to precisely describe the types of prickles that exist in roses,their tissues of origin and their *** performed a detailed histological analysis of prickle initiation and development in a rose F1 *** on the prickle investigation of 110 roses,we proposed the fi rst categorization of prickles in the Rosa *** are mainly divided into two categories,nonglandular prickles(NGPs)and glandular prickles(GPs),and subcategories were defined based on the presence/absence of hairs and *** demonstrated that NGPs and GPs both originate from multiple cells ofthe ground meristem beneath the *** GPs,the gland cells originate from the protoderm of the GP at the early developmental *** findings clearly demonstrate that prickles are notmodified trichomes(which originate from the protoderm).These conclusions are different from the current mainstream *** results provide a foundation for further studies on prickle initiation and development in plants.

关键词： beneath origin Morphological

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Diversity and selection of the continuous-flowering gene, RoKSN, in rose

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Horticulture Research 2021年第1期8卷 1155-1165页

作者： Vanessa Soufflet-Freslon Emilie Araou Julien Jeauffre Tatiana Thouroude Annie Chastellier Gilles Michel Yuki Mikanagi Koji Kawamura Mark Banfield Cristiana Oghina-Pavie Jeremy Clotault Alix Pernet Fabrice Foucher Univ Angers Institut AgroINRAEIRHSSFR QUASAVF-49000 AngersFrance49071 BeaucouzeFrance Natural History Museum and Institute ChibaJapan Osaka Institute of Technology OsakaJapan Department of Biological Chemistry John Innes CentreNorwich Research ParkNorwichUK Univ Angers CNRSTEMOSSFR CONFLUENCESAngers F-49000France

Blooming seasonality is an important trait in ornamental plants and was selected by *** roses flower only in spring whereas most cultivated modern roses can flower *** trait is explained by a mutation of a floral repressor gene,RoKSN,a TFL1 *** this work,we studied the origin,the diversity and the selection of the RoKSN *** analyzed 270 accessions,including wild and old cultivated Asian and European roses as well as modern *** sequencing the RoKSN gene,we proposed that the allele responsible for continuous-flowering,RoKSN copia,originated from Chinese wild roses(Indicae section),with a recent insertion of the copia *** cultivated Asian roses with the RoKSN copia allele were introduced in Europe,and the RoKSN copia allele was progressively selected during the 19th and 20th centuries,leading to continuous-flowering modern ***,we detected a new allele,RoKSN A181,leading to a weak *** allele encodes a functional floral repressor and is responsible for a moderate accumulation of RoKSN transcripts.A transient selection of this RoKSN A181 allele was observed during the 19th *** work highlights the selection of different alleles at the RoKSN locus for recurrent blooming in rose.

关键词： originated selection insertion

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基于GroIMP的水稻功能与结构仿真模型研究

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系统仿真学报 2013年第7期25卷 1476-1483,1489页

作者：徐利锋危扬丁维龙 Gerhard Buck-Sorlin 程志君浙江工业大学计算机科学与技术学院 UMR1345 Institut de Recherche en Horticulture et Semences(irhs) 49045 Angers Cedex 01France

为探索植物仿真模型构建方法及提高仿真模型构建效率,设计并实现了一个基于相关生长语法RGG及扩展L系统的植物模型构建语言XL的水稻秧苗功能与结构模型。该模型包含了光环境模块、植物结构模型、生理功能模型以及环境设置模块,从而能够... 详细信息

为探索植物仿真模型构建方法及提高仿真模型构建效率,设计并实现了一个基于相关生长语法RGG及扩展L系统的植物模型构建语言XL的水稻秧苗功能与结构模型。该模型包含了光环境模块、植物结构模型、生理功能模型以及环境设置模块,从而能够在植物外部形态层面及内部生理功能层面同时来描述虚拟植物的生长过程,并通过对植物生理过程与形态结构及环境因子的交互作用的考虑,能够在开源及交互的建模平台GroIMP上实现对虚拟植物的生长状态进行综合预测与动态可视化。简要地介绍了模型中主要模块及子模型构建的主要方法及模型构建的关键步骤,并通过模型的图形、数据输出验证了模型的有效性。经过简单地扩展,构建的模型可以直接应用到水稻整个生长期的建模仿真研究中。

关键词：植物仿真相关生长语法扩展L系统功能与结构模型光环境 GroIMP

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Radiated Ultrashort High-Power Electromagnetic Pulses Induce ATP Release in B16F10 Murine Melanoma Cells

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Journal of Electromagnetic Analysis and Applications 2015年第3期7卷 66-74页

作者： Sabrina Macaire Alexandre Catrain Stéphane Tortel Jean-Christophe Joly Sébastien Girard Pierre Bonnet Alain Vian CEA DAM Gramat France Institut Pascal Université Blaise Pascal Clermont-Ferrand France CNRS UMR 6602 Aubière France ARCH-E. Université d’Angers UMR 1345 IRHS Angers France

Ultrawideband electromagnetic pulses with high amplitude and short duration are reported to affect several aspects of cell physiology. They are usually delivered to the living material through electrodes in small dedicated chambers. Here we showed, using a totally different experimental setup, that radiated EM pulses illuminating the living material through a specialized antenna (without any direct contact) are able to trigger a rapid release of ATP in cultured murine cells that was concomitant with a drop of intracellular AEC. Despite this rapid and strong response, we found that cell viability and clonogenicity were only slightly affected by the EMF exposure.

关键词： Radiated Electromagnetic Pulses Koshelev Antenna eATP Cell Viability

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The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

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Horticulture Research 2021年第1期8卷 2785-2797页

作者： Nicholas P.Howard Cameron Peace Kevin A.T.Silverstein Ana Poets James J.Luby Stijn Vanderzande Charles-Eric Durel Helene Muranty Caroline Denance Eric van de Weg Institut fur Biologie und Umweltwissenschaften Carl von Ossietzky UniversityOldenburgGermany Department of Horticultural Science University of MinnesotaSt.PaulMNUSA Department of Horticulture and Landscape Architecture Washington State UniversityPullmanWashingtonWAUSA Minnesota Supercomputing Institute University of MinnesotaMinneapolisMNUSA Universited’Angers Institut AgroINRAEIRHSSFR 4207 QuaSaVBeaucouzeFrance Plant Breeding Wageningen University and ResearchWageningenThe Netherlands

Pedigree information is of fundamental importance in breeding programs and related genetics ***,many individuals have unknown *** methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive *** objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPLoSH).A custom Python script,HapShared,was developed to generate SPLoSH data in apple and sweet *** was used to establish empirical distributions of SPLoSH data for known relationships in these *** distributions were then used to estimate previously unknown *** studies in each crop demonstrated various pedigree reconstruction scenarios using SPLoSH *** cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘Windsor’,and the paternal grandparents of‘Stella’were *** apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree *** with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

关键词： Python breeding crops

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Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols

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Horticulture Research 2019年第1期6卷 444-455页

作者： Kendra AMcClure YuiHui Gong Jun Song Melinda Vinqvist-Tymchuk Leslie Campbell Palmer Lihua Fan Karen Burgher-MacLellan ZhaoQi Zhang Jean-Marc Celton Charles FForney ZoëMigicovsky Sean Myles Department of Plant and Animal Sciences Faculty of AgricultureDalhousie UniversityTruroNS B2N 5E3Canada Agriculture and Agri-Food Canada Kentville Research and Development CentreKentvilleNS B4N 1J5Canada College of Horticulture South China Agriculture UniversityGuangzhou 510642China irhs Agrocampus-OuestINRAUniversitéd’AngersSFR 4207 QuaSaVBeaucouzéFrance

Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing,primarily as dietary *** numerous pre-and post-harvest factors can affect the composition of polyphenols in apples,genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple *** we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography(HPLC)data with~100,000 single nucleotide polymorphisms(SNPs)from two diverse apple *** found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars,and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic *** GWAS,we identified candidate genes for the production of quercitrin,epicatechin,catechin,chlorogenic acid,4-O-caffeoylquinic acid and procyanidins B1,B2,and *** observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through markerassisted breeding or gene editing.

关键词： effect apple cultivar

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