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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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Multichannel imaging for monitoring chemical composition and germination capacity of cowpea(Vigna unguiculata) seeds during development and maturation

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The Crop Journal 2022年第5期10卷 1399-1411页

作者： Gamal ElMasry Nasser Mandour Yahya Ejeez Didier demilly Salim Al-Rejaie Jerome Verdier etienne Belin David Rousseau Agricultural engineering department Faculty of AgricultureSuez Canal UniversityIsmailiaEgypt Groupe d’etude et de Controle des Variétés et des semences(GEVES) Station Nationale d’Essais de Semences(SNES)Beaucouze49071AngersFrance department of Pharmacology&Toxicology College of PharmacyKing Saud UniversitySaudi Arabia Laboratoire Angevin de recherche en Ingenierie des Systemes(LARIS) Universited’AngersAngersFrance institut National de la recherche Agronomique(inra) UMR1345 Institut de Recherche en Horticulture et SemencesBeaucouzéF-49071AngersFrance

This study aimed to set a computer-integrated multichannel spectral imaging system as a high-throughput phenotyping tool for the analysis of individual cowpea seeds harvested at different developmental stages. The changes in germination capacity and variations in moisture, protein and different sugars during twelve stages of seed development from 10 to 32 days after anthesis were nondestructively monitored. Multispectral data at 20 discrete wavelengths in the ultraviolet, visible and near infrared regions were extracted from individual seeds and then modelled using partial least squares regression and linear discriminant analysis(LDA) models. The developed multivariate models were accurate enough for monitoring all possible changes occurred in moisture, protein and sugar contents with coefficients of determination in prediction R^(2) of 0.93, 0.80 and 0.78 and root mean square errors in prediction(RMSEP) of 6.045%, 2.236% and 0.890%, respectively. The accuracy of PLS models in predicting individual sugars such as verbascose and stachyose was reasonable with R~2 of 0.87 and 0.87 and RMSEP of 0.071%and 0.485%, respectively;but for the prediction of sucrose and raffinose the accuracy was relatively limited with R^(2) of 0.24 and 0.66 and RMSEP of 0.567% and 0.045%, respectively. The developed LDA model was robust in classifying the seeds based on their germination capacity with overall correct classification of96.33% and 95.67% in the training and validation datasets, respectively. With these levels of accuracy,the proposed multichannel spectral imaging system designed for single seeds could be an effective choice as a rapid screening and non-destructive technique for identifying the ideal harvesting time of cowpea seeds based on their chemical composition and germination capacity. Moreover, the development of chemical images of the major constituents along with classification images confirmed the usefulness of the proposed technique as a non-destructive tool for estim

关键词： Multispectral imaging Multichannel imaging Chemical imaging Spectral analysis Seeds Cowpea

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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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Genome mapping of postzygotic hybrid necrosis in an interspecific pear population

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horticulture Research 2016年第1期3卷 326-337页

作者： Sara Montanari Lester Brewer Robert Lamberts Riccardo Velasco Mickael Malnoy Laure Perchepied Philippe Guérif Charles-Eric Durel Vincent G M Bus Susan E Gardiner David Chagné Research and Innovation Centre Fondazione Edmund MachVia Mach 1San Michele all’Adige38010TNItaly The New Zealand institute for Plant&Food Research Limited Palmerston North Research CentrePalmerston NorthNew Zealand institut de recherche en horticulture et semences-umr1345 Institut National de la Recherche Agronomique(INRA)SFR 4207 Quasav42 rue Georges MorelBeaucouzéF-49071France The New Zealand institute for Plant&Food Research Limited Motueka Research CentreMotuekaNew Zealand institut de recherche en horticulture et semences-umr1345 Universitéd’AngersAngersF-49045France The New Zealand institute for Plant&Food Research Limited Hawke’s Bay Research CentreHavelock NorthNew Zealand

deleterious epistatic interactions in plant inter-and intraspecific hybrids can cause a phenomenon known as hybrid necrosis,characterized by a typical seedling phenotype whose main distinguishing features are dwarfism,tissue necrosis and in some cases *** of the chromosome regions associated with this type of incompatibility is important not only to increase our understanding of the evolutionary diversification that led to speciation but also for breeding *** of molecular markers linked to the lethal genes will allow breeders to avoid incompatible inbred combinations that could affect the expression of important agronomic tratis co-segregating with these *** hybrid necrosis has been reported in several plant taxa,including Rosaceae species,this phenomenon has not been described previously in *** the interspecific pear population resulting from a cross between PEAR3(Pyrus bretschneideri×Pyrus communis)and‘Moonglow’(***),we observed two types of hybrid necrosis,expressed at different stages of plant *** a combination of previously mapped and newly developed genetic markers,we identified three chromosome regions associated with these two types of lethality,which were genetically *** type resulted from a negative epistatic interaction between a locus on linkage group 5(LG5)of PEAR3 and a locus on LG1 of‘Moonglow’,while the second type was due to a gene that maps to LG2 of PEAR3 and which either acts alone or more probably interacts with another gene of unknown location inherited from‘Moonglow’.

关键词： breeding seedling dwarf

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Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple

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horticulture Research 2015年第1期2卷 301-309页

作者： Toshi M Foster Jean-Marc Celton David Chagné D Stuart Tustin Susan E Gardiner The New Zealand institute for Plant&Food Research Ltd Palmerston North Private Bag 11600Palmerston North 4474New Zealand inra umr 1345 institut de recherche en horticulture et semences 49071 BeaucouzéFrance The New Zealand institute for Plant&Food Research Ltd Havelock North Private Bag 1401Havelock North 4175New Zealand

The apple dwarfing rootstock‘Malling9’(‘M9’)has been used worldwide both to reduce scion vigour and as a genetic source for breeding new *** of‘M9’segregate for rootstock-induced dwarfing of the scion,indicating that this trait is controlled by one or more genetic factors.A quantitative trait locus(QTL)analysis of a rootstock population derived from the cross between‘M9’×‘Robusta5’(non-dwarfing)and grafted with‘Braeburn’scions identified a major QTL(Dw1)on linkage group(LG)5,which exhibits a significant influence on dwarfing of the scion.A smaller-effect QTL affecting dwarfing(Dw2)was identified on LG11,and four minor-effect QTLs were found on LG6,LG9,LG10 and *** analysis indicates that the combination of Dw1 and Dw2 has the strongest influence on rootstock-induced dwarfing,and that Dw1 has a stronger effect than *** markers linked to Dw1 and Dw2 were screened over 41 rootstock accessions that confer a range of effects on scion *** majority of the dwarfing and semi-dwarfing rootstock accessions screened carried marker alleles linked to Dw1 and *** suggests that most apple dwarfing rootstocks have been derived from the same genetic source.

关键词： dwarf trait breeding

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整合数量遗传信息的水稻虚拟生长模型研究进展

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生物数学学报 2017年第3期32卷 376-388页

作者：徐利锋 Gerhard Buck-Sorlin 丁维龙高楠浙江工业大学计算机科学与技术学院浙江杭州310023 umr1345 institut de recherche en horticulture et semences(IRHS)

随着全球人口的持续增加和环境的恶化,粮食作物的高产作为解决粮食短缺必不可少的途径,一直受到科学家们的广泛关注.运用可视化技术和作物模型相结合的方法,来研究植物的基因型-表现型相互反馈是一种新型的研究手段.其中,运用植物功能... 详细信息

随着全球人口的持续增加和环境的恶化,粮食作物的高产作为解决粮食短缺必不可少的途径,一直受到科学家们的广泛关注.运用可视化技术和作物模型相结合的方法,来研究植物的基因型-表现型相互反馈是一种新型的研究手段.其中,运用植物功能与结构模型的方法,能够对作物株型研究和传统育种进行辅助,从而促进育种进程.本文以水稻的虚拟生长模型为例,从运用作物模型及功能与结构模型进行QTL定位研究出发,阐述了植物模型研究的研究现状.重点综述了水稻功能与结构模型应用于虚拟育种研究的进展,提出了目前运用水稻生长模型进行虚拟育种研究中存在的问题和弊端,并论述了可能的解决方案,最后进行了相关的讨论和展望.

关键词：遗传信息水稻虚拟植物模型功能与结构

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Accuracy and responses of genomic selection on key traits in apple breeding

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horticulture Research 2015年第1期2卷 1-12页

作者： Hélène Muranty Michela Troggio Inès Ben Sadok Mehdi Al Rifaï Annemarie Auwerkerken Elisa Banchi Riccardo Velasco Piergiorgio Stevanato W.Eric van de Weg Mario Di Guardo Satish Kumar François Laurens Marco C.A.M.Bink institut de recherche en horticulture et semences umr1345 INRASFR 4207 QUASAVF-49071 BeaucouzeFrance Research and Innovation Center Fondazione Edmund MachSan Michele all’AdigeTrentoItaly Better 3 Fruit RillaarBelgium DAFNAE Dipartimentodi Agronomia Animali Alimenti Risorse Naturalie Ambienteviale Università1635020 Legnaro(PD)Universitàdegli Studi di PadovaItaly Wageningen UR Plant Breeding Wageningen University and Research CenterWageningenThe Netherlands The New Zealand institute for Plant&Food Research Limited Private Bag 1401Havelock North 4157New Zealand Biometris Wageningen University and Research CenterWageningenThe Netherlands

The application of genomic selection in fruit tree crops is expected to enhance breeding eficiency by increasing prediction accuracy,increasing selection intensity and decreasing generation *** objectives of this study were to assess the accuracy of prediction and selection response in commercial apple breeding programmes for key *** training population comprised 977 individuals derived from 20 pedigreed fllsib *** phenotypic data were available on 10 traits related to productivity and fruit external appearance and genotypic data for 7829 SNPs obtained with an llumina 20K SNP *** these data,a genome-wide prediction model was built and subsequently used to calculate genomic breeding values of five application fllsib *** application families had genotypes at 364 SNPs from a dedicated 512 SNP array,and these genotypic data were extended to the high-density level by *** five families were phenotyped for 1 year and their phenotypes were compared to the predicted breeding *** of genomic prediction across the 10 traits reached a maximum value of 0.5 and had a median value of *** accuracies were strongly affected by the phenotypic distribution and heritability of *** the largest family,significant selection response was observed for traits with high heritability and symmetric phenotypic *** that showed non-significant response often had reduced and skewed phenotypic variation or low *** the five application families the accuracies were uncorrelated to the degree of relatedness to the training *** results underline the potential of genomic prediction to accelerate breeding progress in outbred fruit tree crops that still need to overcome long generation intervals and extensive phenotyping costs.

关键词： breeding crops traits

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Apple whole genome sequences:recent advances and new prospects

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horticulture Research 2019年第1期6卷 1247-1270页

作者： Cameron P.Peace Luca Bianco Michela Troggio Eric van de Weg Nicholas P.Howard Amandine Cornille Charles-Eric Durel Sean Myles ZoëMigicovsky Robert J.Schaffer Evelyne Costes Gennaro Fazio Hisayo Yamane Steve van Nocker Chris Gottschalk Fabrizio Costa David Chagné Xinzhong Zhang Andrea Patocchi Susan E.Gardiner Craig Hardner Satish Kumar Francois Laurens etienne Bucher Dorrie Main Sook Jung Stijn Vanderzande department of horticulture Washington State UniversityPullmanWA 99164USA Computational Biology Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy department of Genomics and Biology of Fruit Crops Fondazione Edmund MachSan Michele all’AdigeTN 38010Italy Plant Breeding Wageningen University and ResearchWageningen 6708PBThe Netherlands department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA institut für Biologie und Umweltwissenschaften Carl von Ossietzky Universität26129 OldenburgGermany GQE-Le Moulon Institut National de la Recherche AgronomiqueUniversity of Paris-SudCNRSAgroParisTechUniversitéParis-Saclay91190 Gif-sur-YvetteFrance institut National de la recherche Agronomique Institut de Recherche en Horticulture et SemencesUMR 134549071 BeaucouzéFrance department of Plant Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNS B2N 5E3Canada The New Zealand institute for Plant and Food Research Ltd Motueka 7198New Zealand School of Biological Sciences University of AucklandAuckland 1142New Zealand AGAP INRACIRADMontpellier SupAgroUniversity of MontpellierMontpellierFrance Plant Genetic Resources Unit USDA ARSGenevaNY 14456USA Laboratory of Pomology Graduate School of AgricultureKyoto UniversityKyoto 606-8502Japan department of horticulture Michigan State UniversityEast LansingMI 48824USA The New Zealand institute for Plant and Food Research Ltd(Plant&Food Research) Palmerston North Research CentrePalmerston North 4474New Zealand College of horticulture China Agricultural University100193 BeijingChina Agroscope 8820 WädenswilSwitzerland Queensland Alliance of Agriculture and Food Innovation University of QueenslandSt Lucia 4072Australia New Cultivar Innovation Plant and Food ResearchHavelock North 4130New Zealand Agroscope 1260 ChanginsSwitzerland

In 2010,a major scientific milestone was achieved for tree fruit crops:publication of the first draft whole genome sequence(WGS)for apple(Malus domestica).This WGS,v1.0,was valuable as the initial reference for sequence information,fine mapping,gene discovery,variant discovery,and tool development.A new,high quality apple WGS,GDDH13 v1.1,was released in 2017 and now serves as the reference genome for *** the past decade,these apple WGSs have had an enormous impact on our understanding of apple biological functioning,trait physiology and inheritance,leading to practical applications for improving this highly valued *** gene identities for phenotypes of fundamental and practical interest can today be discovered much more ***-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and ***-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for *** understand the species,geographical,and genomic origins of domesticated apple more precisely,as well as its relationship to wild *** WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable,environmentally sound,productive,and consumer-desirable apple *** review includes examples of basic and practical breakthroughs and challenges in using the apple *** for“what’s next”focus on necessary upgrades to the genome sequence data pool,as well as for use of the data,to reach new frontiers in genomics-based scientific understanding of apple.

关键词： breakthrough hundreds frontier

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