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Crop Phenomics and High-Throughput Phenotyping:Past Decades,Current Challenges,and Future Perspectives

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Molecular Plant 2020年第2期13卷 187-214页

作者： Wanneng Yang Hui Feng Xuehai Zhang Jian Zhang john H.doonan William David Batchelor Lizhong Xiong Jianbing Yan Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Huazhong Agricultural UniversityWuhan 430070P.R.China National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy Henan Agricultural UniversityZhengzhou 450002P.R.China The National Plant Pheno mics Centre In stitute of BiologicalEnviron mental and Rural SciencesAberystwyth UniversityAberystwythUK Department of Biosystems Engineering Auburn UniversityAuburnALUSA These authors contributed equally to this article.

Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput ***,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics ***,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming *** this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past *** then discuss the latest multi-omics research combining high-throughput phenotyping with genetic ***,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype *** is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.

关键词： crop phenomics high-throughput field phenotyping root system architecture yield and quality genetic studies

不同光照与水分条件下2种白三叶生长特性比较

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草地学报 2020年第5期28卷 1301-1310页

作者：王国芳张吴平张茜韩冀皖董宽虎 john doonan Luis Mur 山西农业大学资源环境学院山西太谷030801 山西农业大学软件学院山西太谷030801 山西农业大学动物科技学院山西太谷030801 Aberystwyth University Aberystwyth SY23 3EE UK

为探究不同光照和水分条件对不同品种白三叶(Trifolium repens L.)生长特性的影响,本研究以TKPR和TNSP 2个白三叶品种为试验对象,通过温室控制设定了3个光照梯度和3个水分梯度共9个组合处理,分析了不同处理下白三叶形态、生物量积累、... 详细信息

为探究不同光照和水分条件对不同品种白三叶(Trifolium repens L.)生长特性的影响,本研究以TKPR和TNSP 2个白三叶品种为试验对象,通过温室控制设定了3个光照梯度和3个水分梯度共9个组合处理,分析了不同处理下白三叶形态、生物量积累、生物量分配比及其可塑性指标的响应特征。结果表明:品种TKPR各指标受光照强度影响较大,品种TNSP受水分强度、光照与水分交互作用的影响较大;品种TNSP的相对生长速率大于TKPR;在适宜的环境下品种TNSP的生物量积累高于品种TKPR;光照与水分的交互作用对品种TKPR的开花繁殖策略影响较大;在不利的环境下品种TKPR适应可塑性较强,TNSP较弱。本研究结果为培育白三叶的新品种和高效生产栽培管理等方面提供了一定的参考依据。

关键词：白三叶 TKPR TNSP 光照水分可塑性

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植物表型组学:发展、现状与挑战

南京农业大学学报 2018年第4期41卷 580-588页

作者：周济 Francois Tardieu Tony Pridmore john doonan Daniel Reynolds Neil Hall Simon Griffiths 程涛朱艳王秀娥姜东丁艳锋南京农业大学植物表型组学研究中心江苏南京210095 Earlham Institute Norwich Research ParkNorwichNR4 7UZUK University of East Anglia Norwich Research ParkNorwichNR4 7TJUK INRA University of MontpellierLEPSE2 Place VialaE34060 MontpellierFrance University of Nottingham NottinghamNG7 2RDUK Aberystwyth Univerity IBERSAberytwythSY23 3DAUK john Innes Centre Norwich Research ParkNorwichNR4 7UHUK

随着遥感、机器人技术、计算机视觉和人工智能的发展,植物表型组学研究已经步入了快速成长阶段。本文首先介绍了植物表型组学的发展简史,包括其理论核心、研究方法、在生物研究中的应用以及国际上最新的研究动向。然后,针对各类表型技... 详细信息

随着遥感、机器人技术、计算机视觉和人工智能的发展,植物表型组学研究已经步入了快速成长阶段。本文首先介绍了植物表型组学的发展简史,包括其理论核心、研究方法、在生物研究中的应用以及国际上最新的研究动向。然后,针对各类表型技术载体平台如手持、人载、车载、田间实时监控、大型室内外自动化平台和航空机载等,分析这些技术手段在室内、外植物研究中的应用情况和实际问题。为了对表型研究中产生的巨量图像和传感器数据进行量化分析,把大数据转化为有实际意义的性状信息和生物学知识,本文着重讨论了后期表型数据解析和相应的研发过程。最后,提出表型组学的应用前景与未来展望,以期为中国的表型研究提供指导和建议。

关键词：表型组学多层次表型遥感成像技术机器人技术物联网人工智能高通量性状分析

A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits

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Plant Communications 2021年第2期2卷 51-62页

作者： Di Wu Dan Wu Hui Feng Lingfeng Duan Guoxing Dai Xiao Liu Kang Wang Peng Yang Guoxing Chen Alan P.Gay john H.doonan Zhiyou Niu Lizhong Xiong Wanneng Yang National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchHubei Key Laboratory of Agricultural Bioinformatics and College of EngineeringHuazhong Agricultural UniversityWuhan 430070PR China School of Information Engineering Wuhan Technology and Business UniversityWuhan 430065PR China The National Plant Phenomics Centre Institute of BiologicalEnvironmental and Rural SciencesAberystwyth UniversityAberystwythUK

Lodging is a common problemin rice,reducing its yield andmechanical harvesting *** architecture is a key aspect of its domestication and a major factor that limits its high *** ideal rice culm structure,includingmajor_axis_culm,minor axis_culm,andwall thickness_culm,is critical for improving lodging ***,the traditionalmethod ofmeasuring rice culms is destructive,time consuming,and labor *** this study,we used a high-throughput micro-CT-RGB imaging system and deep learning(SegNet)todevelopa high-throughputmicro-CTimageanalysis pipelinethatcanextract 24 riceculmmorphological traits and lodging resistance-related *** manual and automatic measurements were compared at themature stage,the mean absolute percentage errors for major_axis_culm,minor_axis_culm,andwall_thickness_culmin 104 indica rice accessionswere 6.03%,5.60%,and 9.85%,respectively,and the R^(2) valueswere 0.799,0.818,and *** also builtmodels of bending stress using culmtraits at the mature and tillering stages,and the R^(2) values were 0.722 and 0.544,*** modeling results indicated that this method can quantify lodging resistance nondestructively,even at an early growth *** addition,we also evaluated the relationships of bending stress toshoot dryweight,culm density,and drought-related traits and found that plants with greater resistance to bending stress had slightly higher biomass,culm density,and culm area but poorer drought *** conclusion,we developed a deep learning-integrated micro-CT image analysis pipeline to accurately quantify the phenotypic traits of rice culms in4.6 min per plant;this pipeline will assist in future high-throughput screening of large rice populations for lodging resistance.

关键词： rice culm micro-CT lodging resistance SegNet high-throughput deep learning

Crop phenotyping studies with application to crop monitoring

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Challenges and Opportunities in Preserving Key Structural Features of 3D-Printed Metal/Covalent Organic Framework

The Crop Journal 2022年第5期

作者： Xiuliang Jin Wanneng Yang john H.doonan Clement Atzberger

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Nano-Micro Letters 2024年第8期16卷 362-381页

作者： Ximeng Liu Dan Zhao john Wang Department of Materials Science and Engineering National University of SingaporeSingapore 117574Singapore Department of Chemical and Biomolecular Engineering National University of SingaporeSingapore 117585Singapore National University of Singapore(Chongqing)Research Institute Chongqing 401123People’s Republic of China

Metal-organic framework(MOF)and covalent organic framework(COF)are a huge group of advanced porous materials exhibiting attractive and tunable microstructural features,such as large surface area,tunable pore size,and functional surfaces,which have significant values in various application *** emerging 3D printing technology further provides MOF and COFs(M/COFs)with higher designability of their macrostructure and demonstrates large achievements in their performance by shaping them into advanced 3D ***,the currently available 3D printing M/COFs strategy faces a major challenge of severe destruction of M/COFs’microstructural features,both during and after 3D *** is envisioned that preserving the microstructure of M/COFs in the 3D-printed monolith will bring a great improvement to the related *** this overview,the 3D-printed M/COFs are categorized into M/COF-mixed monoliths and M/COF-covered *** differences in the properties,applications,and current research states are *** up-to-date advancements in paste/scaffold composition and printing/covering methods to preserve the superior M/COF microstructure during 3D printing are further discussed for the two types of 3D-printed M/*** the analysis of the current states of 3D-printed M/COFs,the expected future research direction to achieve a highly preserved microstructure in the 3D monolith is proposed.

关键词： Metal-organic frameworks Covalent organic frameworks 3D printing Microstructure Monolith

Experimental and analytical investigation on friction resistance force between buried coated pressurized steel pipes and soil

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Frontiers of Structural and Civil Engineering 2024年第4期18卷 615-629页

作者： Shaurav ALAM Tanvir MANZUR john MATTHEWS Chris BARTLETT Erez ALLOUCHE Brent KEIL john KRAFT Department of Civil Engineering and Construction Engineering Technology Louisiana Tech UniversityRustonLA 71270USA Department of Civil Engineering Bangladesh University of Engineering and TechnologyDhaka 1000Bangladesh Georgia Tech Research Institute AtlantaGA 30332USA Stantec Inc. Edmonton T5J0K4Canada North West Pipe Company VancouverWA 98684USA

This paper presents an analytical approach for estimating frictional resistance to pipe movement at soil and external pipe surface of buried coated pressurized steel pipes relative to the internal thrust *** proposed analytical method was developed based on 36 experiments,which involved three coating types(cement mortar(CM),polyurethane type-I(PT-I),prefabricated plastic tape(PPT))on pipes’surfaces,three different soils(pea-gravel(PG),sand(S),silty-clay(SC)),and four simulated over burden depths above the pipe’s *** showed frictional resistance decreased with increasing over burden depth above the pipe’s *** degree of frictional resistance at the pipe-soil interface was found to be in the order of PG>SC>S for all coating variations and overburden *** coated pipe buried in all three types of soil produced significantly higher frictional resistance as compared to other coating *** on experimental data,the developed analytical introduced a dimensionless factor“Z”,which included effects of types of coatings,soil,and overburden depths for simplified rapid *** showed that the method provided a better prediction of frictional resistance forces,in comparison to previous analytical methods,which were barely close in predicting friction resistance for different coating variations,soil types,and overburden *** resistance force values reported herein could be considered conservative.

关键词： friction resistance force thrust force coated pressurized steel pipe soil type overburden depth

A Population Dynamics Approach to the Distribution of Space Debris in Low Earth Orbit

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Communications on Applied Mathematics and Computation 2024年第1期6卷 340-353页

作者： john Jurkiewicz Peter Hinow Department of Mathematical Sciences University of Wisconsin-MilwaukeeMilwaukeeWI53201USA

The presence of the debris in the Earth’s orbit poses a significant risk to human activity in outer *** debris population continues to grow due to ground launches,the loss of external parts from space ships,and uncontrollable collisions between objects.A computationally feasible continuum model for the growth of the debris population and its spatial distribution is therefore *** we propose a diffusion-collision model for the evolution of the debris density in the low-Earth orbit and its dependence on the ground-launch *** parametrize this model and test it against data from publicly available object catalogs to examine timescales for the uncontrolled ***,we consider sensible launch policies and cleanup strategies and how they reduce the future risk of collisions with active satellites or space ships.

关键词： Population dynamics Space debris Kessler syndrome Diffusion Low-Earth orbit

Surgical treatment of inflammatory bowel disease:From the gastroenterologist’s stand-point

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World Journal of Gastrointestinal Surgery 2024年第5期16卷 1235-1254页

作者： john K Triantafillidis Inflammatory Bowel Disease Unit “Metropolitan General”HospitalHolargos 15562AtticaGreece Hellenic Society of Gastrointestinal Oncology Haidari 12461AthensGreece

Treatment of ulcerative colitis(UC)and Crohn’s disease(CD)represents,in the majority of cases,a real challenge to the gastroenterologist’s abilities and skills as well as a clinical test concerning his/her levels of medical knowledge and *** the last two decades,our pharmaceutical arsenal was significantly strengthened,especially after the introduction of the so-called biological agents,drugs which to a large extent not only improved the results of conservative treatment but also changed the natural history of the ***,colectomy is still necessary for some patients with severe UC although smaller compared to the past,precisely because of the improvements achieved in the available conservative ***,surgeries to treat colon dysplasia and cancer are increasing to some *** the same time,satisfactory improvements in surgical techniques,the pre-and post-operative care of patients,as well as the selection of the appropriate time for performing the surgery have been *** patients with CD,the improvement of conservative treatment did not significantly change the need for surgical treatment since two-thirds of patients need to undergo surgery at some point in the course of their *** the other hand,the outcome of the operation has improved through good preoperative care as well as the wide application of more conservative surgical techniques aimed at keeping as much of the bowel in situ as *** article discusses the indications for surgical management of UC patients from the gastroenterologist’s point of view,the results of the emerging new techniques such as transanal surgery and robotics,as well as alternative operations to the classic ileo-anal-pouch *** author also discusses the basic principles of surgical management of patients with CD based on the results of the relevant *** self-evident is emphasized,that is,to achieve an excellent therapeutic result in patients with se

关键词： Inflammatory bowel disease Ulcerative colitis Crohn’s disease Surgery Treatment Ileo-anal-pouch anastomosis Indications Techniques