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Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant Phenomics 2023年第3期5卷 581-597页

作者： John Lagergren Mirko Pavicic Hari B.Chhetri Larry M.York Doug Hyatt David Kainer Erica M.Rutter Kevin Flores Jack Bailey-Bale Marie Klein Gail Taylor Daniel Jacobson Jared Streich Biosciences Division Oak Ridge National LaboratoryOak RidgeTNUSA Department of Applied Mathematics University of CaliforniaMercedCAUSA Department of Mathematics North Carolina State UniversityRaleighNCUSA Department of Plant Sciences University of CaliforniaDavisCAUSA

Plant phenotyping is typically a time-consuming and expensive endeavor,requiring large groups of researchers to meticulously measure biologically relevant plant traits,and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population *** this work,we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the *** contrast to previous methods,our approach(a)does not require experimental or image preprocessing,(b)uses the raw RGB images at full resolution,and(c)requires very few samples for training(e.g.,just 8 images for vein segmentation).Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools,validated using real-world physical measurements,and used to conduct a genome-wide association study to identify genes controlling the *** this way,the current work is designed to provide the plant phenotyping community with(a)methods for fast and accurate image-based feature extraction that require minimal training data and(b)a new population-scale dataset,including 68 different leaf phenotypes,for domain scientists and machine learning *** of the few-shot learning code,data,and results are made publicly available.

关键词： networks neural image

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Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.)

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Plant Phenomics 2022年第1期4卷 342-356页

作者： Zhanyou Xu Larry M.York Anand Seethepalli Bruna Bucciarelli Hao Cheng Deborah A.Samac USDA-ARS Plant Science Research Unit1991 Upper Buford CircleSt.PaulMN 55108USA Biosciences Division and center for bioenergy innovation Oak Ridge National LaboratoryOak RidgeTN 37830USA Noble Research Institute LLCArdmoreOK 73401USA Department of Agronomy and Plant Genetics University of Minnesota1991 Upper Buford CircleSt.PaulMN 55108USA Department of Animal Science University of California2251 Meyer HallOne Shields Ave.DavisCA 95616USA

Active breeding programs specifically for root system architecture(RSA)phenotypes remain rare;however,breeding for branch and taproot types in the perennial crop alfalfa is *** in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root *** image-based methods have been developed,translation to applied breeding is limited.

关键词： breeding Image Root

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GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

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Horticulture Research 2023年第8期10卷 97-108页

作者： Michael F.Nagle Jialin Yuan Damanpreet Kaur Cathleen Ma Ekaterina Peremyslova Yuan Jiang Bahiya Zahl Alexa Niño de Rivera Wellington Muchero Li Fuxin Steven H.Strauss Department of Forest Ecosystems and Society Oregon State University3180 SW Jefferson WayCorvallisOR97331United States Department of Electrical Engineering and Computer Science Oregon State University110 SW Park TerraceCorvallisOR97331United States Statistics Department Oregon State University103 SW Memorial PlaceCorvallisOR97331United States Biosciences Division Oak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830United States center for bioenergy innovation Oak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830United States Bredesen center for Interdisciplinary Research University of Tennessee821 Volunteer Blvd.KnoxvilleTN37996United States

Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of *** capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its genetic variation is largely *** identify genetic regulators of AR,we performed a genome-wide association study(GWAS)using 1148 genotypes of Populus *** are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale;to help overcome this limitation,we developed a computer vision system to measure an array of traits related to adventitious root development in poplar,including temporal measures of lateral and basal root length and *** was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical *** analyses yielded a total of 277 unique associations,suggesting that genes that control rooting include regulators of hormone signaling,cell division and structure,reactive oxygen species signaling,and other processes with known roles in root *** genes with uncharacterized functions and/or cryptic roles were also *** candidates provide targets for functional analysis,including physiological and epistatic analyses,to better characterize the complex polygenic regulation of AR.

关键词： GWAS breeding overcome

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CRISPR/Cas9-based gene activation and base editing in Populus

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Horticulture Research 2023年第6期10卷 205-213页

作者： Tao Yao Guoliang Yuan Haiwei Lu Yang Liu Jin Zhang Gerald A.Tuskan Wellington Muchero Jin-Gui Chen Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The center for bioenergy innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Chemical and Biological Process Development Group Pacific Northwest National Laboratory902 Battelle BoulevardRichlandWA 99352USA Department of Academic Education Central Community College-HastingsHastingsNE 68901USA State Key Laboratory of Subtropical Silviculture College of Forestry and BiotechnologyZhejiang A&F UniversityHangzhou 311300China

The genus Populus has long been used for environmental,agroforestry and industrial applications *** Populus is also recognized as a desirable crop for biofuel production and a model tree for physiological and ecological *** such,various modern biotechnologies,including CRISPR/Cas9-based techniques,have been actively applied to Populus for genetic and genomic improvements for traits such as increased growth rate and tailored lignin ***,CRISPR/Cas9 has been primarily used as the active Cas9 form to create knockouts in the hybrid poplar clone“717-1B4”(*** x *** clone INRA 717-1B4).Alternative CRISPR/Cas9-based technologies,*** involving modified Cas9 for gene activation and base editing,have not been evaluated in most Populus species for their *** we employed a deactivated Cas9(dCas9)-based CRISPR activation(CRISPRa)technique to fine-tune the expression of two target genes,TPX2 and LecRLK-G which play important roles in plant growth and defense response,in hybrid poplar clone“717-1B4”and poplar clone“WV94”(***“WV94”),*** observed that CRISPRa resulted in 1.2-fold to 7.0-fold increase in target gene expression through transient expression in protoplasts and Agrobacterium-mediated stable transformation,demonstrating the effectiveness of dCas9-based CRISPRa system in *** addition,we applied Cas9 nickase(nCas9)-based cytosine base editor(CBE)to precisely introduce premature stop codons via C-to-T conversion,with an efficiency of 13%–14%,in the target gene PLATZ which encodes a transcription factor involved in plant fungal pathogen response in hybrid poplar clone“717-1B4”.Overall,we showcase the successful application of CRISPR/Cas-based technologies in gene expression regulation and precise gene engineering in two Populus species,facilitating the adoption of emerging genome editing tools in woody species.

关键词： CRISPR/Cas9 activation base

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Expanding the application of a UV-visible reporter for transient gene expression and stable transformation in plants

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Horticulture Research 2021年第1期8卷 3286-3296页

作者： Guoliang Yuan Haiwei Lu Dan Tang Md Mahmudul Hassan Yi Li Jin-Gui Chen Gerald A.Tuskan Xiaohan Yang Bioscie nces Divisi on Oak Ridge Nati onal Lab oratoryOak RidgeTN 37831USA The center for Bioe nergy Inno vati on Oak Ridge Nati onal Lab oratoryOak RidgeTN 37831USA Department of Plant Science and Landscape Architecture University of ConnecticutStorrsCT 06269USA National center for Citrus Improvement College of HorticultureHunan Agricultural UniversityChangsha 410128 HunanChina Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali 8602Bangladesh

Green fl uorescent protein(GFP)has been widely used for monitoring gene expression and protein localization in diverse ***,highly sensitive imaging equipment,like fl uorescence microscope,is usually required for the visualization of GFP,limitings its application to fi xed locations in samples.A reporter that can be visualized in realtime regardless the shape,size and location of the target samples will increase the fl exibility and ef fi ciency of research ***,we report the application of a GFP-like protein,called eYGFPuv,in both transient expression and stable transformation,in two herbaceous plant species(Arabidopsis and tobacco)and two woody plant species(poplar and citrus).We observed bright fl uorescence under UV light in all of the four plant species without any effects on plant growth or *** was shown to be effective for imaging transient expression in leaf and root *** a focus on in vitro transformation,we demonstrated that the transgenic events expressing 1x eYGFPuv could be easily identi fi ed visually during the callus stage and the shoot stage,enabling early and ef fi cient selection of ***,whole-plant level visualization of eYGFPuv revealed its ubiquitous stability in transgenic *** addition,our transformation experiments showed that eYGFPuv can also be used to select transgenic plants without *** work demonstrates the feasibility of utilizing 1x eYGFPuv in studies of gene expression and plant transformation in diverse plants.

关键词： transient transformation application

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Plant Promoters and Terminators for High-Precision Bioengineering

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BioDesign Research 2023年第1期5卷 86-105页

作者： Emily G.Brooks Estefania Elorriaga Yang Liu James R.Duduit Guoliang Yuan Chung-Jui Tsai Gerald A.Tuskan Thomas G.Ranney Xiaohan Yang Wusheng Liu Department of Horticultural Science North Carolina State UniversityRaleighNC 27607USA. Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA. The center for bioenergy innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA. Warnell School of Forestry and Natural Resource University of GeorgiaAthensGA 30602USA. Department of Plant Biology University of GeorgiaAthensGA 30602USA. Department of Genetics University of GeorgiaAthensGA 30602USA. Mountain Crop Improvement Lab Department of Horticultural ScienceMountain Horticultural Crops Research and Extension CenterNorth Carolina State UniversityMills RiverNC 28759USA.

High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional *** transcription is tightly regulated by promoters and *** determine the timing,tissues and cells,and levels of the expression of *** mediate transcription termination of genes and affect mRNA levels posttranscriptionally,e.g.,the 3′-end processing,stability,translation efficiency,and nuclear to cytoplasmic export of *** promoter and terminator combination affects gene *** the present article,we review the function and features of plant core promoters,proximal and distal promoters,and terminators,and their effects on and benchmarking strategies for regulating gene expression.

关键词： expression Promoter proximal

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Prospects for engineering Ralstonia eutropha and Zymomonas mobilis for the autotrophic production of 2,3-butanediol from CO_(2)and H_(2)

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Engineering Microbiology 2023年第2期3卷 33-38页

作者： Hui Wei Wei Wang Yat-Chen Chou Michael E.Himmel Xiaowen Chen Yannick J.Bomble Min Zhang Biosciences center National Renewable Energy LaboratoryGoldenCO 80401USA Renewable Resources and Enabling Sciences center National Renewable Energy LaboratoryGoldenCO 80401USA National bioenergy center National Renewable Energy LaboratoryGoldenCO 80401USA

The decarbonization of the chemical industry and a shift toward circular economies because of high global CO_(2) emissions make CO_(2) an attractive feedstock for manufacturing ***,H_(2) is a low-cost and carbon-free reductant because technologies such as solar-driven electrolysis and supercritical water(scH_(2)O) gasification enable sustainable production of molecular hydrogen(H_(2)).We review the recent advances in engineering Ralsto-nia eutropha,the representative species of“Knallgas”bacteria,for utilizing CO_(2) and H_(2) to autotrophically produce 2,3-butanediol(2,3-BDO).This assessment is focused on state-of-the-art approaches for splitting H_(2) to supply en-ergy in the form of ATP and NADH to power cellular reactions and employing the Calvin-Benson-Bassham cycle for CO_(2) *** challenges and opportunities for application and future perspectives are discussed in the context of developing other promising CO_(2) and H_(2)-utilizing microorganisms,exemplified by Zymomonas mobilis.

关键词： Ralstonia eutropha Zymomonas mobilis Butanediol CO_(2)fixation CO_(2)sequestration Metabolic engineering Hydrogenase Rubisco

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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

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BioDesign Research 2024年第1期6卷 51-67页

作者： Md Torikul Islam Yang Liu Md Mahmudul Hassan Paul E.Abraham Jean Merlet Alice Townsend Daniel Jacobson C.Robin Buell Gerald A.Tuskan Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The center for bioenergy innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali 8602Bangladesh Bredesen center for Interdisciplinary Research and Graduate Education University of Tennessee KnoxvilleKnoxvilleTN 37996USA center for Applied Genetic Technologies University of GeorgiaAthensGA 30602USA Department of Crop and Soil Sciences University of GeorgiaAthensGA 30602USA Institute of Plant Breeding Geneticsand GenomicsUniversity of GeorgiaAthensGA 30602USA

Plants are complex systems hierarchically organized and composed of various cell *** understand the molecular underpinnings of complex plant systems,single-cell RNA sequencing(scRNA-seq)has emerged as a powerful tool for revealing high resolution of gene expression patterns at the cellular level and investigating the cell-type ***,scRNA-seq analysis of plant biosystems has great potential for generating new knowledge to inform plant biosystems design and synthetic biology,which aims to modify plants genetically/epigenetically through genome editing,engineering,or re-writing based on rational design for increasing crop yield and quality,promoting the bioeconomy and enhancing environmental *** particular,data from scRNA-seq studies can be utilized to facilitate the development of high-precision Build-Design-Test-Learn capabilities for maximizing the targeted performance of engineered plant biosystems while minimizing unintended side *** date,scRNA-seq has been demonstrated in a limited number of plant species,including model plants(e.g.,Arabidopsis thaliana),agricultural crops(e.g.,Oryza sativa),and bioenergy crops(e.g.,Populus spp.).It is expected that future technical advancements will reduce the cost of scRNA-seq and consequently accelerate the application of this emerging technology in *** this review,we summarize current technical advancements in plant scRNA-seq,including sample preparation,sequencing,and data analysis,to provide guidance on how to choose the appropriate scRNA-seq methods for different types of plant *** then highlight various applications of scRNA-seq in both plant systems biology and plant synthetic biology ***,we discuss the challenges and opportunities for the application of scRNA-seq in plants.

关键词： application biology systems plant advances single-cell synthetic transcriptomics

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Biosystems Design to Accelerate C3-to-CAM Progression

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BioDesign Research 2020年第1期2020卷 18-33页

作者： Guoliang Yuan MdMahmudul Hassan Degao Liu Sung Don Lim Won Cheol Yim John C.Cushman Kasey Markel Patrick M.Shih Haiwei Lu David J.Weston Jin-Gui Chen Timothy J.Tschaplinski Gerald A.Tuskan Xiaohan Yang Biosciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA The center for bioenergy innovation Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Genetics and Plant Breeding Patuakhali Science and Technology UniversityDumkiPatuakhali 8602Bangladesh Department of Genetics Cell Biology and DevelopmentCenter for Precision Plant Genomicsand Center for Genome EngineeringUniversity of MinnesotaSaint PaulMN 55108USA Department of Applied Plant Sciences Kangwon National UniversityChuncheon 24341Republic of Korea Department of Biochemistry and Molecular Biology University of NevadaRenoNVUSA Department of Plant Biology University of CaliforniaDavisDavisCAUSA Feedstocks Division Joint BioEnergy InstituteEmeryvilleCAUSA

Global demand for food and bioenergy production has increased rapidly,while the area of arable land has been declining for decades due to damage caused by erosion,pollution,sea level rise,urban development,soil salinization,and water scarcity driven by global climate *** order to overcome this conflict,there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency(WUE).Crassulacean acid metabolism(CAM)species have substantially higher WUE than species performing C3 or C4 *** plants are derived from C3 photosynthesis ***,it is extremely unlikely that the C3 or C4 crop plants would evolve rapidly into CAM photosynthesis without human ***,there is growing interest in improving WUE through transferring CAM into C3 ***,engineering a major metabolic plant pathway,like CAM,is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C3 and CAM photosynthesis,as well as overcoming physiometabolic limitations such as diurnal stomatal *** advances in CAM evolutionary genomics research,genome editing,and synthetic biology have increased the likelihood of successful acceleration of C3-to-CAM ***,we first summarize the systems biology-level understanding of the molecular processes in the CAM ***,we review the principles of CAM engineering in an evolutionary ***,we discuss the technical approaches to accelerate the C3-to-CAM transition in plants using synthetic biology toolboxes.

关键词： overcome acceleration evolve

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我国流行的非洲猪瘟病毒颗粒精细三维结构解析

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中国预防兽医学报 2019年第11期41卷 1188-1188页

作者： Wang Nan Zhao Dongming CAS Key Laboratory of Infection and Immunity National Laboratory of Macromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China. University of Chinese Academy of Sciences Beijing 100049 China. State Key Laboratory of Veterinary Biotechnology and National High Containment Laboratory for Animal Diseases Control and Prevention Harbin Veterinary Research Institute Chinese Academy of Agricultural Sciences Harbin 150069 China. Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech University Shanghai 201210 China. Laboratory of Structural Biology School of Medicine Tsinghua University Beijing 100084 China. State Key Laboratory of Medicinal Chemical Biology Nankai University Tianjin 300353 China.

非洲猪瘟(African Swine Fever,ASF)是猪的一种烈性传染性病毒病,死亡率接近100%,被世界动物卫生组织(OIE)列为需要通报的动物疫病,我国列为一类动物疫病。ASF于1921年在肯尼亚首次发现,至今已有近百年的历史。该疫病从非洲传播至欧洲... 详细信息

非洲猪瘟(African Swine Fever,ASF)是猪的一种烈性传染性病毒病,死亡率接近100%,被世界动物卫生组织(OIE)列为需要通报的动物疫病,我国列为一类动物疫病。ASF于1921年在肯尼亚首次发现,至今已有近百年的历史。该疫病从非洲传播至欧洲、南美洲、亚洲等多个国家。近一年来,非洲猪瘟病毒传播速度明显加快,呈现愈演愈烈趋势,据国际动物健康组织通报数据显示,2019年1月至2019年9月期间,曾爆发或者正在爆发非洲猪瘟疫情的国家有23个,包含12个欧洲国家、9个亚洲国家和2个非洲国家,其中亚洲几个国家的疫情尤为严重。

关键词：非洲猪瘟世界动物卫生组织一类动物疫病动物健康 OIE 传播速度三维结构数据显示

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