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Genome editing for plant research and crop improvement

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Journal of Integrative Plant Biology 2021年第1期63卷 3-33页

作者： Xiangqiang Zhan Yuming Lu Jian-Kang Zhu Jose Ramon Botella State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticuture Northwest A&F UniversityXianyang 712100 Shanghai Center for Plant Stress Biology CAS Center of Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteIndiana 47907USA School of Agriculture and Food Sciences University of QueenslandBrisbaneQueensland 4072Australia

The advent of clustered regularly interspaced short palindromic repeat(CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel(insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.

关键词： CRISPR/Cas crop improvement genome editing plant research

Fullerenes for rechargeable battery applications:Recent developments and future perspectives

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Journal of Energy Chemistry 2021年第4期30卷 70-79页

作者： Zhipeng Jiang yuming Zhao Xing lu Jia Xie State Key Laboratory of Advanced Electromagnetic Engineering and Technology School of Electrical and Electronic EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina State Key Laboratory of Materials Processing and Die&Mould Technology School of Materials Science and EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina Shenzhen Power Supply Bureau Co. Ltd.Shenzhen 518000GuangdongChina

The development of high-performance batteries is inseparable from the exploration of new materials.Among them,fullerene C60 as an allotrope of carbon has many unique properties that are beneficial for battery applications,including precise structure,controllable derivatization,good solubility,and rich redox chemistry.In this review,we summarize the recent progress of fullerene-based materials in the field of rechargeable batteries and the key issues that need to be solved in the future application of fullerene.We hope this review can provide guidance and stimulate research about the applications of fullerenes in the field of energy storage.

关键词： Batteries Fullerene Carbon materials Energy storage

Rice Protein Tagging Project:A Call for International Collaborations on Genome-wide In-Locus Tagging of Rice Proteins

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Molecular Plant 2020年第12期13卷 1663-1665页

作者： Yuming Lu Pamela C.Ronald Bin Han Jiayang Li Jian-Kang Zhu Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina Department of Plant Pathology and the Genome Center University of CaliforniaDavisCAUSA National Center for Gene Research CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina State Key Laboratory of Plant Genomics and National Center for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina Department of Horticulture and Landscape Architecture Purdue UniversityWest LafayetteINUSA

In September 1997,the International Rice Genome Sequencing Project was launched.This initiative pooled the resources of ten nations to obtain the first complete rice genome sequence,and promoted rice research and breeding into the post-genomics era(Li et al.,2018).In 2008,an internationally coordinated project named "RICE2020" was proposed to systematically and fully characterize all rice genes,transcripts,and proteins(Zhang et al.,2008).While genes and their transcripts can be readily characterized by sequencing-and PCR-based methods,the characterization of protein dynamics including protein levels,subcellular localizations,post-transla-tional modifications,and interactions with macromolecules(e.g.,proteins,DNA,RNA,carbohydrates,and lipids)and small molecules(e.g.,metabolites and ligands)is much more challenging and usually requires antibodies that specifically recognize the protein of interest.Because it is very difficult to systematically produce reliable antibodies for the specific recognition of individual plant proteins,a common practice is to transform a tag-fused open reading frame(ORF)of a gene to the corresponding loss-of-function mutant plants.However,such an ectopically expressed tagged protein may not fully reca-pitulate the properties of the endogenous protein due to the random insertion of the transgene,even when the transgene is expressed under the endogenous gene promoter.A preferred so-lution is to genetically label the coding sequence of the gene of interest,at its in vivo locus,with a sequence encoding a fluores-cent protein tag or an affinity tag such as FLAG or HA.Such "in-locus" protein tagging,as we are naming it here,has been carried out genome-wide in yeast,Caenorhabditis elegans,fly,and mammalian cultured cells,greatly facilitating the characterization of proteins in these organisms(Jiang et al.,2018).In 2017,a Genome Tagging Project was launched in mice,aiming to label every protein using a CRISPR/Cas9-based "artificial spermatids"method(Jiang et al.,2018).Significant funding and effor

关键词： breeding Genome endogenous

Multiplex Gene Editing in Rice Using the CRISPR-Cpf1 System

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Molecular Plant 2017年第7期10卷 1011-1013页

作者： Mugui Wang Yanfei Mao Yuming Lu Xiaoping Tao Jian-kang Zhu Shanghai Center for Plant Stress Biology and Center for Excellence inMolecular Plant Sciences Chinese Academy of Sciences Shanghai 201602 China Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907 USA

Dear Editor, The class 2/type Ⅱ clustered regularly interspaced short palindromic repeat （CRISPR）/Cas9 system has been used successfully for simultaneous modification of multiple loci in plants. Two general strategies have been applied to coexpress multiple single guide RNAs （sgRNAs） to achieve multiplex gene editing in plant cells.

关键词： TARGETED MUTAGENESIS CPF1

Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems

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Journal of Integrative Plant Biology 2018年第8期60卷 626-631页

作者： Mugui Wang Yanfei Mao Yuming Lu Zhidan Wang Xiaoping Tao Jian-Kang Zhu Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai 201602 China Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907 USA

The class 2 clustered regularly interspaced short palindromic repeat （CRISPR） systems have been widely used for simultaneous modification of multiple loci in plants. Traditionally, the type II CRISPR-Cas9 or type V CRISPR-Cpfl （also known as Cas12a） system is a two-component transcriptional unit （TCTU） in which the Cas9 or Cpf1 protein is expressed from an RNA polymerase （pol） II promoter, whereas the single guide RNA （sgRNA） is typically expressed from a Pol III promoter, such as U6 or U3 promoter.

关键词： Multiplex gene editing in rice with simplified CRISPR-Cpf1 and CRISPR-Cas9 systems PAM Figure LEA

High-throughput genome editing in rice with a virus-based surrogate system

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Journal of Integrative Plant Biology 2023年第3期65卷 646-655页

作者： Yifu Tian Dating Zhong Xinbo Li Rundong Shen Han Han Yuqin Dai Qi Yao Xuening Zhang Qi Deng Xuesong Cao Jian-Kang Zhu Yuming Lu Shanghai Center for Plant Stress Biology Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 201602China Center for Advanced Bioindustry Technologies Institute of Crop SciencesChinese Academy of Agricultural SciencesBeiing 100081China Hainan Yazhou Bay Seed Lab Sanya 572024China Shanghai Collaborative Innovation Center of Agri Seeds Joint Center for Single Cell BiologySchool of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Institute of Advanced Biotechnology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China

With the widespread use of clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas) technologies in plants, large-scale genome editing is increasingly needed. Here, we developed a geminivirus-mediated surrogate system, called Wheat Dwarf Virus-Gate(WDV-surrogate), to facilitate high-throughput genome editing.WDV-Gate has two parts: one is the recipient callus from a transgenic rice line expressing Cas9 and a mutated hygromycin-resistant gene(HygM) for surrogate selection;the other is a WDV-based construct expressing two single guide RNAs(sgRNAs) targeting HygM and a gene of interest, respectively. We evaluated WDV-Gate on six rice loci by producing a total of 874 T_0 plants. Compared with the conventional method, the WDV-Gate system, which was characterized by a transient and high level of sgRNA expression, significantly increased editing frequency(66.8% vs. 90.1%), plantlet regeneration efficiency(2.31-fold increase), and numbers of homozygous-edited plants(36.3%vs. 70.7%). Large-scale editing using pooled sg RNAs targeting the SLR1 gene resulted in a high editing frequency of 94.4%, further demonstrating its feasibility. We also tested WDVGate on sequence knock-in for protein tagging.By co-delivering a chemically modified donor DNA with the WDV-Gate plasmid, 3xFLAG peptides were successfully fused to three loci with an efficiency of up to 13%. Thus, by combining transiently expressed sgRNAs and a surrogate selection system, WDV-Gate could be useful for high-throughput gene knock-out and sequence knock-in.

关键词： genome editing high-throughput protein tagging rice

植物生长潜力而非系统发育关系预测荒废农田土壤生物对外来和本土植物的作用

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Journal of Plant Ecology 2023年第1期16卷 50-60页

作者： Chunqiang Wei Bingbing Jia lunlun Gao Zhen Liu yuming Liang Xin Zhang Xinmin lu School of Life Sciences Central China Normal UniversityWuhan 430079China State Key Laboratory of Agricultural Microbiology Huazhong Agricultural UniversityWuhan 430070China Institute of Invasion Biology and Agriculture Ecological Safety Huazhong Agricultural UniversityWuhan 430070China College of Plant Sciences and Technology Huazhong Agricultural UniversityWuhan 430070China Agricultural and Rural Water Conservancy Bureau of Jixi County Anhui 245300China

植物能够调控土壤生物群落,而后者将对后期发生的植物适合度和群落结构产生显著影响。长期种植的单一农作物能够显著调控土壤生物群落,而新近荒废农田中土壤生物如何调控外来和本土杂草定植目前还不清楚,这严重束缚了农田杂草治理能力... 详细信息

植物能够调控土壤生物群落,而后者将对后期发生的植物适合度和群落结构产生显著影响。长期种植的单一农作物能够显著调控土壤生物群落,而新近荒废农田中土壤生物如何调控外来和本土杂草定植目前还不清楚,这严重束缚了农田杂草治理能力的提升。本研究采集新近荒废的玉米地表层土壤,选取58种华中地区常见农田杂草(28种外来和30种本土植物)为对象开展实验。通过将植物种植于伽马射线灭菌或未灭菌土壤,定量评价了土壤生物对植物地上、地下和总生物量的影响,探讨了实验物种-玉米系统发育距离和土壤效应是否相关,探究了能够预测土壤效应的关键植物性状。结果发现:(i)总体而言,土壤生物显著抑制实验植物生长,表明土壤拮抗生物(如病原菌等)发挥主导作用;(ii)伴随植物生长潜力提升,土壤生物对植物的抑制作用逐渐增强,而土壤生物对实验植物的调控作用与实验物种-玉米系统发育距离无关;(iii)相对于本土植物,外来植物(尤其多年生物种)被土壤生物抑制的程度更高。这些结果表明,植物生长潜力能够有效预测土壤生物对植物生长的调控作用,而且新近荒废农田土壤生物具有抵御外来植物入侵的潜力。

关键词：杂草荒废农田植物性状植物-土壤互作植物入侵系统发育关系土壤生物

Efficient Multi-Tenant Virtual Machine Allocation in Cloud Data Centers

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Tsinghua Science and Technology 2015年第1期20卷 81-89页

作者： Jiaxin Li Dongsheng Li yuming Ye Xicheng lu the National Key Laboratory of Parallel and Distributed Processing (PDL) College of Computer National University of Defense Technology

Virtual Machine（VM） allocation for multiple tenants is an important and challenging problem to provide efficient infrastructure services in cloud data centers. Tenants run applications on their allocated VMs, and the network distance between a tenant＇s VMs may considerably impact the tenant＇s Quality of Service（Qo S）. In this study, we define and formulate the multi-tenant VM allocation problem in cloud data centers, considering the VM requirements of different tenants, and introducing the allocation goal of minimizing the sum of the VMs＇ network diameters of all tenants. Then, we propose a Layered Progressive resource allocation algorithm for multi-tenant cloud data centers based on the Multiple Knapsack Problem（LP-MKP）. The LP-MKP algorithm uses a multi-stage layered progressive method for multi-tenant VM allocation and efficiently handles unprocessed tenants at each stage. This reduces resource fragmentation in cloud data centers, decreases the differences in the Qo S among tenants, and improves tenants＇ overall Qo S in cloud data centers. We perform experiments to evaluate the LP-MKP algorithm and demonstrate that it can provide significant gains over other allocation algorithms.

关键词： virtual machine allocation cloud data center multiple tenants multiple knapsack problem

Gene Targeting by Homology-Directed Repair in Rice Using a Geminivirus-Based CRISPR/Cas9 System

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Molecular Plant 2017年第7期10卷 1007-1010页

作者： Mugui Wang Yuming Lu Jose Ramon Botella Yanfei Mao Kai Hua Jian-kang Zhu Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences Chinese Academy of Sciences Shanghai 201602 China Plant Genetic Engineering Laboratory School of Agriculture and Food Sciences University of Queensland Brisbane QLD 4072 Austraria Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907 USA

Dear Editor, Rice （Oryza sativa） is the staple food for more than half of the world＇s population. Technologies enabling precise and efficient DNA knock-in or replacement, hereinafter referred to as KI, have the pot... 详细信息

关键词： DNA REPLICONS GENOME