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| 1 | Engineering Herbicide-Resistant Rice Plants through CRISPR/Cas9-Mediated Homologous Recombination of Acetolactate Synthase显示文摘 | Sun, Yongwei Zhang, Xin Wu, Chuanyin He, Yubing Ma, Youzhi Hou, Han Guo, Xiuping Du, Wenming Zhao, Yunde Xia, Lanqin | 2016 | Molecular Plant2016，9，4： | 94 |
| 2 | Generation of Targeted Point Mutations in Rice by a Modified CRISPR/Cas9 System显示文摘 | Jingying Li Yongwei Sun Jinlu Du Yunde Zhao Lanqin Xia | 2017 | Molecular Plant2017，10，3： | 72 |
| 3 | Auxin Biosynthesis: A Simple Two-Step Pathway Converts Tryptophan to Indole-3-Acetic Acid in Plants显示文摘Indole-3-acetic 酸(IAA ) ,主要自然地发生的植物生长素,是必要的为几乎植物生长和开发的每个方面。然而,仅仅最近,研究最后建立了在植物把色氨酸(Trp ) 变换成 IAA 的第一条完全的植物生长素生合成小径。Trp 被氨基的 transferases 的 TAA 家庭首先变换成 indole-3-pyruvate (国际语音学协会) ,随后, IAA 被黄素 monooxygenases 的 YUC 家庭从国际语音学协会生产。到 IAA 的 Trp 的二拍子的圆舞变换是在许多发展过程起一个必要作用的主要植物生长素生合成小径。 | Yunde Zhao | 2012 | Molecular Plant2012，5，2： | 45 |
| 4 | Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing显示文摘CRISPR/Cas9 uses a guide RNA(gRNA)molecule to execute sequence-specific DNA cleavage and it has been widely used for genome editing in many organisms.Modifications at either end of the gRNAs often render Cas9/gRNA inactive.So far,production of gRNA in vivo has only been achieved by using the U6 and U3 snRNA promoters.However,the U6 and U3 promoters have major limitations such as a lack of cell specificity and unsuitability for in vitro transcription.Here,we present a versatile method for efficiently producing gRNAs both in vitro and in vivo.We design an artificial gene named RGR that,once transcribed,generates an RNA molecule with ribozyme sequences at both ends of the designed gRNA.We show that the primary transcripts of RGR undergo self-catalyzed cleavage to generate the desired gRNA,which can efficiently guide sequence-specific cleavage of DNA targets both in vitro and in yeast.RGR can be transcribed from any promoters and thus allows for cell-and tissue-specific genome editing ifappropriate promoters are chosen.Detecting mutations generated by CRISPR is often achieved by enzyme digestions,which are not very compatible with high-throughput analysis.Our system allows for the use of universal primers to produce any gRNAs in vitro,which can then be used with Cas9 protein to detect mutations caused by the gRNAs/CRISPR.In conclusion,we provide a versatile method for generating targeted mutations in specific cells and tissues,and for efficiently detecting the mutations generated. | Yangbin Gao Yunde Zhao | 2014 | Journal of Integrative Plant Biology2014，56，4： | 39 |
| 5 | A novel method for purification of recombinant adeno-associated virus vectors on a large scale显示文摘A novel method for recombinant adeno-associ-ated virus (rAAV) purification on large scale is described. The method involves three steps, including chloroform treatment, PEG/NaCl precipitation and chloroform extraction. The whole procedure can be performed in four hours. Using this purification method, we can reproducibly obtain, from 4 × 109 of proviral cells cultured in roller bottles, purified rAAV-GFP stocks with titers of around 5×1013 particles/mL and purity greater than 95%. The infectious titers of the vector stocks were up to 2×1012 TU/mL, thus particle-to-infectivity rate was about 25. Under an electronic microscope, most rAAV particles appeared full and a few were in intermediate form. Empty particles were rarely seen. The purified rAAV-GFP stocks have been successfully used in in vitro and in vivo transfection experiments. Therefore, this new method offers a simple, rapid and cost-effective way for large-scale rAAV purification. | WU Xiaobing DONG Xiaoyan WU Zhijian CAO Hui NIU Dongbin QU Jianguo WANG Hong HOU Yunde | 2001 | Chinese Science Bulletin2001，46，6： | 21 |
| 6 | Programmed Self-Elimination of the CRISPR/Cas9 Construct Greatly Accelerates the Isolation of Edited and Transgene-Free Rice Plants显示文摘 | Yubing He Min Zhu Lihao Wang Junhua Wu Qiaoyan Wang Rongchen Wang Yunde Zhao | 2018 | Molecular Plant2018，11，9： | 18 |
| 7 | A Role for Auxin in Flower Development显示文摘植物生长素长在植物生长和开发包括花开发的许多方面被含有。然而,在花开发的植物生长素的准确角色一直不是明确的直到植物生长素生合成异种的最近的鉴定。植物生长素为花的 primordia 的开始是必要的,并且发信号的植物生长素生合成,极的植物生长素运输或植物生长素的混乱导致花形成的失败。植物生长素也在指定花的机关的数字和身份起一个必要作用。在植物生长素小径和已知的花发展基因之间的关系的进一步的分析将在植物关于瀑形成和模式形成的机制提供批评信息。 | Youfa Cheng Yunde Zhao | 2007 | Journal of Integrative Plant Biology2007，49，1： | 17 |
| 8 | Self-cleaving ribozymes enable the production of guide RNAs from unlimited choices of promoters for CRISPR/Cas9 mediated genome editing显示文摘Development of tools for targeted modifications of specific DNA sequences in plants is of great importance to basic plant biology research as well as crop improvement.The ability to cut DNA at specific locations in the genome to generate doublestrand breaks(DSBs)in vivo is a prerequisite for any genome editing efforts.Several engineered nucleases including zinc finger nucleases(ZFNs)and transcriptional activator-like nucleases(TALENs)have been successfully used to edit genomes.However, | Yubing He Tao Zhang Ning Yang Meilian Xu Lang Yan Lihao Wang Rongchen Wang Yunde Zhao | 2017 | Journal of Genetics and Genomics2017，44，9： | 14 |
| 9 | A method for the production and expedient screening of CRISPR/Cas9-mediated non-transgenic mutant plants显示文摘Developing CRISPR/Cas9-mediated non-transgenic mutants in asexually propagated perennial crop plants is challenging but highly desirable.Here,we report a highly useful method using an Agrobacterium-mediated transient CRISPR/Cas9 gene expression system to create non-transgenic mutant plants without the need for sexual segregation.We have also developed a rapid,cost-effective,and high-throughput mutant screening protocol based on Illumina sequencing followed by high-resolution melting(HRM)analysis.Using tetraploid tobacco as a model species and the phytoene desaturase(PDS)gene as a target,we successfully created and expediently identified mutant plants,which were verified as tetra-allelic mutants.We produced pds mutant shoots at a rate of 47.5%from tobacco leaf explants,without the use of antibiotic selection.Among these pds plants,17.2%were confirmed to be non-transgenic,for an overall non-transgenic mutation rate of 8.2%.Our method is reliable and effective in creating non-transgenic mutant plants without the need to segregate out transgenes through sexual reproduction.This method should be applicable to many economically important,heterozygous,perennial crop species that are more difficult to regenerate. | Longzheng Chen Wei Li Lorenzo Katin-Grazzini Jing Ding Xianbin Gu Yanjun Li Tingting Gu Ren Wang Xinchun Lin Ziniu Deng Richard J.McAvoy Frederick G.Gmitter Jr. Zhanao Deng Yunde Zhao Yi Li | 2018 | Horticulture Research2018，5，1： | 12 |
| 10 | Efficient allelic replacement in rice by gene editing: A case study of the NRT1.1B gene显示文摘Precise replacement of an existing allele in commercial cultivars with an elite allele is a major goal in crop breeding. A single nucleotide polymorphism in the NRT1.1 B gene between japonica and indica rice is responsible for the improved nitrogen use efficiency in indica rice. Herein, we precisely replaced the japonica NRT1.1 B allele with the indica allele, in just one generation, using CRISPR/Cas9 gene-editing technology.No additional selective pressure was needed to enrich the precise replacement events. This work demonstrates the feasibility of replacing any genes with elite alleles within one generation, greatly expanding our ability to improve agriculturally important traits. | Jingying Li Xin Zhang Yongwei Sun Jiahui Zhang Wenming Du Xiuping Guo Shaoya Li Yunde Zhao Lanqin Xia | 2018 | Journal of Integrative Plant Biology2018，60，7： | 11 |
| 11 | NPY Genes Play an Essential Role in Root Gravitropic Responses in Arabidopsis显示文摘植物能察觉到他们保证根在土壤和那被抛锚的生长射击的严肃和东方的方向变得向上。Gravitropism 用 Arabidopsis 遗传,而是准确机制广泛地被学习了因为 gravitropism 充分没被理解。这里,我们证明五 NPY 基因在 Arabidopsis 根 gravitropism 起一个关键作用。NPY 基因以前与 AGC kinases PID, PID2, WAG1,和 WAG2 在一条基因小径作为调停植物生长素的 organogenesis 的管理者被识别。我们证明所有五 NPY 基因高度在主要的根尖端被表示。单个 npy 异种不显示明显的 gravitropism 缺点,而是五倍的异种显示出的 npy1 npy2 npy3 npy4 npy5 戏剧的 gravitropic 显型。所有 npy 的系统的分析双、三倍、四倍的联合证明五 NPY 基因都贡献 gravitropism。我们的工作显示 gravitropism,向光性,和 organogenesis 使用至少一自动增益控制 kinase,一 NPH3/NPY 基因,和一 ARF 在被要求的类似的机制。 | Yuanting Li Xinhua Dai Youfa Cheng Yunde Zhao | 2011 | Molecular Plant2011，4，1： | 7 |
| 12 | Expanding the Scope of CRISPR/Cpfl-Mediatec Senome Editing in Rice显示文摘 | Shaoya Li Xin Zhang Wensheng Wang Xiuping Guo Zhichao wu Wenming Du Yunde Zhao Lanqin Xia | 2018 | Molecular Plant2018，11，7： | 6 |
| 13 | Technological breakthroughs in generating transgene-free and genetically stable CRISPR-edited plants显示文摘CRISPR/Cas9 gene-editing technologies have been very effective in editing target genes in all major crop plants and offer unprecedented potentials in crop improvement.A major challenge in using CRISPR gene-editing technology for agricultural applications is that the target gene-edited crop plants need to be transgene free to maintain trait stability and to gain regulatory approval for commercial production.In this article,we present various strategies for generating transgene-free and target geneedited crop plants.The CRISPR transgenes can be removed by genetic segregation if the crop plants are reproduced sexually.Marker-assisted tracking and eliminating transgenes greatly decrease the time and labor needed for identifying the ideal transgene-free plants.Transgenes can be programed to undergo self-elimination when CRISPR genes and suicide genes are sequentially activated,greatly accelerating the isolation of transgene-free and target gene-edited plants.Transgene-free plants can also be generated using approaches that are considered non-transgenic such as ribonucleoprotein transfection,transient expression of transgenes without DNA integration,and nano-biotechnology.Here,we discuss the advantages and disadvantages of the various strategies in generating transgene-free plants and provide guidance for adopting the best strategies in editing a crop plant. | Yubing He Yunde Zhao | 2020 | aBIOTECH2020，1，1： | 5 |
| 14 | Fast-Suppressor Screening for New Components in Protein Trafficking,Organelle Biogenesis and Silencing Pathway in Arabidopsis thaliana Using DEX-Inducible FREE1-RNAi Plants显示文摘Membrane trafficking is essential for plant growth and responses to external signals.The plant unique FYVE domain-containing protein FREE1 is a component of the ESCRT complex(endosomal sorting complex required for transport).FREE1 plays multiple roles in regulating protein trafficking and organelle biogenesis including the formation of intraluminal vesicles of multivesicular body(MVB),vacuolar protein transport and vacuole biogenesis,and autophagic degradation.FREE1 knockout plants show defective MVB formation,abnormal vacuolar transport,fragmented vacuoles,accumulated autophagosomes,and seedling lethality.To further uncover the underlying mechanisms of FREE1 function in plants,we performed a forward genetic screen for mutants that suppressed the seedling lethal phenotype of FREE1-RNAi transgenic plants.The obtained mutants are termed as suppressors of free1(sof).To date,229 putative sof mutants have been identified.Barely detecting of FREE1 protein with M3plants further identified 84 FREE1-related suppressors.Also145 mutants showing no reduction of FREE1 protein were termed as RNAi-related mutants.Through next-generation sequencing(NGS)of bulked DNA from F2mapping population of two RNAi-related sof mutants,FREE1-RNAi T-DNA inserted on chromosome 1 was identified and the causal mutation of putative sof mutant is being identified similarly.These FREE1-and RNAi-related sof mutants will be useful tools and resources for illustrating the underlying mechanisms of FREE1 function in intracellular trafficking and organelle biogenesis,as well as for uncovering the new components involved in the regulation of silencing pathways in plants. | Qiong Zhao Caiji Gao PoShing Lee Lin Liu Shaofang Li Tangjin Hu Jinbo Shen Shuying Pan Hao Ye Yunru Chen Wenhan Cao Yong Cui Peng Zeng Sheng Yu Yangbin Gao Liang Chen Beixin Mo Xin Liu Shi Xiao Yunde Zhao Silin Zhong Xuemei Chen Liwen Jiang | 2015 | Journal of Genetics and Genomics2015，42，6： | 4 |
| 15 | Allelic Analyses of the Arabidopsis YUC1 Locus Reveal Residues and Domains Essential for the Functions of YUC Family of Flavin Monooxygenases显示文摘Flavin monooxygenases(FMOs) play critical roles in plant growth and development by synthesizing auxin and other signaling molecules.However,the structure and function relationship within plant FMOs is not understood.Here we defined the important residues and domains of the Arabidopsis YUC1 FMO,a key enzyme in auxin biosynthesis.We previously showed that simultaneous inactivation of YUC1 and its homologue YUC4 caused severe defects in vascular and floral development.We mutagenized the yuc4 mutant and screened for mutants with phenotypes similar to those of yuc1 yuc4 double mutants.Among the isolated mutants,five of them contained mutations in the YUC1 gene.Interestingly,the mutations identified in the new yuc1 alleles were concentrated in the two GXGXXG motifs that are highly conserved among the plant FMOs.One such motif presumably binds to flavin adenine dinucleotide(FAD) cofactor and the other binds to nicotinamide adenine dinucleotide phosphate(NADPH).We also identified the Ser139 to Phe conversion in yuc1,a mutation that is located between the two nucleotide-binding sites.By analyzing a series of yuc1 mutants,we identified key residues and motifs essential for the functions of YUC1 FMO. | Xianhui Hou Sainan Liu Florencia Pierri Xinhua Dai Li-Jia Qu Yunde Zhao | 2011 | Journal of Integrative Plant Biology2011，53，1： | 4 |
| 16 | A reporter for noninvasively monitoring gene expression and plant transformation显示文摘Reporters have been widely used to visualize gene expression,protein localization,and other cellular activities,but the commonly used reporters require special equipment,expensive chemicals,or invasive treatments.Here,we construct a new reporter RUBY that converts tyrosine to vividly red betalain,which is clearly visible to naked eyes without the need of using special equipment or chemical treatments.We show that RUBY can be used to noninvasively monitor gene expression in plants.Furthermore,we show that RUBY is an effective selection marker for transformation events in both rice and Arabidopsis.The new reporter will be especially useful for monitoring cellular activities in large crop plants such as a fruit tree under field conditions and for observing transformation and gene expression in tissue culture under sterile conditions. | Yubing He Tao Zhang Hui Sun Huadong Zhan Yunde Zhao | 2020 | Horticulture Research2020，7，1： | 4 |
| 17 | Learning online structural appearance model for robust object tracking显示文摘The main challenge of robust object tracking comes from the difficulty in designing an adaptive appearance model that is able to accommodate appearance variations.Existing tracking algorithms often perform self-updating of the appearance model with examples from recent tracking results to account for appearance changes.However,slight inaccuracy of tracking results can degrade the appearance model.In this paper,we propose a robust tracking method by evaluating an online structural appearance model based on local sparse coding and online metric learning.Our appearance model employs pooling of structural features over the local sparse codes of an object region to obtain a middle-level object representation.Tracking is then formulated by seeking for the most similar candidate within a Bayesian inference framework where the distance metric for similarity measurement is learned in an online manner to match the varying object appearance.Both qualitative and quantitative evaluations on various challenging image sequences demonstrate that the proposed algorithm outperforms the state-of-the-art methods. | YANG Min PEI MingTao WU YuWei JIA YunDe | 2015 | Science China(Information Sciences)2015，58，3： | 4 |
| 18 | Learning a discriminative mid-level feature for action recognition显示文摘In this paper,we address the problem of recognizing human actions from videos.Most of the existing approaches employ low-level features(e.g.,local features and global features)to represent an action video.However,algorithms based on low-level features are not robust to complex environments such as cluttered background,camera movement and illumination change.Therefore,we propose a novel random forest learning framework to construct a discriminative and informative mid-level feature from low-level features of densely sampled 3D cuboids.Each cuboid is classified by the corresponding random forests with a novel fusion scheme,and the cuboid’s posterior probabilities of all categories are normalized to generate a histogram.After that,we obtain our mid-level feature by concatenating histograms of all the cuboids.Since a single low-level feature is not enough to capture the variations of human actions,multiple complementary low-level features(i.e.,optical flow and histogram of gradient 3D features)are employed to describe 3D cuboids.Moreover,temporal context between local cuboids is exploited as another type of low-level feature.The above three low-level features(i.e.,optical flow,histogram of gradient 3D features and temporal context)are effectively fused in the proposed learning framework.Finally,the mid-level feature is employed by a random forest classifier for robust action recognition.Experiments on the Weizmann,UCF sports,Ballet,and multi-view IXMAS datasets demonstrate that out mid-level feature learned from multiple low-level features can achieve a superior performance over state-of-the-art methods. | LIU CuiWei PEI MingTao WU XinXiao KONG Yu JIA YunDe | 2014 | Science China(Information Sciences)2014，57，5： | 3 |
| 19 | ESCRT-dependent vacuolar sorting and degradation of the auxin biosynthetic enzyme YUC1 flavin monooxygenase显示文摘YUC flavin monooxygenases catalyze the ratelimiting step of auxin biosynthesis. Here we report the vacuolar targeting and degradation of GFP-YUC1. GFP-YUC1 fusion expressed in Arabidopsis protoplasts or transgenic plants was primarily localized in vacuoles. Surprisingly, we established that GFP-YUC1, a soluble protein, was sorted to vacuoles through the ESCRT pathway, which has long been recognized for sorting and targeting integral membrane proteins. We further show that GFP-YUC1 was ubiquitinated and in this form GFP-YUC1 was targeted for degradation, a process that was also stimulated by elevated auxin levels. Our findings revealed a molecular mechanism of GFP-YUC1 degradation and demonstrate that the ESCRT pathway can recognize both soluble and integral membrane proteins as cargoes. | Chennan Ge Caiji Gao Qingguo Chen Liwen Jiang Yunde Zhao | 2019 | Journal of Integrative Plant Biology2019，61，9： | 2 |
| 20 | Plant genome editing using xCas9 with expanded PAM compatibility显示文摘CRISPR/Cas enables robust genome editing and has revolution-ized both functional genomics and crop breeding.The specificity of Cas-directed DNA cleavage is strictly determined by a chimeric single guide RNA(SgRNA)and a short protospacer adjacent motif(PAM)in the genome(Cong et al,2013;Zetsche et al,2015).The widely used Cas9 from Streptococcus pyogenes(SpCas9)generally recognizes the canonical NGG PAM(where N indicates any nucleicacid base)(Miao et al.,2013;Ma et al,2015),making many regionsuntargetable by Cas9.SpCas9 VQR and VRER variants,which recog-nize the non-canonical PAM sequences of NGA and NGCG,respectively,have been used to expand targetable sequences in plants(Hu et al.,2016).In addition,the applications of other Cas endonucleases such as SaCas9(Staphylococcus aureus Cas9)(Ran et al..2015). | Jingying Li Jinman Luo Meilian Xu Shaoya Li Jiahui Zhang Huiyuan Li Lei Yan Yunde Zhao Lanqin Xia | 2019 | Journal of Genetics and Genomics2019，46，5： | 2 |
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