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Genome-wide binding analysis of transcription factor Rice Indeterminate 1 reveals a complex network controlling rice floral transition

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Journal of Integrative Plant Biology 2022年第9期64卷 1690-1705页

作者： Shuo Zhang Li Deng Lun Zhao Changyin wu National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan430070 China

RICE INDETERMINATE 1(RID1)plays a critical role in controlling floral transition in rice(Oryza sativa).However,the molecular basis for this effect,particularly the target genes and regulatory specificity,remains largely unclear.Here,we performed chromatin immunoprecipitation followed by sequencing(ChIP-seq)in young leaves at the pre-floral-transition stage to identify the target genes of RID1,identifying 2,680 genes associated with RID1 binding sites genome-wide.RID1 binding peaks were highly enriched for TTTGTC,the direct binding motif of the INDETERMINATE DOMAIN protein family that includes RID1.Interestingly,CACGTG and GTGGGCCC,two previously uncharacterized indirect binding motifs,were enriched through the interactions of RID1 with the novel floweringpromoting proteins OsPIL12 and OsTCP11,respectively.Moreover,the ChIP-seq data demonstrated that RID1 bound to numerous rice heading-date genes,such as HEADING DATE1(HD1)and FLAVIN-BINDING,KELCH REPEAT,F-BOX 1(OsFKF1).Notably,transcriptome sequencing(RNA-seq)analysis revealed roles of RID1 in diverse developmental pathways.Genetic analysis combined with genome-wide ChIP-seq and RNA-seq results showed that RID1 directly binds to the promoter of OsERF#136(a repressor of rice flowering)and negatively regulates its expression.Overall,our findings provide new insights into the molecular and genetic mechanisms underlying rice floral transition and characterize OsERF#136 as a previously unrecognized direct target of RID1.

关键词： ChIP-seq floral transition OsERF#136 rice(Oryza sativa) RID1 RNA-seq

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Fixed-Time Cooperative Tracking for Delayed Disturbed Multi-Agent Systems Under Dynamic Event-Triggered Control

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IEEE/CAA Journal of Automatica Sinica 2022年第5期9卷 930-933页

作者： Jian Liu Yongbao wu Mengwei Sun changyin Sun School of Automation Southeast UniversityNanjing 210096 Key Laboratory of Measurement and Control of Complex System of Engineering Ministry of EducationSoutheast UniversityNanjing 210096China Institutes of Physical Science and Information Technology Anhui UniversityHefei 230601China IEEE

Dear editor,Recently,researchers have obtained many new results about the multi-agent systems(MASs)[1]-[3].In[1],the fixed-time cooperative control(FTCC)algorithm of linear MASs with matched disturbances was proposed.The nonholonomic chained-form dynamics case was considered in[2].In[3],the output tracking problem with data packet dropout was solved for high-order MASs.Moreover,delay frequently occurs because of the non-ideal data transmission[4],and the corresponding FTCC algorithm of MASs with delay was given in[5].

关键词： editor Dynamic Trigger Event

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Effort and Contribution of T-DNA Insertion Mutant Library for Rice Functional Genomics Research in China:Review and Perspective

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Journal of Integrative Plant Biology 2012年第12期54卷 953-966页

作者： Yuxiao Chang Tuan Long Changyin wu National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research(wuhan) Huazhong Agricultural University

With the completion of the rice （Oryza sativa L.） genome-sequencing project, the rice research community proposed to characterize the func- tion of every predicted gene in rice by 2020. One of the most effective and high-throughput strategies for studying gene function is to employ genetic mutations induced by insertion elements such as T-DNA or transposons. Since 1999, with support from the Ministry of Science and Technology of China for Rice Functional Genomics Programs, large-scale T-DNA insertion mutant populations have been generated in Huazhong Agricultural University, the Chinese Academy of Sciences and the Chinese Academy of Agricultural Sciences. Currently, a total of 372,346 mutant lines have been generated, and 58,226 T-DNA or Tos17 flanking sequence tags have been isolated. Using these mutant resources, more than 40 genes with potential applications in rice breeding have already been identified. These include genes involved in biotic or abiotic stress responses, nutrient metabolism, pollen development, and plant architecture. The functional analysis of these genes will not only deepen our understanding of the fundamental biological questions in rice, but will also offer valuable gene resources for developing Green Super Rice that is high-yielding with few inputs even under the poor growth conditions of many regions of Africa and Asia.

关键词： Flanking sequence tags functional genomics insertion site rice T-DNA insertion mutant library.

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Phosphorylation of OsFD1 by OsCIPK3 promotes the formation of RFT1-containing florigen activation complex for long-day flowering in rice

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Molecular Plant 2021年第7期14卷 1135-1148页

作者： Qiang Peng Chunmei Zhu Tao Liu Shuo Zhang Shijing Feng Changyin wu National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China Guizhou Rice Research Institute Guizhou Academy of Agricultural SciencesGuiyang 550006China

Heading date is a critical trait that determines the regional adaptability and grain productivity of many crops.Although rice is a facultative short-day plant,its domestication led to the Ghd7-Ehd1-Hd3a/RFT1 pathway for adaptation to long-day conditions(LDs).The formation of the"florigen activation complex"(FAC)containing florigen Hd3a has been characterized.However,the molecular composition of the FAC that contains RFT1 for long-day flowering is unclear.We show here that RFT1 forms a ternary FAC with 14-3-3 proteins and OsFD1 to promote flowering under LDs.We identified a calcineurin B-like-interacting protein kinase,OsCIPK3,which directly interacts with and phosphorylates OsFD1,thereby facilitating the localization of the FAC to the nucleus.Mutation in OsCIPK3 results in a late heading date under LDs but a normal heading date under short-day conditions.Collectively,our results suggest that OsCIPK3 phosphorylates OsFD1 to promote RFT1-containing FAC formation and consequently induce flowering in rice under LDs.

关键词： rice heading date florigen activation complex OsCIPK3 phosphorylation

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OsMLH1 interacts with OsMLH3 to regulate synapsis and interference-sensitive crossover formation during meiosis in rice

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Journal of Genetics and Genomics 2021年第6期48卷 485-496页

作者： Xiaodong Xin Xingwang Li Junkai Zhu Xiaobin Liu Zhenghu Chu Jiali Shen Changyin wu National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Huazhong Agricultural UniversityWuhan 430070China Jiangsu Kingearth Seed Co. Ltd.Yangzhou 225012China

Meiotic recombination is essential for reciprocal exchange of genetic information between homologous chromosomes and their subsequent proper segregation in sexually reproducing organisms. MLH1 and MLH3 belong to meiosis-specific members of the Mut L-homolog family, which are required for normal level of crossovers(COs) in some eukaryotes. However, their functions in plants need to be further elucidated.Here, we report the identification of Os MLH1 and reveal its functions during meiosis in rice. Using CRISPRCas9 approach, two independent mutants, Osmlh1-1 and Osmlh1-2, are generated and exhibited significantly reduced male fertility. In Osmlh1-1, the clearance of PAIR2 is delayed and partial ZEP1 proteins are not loaded into the chromosomes, which might be due to the deficient in resolution of interlocks at late zygotene. Thus, Os MLH1 is required for the assembly of synapsis complex. In Osmlh1-1, CO number is dropped by ~53% and the distribution of residual COs is consistent with predicted Poisson distribution,indicating that Os MLH1 is essential for the formation of interference-sensitive COs(class I COs). Os MLH1 interacts with Os MLH3 through their C-terminal domains. Mutation in Os MLH3 also affects the pollen fertility. Thus, our experiments reveal that the conserved heterodimer Mut Lg(Os MLH1-Os MLH3) is essential for the formation of class I COs in rice.

关键词： Meiosis Crossover OsMLH1 OsMLH3 Rice

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Output feedback control for mobile robot systems with significant external disturbances

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Science China(Information Sciences) 2020年第9期63卷 277-280页

作者： Kang wu Jinya SU changyin SUN Key Laboratory of Measurement and Control of CSE Ministry of EducationSchool of Automation Southeast University Department of Aeronautical and Automotive Engineering Loughborough University

Dear editor,The control of nonholonomic systems, like those describing mobile robots, has attracted considerable research attention in recent decades owing to its theoretical and practical importance. Brockett’s theo... 详细信息

关键词： Nonlinear system Nonholonomic system Adaptive control Extended state observer(ESO) Disturbance rejection

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An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning

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The Crop Journal 2021年第1期9卷 42-56页

作者： Lejun Yu Jiawei Shi Chenglong Huang Lingfeng Duan Di wu Debao Fu Changyin wu Lizhong Xiong Wanneng Yang Qian Liu Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for OptoelectronicsKey Laboratory of Ministry of Education for Biomedical PhotonicsDepartment of Biomedical EngineeringHuazhong University of Science and TechnologyWuhan 430074HubeiChina National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene ResearchAgricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of EngineeringHuazhong Agricultural UniversityWuhan 430070HubeiChina School of Biomedical Engineering Hainan UniversityHaikou 570228HainanChina

Rice panicle phenotyping is required in rice breeding for high yield and grain quality.To fully evaluate spikelet and kernel traits without threshing and hulling,using X-ray and RGB scanning,we developed an integrated rice panicle phenotyping system and a corresponding image analysis pipeline.We compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy(R~2 of 0.99)and speed.Faster R-CNN was also applied to indica and japonica classification and achieved 91%accuracy.The proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

关键词： Rice(O.satiua) Panicle traits RGB imaging X-ray scanning Faster R-CNN

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Rice Functional Genomics Research： Past Decade and Future

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Molecular Plant 2018年第3期11卷 359-380页

作者： Yan Li Jinghua Xiaot Lingling Chen Xuehui Huang Zhukuan Cheng Bin Han Qifa Zhang Changyin wu National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research (Wuhan) Huazhong Agricultural University Wuhan 430070 China College of Life and Environment Sciences Shanghai Normal University Shanghai 200234 China National Center for Plant Gene Research State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy ofSciences Beijing 100101 China National Center for Gene Research Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of SciencesShanghai 200233 China

Rice （Oryza sativa） is a major staple food crop for more than 3.5 billion people worldwide. Under- standing the regulatory mechanisms of complex agronomic traits in rice is critical for global food security. Rice is also a model plant for genomics research of monocotyledonso Thanks to the rapid development of functional genomic technologies, over 2000 genes controlling important agronomic traits have been cloned, and their molecular biological mechanisms have also been partially char- acterized. Here, we briefly review the advances in rice functional genomics research during the past 10 years, including a summary of functional genomics platforms, genes and molecular regulatory networks that regulate important agronomic traits, and newly developed tools for gene identification. These achievements made in functional genomics research will greatly facilitate the development of green super rice. We also discuss future challenges and prospects of rice functional genomics research.

关键词： functional genomics gene identification green super rice Oryza sativa

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miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice

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Molecular Plant 2022年第4期15卷 671-688页

作者： Zeyu Yang Shugang Hui Yan Lv Miaojing Zhang Dan Chen Jingjing Tian Haitao Zhang Hongbo Liu Jianbo Cao Wenya Xie Changyin wu Shiping Wang Meng Yuan National Key Laboratory of Crop Genetic Improvement National Center of Plant Gene Research(Wuhan)Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

MicroRNAs (miRNAs) play important roles in plant physiological activities. However, their roles and molecular mechanisms in boosting plant immunity, especially through the modulation of macronutrient metabolism in response to pathogens, are largely unknown. Here, we report that an evolutionarily conserved miRNA, miR395, promotes resistance to Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), two destructive bacterial pathogens, by regulating sulfate accumulation and distribution in rice. Specifically, miR395 targets and suppresses the expression of the ATP sulfurylase gene OsAPS1, which functions in sulfate assimilation, and two sulfate transporter genes, OsSULTR2;1 and OsSULTR2;2, which function in sulfate translocation, to promote sulfate accumulation, resulting in broad-spectrum resistance to bacterial pathogens in miR395-overexpressing plants. Genetic analysis revealed that miR395-triggered resistance is involved in both pathogen-associated molecular pattern-triggered immunity and R gene-mediated resistance. Moreover, we found that accumulated sulfate but not S-metabolites inhibits proliferation of pathogenic bacteria, revealing a sulfate-mediated antibacterial defense mechanism that differs from sulfur-induced resistance. Furthermore, compared with other bacteria, Xoo and Xoc, which lack the sulfate transporter CysZ, are sensitive to high levels of extracellular sulfate. Accordingly, miR395-regulated sulfate accumulation impaired the virulence of Xoo and Xoc by decreasing extracellular polysaccharide production and biofilm formation. Taken together, these results suggest that rice miR395 modulates sulfate metabolism to exploit pathogen sensitivity to sulfate and thereby promotes broad-spectrum resistance.

关键词： miR395 sulfate metabolism disease resistance CysZ rice

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Physics-based battery SOC estimation methods:Recent advances and future perspectives

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Journal of Energy Chemistry 2024年第2期89卷 27-40,I0003页

作者： Longxing wu Zhiqiang Lyu Zebo Huang Chao Zhang changyin Wei College of Mechanical Engineering Anhui Science and Technology UniversityChuzhou 233100AnhuiChina Hubei Key Laboratory of Power System Design and Test for Electrical Vehicle Hubei University of Arts and ScienceXiangyang 441053HubeiChina School of Internet Anhui UniversityHefei 230039AnhuiChina School of Mechanical and Electrical Engineering Guilin University of Electronic TechnologyGuilin 541004GuangxiChina

The reliable prediction of state of charge(SOC)is one of the vital functions of advanced battery management system(BMS),which has great significance towards safe operation of electric vehicles.By far,the empirical model-based and data-driven-based SOC estimation methods of lithium-ion batteries have been comprehensively discussed and reviewed in various literatures.However,few reviews involving SOC estimation focused on electrochemical mechanism,which gives physical explanations to SOC and becomes most attractive candidate for advanced BMS.For this reason,this paper comprehensively surveys on physics-based SOC algorithms applied in advanced BMS.First,the research progresses of physical SOC estimation methods for lithium-ion batteries are thoroughly discussed and corresponding evaluation criteria are carefully elaborated.Second,future perspectives of the current researches on physics-based battery SOC estimation are presented.The insights stated in this paper are expected to catalyze the development and application of the physics-based advanced BMS algorithms.

关键词： Lithium-ion batteries State of charge Electrochemical model Battery management system

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