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The Interactions among DWARF10,Auxin and Cytokinin Underlie Lateral Bud Outgrowth in Rice

Journal of Integrative Plant Biology 2010年第7期52卷 626-638页

作者： Shuying Zhang Gang Li Jun Fang Weiqi Chen Haipai Jiang Junhuang Zou Xue Liu Xianfeng Zhao Xiaobing Li chengcai chu Qi Xie Xiangning Jiang Lihuang Zhu The State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China College of Biological Sciences and Biotechnology Beijing Forestry University Beijing 100083 China College of Agronomy Shenyang Agricultural University Shenyang 110161 China Department of Ophthalmology University of Utah Salt Lake City UT 84132 USA Graduate University of Chinese Academy of Sciences Beijing 100049 China

Previous studies have shown that DWARFIO （D10） is a rice ortholog of MAX41RMS1/DAD1, encoding a carotenoid cleavage dioxygenase and functioning in strigolactones/strigolactone-derivatives （SL） biosynthesis. Here we use DIO. RNA interference （RNAi） transgenic plants similar to dlO mutant in phenotypes to investigate the interactions among DIO, auxin and cytokinin in regulating rice shoot branching. Auxin levels in node 1 of both decapitated *** and wild type plants decreased significantly, showing that decapitation does reduce endogenous auxin concentration, but decapitation has no clear effects on auxin levels in node 2 of the same plants. This implies that node 1 may be the location where a possible interaction between auxin and DIO gene would be detected. DIO expression in node 1 is inhibited by decapitation, and this inhibition can be restored by exogenous auxin application, indicating that DIO may play an important role in auxin regulation of SL. The decreased expression of most OsPINs in shoot nodes of DIO-RNAi plants may cause a reduced auxin transport capacity. Furthermore, effects of auxin treatment of decapitated plants on the expression of cytokinin biosynthetic genes suggest that DIO promotes cytokinin biosynthesis by reducing auxin levels. Besides, in DIO-RNAi plants, decreased storage cytokinin levels in the shoot node may partly account for the increased active cytokinin contents, resulting in more tillering phenotypes.

关键词： AUXIN PLANT hormones CYTOKININS RICE PHENOTYPE

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ζ-Carotene Isomerase Suppresses Tillering in Rice through the Coordinated Biosynthesis of Strigolactone and Abscisic Acid

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Molecular Plant 2020年第12期13卷 1784-1801页

作者： Xue Liu Qingliang Hu Jijun Yan Kai Sun Yan Liang Meiru Jia Xiangbing Meng Shuang Fang Yiqin Wang Yanhui Jing Guifu Liu Dianxing Wu chengcai chu Steven M.Smith Jinfang chu Yonghong Wang Jiayang Li Bing Wang 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 SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Rice Biology Institute of Nuclear Agriculture SciencesZhejiang UniversityHangzhou 310029China School of Natural Sciences University of TasmaniaHobart 7001Australia State Key Laboratory of Plant Genomics and National Center for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyThe CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesBeijing 100101China College of Life Sciences Shandong Agricultural UniversityTaian 271018China

Rice tillering is an important agronomic trait affecting grain ***,we identified a high-tillering mutant tillering20(t20),which could be restored to the wild type by treatment with the strigolactone(SL)analog rac-GR24.T20 encodes a chloroplast ζ-carotene isomerase(Z-ISO),which is involved in the biosynthesis of ca-rotenoids and their metabolites,SL and abscisic acid(ABA).The t20 mutant has reduced SL and ABA,raising the question of how SL and ABA biosynthesis is coordinated,and whether they have overlapping functions in *** discovered that rac-GR24 stimulated T20 expression and enhanced all-trans-p-carotene ***,rac-GR24 also stimulated expression of Oryza sativa 9-CIS-EPOXY-CAROTENOID DIOXYGENASE 1(OsNCED1)through induction of Oryza sativa HOMEOBOX12(0sHOX12),promoting ABA biosynthesis in shoot *** the other hand,ABA treatment significantly repressed SL biosynthesis and the ABA biosynthetic mutants displayed elevated SL *** treatment reduced the number of basal tillers in both t20 and wild-type ***,while ABA-deficient mu-tants aba1 and aba2 had the same number of basal tillers as wild type,they had more unproductive upper tillers at *** work demonstrates complex interactions in the biosynthesis of carotenoid,SLs and ABA,and reveals a role for ABA in the regulation of rice tillering.

关键词： rice(Oryza sativa L.) tillering ζ-carotene isomerase carotenoid strigolactones abscisic acid

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Expression Patterns of ABA and GA Metabolism Genes and Hormone Levels during Rice Seed Development and Imbibition: A Comparison of Dormant and Non-Dormant Rice Cultivars

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Journal of Genetics and Genomics 2014年第6期41卷 327-338页

作者： Yang Liu Jun Fang Fan Xu Jinfang chu Cunyu Yan Michael R.Schlappi Youping Wang chengcai chu State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental BiologyChinese Academy of Sciences National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academy of Sciences Department of Biological Sciences Marquette University College of Life Sciences Yangzhou University

Seed dormancy is an important agronomic trait in cereals. Using deep dormant （N22）, medium dormant （ZH11）, and non-dormant （G46B） rice cultivars, we correlated seed dormancy phenotypes with abscisic acid （ABA） and gibberellin （GA） metabolism gene expression profiles and phytohormone levels during seed development and imbibition. A time course analysis of ABA and GA content during seed development showed that N22 had a high ABA level at early and middle seed developmental stages, while at late developmental stage it declined to the level of ZHll; however, its ABA/GA ratio maintained at a high level throughout seed development. By contrast, G46B had the lowest ABA content during seed development though at early developmental stage its ABA level was close to that of ZH11, and its ABA/GA ratio peaked at late developmental stage that was at the same level of ZHll. Compared with N22 and G46B, ZH11 had an even and medium ABA level during seed development and its ABA/GA ratio peaked at the middle developmental stage. Moreover, the seed development time-point having high ABA/GA ratio also had relatively high transcript levels for key genes in ABA and GA metabolism pathways across three cultivars. These indicated that the embryo-imposed dormancy has been induced before the late developmental stage and is determined by ABA/GA ratio. A similar analysis during seed imbibition showed that ABA was synthesized in different degrees for the three cultivars. In addition, water uptake assay for intact mature seeds suggested that water could permeate through husk barrier into seed embryo for all three cultivars; however, all three cultivars showed distinct colors by vanillin-staining indicative of the existence of flavans in their husks, which are dormancy inhibition compounds responsible for the husk-imposed dormancy.

关键词： Seed development Seed imbibition Gene expression Abscisic acid (ABA) Gibberellin (GA) ABA/GA ratio Rice

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The U-box ubiquitin ligase TUD1 promotes brassinosteroid-induced GSK2 degradation in rice

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Plant Communications 2023年第2期4卷 107-118页

作者： Dapu Liu Xiaoxing Zhang Qingliang Li Yunhua Xiao Guoxia Zhang Wenchao Yin Mei Niu Wenjing Meng Nana Dong Jihong Liu Yanzhao Yang Qi Xie chengcai chu Hongning Tong National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyThe Innovative Academy for Seed DesignChinese Academy of SciencesBeijing 100101China National Nanfan Research Institute Chinese Academy of Agricultural SciencesSanya 572024China

Brassinosteroids(BRs)are a class of steroid hormones with great potential for use in crop ***-repression is usually one of the key events in hormone ***,how the stability of GSK2,the central negative regulator of BR signaling in rice(Oryza sativa),is regulated by BRs remains ***,we identify the U-box ubiquitin ligase TUD1 as a GSK2-interacting protein by yeast two-hybrid *** show that TUD1 is able to directly interact with GSK2 and ubiquitinate the *** of the tud1 mutant are highly similar to those of plants with constitutively activated *** with this finding,GSK2 protein accumulates in the tud1 mutant compared with the wild *** addition,inhibition of BR synthesis promotes GSK2 accumulation and suppresses TUD1 *** contrast,BRs can induce GSK2 degradation but promote TUD1 ***,the GSK2 degradation process is largely impaired in tud1 in response to *** conclusion,our study demonstrates the role of TUD1 in BR-induced GSK2 degradation,thereby advancing our understanding of a critical step in the BR signaling pathway of rice.

关键词： brassinosteroid TUD1 GSK2 signal transduction ubiquitination

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Root microbiota shift in rice correlates with resident time in the field and developmental stage

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Science China(Life Sciences) 2018年第6期61卷 613-621页

作者： Jingying Zhang Na Zhang Yong-Xin Liu Xiaoning Zhang Bin Hu Yuan Qin Haoran Xu Hui Wang Xiaoxuan Guo Jingmei Qian Wei Wang Pengfan Zhang Tao Jin chengcai chu Yang Bai State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China CAS-JIC Centre of Excel'lence for Plant and Microbial Science (CEPAMS) Institute of Genetics and Developmental Biology Chinese Academy of Sciences (CAS) Beijing 100101 China College of Life Sciences University of Chinese Academy of Sciences Beijing 100039 China China National Genebank-Shenzhen BGI-Shenzhen Shenzhen 518083 China BGI-Qingdao Qingdao 266510 China

Land plants in natural soil form intimate relationships with the diverse root bacterial microbiota. A growing body of evidence shows that these microbes are important for plant growth and health. Root microbiota composition has been widely studied in several model plants and crops; however, little is known about how root microbiota vary throughout the plant's life cycle under field conditions. We performed longitudinal dense sampling in field trials to track the time-series shift of the root microbiota from two representative rice cultivars in two separate locations in China. We found that the rice root microbiota varied dramatically during the vegetative stages and stabilized from the beginning of the reproductive stage, after which the root microbiota underwent relatively minor changes until rice ripening. Notably, both rice genotype and geographical location influenced the patterns of root microbiota shift that occurred during plant growth. The relative abundance of Deltaproteobacteria in roots significantly increased overtime throughout the entire life cycle of rice, while that of Betaproteobacteria, Firmicutes, and Gammaproteobacteria decreased. By a machine learning approach, we identified biomarker taxa and established a model to correlate root microbiota with rice resident time in the field(e.g., Nitrospira accumulated from 5 weeks/tillering in field-grown rice). Our work provides insights into the process of rice root microbiota establishment.

关键词： rice root microbiota time-series shift biomarker taxa residence time in the field developmental stages modeling machine learning

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Direct Modulation of Protein Level in Arabidopsis

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Molecular Plant 2013年第5期6卷 1711-1714页

作者： Lei Su Aining Li Huali Li chengcai chu Jin-Long Qiu Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China

Dear Editor, The general way to probe functions of a protein in vivo is to perturb its level and then observe subsequent phe- notypic changes. In plants, modulation of protein level is mainly carried out at DNA or RNA level, which is indirect and thus affected by stability of the target protein. Thus, experimental approaches to perturb protein level directly are needed, but still limited in plants. In mammalian cells, a technique to modulate protein level directly has been developed. Engineered destabilizing domain （DD） of the human FKBP12 protein can confer instability to other pro- teins when fused to it. A small synthetic molecule ligand Shield 1 （Shldl） can bind DD and shield it from degrada- tion. The level of DD fused protein can be controlled by adjusting Shldl concentration （Banaszynski et al., 2006）.

关键词：钙调蛋白结合蛋白质类磷蛋白磷酸酶类拟南芥属

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A transceptor-channel complex couples nitrate sensing to calcium signaling in Ambidopsis

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Molecular Plant 2021年第5期14卷 774-786页

作者： Xiaohan Wang Changxin Feng LiLi Tian Congcong Hou Wang Tian Bin Hu Qian Zhang Zhijie Ren Qi Niu Jiali Song Dongdong Kong Liangyu Liu Yikun He Ligeng Ma chengcai chu Sheng Luan Legong Li College of Life Sciences Capital Normal UniversityBeijing 100048China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biologythe Innovative Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Department of Plant and Microbial Biology University of California at BerkeleyBerkeleyCA 94720USA

Nitrate-induced Ca^(2+) signaling is crucial for the primary nitrate response in ***,the molecular mechanism underlying the generation of the nitrate-specific calcium signature remains *** report here that a cyclic nucleotide-gated channel(CNGC)protein,CNGC15,and the nitrate transceptor(NRT1.1)constitute a molecular switch that controls calcium influx depending on nitrate *** expression of CNGC15 is induced by nitrate,and its protein is localized at the plasma membrane after establishment of young *** found that disruption of CNGC15 results in the loss of the nitrate-induced Ca^(2+) signature(primary nitrate response)and retards root growth,reminiscent of the phenotype observed in the nrt1.1 *** further showed that CNGC15 is an active Ca^(2+)-permeable channel that physically interacts with the NRT1.1 protein in the plasma ***,we discovered that CNGC15-NRT1.1 interaction silences the channel activity of the heterocomplex,which dissociates upon a rise in nitrate levels,leading to reactivation of the CNGC15 *** dynamic interactions between CNGC15 and NRT1.1 therefore control the channel activity and Ca^(2+) influx in a nitrate-dependent *** study reveals a new nutrient-sensing mechanism that utilizes a nutrient transceptor-channel complex assembly to couple nutrient status to a specific Ca^(2+) signature.

关键词： primary nitrate response nutrient sensing calcium signature nitrate transceptor calcium channel

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Genomic decoding of breeding history to guide breeding-by-design in rice

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National Science Review 2023年第5期10卷 124-137页

作者： Zhuo Chen Qingyun Bu Guifu Liu Maoqing Wang Hongru Wang Huazhao Liu Xiufeng Li Hong Li Jun Fang Yan Liang Zhenfeng Teng Sai Kang Hong Yu Zhukuan Cheng Yongbiao Xue Chengzhi Liang Jiuyou Tang Jiayang Li chengcai chu State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of Sciences Key Laboratory of Crop Biotechnology Breeding of the Ministry of Agriculture and Rural Affairs Beidahuang Kenfeng Seed Co.Ltd Institute of Botany Chinese Academy of Sciences Guangdong Laboratory for Lingnan Modern Agriculture and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of AgricultureSouth China Agricultural University University of Chinese Academy of Sciences State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of Sciences Hainan Yazhou Bay Seed Laboratory

Deciphering the intrinsic molecular logic of empirical crop breeding from a genomic perspective is a decisive prerequisite for breeding-by-design(BbD),but remains not well ***,we decoded the historical features of past rice breeding by phenotyping and haplotyping 546 accessions covering the majority of cultivars bred in the history of Northeast China(NEC).We revealed that three groups founded the genetic diversities in NEC rice with distinct evolution patterns and traced and verified the breeding footprints to known or genome-wide association study(GWAS)-detected quantitative trait loci(QTLs),or introgressions from indica sub-species with chronological changes in allele *** we summarized a rice breeding trend/principle in NEC,and combined with the successful example in breeding and application of Zhongkefa5 to demonstrate the guiding value of our conclusion for BbD in *** study provides a paradigm for decoding the breeding history of a specific crop to guide BbD,which may have implications in different crop breeding.

关键词： rice breeding-by-design breeding history genome-wide association study genomic decoding

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A Novel QTL qTGW3 Encodes the GSK3/ SHAGGY-Like Kinase OsGSK5/OsSK41 that Interacts with OsARF4 to Negatively Regulate Grain Size and Weight in Rice

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Molecular Plant 2018年第5期11卷 736-749页

作者： Zejun Hu Sun-Jie Lu Mei-Jing Wang Haohua He Le Sun Hongru Wang Xue-Huan Liu Ling Jiang Jing-Liang sun Xiaoyun Xin Wei Kong chengcai chu Hong-Wei Xue Jinshui Yang Xiaojin Luo Jian-Xiang Liu State Key Laboratory of Genetic Engineering Institute of Plant Biology School of Life Sciences Fudan University Shanghai 200433 China Key Laboratory of Crop Physiology Ecology and Genetic Breeding Ministry of Education Jiangxi Agricultural University Nanchang 330045 China State Key Laboratory of Plant Genomics National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China State Key Laboratory of Plant Physiology and Biochemistry College of Life Sciences Zhejiang University Hangzhou 310027 China

Grain size and shape are important determinants of grain weight and yield in rice. Here, we report a new major quantitative trait locus （QTL）, qTGW3, that controls grain size and weight in rice. This locus, qTGW3, encodes OsSK41 （also known as OsGSK5）, a member of the GLYCOGEN SYNTHASE KINASE 3/SHAGGY-like family. Rice near-isogenic lines carrying the loss-of-function allele of OsSK41 have increased grain length and weight. We demonstrate that OsSK41 interacts with and phosphorylates AUXIN RESPONSE FACTOR 4 （OsARF4）. Co-expression of OsSK41 with OsARF4 increases the accumulation of OsARF4 in rice protoplasts. Loss of function of OsARF4 results in larger rice grains. RNA-sequencing analysis suggests that OsARF4 and OsSK41 repress the expression of a common set of downstream genes, including some auxin-responsive genes, during rice grain development. The loss-of-function form of OsSK41 at qTGW3 represents a rare allele that has not been extensively utilized in rice breeding. Suppression of OsSK41 function by either targeted gene editing or QTL pyramiding enhances rice grain size and weight. Thus, our study reveals the important role of OsSK41 in rice grain development and provides new candidate genes for genetic improvement of grain yield in rice and perhaps in other cereal crops.

关键词： QTL mapping GSK3-like family protein OsGSK5 OsARF4 grain size and weight Oryza sativa

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Identification of microRNAs in rice root in response to nitrate and ammonium

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Journal of Genetics and Genomics 2016年第11期43卷 651-661页

作者： Hua Li Bin Hu Wei Wang Zhihua Zhang Yan Liang Xiaokai Gao Peng Li Yongqiang Liu Lianhe Zhang chengcai chu State Key Laboratory of Plant Genomics National Center for Plant Gene Research (Beijing) Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China School of Agriculture Henan University of Science and Technology Luoyang 471023 China

Nitrate and ammonium are two major nitrogen （N） sources for higher plants, but they differ in utilization and signaling. MicroRNAs （miRNAs） play an essential role in N signal transduction; however, knowledge remains limited about the regulatory role of miRNAs responsive to different N sources, especially in crop plants. To get global overview on miRNAs involved in N response in rice, we performed high-throughput small RNA-sequencing under different nitrate and ammonium treatments. The results demonstrated that only 16 and 11 miRNAs were significantly induced by nitrate and ammonium under short-term treat-ment, respectively. However, 60 differentially expressed miRNAs were found between nitrate and ammonium under long-term cultivation. These results suggested that miRNA response greatly differentiates between nitrate and ammonium treatments. Furthermore, 44 miRNAs were found to be differentially expressed between high- and low-N conditions. Our study reveals comprehensive expression profiling of miRNAs responsive to different N sources and different N treatments, which advances our understanding on the regulation of different N signaling and homeostasis mediated by miRNAs.

关键词： Rice MicroRNA Nitrogen Nitrate Ammonium

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