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The rice PLATZ protein SHORT GRAIN6 determines grain size by regulating spikelet hull cell division

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Journal of Integrative Plant Biology 2020年第6期62卷 847-864页

作者： Shi-Rong Zhou hong-wei xue National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and Ecologythe Chinese Academy of SciencesShanghai 200032China State Key Laboratory of Crop Genetics and Germplasm Enhancement Jiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjing 210095China School of Agriculture and Biology Shanghai Jiao Tong UniversityShanghai 200240China

Grain size is a major determinant of cereal grain yields;however,the relevant regulatory mechanisms controlling this trait have not been fully *** rice(Oryza sativa)mutant short grain6(sg6)was identified based on its reduced grain length and ***,we functionally characterized the role of SG6 in determining grain size through the regulation of spikelet hull cell ***6 encodes a previously uncharacterized plant ATrich sequence and zinc-binding(PLATZ)protein that is ubiquitously localized throughout the cell and is preferentially expressed in the early developing panicles but not in the *** overexpression of SG6 resulted in significantly larger and heavier grains,as well as increased plant heights,which is consistent with its elevated spikelet hull cell division *** two-hybrid analyses revealed that SG6 interacts with the core cell cycle machinery DP protein and several other putative cell division regulators,consistent with our transcriptomic analysis,which showed that SG6 activates the expression of many DNA replication and cell-cycle-related *** results confirm the crucial role of SG6 in determining grain size by regulating spikelet hull cell division and provide clues for understanding the functions of PLATZ family proteins and the network regulating cereal grain size.

关键词： sativa) fir cereal

Global Analysis of Expression Profiles of Rice Receptor-Like Kinase Genes

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Molecular Plant 2012年第1期5卷 143-153页

作者： Lin-Lin Gao hong-wei xue National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and EcologyShanghai Institutes for Biological Science(SIBS)ChineseAcademy of Sciences300 Fenglin Road20032 ShanghaiChina

The receptor-like kinases （RLKs） play critical roles in plant development and response to stress stimuli. By perceiving or sensing the extracellular signals, RLK activates the downstream signaling pathway through phosphorylating the specific targets. Up to now, only a few RLKs have been functionally identified, which are even fewer in rice （Oryza sativa L.）. We here report the systemic analysis of the expression profiles of rice RLK coding genes in different tissues, with the emphasis on seed development and in response to both abiotic stress and plant hormones. The results showed that most rice RLK genes are expressed in two or more tissues, of which the RLCK-RLKs have a higher, while WAK- and SD-RLKs have a lower, expression level in the vegetative tissues than other subfamily members. Interestingly, the constitutively highly expressed RLKs in rice and Arabidopsis are conserved, which is consistent with the previous hypothesis that RLKs existed before the differentiation of monocotyledon and dicotyledon plants. Nearly one-third of the detected rice RLKs are expressed during seed development, and the RLCK-RLK members possess a higher percentage during the endosperm de- velopment, suggesting a novel function of RLCK-RLK members in endosperm development. Further analysis revealed that many RLK genes expressed during seed development are also regulated by abiotic stresses （cold, salt, or drought） or hor- mones, indicating that RLKs may take part in the stress-related signaling pathways such as dehydration of endosperm. These results provide informative insights into the RLK studies and will be helpful to reveal the global regulatory network controlling rice seed development.

关键词： Receptor-like kinase rice profiling seed development stress ABA.

OsLEC1/OsHAP3E Participates in the Determination of Meristem Identity in Both Vegetative and Reproductive Developments of Rice

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Journal of Integrative Plant Biology 2013年第3期55卷 232-249页

作者： Jing-Jing Zhang hong-wei xue National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and EcologyShanghai Institutes for Biological SciencesChinese Academy of Sciences

In the vegetative phase of plant development, the shoot apical meristem （SAM） produces leaf primordia in regular phyllotaxy, and transforms to the inflorescence meristem when the plant enters reproductive growth, which will undergo a series of identity differentiations and will finally form a complete and fertile panicle. Our previous studies indicated a tissue-specific expression pattern of the OsLEC1 （leafy cotyledon） gene, which is homologous to the Arabidopsis AtLEC1 gene and belongs to the CCAAT-binding protein HAP3 subfamily, during embryo development. Expression of additional OsLEC1 genomic sequences resulted in abnormalities in the development of leaves, panicles and spikelets. The spikelets in particular presented abnormities, including panicle and spikelet-like structures that occurred reiteratively inside prior spikelets, and the occasional spikelet structures that completely transformed into plantlets （a reproductive habit alteration from sexual to asexual called ＂pseudovivipary＂）. Analysis showed that OsLEC1 interacts with several SEPALLATA-like MADS transcription factors, suggesting that increased levels of the OsLEC1 protein might interfere with the normal interaction network of these MADS proteins and lead to defective spikelet development. The expression of OsMADS1 was dramatically reduced, and the DNA methylation level of cytosine in certain regions of the OsMADS1 promoter was increased under OsLEC1 overexpression. These results indicate that OsLEC1 affects the development of leaves, panicles and spikelets, and is a key regulator of meristem identity determination in both rice （Oryza sativa） vegetative and reproductive development.

关键词： Rice OsLECl meristem identity panicle MADS-box transcription factor.

Lipidomic profiling analysis reveals the dynamics of phospholipid molecules in Arabidopsis thaliana seedling growth

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Journal of Integrative Plant Biology 2016年第11期58卷 890-902页

作者： Yi-Sheng Wang hong-Yan Yao hong-wei xue National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

High-throughput lipidomic profiling provides a sensitive approach for discovering minor lipid species. By using an advance in electrospray ionization tandem mass spectrome- try, a large set of phospholipid molecular species （126 species） with high resolution were identified from Arabidopsis seedling; of them 31 species are newly identified （16 are unique in plants）, including 13 species of phosphatidic acid （PA）, nine phosphati- dylcholine, six phosphatidylinositol and three phosphatidylser- ine. Further analysis of the lipidomic profile reveals dynamics of phospholipids and distinct species alterations during seedling development. PA molecules are found at the lowest levels in imbibition and follow an increasing trend during seedling growth, while phosphatidylethanolamine （PE） molecules show the opposite pattern with highest levels at imbibition and a general decreasing trend at later stages. Of PA molecular species, 34：2-, 34：3-, 36：4, 36：5-, 38：3- and 38：4-PA increase during radicle emergence, and 34：2- and 34：3-PA reach highest levels during hypocotyl and cotyledon emergence from the seed coat. Conversely, molecular species of PE show higher levels in imbibition and decrease in later stages. These results suggest the crucial roles of specific molecular species and homeostasis of phospholipid molecules in seedling growth and provide insights into the mechanisms of how phospholipid molecules are involved in regulating plant development.

关键词： Arabidopsis seedling electrospray ionization massspectrometry lipidomic profile phospholipids

Rice miR394 suppresses leaf inclination through targeting an F-box gene, LEAF INCLINATION 4

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Journal of Integrative Plant Biology 2019年第4期61卷 406-416页

作者： Li Qu Li-Bi Lin hong-wei xue National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant Sciences Shanghai Institute of Plant Physiology and Ecology the Chinese Academy of Sciences University of the Chinese Academy of Sciences

Rice leaf inclination is an important agronomic trait, closely related to plant architecture and *** of genes controlling leaf inclination would assist in crop improvement. Although various factors,including the plant hormones auxin and brassinosteroids,have been shown to regulate lamina joint development,the role of microRNAs in regulating leaf inclination remains largely unknown. Here, we functionally characterize the role of rice miR394 and its target, LEAF INCLINCATION 4(LC4), which encodes an F-box protein, in the regulation of leaf inclination. We show that miR394 and LC4 work,antagonistically, to regulate leaf lamina joint development and rice architecture, by modulating expansion and elongation of adaxial parenchyma cells. Suppressed expression of miR394, or enhanced expression of LC4,results in enlarged leaf angles, whereas reducing LC4 expression by CRISPR/Cas9 leads to reduced leaf inclination, suggesting LC4 as candidate for use in rice architecture improvement. LC4 interacts with SKP1, a component of the SCF E3 ubiquitin ligase complex, and transcription of both miR394 and LC4 are regulated by auxin. Rice plants with altered expression of miR394 or LC4 have altered auxin responses, indicating that the miR394-LC4 module mediates auxin effects important for determining rice leaf inclination and architecture.

关键词： Rice miR394 F-box gene LEAF INCLINATION 4

CRISPR Primer Designer:Design primers for knockout and chromosome imaging CRISPR-Cas system

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Journal of Integrative Plant Biology 2015年第7期57卷 613-617页

作者： Meng Yan Shi-Rong Zhou hong-wei xue National Key Laboratory of Plant Molecular Genetics Shanghai Institute of Plant Physiology and Ecologythe Chinese Academy of Sciences

The clustered regularly interspaced short palin- dromic repeats （CRiSPR）-associated system enables biologists to edit genomes precisely and provides a powerful tool for perturbing endogenous gene regulation, modulation of epigenetic markers, and genome architecture. However, there are concerns about the specificity of the system, especially the usages of knocking out a gene. Previous designing tools either were mostly built-in websites or ran as command-line programs, and none of them ran locally and acquired a user- friendly interface. In addition, with the development of CRISPR-derived systems, such as chromosome imaging, there were still no tools helping users to generate specific end-user spacers. We herein present researchers to design primers CRISPR Primer Designer for for CRISPR applications. Theprogram has a user-frfendly interface, can analyze the BLAST results by using multiple parameters, score for each candidate spacer, and generate the primers when using a certain plasmid. In addition, CRISPR Primer Designer runs locally and can be used to search spacer clusters, and exports primers for the CRiSPR-Cas system-based chromosome imaging system.

关键词： Chromosome imaging CRISPR knockout primer software

Studies on the Rice LEAF INCLINATION1 （LC1）, an IAA-amido Synthetase, Reveal the Effects of Auxin in Leaf Inclination Control

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Molecular Plant 2013年第1期6卷 174-187页

作者： Shu-Qing Zhao Jing-Jing Xiang hong-wei xue National Key Laboratory of Plant Molecular Genetics institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences ChineseAcademy of Sciences Shanghai 200032 China

The angle of rice leaf inclination is an important agronomic trait and closely related to the yields and archi- tecture of crops. Although few mutants with altered leaf angles have been reported, the molecular mechanism remains to be elucidated, especially whether hormones are involved in this process. Through genetic screening, a rice gain-of- function mutant leaf inclination1, Icl-D, was identified from the Shanghai T-DNA Insertion Population （SHIP）. Phenotypic analysis confirmed the exaggerated leaf angles of Icl-D due to the stimulated cell elongation at the lamina joint. LC1 is transcribed in various tissues and encodes OsGH3-1, an indole-3-acetic acid （IAA） amido synthetase, whose homolog of Arabidopsis functions in maintaining the auxin homeostasis by conjugating excess IAA to various amino acids. Indeed, recombinant LC1 can catalyze the conjugation of IAA to Ala, Asp, and Asn in vitro, which is consistent with the decreased free IAA amount in Icl-D mutant. Icl-D is insensitive to IAA and hypersensitive to exogenous BR, in agreement with the microarray analysis that reveals the altered transcriptions of genes involved in auxin signaling and BR biosynthesis. These results indicate the crucial roles of auxin homeostasis in the leaf inclination control.

关键词： rice leaf inclination auxin GH3.

LC2 and OsVIL2 Promote Rice Flowering by Photoperoid-lnduced Epigenetic Silencing of OsLF

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Molecular Plant 2013年第2期6卷 514-527页

作者： Jun Wang Jiang Hu Qian Qian hong-wei xue National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chineseacademy of Sciences Shanghai 200032 People's Republic of China State key Laboratory of Rice Biology China National Rice Research institute Hangzhou Zhejiang 310006 People's Republic of China

Proper flowering time is essential for plant reproduction. Winter annual Arabidopsis thaliana needs ver-nalization before flowering, during which AtVILs （VIN3 and VRNS, components of PRC2 complex） mediate the H3K27 tri- methylation at the FLC locus （a floral repressor） to repress the FLC expression and hence to induce flowering. However, how VILs （VIL, VERNALIZATION INSENSITIVE 3-LIKE） function in rice is unknown. Here we demonstrated that rice LC2 （OsVIL3） and OsVIL2 （two OsVILs, possible components of PRC2 complex） promote rice flowering. Our results showed that expressions of LC2 and OsVIL2 are induced by SD （short-day） conditions and both Ic2 mutant and OsVIL2-RNAi lines display delayed heading date, consistent with the reduced expression levels of Hdl and Hd3a. Interestingly, LC2 binds to the promoter region of a floral repressor OsLF and represses the OsLF expression via H3K27 tri-methylation modification. In addition, OsLF directly regulates the Hdl expression through binding to Hdl promoter. These results first demonstrated that the putative PRC2 in rice is involved in photoperiod flowering regulation, which is different from that of Arabidopsis, and revealed that LC2 binds the promoter region of target gene, presenting a possible mechanism of the recruitment pro-cess of PRC2 complex to its target genes. The studies provide informative clues on the epigenetic control of rice flowering.

关键词： epigenetic control rice flowering LC2 PRC2.

Arabidopsis MSBP1 Is Activated by HY5 and HYH and Is Involved in Photomorphogenesis and Brassinosteroid Sensitivity Regulation

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Molecular Plant 2011年第6期4卷 1092-1104页

作者： Qiu-Ming Shi Xi Yang Li Song hong-wei xue National Key Laboratory of Plant Molecular Genetics Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 300 Fenglin Road 200032 Shanghai PR China

Membrane Steroid Binding Protein 1 （MSBP1） can bind steroids in vitro and negatively regulates brassinosteroid （BR） signaling, as well as cell elongation and expansion. Detailed analysis of the MSBP1 expression pattern based on quantitative real-time RT-PCR and promoter-GUS fusion studies revealed that MSBP1 expression in hypocotyls is stimulated by various light conditions, Interestingly, MSBP1 expression is greatly suppressed in hyS, hyh, or hy5hyh mutants but enhanced in cop1 mutants, Further analysis employing a yeast one-hybrid assay, an electrophoretic mobility shift assay （EMSA）, and a Chromatin IP （CHIP） assay confirmed the direct binding of Long Hypocotyl 5 （HY5） and HY5 Homolog （HYH） to the promoter region of MSBP1, indicating that MSBP1 is involved in light-regulated hypocotyl growth by serving as a direct target for HY5 and HYH. In addition, hy5 and hy5 hyh mutants show altered BR responses to light, which is consistent with the suppressed expression of MSBP1 in these mutants. These results suggest that light triggers MSBP1 ex- pression through direct binding to and activation by HY5 and HYH, thereby inhibiting hypocotyl elongation. The findings also provide informative clues regarding the mechanisms for the negative regulation of BR sensitivity and photomorpho- genesis during the dark-light transition.

关键词： MSBP1 HY5 HYH photomorphogenesis BR signaling.