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Science China(Life Sciences) 2008年第4期51卷 336-345页

作者： WANG ChunMei, WANG HuiWen, ZHANG JinSong & CHEN ShouYi National Key Laboratory of plant Genomics, institute of genetics and Developmental biology, Chinese Academy of Sciences, Bei-jing 100101, China National Key Laboratory of plant Genomics Institute of Genetics Developmental biology Chinese Academy of Sciences Beijing 100101 China

plant seed development and germination are under strict temporal and spatial regulation, and tran-scription factors play important roles in this regulation. In the present study we identified an EST ex-pressed specifically in the developing soybean seeds. The full length of the gene was obtained through further RACE analysis and the gene was named GmSGR. Sequence analysis revealed that this gene belonged to the AP2/ERF transcription factor family. Its AP2 domain had the highest similarity with that of the A-3 member AtABI4 of DREB subgroup in the AP2/ERF family in Arabidopsis. GmSGR did not exhibit transcriptional activation activity in the yeast assay system. GmSGR was overexpressed in Arabidopsis and the germination rates of the transgenic seeds were significantly higher than that of the wild type seeds under higher concentrations of ABA and glucose respectively. However, the germina-tion rates of the transgenic seeds were lower than that of control under salt stress. The expression of AtEm6 and AtRD29B was higher in the seedlings of the transgenic plants than that in the wild-type seedlings. These results suggest that GmSGR may confer reduced ABA sensitivity and enhanced salt sensitivity to the transgenic seeds through regulating the expression of AtEm6 and AtRD29B genes.

关键词： ABA AP2/ERF transcription factor salt stress seed germination soybean

Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene

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Journal of genetics and Genomics 2017年第9期44卷 465-468页

作者： Jun Li Huawei Zhang Xiaomin Si Youhui Tian Kunling Chen Jinxing Liu Huabang Chen Caixia Gao State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biology Chinese Academy of Sciences University of Chinese Academy of Sciences State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of Sciences

Maize（Zea mays L.）is one of the most important cereal crops,with a global production of 1.02 billion tons in 2013（Baldaufa et al.,2016）.Heterosis is widely used to increase the productivity of maize,and the first ... 详细信息

关键词： PCR RE Generation of thermosensitive male-sterile maize by targeted knockout of the ZmTMS5 gene

In memory of Professor Biao Ding(1960–2015)

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Journal of Integrative plant biology 2015年第8期57卷 730-731页

作者： Asuka Itaya William J.Lucas Yijun Qi Feng Qu Ying Wang Xuehua Zhong Chun-Ming Liu Agriculture and Agri-Food Canada Department of plant biology University of California Center for plant biology School of Life Sciences Tsinghua University Department of plant Pathology Ohio State University Department of Molecular genetics Ohio State University Wisconsin institute for Discovery& Laboratory of genetics University of Wisconsin institute of Botany Chinese Academy of Sciences

It is with profound sadness that we mourn the loss of Dr. Biao Ding, a full-professor in the Department of Molecular genetics, Ohio State University （OSU）, and a world-renowned plant biologist with leading authority in viroid research. He died suddenly on June 26, 2015 in Prague, Czech Republic, while attending the international Conference on Viroids and Viroid-Like RNAs as a Keynote Speaker. Dr. Ding was born in 196., in Kunming, Yunnan Province, China. He received his B.S. from Beijing Forestry University in 1982, and was then selected as one of the first group of outstanding young students to study abroad since the imolementation of China＇s Reform and Open Policy.

关键词： COLLEGE teachers MOLECULAR genetics plant diseases plant biotechnology

Filtering for SNPs with high selective constraint augments mid-parent heterosis predictions in wheat(Triticum aestivum L.)

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The Crop Journal 2023年第1期11卷 166-176页

作者： Abhishek Gogna Jie Zhang Yong Jiang Albert W.Schulthess Yusheng Zhao Jochen C.Reif Leibniz institute of plant genetics and Crop plant Research(IPK) 06466 Stadt SeelandGermany

To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis(MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation based on the phylogeny of wheat and investigations were made to:(1) assess the benefit of including deleterious alleles into MPH prediction models and(2) understand the genetic underpinnings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite × elite(Exp. 1) and elite × plant genetic resources(PGR;Exp. 2). In our study, we found a lower allele frequency of moderately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH prediction models: modelling their additive-by-additive effects in Exp. 1 and dominance as well as associated digenic epistatic effects in Exp. 2 significantly boosts prediction accuracies of MPH. Furthermore,heterotic-quantitative trait loci's underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles contributes to grain yield heterosis in elite crosses(Exp. 1).

关键词： Hybrid wheat Genomic evolutionary rate profiling Deleterious SNP Heterotic Quantitative trait loci

Toward Understanding the Stem-Cell Origin and Molecular Regulation of Rice Tillering

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Journal of genetics and Genomics 2015年第2期42卷 47-48页

作者： Chuanyou Li State Key Laboratory of plant Genomics and National Center for plant Gene Research (Beijing) Institute of Genetics and Developmental BiologyChinese Academy of Sciences

Rice tiller is a specialized grain-bearing branch that contrib- utes greatly to grain production. Therefore, rice tillering is an important agronomic trait and provides a model system for the study of branching in monocots. Owing its importance both to agriculture and to fundamental science, much attention has been given to understand the molecular mechanisms under- lying rice tillering.

关键词： MOC Toward Understanding the Stem-Cell Origin and Molecular Regulation of Rice Tillering

Die in pieces:How Drosophila sheds light on neurite degeneration and clearance

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Journal of genetics and Genomics 2019年第4期46卷 187-199页

作者： Maria L.Sapar Chun Han Weill institute for Cell and Molecular biology Department of Molecular Biology and GeneticsCornell University

Dendrites and axons are delicate neuronal membrane extensions that undergo degeneration after physical injuries. In neurodegenerative diseases, they often degenerate prior to neuronal death. Understanding the mechanisms of neurite degeneration has been an intense focus of neurobiology research in the last two decades. As a result, many discoveries have been made in the molecular pathways that lead to neurite degeneration and the cell-cell interactions responsible for the subsequent clearance of neuronal debris. Drosophila melanogaster has served as a prime in vivo model system for identifying and characterizing the key molecular players in neurite degeneration, thanks to its genetic tractability and easy access to its nervous system. The knowledge learned in the fly provided targets and fuel for studies in other model systems that have further enhanced our understanding of neurodegeneration. In this review, we will introduce the experimental systems developed in Drosophila to investigate injuryinduced neurite degeneration, and then discuss the biological pathways that drive degeneration. We will also cover what is known about the mechanisms of how phagocytes recognize and clear degenerating neurites, and how recent findings in this area enhance our understanding of neurodegenerative disease pathology.

关键词： Drosophila Neurite degeneration Axon Dendrite Wallerian degeneration Phagocyte Phagocytosis PS exposure Injury assay

Transcriptome analysis of salt-stress response in three seedling tissues of common wheat

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The Crop Journal 2019年第3期7卷 378-392页

作者： Qiaoling Luo Wan Teng Shuang Fang Hongwei Li Bin Li Jinfang Chu Zhensheng Li Qi Zheng State Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China National Centre for plant Gene Research (Beijing) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Xiaoyan 60(XY60) is a new wheat variety bred in the laboratory of Zhensheng *** salt treatment, seedlings of XY60 maintain green leaves and produce longer roots than the high yielding cultivar Zhongmai 175(ZM175).To explain these different phenotypes we carried out an RNA-Seq analysis using 12 samples from three tissues of both varieties subjected to salt and control *** comparing data from the salt treated plants with the control, 703, 979, and 1197 differentially expressed genes(DEGs) were detected in new leaves, old leaves, and roots of XY60, *** corresponding numbers for ZM175 were 613, 1401, and *** most significantly enriched Gene Ontology(GO) terms and KEGG pathways were associated with polyunsaturated fatty acid(PUFA) metabolism in both new and old leaves from *** were associated with photosynthesis and energy metabolism in *** most significantly enriched KEGG pathway in roots of both varieties was “glucosinolate biosynthesis”.In addition, jasmonic acid(JA) concentration in XY60 was higher than in ZM175, although it increased significantly in both varieties following salt *** in relative expression levels of AOS, MYC2, and JAZ revealed by qRT-PCR were concordant with those from *** results suggest that PUFAs may contribute to salt tolerance in common wheat by enhancing the photosynthetic system and JA-related pathways.

关键词： Jasmonic acid Photosynthesis RNA-Seq Salt tolerance Triticum aestivum

HeteroMeth： A Database of Cell-to-cell Heterogeneity in DNA Methylation

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Genomics, Proteomics & Bioinformatics 2018年第4期16卷 234-243页

作者： Qing Huan Yuliang Zhang Shaohuan Wu Wenfeng Qian State Key Laboratory of plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China Key Laboratory of Genetic Network biology Institute of Genetics and Developmental Biology Chinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//***/HeteroMeth.

关键词： Cell-to-cell heterogeneity DNA methylation Bisulfite sequencing Single cell Shannon entropy

Recent advances in understanding of the epigenetic regulation of plant regeneration

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aBIOTECH 2023年第1期4卷 31-46页

作者： Xuemei Liu Kehui Zhu Jun Xiao Key Laboratory of plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS-JIC Centre of Excellence for plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

Ever since the concept of"plant cell totipotency"was first proposed in the early twentieth century,plant regeneration has been a major focus of ***-mediated organogenesis and genetic transformation are important topics in both basic research and modern *** studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant *** hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA ***,we summarize how various aspects of epigenetic regulation,including histone modifications and variants,chromatin accessibility dynamics,DNA methylation,and microRNAs,modulate plant *** the mechanisms of epigenetic regulation are conserved in many plants,research in this field has potential applications in boosting crop breeding,especially if coupled with emerging single-cell omics technologies.

关键词： plant regeneration Epigenetic regulation Arabidopsis Crop breeding

New guidelines for fluorophore application in peroxisome targeting analyses in transient plant expression systems

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Journal of Integrative plant biology 2019年第7期61卷 884-899页

作者： Christian Falter Nguyen Binh Anh Thu Saugat Pokhrel Sigrun Reumann plant Biochemistry and Infection biology Institute of Plant Science and Microbiology University of Hamburg

Peroxisome research has been revolutionized by proteome studies combined with in vivo subcellular targeting analyses. Yellow and cyan fluorescent protein(YFP and CFP) are the classical fluorophores of plant peroxisome research. In the new transient expression system of Arabidopsis seedlings co-cultivated with Agrobacterium we detected the YFP fusion of one candidate protein in peroxisomes, but only upon co-transformation with the peroxisome marker, CFP-PTS1. The data suggested that the YFP fusion was directed to peroxisomes due to its weak heterodimerization ability with CFP-PTS1,allowing piggy-back import into peroxisomes. Indeed, if co-expressed with monomeric Cerulean-PTS1(mCer-PTS1),the YFP fusion was no longer matrix localized. We systematically investigated the occurrence and extent of dimerization-based piggy-back import for different fluorophore combinations in five major transient plant expression systems. In Arabidopsis seedlings and tobacco leaves both untagged YFP and monomeric Venus were imported into peroxisomes if co-expressed with CFP-PTS1 but not with mCer-PTS1. By contrast, piggy-back import of cytosolic proteins was not observed in Arabidopsis and tobacco protoplasts or in onion epidermal cells for any fluorophore combination at any time point. Based on these important results we formulate new guidelines for fluorophore usage and experimental design to guarantee reliable identification of novel plant peroxisomal proteins.

关键词： transient plant expression systems fluorophore