植物的功能基因组学研究进展 Progress in Functional Genomics in Plants

基因组研究计划包括以全基因组测序为目标的结构基因组学和以基因功能鉴定为目标的功能基因组学两方面的内容。目前基因功能鉴定的方法主要有：基因表达的系统分析(SAGE)、cDNA微阵列、DNA(基因)芯片、蛋白组技术以及基于转座子标签和T_DNA标签的反求遗传学技术等。本文对上述各种技术的优缺点以及它们在植物基因功能鉴定中的应用进行了综述。 Abstract: The genome projects comprise the structural genomics focusing on determining the complete sequences of the genome and the functional genomics focusing on elucidating the biological function of genes.The rapidly evolving tools for functional genomics research include Serial Analysis of Gene Expression (SAGE),cDNA microarray,DNA (or gene) chips,proteome project and the reverse genetics technique based on the well-established transposon tagging and T?DNA tagging systems.In this paper,the advantages and disadvantages of such techniques and application of these techniques in plant functional genomics research are reviewed and future prospective are also presented.     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the spring of 2019,on"Plant Genomics"in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in Summer 2018,on "Plant Genomics" in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the spring of 2019,on‘‘Plant Genomics’’in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

正We are very pleased to announce a special issue,to be published in the fall of 2018,on‘‘Plant Genomics’’in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on ‘‘Plant Genomics”

正We are very pleased to announce a special issue, to be published in the summer of 2019,on ‘‘Plant Genomics’’ in the journal Genomics, ProteomicsBioinformatics (GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions. The multiple released genomes further promote the research on genome evolution and its functional     

Special Issue on “Plant Genomics”

<正>We are very pleased to announce a special issue,to be published in Summer 2018,on"Plant Genomics"in the journal Genomics,ProteomicsBioinformatics(GPB).The development of genomics has greatly accelerated and even renovated the plant research.The sequencing of plant genomes has greatly facilitated the research on gene functions.The multiple released genomes further promote the research on genome evolution and its functional relevance.Meanwhile,the state-of-art epigenetics studies go on a genome-wide level.All these     

Targeted Mutagenesis of Duplicated Genes in Caenorhabditis elegans Using CRISPR-Cas9

正CRISPR(clustered regularly interspaced short palindromic repeats)-Cas9-based genome editing has revolutionized functional genomics in many biological research fields.The specificity and potency of CRISPR-Cas9 genome editing make it ideal for investigating the function of genes in vivo(Hsu     

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.     

Genetic resources offer efficient tools for rice functional genomics research

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T‐DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene‐rich regions, resulting in direct gene knockout or activation of genes within 20–30 kb up‐ and downstream of the T‐DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T‐DNA‐tagged rice mutant population. We also discuss important features of T‐DNA activation‐ and knockout‐tagging and promoter‐trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high‐throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.     

植物功能基因组学研究进展

植物基因组研究已经由以全基因组测序为目标的结构基因组学转向以基因功能鉴定为目标的功能基因组学研究.本简要介绍了植物功能基因组的主要研究方法,如基因表达系列分析法、表达序列标签法、差异表达谱基因芯片法、蛋白质组学分析法以及生物信息学等及其研究现状,并展望了植物功能基因组学的应用前景.     

Perspectives of DNA microarray and next-generation DNA sequencing technologies

DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequencing method was first introduced by the 454 Company in 2003, immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research. Supported by the National High-Tech Research Program of China (Grant No.2006AA020704) and Shanghai Science and Technology Commission (Grant No. 05DZ22201)     

Applications of retrotransposons as genetic tools in plant biology

Retrotransposons are mobile genetic elements that accomplish transposition via an RNA intermediate that is reverse transcribed before integration into a new location within the host genome. They are ubiquitous in eukaryotic organisms and constitute a major portion of the nuclear genome (often more than half of the total DNA) in plants. Furthermore, they are dispersed as interspersed repetitive sequences throughout most of the length of all host chromosomes. These unique properties of retrotransposons have been exploited as genetic tools for plant genome analysis. Major applications are in determining phylogeny and genetic diversity and in the functional analyses of genes in plants. Here, recent advances in molecular markers, gene tagging and functional genomics technologies using plant retrotransposons are described.     

中国基因组学研究进展与发展态势

20 世纪 90 年代初,以完成人类基因组全序列测定和注释为核心任务的人类基因组计划在美国的领导下兴起．自1999年中国加入人类基因组计划到现在的10年时间里,中国基因组学得到了快速的发展,建立了先进的基因组学技术平台,并出色完成了多项重大基因组科学研究项目,对我国生命科学各个领域的发展产生了重要影响．结合我国基因组学研究现状,《中国科学C辑·生命科学》(Sci China Ser C-Life Sci) 2009年第1期发表了中国基因组学专题,综述了基因组测序、分型,功能基因检测技术和生物信息学分析技术,以及肝癌、免疫和环境与工业微生物的基因组学研究等方面的研究工作．     

植物功能基因组学的研究策略

植物基因组学是一门研究植物基因组内基因与遗传信息是如何有机结合并如何决定其功能的一门科学。随着植物基因组计划的顺利进行 ,植物基因组学的研究已从结构基因组学转向功能基因组学。近年来 ,多采用高通量 (highthroughput,HTP)序列分析技术、大规模实验技术及计算机统计分析技术研究植物基因组功能。概述了植物功能基因组学的最新进展。     

水稻插入突变库构建研究进展

水稻是单子叶植物基因组研究的一种模式植物 ,其全基因组测序已经完成 ,在此基础上开展功能基因组的研究。水稻插入突变体库的建立是功能基因组研究的一个重要内容 ,在此基础上也能进行正向遗传学及反向遗传学的研究。水稻插入突变体库构建的方法有T DNA插入突变、Ac Ds系统插入突变、Tos1 7插入突变。分别介绍三种方法的原理及其在水稻突变体库构建中的应用和研究进展。     

激发标签技术在植物功能基因组研究中的应用

获得突变体是研究植物功能基因组的有效方法。与传统的T-DNA插入功能缺失突变相比, 建立在功能获得突变基础之上的激发标签技术具有独特的优势, 主要表现为可以获得功能冗余基因的显性突变体并方便地克隆相关基因。文章对激发标签技术的原理, 及其在拟南芥、水稻等植物功能基因组研究中的进展进行了综述, 并介绍了激发标签技术在植物抗逆、抗病和生长发育机理研究方面的新进展。文章最后探讨了激发标签技术的发展前景。     

三维基因组学研究进展

三维基因组学是一门研究基因组三维空间结构与功能的新兴学科,主要研究基因组序列在细胞核内的三维空间构象,及其对DNA复制、DNA重组、基因表达调控等生物过程的生物学效应。自染色质构象捕获技术 (3C)出现后,三维基因组学相关研究领域飞速发展。借助于3C及其衍生技术、Hi-C和ChIA-PET等技术,科学家能对各类物种的三维基因组进行更为深入的研究,从而揭示微生物、植物和动物基因组的空间构象、染色质的相互作用模式、转录调控以及不同生物学性状的形成机制;挖掘与生命活动和疾病相关的关键基因和信号通路;推动农业科学、生命科学和医学等领域的快速发展。文中就三维基因组学研究进展作一综述,主要阐述三维基因组学的概念和研究技术的发展及其在农业科学、生命科学和医学等领域的应用,尤其是肿瘤领域所取得的阶段性研究成果。     

Ac/Ds标签系统与水稻功能基因组学

自2002年水稻基因组测序完成后,水稻功能基因组学研究正在成为水稻研究的重要内容.构建突变体库是研究功能基因组学的一条重要而有效的途径.利用外源的Ac/Ds (Activator/Dissociation)标签系统是构建插入突变体库较为理想的方法,经过多年发展完善,其在水稻中已有广泛的应用,但仍面临着一些需要解决的实际问题.文章对Ac/Ds标签系统的转座行为及其构建突变体库的问题和优点进行了综述,总结了近年来Ac/Ds标签系统在水稻中的研究进展,分析了利用Ac/Ds标签系统进行功能基因组学研究所面临的挑战.