基因芯片与高通量DNA测序技术前景分析

基因芯片与第二代DNA测序是两种重要的高通量基因组学研究技术,对于揭示基因组的结构与功能已经并正在发挥重要的推动作用．基因芯片技术建立了10多年,技术日渐成熟,在功能基因组、系统生物学、药物基因组的研究中已经得到了广泛的应用．2003年,454公司首先建立了高通量的第二代测序技术,其他公司相继推出了Solexa和Solid测序技术．虽然第二代测序技术建立的时间不长,但发展非常快,已经应用于基因组,包括测序和表观基因组学以及功能基因组学研究的许多方面．本文简要综述了基因芯片和第二代测序技术及其应用进展,并分析了这两种高通量基因组学技术的前景．     

水稻单核苷酸多态性及其应用现状

单核苷酸多态性（single nucleotide polymorphisms, SNPs）在水稻中数量多,分布密度高,遗传稳定性高。水稻SNPs的发现方法主要有对样本DNA的PCR产物直接测序、从SSR区段检测SNPs和从基因组序列直接搜索等。目前已有多种基因分型技术运用到了水稻SNPs检测,SNPs检测的高度自动化使水稻SNPs基因分型非常方便。单核苷酸多态性在水稻遗传图谱的构建、基因克隆和功能基因组学研究、标记辅助选择育种、遗传资源分类及物种进化等方面的应用具有巨大潜力。     

临床宏基因组学应用现状及存在问题分析

众所周知,宏基因组学是一种通过提取样品中微生物的总DNA,构建宏基因组文库,研究环境中全部微生物的遗传组成及其菌落功能的方法。而宏基因组新一代测序(metagenome next-generation sequencing, mNGS)是在宏基因组学基础上进一步发展起来的新一代测序技术,无需对患者标本进行培养,直接分析标本中的微生物DNA或RNA。本文介绍了宏基因组学在临床上的应用,包括传染病的诊断、疾病和健康状态下的微生物组分析、人类宿主反应分析和肿瘤相关病毒及其基因组鉴定,并简要探讨了临床宏基因组学研究中所遇到的挑战及解决方法。     

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.     

T—DNA介导的基因诱捕技术及其在植物功能基因组学研究中的应用

T-DNA介导的基因诱捕技术是近年来发展起来的鉴定和分离基因的方法。在拟南芥和水稻基因组测序已经完成的今天,该技术将在两者基因功能的研究中扮演举足轻重的角色。本文就T—DNA介导的基因诱捕系统、基因克隆和突变体库构建的研究进展及其在植物功能基因组学上的应用等内容进行了综述,并讨论了该技术应用中的一些问题。     

单细胞基因组学分析的技术前沿

基因组学已经深刻地改变了生命科学的诸多领域的面貌。目前它的主要内容是新的全基因组碱基序列的测定和在全基因组范围内鉴定那些在不同水平上影响生命活动的基因群的功能和相互作用。为达此要求,近年出现的第二代测序(深度测序)技术和基因芯片技术发挥了关键作用,但是两者都需要足够的高质量的核酸样品。所以,在只有或只能用单细胞或极少量细胞的情况下,如果没有特殊手段,上述分析往往不能常规、方便地进行。文章以DNA扩增为主线,综合阐述了目前在单细胞(特别是微生物)全基因组测序和大基因组的靶向重测序,以及对单细胞或微量细胞进行的基于深度测序或芯片杂交的功能基因组分析,如转录组、ChIP和DNA的CpG甲基化分析等的最新策略和技术,评价了单细胞基因组测序和功能基因组学各技术的特点并对发展前景进行了展望。     

主要禾谷类作物比较基因组学研究策略与进展

随着拟南芥、水稻等模式植物基因组测序计划的完成, 比较基因组学作为一门新兴学科, 近年来发展迅速, 为植物基因组的进化、结构和功能研究开辟了新的途径。文章综述了比较基因组学在作物比较遗传作图、基因结构区域的微共线性、ESTs和蛋白质水平的比较以及基于比较基因组学的基因和QTL的克隆等方面内容与研究进展, 分析了不同水平上比较基因组学研究策略的原理、特点、可行性, 以期为利用模式生物的基因和基因组数据、采用比较基因组学策略克隆作物重要性状功能基因、阐明基因组结构与进化提供帮助。     

获取全长cDNA若干方法的比较

生物技术突飞猛进大大提高了人类认识自身及与人类息息相关的生命现象的能力。近几年内 ,人类 [1,2 ]、模式生物拟南芥 ( Arabidopsis thaliana) [3 5]及水稻的基因组测序 [6,7]的草图相继完成 ,给人类又提出了新的挑战 :如何鉴定这些序列的功能及如何解析生命现象的基因本质 ,这是一个更加庞大而又极富挑战性的课题 ,正促使一门新的学科即功能基因组学 ( Functional genomics)的产生与蓬勃发展。不论功能基因组学多么深奥 ,其认识基因功能的基本前提是获取可能有相关功能的基因之全长编码序列。其中 ,全长 c DNA序列的获取是正确地注释基…     

水稻功能基因组学研究策略

自80年代第一株可育转基因水稻问世以来,水稻转化研究进展迅速。已采用包括农杆茵介导等许多转化方法。随着水稻基因组测序计划的完成,以功能基因组学研究为代表的后基因组时代已经到来。丰富的信息资源将为水稻功能基因的发掘创造十分有利的条件。本文将对水稻功能基因组的研究进展及其方法等进行简要概括。     

DNA测序技术的发展进程

随着DNA测序技术的发展,生物信息学、分子遗传学、精准医学以及基因组学等新兴学科也随之涌现,推动着生命科学研究的不断深入。本文就DNA测序技术发展进程中的几代测序技术的原理及优缺点进行介绍,并对以后测序技术的发展进行展望。     

Rice functional genomics research in China

Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.     

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.     

插入突变在水稻功能基因组学中的研究进展

构建饱和的基因突变体库是最直接、有效的分析鉴定基因功能的方法.根据插入突变源不同可分为T-DNA插入突变、转座子插入突变等.主要介绍这两种方法的原理及其在水稻功能基因组学研究中的应用和进展,并分析和讨论了插入突变在水稻功能基因组学研究中存在的困难和发展趋势.     

Genome Sequencing and Identification of Gene Function in Rice

Rice is known to be one of the most important crops for human consumption. As the model cereal crop, large-scale sequencing of rice genome must play quite important roles both in theoretical research and practical application in rice breeding, which announces the opening of another new way to resolve the world food crisis. At present, the emphasis of rice genome research has been transferred from structure genomics to functional analysis. The discovery of new genes and annotation of gene function was believed to be an important issue in functional genomics research. In this article, the sequencing and functional research of the rice genome were reviewed. These results may provide some useful clues for rice genetic engineering and breeding practices.     

水稻基因组测序及基因功能的鉴定

水稻是重要的粮食作物。作为单子叶模式植物,水稻基因组的大规模测序具有巨大的理论价值和现实意义。目前已获得了籼稻“93—11”和粳稻“日本晴”高质量的基因组数据,这为在基因组水平上深入研究其生长、发育、抗病和高产等的遗传机理提供了便利,从而为进一步解决世界粮食危机提供了新的突破口和契机。随着水稻基因组计划的顺利结束,其研究重心也已由建立高分辨率的遗传、物理和转录图谱为主的结构基因组学转向基因功能的研究。结构基因组学研究获得的大量序列数据为揭示和开发功能基因开辟了广阔的前景。目前,利用图位克隆和电子克隆等方法已成功分离了多个水稻抗病、抗虫、抗逆境、抗倒伏、高产、优质等重要农艺性状相关的基因,对培育水稻新品种,促进农业的可持续发展意义重大。据估计,水稻至少拥有3．7万个非转座因子相关的蛋白编码基因。因此,完成全基因组序列测定后,重要基因功能的鉴定已成为当前基因组学研究的主要目标。反向遗传学、大规模基因功能表达谱分析和蛋白质组研究等策略已在研究水稻重要基因的功能方面发挥了重要作用。文章综述了水稻基因组测序及基因功能研究的现状,并就新基因发掘和基因功能注释的方法作了评述,期待为水稻遗传工程和育种实践提供参考。     

Towards molecular breeding and improvement of rice in China

China is the largest producer and consumer of rice in the world and a pioneer in applying hybrid rice technology. Although hybrid rice has contributed greatly to Chinese agriculture in the past decades, its potential to improve grain quality further is being questioned. However, to meet the challenges posed by severe crop damage by pests and diseases, the extensive use of pesticides and chemical fertilizers, and a shortage of water and energy, more elite rice cultivars are needed. In recent years, China has seen continued improvements in rice genetics, powered by functional genomics as a way forward to safeguard its rice production. Here, we briefly review the current status of rice breeding in China through strategies integrating hybrid rice technology, molecular marker-assisted breeding, functional genomics and genetically modified rice.     

How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.