植物基因组表达序列标签(EST)计划研究进展

植物表达序列标签(EST)计划是随机挑选cDNA克隆,并对其3′或5′端进行大规模一次性测序,将得到的150～500 bp长度的DNA片段与数据库中的序列进行比较,获得对基因组结构、组织、表达等认识的基因组研究策略.就近年来国际植物EST计划的实施情况、植物EST计划的研究范围、生物信息学在EST研究中的应用、EST数据库及查询、植物EST研究中遇到的问题等方面内容进行了综述.     

EST分子标记开发及在比较基因组学中的应用

数量迅速增加的EST(expressed sequence tags)为分子标记的开发提供了宝贵的资源。与来自于基因组DNA开发的传统标记相比,以EST为基础的分子标记是一种新型分子标记,具有其显著的优势,如开发简便、信息量高和通用性好等,在多方面都有重要的利用价值。本文详细地介绍了目前基于EST开发的5类分子标记以及基于生物信息学方法的开发策略,这些标记包括EST-PCR、EST-SSR、EST-SNP、EST-RFLP和EST-AFLP。此外,对这些标记在比较基因组学研究中的应用进行了评述,包括比较作图、遗传多样性评价及系统发育研究等。     

表达序列标签(EST)在基因组学研究中的应用

表达序列标签 (expressedsequencetags)是一种快捷、高效的揭示基因组信息的方法。本文对EST的产生、概念、技术原理及其在基因组研究中的广泛应用作一详细的介绍     

分子标记及其在海洋动物遗传研究中的应用

分子遗传标记在农业动植物育种和生产上得到了广泛的应用,且取得了可喜的成果,但在水生生物上的应用还处于初始阶段。本文简要介绍了限制性片段长度多态性（RFLP）、随机扩增多态性DNA（RAPD）、扩增片段长度多态性（AFLP）、小卫星DNA和微卫星DNA（或称简单序列重复,SSR）等分子标记的概念、基本原理及其特点,重点介绍了第三代分子标记单核苷酸多态性（SNP）技术。综述了这些分子标记在海洋动物遗传结构分析、亲缘关系鉴定、遗传图谱的构建和标记辅助育种等方面的应用。     

植物表达序列标签(EST)标记及其应用研究进展

简要介绍了植物表达序列标签(EST)标记的研究现状,并对几种植物中利用EST建立分子标记的几种策略和EST标记在绘制遗传图谱、资源分析、品种鉴定及比较基因组学研究方面的应用等进行了综合评述。     

分子标记在百合属植物遗传多样性研究中的应用

介绍分子标记技术及其发展概况,并重点论述几种常见分子标记技术如随机扩增多态性DNA(random amplified polymorphism DNA,RAPD)、简单重复序列间区(inter-simple sequence repeat,ISSR)、扩增片段长度多态性(amplified fragment length polymorphism,AFLP)和内转录间隔区(internal transcribed spacer,ITS)等的基本原理、技术上的优缺点及其在百合属植物遗传多样性研究中的应用现状,同时对分子标记技术在百合属植物遗传多样性研究中的应用前景进行展望.     

SCoT分子标记在植物研究中的应用进展

SCo T是一种新型的目的基因分子标记,该标记不仅能获得与性状联系紧密的目的基因,而且能对性状进行跟踪,已被广泛应用于多种植物的研究。本文概述了SCo T标记的原理、引物设计方法及特点,并从PCR反应体系建立与优化、种质资源遗传多样性与亲缘关系分析、种质鉴定与指纹图谱构建、基因差异表达与分子遗传连锁图谱构建等方面总结了SCo T标记的应用进展。同时,对其存在的问题进行了讨论,并展望了该标记的发展应用前景。     

微卫星DNA标记开发技术进展及其在经济植物研究中的应用

微卫星分子标记技术被广泛应用于分子生物学研究中,具有多态性高、重复性好、共显性表达、杂合度高等特点,在种群遗传多样性、遗传图谱构建等领域发挥不可替代的作用。近年来,随着新一代高通量测序技术的进一步成熟,简单重复序列(simple sequence repeat,SSR)标记的开发技术与应用得到了进一步的发展。现主要对基于高通量测序的微卫星分子标记最新开发技术进行介绍,并从遗传多样性分析、遗传图谱构建、品种鉴定及分子辅助育种等方面,总结近年来SSR标记技术在经济植物研究中的最新应用,最后对SSR技术的应用前景进行展望,以期为利用微卫星技术进行经济植物研究提供参考。     

亚历山大藻属微卫星标记的筛选

采用生物信息学方法,从塔玛亚历山大藻的ESTs数据库中筛选微卫星(Simple Sequence Repeat, SSR)位点,设计SSR引物,利用毛细管电泳对4株塔玛亚历山大藻(Alexandrium tamarense)、2株相关亚历山大藻(Alexandrium affine)和1株链状亚历山大藻(Alexandrium catenella)进行种内、种间遗传多样性分析,获得以下主要结果:(1)从6830条非冗余的ESTs中共查找到222个SSR,平均每18.5kb就有一个SSR,三核苷酸重复在所有的重复类型中所占比例最大,达到48.2%,重复单元CTG/CAG出现频率最高.进一步筛选出12条SSR引物,用于遗传多样性分析.(2)种内遗传多样性水平整体偏低,多态性引物比率仅为41 67%,Nei's基因多样性平均为0.2130.种间遗传多样性水平较高,多态性引物比率为75%,Nei's基因多样性平均水平为0 4643;另外,种间遗传分化系数较高,平均水平为0.7051.(3)对7个样品的聚类图分析发现,A. tamarense CCMP116 与A. affine CCMP112遗传距离极为接近;A. tamarense ATHK9301、CCMP1598和ATDH01相互聚在一起;A. catenella ACDH01与A. tamarense分属两枝.以上结果表明,SSR标记在亚历山大藻种内遗传多样性分析方面是一种非常有用的工具.     

贝母属植物分子标记应用研究

贝母属植物有较高的药用与经济价值,对其开展分子标记研究,不仅能够应用于物种鉴定,而且能为种质资源的保护及选育方针的制定提供理论指导.结合课题组前期开展的贝母属植物分子标记的研究,就随机扩增多态性DNA、简单重复区间序列、单核苷酸多态性、扩增片段长度多态性和DNA条形码等5种分子标记技术,对贝母属植物的种质资源鉴定、遗传...     

A gene‐based SNP linkage map for pacific white shrimp,Litopenaeus vannamei

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex‐averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average‐squared correlation coefficient (r²), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r² increased with decreasing inter‐marker distance from ～80 cm , and increased more rapidly from ～30 cm . A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.     

猕猴桃品种SSR分析的初步研究

通过对16对高多态性的猕猴桃SSR引物筛选,选用了9对稳定、适用性好的引物对我国栽培的48个猕猴桃品种(品系)进行了初步研究,在9个多态性位点上共获得213个等位基因片段,其SSR指纹图谱可将供试品种完全区分开。遗传多样性分析和分辨力检测表明,我国猕猴桃栽培品种具有较高的遗传多样性,SSR标记在猕猴桃品种中有较高鉴定效率。中华／美味品种群拥有高比例的共同等位基因,反应出两者极近的亲缘关系。本研究为进一步建立我国猕猴桃栽培品种的分子指纹鉴定体系奠定了基础,为制定猕猴桃品种资源的有效保育和利用策略提供了科学依据,并对深入研究中华猕猴桃和美味猕猴桃间的系统关系提供了实验数据。     

利用AFLP分析西南特色猕猴桃的遗传多样性

为分析西南地区特色猕猴桃(Actinidia Lindl.)的遗传多样性,建立并优化了猕猴桃DNA 多态性分析的AFLP 体系,AFLP 标记体系为300 ng 基因组DNA 用EcoR Ⅰ/Mse Ⅰ (15 U/5 U)于37℃下酶切2 h,加接头后的混合物稀释5 倍用于预扩增,预扩增产物再稀释10 倍后进行选择性扩增.结果表明,筛选的22 对引物进行扩增反应,共得到979 条条带,其中多态性条带为649 条.采用优化的AFLP 体系,对西南地区的10 种猕猴桃50 个样本进行了遗传多样性分析,包括普通品种中华猕猴桃、美味猕猴桃,及特色品种硬毛猕猴桃、毛被猕猴桃、革叶猕猴桃、四萼猕猴桃、狗枣猕猴桃、葛枣猕猴桃、京梨猕猴桃和紫果猕猴,结果表明种内和种间的聚类关系明显;斑果组(sect. Maculatae)和净果组(sect. Leiocarpae)的种间有聚类交叉,并呈现地理区域性分布.     

Population structure of large yellow croaker (Larimichthys crocea) revealed by single nucleotide polymorphisms

The large yellow croaker, Larimichthys crocea, is one of the most commercially important marine species native to China Seas. In this study, Sequenom MassARRAY was used to analyze 120 individuals from three geographic populations in the East and South China Seas and a cultured stock. Forty-four of 60 single nucleotide polymorphism (SNP) loci were ascertained. Eleven loci, scf117, scf708, scf247, scf595, scf100, scf166, scf305, scf664, scf117, scf187 and scf511 each showed population-specific genotypes. A total of 127 alleles were detected. Averagely, the effective number of alleles was between 1.328 and 1.341, expected heterozygosity and observed heterozygosity ranged from 0.273 to 0.320, and 0.190 to 0.235, respectively, Pic value ranged from 0.215 to 0.247, and F_IS ranged from 0.174 to 0.279. The neighbor-joining tree based on calculated genetic distances showed a concordant topology with the traditional morphological characterization. When the population size of wild large yellow croaker drastically has shrunk over the past 20 years, the genetic diversity in both wild and farmed stocks has declined as well.     

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.