Identification and evaluation of chloroplast uni- and trinucleotide sequence repeats in citrus

A cpDNA fragment of 34 genotypes belonging to Citrus and four related genera was amplified and sequenced. Chloroplast microsatellites were revealed with the length of repeats ranging from 25 to 44 bases. Other than the normal uninucleotide poly(A) repeats, a trinucleotide poly(TAA) motif was also found, the first report of such repeats in a plant chloroplast genome. According to SSR structure variations, 18 Chloroplast SSR Types (CST) were identified. The CST sequences were informative for better understanding the genetic relationships of chloroplast genomes among the analyzed genotypes and confirmed some previous hypotheses about the female parent of several hybrid accessions.     

Comparison of the use of morphological,protein and DNA markers in the genetic characterization of Iranian wild Prunus species

In this study, the genetic diversity of four Iranian wild Prunus species including Prunus eleagnifolia, Prunus hauskenchtii, Prunus scoparia and Prunus lycioides were investigated using morphological, protein and DNA markers. DNA markers included nuclear and chloroplast SSRs and self-incompatibility (S) allele amplification. At the morphological level, leaf width showed significant differences between the four wild Prunus species. Concerning fruit and kernel characters, their values are relatively similar indicating the high degree of homoplasy described in Prunus. Nuclear SSR markers have been the most abundant markers with a higher polymorphism in comparison with morphological, protein and chloroplast SSR markers. Results also indicated the high variability present in the S locus. On the other hand, the correlation between the clustering based on DNA markers and protein were in general low. Dendogram performed using nuclear and chloroplast SSR indicated a more diffuse clustering between the wild almond species probably due to the natural introgression of genes observed in these wild almond species. Data from the analysis of the total protein seems to be more accurate to establish taxonomy relationships in these very close wild species.     

蝴蝶兰叶绿体DNA微卫星分析与标记开发

为开发兰科植物叶绿体微卫星(cpSSR)引物,对台湾蝴蝶兰叶绿体全序列进行cpSSR统计分析。结果表明台湾蝴蝶兰SSR以单碱基重复为主,占总数的78.3%。在单碱基重复中又以A和T重复为主,占95.8%。重复方式以完全重复为主,占总数的70%。开发出3对cpSSR引物。     

两类SSR对苜蓿属种质遗传多样性和亲缘关系的比较研究

利用33对细胞核SSR标记和28对叶绿体SSR标记对38份苜蓿属种质进行了遗传多样性和亲缘关系分析。在38份苜蓿属种质中,叶绿体SSR标记的平均等位变异数高于细胞核SSR标记,而遗传多样性指数则相反;分别用细胞核SSR、叶绿体SSR和61对SSR标记对38份苜蓿属种质进行聚类,结果显示:3次聚类都把38份苜蓿属种质划分为一年生和多年生苜蓿两个大类群;以相似系数0.8为准,3次聚类结果的差异主要显示在一年生苜蓿内部尤其是蒺藜苜蓿种质内的品种(系)划分上。     

枳属种质遗传多样性及其与近缘属植物亲缘关系的SSR和cpSSR标记分析

 应用核基因组SSR和叶绿体基因组SSR,分析了枳属28份枳及枳杂种种质的遗传多样性及其与近缘属植物的亲缘关系。核基因组SSR分析表明普通枳的遗传差异明显,22个SSR位点的平均多态性信息含量（PIC）为0.51,平均期望杂合度为0.52,表明中国枳种质资源具有较丰富的遗传多样性。在遗传距离约0.16时,22份普通枳可以分成4个类型。叶绿体基因组SSR分析则发现普通枳间基本无差异,表明以母系遗传为特征的枳叶绿体基因组相对保守。富民枳与普通枳无论是在核基因组还是在叶绿体基因组上均存在较大差异,支持富民枳种的地位。SSR和cpSSR结合使用可比较准确地鉴定枳杂种。     

基于cpSSR标记的甘薯品种亲缘关系及遗传多样性分析

在甘薯遗传多样性研究中,目前主要采用细胞核基因组的遗传信息。而放任授粉(集团杂交)是甘薯育种的重要手段,但基于叶绿体微卫星(chloroplast simple sequence repeat,cpSSR)标记技术的甘薯的遗传多样性分析和指纹图谱构建的研究报道较少。本研究基于cpSSR标记技术,对16份甘薯品种进行分子鉴别,并建立相对应的指纹图谱。利用在19对cpSSR引物中筛选出的11对特异性引物进行cpSSR扩增,通过聚丙烯酰胺凝胶电泳检测,结果显示,共扩增出43个条带,其中多态性条带33条,平均每对引物扩增出3个多态性条带,多态性百分率为76.74%。16份甘薯品种的遗传距离变异范围为0.0912-0.5067,平均遗传距离是0.2301。聚类分析表明,cpSSR标记能大致反映出不同品种之间的亲缘关系。该指纹图谱的建立,可为中国甘薯品种数据库的完善、近缘甘薯品种的鉴定、育种亲本的选择和品种保护提供参考依据。     

利用cpSSR分子标记法对丹参遗传特征的分析(英文)

[目的]利用cpSSR(叶绿体微卫星)分子标记法对丹参的遗传特征进行分析。[方法]选择12对cpSSR扩增良好、重复性好、条带清晰的SSR引物,对全国8省25县31个采样点的丹参进行cpSSR检测分析。[结果]丹参在细胞质遗传(cpSSR)上,总体均体现为中等水平;在地区上存在不同程度差异。基于Shannon多样性指数和Nei’s基因多样性指数的细胞质遗传多样性各省间大小依次为:山西、河南、山东、河北、四川、江苏、陕西、安徽。8省区间丹参的遗传变异以种群间的遗传变异为主导;省区内种群间的基因流有限,而省区间的基因交流较明显。[结论]综合分析认为道地产区和传统主产区的丹参主要为就地引种栽培,在栽培过程中引入了部分外来种源;在道地产区四川、山东、河南之间很早就存在种质互换,新产区多从道地产区引种。但在遗传分化方面未显示地理相关性,进一步说明全国丹参种质之间存在广泛的基因交流,是由于人类活动中对丹参的异地引种所造成。     

A comparison of genetic diversity and differentiation in five Chinese pines using cpSSR and AFLP markers

Gene diversity and genetic differentiation in five Chinese pines, Pinus henryi, P. tabulaeformis, P. yunnanensis, P. taiwanensis and P. massoniana, were compared using amplified fragment length polymorphism (AFLP) and simple chloroplast sequence repeat (cpSSR). High genetic differentiation and median gene diversity with cpSSR markers were found both at population and species level, while median differentiation and higher gene diversity in AFLP data. Measures of subdivision that consider similarity between haplotypes offered better information on the geographic structure of plants than the standard subdivisions. Among several methods analyzed in AFLPs, the square root method provided downwardly biased estimates of the genetic parameters, while the Lynch and Milligan method over-estimated genetic diversity due to a small sample size. The Bayesian statistic was the most accurate and popular method for these dominant species and its value of species differentiation (θ ^B = 0.1035) was close to the parameter given by analysis of molecular variance (AMOVA). __________ Translated from Acta Botanica Boreali-Occidentalia Sinica, 2007, 27(12): 2385–2392 [译自: 西北植物学报]     

应用cpSSR和EST-SSR标记进行柑橘特异种质资源遗传背景研究

将叶绿体SSR 和EST-SSR 标记用于揭示柑橘及其近缘属的系统发育关系,并阐明保存在重庆国家果树种质柑橘圃内一些特异种质资源的遗传背景。其中50 份材料和44 份材料分别用cpSSR 和EST-SSR 分析。22 对cpSSR 引物产生146 个多态性条带,平均检测到6.64 个多态性条带,平均Shannon’s多样性指数为0.32;18 对EST-SSR 引物产生240 个多态性条带,平均检测到 13.3 个多态性条带,平均多态信息含量（PIC）为0.73,平均期望杂合度为0.78。根据cpSSR 和EST-SSR 分析,结合形态学证据,阐明一些特异柑橘种质资源的遗传背景,同时证明莽山野橘、元橘、宜昌橙有较近的亲缘关系。     

利用cpSSR分子标记法对丹参遗传特征的分析

[目的]利用cpSSR(叶绿体微卫星)分子标记法对丹参的遗传特征进行分析。[方法]选择12对cpSSR扩增良好、重复性好、条带清晰的SSR引物,对全国8省25县31个采样点的丹参进行cpSSR检测分析。[结果]丹参在细胞质遗传(cpSSR)上,总体均体现为中等水平;在地区上存在不同程度差异。基于Shannon多样性指数和Nei’s基因多样性指数的细胞质遗传多样性各省间大小依次为:山西、河南、山东、河北、四川、江苏、陕西、安徽。8省区间丹参的遗传变异以种群间的遗传变异为主导;省区内种群间的基因流有限,而省区间的基因交流较明显。[结论]综合分析认为道地产区和传统主产区的丹参主要为就地引种栽培,在栽培过程中引入了部分外来种源;在道地产区四川、山东、河南之间很早就存在种质互换,新产区多从道地产区引种。但在遗传分化方面未显示地理相关性,进一步说明全国丹参种质之间存在广泛的基因交流,是由于人类活动中对丹参的异地引种所造成。