Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species

Even though lentil has been an important food legume for centuries, genetic studies in lentil are still in their infancy. Genetic diversity and relationships among wild Lens species from Turkey has seldom been investigated. Additionally, a limited number of simple sequence repeat (SSR) markers have been developed for use in breeding and genetic studies of lentil crop. In this study, molecular characterization of 50 accessions mostly from Turkey, belonging to 6 wild and 1 cultivated Lens species, was performed using newly developed inter-primer binding site (iPBS) retrotransposons and inter-SSR (ISSR) markers. The 10 iPBS primers generated a total of 151 scorable bands, of which 150 were polymorphic (99.3%) with an average of 15.0 polymorphic fragments per primer. The 10 ISSR primers detected 138 scorable bands showing 100% polymorphism, with an average of 13.5 bands per primer. The average polymorphism information content (PIC) value for ISSR markers (0.97) was higher than that for iPBS markers (0.90). Lens orientalis was found to be the most diverse species, raising the possibility of wide crosses with cultivated species Lens culinaris. Cultivated varieties also showed high level of polymorphism, at 82.92% and 51.92% with ISSR and iPBS markers, respectively. Lens lamottei and Lens tomentosus were found as the least polymorphic species using both marker systems. The grouping of accessions and species within clusters were almost similar when iPBS and ISSR graphs were compared. Our data also suggested the role of iPBS-retrotransposons as ‘a universal marker’ for molecular characterization of wild and cultivated Lens species.     

Genetic variability and relationships between and within grape cultivated varieties and wild species based on SRAP markers

Sequence-related amplified polymorphism (SRAP) markers were used to assess genetic relationships among 76 grape genotypes including Chinese indigenous and newly bred varieties, representatives of foreign grape varieties, and wild Vitis species. Nineteen informative primers were selected from 100 SRAP primer pairs due to their ability to produce clearly and repeatedly polymorphic and unambiguous bands among the varieties. A total of 228 bands were produced; 78.63% of them were polymorphic; the average polymorphism information content (PIC) is 0.76. Genetic relationships were obtained using Nei and Li similarity coefficients. Cluster analysis of SRAP markers through the unweighted pair-group method of arithmetic averages (UPGMA) analysis and principal coordinate analysis (PCoA) were largely consistent. The definition of clusters in the dendrogram and PCoA plot is the same and some degree of grouping by types of grape, ecogeographical origin, and taxonomic status of the varieties was revealed. Three main groups were found after cluster analysis, i.e., table grape of Vitis vinifera; table grape of Euro-America hybrid and wine grape of V. vinifera; wild Vitis species. Groupings indicated a divergence between the table and wine-type varieties of V. vinifera. The results showed that the wild Vitis species that originated from America and China could be clearly differentiated and Vitis hancockii is the most distant from the others of Asian Vitis species. The results also indicated that SRAP markers are informative and could distinguish bud sports of grape. The present analysis revealed that Chinese cultivated and wild grape germplasm are highly variable and have abundant genetic diversity.     

Genetic diversity in some grape varieties revealed by SCoT analyses

Start codon targeted (SCoT) polymorphic markers were used to assess genetic relationships among 64 grape varieties. Seventeen informative primers were selected from 36 SCoT primers based on their ability to produce clear and repeatable polymorphic and unambiguous bands among the varieties. A total of 131 bands were produced; 93.1% of them were polymorphic; the average polymorphism information content was 0.82. Cluster analysis of SCoT markers through the unweighted pair-group method of arithmetic averages analysis and principal coordinate analysis were largely consistent. The partition of clusters in the dendrogram and PCoA plot was similar and some degree of grouping by types of grape and taxonomic status of the varieties was revealed. Four main groups were found after cluster analysis, i.e. table grape of Vitis vinifera; table grape of Euro-America hybrid; wine grape of V. vinifera and wild Vitis species. The results showed that the wild Vitis species originated from America and China could be clearly differentiated. The results also indicated that SCoT markers are informative and could be used to detect polymorphism for grape varieties.     

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.     

基于SSR分子标记的73份山葡萄及杂交后代的遗传多样性分析

采用SSR分子标记技术,分析俄罗斯葡萄资源及东北山葡萄资源的遗传多样性及亲缘关系,旨在为葡萄种质资源利用与创新及分子标记辅助育种提供依据。筛选11对多态性好的SSR引物分析了10份东北山葡萄品种和63份俄罗斯引种葡萄的遗传多样性及亲缘关系。11对引物在73份葡萄资源中共检测到75个等位基因,每个位点扩增3(VVIN31)-10(VVS2)个等位基因,平均等位基因6.8182个,有效等位基因(Ne)在5.280(VVS2)-1.3050(VVIN31)之间,平均值为3.5196;Shannon多态性信息指数(I)范围1.8830(VVS2)-0.4678(VVIN31),平均值1.3736;各位点多态性信息含量(PIC)变化范围为0.2337(VVIN31)-0.8098(VVS2)平均值0.6440,其中VVIN31、VMCA12位点只具有低中度多态性;Nei’s遗传多样指数在0.8098(VVS2)-0.2337(VVIN31)之间,平均值0.6444,表明各位点遗传多样性存在较大差异,等位基因在群体内的分布不均匀;观测杂合度变化范围为0.1667-0.9315,平均值0.4642,期望杂合度变化范围0.8154-0.2353,平均值为0.6489,不同位点杂合度差异较大,平均观测杂合度低于期望杂合度,表示种群内存在一定的近交率,杂合体缺失,纯合体较多;遗传分化系数Fst平均值为0.1183。基因流Nm平均值为1.8641,种质中度遗传分化,基因流较大。聚类分析结果表明东北山葡萄资源与俄罗斯野生葡萄资源亲缘关系较近,与俄罗斯选育葡萄资源亲缘关系较远;俄罗斯选育品种的遗传多样性高于山葡萄品种与俄罗斯野生葡萄资源。11对SSR引物含有丰富的多态性信息,73份葡萄资源产生了中度的遗传分化,基因流较丰富,俄罗斯葡萄资源的遗传多样性较丰富,可用于山葡萄新品种选育。     

Utility of iPBS retrotransposons markers for molecular characterization of African Gnetum species

Abstract

Species of African Gnetum are lianas used as vegetables, medicines and for generating income. Despite the taxonomic confusion, identification of new species and diverse morphological characters in African Gnetum, molecular markers on these plants are lacking. However, the inter-primer binding site (iPBS) retrotransposons markers could be simple and excellent molecular markers for African Gnetum. The objective of this study was to determine the efficiency of iPBS markers in detecting genetic differentiation in African Gnetum species. A set of 21 iPBS markers were analysed on 14 accessions including G. africanum Welw., G. buchholzianum Engl. and the recently identified species G. latispicum. Six best selected primers generated 103 bands in G. africanum, 95 in G. buchholzianum and 24 in G. latispicum. Cluster analysis divided the accessions into two major groups. The first group contained all the accessions of G. africanum, whereas the second group was further divided in two subgroups representing accessions of G. buchholzianum and G. latispicum. Additionally, the Jaccard similarity coefficient indicated a close relationship between accessions of G. buchholzianum and G. latispicum. The iPBS marker system revealed genetic differentiation within African Gnetum and could be useful for evaluating genetic diversity, conservation, taxonomy and evolution studies.     

Genetic relationship between Chinese wild Vitis species and American and European Cultivars based on ISSR markers

Inter-simple sequence repeat (ISSR) markers were employed to detect the genetic diversity among 70 grape accessions including 52 clones of 17 Chinese wild grape species, seven interspecific hybrids, 10 Vitis vinifera L. cultivars, and one strain of Vitis riparia L. A total of 119 polymorphic bands with an average of 11.9 per primer were observed. The unweighted pair-group method (UPGMA) analysis indicated that the 70 clones or accessions had a similarity range from 0.08 to 0.93, indicating that abundant diversities exist among these accessions. Based on cluster analysis and principal coordinate analysis, all accessions could be divided into two major groups, the Chinese wild grape group, and the American and European cultivar group. The largest distance was found among V. riparia MichX, Vitis piasezkii, V. vinifera L. interspecific hybrid (Vitis binifera × V. labrusca) and the wild grapes native to China.     

Genetic structure in cultivated and wild carrots (Daucus carota L.) revealed by AFLP analysis

Genetic variation within and among five Danish populations of wild carrot and five cultivated varieties was investigated using amplified fragment length polymorphism (AFLP). Ten AFLP primer combinations produced 116 polymorphic bands. Based on the marker data an UPGMA-cluster analysis and principal component analysis (PCA) separated the Daucus collections into three groups, consisting of the wild populations, the old varieties, and the recently bred varieties. The genetic distance between the wild populations reflected the physical distance between collection sites. Analysis of genetic diversity showed that the old varieties released between 1974 and 1976 were more heterogeneous than the newly developed F₁ hybrid varieties. The analysis of molecular variation (AMOVA) showed that the major part of the genetic variation in the plant material was found within populations/varieties. The presence of markers specific to the cultivated carrot makes it possible to detect introgression from cultivated to wild types. Received: 6 October 1999 / Accepted: 4 November 1999     

Genetic diversity among varieties and wild species accessions of pea (Pisum sativum L.) based on molecular markers, and morphological and physiological characters.

Random amplified polymorphic DNA, simple sequence repeat, and inter-simple sequence repeat markers were used to estimate the genetic relations among 65 pea varieties (Pisum sativum L.) and 21 accessions from wild Pisum subspecies (subsp.) abyssinicum, asiaticum, elatius, transcaucasicum, and var. arvense. Fifty-one of these varieties are currently available for growers in western Canada. Nei and Li's genetic similarity (GS) estimates calculated using the marker data showed that pair-wise comparison values among the 65 varieties ranged from 0.34 to 1.00. GS analysis on varieties grouped according to their originating breeding programs demonstrated that different levels of diversity were maintained at different breeding programs. Unweighted pair-group method arithmetic average cluster analysis and principal coordinate analysis on the marker-based GS grouped the cultivated varieties separately from the wild accessions. The majority of the food and feed varieties were grouped separately from the silage and specialty varieties, regardless of the originating breeding programs. The analysis also revealed some genetically distinct varieties such as Croma, CDC Handel, 1096M-8, and CDC Acer. The relations among the cultivated varieties, as revealed by molecular-marker-based GS, were not significantly correlated with those based on the agronomic characters, suggesting that the 2 systems give different estimates of genetic relations among the varieties. However, on a smaller scale, a consistent subcluster of genotypes was identified on the basis of agronomic characters and their marker-based GS. Furthermore, a number of variety-specific markers were identified in the current study, which could be useful for variety identification. Breeding strategies to maintain or enhance the genetic diversity of future varieties are proposed.     

葡萄种质资源初级核心群的构建

以国家果树种质郑州葡萄圃保存的867份栽培种质为材料,对47项表型性状进行了主成分分析。采用欧氏遗传距离、离差平方和法进行种质初选。采用分组和逐步聚类法,分别以15%、20%、25%和30%的比例抽样,依次获得124、170、205和252份种质。通过对初选种质的遗传多样性指数、表型保留比例的分析,检验初级核心群的构建效果。结果表明,按种质类型分组,组内采用平方根策略、15%抽样比例获得的124份初选种质的表型保留比例和遗传多样性代表性均达到96%,表明构建的初级核心群对原始种质具有很好的代表性。     

iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species

Lack of requisite genetic variation in cultivated species has necessitated systematic collection, documentation and evaluation of wild Cicer species for use in chickpea variety improvement programs. Cicer arietinum has very narrow genetic variation, and the use of a wild relative in chickpea breeding could provide a good opportunity for increasing the available genetic variation of cultivated chickpea. Genetic diversity and the relationship of 71 accessions, from the core area of chickpea origin and domestication (Southeastern Turkey), belonging to five wild annual species and one cultivated species (Cicer arietinum) were analysed using iPBS-retrotransposon and ISSR markers. A total of 136 scorable bands were detected using 10 ISSR primers among 71 accessions belonging to 6 species, out of which 135 were polymorphic (99.3 %), with an average of 13.5 polymorphic fragments per primer, whereas iPBS detected 130 bands with 100 % polymorphism with an average of 13.0 bands per primer. C. echinospermum and C. pinnatifidum were the most diverse among species, whereas C. arietinum exhibited lower polymorphism. The average polymorphism information contents (PIC) value for both marker systems was 0.91. The clustering of the accessions and species within groups was almost similar, when iPBS and ISSR NeighborNet (NNet) planar graphs were compared. Further detailed studies are indispensable in order to collect Cicer germplasm, especially C. reticulatum, from southeastern Turkey particularly, from Karacada? Mountain for preservation, management of this species, and to study their genetic diversity at molecular level. This study also demonstrates the utility and role of iPBS-retrotransposons, a dominant and ubiquitous part of eukaryotic genomes, for diversity studies in wild chickpea and in cultivated chickpea.     

The genetic diversity of UK,US and Australian cultivars of <Emphasis Type="Italic">Triticum aestivum</Emphasis> measured by DArT markers and considered by genome

The genetic diversity of UK, US and Australian wheat varieties over the period of modern plant breeding is estimated using diversity array technology markers. Diversity is assessed by both genetic distance between varieties, by AMOVA and as the volumes of multi-dimensional convex hulls estimated from principal co-ordinate analysis. At the whole genome level the three populations are genetically distinct; this is also true of the B genome. However, the US and Australian D genomes are found to occupy the same region of diversity space and the A genomes for these countries are partially overlapping. The use of high-density genotyping with a common marker set allows an unprecedented direct comparison between the diversities of the national populations, between individual genomes and the fluctuation of diversity over time. The highest genetic diversity amongst varieties is reported in the Australian population followed by the US, which in turn is more diverse than the UK. However the average diversity of loci is higher in the US set than in the Australian. Non-random fluctuations in genetic diversity over time are observed.     

葡萄感霜霉病基因的分子标记(英文)

 在葡萄抗病育种中 ,幼苗期排除感霜霉病的后代具有特别重要的意义 .用 BSA,RAPD和SCAR方法研究了葡萄感霜霉病基因的分子标记 .分析了两个种间杂交组合 [毛葡萄 (抗病 )×欧洲葡萄 (感病 ) ]88- 1 1 0和 88- 84与 88- 1 1 0的 F1代自交或互交所得的 3个 F2 代 ,以及欧洲葡萄品种和中国野生葡萄种 .共筛选了 2 80个随机引物 .引物 OPO1 0产生了一个 RAPD标记 OPO1 0 - 80 0与葡萄感霜霉病主效基因紧密联锁 .将该 DNA片段克隆并测序 .OPO1 0 - 80 0的实际长度为 835bp,所以 OPO1 0 - 80 0应为 OPO1 0 - 835.据其两端序列 ,设计了一对长度为 2 6bp和 2 8bp的特异引物分别扩增上述试材 ,获得了与该 RAPD标记相同大小的一条带 ,将 RAPD标记转化为 SCAR标记SCO1 0 - 835.并证实了此 SCAR标记的通用性 ,该 SCAR标记可用于葡萄抗病育种中杂种后代对霜霉病的抗病与感病性鉴定 .     

菊属11个野生种和12个栽培品种遗传关系的ISSR分析

为进一步明确菊属野生种与栽培品种的遗传关系和多样性,本研究利用ISSR分子标记技术对菊属11个野生种和12个栽培品种之间的遗传关系进行比较分析.从75个ISSR引物中筛选出了14个引物,对供试材料的DNA进行扩增,共获得142条清晰可辨的谱带,多态位点比率为95.1%;菊属野生种的平均有效等位基因数(effective number of alleles,Ne)、平均Nei's基因多样性指数(Nei's gene diversity,H)及Shannon信息指数(shannon's information index,I)均高于栽培菊花,说明各野生种间基因差异比较显著,多态性强于栽培品种.UPGMA聚类结果表明:菊属野生种呈现由低倍向高倍进化的趋势;栽培菊花之间遗传关系复杂,大体可以推断出平瓣是菊花的基本瓣形;菊花脑与栽培菊花亲缘关系最近,小红菊、龙脑菊、若狭滨菊与栽培菊花关系亦较近,神农香菊与其它材料关系最远.本研究的结果表明菊属野生种与栽培品种之间遗传关系比较复杂,而ISSR分子标记技术可以较好地从分子水平上揭示出菊属植物间的遗传关系.     

利用产量位点标记分析中国水稻骨干恢复系与南亚及东南亚恢复系的遗传多样性

利用47个根据已报道的QTL位点或者已被精细定位或克隆的与水稻产量性状基因紧密连锁的产量位点标记,对来自中国、印度和越南等国的58份水稻恢复系进行遗传多样性分析。结果表明:(1)在中国恢复系中,47个产量位点标记中有36个具有多态性,共检测到90个等位基因,每个标记检测到等位基因2~4个,平均为2.500个;有效等位基因共62.905个,平均每个标记1.747个;36个有效标记的Shannon信息指数平均值为0.632,变幅为0.271~1.266。(2)在来自国外的材料中,47个产量位点标记均具有多态性,共检测到131个等位基因,每个标记检测到的等位基因数为2~6个,平均2.787个;有效等位基因数共82.686个,平均1.759个;47个标记的Shannon信息指数平均值为0.649,变幅为0.109~1.110。(3)聚类分析显示,在遗传相似系数为0.73水平上,参试资源聚为三大类群,中国资源多聚在第Ⅰ类群下的第1、2、3亚群,越南资源多聚在第Ⅰ-4亚群,孟加拉资源多聚在第Ⅲ-3亚群。由此表明,中国资源遗传基础较为狭窄,而其他国家的恢复系具有较远的亲缘关系。     

Morphological and molecular genetic variations of oat genotypes grown in Kermanshah,Iran

Morphological traits and molecular markers are two common methods for genetic variation studies. Molecular markers, morphological traits methods and relationship between the two were used to study genetic variation among 43 oat genotypes and varieties. For this purpose, an augmented design was conducted in three replicates at 2008–2009 cropping season in the experimental field of Campus of Agriculture and Natural Resources of Razi University, Kermanshah, Iran. Four wild oat accessions (Avena sterilis) were added to evaluated genotypes in molecular experiment. Results showed a significant variation among genotypes for all morphological traits and they were classified based on this variation in four groups by WARD cluster analysis. In molecular experiment, 28 inter simple sequence repeat (ISSR) primers amplified 206 polymorph bands. Based on Jaccard similarity matrix, similarity among genotypes was varied from 0.23 to 0.66 and cluster analysis classified genotypes in seven groups by complete linkage method. The correlation between ISSR marker and morphological traits classifications was not significant. ISSR showed to be a helpful marker for genotype identity and separation as it put wild accessions in a group.     

分子标记在食（药）用真菌遗传多样性研究中的应用

食（药）用真菌在经济和生态方面都具有重要意义,其遗传多样性研究是资源可持续利用和生物保护学研究的基础,有利于食（药）用真菌种质资源的收集、保存、评价和利用,也有助于其分类学、系统学及进化等的研究。遗传多样性的研究方法很多,分子标记是目前最常用最有效的方法之一。综合分析了分子标记在食（药）用真菌遗传多样性研究中的应用,比较了各种标记的应用范围、优缺点,探讨了分子标记用于食（药）用真菌遗传多样性评价的前景及问题。     

云南栽培种及野生种芋头的AFLP指纹分析

目的:分析云南芋头种质资源遗传多样性。方法:应用扩增片段长度多态性(AFLP)指纹技术,用3对AFLP引物对采集自云南省的9份芋头栽培品种及1份野生品种进行研究,分离AFLP多态性条带。结果:共分离到60个AFLP多态性条带,AFLP多态位点百分率为96.77%,云南芋头种质资源在DNA分子水平上表现出丰富的遗传多样性。聚类分析将10份芋头品种分为2组,遗传距离为0.101～0.908。结论:AFLP指纹技术是筛选品种间差异基因的有效方法,研究结果为云南省芋头品种鉴定、遗传相关性分析、特殊功能基因的分离等工作提供了一定的理论基础。     

40份玉米自交系的ISSR遗传多样性分析

利用ISSR分子标记技术对40份玉米自交系进行亲缘关系分析。从59条ISSR引物中筛选出10条重复性高、多态性好的引物,分别对全部供试材料进行扩增,共扩出90条清晰谱带,其中多态性条带81条,多态性比率为90.00%,表明供试材料基因组DNA的多态性较高。用 NTSYSpc-2.10软件中的 UPGMA进行聚类分析,40份玉米自交系的遗传相似系数变化范围在0.65~1.00之间,在此基础上构建聚类分析树状图,揭示了玉米各自交系间的亲缘关系。本研究为今后分子水平上玉米优良自交系的改良与选育提供了一定的参考依据。     

附子野生资源群体遗传多样性的RAPD分析

应用RAPD标记分析了分布在附子主栽区四川、重庆、陕西及湖北16个野生乌头种群的遗传变异。24个引物共检测到643个RAPD位点,多态位点602个,总的多态位点百分率达93．5％。Shannon多样性和Nei遗传分化结果一致显示重庆酉阳种群和重庆城口种群遗传多样性最高,四川盐源种群和陕西勉县种群的遗传多样性最低。Shannon指数测出的种群内的遗传变异（57．6％）略占优势,群体间的遗传分化达到42．4％;Nei基因分化系数（GST）达40．0％;分子方差分析（AMOVA）发现群体间遗传变异仅为25．37％;种群每代迁移数Nm为0．756。Nei相似性系数的UPGMA分析结果显示该地区的野生乌头分布上有一定的地域性,特别是同为附子道地产地江油供种的北川、安县和青川种群间遗传关系密切,说明种质资源在道地药材形成中具有重要作用。研究结果表明,附子主要栽培地区的乌头野生种群之间存在较大的遗传分化,遗传多样性较高,遗传种质资源较丰富,存在一定的特异性资源,为进一步开发利用乌头（川乌、附子）提供了丰富的种质资源。