Fractionation and electrophoretic patterns of seed protein of Opuntia genus. A preliminary survey as a tool for accession differentiation and taxonomy

At present, little is known about Opuntia seed proteins and their contribution to the characterization and taxonomy of genotypes belong to this genus. The variation among 102 accessions of Mexican Opuntia was studied using electrophoretic patterns by sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS–PAGE) of their seed total proteins (STPs) and seed storage proteins (SSPs). Albumins and globulins were the most abundant protein fractions, with contents varied from 2.6 to 11.9 mg/mL and 2.6–9.5 mg/mL, respectively. These were followed by glutelins (2.3–8.5 mg/mL) and prolamins as the lowest (1.1–7.9 mg/mL) of the four protein factions. On the other hand, STPs content varied between 1.13 and 7.12 mg/mL. Regardless of variations in protein content estimated in seeds, the electrophoretic patterns of STPs and SSPs, as outcome of their SDS–PAGE, were not so variable. Furthermore, the individual analysis of each STPs or the SSPs analyses, separately, were not enough to discriminate all accessions, since it was necessary to combine the data resulting from all protein profiles together to differentiate all Opuntia genotypes. The UPGMA analysis indicated that there is no separation between accessions of species of the prickly pear (sweet fruits) and “xoconostle” (acidic fruits), even though the latter were grouped together. Based on biochemical markers analyzed herein, the need for revision of taxonomic assignment of genotypes belonging to the genus Opuntia is suggested.     

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     

野牡丹族数量分类的初步研究

用ＵＰＧＭＡ聚合法对野牡丹族的４２个性状进行Ｒ分析和对该族华南及台湾地区１５个分类群进行Ｑ分析．Ｒ分析的结果反映了性状之间相关进化及性状与分类群之间相关进化的规律性．Ｑ分析对这些分类群的分类系统做了初步的定量研究．其结论与经典分类基本吻合．Ｑ分析的结果还支持将台湾产的耳药花并入野牡丹属。     

Development,cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

Sugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5′UTR and in the ORF (about 27%) and a low frequency was observed in the 3′UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane.     

五味子科比较木材解剖及其系统学意义

在光学显微镜和扫描电镜下观察了南五味子属Kadsura 7种21个样品和五昧子属Schisandra 8种14个样品的木材解剖特征,结果表明次生木质部的导管分子类型、导管一射线间纹孔的排列方式、射线类型、射线细胞形状等性状在科的水平上很稳定,这些共同特征都支持五味子科Schisandraceae是比较自然的类群。在五昧子科中发现木材导管单生、具梯状穿孔板、导管壁具梯形排列的纹孔以及木射线异型等原始性状,支持五味子科在被子植物中的原始地位。此外,该科木材还具有单穿孔板导管、导管次生壁具螺纹加厚、具分隔纤维等较为特化的性状状态,这种性状进化水平的异等级现象,使五味子科表现出不同进化水平性状的镶嵌组合。根据木材解剖性状对五味子科进行UPGMA聚类分析,所得结果显示南五昧子属和五味子属在木材解剖特征方面有一定的交叉和重叠,这与分子系统学的结论一致,表明这两个属关系密切,可能起源于共同的祖先。通过比较五昧子科与八角科Illiciaceae的木材解剖特征,进一步证明两个科的亲缘关系很近,不支持将五味子科从八角目Illiciales中独立出来成立五味子目Schisandrales的观点。     

Genetic diversity analysis of sedges (Carex spp.) in Shandong,China based on inter-simple sequence repeat

As the plants of turfgrass, forage and environment protecting plants, Carex L. has important economic value. The aims of the study were to construct ISSR-PCR amplification reaction system on Carex and to investigate the genetic diversity of 16 Carex populations belonging to 10 species using inter-simple sequence repeat (ISSR) makers. A total of 120 polymorphic amplified bands were obtained from 6 primers, and the percentage of polymorphisms was 100%. Genetic similarity between accessions ranged from 0.4250 to 0.8667 with an average of 0.6459, suggesting that the collected accessions are genetically diverse. All accessions were grouped into 3 clusters according to the UPGMA dendrogram. Most of the populations from the same regions can be basically clustered together and molecular grouping of Carex spp. correlates with geographical distribution and ecological environment. However, a few appeared to be divergent with the geographical distribution. The results showed that ISSR maker is an effective tool for the study of genetic diversity in Carex. As for the genus Carex, such information is needed for successful management and preservation of species to ensure the maintenance of genetic variation.     

K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.     

Assessment of genetic differentiation in the large yellow croaker, Pseudosciaena crocea Richardson,and its first hybrid filial generations with AFLP markers

The genetic diversity (the digital characteristics) of four populations (120 individuals) of breeding large yellow croakers, Pseudosciaena crocea Richardson, was analyzed with amplified fragment length polymorphism (AFLP) markers. Ten primer combinations amplified 248 bands, of which 39.52% were polymorphic. Shannon's information index of the Daiqv (DQ) population was higher than that of the Minyu (MY) population, at 0.2167 and 0.2074, respectively. Additionally, the Shannon's information index value for the minus-hybrid (DQ population♂ × MY population♀) first hybrid generation was higher than the value for the plus-hybrid (MY population♂ × DQ population♀) first hybrid generation at 0.1687 and 0.1613, respectively. The F_ST of the parental generation was lower than that of the filial generation at 0.0329 and 0.0891, respectively. Gene flow was very high according to F_st values in both parental and filial generations. The UPGMA clustering analysis based on genetic similarity organized the four populations into three groups. The minus-hybrid stock was the most distinct as compared to the other populations.     

黄斑蜂族的系统学研究：几何形态测量方法（膜翅目： 切叶蜂科）

利用采集于土耳其安纳托利亚中部(Middle Anatolia) 的切叶蜂科6个种92头标本,选取虫体上的30个特征点(landmarks)(其中前翅16个,后翅6个,头部8个),利用UPGMA等数值分类方法对不同属和种的亲缘关系进行了探讨。据此对一些种的归属和一些属的划分提出了一些与传统分类观点相同或不同的见解,但各种分析方法的结果都支持切叶蜂族Megachilini起源的单系性。     

Genetic diversity assessment in Portugal accessions of <Emphasis Type="Italic">Olea europaea</Emphasis> by RAPD markers

Eighty seven olive (Olea europaea ssp. sativa L.) cultivar accessions from Portugal were characterized by means of randomly amplified polymorphic DNA (RAPD) markers. Of the 11 arbitrary 10-mer primers tested a total of 92 polymorphic bands were obtained, representing 87.6 % of the total amplification products. Twenty nine different genotypes were clearly discriminated. Differences were not found among the amplification profiles from different individuals of the same cultivar. All the genotypes could be identified by the combination of three primers: OPR-1, OPK-14 and OPA-1, seven genotype-specific markers being detected. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA). The genetic analysis of the results showed a gradual distance between the various cultivars, making it difficult to identify well-differentiated phylogenetic groups, although two clusters were distinguishable with 35 % similarity, in addition to three independent branches with lower similarity: Galega, Tentilheira and Redondal. The dendrogram reflect some relationships for most of the cultivars according to the use of the fruit and ecological adaptation.