Extensive dispersal of Roanoke logperch (Percina rex) inferred from genetic marker data

The dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (N_e) for a population of Roanoke logperch Percina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation‐by‐distance model. Estimates of N_e varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half‐sibling pairs, but only one parent–offspring pair and no full‐sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model‐based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics.     

栉孔扇贝、虾夷扇贝及其杂交子代的MSAP分析

运用甲基化敏感扩增多态性(methylation-sensitive amplification polymorphism,MSAP)技术对栉孔扇贝(♀)、虾夷扇贝(♂)及其杂交子一代、子二代基因组DNA胞嘧啶甲基化水平进行了研究,并分析了DNA甲基化与各性状的相关性及其与杂种优势的关系。结果表明,(1)DNA甲基化率与壳宽、总重等表型值呈正相关的关系,而与壳长、壳高、软体重和闭壳肌重4个性状表型值呈负相关的关系,其中闭壳肌重与甲基化率的相关性达到极显著水平(P<0.01);(2)虾夷扇贝、栉孔扇贝、F1代、F2代的总甲基化率分别为32.79%、24.13%、19.98%、20.18%,杂交种F1代的甲基化水平低于双亲,是两种扇贝杂交的结果;F1代的甲基化模式经过了重新调整,其变化相对其亲本主要有4种类型:甲基化水平相同、去甲基化、超甲基化、次甲基化,且去甲基化位点多于超甲基化位点。结果证实杂种优势的产生与杂交种F1代基因组DNA甲基化模式的改变和重新调整有关,丰富了杂种优势机理研究内容。     

Polymorphism and heredity of cpDNA and mtDNA in the Section Leuce of <Emphasis Type="Italic">Populus</Emphasis>

The chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) of 16 Populus species (Section Leuce) and their F1 generation were detected using PCR-RFLP technique. The results show that cpDNA in the F1 generation of 22 hybrid combinations was inherited maternally, which supported the conclusions of the study of plasmid cytology. The mtDNA fragments amplified by PCR were consistent with the restriction maps in all hybrid combinations and no polymorphism was detected, indicating that the Section Leuce is highly conserved in mitochondrial gene sequences. These results provided direct evidence of maternal chloroplast inheritance in Populus tomentosa, P. bolleana, P. davidiana, P. adenopoda, P. tomentosa × P. bolleana, P. alba × P. glandulosa and P. alba × P. tomentosa.     

31个种源东部白松SRAP指纹图谱分析

采用8对SRAP引物对加拿大31个种源的东部白松进行分析,获得104个扩增位点,多态性位点79个,平均多态性水平76%,每对引物产生等位基因7～22个,条带分布100～1 000 bp。各种源相互间相似系数为0.653 8～0.951 9,平均0.830 5。引物组合ME1-EM6与ME7-EM7可将31个种源区分开。     

适合RAPD分析的三种玉米基因组DNA提取方法比较

本文通过对3种玉米基因组DNA提取方法的比较得出，DNA提取时采用一次氯仿／异戊醇抽提方法，得到的DNA质和量都较为理想，并且能够达到RAPD实验的要求。     

Vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping

The sequence‐specific amplification polymorphism (S‐SAP) method, derived from the amplified fragment length polymorphism (AFLP) technique, produces amplified fragments containing retrotransposon long terminal repeat ( LTR ) sequence at one end and a host restriction site at the other. The development and application of this procedure to the LTR of the Vine‐1 element from grapevine is reported. Two primers derived from one of the LTR sequences flanking the retrotransposon were used in combination with MseI degenerated primers on 15 grapevine accessions. S‐SAP results were compared with AFLP data. The heterozygosity and gene diversity values were higher for S‐SAP than for the AFLP procedure. Results show that S‐SAP amplification is effective in identifying polymorphisms and defining genetic distances among cultivars, and could be used for fingerprinting and for ‘Traminer’ clone identification. To the contrary Vine‐1 retrotransposon‐based S‐SAP was not able to distinguish ‘Pinot’ clones.     

直接扩增甜瓜小卫星DNA指纹图谱

以小卫星DNA YNZ22核心序列为引物,甜瓜DNA为模板,在甜瓜上研究了直接扩增小卫星DNA(DAMD)的优化反应体系,结果表明:在20μL的反应体系中,5种主要成分Taq DNA聚合酶、Mg2 、引物、模板DNA和dNTPs的最适浓度分别为1U,2.5 mmol/L,0.5 mmol/L,30 ng,5 mmol/L。在优化的DAMD-PCR反应体系下,利用该引物在28个甜瓜品种上构建了直接扩增小卫星DNA(DAMD)的指纹图谱,分析结果表明,该引物在28个甜瓜品种上共扩增出13位点,其中9位点具有多态性,多态性条带比率为69%,可一次性从28个甜瓜品种中鉴别出其中的21个,鉴别率高达75%。     

Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP,ISSR and SSR markers

Molecular markers provide novel tools to differentiate between the various grades of Basmati rice, maintain fair-trade practices and to determine its relationship with other rice groups in Oryza sativa. We have evaluated the genetic diversity and patterns of relationships among the 18 rice genotypes representative of the traditional Basmati, cross-bred Basmati and non-Basmati (indica and japonica) rice varieties using AFLP, ISSR and SSR markers. All the three marker systems generated higher levels of polymorphism and could distinguish between all the 18 rice cultivars. The minimum number of assay-units per system needed to distinguish between all the cultivars was one for AFLP, two for ISSR and five for SSR. A total of 171 (110 polymorphic), 240 (188 polymorphic) and 160 (159 polymorphic) bands were detected using five primer combinations of AFLP, 25 UBC ISSR primers and 30 well distributed, mapped SSR markers, respectively. The salient features of AFLP, ISSR and SSR marker data analyzed using clustering algorithms, principal component analysis, Mantel test and AMOVA analysis are as given below: (i) the two traditional Basmati rice varieties were genetically distinct from indica and japonica rice varieties and invariably formed a separate cluster, (ii) the six Basmati varieties developed from various indica × Basmati rice crosses and backcrosses were grouped variably depending upon the marker system employed; CSR30 and Super being more closer to traditional Basmati followed by HKR228, Kasturi, Pusa Basmati 1 and Sabarmati, (iii) AFLP, ISSR and SSR marker data-sets showed moderate levels of positive correlation (Mantel test, r = 0.42–0.50), and (iv) the partitioning of the variance among and within rice groups (traditional Basmati, cross-bred Basmati, indica and japonica) using AMOVA showed greater variation among than within groups using SSR data-set, while reverse was true for both ISSR and AFLP data-sets. The study emphasizes the need for using a combination of different marker systems for a comprehensive genetic analysis of Basmati rice germplasm. The high-level polymorphism generated by SSR, ISSR and AFLP assays described in this study shall provide novel markers to differentiate between traditional Basmati rice supplies from cheaper cross-bred Basmati and long-grain non-Basmati varieties at commercial level.The first two authors have equal contribution     

Genetic variability measures among Bromus catharticus Vahl. populations and cultivars with RAPD and AFLP markers

The objectives of this study were to optimize RAPD and AFLP techniques in B. catharticus, and to determine the genetic variability of populations and commercial prairie grass cultivars with the aforementioned molecular markers. Two populations with contrasting morphological characteristics were evaluated from individual and bulked DNA samples using RAPD markers. Both analyses showed a similar information about inter population variability. Each accession was sampled by a single leaf bulk of 10 plants. Accession similarities were established with 276 RAPD and 714 AFLP bands using Jaccard similarity coefficient. The dendrogram of the accessions using RAPD markers showed that they shared high similarity values (>94%). A similar result was obtained with AFLP markers (similarity values >98%), revealing a narrow genetic basis in the analyzed accessions. Consequently, molecular characterization of germplasm should be considered in addition to morphological criteria, to choose the parental genotypes for breeding programs of this forage crop. The AFLP technique was more efficient to detect DNA polymorphism in our experiments and unique fingerprints were detected for all the accessions. RAPD is a simple and non expensive technique, suitable to estimate genetic similarity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Avoiding Obstacle Planning for Robots on Molecular Optimization Algorithm

Interest in DNA computing has increased overwhelmingly since Adleman successfully demonstrated its capability to solve Hamiltonian Path Problem. This article introduces the improving method in virtue of the biological thery of DNA technology, a new molecular algorithm is advanced. After a numerical simulation, the result shows that it avoids the prematurely and lower convergent speed of the classic genetic algorithm, and inherits global search capability, the validity and the speed of the genetic algorithm have been increased. The best result can be obtained in few iterative times. It is fit for solving path planning problem.