Biogeography and Genetic Structure in Populations of a Widespread Lichen (Parmelina tiliacea,Parmeliaceae, Ascomycota)

The genetic diversity and population structure of the foliose lichenized fungus Parmelina tiliacea has been analyzed through its geographical range, including samples from Macaronesia (Canary Islands), the Mediterranean, and Eurosiberia. DNA sequences from the nuclear ribosomal internal transcribed spacer, the mitochondrial large subunit ribosomal RNA gene, and the translation elongation factor 1-α were used as molecular markers. The haplotypes of the three markers and the molecular variance analyses of multilocus haplotypes showed the highest diversity in the Canary Islands, while restricted haplotypes occurred at high frequencies in Mediterranean coastal samples. The multilocus haplotypes formed three unevenly distributed clusters (clusters 1-3). In the Canary Islands all the haplotypes were present in a similar proportion, while the coastal Mediterranean sites had almost exclusively haplotypes of cluster 3; cluster 2 predominated in inland Mediterranean sites; and cluster 1 was more abundant in central and northern Europe (Eurosiberian area). The distribution of clusters is partially explained by climatic factors, and its interaction with local spatial structure, but much of the variation remains unexplained. The high frequency of individuals in the Canary Islands with haplotypes shared with other areas suggests that could be a refugium of genetic diversity, and the high frequency of individuals of the Mediterranean coastal sites with restricted haplotypes indicates that gene flow to contiguous areas may be restricted. This is significant for the selection of areas for conservation purposes, as those with most genetic variation may reflect historical factors and biological properties of the species.     

猕猴桃SCoT遗传多样性分析及指纹图谱的构建

利用SCoT标记对32个猕猴桃品种进行了遗传多样性分析。从47个SCoT引物中筛选了11个引物进行PCR扩增,共扩增出185个条带,其中多态性条带180个,多态性比率为97.30%。各引物Nei's基因多样性指数（H）平均为0.238 4,Shannon's信息指数（I）平均为0.377 8。利用UPGMA构建32份猕猴桃种质资源的聚类树状图。在遗传相似系数为0.78处可将32个猕猴桃品种分为5组,聚类结果与形态学分类基本一致。利用4条引物扩增的16个多态性位点构建了32个猕猴桃品种的DNA指纹图谱,可以将32个猕猴桃品种区分并准确鉴定。     

云南三种稻蝗基因组DNA的RAPD多态性分析

应用RAPD技术对采自云南龙陵两交水和腾冲曲石马鹿冲的24头稻蝗进行了基因组DNA多态性分析,10条随机引物共产生129条清晰、稳定的谱带.基于Jaccard相似系数,用Between-groups Linkage法得出的聚类图与基于Nei's遗传距离分别用UPGMA和NJ法构建的分子系统树基本一致:供试的所有稻蝗个体分为3个聚类簇:龙陵两交水的3、7～8号个体与腾冲曲石马鹿冲(海拔1450m)的8个个体聚为一支,龙陵两交水的1、2、4～6号个体聚为另一支,两支相聚后与腾冲曲石马鹿冲(海拔1 550 m)的8个个体聚为一起.形态学鉴定表明:龙陵两交水的3、7～8号个体为日本稻蝗,1、2、4～6号个体为小稻蝗,腾冲曲石马鹿冲(海拔1450 m)的8个个体均为日本稻蝗,腾冲曲石马鹿冲(海拔1550 m)的个体为有待进一步鉴定的未知种.形态学鉴定结果与聚类结果完全吻合,充分展示了RAPD技术在区分近缘物种方面的独到优势.比较不同采集地的日本稻蝗、小稻蝗的RAPD分析结果,发现云南的这两种稻蝗在同物种不同种群中的遗传多样性最为丰富,从一个侧面显示出我国云南昆虫的物种多样性及物种内部丰富的遗传多样性.     

Assessment of genetic relationships among native and introduced Himalayan balsam (Impatiens glandulifera) plants based on genome profiling

We conducted genomic characterization based on SNP and SilicoDArT markers on the invasive Himalayan balsam (Impatiens glandulifera) plants originating from native and non‐native regions of their distribution. When genetic relationships were explored by PCoA using SNP and SilicoDArT marker data, the first, second, and third principal coordinates explained altogether 37.4% and 31.0% of the variability, respectively. Samples from the UK, Canada, and Pakistan were grouped together, while Indian plants were clearly distinct based on SNP markers but relatively close to the UK–Canada–Pakistan group based on SilicoDArT markers. Constructed trees differentiated individuals into clusters resembling the PCoA patterns. The Bayesian BAPS analysis performed for the SNP data revealed that the individuals were distributed in seven clusters, representing samples from each of the four Finnish populations, India, Pakistan, and the combination of the UK and Canada. Similar clustering was visible in the UPGMA tree. The Indian cluster did not display any ancestral gene flow with the others, while the Pakistani cluster showed ancestral gene flow only with the combined UK and Canada cluster. Furthermore, the latter cluster displayed ancestral gene flow with the Finnish populations varying from 0% to 3.1%. The BAPS analyses conducted for the SilicoDArT data differ slightly: The individuals were distributed in nine clusters, and the Indian cluster exhibited ancestral gene flow with the mixed cluster including Canadian, Pakistani, and UK samples, and one Finnish sample. The AMOVA showed that 45% and 26% of variation was present among the I. glandulifera groups/populations and the rest within them based on SNP and SilicoDArT markers, respectively. The Bayesian BAPS analyses and the gene flow networks were the most informative tools for resolving relationships among native and introduced plants. It is notable that the small sample sizes for non‐Finnish plant materials may affect the accuracy of the gene flow and other estimates.     

Taxa distribution and RAPD markers indicate different origin and regional differentiation of hybrids in the invasive Fallopia complex in central-western Europe

Interspecific hybridization can be a driving force for evolutionary processes during plant invasions, by increasing genetic variation and creating novel gene combinations, thereby promoting genetic differentiation among populations of invasive species in the introduced range. We examined regional genetic structure in the invasive Fallopia complex, consisting of F. japonica var. japonica , F.   sachalinensis and their hybrid F.  ×  bohemica , in seven regions in Germany and Switzerland using RAPD analysis and flow cytometry. All individuals identified as F. japonica var . japonica had the same RAPD phenotype, while F. sachalinensis (11 RAPD phenotypes for 11 sampled individuals) and F.  ×  bohemica (24 RAPD phenotypes for 32 sampled individuals) showed high genotypic diversity. Bayesian cluster analysis revealed three distinct genetic clusters. The majority of F . ×  bohemica individuals were assigned to a unique genetic cluster that differed from those of the parental species, while the other F . ×  bohemica individuals had different degrees of admixture to the three genetic clusters. At the regional scale, the occurrence of male-fertile F. sachalinensis coincided with the distribution of F . ×  bohemica plants showing a high percentage of assignment to both parental species, suggesting that they originated from hybridization between the parental species. In contrast, in regions where male-fertile F. sachalinensis were absent, F . ×  bohemica belonged to the non-admixed genetic group, indicating multiple introductions of hybrids or sexual reproduction among hybrids. We also found regional differentiation in the gene pool of F.  ×  bohemica , with individuals within the same region more similar to each other than to individuals from different regions.     

中国13个民族7个Y-STR基因座遗传关系的研究

选择具有高度遗传多态性与稳定性的7个Y-STR位点分析宁夏回族与国内17个群体之间的群体遗传关系。采用Y-STR复合扩增、ABI全自动测序仪测序方法,结合基因扫描和自动分型技术获得150名宁夏回族个体DYS19、DYS389Ⅰ、DYS389Ⅱ、DYS390、DYS391、DYS392和DYS393七个基因座的基因频率,同时还收集国内17个群体这7个基因座的基因频率数据,计算他们间的遗传距离,进行聚类分析。结果显示:宁夏回族与北京汉族、云南汉族、安徽汉族、天津汉族、湖南汉族先聚为一类,然后与福建汉族相聚,最后与其他少数民族相聚,揭示回族与汉族在遗传结构上具有很大的相似性,为回族起源和发展过程中融入了大量汉族血缘的论点提供了遗传学证据。     

从头骨形态学和古DNA探究公元3～4世纪西藏阿里地区人群的来源

中国社会科学院考古研究所和西藏自治区文物保护研究所于2012年至2014年间在西藏阿里地区噶尔县发现了一个古代墓群,称为故如甲木墓地。其中8座墓葬的时代约为公元3-4世纪,相当于中原的汉晋时期。共发现32例个体,对其中保存较好的16例个体（7例男性,9例女性）的头骨进行了形态观察和测量分析。聚类分析结果显示故如甲木古代居民与四川卡莎湖古代居民最接近,相比与陕西、山西、河南等地区古代居民的关系,故如甲木居民与新疆多岗和察吾乎四号墓地的古代居民更为接近。与近现代人群比较,故如甲木与广西壮族和藏族A型的现代居民接近。线粒体DNA的分析结果表明,故如甲木居民的母系来源多元化,大多数为欧亚东部类群,也有少量是欧亚西部类群,他们对中国现代藏族人群以及西藏的其他一些民族具有母系遗传的贡献。     

利用ISSR分子标记检测空间诱导罗汉果DNA突变

为探究太空环境对罗汉果造成的诱变效应,筛选罗汉果新品种培育优异种质,该研究运用ISSR分子标记技术,对28个航天诱变罗汉果及主栽品种进行了全基因组多态性检测和聚类分析。结果表明:从100个ISSR引物中筛选得到17个引物,共扩增出157个条带,其中83条具有多态性,多态条带百分率为52.87%,遗传相似系数范围为0.707~0.987。根据UPGMA聚类图,28个罗汉果样本可以分为3类:聚类Ⅰ为航天种质B6♂和B3♀;聚类Ⅱ为航天种质A1♀、A14、A18♂与主栽品种;聚类Ⅲ中都为航天罗汉果种质。上述结果暗示A1♀、A14、A18♂与其他航天种质已经产生了一定的遗传分化,具有与主栽品种相似的遗传背景,可能获得了有益突变。该研究结果为罗汉果新品种培育和杂交亲本选配提供了科学依据。     

Population genetics of Wolbachia‐infected,parthenogenetic and uninfected,sexual populations of Tetrastichus coeruleus (Hymenoptera: Eulophidae)

Wolbachia are endosymbiotic bacteria known to manipulate the reproduction of their hosts. These manipulations are expected to have consequences on the population genetics of the host, such as heterozygosity levels, genetic diversity and gene flow. The parasitoid wasp Tetrastichus coeruleus has populations that are infected with parthenogenesis‐inducing Wolbachia and populations that are not infected. We studied the population genetics of T. coeruleus between and within Wolbachia‐infected and uninfected populations, using nuclear microsatellites and mitochondrial DNA. We expected reduced genetic diversity in both DNA types in infected populations. However, migration and gene flow could introduce new DNA variants into populations. We therefore paid special attention to individuals with unexpected (genetic) characteristics. Based on nuclear and mitochondrial DNA, two genetic clusters were evident: a thelytokous cluster containing all Wolbachia‐infected, parthenogenetic populations and an arrhenotokous cluster containing all uninfected, sexual populations. Nuclear and mitochondrial DNA did not exhibit concordant patterns of variation, although there was reduced genetic diversity in infected populations for both DNA types. Within the thelytokous cluster, there was nuclear DNA variation, but no mitochondrial DNA variation. This nuclear DNA variation may be explained by occasional sex between infected females and males, by horizontal transmission of Wolbachia, and/or by novel mutations. Several females from thelytokous populations were uninfected and/or heterozygous for microsatellite loci. These unexpected characteristics may be explained by migration, by inefficient transmission of Wolbachia, by horizontal transmission of Wolbachia, and/or by novel mutations. However, migration has not prevented the build‐up of considerable genetic differentiation between thelytokous and arrhenotokous populations.     

Molecular characterization and genetic structure of the Nero Siciliano pig breed

Nero Siciliano is an autochthonous pig breed that is reared mainly in semi-extensive systems in northeastern Sicily. Despite its economic importance and well-appreciated meat products, this breed is currently endangered. Consequently, an analysis of intra-breed variability is a fundamental step in preserving this genetic resource and its breeding system. In this work, we used 25 microsatellite markers to examine the genetic composition of 147 unrelated Nero Siciliano pigs. The total number of alleles detected (249, 9.96 per locus) and the expected heterozygosity (0.708) indicated that this breed had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups into which the sample could be partitioned was nine. Based on the proportion of each individuals genome derived from ancestry, pigs with at least 70% of their genome belonging to one cluster were assigned to that cluster. The cluster size ranged from 7 to 17 (n = 108). Genetic variability in this sub-population was slightly lower than in the whole sample, genetic differentiation among clusters was moderate (F(ST) 0.125) and the F(IS) value was 0.011. NeighborNet and correspondence analysis revealed two clusters as the most divergent. Molecular coancestry analysis confirmed the good within-breed variability and highlighted the clusters that retained the highest genetic diversity.     

Diversity and seasonal changes of uncultured Planctomycetales in river biofilms

Cell counts of planctomycetes showed that there were high levels of these organisms in the summer and low levels in the winter in biofilms grown in situ in two polluted rivers, the Elbe River and the Spittelwasser River. In this study 16S rRNA-based methods were used to investigate if these changes were correlated with changes in the species composition. Planctomycete-specific clone libraries of the 16S rRNA genes found in both rivers showed that there were seven clusters, which were distantly related to the genera Pirellula, Planctomyces, and Gemmata. The majority of the sequences from the Spittelwasser River were affiliated with a cluster related to Pirellula, while the majority of the clones from the Elbe River fell into three clusters related to Planctomyces and one deeply branching cluster related to Pirellula. Some clusters also contained sequences derived from freshwater environments worldwide, and the similarities to our biofilm clones were as high as 99.8%, indicating the presence of globally distributed freshwater clusters of planctomycetes that have not been cultivated yet. Community fingerprints of planctomycete 16S rRNA genes were generated by temperature gradient gel electrophoresis from Elbe River biofilm samples collected monthly for 1 year. Sixteen bands were identified, and for the most part these bands represented organisms related to the genus Planctomyces. The fingerprints showed that there was strong seasonality of most bands and that there were clear differences in the summer and the winter. Thus, seasonal changes in the abundance of Planctomycetales in river biofilms were coupled to shifts in the community composition.     

镜湖萼花臂尾轮虫（Brachionus calyciflorus）种群遗传多样性的季节变化

运用随机扩增多态DNA（RAPD）技术研究了于2005年春季和夏季采自芜湖市镜湖的萼花臂尾轮虫（Brachionus calyciflorus）种群基因组DNA多态性。从44个随机引物中筛选出10个谱带清晰、重复性好的引物。10个引物共检测到76个位点,其中65个位点显多态性,多态位点比例（P）为85.5%。对RAPD扩增结果进行聚类分析,基于遗传距离指数构建了萼花臂尾轮虫的UPGMA和ME系统树。经计算,各克隆平均遗传距离指数为0.5219,春季种群内遗传距离指数（0.4416）大于夏季种群内遗传距离指数（0.4304）;两季节种群间遗传距离指数为0.6010,明显大于季节种群内遗传距离指数。16个克隆分别聚在2个主要簇群中,在UPGMA系统树中,春季种群和夏季种群明显分聚在两个主要支系中;而在ME树中,除了夏季Su2克隆和春季种群聚到一个支系外,其它夏季种群则聚在一个独立支系中。上述结果表明,春季种群和夏季种群在遗传上具有较大的差异;镜湖萼花臂尾轮虫种群存在着明显的季节更替,而Su2克隆可能是春季和夏季种群间的过渡。     

中国桑树选育品种ISSR指纹图谱的构建及遗传多样性分析

利用ISSR标记构建了24个选育桑品种的指纹图谱,用3种独立的方法（特殊的标记;特异的谱带类型;不同引物提供的谱带类型组合）可以有效地鉴别桑树选育品种,证明ISSR标记在桑树品种的鉴别方面是一个有效的工具和方法。17个ISSR引物共扩增出80条带,40条带具有多态性,占50．0％。24份选育桑树品种间平均遗传相似系数、Nei’S基因多样性（gene diversity）和Shannon’S信息指数分别为0．8731,0．1210和0．1942。桑树选育品种间的遗传多样性较低,说明中国选育桑品种间遗传距离较小,亲缘关系较近,。遗传基础较狭窄。UPGMA法聚类和PCA分析都清楚地显示了24个桑树选育品种的亲缘关系,聚类结果与桑树品种的系谱基本一致。     

利用RAPD技术分析实验用比格犬的遗传背景

目的　运用RAPD技术对实验用比格犬 (Beagle)进行遗传背景分析。方法　筛选的 16个RAPD引物对 4 0个样品的分析 ,共得到 93个扩增条带。结果　所有样品的相似系数 80 4 %到 10 0 %间变动 ,平均相似系数为93 2 8% ,聚类分析得到了这些个体的同源树资料。结论　本遗传背景资料可以为以后的比格犬繁育生产和生物医药学的研究应用提供技术指导     

基于ISSR分子标记的叶子花亲缘关系分析和指纹图谱构建

为分析品种遗传多样性和遗传距离并构建品种聚类图和指纹图谱,该研究从DNA模板浓度、引物浓度、退火温度和循环次数等方面优化了叶子花ISSR-PCR反应体系和反应程序,利用11个ISSR引物对131个叶子花品种进行PCR扩增,扩增产物经琼脂糖凝胶电泳检测.结果表明:优化的ISSR-PCR反应体系中DNA模板浓度为0.5 n...     

冬枣×宁梨巨枣的子代SRAP鉴定及遗传多样性分析

应用SRAP分子标记方法对冬枣×宁梨巨枣的子代进行了分子鉴定及遗传多样性分析。采用构建基因池的方法对SRAP分子标记引物进行筛选,从88对引物中筛选出15对多态性好、主带清晰的引物,并对子代进行了真实性鉴定及多态性分析。结果表明:(1)15对引物共产生95个多态性条带,平均每对引物产生6.3个多态性条带,显示了较高的多态性比率。(2)80个子代中44个具有父本特征带,鉴定为真杂种。子代遗传多样性及UPGMA聚类分析表明,子代个体与亲本间的遗传相似系数在0.55~0.98之间,个体差异明显。该研究结果为枣树杂交育种提供了重要的分子证据。     

Essential oil composition and preliminary molecular study of four Hungarian Thymus species

Chemical and genetic differences of twenty taxa belonging to four Thymus species were studied in order to determine whether molecular characters and essential oil components could be used as taxonomic markers and to examine the correlation between them. Plant samples, representing different taxa and geographic regions, were collected from experimentally grown populations. Essential oil samples were analysed by GC/MS and cluster analysis of volatile composition resulted in segregation of thymol chemotypes from sesquiterpenic ones. Thymol was characteristic for all the populations of Thymus glabrescens and T. pannonicus as well as for certain taxa belonging to T. praecox and T. pulegioides. Sesquiterpenes occurred in only two taxa of T. glabrescens, in each sample of T. praecox and in three taxa of T. pulegioides. Plant samples were analysed by random amplified polymorphic DNA (RAPD). The obtained dendrogram revealed high gene diversity. The 13 primers resulted 114 polymorphic RAPD bands, and the average percentage of polymorphism was 80.8%. The RAPD dendogram showed separation neither at interspecific nor at interpopulational levels. Therefore, further specific molecular studies involving more taxa are suggested. Partial correlation have been found between molecular and chemical assessments.     

Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, <Emphasis Type="Italic">Helianthus annuus</Emphasis> L

Crop germplasm collections are valuable resources for ongoing plant breeding efforts. To fully utilize such collections, however, researchers need detailed information about the amount and distribution of genetic diversity present within collections. Here, we report the results of a population genetic analysis of the primary gene pool of sunflower (Helianthus annuus L.) based on a broad sampling of 433 cultivated accessions from North America and Europe, as well as a range-wide collection of 24 wild sunflower populations. Gene diversity across the cultivars was 0.47, as compared with 0.70 in the wilds, indicating that cultivated sunflower harbors roughly two-thirds of the total genetic diversity present in wild sunflower. Population structure analyses revealed that wild sunflower can be subdivided into four genetically distinct population clusters throughout its North American range, whereas the cultivated sunflower gene pool could be split into two main clusters separating restorer lines from the balance of the gene pool. Use of a maximum likelihood method to estimate the contribution of the wild gene pool to the cultivated sunflower germplasm revealed that the bulk of the cultivar diversity is derived from two wild sunflower population genetic clusters that are primarily composed of individuals from the east-central United States, the same general region in which sunflower domestication is believed to have occurred. We also identified a nested subset of accessions that capture as much of the allelic diversity present within the sampled cultivated sunflower germplasm collection as possible. At the high end, a core set of 288 captured nearly 90% of the alleles present in the full set of 433, whereas a core set of just 12 accessions was sufficient to capture nearly 50% of the total allelic diversity present within this sample of cultivated sunflower.     

Genetic diversity of forest arabica coffee (Coffea arabica L.) in Ethiopia as revealed by random amplified polymorphic DNA (RAPD) analysis

Genetic diversity within the forest Coffea arabica L. gene pool in Ethiopia has not been extensively examined with molecular markers. In the present study, a total of 75 polymorphic RAPD bands generated by twelve random primers were used to assess genetic diversity among 144 genotypes representing 16 C. arabica populations. The number of polymorphic bands detected with each primer ranged from 2 to 9 with a mean of 6.25 bands per primer. Banding patterns ranged in percentage polymorphism from 37% to 73% with an overall mean of 56% for the populations analyzed. The amount of genetic variation among populations estimated by Shannon-Weaver diversity index was (H = 0.30). The within population and between populations differentiation values were 0.65 and 0.35, respectively. Genetic differentiations within and between zones of sample collection sites were 0.80 and 0.20, respectively. Within population average similarities estimated by simple matching coefficients ranged from 0.72 to 0.85, with an overall average of 0.78. In the cluster analysis that used individual samples as operational taxonomic units, most of the representatives of the same population failed to cluster before they joined members of other populations. Nevertheless, most of the populations were clustered on the basis of their geographic closeness and an east west differentiation was observed at approximately 75% similarity. The results obtained provide information on how to select sites for in situ conservation of C. arabica germplasm.     

Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites

Two hundred and sixty maize inbred lines, representative of the genetic diversity among essentially all public lines of importance to temperate breeding and many important tropical and subtropical lines, were assayed for polymorphism at 94 microsatellite loci. The 2039 alleles identified served as raw data for estimating genetic structure and diversity. A model-based clustering analysis placed the inbred lines in five clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. A "phylogenetic" tree was constructed to further assess the genetic structure of maize inbreds, showing good agreement with the pedigree information and the cluster analysis. Tropical and subtropical inbreds possess a greater number of alleles and greater gene diversity than their temperate counterparts. The temperate Stiff Stalk lines are on average the most divergent from all other inbred groups. Comparison of diversity in equivalent samples of inbreds and open-pollinated landraces revealed that maize inbreds capture <80% of the alleles in the landraces, suggesting that landraces can provide additional genetic diversity for maize breeding. The contributions of four different segments of the landrace gene pool to each inbred group's gene pool were estimated using a novel likelihood-based model. The estimates are largely consistent with known histories of the inbreds and indicate that tropical highland germplasm is poorly represented in maize inbreds. Core sets of inbreds that capture maximal allelic richness were defined. These or similar core sets can be used for a variety of genetic applications in maize.