Genetic Diversity in Grapevine Germplasm Resources in the Coruh Valley Revealed by RAPD Markers

Random amplified polymorphic DNA analysis was carried out in 35 autochthonous table grapevine cultivars grown in Coruh valley. Fifty-five oligonucleotide primers were screened on cultivars, and among them, 12 primers showed clear polymorphic patterns. PCR amplification with 12 primers generated a total of 157 polymorphic bands. There was genetic variation among the cultivars with values of genetic diversity ranging from 0.19 to 0.72 using the Jaccard coefficient. UPGMA analysis of the distance matrix resulted in a dendrogram with two main clusters. The first cluster included 28 cultivars and the second 7 cultivars. The greatest genetic similarity was observed between cultivars Gah and Kolik, while the greatest dissimilarity was observed between cultivars Gah and Siyah Kus Uzumu. The dendrogram revealed that the cultivars present in Coruh valley can be distinguished to a relatively high degree.     

利用RAPD 标记技术对白桦种源遗传变异的分析及种源区划

用随机扩增多态DNA(RAPD)分子标记方法对白桦17 个种源152 个个体进行了遗传变异的比较分析, 通过14 个随机引物扩增共检测到233 个位点, 各种源多态位点百分率差异明显, 范围在20.17%~32.19%之间, 多态位点百分率最高的是帽儿山种源和清源种源, 最低的是绰尔种源。遗传变异在种源间占43.53%, 在种源内个体间占56.47%。根据种源间的遗传距离, 构建了白桦17 个种源的遗传关系聚类图, 结果将东北地区的白桦聚为一类, 华北、西北地区的白桦聚为另一类。同时根据地理气候因子和遗传距离对白桦群体进行了种源区的划分。     

Organisation of the variability of abundant proteins in seven geographical origins of maritime pine (Pinus pinaster Ait.)

The comparison of 42 two-dimensional protein patterns from megagametophytes of maritime pine from seven geographical origins enabled the analysis of the genetic variability of abundant proteins. More than 84% of the polypeptides were variable. The intra- and inter-origin variability levels were of a similar magnitude. Correspondence analysis and a dendrogram computed using a dissimilarity index between individuals showed three main groups. The first group included the individuals from Landes (France), Portugal, eastern Spain, and Corsica, without individualising the provenances. The second group was composed of accessions from Italy and Sardinia, and the individuals of each location were separated. The third group included all of the individuals of Moroccan origin. This clustering was in agreement with the Atlantic, Mediterranean and North African structuration of maritime pine established from terpene data.     

Allozyme variation in 16 natural populations of Faidherbia albida (Del.) A. Chev

The objectives of this study were (1) to investigate the genetic variability; and (2) to determine the phylogenetic relationship in the leguminous tree Faidherbia albida through out its range of distribution in East, West and Southern Africa. A total of 16 populations were subjected to enzyme electrophoresis and 6 enzyme systems (Adh, Mdh, G6pdh, Idh, 6Pgdh, and alpha-Est) encoded by 12 loci were scored. A total of fifty one different alleles were detected, with an average of 2.5 alleles per locus. Forty three percent of the loci were polymorphic at a 95% criterion. The average expected heterozygosity (gene diversity index H(e)) was 0.141. All provenances showed significant deviation from Hardy-Weinberg expectation. The UPGMA cluster analysis, based on Modified Rogers distance revealed close similarities between Eastern and Southern African provenances, except Debre zeit from Ethiopia, which was closest to West African populations than to the East African populations. Also, Bignona from West Africa was peculiarly closer to East African provenances. Differentiation of West African populations from Eastern and Southern African provenances was quite evident, emphasising the clinical pattern of variation in these two major geographical races of F. albida in Africa. Wright's F-statistics showed an overall significant deficit of heterozygotes, a common feature in mixed mating, entomophilous, widespread species such as F. albida. The dendrogram analysis showed wide separation among the three Ethiopian provenances indicating a high level of genetic differentiation and diversity among them.     

Genetic relationships between seven Spanish native breeds of cattle

Summary. Ten genetic markers were studied in seven Spanish native cattle breeds, using a total of 725 animals. Of the ten, two were found to be monomorphic in all seven breeds. The genetic relationships of the seven breeds are estimated by three different genetic-statistical methods (genetic distances, main coordinate analysis and cluster analysis), which indicate three clearly distinct groups of populations: one where the Cárdena Andaluza and Alistana Sanabresa are very closely related, one comprising Sayaguesa, Morucha, Asturiana de los Valles and Asturiana de la Montaña cattle, and a third, genetically distant from the other two, comprising only Blanca Cacereña. The dendrogram drawn from the genetic distances matrix would seem to imply that the seven breeds are descended from different ancestors.     

Joint analysis of phenotypic and molecular diversity provides new insights on the genetic variability of the Brazilian physic nut germplasm bank

The genetic variability of the Brazilian physic nut (Jatropha curcas) germplasm bank (117 accessions) was assessed using a combination of phenotypic and molecular data. The joint dissimilarity matrix showed moderate correlation with the original matrices of phenotypic and molecular data. However, the correlation between the phenotypic dissimilarity matrix and the genotypic dissimilarity matrix was low. This finding indicated that molecular markers (RAPD and SSR) did not adequately sample the genomic regions that were relevant for phenotypic differentiation of the accessions. The dissimilarity values of the joint dissimilarity matrix were used to measure phenotypic + molecular diversity. This diversity varied from 0 to 1.29 among the 117 accessions, with an average dissimilarity among genotypes of 0.51. Joint analysis of phenotypic and molecular diversity indicated that the genetic diversity of the physic nut germplasm was 156% and 64% higher than the diversity estimated from phenotypic and molecular data, respectively. These results show that Jatropha genetic variability in Brazil is not as limited as previously thought.     

Study of genetic variation among parsley (<Emphasis Type="Italic">Petroselinum Crispum</Emphasis> (Mill.) Nym.) samples using RAPD and ISSR markers

RAPD and ISSR markers have been used to classify 32 samples of parsley (Petroselinum Crispum (Mill.) Nym. ex A. W. Hill) including the root and leaf plants. In total, 51 RAPD and 66 ISSR markers were amplified by five RAPD and six ISSR primers. On average, the ISSR and RAPD spectra had 11 and 10.2 bands, respectively. The matrix of genetic distances between the samples was constructed using Jaccard coefficients. The dendrogram constructed by the UPGMA method graphically shows the values of genetic distances. The distance between root and leaf forms of parsley was 0.292.     

Structure and Genetic Relationship Among Brazilian Naturalized and Imported Goat Breeds

Fourteen goat populations were studied regarding their genetic relationship and structure. Parameters of genetic diversity (HT, HS and GST) and F statistic (FIS, FIT and FST) were estimated. Undefined breed populations presented high homogeneity, as did imported breed populations. Naturalized breed populations showed high differentiation. The genetic distances separating these 14 goat populations were calculated from gene frequency data for eight blood genetic markers (esterase D, phosphoglucomutase 1, carbonic anhydrase II, peptidase B, amylase, haemoglobin, transferrin, and protein X). Working with the genetic distance matrix of Nei corrected for small samples (DA), we constructed a dendrogram using the unweighted pair group method with arithmetic mean. DA values ranged from 0.0027 to 0.1518. The dendrogram divided the populations into two groups, one consisting of three populations of naturalized breeds, and another including the other populations (imported breeds, undefined breeds and some other naturalized breeds).     

濒危植物猪血木人工繁殖幼苗的遗传多样性及对种群复壮的启示

猪血木为山茶科特有的单型属珍稀濒危植物,目前仅在广东省阳春市八甲镇有分布,且种群数量不足200株,为给濒危植物猪血木的种群成功回归自然和种群复壮提供科学依据,采用AFLP分子技术,对7个种源人工繁殖的猪血木幼苗遗传多样性进行研究。结果表明:6对引物共检测到位点数为115个,其中多态位点数为68个,多态位点所占比率为59.13%,观察等位基因数(Na)为1.5826、有效等位基因数(Ne)为1.3813、Nei′s基因多样性(H)为0.2215、Shannon多样性指数(Ⅰ)为0.3280。UPGMA聚类将7个种源的幼苗划分为3支,不同种源间幼苗的遗传距离与种源地理距离存在显著相关性(P<0.05)。说明不同种源人工繁殖猪血木幼苗仍保持较高的遗传多样性。建议采集不同种源种子进行人工繁殖和人工种群构建,促进物种的种群复壮。     

57株毛头鬼伞遗传多样性分析

运用SRAP、RAPD、ISSR3种分子标记技术对来源不同地区的57株毛头鬼伞Coprinus comatus进行了遗传多样性分析,通过3种分子标记进行聚类分析,当相异系数D为0.48时,可以把57株毛头鬼伞分为4类:Ⅰ类包括Co0001;Ⅱ类包括Co0003;Ⅲ类包括Co0005;Ⅳ类包括其余54个菌种。供试的57个菌株间的相异系数范围从0–0.72,具有一定的遗传多态性。但其中有许多菌株两者之间的相异系数为0,说明毛头鬼伞菌种存在着比较严重的同种异名现象。     

新疆8个绵羊品种遗传多样性和系统发生关系的微卫星分析

为分析新疆北疆地区主要绵羊品种的遗传多样性和系统发生关系,利用10个微卫星标记,采用PCR扩增,12％非变性聚丙烯酰胺凝胶电泳、Sanguinetti银染法显色,对新疆北疆地区8个品种、1个杂交一代绵羊群体遗传多样性进行了检测,统计了各群体的等位基因组成、平均有效等位基因数(E)和平均基因纯合率,利用等位基因频率计算出各群体的平均遗传杂合度(h)、多态信息含量(PIC)和群体间的遗传距离。利用分子进化遗传分析软件,采用邻结法构建系统发生树;同时根据等位基因频率,利用PHYLIP(3．6)分析软件,采用最大似然法构建系统发生树,应用白举检验估计系统树中结点的白引导值,并进行了系统发生分析。结果表明：10个微卫星位点在9个绵羊群体中的多态信息含量除BMI824、MAF65为低、中度多态外,其余8个微卫星均为高度多态,可作为有效的遗传标记用于各绵羊品种的遗传多样性和系统发生关系的分析;所有绵羊群体的平均PIC(0．5631)、h(0．5721)和E(2．9)均低于国外其他品种的绵羊,其基因多态性和遗传多样性相对贫乏;新疆本地土种阿勒泰羊、哈萨克羊和巴什拜羊与国外引进绵羊品种及混有外血的本地培育品种遗传距离较远,他们聚为不同的两类,各绵羊品种的分子系统发生关系与其来源、育成史、分化及地理分布基本一致。     

Genetic diversity of yacon (Smallanthus sonchifolius (Poepp. & Endl.) H. Robinson) and its wild relatives as revealed by ISSR markers

Set of 29 accessions of Smallanthus sonchifolius, an important tuber crop from South America, and its three wild relatives were analysed using the Inter Simple Sequence Repeats (ISSR) markers. Seven primers out of 30 primers screened gave clear and reproducible spectra. The range of amplified bands was from 2500 bp to 300 bp. These seven primers generated in total 77 bands, from which 75 (97.4%) were polymorphic. Nei's genetic distances between samples varied from 0.01 to 0.24. The Shannon's index (I) was estimated as 0.0392. The UPGMA dendrogram created using the Neighbour joining method and based on the Dice's dissimilarity coefficient separated clearly the wild accessions from all S. sonchifolius samples, which remained close to each other, confirming the clonal origin and thus a very low genetic variability within the genus.     

Molecular characterization of sawtooth oak (Quercus acutissima) germplasm based on randomly amplified polymorphic DNA

Sawtooth oak (Quercus acutissima) is a predominant tree species in the deciduous broad-leaved forest in China. It distributes in a large landscape area and can disperse in various ecology types. Molecular study on sawtooth oak can provide valuable information about the genetic diversity level and genetic relatedness on this important tree species. Insight into the genetic structure also provides resources of a species with its current feature and future evolutionary potential. The genetic structure of sawtooth oak was investigated by randomly amplified polymorphic DNA (RAPD). Twelve RAPD markers were used to assess genetic diversity of 408 individuals from 17 provenances enveloping most of the current distribution area of sawtooth oak. A total of 66 amplification products were detected, of which 49 bands (74.24 %) were polymorphic. Nei’s gene diversity, 0.2409, indicated a relatively high level of genetic variation in sawtooth oak germplasm. Analysis of molecular variance showed that most of the genetic diversity (87 %) was allocated within provenances. A combination of UPGMA dendrogram and STRUCTURE analysis was employed to estimate the genetic relationships of sawtooth oak germplasm; interestingly, the two methods presented similar grouping pattern with few discrepancies. Results revealed that 16 out of 17 provenances were clustered into one group, while the other 1 (LQ provenance) constituted a separate cluster. The data presented in this study suggested that the RAPD method was a valuable tool for estimation of genetic diversity and genetic relatedness of sawtooth oak germplasm. The present study also gave useful implications for germplasm conservation and new cultivar development for this promising energy tree species.     

Microsatellite polymorphism in natural populations of wild emmer wheat,Triticum dicoccoides,in Israel

Diversity in 20 microsatellite loci of wild emmer wheat, Triticum dicoccoides, was examined in 15 populations (135 genotypes) representing a wide range of ecological conditions of soil, temperature, and water availability, in Israel and Turkey. An extensive amount of diversity at microsatellite loci was observed despite the predominantly selfing nature of this plant species. The 20 Gatersleben wheat microsatellites (GWM), representing 13 chromosomes of genomes A and B of wheat, revealed a total of 364 alleles, with an average of 18 alleles per GWM marker (range: 5–26). The proportion of polymorphic loci per population averaged 0.90 (range: 0.45– 1.00); genic diversity, He, averaged 0.50 (range 0.094– 0.736); and Shannon’s information index averaged 0.84 (range 0.166–1.307). The coefficients of genetic distance between populations were high and averaged D=1.862 (range 0.876–3.320), an indication of sharp genetic divergence over short distances. Interpopulation genetic distances showed no association with geographic distance between the population sites of origin, which ruled out a simple isolation by distance model. Genetic dissimilarity values between genotypes were used to produce a dendrogram of the relationships among wild wheat populations by the unweighted pair-group method with arithmetic averages (UPGMA). The results showed that all the wild emmer wheat populations could be distinguished. Microsatellite analysis was found to be highly effective in distinguishing genotypes of T. dicoccoides, originating from diverse ecogeographical sites in Israel and Turkey, with 88% of the 135 genotypes correctly classified into sites of origin by discriminant analysis. Our present microsatellite results are non-random and in agreement with the previously obtained allozyme and RAPD patterns, although the genetic-diversity values obtained with microsatellites are much higher. Significant correlates of microsatellite markers with various climatic and soil factors suggest that, as in allozymes and RAPDs, natural selection causes adaptive microsatellite ecogeographical differentiation, not only in coding, but most importantly in non-coding genomic regions. Hence, the concept of ”junk DNA” needs to be replaced by at least partly regulatory DNA. The obtained results suggest that microsatellite markers are useful for the estimation of genetic diversity in natural populations of T. dicoccoides and for the tagging of agronomically important traits derived from wild emmer wheat. Received: 27 February 2001 / Accepted: 22 March 2001     

Comparative analysis of DNA polymorphisms and phylogenetic relationships among Syzygium cumini Skeels based on phenotypic characters and RAPD technique

The Indian black berry (Syzygium cumini Skeels) has a great nutraceutical and medicinal properties. As in other fruit crops, the fruit characteristics are important attributes for differentiation were also determined for different accessions of S. cumini. The fruit weight, length, breadth, length: breadth ratio, pulp weight, pulp content, seed weight and pulp: seed ratio significantly varied in different accessions. Molecular characterization was carried out using PCR based RAPD technique. Out of 80 RAPD primers, only 18 primers produced stable polymorphisms that were used to examine the phylogenetic relationship. A sum of 207 loci were generated out of which 201 loci found polymorphic. The average genetic dissimilarity was 97 per cent among jamun accessions. The phylogenetic relationship was also determined by principal coordinates analysis (PCoA) that explained 46.95 per cent cumulative variance. The two-dimensional PCoA analysis showed grouping of the different accessions that were plotted into four sub-plots, representing clustering of accessions. The UPGMA (r = 0.967) and NJ (r = 0.987) dendrogram constructed based on the dissimilarity matrix revealed a good degree of fit with the cophenetic correlation value. The dendrogram grouped the accessions into three main clusters according to their eco-geographical regions which given useful insight into their phylogenetic relationships.     

Isozyme variation among teak (Tectona grandis L.f.) provenances

Fourteen enzyme systems were analysed in leaf parenchyma of nine native and introduced populations of teak. These enzyme systems were encoded by 20 putative loci of which 18 were polymorphic. Populations showed a general lack of heterozygosity (average F_IS = 0.11). On average over the 18 polymorphic loci, the genetic differentiation among provenances varied according to the estimator: 0.09 for G_ST, 0.12 for F_ST and 0.19 for . The cluster analysis showed two main gene pools, the first consisted of the Indian provenances and the second of African, Indonesian and Thai provenances. Genetic distances among populations of the same group were similar, and lower than the genetic distances between populations from different groups. The factorial analysis on genotypes of seedlings also showed the same geographic differentiation into two major groups. The possible natural distribution of teak in Java is discussed.     

大鳞副泥鳅5个野生群体的遗传多样性分析

利用微卫星分子标记分析了天津地区于桥水库、大黄堡湿地、七里海湿地、团泊水库和潮白新河5个野生大鳞副泥鳅群体的遗传多样性。5个群体在12个微卫星位点共检测到98个等位基因,平均等位基因数为8.500;有效等位基因数为2.713;平均观测杂合度为0.526;平均期望杂合度为0.544。5个群体间的遗传分化指数介于0.021~0.106之间,平均遗传分化指数为0.059,属中低水平的遗传分化。AMOVA分析结果显示,在总的变异中,94.1%的遗传变异来自群体内,5.90%的遗传变异来自于群体间。根据Nei’s遗传距离所绘制的系统树显示,于桥水库、团泊水库、七里海湿地和大黄堡湿地4个群体的遗传距离相对较小聚为一支,潮白新河群体单独为一支。遗传瓶颈效应分析表明,该5个群体近期未经受遗传瓶颈效应,处于突变-漂移平衡。总体来看,天津地区5个野生大鳞副泥鳅群体的遗传多样性较高,可作为品种选育的基础群体。     

Towards a consensus for calculating dendrogram-based functional diversity indices

The widely used FD index of functional diversity is based on the construction of a dendrogram. This index has been the subject of a strong debate concerning the choice of the distance and the clustering method to be used, since the method chosen may greatly affect the FD values obtained. Much of this debate has been centred around which method of dendrogram construction gives a faithful representation of species distribution in multidimensional functional trait space. From artificially generated datasets varying in species richness and correlations between traits, we test whether any single combination of clustering method(s) and distance consistently produces a dendrogram that most closely corresponds to the matrix of functional distances between pairs of species studied. We also test the ability of consensus trees, which incorporate features common to a range of different dendrograms, to summarize distance matrices. Our results show that no combination of clustering method(s) and distance constantly outperforms the others due to the complexity of interactions between correlations of traits, species richness, distance measures and clustering methods. Furthermore, the construction of a consensus tree from a range of dendrograms is often the best solution. Consequently, we recommend testing all combinations of distances and clustering methods (including consensus trees), then selecting the most reliable tree (with the lowest dissimilarity) to estimate FD value. Furthermore we suggest that any index that requires the construction of functional dendrograms potentially benefits from this new approach.     

不同种源太子参的RAPD分析

应用RAPD标记方法分析了15个太子参〔Pseudostellaria heterophylla(Miq.)Pax ex Pax et Hoffm.〕种源间的遗传多样性和亲缘关系。10条随机引物共扩增出65条带,其中多态性条带37条,多态性条带百分率达56.9%。用聚类分析方法可将15个太子参种源分为4类;地理分布越近,太子参种源间的遗传差异越小。来源于安徽宣城的太子参种源遗传变异明显,辽宁凤城的野生太子参与山东地区的太子参栽培种源间的亲缘关系较近,与江苏各地太子参种源的亲缘关系则较远,这些种源均可作为育种材料。自然环境,尤其是生态环境的变化,对太子参的遗传变异有一定的影响。