RAPD polymorphism of wild emmer wheat populations, Triticum dicoccoides, in Israel

 Genetic diversity in random amplified polymorphic DNAs (RAPDs) was studied in 110 genotypes of the tetraploid wild progenitor of wheat, Triticum dicoccoides, from 11 populations sampled in Israel and Turkey. Our results show high level of diversity of RAPD markers in wild wheat populations in Israel. The ten primers used in this study amplified 59 scorable RAPD loci of which 48 (81.4%) were polymorphic and 11 monomorphic. RAPD analysis was found to be highly effective in distinguishing genotypes of T. dicoccoides originating from diverse ecogeographical sites in Israel and Turkey, with 95.5% of the 100 genotypes correctly classified into sites of origin by discriminant analysis based on RAPD genotyping. However, interpopulation genetic distances showed no association with geographic distance between the population sites of origin, negating a simple isolation by distance model. Spatial autocorrelation of RAPD frequencies suggests that migration is not influential. Our present RAPD results are non-random and in agreement with the previously obtained allozyme patterns, although the genetic diversity values obtained with RAPDs are much higher than the allozyme values. Significant correlates of RAPD markers with various climatic and soil factors suggest that, as in the case of allozymes, natural selection causes adaptive RAPD ecogeographical differentiation. The results obtained suggest that RAPD markers are useful for the estimation of genetic diversity in wild material of T. dicoccoides and the identification of suitable parents for the development of mapping populations for the tagging of agronomically important traits derived from T. dicoccoides. Received: 13 July 1998 / Accepted: 13 August 1998     

Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints

The relevance of using dominant random amplified polymorphic DNA (RAPD) fingerprints for estimating population differentiation was investigated when typically small population sample sizes were used. Haploid sexual tissues were first used to determine genotypes at RAPD loci for 75 eastern white pines ( Pinus strobus L.) representing five populations. Dominant RAPD fingerprints were then inferred from genotypic data for each individual at each locus, and gene diversity estimates from both sources of data were compared. Genotypic information at RAPD loci indicated little or no differentiation among populations, similar to allozyme loci. However, estimates of population differentiation derived from dominant RAPD fingerprints according to various common methods of analysis were generally inflated, especially when all fragments were considered. Simulations showed that an increase in loci sampling and population sample sizes did not significantly alleviate the biases observed.     

Qualitative and quantitative characterization of RAPD variation among snap bean (Phaseolus vulgaris) genotypes

Ten snap bean (Phaseolus vulgaris) genotypes were screened for polymorphism with 400 RAPD (random amplified polymorphic DNA) primers. Polymorphic RAPDs were scored and classified into three categories based on ethidium bromide staining intensity. An average of 5.19 RAPD bands were scored per primer for the 364 primers that gave scorable amplification products. An average of 2.15 polymorphic RAPDs were detected per primer. The results show that primer screening may reduce the number of RAPD reactions required for the analysis of genetic relationships among snap-bean genotypes by over 60%. Based on the analysis of the distribution of RAPD amplification, the same number of polymorphic RAPDs were amplified from different genotypes for all RAPD band intensity levels. A comparison of RAPD band amplification frequency among genotypes for the three categories of bands classified by amplification strength revealed a measurable difference in the frequencies of RAPDs classified as faint (weakly amplifying) compared to RAPD bands classified as bold (strongly amplifying) indicating a possible scoring error due to the underscoring of faint bands. Correlation analysis showed that RAPD bands amplified by the same primer are not more closely correlated then RAPD bands amplified by different primers but are more highly correlated then expected by chance. Pairwise comparisons of RAPD bands indicate that the distribution of RAPD amplification among genotypes will be a useful criterion for establishing RAPD band identity. For the average pairwise comparison of genotypes, 50% of primers tested and 15.8% of all scored RAPDs detected polymorphism. Based on RAPD data Nei's average gene diversity at a locus was 0.158 based on all scorable RAPD bands and 0.388 if only polymorphic RAPD loci were considered. RAPD-derived 1 relationships among genotypes are reported for the ten genotypes included in this study. The data presented here demonstrate that many informative, polymorphic RAPDs can be found among snap bean cultivars. These RAPDs may be useful for the unique identification of bean varieties, the organization of bean germplasm, and applications of molecular markers to bean breeding.     

65份野生油茶种质遗传多样性的ISSR和RAPD标记分析

利用ISSR和RAPD标记,对名邛台地野生油茶种质进行遗传多样性分析。从60条简单重复序列引物中筛选出16条引物,在65份样品中共扩增出213条带,其中多态位点为203个,多态位点百分率为95.31%;从30条寡居核苷酸引物中筛选出8条引物,共扩增出105条带,其中多态性位点94个,多态位点百分率为89.52%。结果表明:名邛台地野生油茶种质具有较丰富的遗传多样性,ISSR和RAPD标记可以应用于油茶种质遗传多样性分析。     

Diversity Among a Heterodera glycines Field Isolate and Derived Inbreds Based on RAPD Analysis and Reproduction on Soybean Genotypes

A field population of Heterodera glycines was inbred by a combination of controlled male-female matings and inoculation of soybean with second-stage juveniles (J2) from single cysts. The initial and four F₆ inbred populations were subjected to random amplified polymorphic DNA analysis and were also tested for their ability to reproduce on race differentials. The RAPD patterns of the inbred populations had a lower number of total bands and a lower percentage of polymorphic bands among individual cysts than the initial population. The estimated number of polymorphic loci detected by RAPD analysis was about 25% for the initial population and 4% to 7% for the inbred lines. Reproduction of H. glycines decreased for 6 of 24 inbred-soybean combinations. In particular, reproduction of three inbred populations on PI 90763 was greatly reduced. Inbreeding did not decrease variance of cyst number on soybean genotypes. The inbreeding coefficient calculated from RAPD data was greater than that derived from the known inbreeding pedigree.     

濒危植物资源冷杉遗传多样性研究

资源冷杉(Abies ziyuanensis)属松科(Pinaceae)冷杉属(Abies),是国家一级保护的濒危植物。利用RAPD分子标记对分布于广西资源县银竹老山和湖南省炎陵县大院的2个资源冷杉种群共54株进行了遗传多样性分析。用20个随机引物共扩增到126个位点,其中66个位点是多态性的,总的多态位点百分率为52.4％,在两个种群分别为33.6％和31。2％。Nei's基因多样性为0.312,Shannon信息指数为0.475,两个种群的遗传分化系数Gst为0.455。基于Nei's遗传距离进行了UPGMA聚类分析,结果两种群的样品彼此明显区分开来。分析结果表明资源冷杉种群内的遗传多样性较低,但两种群间的遗传分化明显。需要同时重视两分布地的资源冷杉的保护工作。     

长筒石蒜居群遗传多样性RAPD分析

利用RAPD标记对长筒石蒜3个居群的遗传多样性及分化程度进行了研究。12条随机引物扩增出94个可分析位点,多态位点比率(PPB)为65.96%,表明长筒石蒜具有比较高的遗传多样性。经POP-GENE32分析表明:Nei’s基因多样性指数(h)为0.1897,香农多样性指数(Ⅰ)为0.2945,基因分化系数(GST)为0.1191,基因流(Nm)为3.6980。经WINAMOVA分析表明:居群内遗传变异占71.75%,而居群间只占28.25%。遗传多样性分析表明,各居群的遗传多样性水平由高到低为琅琊山居群>宝华山居群>盱眙居群。遗传分化表明:长筒石蒜各居群间遗传分化程度较低;大部分遗传变异存在于居群内部,表明其具有较强的进化潜力,自然情况下不会处于濒危状态,野生种质资源的破坏,主要来自于人为干扰。     

我国部分金莲花种质资源遗传多样性的RAPD研究

用RAPD标记对来自不同产地的24份金莲花种质从分子水平开展遗传多样性研究,为综舍评价我国金莲花资源现状及植物资源的合理保护提供参考。结果显示,30条RAPD引物共扩增获得194条清晰可辨条带,其中多态性条带108条,多态性位点百分率为55．67％,金莲花总多样性指数为0．1460,居群内遗传多样性为0．0591,Shannon’s多样性指数为0．2248;通过UPGMA进行聚类分析,将24份金莲花种质划分为3个大类,根据总遗传多样性和居群内遗传多样性计算不同居群间遗传分化系数为0．6902,基因流估计平均值为0．2244。研究结果表明,目前我国金莲花种质资源的遗传多样性指教偏低,应该尽快采取相应措施,对不同金莲花资源进行合理保护。     

Identification and Characterization of Malaysian River Catfish, Mystus nemurus (C&V): RAPD and AFLP Analysis

This work represents the first application of the amplified fragment length polymorphism (AFLP) technique and the random amplified polymorphic DNA (RAPD) technique in the study of genetic variation within and among five geographical populations of M. nemurus. Four AFLP primer combinations and nine RAPD primers detected a total of 158 and 42 polymorphic markers, respectively. The results of AFLP and RAPD analysis provide similar conclusions as far as the population clustering analysis is concerned. The Sarawak population, which is located on Borneo Island, clustered by itself and was thus isolated from the rest of the populations located in Peninsular Malaysia. Both marker systems revealed high genetic variability within the Universiti Putra Malaysia (UPM) and Sarawak populations. Three subgroups each from the Kedah, Perak, and Sarawak populations were detected by AFLP but not by RAPD. Unique AFLP fingerprints were also observed in some unusual genotypes sampled in Sarawak. This indicates that AFLP may be a more efficient marker system than RAPD for identifying genotypes within populations.     

Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes

Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars. Fifty-six polymorphic RFLP bands and 181 polymorphic RAPD bands were generated using 15 random cDNA probes and 62 10-mer primers, respectively. The objectives were to compare RFLP and RAPD markers with regard to their (1) sampling variance, (2) rank correlations of genetic distance among sub-samples, and (3) inheritance. A bootstrap procedure was used to generate 200 random samples of size n (n=2,3,5,... 55) independently from the RAPD and RFLP data sets. The coefficient of variance (CV) was estimated for each sample. Pooled regressions of the coefficient of variance on bootstrap sample size indicated that the rate of decrease in CV with increasing sample size was the same for RFLPs and RAPDs. The rank correlation between the Nei-Li genetic similarity values for all pairs of genotypes (990) based on RFLP and RAPD data was 0.745. Differences were observed between the RFLP and RAPD dendrograms of the 45 genotypes. Overlap in the distributions of rank correlations between independent sub-samples from the RAPD data set, compared to correlations between RFLP and RAPD sub-samples, suggest that observed differences in estimation of genetic similarity between RAPDs and RFLPs is largely due to sampling error rather than due to DNA-based differences in how RAPDs and RFLPs reveal polymorphisms. A crossing algorithm was used to generate hypothetical banding patterns of hybrids based on the genotypes of the parents. The results of this study indicate that RAPDs provide a level of resolution equivalent to RFLPs for detemination of the genetic relationships among genotypes.     

Genetic variation of ticks (Ixodes ricinus L.) in the Lithuanian and Norwegian populations

RAPD markers were used to measure the genetic diversity of 119 individuals of Ixodes ricinus collected from Lithuania and Norway. The samples were analysed within and also between the populations. We analysed 74 loci in each of 6 populations. Our results show high levels of diversity within the populations. The percentage of polymorphic loci of the six analysed populations: Birzai, Vilnius, Kretinga, Tjore, Kjosvik and Odderoya were 68.9%, 58.1%, 78.38%, 62.2%, 44.6% and 68.9%, respectively. The percentage of polymorphic loci in the Lithuanian populations was 93.2%, and in the Norwegian populations 81.08%. The genetic distance ranged from 0.019 to 0.079 within Norwegian populations and from 0.005 to 0.0967 within Lithuanian populations and between the countries from 0.022 to 0.146. The genetic variation of I. ricinus among Norwegian populations was lower than among Lithuanian populations. The highest part of genetic variation in I. ricinus ticks depends on variation within Kretinga (Lithuania) and Odderoya (Norway) populations situated in coastal areas where many migratory and sea birds are aggregated.     

内蒙古典型草原羊草种群遗传分化的RAPD分析

运用 RAPD技术对内蒙古典型草原不同生境 8个羊草种群进行分析。采用 2 4个随机引物 (10 nt)在 8个种群中共检测到2 2 4个扩增片断 ,其中多态性片断 173个 ,总的多态位点百分率达 77.2 % ,特异性片断 2 2个 ,占 9.82 % ,平均每个引物扩增的DNA带数为 9.3 3条。利用 Nei指数和 Shannon指数估算了 8个种群的遗传多样性 ,并计算种群相似系数和遗传距离 ,运用UPGMA法进行聚类分析。结果表明 :羊草大部分的遗传变异存在于种群内 ,只有少部分的遗传变异存在于种群间 ,Nei指数和Shannon指数计算结果分别为 85.4%和 66.8% ;羊草不同种群的遗传多样性存在差异 ;8个羊草种群平均遗传距离为 0 .2 3 16,变异范围为 0 .1587～ 0 .2 70 0 ,说明 8个羊草种群间的遗传变异不大 ,即 :在较小地理范围内羊草的遗传分化程度较小 ;8个种群可聚为 3个类群 ,聚类结果显示生境相似的种群能够聚在一起 ,而地理距离最近的种群不一定归为一类 ,说明小范围内羊草种群间的遗传分化与地理距离不存在相关性 ,而与其生境间的相似度相关。影响遗传相似性的不是单一因子而是各种因子的综合作用 ,较小地理范围内羊草种群间的遗传分化主要是由环境的异质性所引起的     

Genetic and biochemical differentiation in Vitis vinifera (Kabarcik) populations grown at different altitudes in Coruh Valley

We examined genetic differences of four Vitis vinifera populations (A, B, C, D) including local Kabarcik cultivar grown along an altitude gradient of 800, 900, 1000, and 1150 m above sea level in the Coruh Valley (800 m: A population; 900 m: B population; 1000 m: C population; 1150 m: D population). Leaf samples were used for both RAPD and fatty acid analysis. A total of 60 individuals with 15 individuals per population were included in this study. RAPD analyses showed various band sizes, which ranged from 250 to 3000 bp. Mean polymorphic locus ratios were determined as 96.29% considering four populations. The highest percentage of polymorphic loci (97.8%) was produced by the highest altitude. Thirty-two different fatty acids were found; linoleic acid was the most common in all four populations. According to the dendograms obtained from statistical analyses of RAPD and fatty acid profiles the populations that were close to each other in terms of geographical distance also were similar genetically.     

Comparison of multivariate methods for the analysis of genetic resources and adaptation in Phytolacca dodecandra using RAPD

The extent of genetic differentiation among 17 Ethiopian populations (249 individuals) of Phytolacca dodecandra (Endod) sampled along altitudinal gradients that varied from 1600 to 3000 m was investigated using random amplified polymorphic DNA (RAPD). The populations were classified into three altitude groups: lowland (1600–2100 m), central-highland (2101–2500 m) and highland (2500–3000 m). Seventy polymorphic loci scored from 12 RAPD primers, singly or in combination with ecogeographical variables (altitude, longitude, latitude, temperature and rainfall), were used for principal component, discriminant, correlation, and stepwise multiple regression analyses. Principal component analysis (PCA) clearly differentiated lowland and the central-highland populations from those of the highlands independent of their geographical regions. Canonical discriminant analysis separated the lowland plants from those of the highlands with the central-highland plants being intermediate. Classificatory discriminant analysis corrected classification of 92.8% of the 249 plants into their respective three altitude groups. Multiple regression analysis identified a strong association between some RAPDs and altitude, temperature and rainfall, while the variation in most RAPDs was explained by combinations of the different ecogeographical variables. It is hypothesised that the different altitude groups may be (1) chemical and/or physiological ecotypes produced as a result of complex interactions of altitude with climatic and/or edaphic factors, or (2) different in ploidy levels. The significant correlations obtained between population means from some RAPDs and altitude and temperature as well as the strong association of some RAPDs with the ecogeographical variables in the multiple regression analysis suggest that part of the RAPD polymorphism could be adaptive, and responsive to environmental selection. Received: 15 December 1999 / Accepted: 12 February 2000     

Genetic differentiation among common and selected hatchery populations of flounder: Evidence from RAPD markers

Randomly amplified polymorphism DNA (RAPD) analysis was performed in order to evaluate one common population and two selected hatchery populations of flounder Paralichthys olivaceus. A total of 90 individuals belonging to three populations were screened using 12 different RAPD primers. A total of 71 loci were produced in the three studied populations, and 43.5%, 42.4% and 42.2% of these loci were polymorphic over all the genotypes tested in common, susceptible and resistant populations, respectively. The number of loci detected by single primers ranged from four to eight. The average heterozygosites of common, susceptible and resistant populations were 0.112, 0.103 and 0.111, respectively. Compared with the common population, the two selected hatchery populations, susceptible and resistant, showed some genetic differences including a smaller number of loci, a smaller number of polymorphic loci, a smaller number of genotypes and a smaller Shannon index. The present study confirmed that it is important to detect the genetic variability of the selected hatchery population for the conservation of natural flounder resources.     

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     

Inheritance of random amplified polymorphic DNA (RAPD-PCR) markers and their use in population genetic studies of Calomys musculinus (Rodentia,Muridae), the reservoir of Argentine hemorrhagic fever

In order to assess the reliability of RAPD markers in the estimation of the genetic structure of natural populations of the murid rodent Calomys musculinus (reservoir of Junin virus, ethiological agent of Argentine Hemorrhagic Fever), we have analyzed the heritability of RAPD bands in 10 parents and their offspring (33 individuals). Fourteen out of a total of 119 bands obtained were absent in the parental patterns, but consistently amplified in offspring from some families. These bands can be eliminated from analyses. Overall degree of band sharing between individuals, including non-parental bands, correctly grouped members of a family in the same cluster in a UPGMA tree, with a high bootstrap percentage. Results support the usefulness of RAPDs as hereditable markers. One hundred polymorphic RAPD loci were identified in three natural populations of C. musculinus. Mean expected heterozygosity in three natural populations ranged from 0.206 to 0.220. Allele frequency based and phenotype based measures of genetic differentiation among natural populations of C. musculinus gave similar results (Weir and Cockerham's theta = 0.133; Excoffier et al.'s phi = 0.127). These values were considerably higher than those found previously using allozymes as genetic markers, and are compatible with moderate to low levels of gene flow among populations.     

羊草种群遗传分化的RAPD分析I：扩增片段频率的变化

松嫩草原上分布着灰绿型和黄绿型两种叶色类型的羊草,为进一步明确这两种叶色类型种群分化的分子基础 ,对其9个种群105个个体进行了RAPD分析。15个随机引物（10nt)共扩增出149个多态性片段,总的多态位点为96．1％,黄绿型与灰绿型种群间在10．1％的多态性片段上明显不同,相似生境或同一地域的种群在一些位点上表现出相似或相同的变化;9个种群都检测到了特异性扩增。     

菜薹种质内不同大小群体问遗传多样性的RAPD鉴定和比较

为了了解菜薹种质内的遗传多样性,确定适宜的更新群体,从一份菜薹地方品种的200株群体中随机抽取10、15、20、25、30、35和．40株组成不同的群体,利用RAPD技术分析各自的多态位点数、计算多态位点百分率、遗传多样性指数和缺失位点数。通过对各参数的比较结果表明,该种质内单株间的遗传差异较大,大于30株的群体能代表200株群体的遗传多样性。在满足其完全随机交配的前提下,可视为更新的有效群体。根据更新时繁种群体应为有效群体2倍的原则,认为不小于60株的群体为菜薹种质更新比较适宜的群体。