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1.
We describe the development and characterization of microsatellite loci from the human oomycete pathogen Pythium insidiosum. Nine of 15 microsatellite loci were shown to be appropriate for population genetic study. All loci were polymorphic with observed heterozygosities ranging from 0.241 to 0.912 and from five to 18 alleles per locus among 65 individuals in Thailand. These markers are being used to ascertain multilocus genotypes for molecular epidemiological and population genetic analyses of this little known human pathogen.  相似文献   

2.
Biodiversity information in available germplasm is very useful for the success of any breeding program. To establish genetic diversity among 44 genotypes of chickpea comprising cultigen, landraces, internationally developed improved lines and wild relatives, genetic distances were evaluated using 19 simple sequence repeat markers with 100 marker loci. Estimation of the number of alleles per locus (n a), the effective allele number (n e), and Wright fixation index F were 6.25, 3.67, and 0.44, respectively. Polymorphism information content values ranged from 0.84 (locus NCPGR6 and TA135) to 0.44 (locus NCPGR7) with an average of 0.68. Dice’s coefficient similarity matrix for studied chickpea genotypes varied from 0.07 to 1.0 indicating a broader genetic base among genotypes studied. The highest similarity, 1.0, was observed between genotypes Sel 96TH11484 and Sel 96TH11485; while, the lowest, 0.07, was observed between genotypes Sel 95TH1716 and Azad. Based on the UPGMA clustering method, all genotypes were clustered in eight groups, which indicated the probable origin and region similarity of landraces and local Iran landraces over the other cultivars and wild species. It also represents a wide diversity among available germplasm. Analysis of molecular variance revealed that 41% of the total variance was due to differences among groups while 59% was due to differences within groups. The results of principal coordinate analysis approximately corresponded to those obtained through cluster analysis. Genetic variation detected in this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs.  相似文献   

3.
Plant clonality may greatly reduce effective population size and influence management strategies of rare and endangered species. We examined genetic diversity and the extent of clonality in four populations of the monotypic herbaceous perennial Japonolirion osense, which is one of the most rare flowering plants in Japan. Allozyme analysis revealed moderate levels of genetic variation, and the proportion of polymorphic loci (P=66.7%) was higher than the value for species with similar life-history traits. With four polymorphic loci, 19 multilocus genotypes were observed among 433 aerial shoot samples and 10 (52%) were found only in single populations. The proportion of distinguishable genotypes (PD=0.10) and Simpson's index of diversity (D=0.52) also exhibited moderate levels of genotypic diversity compared to other clonal plants, with genotype frequencies at Hardy-Weinberg equilibrium. The distributions of genotypes were often localized and they were mostly found within a radius of 5 m. Spatial autocorrelation analysis showed that shoot samples located 4 m apart were expected to be genetically independent. The results suggest that the spatial extent of genets was relatively narrow and thus the clonality was not extensive.  相似文献   

4.
Genetic diversity at variable-number-tandem-repeat (VNTR) loci was examined in the common cattail, Typha latifolia (Typhaceae), using three synthetic DNA probes composed of tandemly repeated “core” sequences (GACA, GATA, and GCAC). The principal objectives of this investigation were to determine whether: (1) the previously reported almost complete lack of polymorphism at allozyme loci in this species was indicative of a reduced amount of genetic diversity at VNTR loci as well; (2) VNTR markers were informative about possible clonal propagation; and (3) significant differences in genetic structure of sampling sites were associated with differences in environmental levels of pollutants at those sites. Previously, widespread sampling across the eastern United States, surveying across ten allozyme loci, has detected only two genotypes, involving a difference at a single locus, among 104 populations. In this study, the amount of genetic diversity detected at VNTR loci: (1) among ramets (N = 40; 40 genotypes detected) collected at ∼8-km intervals along a 320-km transect; (2) among ramets (N = 220; 117 genotypes detected) from five study sites separated by 50–3000 m; and (3) even among ramets within each study site [N = 44 per site; from 13 to 34 genotypes detected per site (270 m2)] exceeds that previously found in those more geographically widespread allozyme surveys. Among the 260 ramets analyzed here, the mean number of bands scored per individual was 48.61 (SD = 2.80). Mean genetic similarity among ramets collected along the 320-km transect was 0.91, which was within the range of mean genetic similarity within the five study sites (range: 0.89–0.95). Among the five study sites, 61% of the samples analyzed appeared to be clonal ramets, with up to 12 clones detected for 44 ramets sampled within a site. Clones grew intermingled and ranged up to 39 m in extent. Permutation tests of genetic similarity revealed significant genetic differentiation between each of the five study sites. Consistent with the previous allozyme studies, T. latifolia was characterized by extremely low genetic variation relative to levels of polymorphism detected at VNTR loci in other plant species. Estimated heterozygosity among ramets along the 320-km transect ranged from 0.11 to 0.13, while that within the five study sites ranged from 0.05 to 0.12. Estimates of Fst (0.32–0.41) also indicated considerable genetic subdivision among these stands. Significantly higher genetic diversity was detected at the two study sites that chemistry and toxicity data indicate to be the most severely impacted by pollutants. Although this correlation does not establish cause and effect, the results of this study indicate that the analysis of genetic diversity at VNTR loci may be a useful tool for monitoring anthropogenic-induced changes in the genetic structure of natural populations of plants.  相似文献   

5.
Variation at 18 allozyme loci was assayed among representatives of the geographically widespread, triploid parthenogenetic form of Heteronotia binoei. A minimum of 52 different genotypes were observed among 143 individuals. Virtually all localities sampled had multiple genotypes among the unisexuals. This represents unusually high genotypic diversity for a unisexual vertebrate. Heterozygosity in the triploids was higher than in diploid bisexual populations of H. binoei. Comparison with the alleles present in the diploid bisexuals confirms that the parthenogens are hybrids and indicates that most of the genotypic diversity stems from repetitive hybrid origins. However, the presence of some alleles unique to the parthenogens suggests that mutation adds to their genetic diversity. The genetic structure of this geographically widespread parthenogen suggests the hypothesis that the persistence and spread of the unisexual lineages is facilitated by genotypic diversity.  相似文献   

6.
Vitex rotundifolia L.f. is a woody perennial and has sexual and asexual modes of reproduction. Allozyme study was conducted on 550 plants in 13 Korean populations. The levels of genetic variability and divergence within and among populations, respectively, are considerably lower and higher than the mean values for woody plants with similar life history tralts. Mean percentage of polymorphic loci (P P), mean number of alleles per locus (A P), and mean genetic diversity (He P) within populations ofV. rotundifolia were: 16.7%, 1.21, and 0.047. On average, about 79% of the total variation inV. rotundifolia was common to all populations (meanG ST=0.208). In addition, significant differences in allele frequencies among populations were found in all polymorphic loci examined (P<0.001). On the other hand, levels of genotypic diversity within and among populations were moderate. About 44% (18/41) of multilocus genotypes were “local genotypes” (genotypes occurring in only one population), whereas only one “widespread genotype” (genotypes occurring in more than 75% of the populations) were detected. The mean number of multilocus genotypes per population (G) and mean genotypic diversity index (D G) were 8.4 and 0.74, respectively. Most common multilocus genotypes found in populations were homozygous for five polymorphic loci. The abundance of ramets of these genets is responsible for the low levels of expected heterozygosity within populations. The results indicate that clonal reproduction may act as an enhancer of genetic drift by reducing effective size of local populations ofV. rotundifolia.  相似文献   

7.
Genetic diversity of six isozyme loci in cultivated barley of Tibet   总被引:9,自引:0,他引:9  
Summary A random sample of 463 accessions of cultivated barley from the Tibet Hordeum germplasm collection was assayed electorphoretically for genetic diversity at six isozyme loci. Two loci (Acp-1 and Got-1) were found to be monomorphic and extensive variation was detected at the remaining four loci (Est-1, Est-2, Est-3 and Est-4). The allelic composition of Tibetan barley appeared to be distinct as compared to the results of previous studies of barleys from other parts of the world. Partitioning of genetic diversity showed that approximately 96% of the total variation was maintained at the within-subregion level and only about 4% was accounted for by differentiation among the eight subregions. Analysis of multilocus genotypes revealed non-random association of the alleles at the four loci, both in the entire sample and in all the subregions, although the four major multilocus genotypes did not show significant departure from the expectation based on complete random association. The possible causes for the establishment of these multilocus associations were discussed.  相似文献   

8.
Present investigation was carried out to evaluate genetic diversity among 38 M6 population of oat cv. JO-1. To validate the observed morpho-physiological variations, these lines were analyzed with 21 ISSR primers. A total of 132 loci were amplified by these 21 ISSR markers and 116 loci were found to be polymorphic (87.87 %). The genetic similarity coefficient values among 39 oat genotypes based on ISSR analysis ranged from 0.305 to 0.957. The cluster analysis divided the oat genotypes into two groups. Mutants JMO 81 and JMO 82 were found to be most divergent, hence can be used as parents in breeding program for the development of superior cultivars.  相似文献   

9.
Five polymorphic microsatellites (simple sequence repeat; SSR) markers were used to estimate the levels of genetic variation within and among natural populations from different islands of the endangered endemic from the Canary Islands Sambucus palmensis Link (Sambucaceae). Genetic data were used to infer potential evolutionary processes that could have led to present genetic differentiation among islands. The levels of genetic variability of S. palmensis were considerably high; proportion of polymorphic loci (P = 100%), mean number of alleles per locus (A = 6.8), average expected heterozygosity (He = 0.499). In spite of its small population size and endemic character, 58 different multilocus genotypes were detected within the 165 individuals analyzed. All samples located in different islands always presented different multilocus genotypes. Principal Coordinates Analysis, genetic differentiation analysis (F ST and G ST ) and Bayesian Cluster Analysis revealed significant genetic differences among populations located in different islands. However, this genetic differentiation was not recorded among Tenerife and La Gomera populations, possibly revealing the uncontrolled transfer of material between both islands. AMOVA analysis attributed 77% of the variance to differences within populations, whereas 8% was distributed between islands. The levels of genetic differentiation observed among populations, and the genetic diversity distribution within populations in S. palmensis, indicate that management should aim to conserve as many of the small populations as possible. Concentrating conservation efforts only on the few large populations would result in the likelihood of loss of genetic variability for the species.  相似文献   

10.
Genetic diversity at 38 microsatellite (short sequence repeats (SSRs)) loci was studied in a sample of 54 plants representing a natural population of wild barley, Hordeum spontaneum, at the Neve Yaar microsite in Israel. Wild barley at the microsite was organized in a mosaic pattern over an area of 3180 m2 in the open Tabor oak forest, which was subdivided into four microniches: (i) sun-rock (11 genotypes), (ii) sun-soil (18 genotypes), (iii) shade-soil (11 genotypes), and (iv) shade-rock (14 genotypes). Fifty-four genotypes were tested for ecological-genetic microniche correlates. Analysis of 36 loci showed that allele distributions at SSR loci were nonrandom but structured by ecological stresses (climatic and edaphic). Sixteen (45.7%) of 35 polymorphic loci varied significantly (p < 0.05) in allele frequencies among the microniches. Significant genetic divergence and diversity were found among the four subpopulations. The soil and shade subpopulations showed higher genetic diversities at SSR loci than the rock and sun subpopulations, and the lowest genetic diversity was observed in the sun-rock subpopulation, in contrast with the previous allozyme and RAPD studies. On average, of 36 loci, 88.75% of the total genetic diversity exists within the four microniches, while 11.25% exists between the microniches. In a permutation test, G(ST) was lower for 4999 out of 5000 randomized data sets (p < 0.001) when compared with real data (0.1125). The highest genetic distance was between shade-soil and sun-rock (D = 0.222). Our results suggest that diversifying natural selection may act upon some regulatory regions, resulting in adaptive SSR divergence. Fixation of some loci (GMS61, GMS1, and EBMAC824) at a specific microniche seems to suggest directional selection. The pattern of other SSR loci suggests the operation of balancing selection. SSRs may be either direct targets of selection or markers of selected haplotypes (selective sweep).  相似文献   

11.
The red blood cell phenotypes for eight polymorphic loci were determined for 293 free-ranging Macaca mulatta living on Cayo Santiago; this number represents the total population of the island, disposed in four social groups plus peripheral males. The rhesus population shows significant genetic heterogeneity over blood group systems (loci) and social groups. No particular genetic locus or social group is solely responsible for the genetic heterogeneity observed. The distributions of genotypes for two loci (G and H) do not deviate significantly from Hardy-Weinberg expectations within social groups or in the population as a whole. Correction of the equilibrium expectations for the effect of population subdivision yields no statistically significant results. Overall, the results suggest that the interaction of a variety of processes (random genetic drift, founder effect, migration and selection) may be responsible for the diversity observed. These data, combined with those from further studies, may allow an application of behavioral and genetic knowledge to the study of microevolutionary processes among nonhuman primates.  相似文献   

12.
Pueraria lobata (kudzu), a clonal, leguminous vine, is invading the southeastern United States at a rate of 50 000 ha per year. Genetic variability and clonal diversity were measured in 20 southeastern U.S. populations using 14 allozyme loci. Within its U.S. range, 92.9% of the loci were polymorphic and overall genetic diversity was 0.290. Such high levels of genetic diversity are consistent with its history of multiple introductions over an extended period of time. The average proportions of polymorphic loci and genetic diversity within populations were 55.7% (range = 28.6–85.7%) and 0.213 (range = 0.114–0.317), respectively. The proportion of total genetic diversity found among populations was similar to species with equivalent life history characters (GST = 0.199). No regional patterns of variation were seen. The number of putative genotypes in each population ranged from 2 to 26. Mean genotypic diversity was 0.694, ranging from 0.223 to 0.955. Such high levels of genotypic diversity indicate that local sites are often colonized by several propagules (most likely seeds) and/or that sexual reproduction occurs within populations after establishment. An excess of heterozygosity was observed in populations with few unique genets, implying that selection for highly heterozygous individuals may occur in populations of P. lobata.  相似文献   

13.
 We have identified, isolated, and characterized microsatellite/simple sequence repeat (SSR) loci in trembling aspen (Populus tremuloides) by screening partial genomic libraries. We have also examined the compatibility and use of the P. tremuloides SSR primers to resolve microsatellites in other Populus species. Fourteen microsatellites were identified from 1600 clones screened. The TC/AG microsatellites were the most abundant. A total of 29 alleles were detected in 36 P. tremuloides individuals at the four SSR loci (two each of di- and tri-nucleotide repeats) characterized. The number of alleles at the SSR loci ranged from 5 to 11, with an average of 7.25 alleles per locus, and the observed heterozygosity ranged from 0.19 to 0.82, with a mean of 0.46 per locus. Although the highest polymorphism was observed for a dinucleotide SSR locus, the trinucleotide SSR loci showed substantial polymorphism. There were 34 unique multilocus genotypes among the 36 P. tremuloides individuals examined, and 89% of the individuals had unique multilocus genotypes. Two pairs of SSR primers were successful in PCR, amplifying genomic DNA and resolving microsatellites of comparable size from Populus deltoides, P. nigra, Pcanadensis, and P. maximowiczii. The microsatellite DNA markers developed could be used for clonal fingerprinting, certification of controlled crosses, genome mapping, marker-assisted early selection, genetic diversity assessments, and conservation and sustainable management of poplar genetic resources. Received: 14 November 1997 / Accepted: 17 November 1997  相似文献   

14.
The objective of this study was to analyze the genetic relationships, using PCR-based ISSR markers, among 70 Indian flax (Linum usitatissimum L.) genotypes actively utilized in flax breeding programs. Twelve ISSR primers were used for the analysis yielding 136 loci, of which 87 were polymorphic. The average number of amplified loci and the average number of polymorphic loci per primer were 11.3 and 7.25, respectively, while the percent loci polymorphism ranged from 11.1 to 81.8 with an average of 63.9 across all the genotypes. The range of polymorphism information content scores was 0.03–0.49, with an average of 0.18. A dendrogram was generated based on the similarity matrix by the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), wherein the flax genotypes were grouped in five clusters. The Jaccard’s similarity coefficient among the genotypes ranged from 0.60 to 0.97. When the omega-3 alpha linolenic acid (ALA) contents of the individual genotypes were correlated with the clusters in the dendrogram, the high ALA containing genotypes were grouped in two clusters. This study identified SLS 50, Ayogi, and Sheetal to be the most diverse genotypes and suggested their use in breeding programs and for developing mapping populations.  相似文献   

15.
Somatic mutations are an underappreciated source of genetic variation within multi-cellular organisms. The resulting genetic mosaicism should be particularly abundant in large clones of vegetatively propagating angiosperms. Little is known on the abundance and ecological correlates of genetic mosaicism in field populations, despite its potential evolutionary significance. Because sexual reproduction restores genetic homogeneity, we predicted that in facultatively clonally reproducing organisms, the prevalence of genetic mosaicism increases with increasing clonality. This was tested among 33 coastal locations colonized by the ecologically important marine angiosperm Zostera marina, ranging from Portugal to Finland. Genetic mosaics were detectable as complex microsatellite genotypes at two hypervariable loci that revealed additional mosaic alleles, suggesting the presence of one or more divergent cell lineages within the same ramet. The proportions of non-mosaic genotypes in a population sharply decreased below a clonal richness of 0.2. Accordingly, more genetic mosaics were found at the southern and northern limit of the distribution of Z. marina in Europe where sexual reproduction is rare or absent. The genetic mosaics observed at neutral microsatellite markers suggest the possibility of within-clone variation at selectively relevant loci and supports the notion that members of clones are seldom genetically identical.  相似文献   

16.
Cyclical parthenogenesis allows study of the genetic and evolutionary characteristics of groups exhibiting both asexual and sexual reproduction. The cladoceran genus Daphnia contains species which vary with respect to the relative incidence of sexual reproduction; pond species tend to undergo sexual reproduction more regularly than species found in large lakes. Previous genetic studies have focused on pond populations, generating expectations about large-lake populations that have not been fully met by recent studies. The present study of the Palearctic species Daphnia galeata further examines the genetic structure of large-lake populations. Nine local populations, from lakes in northern Germany, are examined for genetic variation at seven enzyme loci. Populations exhibit similar allelic arrays and often similar allele frequencies at the five polymorphic loci; values of Nei's genetic distance (D) ranged from 0.002 to 0.239, with a mean of 0.084. FST values range from 0.012 to 0.257, and spatial autocorrelation coefficients range from -0.533 to 0.551, for the eight alleles analyzed. With few exceptions, within-population genotypic frequencies were in Hardy-Weinberg equilibrium. There was, however, significant heterogeneity in genotypic frequencies among populations. The number of coexisting clonal groups, as determined by three locus genotypes, is high within populations. Clonal groups are widely distributed among localities. The amount of genetic divergence observed among these large-lake populations is smaller than that previously observed among pond populations and suggests that different processes may be important in determining the genetic structure and subsequent phenotypic divergence of lake versus pond populations.  相似文献   

17.
Microsatellites are powerful markers to infer population genetic parameters. We used 10 microsatellite loci to characterize the genetic diversity and structure of 79 samples of Sclerotinia sclerotiorum isolated from four Brazilian dry bean populations and observed that eight of them were polymorphic within populations. We identified 102 different haplotypes ranging from 6 to 18 per locus. Analyses based on genetic diversity and fixation indices indicated variability among and within populations of 28.79% (FST = 28793) and 71.21%, respectively. To examine genetic relatedness among S. sclerotiorum isolates, we used internal spacer (ITS1‐5.8S‐ITS2) restriction fragment length polymorphism (PCR‐RFLP) and sequencing analysis. PCR‐RFLP analysis of these regions failed to show any genetic differences among isolates. However, we detected variability within the sequence, which does not support the hypothesis of clonal populations within each population. High variability within and among populations may indicate the introduction of new genotypes in the areas analysed, in addition to the occurrence of clonal and sexual reproduction in the populations of S. sclerotiorum in the Brazilian Cerrado.  相似文献   

18.
The genetic structure of populations of the clone-forming tropical terrestrial bromeliad, Aechmea magdalenae, was examined by electrophoretic analyses in nine populations occurring on and near Barro Colorado Island, Republic of Panama. For the nine populations as a whole, 33% of the loci were polymorphic and the genetic diversity was 0.121. Within populations, the mean percent of polymorphic loci was 24.1% and the mean genetic diversity was 0.084. About one-third of the total allozyme diversity resided among populations (mean GST = 0.356). The distribution of A. magdalenae was patchy in the study area. This, coupled with the relatively small effective population sizes and the possible founding of populations by few individuals may have contributed to the large among-population component of genetic diversity. The extent of clonal growth was inferred by examining the relationship between the proportion of rosette-pairs sharing identical multilocus genotypes and distance between pairs. This method indicates that clonal spread is local; individuals sharing multilocus genotypes most often occur within 10 m of each other.  相似文献   

19.
Red maple (Acer rubum), a common deciduous tree species in Northern Ontario, has shown resistance to soil metal contamination. Previous reports have indicated that this plant does not accumulate metals in its tissue. However, low level of nickel and copper corresponding to the bioavailable levels in contaminated soils in Northern Ontario causes severe physiological damages. No differentiation between metal‐contaminated and uncontaminated populations has been reported based on genetic analyses. The main objective of this study was to assess whether DNA methylation is involved in A. rubrum adaptation to soil metal contamination. Global cytosine and methylation‐sensitive amplified polymorphism (MSAP) analyses were carried out in A. rubrum populations from metal‐contaminated and uncontaminated sites. The global modified cytosine ratios in genomic DNA revealed a significant decrease in cytosine methylation in genotypes from a metal‐contaminated site compared to uncontaminated populations. Other genotypes from a different metal‐contaminated site within the same region appear to be recalcitrant to metal‐induced DNA alterations even ≥30 years of tree life exposure to nickel and copper . MSAP analysis showed a high level of polymorphisms in both uncontaminated (77%) and metal‐contaminated (72%) populations. Overall, 205 CCGG loci were identified in which 127 were methylated in either outer or inner cytosine. No differentiation among populations was established based on several genetic parameters tested. The variations for nonmethylated and methylated loci were compared by analysis of molecular variance (AMOVA). For methylated loci, molecular variance among and within populations was 1.5% and 13.2%, respectively. These values were low (0.6% for among populations and 5.8% for within populations) for unmethylated loci. Metal contamination is seen to affect methylation of cytosine residues in CCGG motifs in the A. rubrum populations that were analyzed.  相似文献   

20.
Levin DA 《Genetics》1975,79(3):477-491
Twenty enzyme loci were studied in 44 Illinois populations of Oenothera biennis; four were polymorphic. Most of the variation was distributed between populations. Fifty-nine percent of the populations had one genotype, 27% two genotypes and the remaining 16% from three to five genotypes; the average was 1.50. The proportion of genetic diversity present in single populations is.38 of that present in the state. Members of single populations were uniformly heterozygous for 1 to 4 loci. The mean heterozygosity per population ranged from 0 to 20%. For Illinois populations collectively, heterozygosity averaged 4.5%. There was much gene frequency heterogeneity between populations. The true standardized genetic variance among populations for alleles at polymorphic loci varied from.40 to.78. Populations from Cook County were much more similar inter se than those downstate, had fewer genotypes and polymorphic loci, and had less heterozygosity than downstate populations. The mean normalized genetic identity among Cook County populations was.987 versus.947 for downstate populations. The mean number of genotypes per population in Cook County was 1.06 versus 2.40 in downstate populations. There was only one polymorphic locus in Cook County, VLP. The genetic structure of Oe. biennis suggests that single populations are colonized by one, or at best a few individuals. Cook County populations are judged to be less variable than downstate populations because the mean age of the populations probably is less than that of those downstate.  相似文献   

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