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Sample records for twenty-two di-nucleotide microsatellite

  1. Development of di-nucleotide microsatellite markers and construction of genetic linkage map in mango (Mangifera indica L.

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    Chataporn Chunwongse

    2015-04-01

    Full Text Available Forty-two di-nucleotide microsatellite, or simple-sequence repeat (SSR, markers were developed using CA and CTenriched genomic libraries of Mangifera indica L. Six cultivated mangoes and two wild species were tested for primer amplifications. Most loci could amplify M. caloneura Kruz and M. foetida. The average number of alleles per locus was 4.4. The average expected heterozygosity and the maximum polymorphism information content value were 0.57 and 0.53, respectively. The SSRs developed in this study together with 65 SSRs and 145 restriction fragment length polymorphism (RFLP markers reported previously were used in the genetic linkage analysis. A partial genetic linkage map was constructed based on 31 F1 progenies from a cross between ‘Alphonso’ and ‘Palmer’. The map spanned a distance of 529.9 centiMorgan (cM and consisted of 9 microsatellite markers (6 from this study and 67 RFLP markers. The new SSR markers and the present map will be useful for mango genetic studies and breeding applications in the future.

  2. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

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    Thomson Pippa

    2003-09-01

    Full Text Available Abstract In a project on the biodiversity of chickens funded by the European Commission (EC, eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line and the most polymorphic population (Gallus gallus spadiceus were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.

  3. The cyclic di-nucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function

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    Precit, Mimi; Delince, Matthieu; Pensinger, Daniel; Huynh, TuAnh Ngoc; Jurado, Ashley R.; Goo, Young Ah; Sadilek, Martin; Iavarone, Anthony T.; Sauer, John-Demian; Tong, Liang; Woodward, Joshua J.

    2014-01-01

    SUMMARY Cyclic di-adenosine monophosphate (c-di-AMP) is a broadly conserved second messenger required for bacterial growth and infection. However, the molecular mechanisms of c-di-AMP signaling are still poorly understood. Using a chemical proteomics screen for c-di-AMP interacting proteins in the pathogen Listeria monocytogenes, we identified several broadly conserved protein receptors, including the central metabolic enzyme pyruvate carboxylase (LmPC). Biochemical and crystallographic studies of the LmPC-c-di-AMP interaction revealed a previously unrecognized allosteric regulatory site 25 Å from the active site. Mutations in this site disrupted c-di-AMP binding and affected enzyme catalysis of LmPC as well as PC from pathogenic Enterococcus faecalis. C-di-AMP depletion resulted in altered metabolic activity in L. monocytogenes. Correction of this metabolic imbalance rescued bacterial growth, reduced bacterial lysis, and resulted in enhanced bacterial burdens during infection. These findings greatly expand the c-di-AMP signaling repertoire and reveal a central metabolic regulatory role for a cyclic di-nucleotide. PMID:25215494

  4. Twenty-Two Hispanic Leaders Discuss Poverty: Results from the Hispanic Leaders Study.

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    Quiroz, Julia Teresa

    This study reports twenty-two Hispanic leaders' responses to interviews assessing their perspectives on the nature, prevalence, and causes of poverty among Hispanics. This report contains six parts. Part 1 is an introduction. Part 2 presents the methodology used in the study. Part 3 gives the leaders' demographic and educational backgrounds. Part…

  5. Twenty-Two Hispanic Leaders Discuss Poverty: Results from the Hispanic Leaders Study.

    Science.gov (United States)

    Quiroz, Julia Teresa

    This study reports twenty-two Hispanic leaders' responses to interviews assessing their perspectives on the nature, prevalence, and causes of poverty among Hispanics. This report contains six parts. Part 1 is an introduction. Part 2 presents the methodology used in the study. Part 3 gives the leaders' demographic and educational backgrounds. Part…

  6. Topical melagenine for repigmentation in twenty-two child patients with vitiligo on the scalp

    Institute of Scientific and Technical Information of China (English)

    许爱娥; 尉晓冬

    2004-01-01

    Background The purpose of this study was to evaluate the efficacy of topical melagenine for repigmentation in child patients with vitiligo on the scalp. Methods Twenty-two child patients with vitiligo on the scalp were treated with 1.2 mg/ml aqueous melagenine in combination with 20 minutes of infrared exposure twice daily. Results In 4 patients (18.2%), melagenine treatment in combination with infrared exposure led to complete recovery; in 6 patients (27.3%), treatment was shown to be effective; in 8 patients(36.3%), treatment led to improvements in patient condition; and only 4 patients (18.2%) showed no response after 1 -2 treatment sessions. The general effective rate of melagenine-infrared combination treatment was 45. 5% for the children with vitiligo on the scalp, and treatment was accompanied by minimal side effects.Conclusion Melagenine may be efficacious and a safe treatment option for childhood vitiligo affecting the scalp.

  7. Characterization of novel microsatellite markers in Musa acuminata subsp. burmannicoides, var. Calcutta 4

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    Amorim Edson P

    2010-05-01

    Full Text Available Abstract Background Banana is a nutritionally important crop across tropical and sub-tropical countries in sub-Saharan Africa, Central and South America and Asia. Although cultivars have evolved from diploid, triploid and tetraploid wild Asian species of Musa acuminata (A genome and Musa balbisiana (B genome, many of today's commercial cultivars are sterile triploids or diploids, with fruit developing via parthenocarpy. As a result of restricted genetic variation, improvement has been limited, resulting in a crop frequently lacking resistance to pests and disease. Considering the importance of molecular tools to facilitate development of disease resistant genotypes, the objectives of this study were to develop polymorphic microsatellite markers from BAC clone sequences for M. acuminata subsp. burmannicoides, var. Calcutta 4. This wild diploid species is used as a donor cultivar in breeding programs as a source of resistance to diverse biotic stresses. Findings Microsatellite sequences were identified from five Calcutta 4 BAC consensi datasets. Specific primers were designed for 41 loci. Isolated di-nucleotide repeat motifs were the most abundant, followed by tri-nucleotides. From 33 tested loci, 20 displayed polymorphism when screened across 21 diploid M. acuminata accessions, contrasting in resistance to Sigatoka diseases. The number of alleles per SSR locus ranged from two to four, with a total of 56. Six repeat classes were identified, with di-nucleotides the most abundant. Expected heterozygosity values for polymorphic markers ranged from 0.31 to 0.75. Conclusions This is the first report identifying polymorphic microsatellite markers from M. acuminata subsp. burmannicoides, var. Calcutta 4 across accessions contrasting in resistance to Sigatoka diseases. These BAC-derived polymorphic microsatellite markers are a useful resource for banana, applicable for genetic map development, germplasm characterization, evolutionary studies and marker

  8. Toxicity of twenty-two plant essential oils against pathogenic bacteria of vegetables and mushrooms.

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    Todorović, Biljana; Potočnik, Ivana; Rekanović, Emil; Stepanović, Miloš; Kostić, Miroslav; Ristić, Mihajlo; Milijašević-Marčić, Svetlana

    2016-12-01

    ASBTRACT Toxicity of twenty-two essential oils to three bacterial pathogens in different horticultural systems: Xanthomonas campestris pv. phaseoli (causing blight of bean), Clavibacter michiganensis subsp. michiganensis (bacterial wilt and canker of tomato), and Pseudomonas tolaasii (causal agent of bacterial brown blotch on cultivated mushrooms) was tested. Control of bacterial diseases is very difficult due to antibiotic resistance and ineffectiveness of chemical products, to that essential oils offer a promising alternative. Minimal inhibitory and bactericidal concentrations are determined by applying a single drop of oil onto the inner side of each plate cover in macrodilution assays. Among all tested substances, the strongest and broadest activity was shown by the oils of wintergreen (Gaultheria procumbens), oregano (Origanum vulgare), and lemongrass (Cymbopogon flexuosus. Carvacrol (64.0-75.8%) was the dominant component of oregano oils, while geranial (40.7%) and neral (26.7%) were the major constituents of lemongrass oil. Xanthomonas campestris pv. phaseoli was the most sensitive to plant essential oils, being susceptible to 19 oils, while 11 oils were bactericidal to the pathogen. Sixteen oils inhibited the growth of Clavibacter michiganensis subsp. michiganensis and seven oils showed bactericidal effects to the pathogen. The least sensitive species was Pseudomonas tolaasii as five oils inhibited bacterial growth and two oils were bactericidal. Wintergreen, oregano, and lemongrass oils should be formulated as potential biochemical bactericides against different horticultural pathogens.

  9. Microsatellite loci isolation from river buffalo using enriched partial genomic libraries

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    A.L. Silva

    2010-02-01

    Full Text Available The extensive use of buffalo in agriculture, especially in developing countries, begs for genetic resources to evaluate and improve traits important to local and regional economies. Brazil presents the largest water buffalo populations in the New World, with 1.1 million heads including swamp and river types. To design rational breeding strategies for optimum utilization and conservation of available genetic variability in the Brazilian buffalo’s population, it is essential to understand their genetic architecture and relationship among various breeds. This depends, in part, on the knowledge of their genetic structure based on molecular markers like microsatellites. In the present study, we developed six enriched partial genomic libraries for river buffalo using selective hybridization methods. Genomic DNA was hybridized with six different arrays of repeat motif, 5’ biotinylated - (CA15, (CT15, (AGG8, (GAAA8, (GATA8, (AAAAC8 – and bound to streptavidin coated beads. The cloning process generated a total of 1920 recombinant clones. Up to date, 487 were directly sequenced for the presence of repeats, from which 13 have been positive for presence of repeats as follows: 9 for di-nucleotide repeats, 3 for tri-nucleotide repeats and 1 for tetra-nucleotide repeat. PCR primer pairs for the isolated microsatellites are under construction to determine optimum annealing temperature. These microsatellites will be useful for studies involving phylogenetic relationships, genome mapping and genetic diversity analysis within buffalo populations worldwide.

  10. Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

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    Qun Wang

    2012-12-01

    Full Text Available Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%; the second most abundant were the tri-nucleotide repeats (42,657, 30.11%. Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32% of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR. To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82% produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2–14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites.

  11. Chapter Twenty Two

    African Journals Online (AJOL)

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    As a matter of fact, the act of writing novel in English language in Africa began ... advent of European colonial masters and the myths with which they have been ..... According to Odili, the surrogate author: “A common saying, in the country after.

  12. A new treatment strategy for severe arthrofibrosis of the knee. A review of twenty-two cases.

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    Wang, Jian-Hua; Zhao, Jin-Zhong; He, Yao-Hua

    2006-06-01

    To reduce the morbidity of traditional quadricepsplasty for the treatment of severe arthrofibrosis of the knee, we instituted a treatment regimen consisting of an initial extra-articular mini-invasive quadricepsplasty and subsequent intra-articular arthroscopic lysis of adhesions during the same anesthesia session. The purpose of the present study was to determine the results of this technique. From 1998 to 2001, twenty-two patients with severely arthrofibrotic knees were managed with this operative technique. The mean age of the patients at the time of the operation was thirty-seven years. After a mean duration of follow-up of forty-four months (minimum, twenty-four months), all patients were evaluated according to the criteria of Judet and The Hospital for Special Surgery knee-rating system. The average maximum degree of flexion increased from 27 degrees preoperatively to 115 degrees at the time of the most recent follow-up (p < 0.001). According to the criteria of Judet, the result was excellent for sixteen knees, good for five, and fair for one. The average Hospital for Special Surgery knee score improved from 74 points preoperatively to 94 points at the time of the most recent follow-up (p < 0.001). A superficial wound infection occurred in one patient. Only one patient had a persistent 15 degrees extension lag. This mini-invasive operation for the severely arthrofibrotic knee can be used to increase the range of motion and enhance functional outcome.

  13. Screening of antiangiogenic potential of twenty two marine invertebrate extracts of phylum Mollusca from South East Coast of India

    Institute of Scientific and Technical Information of China (English)

    Pankaj Gupta; Muthuvel Arumugam; Raj Vardhan Azad; Rohit Saxena; Supriyo Ghose; Nihar Ranjan Biswas; Thirumurthy Velpandian

    2014-01-01

    Objective: To evaluate the antiangiogenic potential of twenty two marine invertebrate species of Phylum Mollusca from south east coast of India.Methods:Live specimens of molluscan species were collected and their methanolic extracts were evaluated for preliminary antiangiogenic activity using the in ovo chick chorio-allantoic membrane assay. The extracts were further evaluated for in vivo antiangiogenic activity using chemical cautery induced corneal neovascularization assay in rats and oxygen induced retinopathy assay in rat pups.Results:In the chick chorio-allantoic membrane assay, four methanolic extracts of marine molluscan species viz. Meretrix meretrix, Meretrix casta, Telescopium telescopium and Bursacrumena methanolic extracts exhibited noticeable antiangiogenic activity at the tested concentration of 200 µg whereby they significantly inhibited the VEGF induced proliferation of new blood vessels. Among these four extracts, the methanolic extract of Meretrix casta exhibited relatively higher degree of antiangiogenic activity with an inhibitiory percentage (64.63%) of the VEGF induced neovascularization followed by the methanolic extracts of Telescopium telescopium (62.02%), Bursa crumena (60.48%) and Meretrix meretrix (47.01%). These four methanolic extracts were further evaluated for in vivo antiangiogenic activity whereby the methanolic extract of Telescopium telescopium exhibited most noticeable inhibition (42.58%) of the corneal neovascularization in rats in comparison to the sham treated group, and also exhibited most noticeable inhibition (31.31%) of the oxygen induced retinal neovascularization in rat pups in comparison to the hyperoxia group that was observed for considerable retinal neovascularization.Conclusions:The significant antiangiogenic activity evinced by the extract of Telescopium telescopium merits further investigation for ocular neovascular diseases.

  14. Twenty-Two Years of Combined GPS Daily Coordinate Time Series and Derived Parameters: Implications for ITRF

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    Bock, Y.; Kedar, S.; Moore, A. W.; Fang, P.; Liu, Z.; Owen, S. E.; Squibb, M. B.

    2014-12-01

    The NASA-funded "Solid Earth Science ESDR System (SESES)" MEaSUREs project publishes long-term Earth Science Data Records (ESDRs), the result of a combined solution of independent daily JPL (GIPSY-OASIS software) and SIO (GAMIT software) GPS analyses, using a common source of metadata from the SOPAC database. The project has now produced up to twenty-two years of consistent, calibrated and validated ESDR products for over 3200 GPS stations from Western North America, other plate boundaries, and global networks made available through the GPS Explorer data portal and NASA's CDDIS archive. The combined solution of daily coordinate time series uses SOPAC h-files and JPL STACOV files as input to the st_filter software. The combined time series are then fit with the analyze_tseri software for daily positions/displacements, secular velocities, coseismic and postseismic displacements, as well as annual and semi-annual signatures and non-coseismic offsets due primarily to equipment (antenna) changes. Published uncertainties for the estimated parameters take into account temporal noise in the daily coordinate time series. The resulting residual coordinate time series with typical daily RMS values of 1.5-4.0 mm in the horizontal and 4.0-8.0 mm in the vertical can then can be mined for other signals such as transient deformation associated with earthquake tremor and slip (ETS) and hydrological effects. As part of this process we have catalogued and characterized coseismic displacements due to more than 80 earthquakes affecting over hundreds of regional and global stations, as well as significant postseismic deformation for the larger events. The larger events can affect stations 1000's of km from the earthquake epicenters and thus significantly affect the positions of stations used in defining the reference frame. We discuss the implications and contributions of our ongoing analysis to the long-term maintenance of the international terrestrial reference frame.

  15. Genome-wide identification of microsatellites in white clover (Trifolium repens L. using FIASCO and phpSSRMiner

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    Bouton Joseph H

    2008-07-01

    Full Text Available Abstract Background Allotetraploid white clover (Trifolium repens L. is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover. Results Genomic libraries containing simple sequence repeat (SSR sequences were constructed using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO procedure and phpSSRMiner was used to develop the microsatellite markers. SSR motifs were isolated using two biotin-labeled probes, (CA17 and (ATG12. The sequences of 6,816 clones were assembled into 1,698 contigs, 32% of which represented novel sequences based on BLASTN searches. Approximately 32%, 28%, and 16% of these SSRs contained hexa-, tri-, and di-nucleotide repeats, respectively. The most frequent motifs were the CA and ATG complementary repeats and the associated compound sequences. Primer pairs were designed for 859 SSR loci based on sequences from these genomic libraries and from GenBank white clover nucleotide sequences. A total of 191 SSR primers developed from the two libraries were tested for polymorphism in individual clones from the parental genotypes GA43 ('Durana', 'SRVR' and six F1 progeny from a mapping population. Ninety two percent produced amplicons and 66% of these were polymorphic. Conclusion The combined approach of identifying SSR-enriched fragments by FIASCO coupled with the primer design and in silico amplification using phpSSRMiner represents an efficient and low cost pipeline for the large-scale development of microsatellite markers in plants. The approach described here could be readily adapted and utilized in other non-related species with none or limited genomic resources.

  16. Identification and Characterization of 43 Microsatellite Markers Derived from Expressed Sequence Tags of the Sea Cucumber (Apostichopusjaponicus)

    Institute of Scientific and Technical Information of China (English)

    JIANG Qun; LI Qi; YU Hong; KONG Lingfeng

    2011-01-01

    The sea cucumber Apostichopus japonicus is a commercially and ecologically important species in China. A total of 3056 potential unigenes were generated after assembling 7597 A. japonicus expressed sequence tags (ESTs) downloaded from GenBank. Two hundred and fifty microsatellite-containing ESTs (8.18%) and 299 simple sequence repeats (SSRs) were detected. The average density of SSRs was 1 per 7.403 kb of EST after redundancy elimination. Di-nucleotide repeat motifs appeared to be the most abundant type with a percentage of 69.90%. Of the 126 primer pairs designed, 90 amplified the expected products and 43 showed polymorphism in 30 individuals tested. The number of alleles per locus ranged from 2 to 26 with an average of 7.0 alleles,and the observed and expected heterozygosities varied from 0.067 to 1.000 and from 0.066 to 0.959, respectively. These new EST-derived microsatellite markers would provide sufficient polymorphism for population genetic studies and genome mapping of this sea cucumber species.

  17. [Aspirin suppresses microsatellite instability].

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    Wallinger, S; Dietmaier, W; Beyser, K; Bocker, T; Hofstädter, F; Fishel, R; Rüschoff, J

    1999-01-01

    Nonsteroidal anti-inflammatory drugs (NSAIDs) exhibit cancer preventive effects and have been shown to induce regression of adenomas in FAP patients. In order to elucidate the probable underlying mechanism, the effect of NSAIDs on mismatch repair related microsatellite instability was investigated. Six colorectal cancer cell lines all but one deficient for human mismatch repair (MMR) genes were examined for microsatellite instability (MSI) prior and after treatment with Aspirin or Sulindac. For rapid in vitro analysis of MSI a microcloning assay was developed by combining Laser microdissection and random (PEP-) PCR prior to specific MSI-PCR. Effects of NSAIDs on cell cycle and apoptosis were systematically investigated by using flow cytometry and cell-sorting. MSI frequency in cells deficient of MMR genes (hMSH2, hMLH1, hMSH6) was markedly reduced after long-term (> 10 weeks) NSAID treatment. This effect was reversible, time- and concentration dependent. However, in the hPMS2 deficient endometrial cancer cell line (HEC-1-A) the MSI phenotype kept unchanged. According to cell sorting, non-apoptotic cells were stable and apoptotic cells were unstable. These results suggest that aspirin/sulindac induces a genetic selection for microsatellite stability in a subset of MMR-deficient cells and may thus provide an effective prophylactic therapy for HNPCC related colorectal carcinomas.

  18. Microsatellite genotyping of carnation varieties

    NARCIS (Netherlands)

    Smulders, M.J.M.; Noordijk, Y.; Rus-Kortekaas, W.; Bredemeijer, G.M.M.; Vosman, B.

    2003-01-01

    A set of 11 sequence-tagged microsatellite markers for carnation (Dianthus caryophyllus) was developed using a DNA library enriched for microsatellites. Supplemented with three markers derived from sequence database entries, these were used to genotype carnation varieties using a semi-automated fluo

  19. Microsatellite instability in bladder cancer

    DEFF Research Database (Denmark)

    Gonzalez-Zulueta, M; Ruppert, J M; Tokino, K;

    1993-01-01

    Somatic instability at microsatellite repeats was detected in 6 of 200 transitional cell carcinomas of the bladder. Instabilities were apparent as changes in (GT)n repeat lengths on human chromosome 9 for four tumors and as alterations in a (CAG)n repeat in the androgen receptor gene on the X...... chromosome for three tumors. Single locus alterations were detected in three tumors, while three other tumors revealed changes in two or more loci. In one tumor we found microsatellite instability in all five loci analyzed on chromosome 9. The alterations detected were either minor 2-base pair changes...

  20. Analysis of Twenty-Two Performance Properties of Diesel, Gasoline, and Jet Fuels Using a Field-Portable Near-Infrared (NIR) Analyzer.

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    Brouillette, Carl; Smith, Wayne; Shende, Chetan; Gladding, Zack; Farquharson, Stuart; Morris, Robert E; Cramer, Jeffrey A; Schmitigal, Joel

    2016-05-01

    The change in custody of fuel shipments at depots, pipelines, and ports could benefit from an analyzer that could rapidly verify that properties are within specifications. To meet this need, the design requirements for a fuel analyzer based on near-infrared (NIR) spectroscopy, such as spectral region and resolution, were examined. It was found that the 1000 to 1600 nm region, containing the second CH overtone and combination vibrational modes of hydrocarbons, provided the best near-infrared to fuel property correlations when path length was taken into account, whereas 4 cm(-1) resolution provided only a modest improvement compared to 16 cm(-1) resolution when four or more latent variables were used. Based on these results, a field-portable near-infrared fuel analyzer was built that employed an incandescent light source, sample compartment optics to hold 2 mL glass sample vials with ∼1 cm path length, a transmission grating, and a 256 channel InGaAs detector that measured the above stated wavelength range with 5-6 nm (∼32 cm(-1)) resolution. The analyzer produced high signal-to-noise ratio (SNR) spectra of samples in 5 s. Twenty-two property correlation models were developed for diesel, gasoline, and jet fuels with root mean squared error of correlation - cross-validated values that compared favorably to corresponding ASTM reproducibility values. The standard deviations of predicted properties for repeat measurements at 4, 24, and 38℃ were often better than ASTM documented repeatability values. The analyzer and diesel property models were tested by measuring seven diesel samples at a local ASTM certification laboratory. The standard deviations between the analyzer determined values and the ASTM measured values for these samples were generally better than the model root mean squared error of correlation-cross-validated values for each property.

  1. Detection of respiratory viruses and bacteria in children using a twenty-two target reverse-transcription real-time PCR (RT-qPCR) panel.

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    Ellis, Chelsey; Misir, Amita; Hui, Charles; Jabbour, Mona; Barrowman, Nicholas; Langill, Jonathan; Bowes, Jennifer; Slinger, Robert

    2016-05-01

    Rapid detection of the wide range of viruses and bacteria that cause respiratory infection in children is important for patient care and antibiotic stewardship. We therefore designed and evaluated a ready-to-use 22 target respiratory infection reverse-transcription real-time polymerase chain reaction (RT-qPCR) panel to determine if this would improve detection of these agents at our pediatric hospital. RT-qPCR assays for twenty-two target organisms were dried-down in individual wells of 96 well plates and saved at room temperature. Targets included 18 respiratory viruses and 4 bacteria. After automated nucleic acid extraction of nasopharyngeal aspirate (NPA) samples, rapid qPCR was performed. RT-qPCR results were compared with those obtained by the testing methods used at our hospital laboratories. One hundred fifty-nine pediatric NPA samples were tested with the RT-qPCR panel. One or more respiratory pathogens were detected in 132/159 (83%) samples. This was significantly higher than the detection rate of standard methods (94/159, 59%) (Pviruses, bocavirus, and coronaviruses. The panel internal control assay performance remained stable at room temperature storage over a two-month testing period. The RT-qPCR panel was able to identify pathogens in a high proportion of respiratory samples. The panel detected more positive specimens than the methods in use at our hospital. The pre-made panel format was easy to use and rapid, with results available in approximately 90 minutes. We now plan to determine if use of this panel improves patient care and antibiotic stewardship.

  2. A novel microsatellite control system

    Energy Technology Data Exchange (ETDEWEB)

    Moore, K.R.; Frigo, J.R.; Tilden, M.W.

    1998-02-01

    The authors are researching extremely simple yet quite capable analog pulse-coded neural networks for ``smaller-faster-cheaper`` spacecraft attitude and control systems. The will demonstrate a prototype microsatellite that uses their novel control method to autonomously stabilize itself in the ambient magnetic field and point itself at the brightest available light source. Though still in design infancy, the ``Nervous Net`` controllers described could allow for space missions not currently possible given conventional satellite hardware. Result, prospects and details are presented.

  3. Recovery of a lowland dipterocarp forest twenty two years after selective logging at Sekundur, Gunung Leuser National Park, North Sumatra, Indonesia

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    Dolly - Priatna

    2006-12-01

    Full Text Available PRIATNA, D.; KARTAWINATA, K.; ABDULHADI, R. 2004. Recovery of a lowland dipterocarp forest twenty two years after selective logging at Sekundur, Gunung Leuser National Park, North Sumatra, Indonesia. Reinwardtia 12 (3: 237–255. — A permanent 2-ha plot of lowland forest selectively logged in 1978 at Sekundur, Gunung Leuser National Park, which is also a Biosphere Reserve and a World Heritage Site, North Sumatra, was established and investigated in 1982. It was re-examined in 2000, where remeasurement and reidentification of all trees with DBH 10 cm were made. The areas of gap, building and mature phases of the canopy were also measured and mapped. Within this plot, 133 species, 87 genera and 39 families were recorded, with the total number of trees of 1145 or density of 572.5/ha. Euphorbiaceae was the richest family with 18 species (13.5 % of the total and total number of trees of 248 (21.7 % of the total or density of 124 trees/ha. The most important families were Dipterocarpaceae with IV (Importance Value = 52.0, followed by Euphorbiaceae with IV = 51.8. The most prevalent species was Shorea kunstleri (Dipterocarpaceae with IV =24.4, followed by Macaranga diepenhorstii (Euphorbiaceae with IV = 12.4. They were the species with highest density, 34 trees/ha and 23.5 trees/ha, respectively. During the period of 18 years there has been no shift in the richest families, most important families and most important species. Euphorbiaceae was the richest family and Dipterocarpaceae was the most important family, with Shorea kunstleri as the most important species with highest importance value throughout the period. The number of species increased from 127 to 133 with increase in density by 36.8% , from 418.5 trees/ha to 572.5 trees/ha. The mortality was 25.57 % or 1.4 % per year. The diameter class distribution indicated that the forest recovery has not been complete. Trees were small, comprising 67.6 % with diameters of 10-20 cm and only two trees

  4. Origin, evolution and genome distribution of microsatellites

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    Eder Jorge Oliveira

    2006-01-01

    Full Text Available Microsatellites, or simple sequence repeats (SSRs, have been the most widely applied class of molecular markers used in genetic studies, with applications in many fields of genetics including genetic conservation, population genetics, molecular breeding, and paternity testing. This range of applications is due to the fact that microsatellite markers are co-dominant and multi-allelic, are highly reproducible, have high-resolution and are based on the polymerase chain reaction (PCR. When first introduced, the development of microsatellite markers was expensive but now new and efficient methods of repetitive sequence isolation have been reported, which have led to reduced costs and microsatellite-technology has been increasingly applied to several species, including non-model organisms. The advent of microsatellite markers revolutionized the use of molecular markers but the development of biometric methods for analyzing microsatellite data has not accompanied the progress in the application of these markers, with more effort being need to obtain information on the evolution of the repetitive sequences, which constitute microsatellites in order to formulate models that fit the characteristics of such markers. Our review describes the genetic nature of microsatellites, the mechanisms and models of mutation that control their evolution and aspects related to their genesis, distribution and transferability between taxa. The implications of the use of microsatellites as a tool for estimating genetic parameters are also discussed.

  5. Sequence determinants of human microsatellite variability

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    Jakobsson Mattias

    2009-12-01

    Full Text Available Abstract Background Microsatellite loci are frequently used in genomic studies of DNA sequence repeats and in population studies of genetic variability. To investigate the effect of sequence properties of microsatellites on their level of variability we have analyzed genotypes at 627 microsatellite loci in 1,048 worldwide individuals from the HGDP-CEPH cell line panel together with the DNA sequences of these microsatellites in the human RefSeq database. Results Calibrating PCR fragment lengths in individual genotypes by using the RefSeq sequence enabled us to infer repeat number in the HGDP-CEPH dataset and to calculate the mean number of repeats (as opposed to the mean PCR fragment length, under the assumption that differences in PCR fragment length reflect differences in the numbers of repeats in the embedded repeat sequences. We find the mean and maximum numbers of repeats across individuals to be positively correlated with heterozygosity. The size and composition of the repeat unit of a microsatellite are also important factors in predicting heterozygosity, with tetra-nucleotide repeat units high in G/C content leading to higher heterozygosity. Finally, we find that microsatellites containing more separate sets of repeated motifs generally have higher heterozygosity. Conclusions These results suggest that sequence properties of microsatellites have a significant impact in determining the features of human microsatellite variability.

  6. RAPD identification of microsatellites in Daphnia

    NARCIS (Netherlands)

    Ender, A.; Schwenk, K.; Stadler, T.; Streit, B.; Schierwater, B.

    1996-01-01

    Simple sequence repeats (SSRs, or microsatellites) have been constantly gaining importance as single-locus DNA markers in population genetics and behavioural ecology. We tested a PCR- based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and s

  7. Large proportion of low frequency microsatellite-instability and loss of heterozygosity in pheochromocytoma and endocrine tumors detected with an extended marker panel.

    Science.gov (United States)

    Kupka, Susan; Haack, Birgit; Zdichavsky, Marty; Mlinar, Tanja; Kienzle, Christine; Bock, Thomas; Kandolf, Reinhard; Kroeber, Stefan-Martin; Königsrainer, Alfred

    2008-04-01

    Pheochromocytoma (PCC) is a usually benign tumor originated in the majority of patients from the adrenal medulla. Regarding sporadic forms of PCC, mechanisms of pathogenesis are largely unknown. Recently, microsatellite-instability (MSI) was discussed as genetic factor contributing to PCC development. Since microsatellite markers used for MSI detection have only been recommended for colorectal carcinoma (CRC), we established an extended marker set for MSI detection in PCC. Twenty-two PCC patients were analyzed applying 11 microsatellite markers. Our marker set comprised the reference panel for CRC and six additional markers, which have already been described to detect MSI in tumors other than CRC. Moreover, 23 endocrine tumors with gastrointestinal origin were examined in order to test the applicability of this marker panel. Microsatellite-instability was detected in 41% of PCCs. Twenty-seven percent showed loss of heterozygosity (LOH) events affecting different chromosomal regions. Among the 23 patients with endocrine tumors, only three (one pancreatic endocrine tumor, one duodenal neuro-endocrine tumor, one hepatic metastasis of a primary tumor with unknown origin) demonstrated MSI. The extended microsatellite panel is qualified to detect MSI in PCC. Nine percent of MSI-positive cases would have not been noticed by the use of the reference panel alone. PCCs are characterized by low frequency MSI pointing to failures in factors involved in DNA replication.

  8. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae).

    Science.gov (United States)

    Zheng, Xingfei; Pan, Cheng; Diao, Ying; You, Yongning; Yang, Chaozhu; Hu, Zhongli

    2013-07-19

    Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of Amorphophallus have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in Amorphophallus. Here, we report large scale of transcriptome sequencing of two species: Amorphophallus konjac and Amorphophallus bulbifer using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences. cDNAs of A. konjac and A. bulbifer were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard's similarity coefficients was constructed, which showed a distinct cluster of 25 Amorphophallus individuals. A total of 10,754 SSR markers have been identified in Amorphophallus using transcriptome sequencing. One hundred and seventy-seven polymorphic

  9. Microsatellite DNA capture from enriched libraries.

    Science.gov (United States)

    Gonzalez, Elena G; Zardoya, Rafael

    2013-01-01

    Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

  10. Microsatellites and agronomic traits for assessing genetic ...

    African Journals Online (AJOL)

    GRACE

    2006-05-16

    May 16, 2006 ... The Africa Rice Center (WARDA) has developed several interspecific rice ... distribution (banding pattern) observed between NERICAs 8 and 9 is highly .... position on the microsatellite framework map published by Chen et al.

  11. HMSRP Hawaiian Monk Seal Microsatellite Genotypes

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Currently ~2,400 Hawaiian monk seal specimens have been analyzed genetically, providing genotypes at 18 microsatellite loci. These data are organized by individual,...

  12. A Preliminary Screening and Characteristic Analysis of Microsatellite Markers from Transcriptome Sequences in Mugilogobius chulae%诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析

    Institute of Scientific and Technical Information of China (English)

    蔡磊; 余露军; 陈小曲; 叶惠欣; 陈琳; 李建军

    2015-01-01

    旨在为大规模开发诸氏鲻虾虎鱼微卫星标记,采用高通量测序技术,对诸氏鲻虾虎鱼肝脏转录组进行了测序。结果共获得47979条Unigenes,利用微卫星查找程序在47979条Unigenes中共获得6225个微卫星位点(12.97%),平均每7.02 kb就出现1个微卫星位点。6225个微卫星位点由226种重复基序组成,主要分布在三、四和五碱基重复类型中。在数量上,单碱基重复类型微卫星位点最多,占42.49%,二碱基和三碱基重复类型所占比例相似,分别为25.22%和26.27%,四、五、六重复类型较少,合计占6.03%。单碱基重复序列中最多的类型为A/T,二碱基重复序列中以AG/CT重复单元为主,三碱基重复序列中以AGC/TCG为优势类型。挑选部分二、三和四单元重复类型微卫星序列,共设计76对引物,可稳定扩增出目的条带的有55对,其中32对具有多态性。结果表明,利用诸氏鲻虾虎鱼转录组数据可快速大量开发微卫星标记。%In order to explore microsatellite markers in large-scale, the liver transcriptome of Mugilogobius chulae was sequenced by high-throughput sequencing technology. A total of 6 225(12.97%)microsatellite markers were screened from 47 979 Unigenes by microsatellite software, averagely 1 microsatellite marker in every 7.02 kb. The 6 225 microsatellite markers consisted of 226 repeat motifs, which mainly distributed in tri-nucleotide, quad-nucleotide and penta-nucleotide repeats. The mono-nucleotide repeats were of the most by number, accounting for 42.49% of all the microsatellite markers, the di-nucleotide repeats and tri-nucleotide repeats had the similar proportion(25.22% and 26.27%of all the markers, respectively), the rest were the quad-nucleotide, penta-nucleotide and hexa-nucleotide repeats, together accounting for 6.03%. A/T, AG/CT and AGC/TCG were the most frequent motifs in mono-nucleotide, di-nucleotide and tri-nucleotide repeats

  13. Microsatellites as targets of natural selection.

    Science.gov (United States)

    Haasl, Ryan J; Payseur, Bret A

    2013-02-01

    The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to selection that targets single nucleotide variants, fundamentally different types of mutation generate abundant polymorphism in genomes. Moreover, recent empirical results suggest that mutationally complex, multiallelic loci including microsatellites and copy number variants are sometimes targeted by natural selection. Given their abundance, the lack of inference methods tailored to the mutational peculiarities of these types of loci represents a notable gap in our ability to interrogate genomes for signatures of natural selection. Previous theoretical investigations of mutation-selection balance at multiallelic loci include assumptions that limit their application to inference from empirical data. Focusing on microsatellites, we assess the dynamics and population-level consequences of selection targeting mutationally complex variants. We develop general models of a multiallelic fitness surface, a realistic model of microsatellite mutation, and an efficient simulation algorithm. Using these tools, we explore mutation-selection-drift equilibrium at microsatellites and investigate the mutational history and selective regime of the microsatellite that causes Friedreich's ataxia. We characterize microsatellite selective events by their duration and cost, note similarities to sweeps from standing point variation, and conclude that it is premature to label microsatellites as ubiquitous agents of efficient adaptive change. Together, our models and simulation algorithm provide a powerful framework for statistical inference, which can be used to test the neutrality of microsatellites and other multiallelic variants.

  14. Highly informative single-copy nuclear microsatellite DNA markers developed using an AFLP-SSR approach in black spruce (Picea mariana and red spruce (P. rubens.

    Directory of Open Access Journals (Sweden)

    Yong-Zhong Shi

    Full Text Available Microsatellites or simple sequence repeats (SSRs are highly informative molecular markers for various biological studies in plants. In spruce (Picea and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana and red spruce (Picea rubens using a simple but efficient method based on a combination of AFLP and microsatellite technologies.A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean = 0.67 in black spruce and from 0.161 to 0.851 (mean = 0.62 in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies.The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for

  15. Multiplexed microsatellite recovery using massively parallel sequencing.

    Science.gov (United States)

    Jennings, T N; Knaus, B J; Mullins, T D; Haig, S M; Cronn, R C

    2011-11-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

  16. 柑橘全爪螨微卫星位点鉴定与信息分析%Analysis of Microsatellite Loci fromPanonychus citri Based on Enriched Microsatellite Library and Transcriptome Dataset

    Institute of Scientific and Technical Information of China (English)

    魏丹丹; 刘燕; 杜洋; 李刚; 李婷; 袁明龙; 王进军

    2016-01-01

    , msatcommander software and bioinformatics methods were used to identify and assess of the quality and quantity of EST-SSR loci from P. citritranscriptome dataset. Primer Premier 5 was used to designP. citriSSR primers, and then these primer pairs were verified by PCR.[Result]Three microsatellite-enriched libraries of AC-repeat, TC-repeat, and ATG-repeat were constructed forP. citri. The positive clone rates of these three libraries were about 30%, 28% and 25%, respectively. The sequencing results showed that the AC library had the highest redundancy rate, and the TC library followed. However, the same clone of SSR in the ATG library was not found. Intriguingly, in the AC library, some AC-repeat types of SSRs existed in many copies with similar or almost identical sequences in one of the flanking regions. Totally, 44 unique microsatellite loci (GenBank number JF776418-JF776461) were obtained. Among these SSRs, 20 primer pairs were synthesized, and 11 primer pairs could be steadily amplified. In gSSR, perfect SSR accounted for 54.5%, and imperfect perfected and compound SSR accounted for 27.3% and 18.2%, respectively. In perfect gSSR, the repeat times (13-42 times) of the di-nucleotide repeat SSR were much higher than tri-nucleotide repeat SSR (5-9 times). A total of 8 023 EST-SSR loci were identified fromP. citri transcriptome, and 2 540 SSR sequences could be used for primer design. A total of 35 primer pairs were synthesized (GenBank number KT261306-KT261340), and 8 primer pairs could be steadily amplified. The average distribution distance of the transcriptomic SSRs was 3.55 kb. Tri-nucleotide repeat SSR was the most frequently occurring type in P. citri EST-SSR (53.86%), and di-nucleotide repeat SSR was followed (43.36%). The tetra-, penta-, hexa- nucleotide repeat and compound SSR were very scarce with similar numbers, and accounted for 2.78% in total. The repeat of times of the EST-SSR motifs were mainly concentrated in 5-10 times.[Conclusion]Microsatellite enrichment by

  17. Eguchipsammia fistula Microsatellite Development and Population Analysis

    KAUST Repository

    Mughal, Mehreen

    2012-12-01

    Deep water corals are an understudied yet biologically important and fragile ecosystem under threat from recent increasing temperatures and high carbon dioxide emissions. Using 454 sequencing, we develop 14 new microsatellite markers for the deep water coral Eguchipsammia fistula, collected from the Red Sea but found in deep water coral ecosystems globally. We tested these microsatellite primers on 26 samples of this coral collected from a single population. Results show that these corals are highly clonal within this population stemming from a high level of asexual reproduction. Mitochondrial studies back up microsatellite findings of high levels of genetic similarity. CO1, ND1 and ATP6 mitochondrial sequences of E. fistula and 11 other coral species were used to build phylogenetic trees which grouped E. fistula with shallow water coral Porites rather than deep sea L. Petusa.

  18. A Phylogenetic Index for Cichlid Microsatellite Primers

    Directory of Open Access Journals (Sweden)

    Robert D. Kunkle

    2010-01-01

    Full Text Available Microsatellites abound in most organisms and have proven useful for a range of genetic and genomic studies. Once primers have been created, they can be applied to populations or taxa that have diverged from the source taxon. We use PCR amplification, in a 96-well format, to determine the presence and absence of 46 microsatellite loci in 13 cichlid species. At least one primer set amplified a product in each species tested, and some products were present in nearly all species. These results are compared to the known phylogenetic relationships among cichlids. While we do not address intraspecies variation, our results present a phylogenetic index for the success of microsatellite PCR primer product amplification, thus providing information regarding a collection of primers that are applicable to wide range of species. Through the use of such a uniform primer panel, the potential impact for cross species would be increased.

  19. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants.......We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...

  20. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants.......We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...

  1. Functionally relevant microsatellites in sugarcane unigenes

    Directory of Open Access Journals (Sweden)

    Singh Nagendra K

    2010-11-01

    Full Text Available Abstract Background Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance in silico, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane. Results The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined in silico. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome. Conclusion Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6% of which functions were determined in silico. High level of

  2. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  3. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  4. Optimization of microsatellite DNA Gelred fluorescence imaging ...

    African Journals Online (AJOL)

    user1

    2012-10-11

    Oct 11, 2012 ... In order to explore the best microsatellite DNA Gelred imaging technology, this study .... The cycling parameters were: 4 min at 94°C, followed by 35 cycles of ..... double-strand breaks in mammalian cells. Nucleic Acids Res.

  5. Microsatellite Markers for Raspberries and Blackberries

    Science.gov (United States)

    Twelve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, w...

  6. Microsatellite markers for raspberry and blackberry

    Science.gov (United States)

    welve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, we...

  7. MICROSATELLITE ANALYSIS OF INTRA CULTIVAR DIVERSITY IN ...

    African Journals Online (AJOL)

    ACSS

    were sampled to study intracultivar diversity following microsatellite analysis. The dendrogram ... composition are available on the Indian market. Notable local juicy ..... management and genetic identification of ... the application of the SSR technique allows to discriminate all .... and multivariate analysis system, version 2.1.

  8. DNA microsatellite analysis for tomato genetic differentiation

    Directory of Open Access Journals (Sweden)

    Miskoska-Milevska Elizabeta

    2015-01-01

    Full Text Available Commonly used method for determination of the genetic diversity among the populations is the test for genetic differentiation. DNA microsatellite markers are usually used to investigate the genetic structure of natural populations. The aim of this study was to evaluate the applicability of eight DNA microsatellite loci (LECH13, LE21085, LEMDDNa, LEEF1Aa, LELEUZIP, LE20592, TMS9 and LE2A11 in genetic differentiation of six morphologically different tomato varieties (var. grandifolium from subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme and var. pyriforme from subsp. subspontaneum; and var. racemigerum from subsp. spontaneum. The fragment analyses was performed using Applied Biosystems DNA analyzer (ABI 3130 and GeneMapper® Software program. The data were analysed using the specific program Power Marker Software. The average number of detected alleles was 3,625. Also, the average PIC value for all 8 DNA microsatellites loci was 0,3571. The genetic differentiation test in the researched tomato subspecies showed minor differentiation for locus LELEUZIP (- 0,0009, modest differentiation for locus LECH13 (0,0896, locus LEMDDNa (0,0896 and locus LE21085 (0,0551 and major differentiation for locus LE2A11 (0,7633, locus LEEF1Aa (0,6167, locus TMS9 (0.4967 and locus LE20592 (0,4263. On the other hand, in the estimated tomato varieties, locus LE21085 (0,0297, locus LECH13 (0,0256 and locus LELEUZIP (0,0005 showed minor differentiation, locus LEMDDNa (0,1333 showed modest differentiation, while locus TMS9 (0,5929, locus LEEF1Aa (0,5006, locus LE2A11 (0,4013 and locus LE20592 (0,2606 showed major differentiation. The eight DNA microsatellite loci can be applicable solution for tomato genetic differentiation. The overall results suggest that these microsatellite loci could be used in further population genetic studies of tomatoes.

  9. Microsatellite flanking region similarities among different loci within insect species.

    Science.gov (United States)

    Meglécz, E; Anderson, S J; Bourguet, D; Butcher, R; Caldas, A; Cassel-Lundhagen, A; d'Acier, A C; Dawson, D A; Faure, N; Fauvelot, C; Franck, P; Harper, G; Keyghobadi, N; Kluetsch, C; Muthulakshmi, M; Nagaraju, J; Patt, A; Péténian, F; Silvain, J-F; Wilcock, H R

    2007-04-01

    Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.

  10. MICROSATELLITE ALTERATION AND ITS CHARACTERISTICS IN COLORECTAL CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Objective: To determine the role of microsatellite alterations incarcinogenesis of colorectal carcinoma (CRC). Methods: Alterations of 10 microsatellite loci from 5 different chromosomes were detected in 92 colorectal cancers and their paired normal mucosa by PCR, denatured polyacrylamide gel electrophoresis and silver staining. Associations of microsatellite alterations with clinopathologic parameters were statistically clarified.Results: Alterations of microsatellite were classified into microsatellite instability type I, type II and loss of heterozygosity (LOH). The carcinoma with ≥30% loci microsatellite alterations was defined as replication error(RER) positive tumors. Of 92 cases, 14 were RER+. Microsatellite alterations of P53(1) and D18S363 loci (64.29% ) was most commonly identified in the RER+ tumors. RER+ were more commonly seen in poorly differentiated carcinomas and tended to occur in mucoid carcinomas. The type of microsatellite alterations varied in different histological types of CRC. Conclusions: Microsatellite alteration is a common molecular event in CRC. Different microsatellite loci showed various biologic significance. P53(1) and D18S363 should be essentially detected loci that can show the RER status of tumors.

  11. Microsatellite Instability Assay — EDRN Public Portal

    Science.gov (United States)

    Microsatellite analysis (MSA) is a promising new technique for the surveillance of bladder cancer. The technology, which permits the separation by electrophoresis of polymerase chain reaction (PCR)-amplified sequences from non-malignant and malignant sources, has been applied to the diagnosis of solid tumors arising in colon, lung, oropharynx, kidney and bladder. MSA can detect genetic changes indicative of carcinoma from urothelial cells obtained in voided urine specimens. The genetic profile of DNA purified from urine is compared to that of DNA purified from peripheral lymphocytes that are considered normal. Once the DNA from uroepithelial cells has been obtained, PCR is performed with specific oligonucleotide primers for each chromosomal locus. The PCR products are then examined for evidence of microsatellite instability (MSI) and loss of heterozygosity (LOH), which are genetic characteristics of epithelial tumors. Preliminary work shows that MSA detects 95% of cancers.

  12. Microsatellite data analysis for population genetics.

    Science.gov (United States)

    Kim, Kyung Seok; Sappington, Thomas W

    2013-01-01

    Theories and analytical tools of population genetics have been widely applied for addressing various questions in the fields of ecological genetics, conservation biology, and any context where the role of dispersal or gene flow is important. Underlying much of population genetics is the analysis of variation at selectively neutral marker loci, and microsatellites continue to be a popular choice of marker. In recent decades, software programs to estimate population genetics parameters have been developed at an increasing pace as computational science and theoretical knowledge advance. Numerous population genetics software programs are presently available to analyze microsatellite genotype data, but only a handful are commonly employed for calculating parameters such as genetic variation, genetic structure, patterns of spatial and temporal gene flow, population demography, individual population assignment, and genetic relationships within and between populations. In this chapter, we introduce statistical analyses and relevant population genetic software programs that are commonly employed in the field of population genetics and molecular ecology.

  13. The FLP microsatellite platform flight operations manual

    CERN Document Server

    2016-01-01

    This book represents the Flight Operations Manual for a reusable microsatellite platform – the “Future Low-cost Platform” (FLP), developed at the University of Stuttgart, Germany. It provides a basic insight on the onboard software functions, the core data handling system and on the power, communications, attitude control and thermal subsystem of the platform. Onboard failure detection, isolation and recovery functions are treated in detail. The platform is suited for satellites in the 50-150 kg class and is baseline of the microsatellite “Flying Laptop” from the University. The book covers the essential information for ground operators to controls an FLP-based satellite applying international command and control standards (CCSDS and ECSS PUS). Furthermore it provides an overview on the Flight Control Center in Stuttgart and on the link to the German Space Agency DLR Ground Station which is used for early mission phases. Flight procedure and mission planning chapters complement the book. .

  14. Elevated Triglyceride Level Is Independently Associated With Increased All-Cause Mortality in Patients With Established Coronary Heart Disease: Twenty-Two-Year Follow-Up of the Bezafibrate Infarction Prevention Study and Registry.

    Science.gov (United States)

    Klempfner, Robert; Erez, Aharon; Sagit, Ben-Zekry; Goldenberg, Ilan; Fisman, Enrique; Kopel, Eran; Shlomo, Nir; Israel, Ariel; Tenenbaum, Alexander

    2016-03-01

    The independent association between elevated triglycerides and all-cause mortality among patients with established coronary heart disease is controversial. The aim of this study was to investigate this association in a large cohort of patients with proven coronary heart disease. The study cohort comprised 15 355 patients who were screened for the Bezafibrate Infarction Prevention (BIP) trial. Twenty-two-year mortality data were obtained from the national registry. Patients were divided into 5 groups according to strata of fasting serum triglycerides: (1) low-normal triglycerides (triglycerides (100-149 mg/dL); (3) borderline hypertriglyceridemia triglycerides (150-199 mg/dL); (4) moderate hypertriglyceridemia triglycerides (200-499 mg/dL); (5) severe hypertriglyceridemia triglycerides (≥500 mg/dL). Age- and sex-adjusted survival was 41% in the low-normal triglycerides group than 37%, 36%, 35%, and 25% in groups with progressively higher triglycerides (Ptriglycerides elevation was associated with a corresponding 6% (P=0.016) increased risk of 22-year all-cause mortality. The 22-year mortality risk for patients with severe hypertriglyceridemia was increased by 68% when compared with patients with low-normal triglycerides (Pdisease, higher triglycerides levels are independently associated with increased 22-year mortality. Even in patients with triglycerides of 100 to 149 mg/dL, the elevated risk for death could be detected than in patients with lower triglycerides levels, whereas severe hypertriglyceridemia denotes a population with particularly increased mortality risk. © 2016 American Heart Association, Inc.

  15. Identification of Carnation varieties using microsatellite markers

    OpenAIRE

    Arens, P.F.P.; Esselink, G.; Noordijk, Y.; Kodde, L.P.; Hof, L.; Wietsma, W.A.; Vosman, B.

    2009-01-01

    As in many ornamentals, also in carnation the number of varieties in common knowledge is large and identification throughout the chain from breeder to consumer using plant material from different stages and organs may be needed. Results in this study on the use of microsatellite markers from Dianthus caryophyllus L. for the characterization of carnation varieties as well as the construction and evaluation of a molecular database show that these markers show potential for identification purposes

  16. XSS-10 microsatellite flight demonstration program results

    Science.gov (United States)

    Davis, Thomas M.; Melanson, David

    2004-08-01

    Air Force Research Laboratory"s space experiment XSS-10 was flown on the Air Force Global Positioning Satellite (GPS) mission IIR-8 launched on January 29, 2003. The mission objectives of XSS-10 were to demonstrate autonomous navigation, proximity operations, and inspection of a Resident Space Object (RSO). XSS-10 was a 28-kilogram micro-satellite was launched as a secondary mission on a Delta II expendable launch vehicle carrying a GPS satellite. XSS-10 was equipped with a visible camera, a star sensor, and mini SGLS system, all specially built for this program. In addition, a visible camera was attached to the second stage to observe the release of the micro-satellite and observe its maneuvers. Following the release of the GPS satellite, the Delta II initiated three depletion burns to reorient into an 800 KM circular orbit. The XSS-II was ejected from the Delta II second stage approximately 18 hours after launch. Operating autonomously on a preplanned course, XSS-10 performed its mission of navigating around the Delta II second stage at preplanned positions; the micro-satellite took images of the second stage and send them back to earth in real time. During these demonstrations the XSS-10 mission operations team accomplished responsive checkout of the micro-satellite and all of its subsystems, autonomous navigation on a preplanned course and a variety of algorithms and mission operations that pave the way for more ambitious missions in the future. This paper will discuss the results of the mission and post mission analysis of the XSS-10 space flight.

  17. Microsatellites in varied arenas of research

    Directory of Open Access Journals (Sweden)

    K S Remya

    2010-01-01

    Full Text Available Microsatellites known as simple-sequence repeats (SSRs or short-tandem repeats (STRs, represent specific sequences of DNA consisting of tandemly repeated units of one to six nucleotides. The repetitive nature of microsatellites makes them particularly prone to grow or shrink in length and these changes can have both good and bad consequences for the organisms that possess them. They are responsible for various neurological diseases and hence the same cause is now utilized for the early detection of various diseases, such as, Schizophrenia and Bipolar Disorder, Congenital generalized Hypertrichosis, Asthma, and Bronchial Hyperresponsiveness. These agents are widely used for forensic identification and relatedness testing, and are predominant genetic markers in this area of application. The application of microsatellites is an extending web and covers the varied scenarios of science, such as, conservation biology, plant genetics, and population studies. At present, researches are progressing round the globe to extend the use of these genetic repeaters to unmask the hidden genetic secrets behind the creation of the world.

  18. Isolation and Characterization of Microsatellite Markers in Beilschmiedia roxburghiana (Lauraceae

    Directory of Open Access Journals (Sweden)

    Lu Liu

    2013-07-01

    Full Text Available Premise of the study: Although there are as many as 250 species in the genus Beilschmiedia, their genetic diversity has been poorly investigated. Our objective was to develop microsatellite markers for B. roxburghiana to study its genetic diversity for the sustainable management of this species. Methods and Results: Using the microsatellite-enriched library and PCR-based screening method, 22 microsatellite markers were developed and 10 showed high polymorphism in a population. The number of alleles per locus for these 10 microsatellites ranged from five to 19. The observed and expected heterozygosities ranged from 0.298 to 1.000 and from 0.314 to 0.878, respectively. Conclusions: Our results from the 10 highly polymorphic microsatellites indicate that the principal reproductive mode of B. roxburghiana is clonal in the studied population. These microsatellites will facilitate further studies on genetic diversity and structure in B. roxburghiana.

  19. Potential of Microsatellites Markers for the Genetic Analysis of Bryophytes

    Directory of Open Access Journals (Sweden)

    Saumy PANDEY

    2016-03-01

    Full Text Available Microsatellites have increasingly being used to study genetic diversity, phylogeny, population genetics, population ecology and genetic mapping of bryophytes. Due to co-dominant and highly reproducible features, microsatellites became markers of choice for several genetic analyses of bryophytes. However, the major limitation is de novo isolation of microsatellites from the interest species which were studied and gave genomic libraries. Initially, traditional methods of microsatellite development were tedious and time consuming, but due to the sequencing of several bryophytes available in public databases, advancement in PCR technologies and computer software, have cumulatively facilitated the development of microsatellites for bryophytes study. This review examines the features, strategies for the development of microsatellites and their utilization in many aspects of genetic and ecological studies of bryophytes.

  20. Microsatellite markers for Russian olive (Elaeagnus angustifolia; Elaeagnaceae) 1

    OpenAIRE

    Gaskin, John F; Hufbauer, Ruth A; Bogdanowicz, Steven M.

    2013-01-01

    Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. Conclusions: These microsatellites have sufficient potential variability to define...

  1. Microsatellite Markers for Russian Olive (Elaeagnus angustifolia; Elaeagnaceae

    Directory of Open Access Journals (Sweden)

    John F. Gaskin

    2013-09-01

    Full Text Available Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. Conclusions: These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion.

  2. Detecting microsatellites within genomes: significant variation among algorithms

    Directory of Open Access Journals (Sweden)

    Rivals Eric

    2007-04-01

    Full Text Available Abstract Background Microsatellites are short, tandemly-repeated DNA sequences which are widely distributed among genomes. Their structure, role and evolution can be analyzed based on exhaustive extraction from sequenced genomes. Several dedicated algorithms have been developed for this purpose. Here, we compared the detection efficiency of five of them (TRF, Mreps, Sputnik, STAR, and RepeatMasker. Results Our analysis was first conducted on the human X chromosome, and microsatellite distributions were characterized by microsatellite number, length, and divergence from a pure motif. The algorithms work with user-defined parameters, and we demonstrate that the parameter values chosen can strongly influence microsatellite distributions. The five algorithms were then compared by fixing parameters settings, and the analysis was extended to three other genomes (Saccharomyces cerevisiae, Neurospora crassa and Drosophila melanogaster spanning a wide range of size and structure. Significant differences for all characteristics of microsatellites were observed among algorithms, but not among genomes, for both perfect and imperfect microsatellites. Striking differences were detected for short microsatellites (below 20 bp, regardless of motif. Conclusion Since the algorithm used strongly influences empirical distributions, studies analyzing microsatellite evolution based on a comparison between empirical and theoretical size distributions should therefore be considered with caution. We also discuss why a typological definition of microsatellites limits our capacity to capture their genomic distributions.

  3. MISA-web: a web server for microsatellite prediction.

    Science.gov (United States)

    Beier, Sebastian; Thiel, Thomas; Münch, Thomas; Scholz, Uwe; Mascher, Martin

    2017-08-15

    Microsatellites are a widely-used marker system in plant genetics and forensics. The development of reliable microsatellite markers from resequencing data is challenging. We extended MISA, a computational tool assisting the development of microsatellite markers, and reimplemented it as a web-based application. We improved compound microsatellite detection and added the possibility to display and export MISA results in GFF3 format for downstream analysis. MISA-web can be accessed under http://misaweb.ipk-gatersleben.de/. The website provides tutorials, usage note as well as download links to the source code. scholz@ipk-gatersleben.de.

  4. Chloroplast microsatellite primers for cacao (Theobroma cacao) and other Malvaceae.

    Science.gov (United States)

    Yang, Ji Y; Motilal, Lambert A; Dempewolf, Hannes; Maharaj, Kamaldeo; Cronk, Q C B

    2011-12-01

    Chloroplast microsatellites were developed in Theobroma cacao to examine the genetic diversity of cacao cultivars in Trinidad and Tobago. Nine polymorphic microsatellites were designed from the chloroplast genomes of two T. cacao accessions. These microsatellites were tested in 95 hybrid accessions from Trinidad and Tobago. An average of 2.9 alleles per locus was found. These chloroplast microsatellites, particularly the highly polymorphic pentameric repeat, were useful in assessing genetic variation in T. cacao. In addition, these markers should also prove to be useful for population genetic studies in other species of Malvaceae.

  5. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species

    Science.gov (United States)

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in three other Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Nineteen microsatellite primers were tes...

  6. Microsatellite-assisted backcross selection in maize

    Directory of Open Access Journals (Sweden)

    Luciana Lasry Benchimol

    2005-12-01

    Full Text Available A microsatellite marker (SSR was chosen to simulate a target allele and three criteria (02, 04 and 06 markers per chromosome were tested to evaluate the most efficient parameters for performing marker-assisted backcross (MAB selection. We used 53 polymorphic SSRs to genotype 186 BC1 maize (Zea mays L. plants produced by crossing the inbred maize lines L-08-05 (donor parent and L-14-4B (recurrent parent. The second backcross (BC2 generation was produced with 180 plants and screened with markers which were not recovered from the first backcross (BC1 generation. A total of 480 plants were evaluated in the third backcross (BC3 generation from which 48 plants were selected for parental genotype recovery. Recurrent genotype recovery averages in three backcross generations were compatible with those expected in BC4 or BC5, indicating genetic gain due to the marker-assisted backcrossing. The target marker (polymorphic microsatellite PHI037 was efficiently transferred. Six markers per chromosome showed a high level of precision for parental estimates at different levels of maize genome saturation and donor alleles were not present in the selected recovered pure lines. Phenotypically, the plants chosen based on this criterion (06 markers per chromosome were closer to the recurrent parent than any other selected by other criteria (02 or 04 markers per chromosome. This approach allowed the understanding that six microsatellites per chromosome is a more efficient parameter than 02 and 04 markers per chromosome for deriving a marker-assisted backcross (MAB experiment in three backcross generations.

  7. New microsatellite markers for bananas (Musa spp).

    Science.gov (United States)

    Amorim, E P; Silva, P H; Ferreira, C F; Amorim, V B O; Santos, V J; Vilarinhos, A D; Santos, C M R; Souza Júnior, M T; Miller, R N G

    2012-04-27

    Thirty-four microsatellite markers (SSRs) were identified in EST and BAC clones from Musa acuminata burmannicoides var. Calcutta 4 and validated in 22 Musa genotypes from the Banana Germplasm Bank of Embrapa-CNPMF, which includes wild and improved diploids. The number of alleles per locus ranged from 2 to 14. The markers were considered highly informative based on their polymorphism information content values; more than 50% were above 0.5. These SSRs will be useful for banana breeding programs, for studies of genetic diversity, germplasm characterization and selection, development of saturated genetic linkage maps, and marker assisted selection.

  8. Mitochondrial microsatellite instability in patients with metastatic colorectal cancer

    NARCIS (Netherlands)

    Venderbosch, S.; van Vliet, S.; Craenmehr, M. H C; Simmer, F.; de Haan, A. F J; Punt, C. J A; Koopman, M.; Nagtegaal, I. D.

    2015-01-01

    Mitochondrial microsatellite instability (mtMSI), a change in length in mtDNA microsatellite sequences between normal and tumor tissue, has been described as a frequent occurrence in colorectal cancer (CRC). We evaluated the prevalence and prognostic value of mtMSI and its relation to nuclear

  9. Evidence for widespread convergent evolution around human microsatellites.

    Directory of Open Access Journals (Sweden)

    Edward J Vowles

    2004-08-01

    Full Text Available Microsatellites are a major component of the human genome, and their evolution has been much studied. However, the evolution of microsatellite flanking sequences has received less attention, with reports of both high and low mutation rates and of a tendency for microsatellites to cluster. From the human genome we generated a database of many thousands of (AC(n flanking sequences within which we searched for common characteristics. Sequences flanking microsatellites of similar length show remarkable levels of convergent evolution, indicating shared mutational biases. These biases extend 25-50 bases either side of the microsatellite and may therefore affect more than 30% of the entire genome. To explore the extent and absolute strength of these effects, we quantified the observed convergence. We also compared homologous human and chimpanzee loci to look for evidence of changes in mutation rate around microsatellites. Most models of DNA sequence evolution assume that mutations are independent and occur randomly. Allowances may be made for sites mutating at different rates and for general mutation biases such as the faster rate of transitions over transversions. Our analysis suggests that these models may be inadequate, in that proximity to even very short microsatellites may alter the rate and distribution of mutations that occur. The elevated local mutation rate combined with sequence convergence, both of which we find evidence for, also provide a possible resolution for the apparently contradictory inferences of mutation rates in microsatellite flanking sequences.

  10. CMD: a Cotton Microsatellite Database resource for Gossypium genomics

    Directory of Open Access Journals (Sweden)

    Liu Shaolin

    2006-05-01

    Full Text Available Abstract Background The Cotton Microsatellite Database (CMD http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. Description At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. Conclusion The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

  11. Candidate driver genes in microsatellite-unstable colorectal cancer

    NARCIS (Netherlands)

    Alhopuro, Pia; Sammalkorpi, Heli; Niittymaki, Iina; Bistrom, Mia; Raitila, Anniina; Saharinen, Juha; Nousiainen, Kari; Lehtonen, Heli J.; Heliovaara, Elina; Puhakka, Jani; Tuupanen, Sari; Sousa, Sonia; Seruca, Raquel; Ferreira, Ana M.; Hofstra, Robert M. W.; Mecklin, Jukka-Pekka; Jarvinen, Heikki; Ristimaki, Ari; Orntoft, Torben F.; Hautaniemi, Sampsa; Arango, Diego; Karhu, Auli; Aaltonen, Lauri A.

    2012-01-01

    Defects in the mismatch repair system lead to microsatellite instability (MSI), a feature observed in similar to 15% of all colorectal cancers (CRCs). Microsatellite mutations that drive tumourigenesis, typically inactivation of tumour suppressors, are selected for and are frequently detected in MSI

  12. Ancient conservation of trinucleotide microsatellite loci in polistine wasps

    DEFF Research Database (Denmark)

    Ezenwa, V O; Peters, J M; Zhu, Y

    1998-01-01

    Microsatellites have proven to be very useful genetic markers for studies of kinship, parentage, and gene mapping. If microsatellites are conserved among species, then those developed for one species can be used on related species, which would save the time and effort of developing new loci. We e...

  13. [Construction and identification on enriched microsatellite library from yak genome].

    Science.gov (United States)

    Li, Qi-Fa; Zhao, Xing-Bo; Luo, Xiao-Lin; Yao, Ping; Li, Ning; Tian, Zhi-Hua; Wu, Chang-Xin; Xie, Zhuang

    2004-05-01

    We constructed the first microsatellite-enriched library of yak according to the strong affinity between biotin and streptavidin. The method included ligation of 300 approximately 1 000 bp enzyme-digested fragments and adaptors, affinity capture of microsatellite repeat using biotinylated oligoprobe ((CA)12, (CCG) 8, (CAG)8, (TTTC) 8) attached to streptavidin-coated magnetic beads, PCR amplification using the 21-mer adaptor oligonucleotide as primer to obtain double-stranded targeted fragments, religated into pMD18-T vector and transformed to DH5alpha. The results of sequencing showed that 37 of 48 readable sequences contained microsatellites indicating a high degree of microsatellite enrichment. The new polymorphic microsatellite markers we have identified and characterized will contribute to the yak genetic linkage mapping, molecular evolution and phylogenetic studies, marker assistant selection and QTLs location of yak main economic traits.

  14. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  15. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries.

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3%) sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds). Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8%) contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds). The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds). From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  16. Microsatellites in the Genome of the Edible Mushroom, Volvariella volvacea

    Directory of Open Access Journals (Sweden)

    Ying Wang

    2014-01-01

    Full Text Available Using bioinformatics software and database, we have characterized the microsatellite pattern in the V. volvacea genome and compared it with microsatellite patterns found in the genomes of four other edible fungi: Coprinopsis cinerea, Schizophyllum commune, Agaricus bisporus, and Pleurotus ostreatus. A total of 1346 microsatellites have been identified, with mono-nucleotides being the most frequent motif. The relative abundance of microsatellites was lower in coding regions with 21 No./Mb. However, the microsatellites in the V. volvacea gene models showed a greater tendency to be located in the CDS regions. There was also a higher preponderance of trinucleotide repeats, especially in the kinase genes, which implied a possible role in phenotypic variation. Among the five fungal genomes, microsatellite abundance appeared to be unrelated to genome size. Furthermore, the short motifs (mono- to tri-nucleotides outnumbered other categories although these differed in proportion. Data analysis indicated a possible relationship between the most frequent microsatellite types and the genetic distance between the five fungal genomes.

  17. A microsatellite platform for hot spot detection

    Energy Technology Data Exchange (ETDEWEB)

    Walter, I.; Briess, K.; Baerwald, W.; Lorenz, E.; Skrbek, W.; Schrandt, F. [DLR, Berlin (Germany). Inst. of Space Sensor Technology & Planetary Exploration

    2005-01-01

    The main payload of the BIRD micro-satellite is the newly developed hot spot recognition system. It's a dual-channel instrument for middle and thermal infrared imagery based on cooled MCT line detectors. The miniaturisation by integrated detector/cooler assemblies provides a highly efficient design. Since the launch in October 2001 from SHAR/India the BIRD payload, claiming 30% of the BIRD mass of 92 kg, is fully operational. Among others forest fires (Australia), volcanoes (Etna, Chile) and burning coal mines (China) have been detected and their parameters like size, temperature and energy release could be determined. As the status of the payload system is satisfactorily it has a potential to be applied in new missions with the help of modern detector technology.

  18. Identification of microsatellites in cattle unigenes

    Institute of Scientific and Technical Information of China (English)

    Qiuliang Yan; Yinghan Zhang; Hongbin Li; Caihong Wei; Lili Niu; Shan Guan; Shangang Li; Lixin Du

    2008-01-01

    To identify EST-SSR molecular markers, 41,986 cattle UniGene sequences from NCBI were mined for analyzing SSRs. A total of 1,831 SSRs were identified from 1,666 ESTs, which represented an average density of 19.88 kb per SSR. The frequency of EST-SSRs was 4.0%. The dinucleotide repeat motif was the most abundant SSR, accounting for 54%, followed by 22%, 13%, 7% and 4%, respec-tively, for tri-, hexa-, penta- and tetra-nucleotide repeats. Depending upon the length of the repeat unit, the length of microsatellites varied from 14 to 86 bp. Among the di- and tri-nucleotide repeats, AC/TG (57%) and AGC (12%) were the most abundant type. Annotation of EST-SSRs was also carried out. Three hundred primer pairs were randomly designed using Prime Premier 5.0 program and Oligo 5.0 for further experimental validation.

  19. Micro-Satellite Attitude Determination Using GPS Carrier Phases

    Institute of Scientific and Technical Information of China (English)

    He Xiu-feng; Ling Keck-voon

    2003-01-01

    GPS is an attractive attitude sensor for micro-satellites due to small package and advantage for cost savings. However, the major difficulty in attitude determination for a micro-satellite is that baseline lengths are short (less than a meter) . Thus , to obtain precise accuracy of attitudes for a micro-satellite, the algorithm selection and error source calibration are important. In this paper, a technique based on the attitude cost function is proposed. To verify the method proposed, the experiments have been conducted. The results indicate that attitude errors are less than 1 deg.

  20. Gene expression signatures for colorectal cancer microsatellite status and HNPCC

    DEFF Research Database (Denmark)

    Kruhøffer, M; Jensen, J L; Laiho, P;

    2005-01-01

    The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary non-polyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI...... of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated...

  1. Microsatellite markers for Russian olive (Elaeagnus angustifolia; Elaeagnaceae)1

    Science.gov (United States)

    Gaskin, John F.; Hufbauer, Ruth A.; Bogdanowicz, Steven M.

    2013-01-01

    • Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. • Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. • Conclusions: These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion. PMID:25202584

  2. Microsatellite Primers in the Lichen Symbiotic Alga Trebouxia decolorans (Trebouxiophyceae

    Directory of Open Access Journals (Sweden)

    Francesco Dal Grande

    2013-03-01

    Full Text Available Premise of the study: Polymorphic microsatellite markers were developed for the symbiotic green alga Trebouxia decolorans to study fine-scale population structure and clonal diversity. Methods and Results: Using Illumina pyrosequencing, 20 microsatellite primer sets were developed for T. decolorans. The primer sets were tested on 43 individuals sampled from four subpopulations in Germany. The primers amplified di-, tri-, and tetranucleotide repeats with three to 15 alleles per locus, and the unbiased haploid diversity per locus ranged from 0.636 to 0.821. Conclusions: The identified microsatellite markers will be useful to study the genetic diversity, dispersal, and reproductive mode of this common lichen photobiont.

  3. Dendritic cell and macrophage infiltration in microsatellite-unstable and microsatellite-stable colorectal cancer.

    Science.gov (United States)

    Bauer, Kathrin; Michel, Sara; Reuschenbach, Miriam; Nelius, Nina; von Knebel Doeberitz, Magnus; Kloor, Matthias

    2011-09-01

    High level microsatellite instability (MSI-H) is a hallmark of Lynch syndrome-associated colorectal cancer (CRC). MSI-H CRC express immunogenic tumour antigens as a consequence of DNA mismatch repair deficiency-induced frameshift mutations. Consequently, frameshift antigen-specific immune responses are commonly observed in patients with Lynch syndrome-associated MSI-H CRC. Dendritic cells (DC) and macrophages play a crucial role in the induction and modulation of immune responses. We here analysed DC and macrophage infiltration in MSI-H and microsatellite-stable CRC. Sixty-nine CRC (MSI-H, n = 33; microsatellite-stable, n = 36) were examined for the density of tumour-infiltrating DC, Foxp3-positive regulatory T cells, and CD163-positive macrophages. In MSI-H lesions, S100-positive and CD163-positive cell counts were significantly higher compared to microsatellite-stable lesions (S100: epithelium P = 0.018, stroma P = 0.042; CD163: epithelium P < 0.001, stroma P = 0.046). Additionally, numbers of CD208-positive mature DC were significantly elevated in the epithelial compartment of MSI-H CRC (P = 0.027). High numbers of tumour-infiltrating Foxp3-positive T cells were detected in tumours showing a low proportion of CD208-positive, mature DC among the total number of S100-positive cells. Our study demonstrates that infiltration with DC, mature DC, and macrophages is elevated in MSI-H compared to microsatellite-stable CRC. The positive correlation of Foxp3-positive Treg cell density with a low proportion of mature DC suggests that impaired DC maturation may contribute to local immune evasion in CRC. Our results demonstrate that DC and macrophages in the tumour environment likely play an important role in the induction of antigen-specific immune responses in Lynch syndrome. Moreover, impaired DC maturation might contribute to local immune evasion in CRC.

  4. Evidence for heterozygote instability in microsatellite loci in house wrens.

    Science.gov (United States)

    Masters, Brian S; Johnson, L Scott; Johnson, Bonnie G P; Brubaker, Jessica L; Sakaluk, Scott K; Thompson, Charles F

    2011-02-23

    Microsatellite loci have high mutation rates and high levels of allelic variation, but the factors influencing their mutation rate are not well understood. The proposal that heterozygosity may increase mutation rates has profound implications for understanding the evolution of microsatellite loci, but currently has limited empirical support. We examined 20 microsatellite mutations identified in an analysis of 12 260 meiotic events across three loci in two populations of a songbird, the house wren (Troglodytes aedon). We found that for an allele of a given length, mutation was significantly more likely when there was a relatively large difference in size between the allele and its homologue (i.e. a large 'allele span'). Our results support the proposal of heterozygote instability at microsatellite loci.

  5. CHARACTERIZATION OF MICROSATELLITE LOCI IN SCHOENOPLECTUS AMERICANUS (CYPERACEAE)

    Science.gov (United States)

    Schoenoplectus americanus is a model organism for studying ecological and ecosystem responses of salt marsh plant communities to global climate change. Here we characterize 16 microsatellite loci in S. americanus to facilitate studies on the genetic basis of phenotypic responses...

  6. Development of microsatellite markers for Carallia brachiata (Rhizophoraceae)1

    Science.gov (United States)

    Qiang, Yinmeng; Xie, Hongxian; Qiao, Sitan; Yuan, Yang; Liu, Ying; Shi, Xianggang; Shu, Mi; Jin, Jianhua; Shi, Suhua; Tan, Fengxiao; Huang, Yelin

    2015-01-01

    Premise of the study: Microsatellite markers were developed for Carallia brachiata to assess the genetic diversity and structure of this terrestrial species of the Rhizophoraceae. Methods and Results: Based on transcriptome data for C. brachiata, 40 primer pairs were initially designed and tested, of which 18 were successfully amplified and 11 were polymorphic. For these microsatellites, one to three alleles per locus were identified. The observed and expected heterozygosities ranged from 0 to 0.727 and 0 to 0.520, respectively. In addition, all primers were successfully amplified in two congeners: C. pectinifolia and C. garciniifolia. Conclusions: The microsatellite markers described here will be useful in population genetic studies of C. brachiata and related species, suggesting that developing microsatellite markers from next-generation sequencing data can be efficient for genetic studies across this genus. PMID:25798345

  7. Genetic diversity studies of Kherigarh cattle based on microsatellite markers

    Indian Academy of Sciences (India)

    A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat

    2006-08-01

    We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles were distinguished by the 21 microsatellite markers used. All the microsatellites were highly polymorphic, with mean (± s.e.) allelic number of 6.24 ± 1.7, ranging 4–10 per locus. The observed heterozygosity in the population ranged between 0.261 and 0.809, with mean (± s.e.) of 0.574 ± 0.131, indicating considerable genetic variation in this population. Genetic bottleneck hypotheses were also explored. Our data suggest that the Kherigarh breed has not experienced a genetic bottleneck in the recent past.

  8. Microsatellite loci and peroxidase alleles correlation in somaclonal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... POD is affected by environmental factors, genotype and their interaction. It is considered to ..... University of Ireland, Ph.D. thesis pp. 1-200. Brondani .... Elymus species using wheat microsatellite markers and RAPD markers.

  9. Basmati aromatic rice genotypes of India using microsatellite markers

    African Journals Online (AJOL)

    Administrator

    Aromatic rice is preferred by consumers all over the world due to its flavor and palatability. ... A dendrogram based on cluster analysis by microsatellite polymorphism grouped all the ..... and Basmati 370) showed a higher degree of similarity.

  10. Quasimonomorphic Mononucleotide Repeats for High-Level Microsatellite Instability Analysis

    Directory of Open Access Journals (Sweden)

    Olivier Buhard

    2004-01-01

    Full Text Available Microsatellite instability (MSI analysis is becoming more and more important to detect sporadic primary tumors of the MSI phenotype as well as in helping to determine Hereditary Non-Polyposis Colorectal Cancer (HNPCC cases. After some years of conflicting data due to the absence of consensus markers for the MSI phenotype, a meeting held in Bethesda to clarify the situation proposed a set of 5 microsatellites (2 mononucleotide repeats and 3 dinucleotide repeats to determine MSI tumors. A second Bethesda consensus meeting was held at the end of 2002. It was discussed here that the 1998 microsatellite panel could underestimate high-level MSI tumors and overestimate low-level MSI tumors. Amongst the suggested changes was the exclusive use of mononucleotide repeats in place of dinucleotide repeats. We have already proposed a pentaplex MSI screening test comprising 5 quasimonomorphic mononucleotide repeats. This article compares the advantages of mono or dinucleotide repeats in determining microsatellite instability.

  11. Microsatellite Primers for the Pacific Northwest Conifer Callitropsis nootkatensis (Cupressaceae

    Directory of Open Access Journals (Sweden)

    Tara N. Jennings

    2013-09-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Nootka cypress (Callitropsis nootkatensis to provide quantitative measures for gene conservation that can assist in guiding management decisions for a species experiencing climate-induced decline. Methods and Results: Using multiplexed massively parallel sequencing, we identified 136,785 microsatellite-containing sequences from 489,625 Illumina paired-end 80-bp reads. After stringent filtering, we selected 144 primer pairs and screened variation at these loci in five populations of C. nootkatensis. Loci show between three and 36 dinucleotide repeats per locus, with an average of 13. Screening of these markers in the Pacific Northwest relative Chamaecyparis lawsoniana demonstrated no marker transferability. This finding highlights the narrow taxonomic utility of microsatellite markers in Callitropsis. Conclusions: These microsatellites show high polymorphism and can be used for routine screening of natural variation in Callitropsis nootkatensis, and will be particularly helpful in identifying clones and inbred relatives at the stand-level.

  12. The pathological phenotype of colon cancer with microsatellite instability

    DEFF Research Database (Denmark)

    Andersen, Helene Schou; Bertelsen, Claus Anders; Henriksen, Rikke;

    2016-01-01

    clinicopathological features of microsatellite unstable tumours with stable ones. METHODS: Data were collected retrospectively, but the pathological analyses were all made prospectively. The study included a total of 833 patients undergoing resection of their colon tumour at Nordsjællands Hospital - Hillerød......, with mismatch repair analysis from 1 January 2007 to 30 November 2012. The study was performed in a setting with complete mesocolic excision surgery and post-operative expert pathological examination of the tumours. Mismatch repair analysis was done by immuno-histochemical staining for the mismatch repair...... proteins: pMLH1, pMSH2, pMSH6 and pPMS2 for the determination of microsatellite instability. Microsatellite instability was defined as deficient expression of one or more of these proteins. RESULTS: Of the 833 patients, 177 had microsatellite instable tumours (21%). Using multivariable logistic regression...

  13. High frequency of microsatellites in S. cerevisiae meiotic recombination hotspots

    Directory of Open Access Journals (Sweden)

    Pitt Joel PW

    2008-01-01

    Full Text Available Abstract Background Microsatellites are highly abundant in eukaryotic genomes but their function and evolution are not yet well understood. Their elevated mutation rate makes them ideal markers of genetic difference, but high levels of unexplained heterogeneity in mutation rates among microsatellites at different genomic locations need to be elucidated in order to improve the power and accuracy of the many types of study that use them as genetic markers. Recombination could contribute to this heterogeneity, since while replication errors are thought to be the predominant mechanism for microsatellite mutation, meiotic recombination is involved in some mutation events. There is also evidence suggesting that microsatellites could function as recombination signals. The yeast S. cerevisiae is a useful model organism with which to further explore the link between microsatellites and recombination, since it is very amenable to genetic study, and meiotic recombination hotspots have been mapped throughout its entire genome. Results We examined in detail the relationship between microsatellites and hotspots of meiotic double-strand breaks, the precursors of meiotic recombination, throughout the S. cerevisiae genome. We included all tandem repeats with motif length (repeat period between one and six base pairs. Long, short and two-copy arrays were considered separately. We found that long, mono-, di- and trinucleotide microsatellites are around twice as frequent in hot than non-hot intergenic regions. The associations are weak or absent for repeats with less than six copies, and also for microsatellites with 4–6 base pair motifs, but high-copy arrays with motif length greater than three are relatively very rare throughout the genome. We present evidence that the association between high-copy, short-motif microsatellites and recombination hotspots is not driven by effects on microsatellite distribution of other factors previously linked to both

  14. Highly polymorphic microsatellite markers for Radix balthica (Linnaeus 1758).

    Science.gov (United States)

    Salinger, M; Pfenninger, M

    2009-07-01

    We present data for eight polymorphic microsatellite markers isolated from a microsatellite-enriched DNA library for the freshwater snail Radix balthica. Three of them were specific for R. balthica while five also amplified polymorphic products in two congeneric species. Test application on populations from all over the species range has shown that these loci are highly informative for analysing population structure and estimating migration rates. Observed deviations from Hardy-Weinberg equilibrium are attributed to a mixed mating system.

  15. Microsatellite genotyping reveals a signature in breast cancer exomes.

    Science.gov (United States)

    McIver, L J; Fonville, N C; Karunasena, E; Garner, H R

    2014-06-01

    Genomic instability at microsatellite loci is a hallmark of many cancers, including breast cancer. However, much of the genomic variation and many of the hereditary components responsible for breast cancer remain undetected. We hypothesized that variation at microsatellites could provide additional genomic markers for breast cancer risk assessment. A total of 1,345 germline and tumor DNA samples from individuals diagnosed with breast cancer, exome sequenced as part of The Cancer Genome Atlas, were analyzed for microsatellite variation. The comparison group for our analysis, representing healthy individuals, consisted of 249 females which were exome sequenced as part of the 1,000 Genomes Project. We applied our microsatellite-based genotyping pipeline to identify 55 microsatellite loci that can distinguish between the germline of individuals diagnosed with breast cancer and healthy individuals with a sensitivity of 88.4 % and a specificity of 77.1 %. Further, we identified additional microsatellite loci that are potentially useful for distinguishing between breast cancer subtypes, revealing a possible fifth subtype. These findings are of clinical interest as possible risk diagnostics and reveal genes that may be of potential therapeutic value, including genes previously not associated with breast cancer.

  16. megasat: automated inference of microsatellite genotypes from sequence data.

    Science.gov (United States)

    Zhan, Luyao; Paterson, Ian G; Fraser, Bonnie A; Watson, Beth; Bradbury, Ian R; Nadukkalam Ravindran, Praveen; Reznick, David; Beiko, Robert G; Bentzen, Paul

    2017-03-01

    megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length-frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0-1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.

  17. Microsatellite discovery by deep sequencing of enriched genomic libraries.

    Science.gov (United States)

    Santana, Quentin; Coetzee, Martin; Steenkamp, Emma; Mlonyeni, Osmond; Hammond, Gifty; Wingfield, Michael; Wingfield, Brenda

    2009-03-01

    Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2-1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose.

  18. SnoN expression is differently regulated in microsatellite unstable compared with microsatellite stable colorectal cancers

    Directory of Open Access Journals (Sweden)

    Leggett Barbara A

    2006-10-01

    Full Text Available Abstract Background SnoN is an important regulator of the transforming growth factor beta (TGFβ signalling pathway and has been shown to exhibit both tumour promotion and suppression activity. Methods To further explore the role of this complex molecule in colorectal tumorigenesis, we examined 52 paired normal and tumour colorectal specimens stratified by level of microsatellite instability; 18 with high-level microsatellite instability (MSI-H and 34 microsatellite stable (MSS. SnoN transcript expression was quantitated by real-time PCR and analysed with respect to clinical indicators of prognosis. Results Within the MSI-H subgroup, SnoN was commonly either up-regulated (6/18, 33% or down-regulated (7/18, 39%. A significantly different distribution of SnoN expression was observed in MSS cancers compared with MSI-H (P ≤ 0.001. Whilst 17/34 (50% of MSS tumours demonstrated up-regulation, none showed down-regulated expression. Within the MSI-H subgroup, up-regulation was significantly correlated with lack of repeat tract mutation in the TGFβRII gene (P ≤ 0.025, suggesting that SnoN is more frequently up-regulated in the presence of functional TGFβ signalling. Conclusion Together these data support the notion that SnoN has both oncogenic and tumour suppressive properties depending on other genetic changes within the tumour, and that the MSI-H pathway of colorectal tumorigenesis presents an excellent model for the study of these opposing functions.

  19. Detected microsatellite polymorphisms in genetically altered inbred mouse strains.

    Science.gov (United States)

    Du, Xiaoyan; Cui, Jing; Wang, Chao; Huo, Xueyun; Lu, Jing; Li, Yichen; Chen, Zhenwen

    2013-08-01

    Microsatellites are 50-200 repetitive DNA sequences composed of 1- to 6-base-pair-long reiterative motifs within the genome. They are vulnerable to DNA modifications, such as recombination and/or integration, and are recognized as "sentinel" DNA. Our previous report indicated that the genotypes of the microsatellite loci could change from mono- to poly-morphisms (CMP) in gene knockout (KO) mice, implying that genetic modification induces microsatellite mutation. However, it is still unclear whether the random insertion of DNA fragments into mice genomes produced via transgene (Tg) or N-ethyl-N-nitrosourea (ENU) would also result in microsatellite mutations or microsatellite loci genotypes changes. This study was designed to find possible clues to answer this question. In brief, 198 microsatellite loci that were distributed among almost all of the chromosomes (except for the Y) were examined through polymerase chain reaction to screen possible CMPs in six Tg strains. First, for each strain, the microsatellite sequences of all loci were compared between Tg and the corresponding background strain to exclude genetic interference. Simultaneously, to exclude spontaneous mutation-related CMPs that might exist in the examined six strains, mice from five spontaneously mutated inbred strains were used as the negative controls. Additionally, the sequences of all loci in these spontaneous mutated mice were compared to corresponding genetic background controls. The results showed that 40 of the 198 (20.2%) loci were identified as having CMPs in the examined Tg mice strains. The CMP genotypes were either homozygous or heterozygous compared to the background controls. Next, we applied the 40 CMP positive loci in ENU-mutated mice and their corresponding background controls. After that, a general comparison of CMPs that exist among Tg, ENU-treated and KO mouse strains was performed. The results indicated that four (D11mit258, D13mit3, D14mit102 and DXmit172) of the 40 (10%) CMP

  20. Microsatellite polymorphisms of Sichuan golden monkeys

    Institute of Scientific and Technical Information of China (English)

    PAN Deng; LI Ying; HU Hongxing; MENG Shijie; MEN Zhengrning; FU Yunxin; ZHANG Yaping

    2005-01-01

    Previous study using protein electrophoresis shows no polymorphism in 44 nuclear loci of Sichuan golden monkey (Rhinopithecus roxellana), which limits our understandings of its population genetic patterns in the nuclear genome. In order to obtain sufficient information, we scanned 14 microsatellite loci in a sample of 32 individuals from its three major habitats (Minshan, Qinling and Shennongjia). A considerable amount of polymorphisms were detected. The average heterozygosities in the local populations were all above 0.5. The differentiations among local populations were significant. There was evidence of geneflow among subpopulations, but geneflow between Qinling and Shennongjia local populations was the weakest. Minshan and Qinling populations might have gone through recent bottlenecks. The estimation of the ratio of the effective population sizes among local populations was close to that from census sizes. Comparisons to available mitochondria data suggested that R. roxellana's social structures played an important role in shaping its population genetic patterns. Our study showed that the polymorphism level of R. roxellana was no higher than other endangered species; therefore, measures should be taken to preserve genetic diversity of this species.

  1. Mutation rate analysis at 19 autosomal microsatellites.

    Science.gov (United States)

    Qian, Xiao-Qin; Yin, Cai-Yong; Ji, Qiang; Li, Kai; Fan, Han-Ting; Yu, Yan-Fang; Bu, Fan-Li; Hu, Ling-Li; Wang, Jian-Wen; Mu, Hao-Fang; Haigh, Steven; Chen, Feng

    2015-07-01

    Previous studies have demonstrated that a large sample size is needed to reliably estimate population- and locus-specific microsatellite mutation rates. Therefore, we conducted a long-term collaboration study and performed a comprehensive analysis on the mutation characteristics of 19 autosomal short tandem repeat (STR) loci. The STR loci located on 15 of 22 autosomal chromosomes were analyzed in a total of 21,106 samples (11,468 parent-child meioses) in a Chinese population. This provided 217,892 allele transfers at 19 STR loci. An overall mutation rate of 1.20 × 10(-3) (95% CI, 1.06-1.36 × 10(-3) ) was observed in the populations across 18 of 19 STR loci, except for the TH01 locus with no mutation found. Most STR mutations (97.7%) were single-step mutations, and only a few mutations (2.30%) comprised two and multiple steps. Interestingly, approximately 93% of mutation events occur in the male germline. The mutation ratios increased with the paternal age at child birth (r = 0.99, ptesting, kinship analysis, and population genetics.

  2. Microsatellite analysis of medfly bioinfestations in California.

    Science.gov (United States)

    Bonizzoni, M; Zheng, L; Guglielmino, C R; Haymer, D S; Gasperi, G; Gomulski, L M; Malacrida, A R

    2001-10-01

    The Mediterranean fruit fly, Ceratitis capitata, is a destructive agricultural pest with a long history of invasion success. This pest has been affecting different regions of the United States for the past 30 years, but a number of studies of medfly bioinfestations has focused on the situation in California. Although some progress has been made in terms of establishing the origin of infestations, the overall status of this pest in this area remains controversial. Specifically, do flies captured over the years represent independent infestations or the persistence of a resident population? We present an effort to answer this question based on the use of multilocus genotyping. Ten microsatellite loci were used to analyse 109 medflies captured in several infestations within California between 1992 and 1998. Using these same markers, 242 medflies from regions of the world having 'established' populations of this pest including Hawaii, Guatemala, El Salvador, Ecuador, Brazil, Argentina and Peru, were also analysed. Although phylogenetic analysis, amova analysis, the IMMANC assignment test and geneclass exclusion test analysis suggest that some of the medflies captured in California are derived from independent invasion events, analysis of specimens from the Los Angeles basin provides support for the hypothesis that an endemic population, probably derived from Guatemala, has been established.

  3. Spin-Stabilized Microsatellites with Solar Concentrators

    Science.gov (United States)

    Timmerman, Paul; Shields, Virgil

    2008-01-01

    A document proposes the development of spin-stabilized microsatellites powered by solar photovoltaic cells aided by solar concentrators. Each such satellite would have a cylindrical or other axisymmetric main body with solar cells mounted in a circumferential belt-like array on its exterior surface. The solar concentrator would be a halo-like outrigger cylindrical Fresnel lens array that would be deployed from and would surround the main body, connected to the main body via spokes or similar structural members. The spacecraft would be oriented with its axis of symmetry perpendicular to the line of sight to the Sun and would be set into rotation about this axis. In effect, the solar cells and concentrator would be oriented and rotated in a "rotisserie" mode, making it possible to take advantage of the concentration of solar light while preventing localized overheating of the solar cells. In addition, the mechanical stabilization inherently afforded by the rotation could be exploited as a means of passive attitude control or, at least, of reducing the requirement for active attitude control.

  4. Microsatellites grant more stable flanking genes

    Directory of Open Access Journals (Sweden)

    Joukhadar Reem

    2012-10-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are DNA sequences that include tandem copies of specific sequences no longer than six bases. SSRs are ubiquitous in all genomes and highly mutable. Presentation of the hypothesis Results from previous studies suggest that flanking regions of SSR are exhibit high stability in a wide range of organisms. We hypothesized that the SSRs ability to discard weak DNA polymerases could be responsible for this unusual stability. . When the weak polymerases are being decayed over SSRs, the flanking sequences would have higher opportunity to be replicated by more stable DNA polymerases. We present evidence of the molecular basis of our hypothesis. Testing the hypothesis The hypothesis could be tested by examining the activity of DNA polymerase during and after a number of PCRs. The PCR reactions should be run with the same SSR locus possessing differences in the SSR length. The hypothesis could also be tested by comparing the mutational rate of a transferred gene between two transformations. The first one has a naked T-DNA (transferred DNA, while the second one has the same T-DNA flanked with two SSRs. Implications of the hypothesis In any transformation experiment, flanking the T-DNA fragment with SSR sequences would result in more stably transferred genes. This process would decrease the unpredictable risks that may occur because of the mutational pressure on this foreign segment.

  5. Microsatellite data support subpopulation structuring among Basques.

    Science.gov (United States)

    Pérez-Miranda, Ana M; Alfonso-Sánchez, Miguel A; Kalantar, Arif; García-Obregón, Susana; de Pancorbo, Marian M; Peña, José A; Herrera, Rene J

    2005-01-01

    Genomic diversity based on 13 short tandem repeat (STR) loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, and CSF1PO) is reported for the first time in Basques from the provinces of Guipúzcoa and Navarre (Spain). STR data from previous studies on Basques from Alava and Vizcaya provinces were also examined using hierarchal analysis of molecular variance (AMOVA) and genetic admixture estimations to ascertain whether the Basques are genetically heterogeneous. To assess the genetic position of Basques in a broader geographic context, we conducted phylogenetic analyses based on F(ST) genetic distances [neighbor-joining trees and multidimensional scaling (MDS)] using data compiled in previous publications. The genetic profile of the Basque groups revealed distinctive regional partitioning of short tandem repeat (STR) diversity. Consistent with the above, native Basques clearly segregated from other populations from Europe (including Spain), North Africa, and the Middle East. The main line of genetic discontinuity inferred from the spatial variability of the microsatellite diversity in Basques significantly overlapped the geographic distribution of the Basque language. The genetic heterogeneity among native Basque groups correlates with the peculiar geography of peopling and marital structure in rural Basque zones and with language boundaries resulting from the uneven impact of Romance languages in the different Basque territories.

  6. Microsatellite variation in Avena sterilis oat germplasm.

    Science.gov (United States)

    Fu, Yong-Bi; Chong, James; Fetch, Tom; Wang, Ming-Li

    2007-04-01

    The Avena sterilis L. collection in the Plant Gene Resources of Canada (PGRC) consists of 11,235 accessions originating from 27 countries and is an invaluable source of genetic variation for genetic improvement of oats, but it has been inadequately characterized, particularly using molecular techniques. More than 35 accessions have been identified with genes for resistance to oat crown and stem rusts, but little is known about their comparative genetic diversity. This study attempted to characterize a structured sample of 369 accessions representing 26 countries and two specific groups with Puccinia coronata avenae (Pc) and Puccinia graminis avenae (Pg) resistance genes using microsatellite (SSR) markers. Screening of 230 SSR primer pairs developed from other major crop species yielded 26 informative primer pairs for this characterization. These 26 primer pairs were applied to screen all the samples and 125 detected alleles were scored for each accession. Analyses of the SSR data showed the effectiveness of the stratified sampling applied in capturing country-wise SSR variation. The frequencies of polymorphic alleles ranged from 0.01 to 0.99 and averaged 0.28. More than 90% of the SSR variation resided within accessions of a country. Accessions from Greece, Liberia, and Italy were genetically most diverse, while accessions from Egypt, Georgia, Ethiopia, Gibraltar, and Kenya were most distinct. Seven major clusters were identified, each consisting of accessions from multiple countries and specific groups, and these clusters were not well congruent with geographic origins. Accessions with Pc and Pg genes had similar levels of SSR variation, did not appear to cluster together, and were not associated with the other representative accessions. These SSR patterns are significant for understanding the progenitor species of cultivated oat, managing A. sterilis germplasm, and exploring new sources of genes for oat improvement.

  7. Evolution of coding microsatellites in primate genomes.

    Science.gov (United States)

    Loire, Etienne; Higuet, Dominique; Netter, Pierre; Achaz, Guillaume

    2013-01-01

    Microsatellites (SSRs) are highly susceptible to expansions and contractions. When located in a coding sequence, the insertion or the deletion of a single unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR creates a frameshift. As a consequence, one would expect to find only very few of these SSRs in coding sequences because of their strong deleterious potential. Unexpectedly, genomes contain many coding SSRs of all types. Here, we report on a study of their evolution in a phylogenetic context using the genomes of four primates: human, chimpanzee, orangutan, and macaque. In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions. We show that the rate of substitution in all types of coding SSRs is typically two times higher than in the rest of coding sequences. Additionally, we observe that although numerous coding SSRs are created and lost by substitutions in the lineages, their numbers remain constant. This last observation suggests that the coding SSRs have reached equilibrium. We hypothesize that this equilibrium involves a combination of mutation, drift, and selection. We thus estimated the fitness cost of mono-SSRs and show that it increases with the number of units. We finally show that the cost of coding mono-SSRs greatly varies from function to function, suggesting that the strength of the selection that acts against them can be correlated to gene functions.

  8. Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome

    Indian Academy of Sciences (India)

    Sreepriya Pramod; Andy D. Perkins; Mark E. Welch

    2014-08-01

    The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5′UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.

  9. Patterns of microsatellite evolution inferred from the Helianthus annuus (Asteraceae) transcriptome.

    Science.gov (United States)

    Pramod, Sreepriya; Perkins, Andy D; Welch, Mark E

    2014-08-01

    The distribution of microsatellites in exons, and their association with gene ontology (GO) terms is explored to elucidate patterns of microsatellite evolution in the common sunflower, Helianthus annuus. The relative position, motif, size and level of impurity were estimated for each microsatellite in the unigene database available from the Compositae Genome Project (CGP), and statistical analyses were performed to determine if differences in microsatellite distributions and enrichment within certain GO terms were significant. There are more translated than untranslated microsatellites, implying that many bring about structural changes in proteins. However, the greatest density is observed within the UTRs, particularly 5'UTRs. Further, UTR microsatellites are purer and longer than coding region microsatellites. This suggests that UTR microsatellites are either younger and under more relaxed constraints, or that purifying selection limits impurities, and directional selection favours their expansion. GOs associated with response to various environmental stimuli including water deprivation and salt stress were significantly enriched with microsatellites. This may suggest that these GOs are more labile in plant genomes, or that selection has favoured the maintenance of microsatellites in these genes over others. This study shows that the distribution of transcribed microsatellites in H. annuus is nonrandom, the coding region microsatellites are under greater constraint compared to the UTR microsatellites, and that these sequences are enriched within genes that regulate plant responses to environmental stress and stimuli.

  10. EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

    Directory of Open Access Journals (Sweden)

    Grover Atul

    2007-07-01

    Full Text Available Abstract Background Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database http://ipu.ac.in/usbt/EuMicroSatdb.htm is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes. Description A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP. The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect, repeat unit length (mono- to hexa-nucleotide, repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided. Conclusion The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

  11. Microsatellites with Macro-Influence in Ewing Sarcoma

    Directory of Open Access Journals (Sweden)

    Stephen L. Lessnick

    2012-07-01

    Full Text Available Numerous molecular abnormalities contribute to the genetic derangements involved in tumorigenesis. Chromosomal translocations are a frequent source of these derangements, producing unique fusion proteins with novel oncogenic properties. EWS/ETS fusions in Ewing sarcoma are a prime example of this, resulting in potent chimeric oncoproteins with novel biological properties and a unique transcriptional signature essential for oncogenesis. Recent evidence demonstrates that EWS/FLI, the most common EWS/ETS fusion in Ewing sarcoma, upregulates gene expression using a GGAA microsatellite response element dispersed throughout the human genome. These GGAA microsatellites function as enhancer elements, are sites of epigenetic regulation and are necessary for EWS/FLI DNA binding and upregulation of principal oncogenic targets. An increasing number of GGAA motifs appear to substantially enhance EWS/FLI-mediated gene expression, which has compelling biological implications as these GGAA microsatellites are highly polymorphic within and between ethnically distinct populations. Historically regarded as junk DNA, this emerging evidence clearly demonstrates that microsatellite DNA plays an instrumental role in EWS/FLI-mediated transcriptional regulation and oncogenesis in Ewing sarcoma. This unprecedented role of GGAA microsatellite DNA in Ewing sarcoma provides a unique opportunity to expand our mechanistic understanding of how EWS/ETS fusions influence cancer susceptibility, prognosis and transcriptional regulation.

  12. DNA microsatellite characterization of the jaguar (Panthera onca) in Colombia.

    Science.gov (United States)

    Ruiz-Garcia, Manuel; Payán, Esteban; Murillo, Andrea; Alvarez, Diana

    2006-04-01

    The Colombian jaguar population is thought to contain two different subspecies, Panthera onca centralis and Panthera onca onca. The genetic structure of this population was evaluated using 12 microsatellite loci (n = 62 samples). In addition, 22 jaguar DNA samples from Guatemala, Paraguay, Perú, Bolivia, Venezuela and Brazil were analyzed for these microsatellite loci (n = 84 samples). The results of this study indicate six primary themes. First, the levels of gene diversity were very high. Second, the majority of the loci analyzed showed an absence of Hardy-Weinberg equilibrium, probably due to the Wahlund effect (= population subdivision). Third, several microsatellite loci showed significant heterogeneity between the two supposed subspecies in the country. Nevertheless, gene flow was present between them, and heterogeneity was relatively low, although the assignment analyses showed good classification of the jaguars studied into their respective subspecies. Fourth, the long-term historical effective population sizes were calculated through a maximum likelihood procedure for single and multi-step mutation models. Fifth, seven out of twelve DNA microsatellites studied significantly deviated from a single-step mutation model. However, the overall mean multi-step mutation percentage for these 12 DNA microsatellites was only 6%. Therefore, 94% of mutations were uni-step. Sixth, no bottleneck events were detected in the Colombian jaguar population overall.

  13. varver: a database of microsatellite variation in vertebrates.

    Science.gov (United States)

    Yashima, Akiko Sato; Innan, Hideki

    2016-10-31

    Understanding how genetic variation is maintained within a species is important in ecology, evolution, conservation and population genetics. Tremendous efforts have been made to evaluate the patterns of genetic variation in natural populations of various species. For this purpose, microsatellites have played a major role since the 1990s. Here we describe a comprehensive database, varver (Variation in Vertebrates) that provides complete information regarding microsatellite variation in natural populations of vertebrates. For each species, varver includes basic information of the species, a list of publications reporting the microsatellite variation, and tables of genetic variation within and between populations (heterozygosity and FST ). The geographic location and rough sampling range are also shown for each sampled population. The database should be useful for researchers interested in not only specific species but also comparing multiple species. We discuss the utility of microsatellite data, particularly for meta-analyses that involve multiple microsatellite loci from various species. We show that in such analyses, it is extremely important to correct for biases caused by differences in mutation rate, mainly due to repeat unit and number.

  14. A novel approach for characterizing microsatellite instability in cancer cells.

    Directory of Open Access Journals (Sweden)

    Yuheng Lu

    Full Text Available Microsatellite instability (MSI is characterized by the expansion or contraction of DNA repeat tracts as a consequence of DNA mismatch repair deficiency (MMRD. Accurate detection of MSI in cancer cells is important since MSI is associated with several cancer subtypes and can help inform therapeutic decisions. Although experimental assays have been developed to detect MSI, they typically depend on a small number of known microsatellite loci or mismatch repair genes and have limited reliability. Here, we report a novel genome-wide approach for MSI detection based on the global detection of insertions and deletions (indels in microsatellites found in expressed genes. Our large-scale analyses of 20 cancer cell lines and 123 normal individuals revealed striking indel features associated with MSI: there is a significant increase of short microsatellite deletions in MSI samples compared to microsatellite stable (MSS ones, suggesting a mechanistic bias of repair efficiency between insertions and deletions in normal human cells. By incorporating this observation into our MSI scoring metric, we show that our approach can correctly distinguish between MSI and MSS cancer cell lines. Moreover, when we applied this approach to primal tumor samples, our metric is also well consistent with diagnosed MSI status. Thus, our study offers new insight into DNA mismatch repair system, and also provides a novel MSI diagnosis method for clinical oncology with better reliability.

  15. The pathological phenotype of colon cancer with microsatellite instability

    DEFF Research Database (Denmark)

    Andersen, Helene Schou; Bertelsen, Claus Anders; Henriksen, Rikke;

    2016-01-01

    INTRODUCTION: Colorectal cancer is a common malignant disease, caused by different aetiologies and molecular pathways. Heterogeneous results have been published regarding the association of microsatellite instability and clinicopathological features. The aim of this study was to compare clinicopa......INTRODUCTION: Colorectal cancer is a common malignant disease, caused by different aetiologies and molecular pathways. Heterogeneous results have been published regarding the association of microsatellite instability and clinicopathological features. The aim of this study was to compare...... clinicopathological features of microsatellite unstable tumours with stable ones. METHODS: Data were collected retrospectively, but the pathological analyses were all made prospectively. The study included a total of 833 patients undergoing resection of their colon tumour at Nordsjællands Hospital - Hillerød...... analysis, we demonstrated that microsatellite unstable cancers were significantly associated with a lower degree of lymph node metastases (odds ratio (OR) = 0.92), distant metastases (OR = 0.33) and tumour budding (OR = 0.41). CONCLUSIONS: We found that microsatellite unstable tumours show a pathological...

  16. The same but different: monomorphic microsatellite markers as a new tool for genetic analysis

    National Research Council Canada - National Science Library

    Nazareno, Alison G; dos Reis, Mauricio S

    2011-01-01

    .... From a set of microsatellite markers, a monomorphic microsatellite locus developed for the palm species Butia eriospatha was used to elucidate whether there are polymorphic sites in its flanking regions. DNA sequences...

  17. Characterization of microsatellite DNA libraries from three mealybug species and development of microsatellite markers for Pseudococcus viburni (Hemiptera: Pseudococcidae).

    Science.gov (United States)

    Correa, M C G; Zaviezo, T; Le Maguet, J; Herrbach, E; Malausa, T

    2014-04-01

    Mealybugs (Hemiptera: Pseudococcidae) are important pests for crops worldwide. Different species, cryptic taxa under the same species name or even populations within a species can differ in biological characteristics, such as phenology, resistance to insecticides, virus transmission and susceptibility to natural enemies. Therefore, their management efficacy depends on their accurate identification. Microsatellite genetic markers are efficient in revealing the fine-scale taxonomic status of insects, both at inter- and intra-specific level. Despite their potential uses, microsatellites have been developed only for one mealybug species so far. Hence, it is unclear whether microsatellites may be useful to assess mealybug population differentiation and structuring. In this work, we tested the feasibility of developing microsatellite markers in mealybugs by: (i) producing and characterizing microsatellite DNA libraries for three species: Pseudococcus viburni, Pseudococcus comstocki and Heliococcus bohemicus, and (ii) by developing and testing markers for Ps. viburni. The obtained libraries contained balanced percentages of dinucleotide (ranging from 15 to 25%) and trinucleotide (from 5 to 17%) motifs. The marker setup for Ps. viburni was successful, although 70% of the primers initially tested were discarded for a lack of polymorphism. Finally, 25 markers were combined in two multiplex polymerase chain reactions with 21 displaying no evidence of deviation from Hardy-Weinberg equilibrium. Ps. viburni markers were tested on one population from France and one from Chile. The markers revealed a significant genetic differentiation between the two populations with an Fst estimate of 0.266.

  18. Genetic diversity in some local chicken breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    M. Cassandro

    2010-04-01

    Full Text Available Genetic relationships among Veneto native breeds of chickens were studied on the basis of microsatellites polymorphisms. A total of 100 DNA samples from 2 local chicken breeds (45 Robusta Lionata and 43 Robusta Maculata and a commercial broiler line (12 Golden Comet were analyzed using 19 microsatellite markers. The average number of alleles per locus was 4.05 and the expected heterozigosity resulted lower for the local breeds than the broiler line. The Robusta Lionata breed and the broiler line showed a significant deficit and excess of heterozygotes, respectively, deviating from Hardy-Weinberg equilibrium. Nei’s standard genetic distances corrected for bias due to sampling of individuals (Da, based on allele frequencies, were calculated among breeds. The local breeds resulted very similar confirming the same genetic origin. The results suggested that microsatellite markers are a useful tool for studying the genetic diversity among local chicken breeds.

  19. Tracing Asian seabass individuals to single fish farms using microsatellites.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    Full Text Available Traceability through physical labels is well established, but it is not highly reliable as physical labels can be easily changed or lost. Application of DNA markers to the traceability of food plays an increasingly important role for consumer protection and confidence building. In this study, we tested the efficiency of 16 polymorphic microsatellites and their combinations for tracing 368 fish to four populations where they originated. Using the maximum likelihood and Bayesian methods, three most efficient microsatellites were required to assign over 95% of fish to the correct populations. Selection of markers based on the assignment score estimated with the software WHICHLOCI was most effective in choosing markers for individual assignment, followed by the selection based on the allele number of individual markers. By combining rapid DNA extraction, and high-throughput genotyping of selected microsatellites, it is possible to conduct routine genetic traceability with high accuracy in Asian seabass.

  20. Methods for Development of Microsatellite Markers: An Overview

    Directory of Open Access Journals (Sweden)

    Siju SENAN

    2014-03-01

    Full Text Available Microsatellite or Simple Sequence Repeat (SSR markers have evolved to the status of a most versatile and popular genetic marker in a ubiquity of plant systems. Due to their co-dominant, hyper-variable and multiallelic nature, they are the prominent markers of choice for fingerprinting, conservation genetics, plant breeding and phylogenetic studies. Despite its development of a new set of SSR markers for a species remained time consuming and expensive for many years. However, with the recent advancement in genomics, new strategies/protocols are now available for the generation of SSR markers. This review presents an overview on microsatellite markers with a special emphasis on the various strategies used for the development of microsatellite markers

  1. Development and Characterization of Microsatellite Markers for Lilium longiflorum (Liliaceae

    Directory of Open Access Journals (Sweden)

    Satomi Sakazono

    2013-09-01

    Full Text Available Premise of the study: Ten microsatellite primers were developed to obtain information on genetic variation in Lilium longiflorum, a bulbous species showing high intraspecific genetic differentiation. Methods and Results: Of 61 microsatellite loci isolated using the dual suppression PCR technique, 10 loci were effective to characterize and estimate genetic variation in two populations of L. longiflorum. The number of alleles at each locus was different between the populations (averages = 3.2 and 10.3 alleles per locus, and the mean observed heterozygosity values were 0.245 and 0.732. Conclusions: Our results demonstrate that there is significant genetic variation between the populations and that the microsatellite markers developed in this study will be useful tools for the investigation of the genetic structure and mating system of natural L. longiflorum populations.

  2. Analysis of microsatellite polymorphism in inbred knockout mice.

    Science.gov (United States)

    Zuo, Baofen; Du, Xiaoyan; Zhao, Jing; Yang, Huixin; Wang, Chao; Wu, Yanhua; Lu, Jing; Wang, Ying; Chen, Zhenwen

    2012-01-01

    Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)(n) (50%, 2/4), followed by (GT)(n) (27.27%, 3/11) and (CA)(n) (23.08%, 3/13). The microsatellite CMP in (CT)(n) and (AG)(n) repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  3. Analysis of microsatellite polymorphism in inbred knockout mice.

    Directory of Open Access Journals (Sweden)

    Baofen Zuo

    Full Text Available Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR in 29 KO inbred mouse strains via short tandem sequence repeat (STR scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8% loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95% showed CMPs among detected mouse strains. However, 11 out of 29 (37.9% KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG(n (50%, 2/4, followed by (GT(n (27.27%, 3/11 and (CA(n (23.08%, 3/13. The microsatellite CMP in (CT(n and (AG(n repeats were 20% (1/5. According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102 revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3 simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice.

  4. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species 1

    OpenAIRE

    Colby Witherup; Diane Ragone; Tyr Wiesner-Hanks; Brian Irish; Brian Scheffler; Sheron Simpson; Francis Zee; M. Iqbal Zuberi; Zerega, Nyree J. C.

    2013-01-01

    Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (1...

  5. Laser microdissection and microsatellite analysis of colorectal adenocarcinomas

    DEFF Research Database (Denmark)

    Jensen, Lars Henrik; Cruger, Dorthe G; Lindebjerg, Jan;

    2006-01-01

    BACKGROUND: Microsatellite instability (MSI) is an important marker in colorectal cancer. The analysis may be difficult if the tumour is heterogeneous or only scarce material is available. The aim of this study was to apply laser microdissection (LMD) to MSI analysis in an attempt to allow...... the MSI status. RESULTS: The method proved efficient in as little as 4,000 microm3 formalin-treated and paraffin-embedded tumour tissue. The result of microsatellite analysis was independent of sample location in the primary tumour and its metastasis. CONCLUSION: LMD followed by a multiplex PCR...

  6. Microsatellites from the charcoal rot fungus (Macrophomina phaseolina).

    Science.gov (United States)

    Baird, Richard E; Wadl, Phillip A; Wang, Xinwang; Johnson, Denita H; Rinehart, Timothy A; Abbas, Hamed K; Shier, Thomas; Trigiano, Robert N

    2009-05-01

    Microsatellite loci were identified from the charcoal rot fungus (Macrophomina phaseolina). Primer pairs for 46 loci were developed, and of these, 13 were optimized and screened using genomic DNA from 55 fungal isolates collected predominantly from two soybean fields in Mississippi. Twelve of the optimized loci were polymorphic and the number of alleles per locus ranged from 6 to 22. These microsatellites will be useful in population and pathogenicity studies to correspond with development of potential disease-resistant soybean and other susceptible crops. © 2009 Blackwell Publishing Ltd. No claim to original US government works.

  7. Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae).

    Science.gov (United States)

    Quan, Zhiwu; Pan, Lei; Ke, Weidong; Ding, Yi

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated and identified in the aquatic plant Euryale ferox Salisb. (Nymphaeaceae). This species, which belongs to basal Magnoliophyta, reproduces sexually. All of these 11 microsatellite markers yielded 25 alleles in a survey of a wild population of 34 individuals. Two or three alleles per locus were detected, with expected heterozygosity ranging from 0.056 to 0.634 and observed heterozygosity from 0.000 to 0.088. These simple sequence repeat markers will be useful for evaluating the genetic structure of the E. ferox population in the future.

  8. Characterization of 11 new microsatellite loci in taro (Colocasia esculenta).

    Science.gov (United States)

    Hu, Kan; Huang, Xing Fang; Ke, Wei Dong; Ding, Yi

    2009-03-01

    Eleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty-eight primer pairs were designed from a microsatellite-enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.

  9. Identification of cut-rose (Rosa hybrida) and rootstock varieties using robust Sequence Tagged Microsatellite markers

    NARCIS (Netherlands)

    Esselink, D.; Smulders, M.J.M.; Vosman, B.

    2003-01-01

    In this study a DNA fingerprinting protocol was developed for the identification of rose varieties based on the variability of microsatellites. Microsatellites were isolated from Rosa hybrida L. using enriched small insert libraries. In total 24 polymorphic sequenced tagged microsatellite site

  10. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

    Science.gov (United States)

    Adams, Richard H; Blackmon, Heath; Reyes-Velasco, Jacobo; Schield, Drew R; Card, Daren C; Andrew, Audra L; Waynewood, Nyimah; Castoe, Todd A

    2016-05-01

    The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.

  11. Microsatellite loci for genetic mapping in the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Reed, K M; Chaves, L D; Hall, M K; Knutson, T P; Rowe, J A; Torgerson, A J

    2003-11-01

    New microsatellite loci for the turkey (Meleagris gallopavo) were developed from two small insert DNA libraries. Polymorphism at these new loci was examined in domestic birds and two resource populations designed for genetic linkage mapping. The majority of loci (152 of 168) was polymorphic in domestic turkeys and informative in two mapping resource populations and thus will be useful for genetic linkage mapping.

  12. Development and use of microsatellite markers in Marama bean

    African Journals Online (AJOL)

    Prof. Adipala Ekwamu

    develop SSR's for detection of polymorphisms in Marama bean. The microsatellite regions of the .... primer by combining 20 µl PCR product (200 µg) and 1 µl primer (10 µM) ... unrelated DNA (sheared herring sperm at 1 mg ml-1) was added to ...

  13. A Multiplexed Microsatellite Fingerprinting Set for Hazelnut Cultivar Identification

    Science.gov (United States)

    The objective of this study was to develop a robust and cost-effective fingerprinting set for hazelnuts using microsatellite (SSR) markers. Twenty SSRs containing repeat motifs of = three nucleotides distributed throughout the hazelnut genome were screened on eight genetically diverse cultivars to a...

  14. Larus Gull Microsatellite DNA Data, 2006-2009

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This data set describes nuclear microsatellite genotypes derived from eleven autosomal loci (Hg16, Hg18, Hg25, K16, Lar12, Lar19, Lar24, Lar26, Rbg13, Rbg18, and...

  15. Microsatellite loci for the invasive colonial hydrozoan Cordylophora caspia

    Science.gov (United States)

    Cordylophora caspia, a colonial hydrozoan native to the Ponto-Caspian region, has become a common invader of both fresh and brackish water ecosystems of North America and Europe. Here we describe 11 polymorphic microsatellite loci for this species. Preliminary analyses indicate ...

  16. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

    Science.gov (United States)

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus (A.) altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: 15 simple seque...

  17. Polymorphic microsatellite DNA markers in the penduline tit, Remiz pendulinus

    NARCIS (Netherlands)

    Meszaros, L. A.; Frauenfelder, N.; Van Der Velde, M.; Komdeur, J.; Szabad, J.

    2008-01-01

    To describe the exceptional mating system of the penduline tit, Remiz pendulinus, we aim to combine field observation records with DNA analysis based on polymorphic microsatellite DNA markers. Here we describe features of nine loci and their corresponding polymerase chain reaction primers. The obser

  18. Microsatellite analysis in two populations of Kunming mice

    DEFF Research Database (Denmark)

    Shang, Haitao; Wei, Hong; Yue, Bingfei;

    2009-01-01

    populations are unclear. Fifteen microsatellite markers were screened by a fluorescence-based semi-automated genotyping method for the two main populations of Kunming mice from Beijing (BJ) and Shanghai (SH) in China. The observed number of alleles, effective number of alleles, observed heterozygosity...

  19. A test of mink microsatellite markers in the ferret

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Christensen, Knud

    2006-01-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variations at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite...

  20. PCR-amplified microsatellites as markers in plant genetics.

    Science.gov (United States)

    Morgante, M; Olivieri, A M

    1993-01-01

    In order to assess the feasibility of using microsatellites as markers in plant genetics, a survey of published DNA sequence data for presence, abundance and ubiquity in higher plants of all types of dinucleotide and trinucleotide repeats with a minimum number of 10 and 7 units, respectively, was conducted. This search revealed that such microsatellites are frequent and widely distributed; they were uncovered in 34 species, with a frequency of one every 50 kb. AT repeats were by far the most frequently observed class of dinucleotide microsatellites, whereas AC/TG repeats, which are common in animals, were observed only once. TAT repeats prevailed among trinucleotides. Polymerase chain reaction amplification of (AT)n and (TAT)n microsatellites in soybean (Glycine max (L.) Merr.) revealed that they are highly polymorphic, as a consequence of length variation, somatically stable and inherited in a co-dominant Mendelian manner. The abundance and amount of information derived from such markers, together with the ease by which they can be identified, make them ideal markers for plant genetic linkage and physical mapping, population studies and varietal identification.

  1. Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

    NARCIS (Netherlands)

    Silfverberg-Dilworth, E.; Matasci, C.L.; Weg, van de W.E.; Kaauwen, van M.P.W.; Walser, M.; Kodde, L.P.; Soglio, V.; Gianfranceschi, L.; Durel, C.E.; Costa, F.; Yamamoto, T.; Koller, B.; Gessler, C.; Patocchi, A.

    2006-01-01

    A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers

  2. Microsatellite instability and MLH1 promoter hypermethylation in colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    Yaron Niv

    2007-01-01

    Colorectal cancer (CRC) is caused by a series of genetic or epigenetic changes, and in the last decade there has been an increased awareness that there are multiple forms of colorectal cancer that develop through different pathways. Microsatellite instability is involved in the genesis of about 15% of sporadic colorectal cancers and most of hereditary nonpolyposis cancers. Tumors with a high frequency of microsatellite instability tend to be diploid, to possess a mucinous histology, and to have a surrounding lymphoid reaction. They are more prevalent in the proximal colon and have a fast pass from polyp to cancer. Nevertheless, they are associated with longer survival than stage-matched tumors with microsatellite stability. Resistance of colorectal cancers with a high frequency of microsatellite instability to 5-fluorouracil-based chemotherapy is well established. Silencing the MLH1 gene expression by its promoter methylation stops the formation of MLH1 protein, and prevents the normal activation of the DMA repair gene. This is an important cause for genomic instability and cell proliferation to the point of colorectal cancer formation. Better knowledge of this process will have a huge impact on colorectal cancer management, prevention, treatment and prognosis.

  3. Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

    Science.gov (United States)

    Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

    2002-01-01

    We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

  4. Isolation and characterization of the bovine microsatellite loci.

    Science.gov (United States)

    Chung, H Y; Kim, T H; Choi, B H; Jang, G W; Lee, J W; Lee, K T; Ha, J M

    2006-12-01

    Microsatellite loci were isolated using five repetitive probes for Korean native cattle. Eleven microsatellite loci were developed based on a biotin hybrid capture method, and enrichment of the genomic libraries (AAAT, TG, AG, T, and TGC repeats) was performed using Sau3AI adapters. The isolated markers were tested in two half-sib Korean cattle families and four imported breeds (Angus, Limousine, Holstein, and Shorthorn). Nine informative microsatellite loci were observed, and two microsatellite loci were revealed as monomorphic in Korean cattle. In the imported breeds, however, all of the markers were informative. In total, 213 alleles were obtained at the 11 loci across five breeds, and the average number of alleles found per locus, considering all populations, was 4.26. Heterozygosity was 0.71 (expected) and 0.57 (observed). The range of the polymorphic information content for the markers in all cattle populations was 0.43-0.69. Eleven percent of genetic variation was attributed to differentiation between populations as determined by the mean F (ST) values. The remaining 89% corresponded to differences among individuals. The isolated markers may be used to identify and classify the local breeds on a molecular basis.

  5. Genetic diversity as assessed by morphological and microsatellite ...

    African Journals Online (AJOL)

    lap

    2012-10-18

    Oct 18, 2012 ... combination of morphological and molecular markers increases the efficiency of diversity measured and the adzuki bean microsatellite markers are highly polymorphic and can be successfully used .... information about the magnitude of genetic variability. ... Two primers MB77 and CP37 were monomorphic.

  6. Frequent allelic imbalance but infrequent microsatellite instability in gastric lymphoma

    NARCIS (Netherlands)

    Hoeve, M A; Ferreira Mota, S C; Schuuring, E; de Leeuw, W J; Chott, A; Meijerink, J P; Kluin, P M; van Krieken, J H

    1999-01-01

    Specific defects in DNA repair pathways are reflected by DNA microsatellite instability (MSI) and play an important role in carcinogenesis. Reported frequencies in gastric non-Hodgkin's lymphomas (NHL) vary from 14% to as high as 90%. Another form of genetic instability in tumours is allelic imbalan

  7. Polymorphic microsatellite markers in the brown seaweed Fucus vesiculosus.

    Science.gov (United States)

    Candeias, Rui; Casado-Amezúa, Pilar; Pearson, Gareth A; Serrão, Ester A; Teixeira, Sara

    2015-03-08

    Fucus vesiculosus is a brown seaweed dominant on temperate rocky shores of the northern hemisphere and, is typically distributed in the mid-upper intertidal zone. It is an external fertilizer that reproduces sexually, providing an excellent model to address conflicting theories related to mating systems and sexual selection. Microsatellite markers have been reported for several Fucus species, however the genomic libraries from where these markers have been isolated, have originated from two or more species pooled together (F. vesiculosus and F. serratus in one library; F. vesiculosus, F. serratus and Ascophyllum nodosum in a second library), or when the genomic DNA originated from only one species it was from Fucus spiralis. Although these markers cross-amplify F. vesiculosus individuals, the level of polymorphism has been low for relatedness studies. The microsatellite markers described here were obtained from an enriched genomic library, followed by 454 pyrosequencing. A total of 9 microsatellite markers were tested across 44 individuals from the North of Portugal. The mean number of alleles across loci was 8.7 and the gene diversity 0.67. The high variability displayed by these microsatellite loci should be useful for paternity analysis, assessing variance of reproductive success and in estimations of genetic variation within and between populations.

  8. Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

    NARCIS (Netherlands)

    Silfverberg-Dilworth, E.; Matasci, C.L.; Weg, van de W.E.; Kaauwen, van M.P.W.; Walser, M.; Kodde, L.P.; Soglio, V.; Gianfranceschi, L.; Durel, C.E.; Costa, F.; Yamamoto, T.; Koller, B.; Gessler, C.; Patocchi, A.

    2006-01-01

    A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers

  9. Microsatellite Organization in the B Chromosome and A Chromosome Complement in Astyanax (Characiformes, Characidae) Species.

    Science.gov (United States)

    Piscor, Diovani; Parise-Maltempi, Patricia P

    2016-01-01

    The organization of microsatellites in B and sex chromosomes has been linked to chromosomal evolution in a number of animal groups. Here, the chromosomal organizations of (CA)15, (GA)15, (CG)15, (GACA)4, and (GATA)8 microsatellites were examined in several Astyanax species with different diploid numbers: Astyanax mexicanus (2n = 50 + 1 B chromosome), A. altiparanae (2n = 50), A. marionae (2n = 48), A. fasciatus (2n = 46), and A. schubarti (2n = 36). The (CA)15 and (GA)15 microsatellites were dispersed across the chromosomes of A. altiparanae and A. fasciatus but were also observed as clusters (CA and GA for A. altiparanae, and CA for A. fasciatus). In A. marionae and A. schubarti, the (CA)15 and (GA)15 microsatellites were dispersed but were also observed as clustered signals and coincident with heterochromatic regions. In all 4 of these species, the (CG)15 and (GACA)4 microsatellites were dispersed across chromosomes, and the (GATA)8 microsatellite was co-localized with 5S rDNA. In A. mexicanus, the (CA)15, (GA)15, (CG)15, (GATA)8, and (GACA)4 microsatellites were weakly detected and dispersed across the chromosomes of the A complement. On the B chromosome, signals for the different microsatellites were weak, strong, absent, weak, and absent, respectively. The distribution of microsatellites and the locational relationship between microsatellites and 5S rDNA are discussed, and a possible evolutionary pathway is proposed for microsatellites in Astyanax. © 2016 S. Karger AG, Basel.

  10. Conjunctival melanoma: survival analysis in twenty-two Mexican patients

    Directory of Open Access Journals (Sweden)

    Rosa Angélica Salcedo-Hernández

    2014-06-01

    Full Text Available Objetivo: Descrever o intervalo livre de doença (DFI e sobrevida global (OS de pacientes com melanoma conjuntival (CM. Método: Prontuários de 22 pacientes que foram internados em dois hospitais entre 1985 e 2006 foram revisados para dados pertinentes, incluindo dados demográficos, local de envolvimento na conjuntiva e outros locais de acometimento, tratamento cirúrgico e tratamento adjuvante. Resultados: Dez (45,45% homens e 12 (54,55% mulheres foram selecionados. A média de idade foi de 52,3 anos. Em 15 pacientes (68,1% CM envolveu a conjuntiva bulbar, e em 7 (31,9% envolveu a conjuntiva palpebral. Dos 22 pacientes, 72,72% tinham história de melanose conjuntival. O tamanho médio do tumor foi de 20,4 mm. Oito (36,36% pacientes foram submetidos à exenteração orbital, 2 (9,06% à enucleação, 5 (22,72% à ampla excisão da lesão seguida de radioterapia, 2 (9,06% à exenteração orbital com esvaziamento cervical e os restantes 5 pacientes (22,72% foram considerados adequadamente tratados apenas com excisão ampla. Oito (36,36% pacientes receberam tratamento adjuvante. Sobrevida livre de doença em 5 anos foi de 51% e sobrevida global em 5 e 10 anos foi de 50% e 37%, respectivamente. Conclusão: Melanoma conjuntival é uma entidade rara. Comportamento do tumor é agressivo, e o melhor tratamento é a cirurgia com terapia adjuvante.

  11. Twenty-two cases of low-frequency noise complaints

    DEFF Research Database (Denmark)

    Pedersen, Christian Sejer; Møller, Henrik; Persson-Waye, Kerstin

    2006-01-01

    In Denmark and in other industrialized countries there are cases where people complain about annoying low-frequency or infrasonic noise in their homes. Besides noise annoyance people often report other adverse effects such as insomnia, headache, lack of concentration etc. In many cases the noise...

  12. Lesson Twenty-two The early repolarization variant

    Institute of Scientific and Technical Information of China (English)

    鲁端; 王劲

    2007-01-01

    @@ The ST-segment elevation seen in apparently healthy and asymptomatic persons,the so-called early repolarization variant (ERPV)1.Hiss et al reported that 91% of 6014 healthy men in the US Air Force who were between 16 and 58 years old had an ST-segment elevation of 0.1 to 0.3 mV in one or more precordial leads2.The elevation was most common and marked in lead V2.

  13. Surgical treatment of chronic pancreatitis. Twenty-two years' experience.

    Science.gov (United States)

    Traverso, L W; Tompkins, R K; Urrea, P T; Longmire, W P

    1979-01-01

    Seventy-four patients underwent operation for chronic pancreatitis during a 22 year period at UCLA Hospital. Follow-up data obtained for 60% of these patients an average of 3.2 years postoperation were analyzed by computer for statistically significant benefit between paired operation combinations and the variables of pain relief, stool habits, alcohol use, readmission for pancreatitis, and narcotic use. The combined group of total and cephalic pancreaticoduodenectomy proved more effective with respect to pain relief and readmission (p less than 0.05) than the group that had pseudocyst drainage. The comparison of groups that underwent resection or ductal drainage showed no statistical differences for the above variables. Regardless of type of operation, if the patient had evidence of pancreatic calcifications and had abstained from alcohol postoperatively, the likelihood of a return to normal activity was more favorable (p less than 0.05). PMID:485605

  14. 滇西亚种树鼩微卫星分子标记的筛选%Isolation and chatracterization of microsatellite markers in Tupaia belangeri chinensis

    Institute of Scientific and Technical Information of China (English)

    张媛; 李晓飞; 李振宇; 仝品芬; 陈玲霞; 尹博文; 代解杰

    2015-01-01

    Objective To screen out specific microsatellite markers for use in Tupaia belangeri chinensis genetic testing. Methods Firstly to screen about 700 microsatellite loci from whole genome.Secondly to choose about 100 better loci without defect factors.Lastly 46 primers were designed by 33 tree shrew’ s microsatellite loci obtained from whole genome and other references.Agarose gel electrophoresis and polyacrylamide gel electrophoresis were used for PCR products, and better loci based on electrophoresis results were chosen.Then STR scan was used to select the microsatellite loci combination for genetic testing.Results Twenty-two microsatellite loci were selected with a significant Stutter peak on STR scanning.Comparing the alternative loci and ultimately selected loci, there were two loci available in the five alternative loci of T.glis.The coincidence rate between T.glis and T.b.chinensis was 40%.There were two loci available in the five alternative loci of T.minor, and the coincidence rate between T.minor and T.b.chinensis was 40%.There were two loci available in the three alternative loci of T.belangeri, and the coincidence rate between T.belangeri and T.b. chinensis was about 70%.Conclusions The 22 microsatellite loci screened in this study are well applied for genetic testing of Tupaia belangeri chinensis, therefore, provide a scientific basis for the genetic quality monitoring of tree shrews.%目的:筛选出适用于滇西亚种树鼩种群遗传质量控制的特异性微卫星分子标记。方法首先从树鼩全基因组序列中筛选出约700个微卫星位点,择优选出约100个位点设计引物,去除有不良因素的,最后保留33对和文献报道的13对引物对滇西亚种树鼩DNA进行 PCR扩增,根据琼脂糖电泳和聚丙烯酰胺电泳结果筛选保留,进行STR扫描再次筛选适于树鼩遗传检测的微卫星位点组合。结果筛选出树鼩微卫星位点22个,STR基因扫描有

  15. Population study and validation of paternity testing for Thoroughbred horses by 15 microsatellite loci.

    Science.gov (United States)

    Tozaki, T; Kakoi, H; Mashima, S; Hirota, K; Hasegawa, T; Ishida, N; Miura, N; Choi-Miura, N H; Tomita, M

    2001-11-01

    Microsatellite 15 TKY System was characterized for parentage verification of horse registry. The Microsatellite 15 TKY System was constructed by using 15 microsatellites, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394, to provide stringent PCR-based microsatellite typing specifically optimized for multicolor fluorescence detection. The Microsatellite 15 TKY System showed good resolutions for 250 unrelated Thoroughbred horses, and the probability of exclusion (PE) at each microsatellite ranged from 0.437 to 0.621, resulting in a total PE value of 99.998% for Thoroughbred horses. These results indicated that the Microsatellite 15 TKY System is useful for paternity testing of Thoroughbred horses. A paternity testing case for a Thoroughbred horse family, in which candidate sires had close relations, was analyzed using the Microsatellite 15 TKY System. In this case, the Microsatellite 15 TKY System excluded paternity of a false sire. We concluded that the Microsatellite 15 TKY System can give sufficient and reliable information for paternity testing.

  16. Isolation and Characterization of Microsatellite Markers for Shorea platyclados (Dipterocarpaceae

    Directory of Open Access Journals (Sweden)

    Chin Hong Ng

    2013-06-01

    Full Text Available Premise of the study: Microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae for DNA profiling and genetic diversity assessment of this tropical timber species. Methods and Results: Fifteen polymorphic microsatellite loci were developed and characterized in S. platyclados using a genomic library enriched for dinucleotide (CT repeats. The primers amplified dinucleotide repeats with 3–14 alleles per locus across four natural populations. The observed and expected heterozygosities ranged from 0.292 to 1.000 and from 0.301 to 0.894, respectively. No significant deviation from Hardy–Weinberg equilibrium was detected in the 15 loci. Four loci pairs displayed linkage disequilibrium. Conclusions: These highly polymorphic markers are adequate for DNA profiling and studies of population genetics in S. platyclados.

  17. Characterization of new microsatellite markers of Siganus fuscescens (Siganidae).

    Science.gov (United States)

    Li, Q H; Li, Z B; Dai, G; Chen, X J; Chen, L N; Cao, Y Y; Shangguan, J B; Ning, Y F

    2013-07-30

    Siganus fuscescens, which is a small commercially important marine fish, is wildly distributed in shallow waters throughout the tropical and subtropical Indo-Pacific and Eastern Mediterranean regions. It is part of a group known as rabbitfish. Fifteen new polymorphic microsatellite markers for S. fuscescens were identified, and 32 wild individuals were used to evaluate the degree of polymorphism of these markers. The number of alleles per locus ranged from 2 to 12, and the polymorphism information content ranged from 0.210 to 0.849. The observed and expected heterozygosities were 0.142-0.808 and 0.225-0.853, respectively. Although significant deviations from Hardy-Weinberg equilibrium were detected at 2 loci (Sf1-37-2 and Sf1-47), no significant deviations were detected at the other 13 loci. These microsatellite markers will provide a useful tool for studies on genetic diversity and differentiation of S. fuscescens.

  18. An Example of Yak Paternity Assignment by Microsatellite Genotyping

    Institute of Scientific and Technical Information of China (English)

    王敏强

    2005-01-01

    12 cattle microsatellite DNA markers were used for establishing the paternity of 4 Datong Yak calves.The results indicated that paternity can be assigned by use of exclusion method directely when the mother is clearly known and data of all likely sires were obtained. The more the alleles of a locus possessed, the more effectively the paternity can be assigned. Not only the microsatellite DNA marker is a promising tool in establishment of yak detail pedigrees, but also can provide us information of reproductive efficiency of the bull(s) based on the numbers of calves it produced in the herd, which will be useful in speeding up the processes of yak genetics improvement.

  19. Development of Microsatellite Markers for Isodon longitubus (Lamiaceae

    Directory of Open Access Journals (Sweden)

    Tadashi Yamashiro

    2013-10-01

    Full Text Available Premise of the study: Microsatellite markers were developed for Isodon longitubus to study the natural hybridization of the species and its congeners. Methods and Results: A total of 10 primer sets were developed for I. longitubus. From the initial screening, all of 10 loci were polymorphic with five to 19 alleles per locus in the Mt. Ishizuchi population, whereas nine loci were polymorphic with two to 12 alleles per loci in the Toon population. Although one locus was monomorphic at one population, the observed and expected heterozygosity values estimated from 34 I. longitubus samples ranged from 0.273 to 1.000 and from 0.483 to 0.918, respectively. Six primer sets could amplify all three species examined in this study (I. inflexus, I. japonicus, and I. shikokianus. Conclusions: The 10 microsatellite markers developed here will be useful in analyzing the population genetic structure of I. longitubus and in studying the natural hybridization between Isodon species.

  20. Microsatellite analysis of paternity and reproduction in Arctic grizzly bears.

    Science.gov (United States)

    Craighead, L; Paetkau, D; Reynolds, H V; Vyse, E R; Strobeck, C

    1995-01-01

    We report data from analyses of microsatellite loci of 30 grizzly bear family groups which demonstrate that each cub in a litter can be sired independently, and we derive estimates of maximum reproductive success for males, from an Arctic population in northwestern Alaska that is minimally affected by human activities. These analyses were made possible by the use of single-locus primers that amplified both of an individual's alleles at eight microsatellite loci and by detailed knowledge of maternal/offspring relationships that allowed the identification of paternal alleles. No single male was responsible for more than approximately 11% of known offspring, and no more than 49% of breeding-age males successfully bred. These data contribute to an understanding of the genetic and demographic basis of male reproductive success, which is of vital importance in the maintenance of small, isolated grizzly bear populations.

  1. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Science.gov (United States)

    Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

    2016-01-01

    Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  2. Propulsion options for very low Earth orbit microsatellites

    Science.gov (United States)

    Leomanni, Mirko; Garulli, Andrea; Giannitrapani, Antonio; Scortecci, Fabrizio

    2017-04-01

    The growing competitiveness in the commercial space market has raised the interest in operating small spacecraft at very low altitudes. To make this feasible, the space industry has started developing propulsion options tailored specifically to these platforms. This paper presents a review of emerging micropropulsion technologies and evaluates their applicability to microsatellite missions in the altitude range 250-500 km. The results of the proposed analysis are demonstrated on two different remote sensing applications.

  3. Study on Five Microsatellite Markers in Beef Cattle Population

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Five microsatellites, IDVGA-2, IDVGA-27, IDVGA-46, IDVGA-55 and TGLA-44,were analyzed for polymorphisms in beef cattle. The number of alleles and polymorphism information content (PIC) values were 12/0. 82, 5/0. 58, 8/0. 70, 6/0. 57 and 11/0. 86 respectively. Each microstellite was typed on a half-sib family in order to verify the segregation of the alleles.

  4. On the simulation of the UPMSAT-2 microsatellite power

    OpenAIRE

    Manuel Navío, Carlos de; Cubas Cano, Javier; Pindado Carrion, Santiago

    2014-01-01

    Simulation of satellite subsystems behaviour is extramely important in the design at early stages. The subsystems are normally simulated in the both ways : isolated and as part of more complex simulation that takes into account imputs from other subsystems (concurrent design). In the present work, a simple concurrent simulation of the power subsystem of a microsatellite, UPMSat-2, is described. The aim of the work is to obtain the performance profile of the system (battery charging level, ...

  5. Characterization of microsatellite loci for the littorine snail Bembicium vittatum.

    Science.gov (United States)

    Kennington, W J; Lukehurst, S S; Johnson, M S

    2008-11-01

    We describe the isolation and development of 17 polymorphic microsatellite loci for the intertidal snail Bembicium vittatum (Gastropoda: Littorinidae). The loci were tested in 46 individuals from a single population situated near the centre of the species distribution. No evidence of linkage disequilibrium was detected between any pair of loci. However, two loci showed significant departures from Hardy-Weinberg expectations. The number of alleles per locus ranged from two to 15. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  6. Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

    Directory of Open Access Journals (Sweden)

    Bénédicte Coupat-Goutaland

    Full Text Available Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM. Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis. They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

  7. Microsatellite analyses of the trout of northwest Mexico

    Science.gov (United States)

    Nielsen, J.L.; Sage, G.K.

    2001-01-01

    The trout of northwest Mexico represent an undescribed group of fish considered part of the Oncorhynchus mykiss (Pacific trout) complex of species and subspecies. Recent genetic studies have shown these fish to have important genetic diversity and a unique evolutionary history when compared to coastal rainbow trout. Increased levels of allelic diversity have been found in this species at the southern extent of its range. In this study we describe the trout in the Sierra Madre Occidental from the rios Yaqui, Mayo, Casas Grandes and de Bavispe, and their relationship to the more southern distribution of Mexican golden trout (O. chrysogaster) using 11 microsatellite loci. Microsatellite allelic diversity in Mexican trout was high with a mean of 6.6 alleles/locus, average heterozygosity = 0.35, and a mean Fst = 0.43 for all loci combined. Microsatellite data were congruent with previously published mtDNA results showing unique panmictic population structure in the Rio Yaqui trout that differs from Pacific coastal trout and Mexican golden trout. These data also add support for the theory of headwaters transfer of trout across the Continental Divide from tributaries of the Rio de Bavispe into the Rio Casas Grandes. Rio Mayo trout share a close genetic relationship to trout in Rio Yaqui, but sample sizes from the Rio Mayo prevent significant comparisons in this study. Microsatellite analyses show significant allelic frequency differences between Rio Yaqui trout and O. chrysogaster in Sinaloa and Durango Mexico, adding further support for a unique evolutionary status for this group of northwestern Mexican trout.

  8. Evolutionary process of a tetranucleotide microsatellite locus in Acipenseriformes

    Indian Academy of Sciences (India)

    Zhao Jun Shao; Eric Rivals; Na Zhao; Sovan Lek; Jianbo Chang; Patrick Berrebi

    2011-08-01

    The evolutionary dynamics of the tetra-nucleotide microsatellite locus Spl-106 were investigated at the repeat and flanking sequences in 137 individuals of 15 Acipenseriform species, giving 93 homologous sequences, which were detected in 11 out of 15 species. Twenty-three haplotypes of flanking sequences and three distinct types of repeats, type I, type II and type III, were found within these 93 sequences. The MS-Align phylogenetic method, newly applied to microsatellite sequences, permitted us to understand the repeat and flanking sequence evolution of Spl-106 locus. The flanking region of locus Spl-106 was highly conserved among the species of genera Acipenser, Huso and Scaphirhynchus, which diverged about 150 million years ago (Mya). The rate of flanking sequence divergence at the microsatellite locus Spl-106 in sturgeons is between 0.011% and 0.079% with an average at 0.028% per million years. Sequence alignment and phylogenetic trees produced by MS-Align showed that both the flanking and repeat regions can cluster the alleles of different species into Pacific and Atlantic lineages. Our results show a synchronous evolutionary pattern between the flanking and repeat regions. Moreover, the coexistence of different repeat types in the same species, even in the same individual, is probably due to two duplication events encompassing the locus Spl-106 that occurred during the divergence of Pacific lineage. The first occured before the diversification of Pacific species (121–96 Mya) and led to repeat types I and II. The second occurred more recently, just before the speciation of A. sinensis and A. dabryanus (69–10 Mya), and led to repeat type III. Sequences in the same species with different repeat types probably corresponds to paralogous loci. This study sheds a new light on the evolutionary mechanisms that shape the complex microsatellite loci involving different repeat types.

  9. A Microsatellite Genetic Map of the Turbot (Scophthalmus maximus)

    Science.gov (United States)

    Bouza, Carmen; Hermida, Miguel; Pardo, Belén G.; Fernández, Carlos; Fortes, Gloria G.; Castro, Jaime; Sánchez, Laura; Presa, Pablo; Pérez, Montse; Sanjuán, Andrés; de Carlos, Alejandro; Álvarez-Dios, José Antonio; Ezcurra, Susana; Cal, Rosa M.; Piferrer, Francesc; Martínez, Paulino

    2007-01-01

    A consensus microsatellite-based linkage map of the turbot (Scophthalmus maximus) was constructed from two unrelated families. The mapping panel was derived from a gynogenetic family of 96 haploid embryos and a biparental diploid family of 85 full-sib progeny with known linkage phase. A total of 242 microsatellites were mapped in 26 linkage groups, six markers remaining unlinked. The consensus map length was 1343.2 cM, with an average distance between markers of 6.5 ± 0.5 cM. Similar length of female and male maps was evidenced. However, the mean recombination at common intervals throughout the genome revealed significant differences between sexes, ∼1.6 times higher in the female than in the male. The comparison of turbot microsatellite flanking sequences against the Tetraodon nigroviridis genome revealed 55 significant matches, with a mean length of 102 bp and high sequence similarity (81–100%). The comparative mapping revealed significant syntenic regions among fish species. This study represents the first linkage map in the turbot, one of the most important flatfish in European aquaculture. This map will be suitable for QTL identification of productive traits in this species and for further evolutionary studies in fish and vertebrate species. PMID:18073440

  10. Genetic diversity of bovine Neospora caninum determined by microsatellite markers.

    Science.gov (United States)

    Salehi, N; Gottstein, B; Haddadzadeh, H R

    2015-10-01

    Neospora caninum is one of the most significant parasitic organisms causing bovine abortion worldwide. Despite the economic impact of this infection, relatively little is known about the genetic diversity of this parasite. In this study, using Nc5 and ITS1 nested PCR, N. caninum has been detected in 12 brain samples of aborted fetuses from 298 seropositive dairy cattle collected from four different regions in Tehran, Iran. These specimen (Nc-Iran) were genotyped in multilocus using 9 different microsatellite markers previously described (MS4, MS5, MS6A, MS6B, MS7, MS8, MS10, MS12 and MS21). Microsatellite amplification was completely feasible in 2 samples, semi-completely in 8 samples, and failed in 2 samples. Within the two completely performed allelic profiles of Nc-Iran strains, unique multilocus profiles were obtained for both and novel allelic patterns were found in the MS8 and MS10 microsatellite markers. The Jaccard's similarity index showed significant difference between these two strains and from other standard isolates derived from GenBank such as Nc-Liv, Nc-SweB1, Nc-GER1, KBA1, and KBA2. All samples originating from the same area showed identical allelic numbers and a correlation between the number of repeats and geographic districts was observed.

  11. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers

    Directory of Open Access Journals (Sweden)

    Jordana Jordi

    2001-07-01

    Full Text Available Abstract Genetic diversity at 13 equine microsatellite loci was compared in five endangered Spanish donkey breeds: Andaluza, Catalana, Mallorquina, Encartaciones and Zamorano-Leonesa. All of the equine microsatellites used in this study were amplified and were polymorphic in the domestic donkey breeds with the exception of HMS1, which was monomorphic, and ASB2, which failed to amplify. Allele number, frequency distributions and mean heterozygosities were very similar among the Spanish donkey breeds. The unbiased expected heterozygosity (HE over all the populations varied between 0.637 and 0.684 in this study. The low GST value showed that only 3.6% of the diversity was between breeds (P A distance matrix showed little differentiation between Spanish breeds, but great differentiation between them and the Moroccan ass and also with the horse, used as an outgroup. These results confirm the potential use of equine microsatellite loci as a tool for genetic studies in domestic donkey populations, which could also be useful for conservation plans.

  12. Microsatellite Primer Development for Post Oak, Quercus stellata (Fagaceae

    Directory of Open Access Journals (Sweden)

    Warren B. Chatwin

    2014-10-01

    Full Text Available Premise of the study: The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata. This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. Methods and Results: Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. Conclusions: We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants.

  13. Tsinghua-1 Micro-Satellite Power System Architecture and Design

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The Tsinghua-1 Micro-satellite, the first satellite made by Tsinghua University, was launched in 2000. The power system of the Tsinghua-1 Micro-satellite is one of the most important subsystems. It provides all the power for the satellite platform and the payloads. The power system design includes the regulation,protection and distribution of a 4 × 35 W solar array and 7 Ah NiCd batteries. This subsystem essentially offerstwo buses: an unregulated 14 V bus and a regulated 5 V bus. All distributed power lines to the users areprotected by current tripping switches. In addition, some essential loads, such as the tele-command system,are supplied through fuses. The Tsinghua-1 Micro-satellite power system provides an efficient, flexible,reliable, and cost-effective solution for small satellites in low earth orbit. A better maximum power pointtracking method has been used to increase reliability margins and to increase the efficiency of the powersystem. The power system reliability was evaluated using several different tests, such as the power boardtest, the assembly integrate test (AIT), the electromagnetic compatibility (EMC) test and the thermal vacuumtest (TVT).``

  14. Genotyping of mature trees of Entandrophragma cylindricum with microsatellites.

    Science.gov (United States)

    Garcia, F; Noyer, J-L; Risterucci, A-M; Chevallier, M-H

    2004-01-01

    We have characterized 10 microsatellite loci for the tropical tree Entandrophragma cylindricum (Sprague) Sprague (sapelli) in order to genotype individuals in forest stands for estimation of the genetic diversity of the species. We used the technique of building a (GA)n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 186 mature trees in a selectively logged stand (Dimako) and an unlogged stand (Ndama), both in Cameroon. All the loci were polymorphic, and the number of alleles was high, ranging from eight to 36, with a mean of 22.1. Both stands showed the same high level of genetic diversity (mean H(E) = 0.85) and a low genetic differentiation (FST = 0.007), indicating that genetic diversity was within rather than among populations. Five and three out seven loci in Dimako and Ndama, respectively, showed a deficit of heterozygotes. The seven loci enabled more than 97% of the mature trees in each stand to be identified. It was concluded that these markers can be efficiently used for gene flow studies.

  15. Polymorphism, monomorphism, and sequences in conserved microsatellites in primate species.

    Science.gov (United States)

    Blanquer-Maumont, A; Crouau-Roy, B

    1995-10-01

    Dimeric short tandem repeats are a source of highly polymorphic markers in the mammalian genome. Genetic variation at these hypervariable loci is extensively used for linkage analysis, for the identification of individuals, and may be useful for interpopulation and interspecies studies. In this paper, we analyze the variability and the sequences of a segment including three microsatellites, first described in man, in several species of primates (chimpanzee, orangutan, gibbon, and macaque) using the heterologous primers (man primers). This region is located on the human chromosome 6p, near the tumor necrosis factor genes, in the major histocompatibility complex. The fact that these primers work in all species studied indicates that they are conserved throughout the different lineages of the two superfamilies, the Hominoidea and the Cercopithecidea, represented by the macaques. However, the intervening sequence displays intraspecific and interspecific variability. The sites of base substitutions and the insertion/deletion events are not evenly distributed within this region. The data suggest that it is necessary to have a minimal number of repeats to increase the rate of mutation sufficiently to allow the development of polymorphism. In some species, the microsatellites present single base variations which reduce the number of contiguous repeats, thus apparently slowing the rate of additional slippage events. Species with such variations or a low number of repeats are monomorphic. These microsatellite sequences are informative in the comparison of closely related species and reflect the phylogeny of the Old World monkeys, apes, and man.

  16. Microsatellite instability and cytogenetic survey in myeloid leukemias

    Directory of Open Access Journals (Sweden)

    E.M.S.F. Ribeiro

    2002-02-01

    Full Text Available Microsatellites are short tandem repeat sequences dispersed throughout the genome. Their instability at multiple genetic loci may result from mismatch repair errors and it occurs in hereditary nonpolyposis colorectal cancer. This instability is also found in many sporadic cancers. In order to evaluate the importance of this process in myeloid leukemias, we studied five loci in different chromosomes of 43 patients, 22 with chronic myelocytic leukemia (CML in the chronic phase, 7 with CML in blast crisis, and 14 with acute myeloid leukemia (AML, by comparing leukemic DNA extracted from bone marrow and constitutional DNA obtained from buccal epithelial cells. Only one of the 43 patients (2.1%, with relapsed AML, showed an alteration in the allele length at a single locus. Cytogenetic analysis was performed in order to improve the characterization of leukemic subtypes and to determine if specific chromosome aberrations were associated with the presence of microsatellite instability. Several chromosome aberrations were observed, most of them detected at diagnosis and during follow-up of the patients, according to current literature. These findings suggest that microsatellite instability is an infrequent genetic event in myeloid leukemias, adding support to the current view that the mechanisms of genomic instability in solid tumors differ from those observed in leukemias, where specific chromosome aberrations seem to play a major role.

  17. First Identification of Polymorphic Microsatellite Markers in the Burgundy Truffle, Tuber aestivum (Tuberaceae

    Directory of Open Access Journals (Sweden)

    Virginie Molinier

    2013-02-01

    Full Text Available Premise of the study: Tuber aestivum, the most common truffle in Europe, plays an important role in the commercial truffle market. For the first time, microsatellite primers were developed to investigate polymorphism within this species. Methods and Results: Using direct shotgun pyrosequencing, 15 polymorphic microsatellites were identified out of the 7784 perfect microsatellites present in the 534620 reads obtained. Tested on 75 samples, these microsatellites were highly polymorphic. The number of alleles varied from four to 15, and the expected heterozygosity ranged from 0.266 to 0.620. A multilocus analysis allowed the identification of 63 genotypes over the 75 samples analyzed. Conclusions: Direct shotgun pyrosequencing is a fast and relatively low-cost technique allowing identification of microsatellites in nonmodel species. The microsatellites developed in this study will be useful in population genetic studies to infer the evolutionary history of this species.

  18. Comparison of microsatellite distribution in genomes of Centruroides exilicauda and Mesobuthus martensii.

    Science.gov (United States)

    Wang, Chen; Kubiak, Lukasz Jakub; Du, Lian-Ming; Li, Wu-Jiao; Jian, Zuo-Yi; Tang, Ce; Fan, Zhen-Xin; Zhang, Xiu-Yue; Yue, Bi-Song

    2016-12-05

    In this study, we characterized the distribution of microsatellites in the genomes and genes of Centruroides exilicauda and Mesobuthus martensii, carried out Gene Ontology (GO) analysis and GO enrichment analysis of coding sequences (CDSs) with microsatellite (SSR). In addition, over-represented GO functions related to environmental interactions, development process and methylation were identified to develop functional markers and facilitate further analysis of microsatellite function in the genes of scorpions. Location analysis indicated that microsatellites were predominantly concentrated at both ends of genes. Most genes containing microsatellite had the SSR present at only one locus, from which we infer that the number of SSRs per gene is limited even though intragenic tandem repeats can generate functional variability. Lastly, we identified 75 SSRs in 64 genes of 54 expanded gene families and 1 SSR in the toxin gene of Mesobuthus martensii, allowing future studies on the effect of microsatellites on gene function.

  19. Microsatellite instability confounds engraftment analysis of hematopoietic stem-cell transplantation.

    Science.gov (United States)

    Tseng, Li-Hui; Tang, Jih-Luh; Haley, Lisa; Beierl, Katie; Gocke, Christopher D; Eshleman, James R; Lin, Ming-Tseh

    2014-07-01

    Polymorphic short tandem-repeat, or microsatellite, loci have been widely used to analyze chimerism status after allogeneic hematopoietic stem-cell transplantation. In molecular diagnostic laboratories, it is recommended to calculate mixed chimerism for at least 2 informative loci and to avoid microsatellite loci on chromosomes with copy number changes. In this report, we show that microsatellite instability observed in 2 patients with acute leukemia may confound chimerism analysis. Interpretation errors may occur even if 2 to 3 loci are analyzed because of length variation in multiple microsatellite loci. Although microsatellite loci with length variation should not be selected for chimerism analysis, the presence of microsatellite instability, like copy number alteration because of aberrant chromosomes, provides evidence of recurrent or residual cancer cells after hematopoietic stem-cell transplantation.

  20. Microsatellite markers of water buffalo, Bubalus bubalis - development, characterisation and linkage disequilibrium studies

    Directory of Open Access Journals (Sweden)

    Vaidhegi R

    2009-10-01

    Full Text Available Abstract Background Microsatellite markers are highly polymorphic and widely used in genome mapping and population genetic studies in livestock species. River buffalo, Bubalus bubalis is an economically important livestock species, though only a limited number of microsatellite markers have been reported thus far in this species. Results In the present study, using two different approaches 571 microsatellite markers have been characterized for water buffalo. Of the 571 microsatellite markers, 498 were polymorphic with average heterozygosity of 0.51 on a panel of 24 unrelated buffalo. Fisher exact test was used to detect LD between the marker pairs. Among the 137550 pairs of marker combination, 14.58% pairs showed significant LD (P Conclusion The high conservation of cattle microsatellite loci in water buffalo promises the usefulness of the cattle microsatellites markers on buffalo. The polymorphic markers characterised in this study will contribute to genetic linkage and radiation hybrid mapping of water buffalo and population genetic studies.

  1. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.

    Science.gov (United States)

    Fernandez-Silva, Iria; Whitney, Jonathan; Wainwright, Benjamin; Andrews, Kimberly R; Ylitalo-Ward, Heather; Bowen, Brian W; Toonen, Robert J; Goetze, Erica; Karl, Stephen A

    2013-01-01

    Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.

  2. Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses.

    Science.gov (United States)

    Fernandez-Silva, Iria; Toonen, Robert J

    2013-01-01

    The comparatively low cost of massive parallel sequencing technology, also known as next-generation sequencing (NGS), has transformed the isolation of microsatellite loci. The most common NGS approach consists of obtaining large amounts of sequence data from genomic DNA or enriched microsatellite libraries, which is then mined for the discovery of microsatellite repeats using bioinformatics analyses. Here, we describe a bioinformatics approach to isolate microsatellite loci, starting from the raw sequence data through a subset of microsatellite primer pairs. The primary difference to previously published approaches includes analyses to select the most accurate sequence data and to eliminate repetitive elements prior to the design of primers. These analyses aim to minimize the testing of primer pairs by identifying the most promising microsatellite loci.

  3. Development of microsatellite markers in potato and their transferability in some members of Solanaceae.

    Science.gov (United States)

    Grover, Atul; Ramesh, B; Sharma, P C

    2009-10-01

    We have developed thirty new microsatellite markers in potato by screening genomic libraries and ESTs. Genomic libraries of potato cultivar Kufri Bahar were screened for sequences containing microsatellite motifs GA, GT, ACA, ATC, GAA, TAA and GATA. Using flanking sequences, PCR primers were designed for microsatellites identified from genomic libraries and ESTs. Sixteen new primer pairs from genomic libraries and fourteen from ESTs along with seven previously published primer pairs amplified PCR products in the selected genotypes comprising of 65 Solanum tuberosum lines and 14 other species of the potato gene pool. Neighbor-joining tree based on genetic distance matrix developed using microsatellite markers successfully distinguished all these genotypes in the expected size range. Seventeen microsatellites could also be cross-amplified in at least one of the five members of solanaceae, namely tomato, eggplant, pepper, petunia and tobacco. The new microsatellite markers obtained in this study will be useful in various genetic and taxonomic studies in potato and related genomes.

  4. Narrowing the position of the Treacher Collins syndrome locus to a small interval between three new microsatellite markers at 5q32-33. 1

    Energy Technology Data Exchange (ETDEWEB)

    Dixon, M.J.; Dixon, J. (Univ. of Manchester (United Kingdom)); Houseal, T.; Klinger, K.; Landes, G.M. (Integrated Genetics, Inc., Framingham, MA (United States)); Bhatt, M.; Ward, D.C. (Yale Univ. School of Medicine, New Haven (United States))

    1993-05-01

    Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development, the features of which include conductive hearing loss and cleft palate. The TCOF1 locus has been localized to chromosome 5q32-33.2. In the present study the authors have used the combined techniques of genetic linkage analysis and fluorescence in situ hybridization (FISH) to more accurately define the TCOF1 critical region. Cosmids IG90 and SPARC, which map to distal 5q, encompass two and one hypervariable microsatellite markers, respectively. The heterozygosity values of these three markers range from .72 to .81. Twenty-two unrelated TCOF1 families have been analyzed for linkage to these markers. There is strong evidence demonstrating linkage to all three markers, the strongest support for positive linkage being provided by haplotyping those markers at the locus encompassed by the cosmid IG90 (Z[sub max]= 19.65; 0 = .010). FISH to metaphase chromosomes and interphase nuclei established that IG90 lies centromeric to SPARC. This information combined with the data generated by genetic linkage analysis demonstrated that the TCOF1 locus is closely flanked proximally by IG90 and distally by SPARC. 30 refs., 2 figs., 4 tabs.

  5. Characterization of nine polymorphic microsatellite markers in sprat ( Sprattus sprattus L.)

    DEFF Research Database (Denmark)

    Dailianis, T.; Limborg, Morten; Hanel, R.;

    2008-01-01

    Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(12) probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number...... of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis....

  6. THE USE OF MICROSATELLITE MARKERS TO STUDY GENETIC DIVERSITY IN INDONESIAN SHEEP

    OpenAIRE

    Jakaria; M.S.A. Zein; S. Sulandari; Subandriyo,; Muladno

    2014-01-01

    The purpose of this research was to study genetic diversity in Indonesian sheep population using microsatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep. Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci data were analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from ...

  7. 荒诞世界里的自由选择——《第二十二条军规》中的存在主义解读%The free choice in absurd world—— Existentialism in "twenty-two military discipline"

    Institute of Scientific and Technical Information of China (English)

    黄新川

    2012-01-01

      作为黑色幽默文学流派的重要作家,约瑟夫·海勒和他的代表作《第二十二条军规》在世界文坛上占有重要的地位。海勒是黑色幽默的代表作家,但是他的写作过程中深受存在主义的影响。作为流行于二十世纪欧美的一种非理性主义哲学思潮,存在主义可以概括为三个方面:“自由选择”,“存在先于本质”,“世界是荒诞的,人生是痛苦的”。本文试图通过分析小说中主要人物尤索林的行为选择来解读海勒的《第二十二条军规》中的存在主义思想,以期能对这部经典有更好的理解%  As the writer of black humor literature genre, Joseph Heller and his masterpiece "twenty-two military discipline" occupies an important position in the world literature. Heller is the representative writer of black humor, but influenced by the existentialism in his writing process. As a non rationalist philosophy popular in Europe and the United States in twentieth Century, existentialism can be summarized as three respects:" freedom of choice"," existence precedes essence"," the world is absurd, life is painful". This paper attempts to analyze the major characters in the novel Usolin's choice behavior to explain existentialism in Heller's "twenty-two military discipline", in order to have a better understanding of this classic.

  8. Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs.

    Science.gov (United States)

    Liewlaksaneeyanawin, Cherdsak; Ritland, Carol E; El-Kassaby, Yousry A; Ritland, Kermit

    2004-07-01

    Microsatellites, or simple sequence repeats (SSRs), are usually regarded as the "markers of choice" in population genetics research because they exhibit high variability. The development cost of these markers is usually high. In addition, microsatellite primers developed for one species often do not cross-amplify in related species, requiring separate development for each species. However, microsatellites found in expressed sequence tags (ESTs) might better cross-amplify as they reside in or near conserved coding DNA. In this study, we identified 14 Pinus taeda (loblolly pine) EST-SSRs from public EST databases and tested for their cross-species transferability to P. contorta ssp. latifolia, P. ponderosa, and P. sylvestris. As part of our development of a P. contorta microsatellite set, we also compared their transferability to that of 99 traditional microsatellite markers developed in P. taeda and tested on P. contorta ssp. latifolia. Compared to traditional microsatellites, EST-SSRs had higher transfer rates across pine species; however, the level of polymorphism of microsatellites derived from ESTs was lower. Sequence analyses revealed that the frequencies of insertions/deletions and base substitutions were lower in EST-SSRs than in other types of microsatellites, confirming that EST-SSRs are more conserved than traditional SSRs. Our results also provide a battery of 23 polymorphic, robust microsatellite primer pairs for lodgepole pine.

  9. Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing.

    Science.gov (United States)

    Schoebel, C N; Brodbeck, S; Buehler, D; Cornejo, C; Gajurel, J; Hartikainen, H; Keller, D; Leys, M; Ríčanová, S; Segelbacher, G; Werth, S; Csencsics, D

    2013-03-01

    Microsatellites, also known as simple sequence repeats (SSRs), are among the most commonly used marker types in evolutionary and ecological studies. Next Generation Sequencing techniques such as 454 pyrosequencing allow the rapid development of microsatellite markers in nonmodel organisms. 454 pyrosequencing is a straightforward approach to develop a high number of microsatellite markers. Therefore, developing microsatellites using 454 pyrosequencing has become the method of choice for marker development. Here, we describe a user friendly way of microsatellite development from 454 pyrosequencing data and analyse data sets of 17 nonmodel species (plants, fungi, invertebrates, birds and a mammal) for microsatellite repeats and flanking regions suitable for primer development. We then compare the numbers of successfully lab-tested microsatellite markers for the various species and furthermore describe diverse challenges that might arise in different study species, for example, large genome size or nonpure extraction of genomic DNA. Successful primer identification was feasible for all species. We found that in species for which large repeat numbers are uncommon, such as fungi, polymorphic markers can nevertheless be developed from 454 pyrosequencing reads containing small repeat numbers (five to six repeats). Furthermore, the development of microsatellite markers for species with large genomes was also with Next Generation Sequencing techniques more cost and time-consuming than for species with smaller genomes. In this study, we showed that depending on the species, a different amount of 454 pyrosequencing data might be required for successful identification of a sufficient number of microsatellite markers for ecological genetic studies.

  10. Microsatellite instability and the association with plasma homocysteine and thymidylate synthase in colorectal cancer

    DEFF Research Database (Denmark)

    Jensen, Lars Henrik; Lindebjerg, Jan; Crüger, Dorthe G.;

    2008-01-01

    The possible associations between microsatellite instability, homocysteine and thymidylate synthase were investigated in tumors and plasma from 130 patients with colorectal cancer. Other analyses included thymidylate synthase and 5,10-methylene-tetrahydrofolate reductase gene polymorphisms......, carcinoembryonic antigen, vitamin B12, and folate. Microsatellite instability of tumors was associated with higher levels of plasma homocysteine (p = 0.008) and higher protein expression of thymidylate synthase (p ... factors. CEA was not associated with neither homocysteine nor microsatellite instability. The data suggests that there is a more pronounced methyl unit deficiency in microsatellite instable tumors....

  11. Analysis of microsatellite markers in the genome of the plant pathogen Ceratocystis fimbriata.

    Science.gov (United States)

    Simpson, Melissa C; Wilken, P Markus; Coetzee, Martin P A; Wingfield, Michael J; Wingfield, Brenda D

    2013-01-01

    Ceratocystis fimbriata sensu lato represents a complex of cryptic and commonly plant pathogenic species that are morphologically similar. Species in this complex have been described using morphological characteristics, intersterility tests and phylogenetics. Microsatellite markers have been useful to study the population structure and origin of some species in the complex. In this study we sequenced the genome of C. fimbriata. This provided an opportunity to mine the genome for microsatellites, to develop new microsatellite markers, and map previously developed markers onto the genome. Over 6000 microsatellites were identified in the genome and their abundance and distribution was determined. Ceratocystis fimbriata has a medium level of microsatellite density and slightly smaller genome when compared with other fungi for which similar microsatellite analyses have been performed. This is the first report of a microsatellite analysis conducted on a genome sequence of a fungal species in the order Microascales. Forty-seven microsatellite markers have been published for population genetic studies, of which 35 could be mapped onto the C. fimbriata genome sequence. We developed an additional ten microsatellite markers within putative genes to differentiate between species in the C. fimbriata s.l. complex. These markers were used to distinguish between 12 species in the complex.

  12. Development of 13 Microsatellite Markers in the Endangered Sinai Primrose (Primula boveana, Primulaceae

    Directory of Open Access Journals (Sweden)

    Hassan Mansour

    2013-06-01

    Full Text Available Premise of the study: We developed microsatellite markers for the endangered plant Primula boveana, the Sinai primrose, and assessed the cross-transferability of these markers to six related taxa. Methods and Results: DNA sequences containing microsatellites were isolated from a microsatellite-enriched library. We obtained successful amplification of 13 microsatellite primer pairs, seven of which were polymorphic in P. boveana. Eleven of these primers successfully cross-amplified to related taxa. Conclusions: The markers reported herein will be useful to characterize the genetic diversity of the endangered P. boveana and to evaluate its mating system, and have the potential to be useful for similar studies in close relatives.

  13. Sequences Characterization of Microsatellite DNA Sequences in Pacific Abalone (Haliotis discus hannat)

    Institute of Scientific and Technical Information of China (English)

    LI Qi; Kijima Akihiro

    2007-01-01

    The microsatellite-enriched library was constructed using magnetic bead hybridization selection method, and the microsatellite DNA sequences were analyzed in Pacific abalone Haliotis discus hannai. Three hundred and fifty white colonies were screened using PCR-based technique, and 84 clones were identified to potentially contain microsatellite repeat motif. The 84 clones were sequenced, and 42 microsatellites and 4 minisatellites with a minimum of five repeats were found (13.1% of white colonies screened). Besides the motif of CA contained in the oligoprobe, we also found other 16 types of microsatellite repeats including a dinucleotide repeat, two tetranucleotide repeats, twelve pentanucleotide repeats and a hexanucleotide repeat. According to Weber(1990), the microsatellite sequences obtained could be categorized structurally into perfect repeats (73.3%), imperfect repeats(13.3%), and compound repeats (13.4%). Among the microsatellite repeats, relatively short arrays (< 20 repeats) were most abundant,accounting for 75.0%. The largest length of microsatellites was 48 repeats, and the average number of repeats was 13.4. The data on the composition and length distribution of microsatellites obtained in the present study can be useful for choosing the repeat motifs for microsatetlite isolation in other abalone species.

  14. Isolation of microsatellite loci in the pollinating fig wasp of Ficus hispida, Ceratosolen solmsi

    Institute of Scientific and Technical Information of China (English)

    Hao Yu; Tong-Xin Zhang; Hao-Yuan Hu; Li-Ming Niu; Hui Xiao; Yan-Zhou Zhang; Da-Wei Huang

    2008-01-01

    Microsatellite loci were isolated for Ceratosolen solmsi, pollinator of the dioecious Ficus hispida. We developed nine polymorphic microsatellite loci based on the method of polymerase chain reaction isolation of microsatellite arrays (PIMA). Enrichment of genomic libraries was performed by random amplified polymorphic DNA (RAPD). A subset of 38 positive clones was sequenced; 15 clones showed microsatellite loci. We tested 15 designed primer pairs and nine of them produced polymorphic amplification in 48 individual wasps collected from different fruits of the dioecious host fig Ficus hispida in China. Among the 48 individuals, 49 alleles were obtained at the nine loci. The observed heterozygosity ranged between 0.357 and 0.634.

  15. Distribution of trinucleotide microsatellites in different categories of mammalian genomic sequence: Implications for human genetic diseases

    Energy Technology Data Exchange (ETDEWEB)

    Stallings, R.L. (Univ. of Pittsburgh, PA (United States))

    1994-05-01

    The distribution of all trinucleotide microsatellite sequences in the GenBank database was surveyed to provide insight into human genetic disease syndromes that result from expansion of microsatellites. The microsatellite motif (CAG)[sub n] is one of the most abundant microsatellite motifs in human GenBank DNA sequences and is the most abundant microsatellite found in exons. This fact may explain why (CAG)[sub n] repeats are thus far the predominant microsatellites expanded in human genetic diseases. Surprisingly, (CAG)[sub n] microsatellites are excluded from intronic regions in a strand-specific fashion, possibly because of similarity to the 3[prime] consensus splice site, CAGG. A comparison of the positions of microsatellites in human vs rodent homologous sequences indicates that some arrays are not extensively conserved for long periods of time, even when they form parts of protein coding sequences. The general lack of conservation of trinucleotide repeat loci in diverse mammals indicates that animal models for some human microsatellite expansion syndromes may be difficult to find. 20 refs., 5 tabs.

  16. Fragile X gene instability: Anchoring AGGs and linked microsatellites

    Energy Technology Data Exchange (ETDEWEB)

    Zhong, Nan; Yang, Weihong; Dobkin, C. [Institute for Basic Research in Developmental Disabilities, Staten Island, NY (United States)] [and others

    1995-08-01

    Interspersed AGGs within the FMR1 gene CGG repeat region may anchor the sequence and prevent slippage during replication. In order to detect the AGG position variations, we developed a method employing partial MnlI restriction analysis and analyzed X chromosomes from 187 males, including 133 normal controls (17 with 20-34 and 16 with 35-52 repeats), plus 54 fragile X premutations with 56-180 repeats. Among controls, the interspersed AGG positions were highly polymorphic, with heterozygosity of 91%. Among the control samples, 1.5% had no AGG positions, 25% had one, 71% had two, and 3% had three. Among the fragile X premutation samples, 63% had no AGG, while 37% had only one AGG. Analysis of premutation samples within fragile X families showed that variation occurred only within the 3{prime} end of the region. Thus, the instability was polar. Controls with {ge}15 pure CGG repeats were associated with the longest alleles of two nearby microsatellites, FRAXAC1 with 20-21 repeats and DXS548 with 202-206 bp and with increased microsatellite heterzygosity. The association of long pure CGG regions, as with fragile X chromosomes, with the longer and more heterozygous microsatellite alleles suggests they may be related mechanistically. Further, our results do not support a recent suggestion that the frequency of fragile X alleles may be increasing. Finally, analysis of a set of nonhuman primate samples showed that long pure CGG tracks are variable in size and are located within the 3{prime} region, which suggests that polar instability within FMR1 is evolutionarily quite old. 55 refs., 3 figs., 4 tabs.

  17. Microsatellite Instability in Young Women with Endometrioid type Endometrial Cancer

    Directory of Open Access Journals (Sweden)

    MR Abbaszadegan

    2009-09-01

    Full Text Available "nBackground: This study was designed to determine the frequency of Microsatellite Instability (MSI in young Iranian pa­tients with endometrial carcinoma and to evaluate its association with histopathologic and clinical features of disease."nMethods: Microsatellite status was analyzed in 23 patients with endometrioid type endometrial cancer who were less than 55 years. Clinicopathologic characteristics such as age, International Federation of Gynecology and Obstetric (FIGO grad­ing and staging of tumor, family history of Hereditary Non-polyposis Colorectal Cancer (HNPCC, oral conception (OC consump­tion, number of pregnancies, fertility, menstrual cycles and underlying disease were considered. Chi-square and Fisher exact tests were used to find the significant relationships."nResults: MSI analysis showed 8 patients (34.8% were MSS (Microsatellite Stable, 15 patients (62.5% were MSI positive. Among cases with MSI phenotype, 4 cases (17.4% had low instability (MSI-L and 11 cases (47.8% had high instability (MSI-H. Three cases with MSI-H had family history of HNPCC related cancers. Five cases (21.7% had infertility in which 4 of them (80% had MSI phenotype. There was no statistically significant relationship between MSI phenotype and tumor grade and stage."nConclusion: Few studies reported high frequency of MSI among young patients. Some studies mentioned similar results in endo­metrioid type of tumor. This study showed even higher frequency (65% when MSI analyzed in young endometrioid type endometrial patients. Most cases with infertility had MSI-H phenotype. It may suggest that beside women with family his­tory of HNPCC, EC screening using MSI would be beneficial in infertile women too.  

  18. The New Fault Tolerant Onboard Computer for Microsatellite Missions

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    This paper describes an onboard computer with dual processing modules. Each processing module is composed of 32 bit ARM reduced instruction set computer processor and other commercial-off-the-shelf devices. A set of fault handling mechanisms is implemented in the computer system, which enables the system to tolerate a single fault. The onboard software is organized around a set of processes that communicate among each other through a routing process. Meeting an extremely tight set of constraints that include mass, volume, power consumption and space environmental conditions, the fault-tolerant onboard computer has excellent data processing capability that can meet the erquirements of micro-satellite missions.

  19. Nine microsatellite loci developed from the octocoral, Paragorgia arborea

    Science.gov (United States)

    Coykendall, Dolly K.; Morrison, Cheryl L.

    2015-01-01

    Paragorgia arborea, or bubblegum coral, occurs in continental slope habitats worldwide, which are increasingly threatened by human activities such as energy development and fisheries practices. From 101 putative loci screened, nine microsatellite markers were developed from samples taken from Baltimore canyon in the western North Atlantic Ocean. The number of alleles ranged from two to thirteen per locus and each displayed equilibrium. These nuclear resources will help further research on population connectivity in threatened coral species where mitochondrial markers are known to lack fine-scale genetic diversity.

  20. Immunotherapy and patients treated for cancer with microsatellite instability.

    Science.gov (United States)

    Colle, Raphaël; Cohen, Romain; Cochereau, Delphine; Duval, Alex; Lascols, Olivier; Lopez-Trabada, Daniel; Afchain, Pauline; Trouilloud, Isabelle; Parc, Yann; Lefevre, Jérémie H; Fléjou, Jean-François; Svrcek, Magali; André, Thierry

    2017-01-01

    Microsatellite instability (MSI) is a tumor phenotype linked to somatic or germline (Lynch syndrome) inactivating alterations of DNA mismatch repair genes. A broad spectrum of neoplasms exhibits MSI phenotype, mainly colorectal cancer, endometrial cancer, and gastric cancer. MSI tumors are characterized by dense immune infiltration and high load of tumor neo-antigens. Growing evidence is accumulating on the efficacy of immune checkpoint inhibition for patients treated for MSI solid tumors. We present a comprehensive overview of MSI phenotype, its biological landscape and current diagnostic methods. Then we focus on MSI as a predictive biomarker of response to immune checkpoint inhibition in the context of colorectal cancer and non-colorectal tumors.

  1. Microsatellites reveal high genetic diversity within colonies of Camponotus ants.

    Science.gov (United States)

    Gertsch, P; Pamilo, P; Varvio, S L

    1995-04-01

    In order to characterize the sociogenetic structure of colonies in the carpenter ants Camponotus herculeanus and C. ligniperda, we have developed microsatellite markers. The three loci studied were either fixed for different alleles in the two species or showed different patterns of polymorphisms. Genotyping of workers and males showed that the broods of C. ligniperda include several matrilines, a rare phenomenon in the genus. Five alleles from a locus polymorphic in both species were sequenced from the respective PCR-products. A part of the length variation appeared to be due to changes outside the repeat sequence, and some PCR products of an equal length had a different number of dinucleotide repeats.

  2. Polymorphic microsatellite loci for the crimson snapper (Lutjanus erythropterus).

    Science.gov (United States)

    Liu, L; Lin, L; Li, C H; Xu, S N; Liu, Y; Zhou, Y B

    2014-07-24

    We isolated and characterized 22 polymorphic microsatellite loci in Lutjanus erythropterus using a (GT)13-enriched genomic library. We found between 2 and 8 alleles per locus, with a mean of 4.85. The observed and expected heterozygosities ranged from 0.065 to 0.867 and from 0.085 to 0.832, respectively, with means of 0.461 and 0.529, respectively. Allele frequencies in three loci were found to deviate from Hardy-Weinberg equilibrium. Evidence for null alleles was found for three loci. These markers will be useful for distinguishing released captive-bred L. erythropterus individuals from wild individuals.

  3. Space-Based Observations of Satellites From the MOST Microsatellite

    Science.gov (United States)

    2006-11-01

    observations spatiales canadiennes d’un objet en orbite terrestre . Deux satellites de géolocalisation GPS ont été suivis à l’aide du télescope optique monté...the derived orbital metric data with high precision ephemerides yielded root mean square errors of 13 arcseconds. The errors are shown to result...space surveillance from an orbiting platform. Résumé Le 12 octobre 2005, le microsatellite MOST du Canada a acquis les premières images

  4. Microsatellite profiles as a basis for intellectual property protection in grape

    NARCIS (Netherlands)

    Ibanez, J.; Eeuwijk, van F.A.

    2003-01-01

    The use of microsatellite analysis in a forensic procedure for establishing infringement on plant breeders¿ rights in vegetatively propagated crops was evaluated. A reference collection of 45 seedless grape varieties was chosen as reference collection. Matching probabilities of grape microsatellite

  5. Dinucleotide repeat microsatellite markers for buck's-horn plantain (Plantago coronopus)

    NARCIS (Netherlands)

    Koorevaar, G.N.; Ivanovic, S.; Van Damme, J.M.M.; Koelewijn, H.P.; Van 't Westende, W.P.C.; Smulders, M.J.M.; Vosman, B.

    2002-01-01

    Eleven polymorphic microsatellite loci were obtained from a GA enriched genomic library, constructed from DNA of buck's-horn plantain (Plantago coronopus). The microsatellite loci were tested on 24 genotypes. These plants were collected from meadows along the coast, located on 11 sites ranging from

  6. Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii

    DEFF Research Database (Denmark)

    Barker, J.S.F.; Frydenberg, Jane; González, J.;

    2009-01-01

    variation for 15 microsatellite loci in each of nine populations in eastern Australia was used to estimate the size of the bottleneck, and to determine if any of these microsatellites marked genomic regions subject to recent selection. We estimate that on its introduction to Australia, D. buzzatii went...

  7. Microsatellites of the parasitic nematode Haemonchus contortus: polymorphism and linkage with a direct repeat

    NARCIS (Netherlands)

    Hoekstra, R.; Criado-Fornelio, A.; Fakkeldij, J.; Bergman, J.; Roos, M.H.

    1997-01-01

    To develop tools to analyse parasitic nematode population structures and the effects of selection pressure on the nematode population, we isolated and characterised 13 microsatellite markers of the nematode Haemonchus contortus. The density of CA/GT microsatellites, once in 575 kb, is lower than in

  8. Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo.

    Science.gov (United States)

    Wu, Chieh-Hsi; Drummond, Alexei J

    2011-05-01

    We provide a framework for Bayesian coalescent inference from microsatellite data that enables inference of population history parameters averaged over microsatellite mutation models. To achieve this we first implemented a rich family of microsatellite mutation models and related components in the software package BEAST. BEAST is a powerful tool that performs Bayesian MCMC analysis on molecular data to make coalescent and evolutionary inferences. Our implementation permits the application of existing nonparametric methods to microsatellite data. The implemented microsatellite models are based on the replication slippage mechanism and focus on three properties of microsatellite mutation: length dependency of mutation rate, mutational bias toward expansion or contraction, and number of repeat units changed in a single mutation event. We develop a new model that facilitates microsatellite model averaging and Bayesian model selection by transdimensional MCMC. With Bayesian model averaging, the posterior distributions of population history parameters are integrated across a set of microsatellite models and thus account for model uncertainty. Simulated data are used to evaluate our method in terms of accuracy and precision of estimation and also identification of the true mutation model. Finally we apply our method to a red colobus monkey data set as an example.

  9. Constraints on Allele size at microsatellite loci : Implications for genetic differentiation

    NARCIS (Netherlands)

    Nauta, M.J.; Weissing, F.J.

    1996-01-01

    Microsatellites are promising genetic markers for studying the demographic structure and phylogenetic history of populations. We present theoretical arguments indicating that the usefulness of microsatellite data for these purposes may be limited to a short time perspective and to relatively small p

  10. Use of microsatellite markers in an American beech (Fagus grandifolia) population and paternity testing

    Science.gov (United States)

    Jennifer Koch; Dave Carey; M.E. Mason

    2010-01-01

    Cross-species amplification of six microsatellite markers from European beech (Fagus sylvatica Linn) and nine markers from Japanese beech (Fagus crenata Blume) was tested in American beech (Fagus grandifolia Ehrh.). Three microsatellites from each species were successfully adapted for use in American beech...

  11. Diploid Musa acuminata genetic diversity assayed with sequence-tagged microsatellite sites.

    Science.gov (United States)

    Grapin, A; Noyer, J L; Carreel, F; Dambier, D; Baurens, F C; Lanaud, C; Lagoda, P J

    1998-06-01

    The sequence-tagged microsatellite site (STMS) discrimination potential was explored using nine microsatellite primer pairs. STMS polymorphism was assayed by nonradioactive urea-polyacrylamide gel electrophoresis. Genetic relationships were examined among 59 genotypes of wild or cultivated accessions of diploid Musa acuminata. The organization of the subspecies was confirmed and some clone relationships were clarified.

  12. Novel Microsatellite Loci for Sebaea aurea (Gentianaceae and Cross-Amplification in Related Species

    Directory of Open Access Journals (Sweden)

    Jonathan Kissling

    2013-12-01

    Full Text Available Premise of the study: Microsatellite loci were developed in Sebaea aurea (Gentianaceae to investigate the functional role of diplostigmaty (i.e., the presence of additional stigmas along the style. Methods and Results: One hundred seventy-four and 180 microsatellite loci were isolated through 454 shotgun sequencing of genomic and microsatellite-enriched DNA libraries, respectively. Sixteen polymorphic microsatellite loci were characterized, and 12 of them were selected to genotype individuals from two populations. Microsatellite amplification was conducted in two multiplex groups, each containing six microsatellite loci. Cross-species amplification was tested in seven other species of Sebaea. The 12 novel microsatellite loci amplified only in the two most closely related species to S. aurea (i.e., S. ambigua and S. minutiflora and were also polymorphic in these two species. Conclusions: These results demonstrate the usefulness of this set of newly developed microsatellite loci to investigate the mating system and population genetic structure in S. aurea and related species.

  13. A microsatellite marker linkage map of the housefly, Musca domestica : Evidence for male recombination

    NARCIS (Netherlands)

    Feldmeyer, B.; Pen, I.; Beukeboom, L. W.

    2010-01-01

    We present the first molecular marker linkage map for Musca domestica containing 35 microsatellite plus six visible markers. We report the development of 33 new microsatellite markers of which 19 are included in the linkage map. Two hundred and thirty-six F2 individuals were genotyped from three cro

  14. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae).

    Science.gov (United States)

    Bonatelli, Isabel A S; Carstens, Bryan C; Moraes, Evandro M

    2015-01-01

    Microsatellite markers (also known as SSRs, Simple Sequence Repeats) are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq) on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  15. Using Next Generation RAD Sequencing to Isolate Multispecies Microsatellites for Pilosocereus (Cactaceae.

    Directory of Open Access Journals (Sweden)

    Isabel A S Bonatelli

    Full Text Available Microsatellite markers (also known as SSRs, Simple Sequence Repeats are widely used in plant science and are among the most informative molecular markers for population genetic investigations, but the development of such markers presents substantial challenges. In this report, we discuss how next generation sequencing can replace the cloning, Sanger sequencing, identification of polymorphic loci, and testing cross-amplification that were previously required to develop microsatellites. We report the development of a large set of microsatellite markers for five species of the Neotropical cactus genus Pilosocereus using a restriction-site-associated DNA sequencing (RAD-seq on a Roche 454 platform. We identified an average of 165 microsatellites per individual, with the absolute numbers across individuals proportional to the sequence reads obtained per individual. Frequency distribution of the repeat units was similar in the five species, with shorter motifs such as di- and trinucleotide being the most abundant repeats. In addition, we provide 72 microsatellites that could be potentially amplified in the sampled species and 22 polymorphic microsatellites validated in two populations of the species Pilosocereus machrisii. Although low coverage sequencing among individuals was observed for most of the loci, which we suggest to be more related to the nature of the microsatellite markers and the possible bias inserted by the restriction enzymes than to the genome size, our work demonstrates that an NGS approach is an efficient method to isolate multispecies microsatellites even in non-model organisms.

  16. Comparison of information content for microsatellites and SNPs in poultry and cattle

    NARCIS (Netherlands)

    Schopen, G.C.B.; Bovenhuis, H.; Visker, M.H.P.W.; Arendonk, van J.A.M.

    2008-01-01

    Data were available for 12 poultry microsatellites and 29 poultry single nucleotide polymorphisms (SNPs), and for 34 cattle microsatellites and 36 cattle SNPs. Stochastic permutation was used to determine the number of SNPs needed to obtain the same average information content as a given number of m

  17. Isolation of novel microsatellites using FIASCO by dual probe enrichment from Jatropha curcas L. and study on genetic equilibrium and diversity of Indian population revealed by isolated microsatellites

    KAUST Repository

    Pamidimarri, D. V N N Sudheer

    2010-03-11

    Jatropha curcas L. belongs to family Euphorbiaceae, native to South America attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petrodiesel. Very few attempts were made to isolate novel microsatellite markers and assessment of the extent of genetic equilibrium and diversity that exists in J. curcas. Therefore, the present investigation was undertaken to isolate the novel microsatellites and access genetic equilibrium, diversity that exists among 44 diverse germplasm collected from distinct geographical areas in India using isolated microsatellites. The overall efficiency of the enrichment of microsatellite by dual probe in the present study found to be 54% and among the sequences obtained the percentage of sequences having suitable flanking regions for the primer designing was found to be 89.58%. The mean co-efficient of genetic similarity (CGS) was found to be 0.97. The overall diversity obtained by microsatellites was found to be low in comparison with the diversity reported by multilocus markers systems observed in earlier studies; however, the good allele polymorphism was observed. The overall dendrogram of microsatellite analysis resulted in random clustering of germplasm and not in accordance to geographical area of collection. The present study, diversity analysis using microsatellite markers concludes the low genetic diversity and genetic disequlibrium of J. curcas in India and will provide pavement for further intra-population studies on narrow geographical areas to understand the population genetic structure, phylogeography and molecular ecological studies. The germplasm characterized, and the microsatellite markers isolated and characterized in the present study can be employed efficiently in breeding programs for genetic improvement of the species through marker assisted selection and QTL analysis, for further genetic resource management and help in making the J

  18. Evaluation of the genetic variability of 13 microsatellite markers in native Indian pigs

    Indian Academy of Sciences (India)

    Rajeev Kaul; Atar Singh; R. K. Vijh; M. S. Tantia; Rahul Behl

    2001-12-01

    We analysed polymorphism of 13 microsatellites in two Indian domesticated pig types (North Indian and Northeast Indian). Heterozygosity, polymorphism information content, and probability of identity of two random individuals were calculated for all microsatellites in both types. The number of alleles observed at a locus varied between five and 12. The evaluated microsatellites exhibited a very high heterozygosity and polymorphism information content. The probability of identity of two random individuals from different populations taking into account all the 13 microsatellites was as low as 3.51 × 10-19. On the basis of these results, we propose that these microsatellite markers may be used with reliability for studying the genetic diversity and for identification of individuals in Indian pig types.

  19. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species.

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M Iqbal; Zerega, Nyree J C

    2013-07-01

    Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  20. Development of microsatellite loci in Artocarpus altilis (Moraceae) and cross-amplification in congeneric species1

    Science.gov (United States)

    Witherup, Colby; Ragone, Diane; Wiesner-Hanks, Tyr; Irish, Brian; Scheffler, Brian; Simpson, Sheron; Zee, Francis; Zuberi, M. Iqbal; Zerega, Nyree J. C.

    2013-01-01

    • Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit) and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. • Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241), A. camansi (34), A. mariannensis (15), and A. altilis × mariannensis (64) samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426) samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. • Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit. PMID:25202565

  1. Development of Microsatellite Loci in Artocarpus altilis (Moraceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Colby Witherup

    2013-07-01

    Full Text Available Premise of the study: Microsatellite loci were isolated and characterized from enriched genomic libraries of Artocarpus altilis (breadfruit and tested in four Artocarpus species and one hybrid. The microsatellite markers provide new tools for further studies in Artocarpus. Methods and Results: A total of 25 microsatellite loci were evaluated across four Artocarpus species and one hybrid. Twenty-one microsatellite loci were evaluated on A. altilis (241, A. camansi (34, A. mariannensis (15, and A. altilis × mariannensis (64 samples. Nine of those loci plus four additional loci were evaluated on A. heterophyllus (jackfruit, 426 samples. All loci are polymorphic for at least one species. The average number of alleles ranges from two to nine within taxa. Conclusions: These microsatellite primers will facilitate further studies on the genetic structure and evolutionary and domestication history of Artocarpus species. They will aid in cultivar identification and establishing germplasm conservation strategies for breadfruit and jackfruit.

  2. Establishment of paternity testing system using microsatellite markers in Chinese Holstein

    Institute of Scientific and Technical Information of China (English)

    Fei Tian; Dongxiao Sun; Yuan Zhang

    2008-01-01

    To estimate the efficiency of microsatellite markers in paternity testing among Chinese Holstein, 30 microsatellite loci were used to differentiate 330 Chinese Holstein genotypes, according to the calculation of the allele frequency, number of alleles, effective number of alleles, genetic heterozygosity, polymorphic information content (PIC), and the exclusion probability in this cattle population. The results demonstrated that the exclusion probability ranged from 0.620 in locus BM1818 to 0.265 in locus INRA005 with the average of 0.472 and 11 microsatellite markers exceeding 0.5. The combined exclusion probability of nine microsatellite markers was over 0.99. The result showed that paternity testing of Chinese Holstein was basically resolved using the nine microsatellite markers selected.

  3. Development and characterization of microsatellite primers for Chamaecyparis obtusa (Cupressaceae)1

    Science.gov (United States)

    Kim, Young Mi; Shin, Yu Seung; Jeong, Ji Hee

    2016-01-01

    Premise of the study: Although several microsatellite markers of Chamaecyparis obtusa (Cupressaceae) have been reported in previous studies, we newly developed and evaluated polymorphic microsatellite markers of C. obtusa, an economically important species in Korea as a major forestation tree species, for further genetic studies. Methods and Results: Microsatellite-enrichment libraries were constructed according to the selective hybridization method. From this output, we obtained 10 polymorphic and five monomorphic microsatellite markers for C. obtusa. Five of these developed markers were successfully amplified for C. pisifera, a related species. Conclusions: These microsatellite markers can be valuable tools for further genetic studies of C. obtusa, and gathered genetic information may be useful for breeding program management. PMID:27213124

  4. Characterization of Microsatellites in Xanthosoma sagittifolium (Araceae and Cross-Amplification in Related Species

    Directory of Open Access Journals (Sweden)

    Chloe Cathebras

    2014-06-01

    Full Text Available Premise of the study: To investigate the genetic diversity of a root crop, Xanthosoma sagittifolium, and to facilitate germplasm conservation, microsatellite loci were developed and characterized by genotyping 39 accessions from different geographic origins. Methods and Results: Using a microsatellite-enriched library approach, 17 polymorphic microsatellite markers were identified and characterized. The number of alleles for each locus ranged from two to six. Observed and expected heterozygosities ranged from 0.00 to 0.97 and from 0.09 to 0.78, respectively. Additionally, cross-amplification of these microsatellite markers was tested successfully in other species of Xanthosoma and Caladium, with rates varying from 23.5% to 100%. Conclusions: These results indicate the effectiveness of microsatellite loci developed for the characterization of X. sagittifolium genetic diversity. They are crucial for the future investigation of population dynamics and clonal identification and, therefore, for prioritizing germplasm conservation. They should also enable research on other related species.

  5. Development of Microsatellite Loci in Scrophularia incisa (Scrophulariaceae and Cross-Amplification in Congeneric Species

    Directory of Open Access Journals (Sweden)

    Rui-Hong Wang

    2014-02-01

    Full Text Available Premise of the study: To elucidate the population genetics and phylogeography of Scrophularia incisa, microsatellite primers were developed. We also applied these microsatellite markers to its closely related species S. dentata and S. kiriloviana. Methods and Results: Using the compound microsatellite marker technique, 12 microsatellite primers were identified in S. incisa. The number of alleles ranged from 14 to 26 when assessed in 78 individuals from four populations. With high cross-species transferability, these primers also amplified in S. dentata and S. kiriloviana. Conclusions: These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure in the Chinese species of sect. Tomiophyllum at fine and range-wide geographical scales.

  6. An Efficient Procedure for Isolating Microsatellite DNAs from Sea Cucumber (Apostichopus japonicus)

    Institute of Scientific and Technical Information of China (English)

    HU Jingjie; ZHAN Aibin; LU Wei; HU Xiaoli; BAO Zhenmin

    2007-01-01

    The construction of enrichment library proves to be one of the efficient approaches for isolating microsatellites in this study. The genomic DNA of sea cucumber was digested with HaeⅢ and size-selected DNA fragments (250-700bp) were ligated to an adaptor. Microsatellite-containing sequences were captured by using a combination of GA and CA probes, which were attached to a nylon membrane. The microsatellite enrichment library constructed in this study consisted of approximately 700 clones. Two hundred and thirty-two clones reacted positively after the library screening procedure. Of the 50 clones sequenced, all contained at least one microsatellite and one duplicate clone was found. Approximately 86% of the sequenced fragments permitted to design primers for sequence tagged microsatellite site (STMS).

  7. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  8. High polymorphism at microsatellite loci in the Chinese donkey.

    Science.gov (United States)

    Zhang, R F; Xie, W M; Zhang, T; Lei, C Z

    2016-06-24

    To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

  9. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  10. Microsatellite Instability Is Common in Colorectal Cancer in Native Nigerians.

    Science.gov (United States)

    Irabor, David O; Oluwasola, Olayiwola A; Ogunbiyi, Olufemi J; Ogun, Olabiyi G; Okolo, Clement A; Melas, Marilena; Gruber, Stephen B; Shi, Chanjuan; Raskin, Leon

    2017-05-01

    Colorectal cancer (CRC) is the fifth most common cancer in Africa, with significant differences in incidence, biology and clinical behavior from other populations. We studied prevalence and clinicopathological features of microsatellite instability (MSI) and young onset CRC in 83 archival samples from the University of Ibadan, Nigeria. Nigerian cases of CRC were MSI-high in 43% and MSI-high CRC had significantly lower histological heterogeneity than microsatellite-stable CRC (20% vs. 55% respectively, p=0.046). Presence of signet ring cell differentiation (10-50% of tumor) was significantly higher in younger patients with CRC (prevalence of mucinous (10%) and signet ring cell adenocarcinomas (4%) were among distinct features of Nigerian patients with CRC. MSI-high CRC is more common in West Africa and more detailed molecular and genetic analysis is warranted as CRC incidence and mortality continue to increase in the Sub-Saharan Africa. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  11. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

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    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  12. THE STUDY OF MICROSATELLITES ALTERATION IN DIAGNOSES OF BLADDER CANCER

    Institute of Scientific and Technical Information of China (English)

    Zhao Jun; He Dalin; Yang Lin; He Hui; Nan Xunyi

    2006-01-01

    Objective To investigate the possibility of microsatellite alteration (MA) in diagnosis of bladder cancer of Chinese people, and find the better panel which will be used in clinic. Methods A total of 6 and 10microsatellite markers were chosen, PCR-SSLP silver staining assay was performed in 31 and 32 bladder cancers tissue,exfoliate cells in urine and 10, 15 non-bladder cancers exfoliate cells in urine, respectively. Results MA (+) was found in 28 out of 31, 30 out of 32 bladder cancers, and the sensitivity was 90.3%, 93.7% respectively. The MA of urine sediment of 25 non-bladder cancers was negative, and the specificity was 100%. The cytology was carried out among 19 out of 31, 20 out of 32 bladder cancers at the same time, 2 cases ( 10.3 %) and 3 cases ( 15 % ) were found cancer positive, and the sensitivity is significantly lower than that by the analysis of MA in exfoliated cells. Conclusion MA was not associated with grade and stage of the bladder cancer. MA assay is a sensitive and effective method for the early detection of bladder cancer and post-operation surveillance.

  13. FullSSR: Microsatellite Finder and Primer Designer

    Science.gov (United States)

    Metz, Sebastián; Cabrera, Juan Manuel; Rueda, Eva; Giri, Federico; Amavet, Patricia

    2016-01-01

    Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR) loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user. PMID:27366148

  14. Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels

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    Mei-Chen Tseng

    2012-04-01

    Full Text Available Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: do temperate and tropical Anguilla eels have different genetic polymorphic patterns?; and do temperate Anguilla japonica and Anguilla anguilla have a closer relationship to each other than to tropical eels? In total, 274 sequences were cloned and sequenced from six conserved microsatellite loci to examine polymorphic patterns of these four catadromous eels. Different mutational events, including substitutions, and repeat-unit deletions and insertions, appeared in major regions, while different point mutations were observed in flanking regions. The results implied that parallel patterns of microsatellite sequences occurred within both tropical and temperate freshwater eels. Consensus flanking sequences of six homologous loci from each of the four species were constructed. Genetic distances ranged from 0.044 (Anguilla bicolor pacifica vs. Anguilla marmorata to 0.061 (Anguilla marmorata vs. Anguilla anguilla. The tree topology suggests the hypothesis of Anguilla japonica and Anguilla anguilla being a sister group must be rejected.

  15. Partners in crime: bidirectional transcription in unstable microsatellite disease.

    Science.gov (United States)

    Batra, Ranjan; Charizanis, Konstantinos; Swanson, Maurice S

    2010-04-15

    Nearly two decades have passed since the discovery that the expansion of microsatellite trinucleotide repeats is responsible for a prominent class of neurological disorders, including Huntington disease and fragile X syndrome. These hereditary diseases are characterized by genetic anticipation or the intergenerational increase in disease severity accompanied by a decrease in age-of-onset. The revelation that the variable expansion of simple sequence repeats accounted for anticipation spawned a number of pathogenesis models and a flurry of studies designed to reveal the molecular events affected by these expansions. This work led to our current understanding that expansions in protein-coding regions result in extended homopolymeric amino acid tracts, often polyglutamine or polyQ, and deleterious protein gain-of-function effects. In contrast, expansions in noncoding regions cause RNA-mediated toxicity. However, the realization that the transcriptome is considerably more complex than previously imagined, as well as the emerging regulatory importance of antisense RNAs, has blurred this distinction. In this review, we summarize evidence for bidirectional transcription of microsatellite disease genes and discuss recent suggestions that some repeat expansions produce variable levels of both toxic RNAs and proteins that influence cell viability, disease penetrance and pathological severity.

  16. Heterologous microsatellite primer pairs informative for the whole genus Arachis

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    Andrea Akemi Hoshino

    2006-01-01

    Full Text Available The genus Arachis currently comprises 69 described species, some of which have potential and real value as human and animal foods. These Arachis species have been collected and maintained in germplasm banks to provide material that can be used as sources of genes in breeding programs and for the selection of new cultivars. One of the principal objectives of germplasm conservation is the evaluation of genetic variability, which is best conducted using molecular markers. We investigated the use of heterologous primers to amplify microsatellite loci that could be used to evaluate genetic variability in Arachis germplasm. Fifteen microsatellite primer pairs were tested in 76 accessions of 34 species from the nine Arachis sections. The data indicated that heterologous primers were very useful in Arachis since they had high transferability among the species (91% and allowed the amplification of very polymorphic putative loci, which allowed both the characterization of most accessions and to make inferences about the mating systems of some species analyzed. Our data also revealed that the germplasm analyzed showed high variability, even when represented by few accessions.

  17. Eucalyptus microsatellites mined in silico: survey and evaluation

    Indian Academy of Sciences (India)

    R. Yasodha; R. Sumathi; P. Chezhian; S. Kavitha; M. Ghosh

    2008-04-01

    Eucalyptus is an important short rotation pulpy woody plant, grown widely in the tropics. Recently, many genomic programmes are underway leading to the accumulation of voluminous genomic and expressed sequence tag sequences in public databases. These sequences can be utilized for analysis of simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) available in the transcribed genes. In this study, in silico analysis of 15,285 sequences representing partial and full-length mRNA from Eucalyptus species for their use in developing SSRs or microsatellites were carried out. A total of 875 EST-SSRs were identified from 772 SSR containing ESTs. Motif size of 6 for dinucleotide and 5 for trinucleotide, tetranucleotide, and pentanucleotides were considered in locating the microsatellites. The average frequency of identified SSRs was 12.9%. The dinucleotide repeats were the most abundant among the dinucleotide, trinucleotide and tetranucleotide motifs and accounted for 50.9% of the Eucalyptus genome. Primer designing analysis showed that 571 sequences with SSRs had sufficient flanking regions for polymerase chain reaction (PCR) primer synthesis. Evaluation of the usefulness of the SSRs showed that EST-derived SSRs can generate polymorphic markers as all the primers showed allelic diversity among the 16 provenances of E. tereticornis.

  18. Genetic diversity of microsatellite loci in hierarchically structured populations.

    Science.gov (United States)

    Song, Seongho; Dey, Dipak K; Holsinger, Kent E

    2011-08-01

    Microsatellite loci are widely used for investigating patterns of genetic variation within and among populations. Those patterns are in turn determined by population sizes, migration rates, and mutation rates. We provide exact expressions for the first two moments of the allele frequency distribution in a stochastic model appropriate for studying microsatellite evolution with migration, mutation, and drift under the assumption that the range of allele sizes is bounded. Using these results, we study the behavior of several measures related to Wright's F(ST), including Slatkin's R(ST). Our analytical approximations for F(ST) and R(ST) show that familiar relationships between N(e)m and F(ST) or R(ST) hold when the migration and mutation rates are small. Using the exact expressions for F(ST) and R(ST), our numerical results show that, when the migration and mutation rates are large, these relationships no longer hold. Our numerical results also show that the diversity measures most closely related to F(ST) depend on mutation rates, mutational models (stepwise versus two-phase), migration rates, and population sizes. Surprisingly, R(ST) is relatively insensitive to the mutation rates and mutational models. The differing behaviors of R(ST) and F(ST) suggest that properties of the among-population distribution of allele frequencies may allow the roles of mutation and migration in producing patterns of diversity to be distinguished, a topic of continuing investigation.

  19. Using Microsatellites to Identify Yeast Strains in Beer

    Science.gov (United States)

    Bruke, Alexandria; Van Brocklin, Jennifer; Rivest, Jason; Prenni, Jessica E.; Ibrahim, Hend

    2012-01-01

    Yeast is an integral part of the brewing process and is responsible for much of the taste and characteristics of beer. During the brewing process, yeast is subject to ageing and stress factors that can result in growth inhibition, decreased genetic stability, and changes in cell membrane stability. Characterization of yeast species used in industrial fermentation (e.g. S. cerevisiae) is of great importance to the brewing industry. The objective of this study was to develop an assay to identify yeast strains commonly used in the production of beer. Six microsatellite regions of DNA (comprised of AAT) were used as sequence tagged site markers (STR) to identify and compare yeast samples and to determine strain within a species. Labeled primers ScATT (1-6) targeting these six microsatellite regions were designed using 6-FAM, VIC, NED and PET 5′-fluorescent labels. The six regions were amplified, in a single reaction, from extracted yeast genomic DNA using a modified multiplex-PCR protocol and the labeled PCR products were analyzed on an ABI 3130xl Genetic Analyzer. Using this approach 6 STR markers were amplified in a single multiplex reaction from a commercially utilized yeast strain provided by Odell Brewing. Different alleles were distinguished based on the size of each STR and the labeling fluorophore. The procedures developed in this study will provide an invaluable tool for the quality control of yeast strains in the brewing industry.

  20. Segregation of microsatellite alleles and residual heterogosity at single loci in homozygous androgenetic common carp (Cyprino carpio L.)

    NARCIS (Netherlands)

    Tanck, M.W.T.; Palstra, A.P.; Weerd, van de M.; Leffering, C.P.; Poel, van der J.J.; Bovenhuis, H.; Komen, J.

    2001-01-01

    Thirty-three androgenetic progeny groups of common carp were analysed using 11 microsatellite markers to (i) verify the homozygous status of the 566 androgenetic individuals, (ii) analyse the microsatellite allele segregation, and (iii) study the possible association of microsatellite alleles with p

  1. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs

    Directory of Open Access Journals (Sweden)

    Bosch Montserrat

    2006-10-01

    Full Text Available Abstract Background The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. Results We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the insterspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Conclusion Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes. Finally, due to their higher complexity and lower potential informative content of microsatellites

  2. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.

    Science.gov (United States)

    López-Giráldez, Francesc; Andrés, Olga; Domingo-Roura, Xavier; Bosch, Montserrat

    2006-10-23

    The popularity of microsatellites has greatly increased in the last decade on account of their many applications. However, little is currently understood about the factors that influence their genesis and distribution among and within species genomes. In this work, we analyzed carnivore microsatellite clones from GenBank to study their association with interspersed repeats and elucidate the role of the latter in microsatellite genesis and distribution. We constructed a comprehensive carnivore microsatellite database comprising 1236 clones from GenBank. Thirty-three species of 11 out of 12 carnivore families were represented, although two distantly related species, the domestic dog and cat, were clearly overrepresented. Of these clones, 330 contained tRNALys-derived SINEs and 357 contained other interspersed repeats. Our rough estimates of tRNA SINE copies per haploid genome were much higher than published ones. Our results also revealed a distinct juxtaposition of AG and A-rich repeats and tRNALys-derived SINEs suggesting their coevolution. Both microsatellites arose repeatedly in two regions of the interspersed repeat. Moreover, microsatellites associated with tRNALys-derived SINEs showed the highest complexity and less potential instability. Our results suggest that tRNALys-derived SINEs are a significant source for microsatellite generation in carnivores, especially for AG and A-rich repeat motifs. These observations indicate two modes of microsatellite generation: the expansion and variation of pre-existing tandem repeats and the conversion of sequences with high cryptic simplicity into a repeat array; mechanisms which are not specific to tRNALys-derived SINEs. Microsatellite and interspersed repeat coevolution could also explain different distribution of repeat types among and within species genomes.Finally, due to their higher complexity and lower potential informative content of microsatellites associated with tRNALys-derived SINEs, we recommend avoiding

  3. A matter of life or death: how microsatellites emerge in and vanish from the human genome.

    Science.gov (United States)

    Kelkar, Yogeshwar D; Eckert, Kristin A; Chiaromonte, Francesca; Makova, Kateryna D

    2011-12-01

    Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypothesized to follow a life cycle, wherein they are born and expand into adulthood, until their degradation and death. Here we identified microsatellite births/deaths in human, chimpanzee, and orangutan genomes, using macaque and marmoset as outgroups. We inferred mutations causing births/deaths based on parsimony, and investigated local genomic environments affecting them. We also studied birth/death patterns within transposable elements (Alus and L1s), coding regions, and disease-associated loci. We observed that substitutions were the predominant cause for births of short microsatellites, while insertions and deletions were important for births of longer microsatellites. Substitutions were the cause for deaths of microsatellites of virtually all lengths. AT-rich L1 sequences exhibited elevated frequency of births/deaths over their entire length, while GC-rich Alus only in their 3' poly(A) tails and middle A-stretches, with differences depending on transposable element integration timing. Births/deaths were strongly selected against in coding regions. Births/deaths occurred in genomic regions with high substitution rates, protomicrosatellite content, and L1 density, but low GC content and Alu density. The majority of the 17 disease-associated microsatellites examined are evolutionarily ancient (were acquired by the common ancestor of simians). Our genome-wide investigation of microsatellite life cycle has fundamental applications for predicting the susceptibility of birth/death of microsatellites, including many disease-causing loci.

  4. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

    Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite

  5. Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing.

    Science.gov (United States)

    Vianna, Juliana A; Noll, Daly; Mura-Jornet, Isidora; Valenzuela-Guerra, Paulina; González-Acuña, Daniel; Navarro, Cristell; Loyola, David E; Dantas, Gisele P M

    Microsatellites are valuable molecular markers for evolutionary and ecological studies. Next generation sequencing is responsible for the increasing number of microsatellites for non-model species. Penguins of the Pygoscelis genus are comprised of three species: Adélie (P. adeliae), Chinstrap (P. antarcticus) and Gentoo penguin (P. papua), all distributed around Antarctica and the sub-Antarctic. The species have been affected differently by climate change, and the use of microsatellite markers will be crucial to monitor population dynamics. We characterized a large set of genome-wide microsatellites and evaluated polymorphisms in all three species. SOLiD reads were generated from the libraries of each species, identifying a large amount of microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P. antarcticus and P. papua, respectively. A large number of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849) microsatellites are described. Microsatellite abundance, diversity and orthology were characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci in all three species, which allow to perform comparative studies. Polymorphic markers presented here enable a number of ecological, population, individual identification, parentage and evolutionary studies of Pygoscelis, with potential use in other penguin species.

  6. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  7. De novo assembly of pen shell ( Atrina pectinata) transcriptome and screening of its genic microsatellites

    Science.gov (United States)

    Sun, Xiujun; Li, Dongming; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Yang, Aiguo

    2017-10-01

    The pen shell ( Atrina pectinata) is a large wedge-shaped bivalve, which belongs to family Pinnidae. Due to its large and nutritious adductor muscle, it is the popular seafood with high commercial value in Asia-Pacific countries. However, limiting genomic and transcriptomic data have hampered its genetic investigations. In this study, the transcriptome of A. pectinata was deeply sequenced using Illumina pair-end sequencing technology. After assembling, a total of 127263 unigenes were obtained. Functional annotation indicated that the highest percentage of unigenes (18.60%) was annotated on GO database, followed by 18.44% on PFAM database and 17.04% on NR database. There were 270 biological pathways matched with those in KEGG database. Furthermore, a total of 23452 potential simple sequence repeats (SSRs) were identified, of them the most abundant type was mono-nucleotide repeats (12902, 55.01%), which was followed by di-nucleotide (8132, 34.68%), tri-nucleotide (2010, 8.57%), tetra-nucleotide (401, 1.71%), and penta-nucleotide (7, 0.03%) repeats. Sixty SSRs were selected for validating and developing genic SSR markers, of them 23 showed polymorphism in a cultured population with the average observed and expected heterozygosities of 0.412 and 0.579, respectively. In this study, we established the first comprehensive transcript dataset of A. pectinata genes. Our results demonstrated that RNA-Seq is a fast and cost-effective method for genic SSR development in non-model species.

  8. Colon and rectal cancer survival by tumor location and microsatellite instability: the Colon Cancer Family Registry.

    Science.gov (United States)

    Phipps, Amanda I; Lindor, Noralane M; Jenkins, Mark A; Baron, John A; Win, Aung Ko; Gallinger, Steven; Gryfe, Robert; Newcomb, Polly A

    2013-08-01

    Cancers in the proximal colon, distal colon, and rectum are frequently studied together; however, there are biological differences in cancers across these sites, particularly in the prevalence of microsatellite instability. We assessed the differences in survival by colon or rectal cancer site, considering the contribution of microsatellite instability to such differences. This is a population-based prospective cohort study for cancer survival. This study was conducted within the Colon Cancer Family Registry, an international consortium. Participants were identified from population-based cancer registries in the United States, Canada, and Australia. Information on tumor site, microsatellite instability, and survival after diagnosis was available for 3284 men and women diagnosed with incident invasive colon or rectal cancer between 1997 and 2002, with ages at diagnosis ranging from 18 to 74. Cox regression was used to calculate hazard ratios for the association between all-cause mortality and tumor location, overall and by microsatellite instability status. Distal colon (HR, 0.59; 95% CI, 0.49-0.71) and rectal cancers (HR, 0.68; 95% CI, 0.57-0.81) were associated with lower mortality than proximal colon cancer overall. Compared specifically with patients with proximal colon cancer exhibiting no/low microsatellite instability, patients with distal colon and rectal cancers experienced lower mortality, regardless of microsatellite instability status; patients with proximal colon cancer exhibiting high microsatellite instability had the lowest mortality. Study limitations include the absence of stage at diagnosis and cause-of-death information for all but a subset of study participants. Some patient groups defined jointly by tumor site and microsatellite instability status are subject to small numbers. Proximal colon cancer survival differs from survival for distal colon and rectal cancer in a manner apparently dependent on microsatellite instability status. These

  9. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya.

    Science.gov (United States)

    Oliveira, G A F; Dantas, J L L; Oliveira, E J

    2015-10-01

    The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.

  10. Both microsatellite length and sequence context determine frameshift mutation rates in defective DNA mismatch repair.

    Science.gov (United States)

    Chung, Heekyung; Lopez, Claudia G; Holmstrom, Joy; Young, Dennis J; Lai, Jenny F; Ream-Robinson, Deena; Carethers, John M

    2010-07-01

    It is generally accepted that longer microsatellites mutate more frequently in defective DNA mismatch repair (MMR) than shorter microsatellites. Indeed, we have previously observed that the A10 microsatellite of transforming growth factor beta type II receptor (TGFBR2) frameshifts -1 bp at a faster rate than the A8 microsatellite of activin type II receptor (ACVR2), although both genes become frameshift-mutated in >80% of MMR-defective colorectal cancers. To experimentally determine the effect of microsatellite length upon frameshift mutation in gene-specific sequence contexts, we altered the microsatellite length within TGFBR2 exon 3 and ACVR2 exon 10, generating A7, A10 and A13 constructs. These constructs were cloned 1 bp out of frame of EGFP, allowing a -1 bp frameshift to drive EGFP expression, and stably transfected into MMR-deficient cells. Subsequent non-fluorescent cells were sorted, cultured for 7-35 days and harvested for EGFP analysis and DNA sequencing. Longer microsatellites within TGFBR2 and ACVR2 showed significantly higher mutation rates than shorter ones, with TGFBR2 A13, A10 and A7 frameshifts measured at 22.38x10(-4), 2.17x10(-4) and 0.13x10(-4), respectively. Surprisingly, shorter ACVR2 constructs showed three times higher mutation rates at A7 and A10 lengths than identical length TGFBR2 constructs but comparably lower at the A13 length, suggesting influences from both microsatellite length as well as the sequence context. Furthermore, the TGFBR2 A13 construct mutated into 33% A11 sequences (-2 bp) in addition to expected A12 (-1 bp), indicating that this construct undergoes continual subsequent frameshift mutation. These data demonstrate experimentally that both the length of a mononucleotide microsatellite and its sequence context influence mutation rate in defective DNA MMR.

  11. Microsatellite primers for the rare sedge Lepidosperma bungalbin (Cyperaceae)1

    Science.gov (United States)

    Nevill, Paul G.; Wardell-Johnson, Grant

    2016-01-01

    Premise of the study: Microsatellite markers were developed for the rare sedge Lepidosperma bungalbin (Cyperaceae) to assess genetic variation and its spatial structuring. Methods and Results: We conducted shotgun sequencing on an Illumina MiSeq and produced 6,215,872 sequence reads. The QDD pipeline was used to design 60 primer pairs that were screened using PCR. We developed 17 loci, of which 12 loci were identified that were polymorphic, amplified reliably, and could be consistently scored. We then screened these loci for variation in individuals from three populations. The number of alleles observed for these 12 loci across the three populations ranged from nine to 19 and expected heterozygosity ranged from 0.41 to 0.89. Conclusions: These markers will enable the quantification of the potential impact of mining on genetic variation within L. bungalbin and establish a baseline for future management of genetic variation of the rare sedge. PMID:27843727

  12. In Silico Retrieving of Opium Poppy (Papaver Somniferum L. Microsatellites

    Directory of Open Access Journals (Sweden)

    Masárová Veronika

    2015-12-01

    Full Text Available Repetitive tandem sequences were retrieved within nucleotide sequences of opium poppy (Papaver somniferum L. genomic DNA available in the GenBank® database. Altogether 538 different microsatellites with the desired length characteristics of tandem repeats have been identified within 450 sequences of opium poppy DNA available in the database. The most frequented were mononucleotide repeats (246; nevertheless, 44 dinucleotide, 148 trinucleotide, 62 tetranucleotide, 28 pentanucleotide and 5 hexanucleotide tandem repeats have also been found. The most abundant were trinucleotide motifs (27.50%, and the most abundant motifs within each group of tandem repeats were TA/AT, TTC/GAA, GGTT/AACC and TTTTA/ TAAAA. Five hexanucleotide repeats contained four different motifs.

  13. Amplification of rainbow trout microsatellites in Brachymystax lenok.

    Science.gov (United States)

    Jia, Z Y; Zhang, Y Y; Shi, L Y; Bai, Q L; Jin, S B; Mou, Z B

    2008-11-01

    Brachymystax lenok is a cold freshwater fish accustomed to inhabit relatively high concentration of dissolved oxygen and clean upper streams. Here we present 13 polymorphic microsatellite primer pairs from rainbow trout to amplify in 32 B. lenok individuals from Ussuri River of China. The number of alleles ranged from two to seven with an average of 3.9 per locus. Observed heterozygosity ranged from 0.0625 to 0.9677. One locus showed significant deviation from Hardy-Weinberg equilibrium. These 13 loci will provide a good basis for investigation of B. lenok population structure and genetic diversity in different distribution region. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  14. Development of eighteen microsatellite loci in walleye (Sander vitreus)

    Science.gov (United States)

    Coykendall, Dolly K.; Morrison, Cheryl L.; Stott, Wendylee; Springmann, Marcus J.

    2014-01-01

    A suite of tri- and tetra-nucleotide microsatellite loci were developed for walleye (Sander vitreus) from 454 pyrosequencing data. Eighteen of the 50 primer sets tested amplified consistently in 35 walleye from two lakes on Isle Royale, Lake Superior: Chickenbone Lake and Whittlesey Lake. The loci displayed moderate levels of allelic diversity (average 5.5 alleles/locus) and heterozygosity (average 35.8 %). Levels of genetic diversity were sufficient to produce unique multi-locus genotypes and detect phylogeographic structuring as individuals assigned back to their population of origin. Cross-species amplification within S. canadensis(sauger) was successful for 15 loci, and 11 loci were diagnostic to species. The loci characterized here will be useful for detecting fine-scale spatial structuring, resolving the taxonomic status of Sander species and sub-species, and detecting walleye/sauger hybrids.

  15. Identification and Characterization of Microsatellites from Calafate (Berberis microphylla, Berberidaceae

    Directory of Open Access Journals (Sweden)

    Benjamín Varas

    2013-07-01

    Full Text Available Premise of the study: Southern barberry or calafate (Berberis microphylla is a shrub species endemic to the Patagonian region of South America that is used for human consumption. The fruit is very rich in vitamin C and anthocyanins and has a very high antioxidant capacity. There have been only a few genetic studies of this and other closely related species. Methods and Results: Here we present the first 18 microsatellite markers of B. microphylla that were characterized using 66 accessions of calafate from Patagonia. On average, they had 7.6 alleles per marker, with an expected heterozygosity of 0.688. The informativeness of these markers was also evaluated in another 15 Berberis species, including most of the native and endemic Chilean species. Conclusions: The results confirm that these new simple sequence repeat markers are very polymorphic and potentially useful in genetic studies in any species of the genus Berberis.

  16. Microsatellite markers derived from Calophyllum inophyllum (Clusiaceae) expressed sequence tags.

    Science.gov (United States)

    Setsuko, Suzuki; Uchiyama, Kentaro; Sugai, Kyoko; Hanaoka, So; Yoshimaru, Hiroshi

    2012-01-01

    Robust markers are required (inter alia) for assessing origins of Calophyllum inophyllum populations on the Bonin Islands, Japan. Therefore, informative expressed sequence tag (EST)-based microsatellite or simple sequence repeat (SSRs) markers in the species were sought. Using 135378 ESTs derived from de novo pyrosequencing, primers for 475 EST-SSRs were developed, 48 of which were tested for PCR amplification. Thirty-six of the 48 primers showed clear amplification, with 23 displaying polymorphism in sampled populations. Expected heterozygosity in the samples from the Bonin Islands and Ryukyu Islands populations ranged from 0.041 to 0.697 and from 0.041 to 0.773, respectively. As EST-SSRs are potentially tightly linked with functional genes, and reportedly more transferable to related species than anonymous genomic SSRs, the developed primers have utility for future studies of the origins, genetic structure, and conservation of C. inophyllum and related species.

  17. Preliminary of Optical Lens Design for Micro-Satellite

    Science.gov (United States)

    Rachim, Elvira; Mukhtar Tahir, Andi; Herawan, Agus

    2017-01-01

    The development of micro satellites for the last two decades is emerging rapidly as the need of satellite communication usage is increasing. Earth observation is one of the example of how satellites are on demand. Most observation satellites consist of sensors and imaging system on-board. One of the key element to have a good imaging system is a special optical lens system design. Such lens is designed specifically by calculating every parameter such as refractive, reflective indexes, type of surface, distance and many more. Manufactured lenses sometimes do not match the requirement of an imager system hence the special lens design is needed. This paper will first briefly describe the history of optic, theory related to lens system, then the design and the analysis of lens system for micro-satellites generally and LAPAN A4 particularly.

  18. Characterization of microsatellite loci in the SLA class I region.

    Science.gov (United States)

    Chung, Hoyoung; McClure, Matthew Charles

    2011-04-01

    Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18 Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. MS markers identified from this analysis can be used to provide an alternative method to direct typing for determining an individual's SLA-1 haplotype. Copyright © 2010 Elsevier Inc. All rights reserved.

  19. Microsatellite instability in cancer of the proximal colon

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, S.N.; Bren, G.; Schaid, D. (Mayo Clinic and Foundation, Rochester, MN (United States))

    1993-05-07

    Colorectal tumor DNA was examined for somatic instability at (CA)[sub n] repeats on human chromosomes 5q, 15q, 17p, and 18q. Differences between tumor and normal DNA were detected in 25 of the 90 (28 percent) tumors examined. This instability appeared as either a substantial change in repeat length (often heterogeneous in nature) or a minor change (typically two base pairs). Microsatellite instability was significantly correlated with the tumor's location in the proximal colon (P = 0.003), with increased patient survival (P = 0.02), and, inversely, with loss of heterozygosity for chromosomes 5q, 17p, and 18q. These data suggest that some colorectal cancers may arise through a mechanism that does not necessarily involve loss of heterozygosity. 23 refs., 2 figs., 3 tabs.

  20. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences.

    Science.gov (United States)

    Gardner, Elliot M; Laricchia, Kristen M; Murphy, Matthew; Ragone, Diane; Scheffler, Brian E; Simpson, Sheron; Williams, Evelyn W; Zerega, Nyree J C

    2015-09-01

    Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Fifteen simple sequence repeats (SSRs) were identified in chloroplast sequences from four Artocarpus transcriptome assemblies. The markers were evaluated using capillary electrophoresis in A. odoratissimus (105 accessions) and A. altilis (73). They were also evaluated in silico in A. altilis (10), A. camansi (6), and A. altilis × A. mariannensis (7) transcriptomes. All loci were polymorphic in at least one species, with all 15 polymorphic in A. camansi. Per species, average alleles per locus ranged between 2.2 and 2.5. Three loci had evidence of fragment-length homoplasy. These markers will complement existing nuclear markers by enabling confident identification of maternal and clone lines, which are often important in vegetatively propagated crops such as breadfruit.

  1. Genome Variability and Gene Content in Chordopoxviruses: Dependence on Microsatellites

    Science.gov (United States)

    Hatcher, Eneida L.; Wang, Chunlin; Lefkowitz, Elliot J.

    2015-01-01

    To investigate gene loss in poxviruses belonging to the Chordopoxvirinae subfamily, we assessed the gene content of representative members of the subfamily, and determined whether individual genes present in each genome were intact, truncated, or fragmented. When nonintact genes were identified, the early stop mutations (ESMs) leading to gene truncation or fragmentation were analyzed. Of all the ESMs present in these poxvirus genomes, over 65% co-localized with microsatellites—simple sequence nucleotide repeats. On average, microsatellites comprise 24% of the nucleotide sequence of these poxvirus genomes. These simple repeats have been shown to exhibit high rates of variation, and represent a target for poxvirus protein variation, gene truncation, and reductive evolution. PMID:25912716

  2. Microsatellite Markers for the Yam Bean Pachyrhizus (Fabaceae

    Directory of Open Access Journals (Sweden)

    Marc Delêtre

    2013-06-01

    Full Text Available Premise of the study: Microsatellite loci were developed for the understudied root crop yam bean (Pachyrhizus spp. to investigate intraspecific diversity and interspecific relationships within the genus Pachyrhizus. Methods and Results: Seventeen nuclear simple sequence repeat (SSR markers with perfect di- and trinucleotide repeats were developed from 454 pyrosequencing of SSR-enriched genomic libraries. Loci were characterized in P. ahipa and wild and cultivated populations of four closely related species. All loci successfully cross-amplified and showed high levels of polymorphism, with number of alleles ranging from three to 12 and expected heterozygosity ranging from 0.095 to 0.831 across the genus. Conclusions: By enabling rapid assessment of genetic diversity in three native neotropical crops, P. ahipa, P. erosus, and P. tuberosus, and two wild relatives, P. ferrugineus and P. panamensis, these markers will allow exploration of the genetic diversity and evolutionary history of the genus Pachyrhizus.

  3. Candidate driver genes in microsatellite-unstable colorectal cancer

    DEFF Research Database (Denmark)

    Alhopuro, Pia; Sammalkorpi, Heli; Niittymäki, Iina;

    2012-01-01

    . Here, we evaluated somatic mutations in microsatellite repeats of 790 genes chosen based on reduced expression in MSI CRC and existence of a coding mononucleotide repeat of 6–10 bp in length. All the repeats were initially sequenced in 30 primary MSI CRC samples and whenever frameshift mutations were...... types (A/T and C/G, 6–10 bp). Along with several know target genes, including TGFBR2, ACVR2, and MSH3, six novel candidate driver genes emerged that harbored significantly more mutations than identical control repeats. The mutation frequencies in 100 MSI CRC samples were 51% in G8 of GLYR1, 47% in T9...... genes that when mutated are likely to contribute to MSI CRC development....

  4. Microsatellite variability of Sardinian pine martens, Martes martes.

    Science.gov (United States)

    Colli, Licia; Cannas, Rita; Deiana, Anna M; Tagliavini, James

    2011-08-01

    The pine marten, Martes martes, is a medium-sized terrestrial carnivore associated with woodland habitats of the western Palearctic region. The present distribution area of the species also includes six islands of the western Mediterranean basin. The origin of these insular populations and their taxonomic status are still debated; their molecular characterization appears relevant for conservation purposes. To describe the genetic variability of the pine martens from Sardinia we characterized 40 insular and 14 Italian individuals at seven nuclear microsatellite loci. The identification of private alleles and the calculated F(ST) value of 0.074 revealed some genetic differentiation between the two populations, which accounts for the high percentages of correct allocation (96.39-98.80%) scored by the genotype assignment test. The presence of two distinct clusters corresponding to Sardinia and mainland Italy was further confirmed by the multivariate Factorial Correspondence Analysis of individual genotypes. Moreover, the genome of the Sardinian individuals bore signs of past demographic fluctuations, i.e. the presence of the monomorphic locus Ma-4, a lower allelic richness and a lower number of private alleles, which may derive from the combination of drift, founder effects, and human overexploitation. Anyway, if such events ever affected the Sardinian population, this is likely to have happened in the past since, according to our microsatellite data, the present-day population does not show evidence of recent bottlenecks or inbreeding, the Wilcoxon sign-rank test and the F(IS) index being not statistically significant (both P > 0.05). Based on this genetic evidence, we advance hypotheses about the distinctiveness of the Sardinian population and its significance for taxonomy and conservation.

  5. Imbalanced adaptive responses associated with microsatellite instability in cholangiocarcinoma

    Science.gov (United States)

    Loilome, Watcharin; Kadsanit, Sasithorn; Muisook, Kanha; Yongvanit, Puangrat; Namwat, Nisana; Techasen, Anchalee; Puapairoj, Anucha; Khuntikeo, Narong; Phonjit, Pichai

    2017-01-01

    The adaptive response of the genome protection mechanism occurs in cells when exposed to genotoxic stress due to the overproduction of free radicals via inflammation and infection. In such circumstances, cells attempt to maintain health via several genome protection mechanisms. However, evidence is increasing that this adaptive response may have deleterious effect; a reduction of antioxidant enzymes and/or imbalance in the DNA repair system generates microsatellite instability (MSI), which has procarcinogenic implications. Therefore, the present study hypothesized that MSI caused by imbalanced responses of antioxidant enzymes and/or DNA repair enzymes as a result of oxidative/nitrative stress arising from the inflammatory response is involved in liver fluke-associated cholangiocarcinogenesis. The present study investigated this hypothesis by identifying the expression patterns of antioxidant enzymes, including superoxide dismutase 2 (SOD2) and catalase (CAT), and DNA repair enzymes, including alkyladenine DNA glycosylase (AAG), apurinic endonuclease (APE) and DNA polymerase β (DNA pol β). In addition, the activities of the antioxidant enzymes, SOD2 and CAT, were examined in human cholangiocarcinoma (CCA) tissues using immunohistochemical staining. MSI was also analyzed in human CCA tissues. The resulting data demonstrated that the expression levels of the SOD2 and CAT enzymes decreased. The activities of SOD2 and CAT decreased significantly in the CCA tissues, compared with the hepatic tissue of cadaveric donors. In the DNA repairing enzymes, it was found that the expression levels of AAG and DNA pol β enzymes increased, whereas the expression of APE decreased. In addition, it was found that MSI-high was present in 69% of patients, whereas MSI-low was present in 31% of patients, with no patients classified as having microsatellite stability. In the patients, a MSI-high was correlated with poor prognosis, indicated by a shorter survival rate. These results

  6. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    Science.gov (United States)

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-01

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  7. Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

    Directory of Open Access Journals (Sweden)

    Suping Feng

    2013-01-01

    Full Text Available Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8% of the 94 Simple Sequence Repeat (SSR loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp., and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus. Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

  8. Characterisation and cross-amplification of polymorphic microsatellite loci in ant-associated root-aphids

    DEFF Research Database (Denmark)

    Ivens, A.B.F.; Kronauer, Daniel Jan Christoph; Boomsma, J.J.

    2011-01-01

    Twenty-six polymorphic microsatellite loci were developed for four species of ant-associated root-aphids: Geoica utricularia, Forda marginata, Tetraneura ulmi and Anoecia corni. We found up to 9 alleles per locus, with an average of 4.8. We also report polymorphic cross-amplification of eleven...... of these markers between different pairs of study species. Furthermore, we tested previously published aphid microsatellites and found one locus developed for Pemphigus bursarius to be polymorphic in G. utricularia. These microsatellite markers will be useful to study the population structure of aphids associated...

  9. Development of microsatellite markers from an enriched genomic library of pumpkin (Cucurbita moschata L.

    Directory of Open Access Journals (Sweden)

    Nuchjaree Watcharawongpaiboon

    2007-09-01

    Full Text Available Development of microsatellite markers in Pumpkin (Cucurbita moschata L. was performed using the biotin-streptavidin enrichment procedure. One hundred and thirty three clones were randomly selected. After sequence analysis of 31 randomly picked positive colonies, 100% of the colonies were found to contain microsatellite sequences, and 9 primer pairs were designed. Five of the primers tested could amplify pumpkins DNA and can be used for genetic purity testing of the commercial hybrids. This paper reports the first isolation and utilization of microsatellite markers in pumpkin.

  10. Isolation and characterization of microsatellite loci for the herbaceous tuber crop, Amorphophallus konjac (Araceae).

    Science.gov (United States)

    Pan, C; You, Y N; Diao, Y; Hu, Z L; Chen, J M

    2012-12-19

    Amorphophallus konjac is an herbaceous tuber crop with tremendous potential for commercial development. We report the development of microsatellite primers for this important crop species. Thirteen polymorphic microsatellite markers were developed and tested in two populations of A. konjac from the Wuling Mountain Region (WL population) and the Yunnan Province (YN population) in China. The number of alleles per locus ranged from 1 to 7; the observed and expected heterozygosities ranged from 0 to 1 and from 0 to 0.844, respectively, in the two populations. These microsatellite markers will facilitate further studies in population genetics and utilization of A. konjac.

  11. Isolation and Characterization of 20 Polymorphic Microsatellite Markers for Juglans mandshurica (Juglandaceae

    Directory of Open Access Journals (Sweden)

    Chang-Mei Chen

    2013-06-01

    Full Text Available Premise of the study: Fifty microsatellite loci were developed for the endangered species Juglans mandshurica to investigate its genetic diversity and population structure. Methods and Results: In all, 50 microsatellite markers were isolated from J. mandshurica, using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO protocol. Twenty of these polymorphic markers were assessed in samples collected from 98 individuals among five populations in northeastern China. Across all of the J. mandshurica samples, the number of alleles per locus ranged from one to 17. Conclusions: These new microsatellite loci will be useful for conservation genetics studies of J. mandshurica.

  12. Microsatellites for the mangrove tree Avicennia germinans (Acanthaceae): Tools for hybridization and mating system studies.

    Science.gov (United States)

    Mori, Gustavo M; Zucchi, Maria I; Sampaio, Iracilda; Souza, Anete P

    2010-09-01

    We developed a new set of microsatellite markers for the black mangrove Avicennia germinans, to provide new informative tools for further studies of the mating system, interspecific hybridization, and population genetics. • We used the microsatellite-enriched library approach to isolate and characterize 25 new primer pairs. Sixteen of them are polymorphic, showing a variable degree of variation in A. germinans, while nine were monomorphic in the samples examined. Eight exhibited private alleles in A. schaueriana. • These results indicate that these new microsatellite markers will be useful molecular tools for further studies of A. germinans and A. schaueriana population genetics, mating systems, and hybridization.

  13. Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences

    DEFF Research Database (Denmark)

    Karlskov-Mortensen, Peter; Hu, Z.L.; Gorodkin, Jan

    2007-01-01

    the human genome (BLAST cut-off threshold = 1 x 10-5). All microsatellite sequences placed on the comparative map are accessible at http://www.animalgenome.org/QTLdb/pig.html . These sequences increase the number of identified microsatellites in the porcine genome by several orders of magnitude......A total of 10 882 porcine microsatelite repeats were identified in genomic shotgun sequences from the Sino-Danish Pig Genome Sequencing Consortium ( http://piggenome.dk ). Of these, 4528 microsatellites were placed on a pig-human comparative map by BLAST analysis of porcine sequences against...

  14. Isolation and characterization of microsatellite markers from the phytopathogenic fungus Alternaria dauci.

    Science.gov (United States)

    Benichou, Soumaya; Dongo, Anita; Henni, Djamel Eddine; Peltier, Didier; Simoneau, Philippe

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated from the necrotrophic phytopathogenic fungus Alternaria dauci based on enriched genomic libraries. In order to assess allelic variability, the microsatellite loci were analysed in a collection of 43 isolates. The number of detected alleles in 11 loci ranged from two to 24 (mean 10.4). Test of cross-species amplification and sequencing of the resulting amplicons showed that some of these microsatellites could be used in different species such as Alternaria solani, Alternaria bataticola and Alternaria zinniae. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  15. Development of a novel set of microsatellite markers for castor bean, Ricinus communis (Euphorbiaceae).

    Science.gov (United States)

    Bajay, Miklos Maximiliano; Zucchi, Maria Imaculada; Kiihl, Tammy Aparecida Manabe; Batista, Carlos Eduardo Araújo; Monteiro, Mariza; Pinheiro, José Baldin

    2011-04-01

    Microsatellite primers were developed for castor bean (Ricinus communis L.) to investigate genetic diversity and population structure, and to provide support to germplasm management. Eleven microsatellite loci were isolated using an enrichment cloning protocol and used to characterize castor bean germplasm from the collection at the Instituto Agronômico de Campinas (IAC). In a survey of 76 castor bean accessions, the investigated loci displayed polymorphism ranging from two to five alleles. The information derived from microsatellite markers led to significant gains in conserved allelic richness and provides support to the implementation of several molecular breeding strategies for castor bean.

  16. Detection of Bladder CA by Microsatellite Analysis (MSA) — EDRN Public Portal

    Science.gov (United States)

    Goal 1: To determine sensitivity and specificity of microsatellite analysis (MSA) of urine sediment, using a panel of 15 microsatellite markers, in detecting bladder cancer in participants requiring cystoscopy. This technique will be compared to the diagnostic standard of cystoscopy, as well as to urine cytology. Goal 2: To determine the temporal performance characteristics of microsatellite analysis of urine sediment. Goal 3: To determine which of the 15 individual markers or combination of markers that make up the MSA test are most predictive of the presence of bladder cancer.

  17. The Lack of Affect and Imbalances of Character--An Interpretation of Mao Zhen in Twenty-two Nights in Spring%情感缺失与角色失衡--《春天的二十二个夜晚》主人公毛榛形象解析

    Institute of Scientific and Technical Information of China (English)

    单静

    2014-01-01

    《春天的二十二个夜晚》是徐坤的一部半自叙传小说,是徐坤人生体验的艺术再现和审美创造。它通过对主人公毛榛的成长经历的内部和外部的描述展现了一代女人甚至一类女人的生存遭际和情感体验,展现了职业女性成长过程中的得与失,以及她们在事业与家庭之间角色转换的失衡。这部小说强烈的时代特征,对当代文学中职业女性的生存状况的研究具有重要意义。%Twenty-two Nights in Spring is a Semi-autobiographical novel of Xu Kun,and it is aesthetic creation and art reproduction of his life experience . Based on internal and external description of Mao Zhen's grow-up experience , this paper presents the living condition and emotional experience of generation of women's , even a type of women , as well as the gain or loss in the process of female professional grow-up , the balance of changing roles between family and enterprise . The prominent feature of times in this novel has important role in the research for living condition of professional female.

  18. Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae)1

    Science.gov (United States)

    Zhou, Juannan; Dudash, Michele R.; Fenster, Charles B.; Zimmer, Elizabeth A.

    2016-01-01

    Premise of the study: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. Methods and Results: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. virginica and S. caroliniana and were also polymorphic. Conclusions: The microsatellite markers reported here provide a valuable tool for paternity analysis in S. stellata. They will also be useful for investigating the population genetic structures of S. stellata and related species. PMID:28101439

  19. Microsatellite loci for tucumã of Amazonas (Astrocaryum aculeatum) and amplification in other Arecaceae.

    Science.gov (United States)

    Ramos, Santiago L Ferreyra; de Macêdo, Jeferson L Vasconcelos; Lopes, Maria T Gomes; Batista, Jacqueline S; Formiga, Kyara M; da Silva, Perla Pimentel; Saulo-Machado, Antonio C; Veasey, Elizabeth Ann

    2012-12-01

    Microsatellite loci were developed for tucumã of Amazonas (Astrocaryum aculeatum), and cross-species amplification was performed in six other Arecaceae, to investigate genetic diversity and population structure and to provide support for natural populations management. • Fourteen microsatellite loci were isolated from a microsatellite-enriched genomic library and used to characterize two wild populations of tucumã of Amazonas (Manaus and Manicoré cities). The investigated loci displayed high polymorphism for both A. aculeatum populations, with a mean observed heterozygosity of 0.498. Amplification rates ranging from 50% to 93% were found for four Astrocaryum species and two additional species of Arecaceae. • The information derived from the microsatellite markers developed here provides significant gains in conserved allelic richness and supports the implementation of several molecular breeding strategies for the Amazonian tucumã.

  20. Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans.

    Science.gov (United States)

    Li, Juan; Bai, Feng-Yan

    2007-11-01

    Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.

  1. Interpretation of electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx.

    Science.gov (United States)

    Arif, I A; Khan, H A; Shobrak, M; Al Homaidan, A A; Al Sadoon, M; Al Farhan, A H; Bahkali, A H

    2010-02-09

    Microsatellite markers are commonly used for examining population structure, especially inbreeding, outbreeding and gene flow. An array of microsatellite loci, preferably with multiallelic presentation, is preferable for ensuring accurate results. However, artifact peaks or stutters in the electrophoretograms significantly hamper the reliable interpretation of genotypes. We interpreted electrophoretograms of seven microsatellite loci to determine the genetic diversity of the Arabian Oryx. All the alleles of different loci exhibited good peak resolutions and hence were clearly identified. Moreover, none of the stutter peaks impaired the recognition or differentiation between homozygote and heterozygote. Our findings suggest that correct identification of alleles in the presence of co-amplified nonspecific fragments is important for reliable interpretation of microsatellite data.

  2. New Microsatellite Markers for Wild and Commercial Species of Passiflora (Passifloraceae and Cross-Amplification

    Directory of Open Access Journals (Sweden)

    Carlos B. M. Cerqueira-Silva

    2014-02-01

    Full Text Available Premise of the study: We developed the first microsatellites for Passiflora setacea and characterized new sets of markers for P. edulis and P. cincinnata, enabling further genetic diversity studies to support the conservation and breeding of passion fruit species. Methods and Results: We developed 69 microsatellite markers and, in conjunction with assessments of cross-amplification using primers available from the literature, present 43 new polymorphic microsatellite loci for three species of Passiflora. The mean number of alleles per locus was 3.1, and the mean values of the expected and observed levels of heterozygosity were 0.406 and 0.322, respectively. Conclusions: These microsatellite markers will be valuable tools for investigating the genetic diversity and population structure of wild and commercial species of passion fruit (Passiflora spp. and may be useful for developing conservation and improvement strategies by contributing to the understanding of the mating system and hybridization within the genus.

  3. Whole-genome linkage analysis in mapping alcoholism genes using single-nucleotide polymorphisms and microsatellites.

    Science.gov (United States)

    Wang, Shuang; Huang, Song; Liu, Nianjun; Chen, Liang; Oh, Cheongeun; Zhao, Hongyu

    2005-12-30

    There is currently a great interest in using single-nucleotide polymorphisms (SNPs) in genetic linkage and association studies because of the abundance of SNPs as well as the availability of high-throughput genotyping technologies. In this study, we compared the performance of whole-genome scans using SNPs with microsatellites on 143 pedigrees from the Collaborative Studies on Genetics of Alcoholism provided by Genetic Analysis Workshop 14. A total of 315 microsatellites and 10,081 SNPs from Affymetrix on 22 autosomal chromosomes were used in our analyses. We found that the results from the two scans had good overall concordance. One region on chromosome 2 and two regions on chromosome 7 showed significant linkage signals (i.e., NPL >or= 2) for alcoholism from both the SNP and microsatellite scans. The different results observed between the two scans may be explained by the difference observed in information content between the SNPs and the microsatellites.

  4. Development of 57 Novel Polymorphic Microsatellite Markers in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

    Institute of Scientific and Technical Information of China (English)

    MIAO Guidong; XU Ying; WANG Di; CHEN Songlin; FAN Tingjun; TIAN Yongsheng

    2011-01-01

    Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C.semilaevis is under threat from environmental factors.Microsatellite markers are very suitable for assessing genetic diversity.Four microsatellite-enriched libraries of half smooth tongue sole (Cynoglossus semilaevis) were constructed,from which 57 polymorphic microsatellites were isolated and characterized.The polymorphism of these microsatellites was assessed by genotyping in 30 individual fish.The number of alleles ranged from 2 to 11,with an average of 4.614 alleles per locus.The values of observed and expected heterozygosities ranged from 0.1000 to 1.0000 and from 0.0966 to 0.8847 respectively.Polymorphism information content (PIC) ranged from 0.0905 to 0.862.These markers would be useful for population structure assessment,genetic linkage map construction and parentage analysis for this species.

  5. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE WIDELY INTRODUCED ESTUARINE ANEMONE NEMATOSTELLA VECTENSIS

    Science.gov (United States)

    We characterized ten polymorphic microsatellite loci from Nematostella vectensis, a burrowing anemone recently introduced to estuaries along the Pacific coast of North America and the southeast coast of England. Preliminary results indicate high variability and significant depar...

  6. CHARACTERIZATION OF MICROSATELLITE LOCI IN THE EUROPEAN GREEN CRAB (CARCINUS MAENAS)

    Science.gov (United States)

    Carcinus maenas (Decapoda: Portunidae) has proven a highly successful invasive marine species whose potential economic and ecological impacts are of great concern worldwide. Here, we characterize fourteen polymorphic microsatellite loci in C. maenas and its sister species C. Ae...

  7. Development of microsatellite loci in Mediterranean sarsaparilla (Smilax aspera; Smilacaceae) using transcriptome data.

    Science.gov (United States)

    Qi, Zhe-Chen; Shen, Chao; Han, Yu-Wei; Shen, Wei; Yang, Man; Liu, Jinliang; Liang, Zong-Suo; Li, Pan; Fu, Cheng-Xin

    2017-04-01

    Although several microsatellite markers of Smilax aspera (Smilacaceae) have been reported in a previous study, due to universality issues in cross-population amplification, we have newly developed microsatellite markers for S. aspera based on transcriptome data to further investigate gene flow and genetic structure of its circum-Mediterranean, East African, and South Asian populations. A total of 4854 simple sequence repeat (SSR) primer pairs were designed from 99,193 contigs acquired from public transcriptome data of S. bona-nox. Forty-six microsatellite loci were selected for further genotyping in 12 S. aspera populations. The number of alleles varied from three to 28, and 93.5% of the developed microsatellite markers could be cross-amplified in least one of three congeneric Smilax species. The SSR markers developed in this study will facilitate further studies on genetic diversity and phylogeographic patterns of S. aspera in intercontinental geographical scales.

  8. Innovative X-ray Star Scanner for Spin Stabilized Microsatellites Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Recent advances in the design of microsatellites have led to renewed interest in the missions that can be flown with small spacecraft and small payloads. The CubeSat...

  9. Servo-Drive Amplifier for Micro-Satellite Superconductor-Levitated Flywheels Project

    Data.gov (United States)

    National Aeronautics and Space Administration — A new servo-drive technology is available to support energy storage and navigation for micro-satellites. Exploiting the ?pinning? effect of high-temperature...

  10. Isolation and characterization of microsatellite markers for Jasminum sambac (Oleaceae) using Illumina shotgun sequencing.

    Science.gov (United States)

    Li, Yong; Zhang, Weirui

    2015-10-01

    Microsatellite markers of Jasminum sambac (Oleaceae) were isolated to investigate wild germplasm resources and provide markers for breeding. Illumina sequencing was used to isolate microsatellite markers from the transcriptome of J. sambac. A total of 1322 microsatellites were identified from 49,772 assembled unigenes. One hundred primer pairs were randomly selected to verify primer amplification efficiency. Out of these tested primer pairs, 31 were successfully amplified: 18 primer pairs yielded a single allele, seven exhibited fixed heterozygosity with two alleles, and only six displayed polymorphisms. This study obtained the first set of microsatellite markers for J. sambac, which will be helpful for the assessment of wild germplasm resources and the development of molecular marker-assisted breeding.

  11. Development of microsatellite markers for the clonal shrub Orixa japonica (Rutaceae) using 454 sequencing1

    Science.gov (United States)

    Tamaki, Ichiro; Setsuko, Suzuki; Sugai, Kyoko; Yanagisawa, Nao

    2016-01-01

    Premise of the study: Microsatellite markers were developed for a dioecious shrub, Orixa japonica (Rutaceae). Because O. japonica vigorously propagates by vegetative growth, microsatellite markers can be used to identify clonal relationships among its ramets. Methods and Results: Sixteen polymorphic microsatellite markers were identified by 454 next-generation sequencing. The number of alleles and expected heterozygosity for each locus among four populations ranged from two to 10 and from 0.140 to 0.875, respectively. Five of the 16 loci showed a low null allele frequency. Because Orixa is a monotypic genus, cross-amplification in a consubfamilial species, Skimmia japonica, was tested, and only one locus showed polymorphism. Conclusions: These microsatellite markers developed for O. japonica contribute to clone identification for studies examining the clonal structure and true sex ratio in the wild. Moreover, five markers that have a low null allele frequency can also be used for estimating mating systems or performing parentage analysis. PMID:27785383

  12. Development of Microsatellite Loci for the Riparian Tree Species Melaleuca argentea (Myrtaceae Using 454 Sequencing

    Directory of Open Access Journals (Sweden)

    Paul G. Nevill

    2013-05-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Melaleuca argentea (Myrtaceae to evaluate genetic diversity and population genetic structure of this broadly distributed northern Australian riparian tree species. Methods and Results: 454 GS-FLX shotgun sequencing was used to obtain 5860 sequences containing putative microsatellite motifs. Two multiplex PCRs were optimized to genotype 11 polymorphic microsatellite loci. These loci were screened for variation in individuals from two populations in the Pilbara region, northwestern Western Australia. Overall, observed heterozygosities ranged from 0.27 to 0.86 (mean: 0.52 and the number of alleles per locus ranged from two to 13 (average: 4.3. Conclusions: These microsatellite loci will be useful in future studies of the evolutionary history and population and spatial genetic structure in M. argentea, and inform the development of seed sourcing strategies for the species.

  13. Microsatellite-Based Fingerprinting of Western Blackberries from Plants, IQF Berries and Puree

    Science.gov (United States)

    The blackberry industry needs a reliable method to ensure trueness-to-type of blackberry products. Microsatellite markers or simple sequence repeats (SSRs) are ideal for cultivar fingerprinting, paternity testing and identity certification. Fingerprinting is valuable for variety identification, qual...

  14. Isolation and characterization of 10 microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean relict plant.

    Science.gov (United States)

    García-Fernández, Alfredo; Lázaro-Nogal, Ana; Traveset, Anna; Valladares, Fernando

    2012-08-01

    The main aim of this study was to isolate and characterize microsatellite loci in Cneorum tricoccon (Cneoraceae), a Mediterranean shrub relict of the early Tertiary, which inhabits western Mediterranean islands and coasts. Microsatellites will be useful for investigating biogeography and landscape genetics across the species distribution range, including current or past gene flow. Seventeen microsatellite loci were characterized, of which 10 were polymorphic and amplified for a total of 56 alleles in three populations of C. tricoccon. The markers revealed average coefficients of expected heterozygosity (H(e) = 0.425), observed heterozygosity (H(o) = 0.282), and inbreeding coefficient value per population (F(IS) = 0.408). These microsatellite primers will potentially be useful in the study of population and landscape genetics, conservation status of isolated populations, island-continental distribution, current or historical movements between populations, and in the investigation of the consequences of dispersal mechanisms of these plants.

  15. Microsatellite DNA markers discriminate between two Octopus vulgaris (Cephalopoda: Octopoda) fisheries along the northwest African coast

    National Research Council Canada - National Science Library

    Murphy, J.M; Balguerias, E; Key, L.N; Boyle, P.R

    2002-01-01

    .... This study aims to determine, using microsatellite DNA loci, whether octopus in the two fisheries are genetically distinct and to try to locate the origin of the samples by comparison with samples...

  16. Microsatellite isolation and characterization for Colletotrichum spp, causal agent of anthracnose in Andean blackberry.

    Science.gov (United States)

    Marulanda, M L; López, A M; Isaza, L; López, P

    2014-09-26

    The genus Colletotrichum, comprised of pathogenic fungi that affect plants grown worldwide, causes the disease known as anthracnose in several fruit and vegetable species. Several studies conducted on plants have shown that the disease is characterized by the presence of one or several species of the fungus attacking the fruit or other organs of the same host. To develop and implement effective control strategies, it is vital to understand the genetic structure of the fungus in agricultural systems, identify associated Colletotrichum species, and define the subpopulations responsible for the disease. Molecular tools were accordingly developed to characterize genotypic populations of Colletotrichum spp, causal agent of anthracnose in commercial crops of Andean blackberry (Rubus glaucus Benth.). A microsatellite-enriched library for Colletotrichum gloeosporioides was developed to identify and characterize microsatellite loci among isolates collected in R. glaucus plantations. Thirty microsatellites were developed and tested in 36 isolates gathered from eight different blackberry-production areas of Colombia. Ten pairs of microsatellites were polymorphic.

  17. Microsatellite development and survey of genetic variation in skipjack tuna Katsuwonus pelamis

    Digital Repository Service at National Institute of Oceanography (India)

    Menezes, M.R.; Noguchi, D.; Nakajima, M.; Taniguchi, N.

    of Population Genetic Informatics, Tohoku University, Sendai, Miyagi 981-8555, Japan (Received 23 October 2007, Accepted 26 March 2008) A survey of five newly developed microsatellite DNA markers in skipjack tuna Katsuwonus pelamis revealed high levels...

  18. Genetic characterisation of four strains of Nile tilapia (Oreochromie Niloticus L.) using microsatellite markers

    NARCIS (Netherlands)

    Rutten, M.J.M.; Komen, J.; Deerenberg, R.M.; Siwek-Gapinska, M.Z.; Bovenhuis, H.

    2004-01-01

    Four domesticated strains of Nile tilapia (Oreochromis niloticus L.) were genetically characterized using 14 microsatellite markers and 64 animals per strain. Two strains, Chitralada (AIT) and International Development Research Centers (IDRC) were obtained from the AIT institute, Bangkok, Thailand.

  19. The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio.

    Science.gov (United States)

    Wei, Na; Bemmels, Jordan B; Dick, Christopher W

    2014-09-01

    The advent of next-generation sequencing (NGS) technologies has transformed the way microsatellites are isolated for ecological and evolutionary investigations. Recent attempts to employ NGS for microsatellite discovery have used the 454, Illumina, and Ion Torrent platforms, but other methods including single-molecule real-time DNA sequencing (Pacific Biosciences or PacBio) remain viable alternatives. We outline a workflow from sequence quality control to microsatellite marker validation in three plant species using PacBio circular consensus sequencing (CCS). We then evaluate the performance of PacBio CCS in comparison with other NGS platforms for microsatellite isolation, through simulations that focus on variations in read length, read quantity and sequencing error rate. Although quality control of CCS reads reduced microsatellite yield by around 50%, hundreds of microsatellite loci that are expected to have improved conversion efficiency to functional markers were retrieved for each species. The simulations quantitatively validate the advantages of long reads and emphasize the detrimental effects of sequencing errors on NGS-enabled microsatellite development. In view of the continuing improvement in read length on NGS platforms, sequence quality and the corresponding strategies of quality control will become the primary factors to consider for effective microsatellite isolation. Among current options, PacBio CCS may be optimal for rapid, small-scale microsatellite development due to its flexibility in scaling sequencing effort, while platforms such as Illumina MiSeq will provide cost-efficient solutions for multispecies microsatellite projects.

  20. Characterization of genome-wide microsatellites of Saccharina japonica based on a preliminary assembly of Illumina sequencing reads

    Science.gov (United States)

    Zhang, Linan; Peng, Jie; Li, Xiaojie; Cui, Cuiju; Sun, Juan; Yang, Guanpin

    2016-06-01

    Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp ( Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N50 of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp.

  1. Geographic structure of Plasmodium vivax: microsatellite analysis of parasite populations from Sri Lanka, Myanmar, and Ethiopia

    DEFF Research Database (Denmark)

    Gunawardena, Sharmini; Karunaweera, Nadira D; Ferreira, Marcelo U;

    2010-01-01

    , Myanmar, and Ethiopia using 12 trinucleotide and tetranucleotide microsatellite markers. All three parasite populations were highly polymorphic with 3-44 alleles per locus. Approximately 65% were multiple-clone infections. Mean genetic diversity (H(E)) was 0.7517 in Ethiopia, 0.8450 in Myanmar, and 0...... as a model identified 78.2% of isolates accurately as being African or Asian. Microsatellite analysis is a useful tool for mapping short-term outbreaks of malaria and for predicting ancestry....

  2. Design and implementation of degenerate microsatellite primers for the mammalian clade.

    Directory of Open Access Journals (Sweden)

    Emmanuel Buschiazzo

    Full Text Available Microsatellites are popular genetic markers in molecular ecology, genetic mapping and forensics. Unfortunately, despite recent advances, the isolation of de novo polymorphic microsatellite loci often requires expensive and intensive groundwork. Primers developed for a focal species are commonly tested in a related, non-focal species of interest for the amplification of orthologous polymorphic loci; when successful, this approach significantly reduces cost and time of microsatellite development. However, transferability of polymorphic microsatellite loci decreases rapidly with increasing evolutionary distance, and this approach has shown its limits. Whole genome sequences represent an under-exploited resource to develop cross-species primers for microsatellites. Here we describe a three-step method that combines a novel in silico pipeline that we use to (1 identify conserved microsatellite loci from a multiple genome alignments, (2 design degenerate primer pairs, with (3 a simple PCR protocol used to implement these primers across species. Using this approach we developed a set of primers for the mammalian clade. We found 126,306 human microsatellites conserved in mammalian aligned sequences, and isolated 5,596 loci using criteria based on wide conservation. From a random subset of ~1000 dinucleotide repeats, we designed degenerate primer pairs for 19 loci, of which five produced polymorphic fragments in up to 18 mammalian species, including the distinctly related marsupials and monotremes, groups that diverged from other mammals 120-160 million years ago. Using our method, many more cross-clade microsatellite loci can be harvested from the currently available genomic data, and this ability is set to improve exponentially as further genomes are sequenced.

  3. Characterization of microsatellite loci for the Australian sea urchin Heliocidaris erythrogramma.

    Science.gov (United States)

    Binks, Rachel M; Lukehurst, Sherralee S; García-González, Francisco; Evans, Jonathan P

    2009-07-01

    We report 16 polymorphic microsatellite loci from Heliocidaris erythrogramma, a common sea urchin endemic to temperate Australian waters. These microsatellites were tested in a minimum of 30 individuals, which yielded between five and 14 alleles per locus. Expected heterozygosity ranged from 0.52 to 0.92 with four loci deviating from Hardy-Weinberg expectations. These markers are expected to be useful for experimental studies involving paternity analysis and for quantifying population structure in H. erythrogramma across its geographic range.

  4. High Resolution Microsatellite Marker Analysis of Some Rice Landraces Using Metaphor Agarose Gel Electrophoresis

    OpenAIRE

    K. Kristamtini; T. Taryono; Panjisakti Basunanda; Rudi Hari Murti

    2016-01-01

    Microsatellite markers or simple sequences repeats are DNA - based molecular techniques that are used to see the different among accessions and inbred lines. There are three methods to analysis the results of the polymerase chain reaction of microsatellite markers namely polyacrylamide gel electrophoresis (PAGE), capillary electroforesis, and Metaphor Agarose Gel Electroforesis (MAGE), and the Use of MAGE assessed more easily and economically the polymorphic pattern of DNA markers...

  5. Genomic Integrity Detection of In Vitro Irradiated Banana Using Microsatellite Marker.

    OpenAIRE

    Nina Ratna Djuita; Rita Megia

    2010-01-01

    Genomic Integrity Detection of In Vitro Irradiated Banana Using Microsatellite Marker. The research aims todetect genomic integrity of in vitro irradiated banana using microsatellite marker. These studies were done on bananacv. Pisang Mas irradiated by 15 Gy of gamma ray. The DNA was isolated from each accesion following Dixie.Amplification of DNA products were done by Perkin Elmer Gene Amp PCR 2400 using ten primers, and thenelectroforesis in agarose 1%. Finally a vertical polyacrylamide gel...

  6. Characterization and transferability of microsatellite markers of the cultivated peanut (Arachis hypogaea

    Directory of Open Access Journals (Sweden)

    Palmieri Dario A

    2007-02-01

    Full Text Available Abstract Background The genus Arachis includes Arachis hypogaea (cultivated peanut and wild species that are used in peanut breeding or as forage. Molecular markers have been employed in several studies of this genus, but microsatellite markers have only been used in few investigations. Microsatellites are very informative and are useful to assess genetic variability, analyze mating systems and in genetic mapping. The objectives of this study were to develop A. hypogaea microsatellite loci and to evaluate the transferability of these markers to other Arachis species. Results Thirteen loci were isolated and characterized using 16 accessions of A. hypogaea. The level of variation found in A. hypogaea using microsatellites was higher than with other markers. Cross-transferability of the markers was also high. Sequencing of the fragments amplified using the primer pair Ah11 from 17 wild Arachis species showed that almost all wild species had similar repeated sequence to the one observed in A. hypogaea. Sequence data suggested that there is no correlation between taxonomic relationship of a wild species to A. hypogaea and the number of repeats found in its microsatellite loci. Conclusion These results show that microsatellite primer pairs from A. hypogaea have multiple uses. A higher level of variation among A. hypogaea accessions can be detected using microsatellite markers in comparison to other markers, such as RFLP, RAPD and AFLP. The microsatellite primers of A. hypogaea showed a very high rate of transferability to other species of the genus. These primer pairs provide important tools to evaluate the genetic variability and to assess the mating system in Arachis species.

  7. Microsatellite markers in the traditional Chinese medicinal herb Gynostemma pentaphyllum (Cucurbitaceae).

    Science.gov (United States)

    Liao, Hui; Zhao, Yao; Zhou, Yin; Wang, Yuguo; Wang, Xiaofan; Lu, Fan; Song, Zhiping

    2011-03-01

    Microsatellite primers were developed for Gynostemma pentaphyllum, a traditional Chinese medicinal herb, to investigate its population genetic diversity. Using the Microsatellite Sequence Enrichment protocol, 14 polymorphic primers sets were identified in four Chinese Gynostemma pentaphyllum populations. The primers amplified di- and trinucleotide repeats with 1-6 alleles per locus, and the observed heterozygosities ranged from 0.000 to 1.000 per population. These markers will facilitate further studies on genetic structure and gene flow of Gynostemma pentaphyllum populations.

  8. Isolation and characterization of microsatellite loci in the common milkweed, Asclepias syriaca (Apocynaceae).

    Science.gov (United States)

    Kabat, Susan M; Dick, Christopher W; Hunter, Mark D

    2010-05-01

    Microsatellite primers were developed for the common milkweed, Asclepias syriaca L., to assist in genet identification and the analysis of spatial genetic structure. Using an enrichment cloning protocol, eight microsatellite loci were isolated and characterized in a Michigan population of A. syriaca. The primers amplified di- and trinucleotide repeats with 4-13 alleles per locus. The primers will be useful for studies of clonality and gene flow in natural populations.

  9. Prognostic values of chromosome 18q microsatellite alterations in stage Ⅱ colonic carcinoma

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM: To investigate the prognostic value of chromosome 18q microsatellite alterations (MA) in stage Ⅱ colon cancer. METHODS: One hundred and six patients with sporadic stage Ⅱ colon cancer were enrolled in this study. DNA was extracted from formalin-fixed, paraffin-embedded tumor and adjacent normal mucosal tissue samples. MA, including loss of heterozygosity (LOH) and microsatellite instability (MSI), was analyzed by polymerase chain reaction, polyacrylamide gel-electrophoresis and DNA sequencing at 5 micr...

  10. The Impacts of Complex Allele Structure on Genotyping Accuracy of Microsatellite: a Lesson from Bear Microsatellites UamD116 and UamB1%微卫星复杂结构对分型的影响:以熊UamD116和UamB1为例

    Institute of Scientific and Technical Information of China (English)

    张小芳; 杨淑慧; 马跃; 徐艳春; 宋伟杰

    2012-01-01

    群体遗传学结论.%Objective: Microsatellite refers to a kind of polymorphic. DNA fragments on the genome which contains variable number of tandem repeats of a short specific sequence of nucleotides (motif). The polymorphism of micorsatellite is reflected by variation of repeating number of motifs resulting in variation of fragment length among alleles. Therefore, routine genotyping approach is based on the fragment length of amplified alleles using polymerase chain reaction (PCR) method. Tetra-nucleotide microsatellites are preferable than di-nucleotide ones because of the influence of stutters on genotyping of the later. However, tetra-nucleotide microsatellites often contain complex motif structure potentially impacting genotyping and such problem is-usually ignored in studies. To address the impacts of complex allele structure on the genotyping, we genotyped two tetra-nucleotide loci of the Asiatic black bear (Ursus thibetanus), UamDl 16 and UamBl, using fragment length based approach and sequence based approach, and compared the results. Methods: A total of 96 samples including muscle, blood and hair were used in the experiments. PCR using fluorescently labeled upper primers were performed for each sample. PCR products were isolated using capillary electrophoresis on an automated DNA sequencer. Results: UamDl 16 contained multiple types of motifs, and mono-, di- tri-nucloetide insertions between motifs. Meanwhile, a 1-bp deletion occurred in the downstream flanking region of some alleles. Fragment length based genotyping was not able to discriminate the differences and sorted different alleles with similar length as a single one. UamBl contained 2 types of alleles, one type contained a 3-bp insertion resulting in the shifts of size difference between the two types of alleles from 4 bp to 1 bp. In addition, alleles with different motifs had similar size. Fragment length based genotyping identified 8 alleles, while sequence based approach identified 12 ones. Conclusion: For complex tetra

  11. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus

    Directory of Open Access Journals (Sweden)

    Williams Emlyn R

    2006-09-01

    Full Text Available Abstract Background Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. Results The consensus map covers ~90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. Conclusion This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and

  12. Development of novel microsatellite markers for strain-specific identification of Chlorella vulgaris.

    Science.gov (United States)

    Jo, Beom-Ho; Lee, Chang Soo; Song, Hae-Ryong; Lee, Hyung-Gwan; Oh, Hee-Mock

    2014-09-01

    A strain-specific identification method is required to secure Chlorella strains with useful genetic traits, such as a fast growth rate or high lipid productivity, for application in biofuels, functional foods, and pharmaceuticals. Microsatellite markers based on simple sequence repeats can be a useful tool for this purpose. Therefore, this study developed five novel microsatellite markers (mChl-001, mChl-002, mChl-005, mChl-011, and mChl-012) using specific loci along the chloroplast genome of Chlorella vulgaris. The microsatellite markers were characterized based on their allelic diversities among nine strains of C. vulgaris with the same 18S rRNA sequence similarity. Each microsatellite marker exhibited 2~5 polymorphic allele types, and their combinations allowed discrimination between seven of the C. vulgaris strains. The two remaining strains were distinguished using one specific interspace region between the mChl-001 and mChl-005 loci, which was composed of about 27 single nucleotide polymorphisms, 13~15 specific sequence sites, and (T)n repeat sites. Thus, the polymorphic combination of the five microsatellite markers and one specific locus facilitated a clear distinction of C. vulgaris at the strain level, suggesting that the proposed microsatellite marker system can be useful for the accurate identification and classification of C. vulgaris.

  13. Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.

    Science.gov (United States)

    Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2014-02-01

    Although much research has been conducted, the pattern of microsatellite distribution has remained ambiguous, and the development/utilization of microsatellite markers has still been limited/inefficient in Brassica, due to the lack of genome sequences. In view of this, we conducted genome-wide microsatellite characterization and marker development in three recently sequenced Brassica crops: Brassica rapa, Brassica oleracea and Brassica napus. The analysed microsatellite characteristics of these Brassica species were highly similar or almost identical, which suggests that the pattern of microsatellite distribution is likely conservative in Brassica. The genomic distribution of microsatellites was highly non-uniform and positively or negatively correlated with genes or transposable elements, respectively. Of the total of 115 869, 185 662 and 356 522 simple sequence repeat (SSR) markers developed with high frequencies (408.2, 343.8 and 356.2 per Mb or one every 2.45, 2.91 and 2.81 kb, respectively), most represented new SSR markers, the majority had determined physical positions, and a large number were genic or putative single-locus SSR markers. We also constructed a comprehensive database for the newly developed SSR markers, which was integrated with public Brassica SSR markers and annotated genome components. The genome-wide SSR markers developed in this study provide a useful tool to extend the annotated genome resources of sequenced Brassica species to genetic study/breeding in different Brassica species.

  14. Sequence analysis of trinucleotide repeat microsatellites from an enrichment library of the equine genome.

    Science.gov (United States)

    Tozaki, T; Inoue, S; Mashima, S; Ohta, M; Miura, N; Tomita, M

    2000-04-01

    Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG)n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG)n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10(4)-fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG)n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG)n repeats showed homology to human (CAG)n-containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans.

  15. Development of an integrative database with 499 novel microsatellite markers for Macaca fascicularis

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    Higashino Atsunori

    2009-06-01

    Full Text Available Abstract Background Cynomolgus macaques (Macaca fascicularis are a valuable resource for linkage studies of genetic disorders, but their microsatellite markers are not sufficient. In genetic studies, a prerequisite for mapping genes is development of a genome-wide set of microsatellite markers in target organisms. A whole genome sequence and its annotation also facilitate identification of markers for causative mutations. The aim of this study is to establish hundreds of microsatellite markers and to develop an integrative cynomolgus macaque genome database with a variety of datasets including marker and gene information that will be useful for further genetic analyses in this species. Results We investigated the level of polymorphisms in cynomolgus monkeys for 671 microsatellite markers that are covered by our established Bacterial Artificial Chromosome (BAC clones. Four hundred and ninety-nine (74.4% of the markers were found to be polymorphic using standard PCR analysis. The average number of alleles and average expected heterozygosity at these polymorphic loci in ten cynomolgus macaques were 8.20 and 0.75, respectively. Conclusion BAC clones and novel microsatellite markers were assigned to the rhesus genome sequence and linked with our cynomolgus macaque cDNA database (QFbase. Our novel microsatellite marker set and genomic database will be valuable integrative resources in analyzing genetic disorders in cynomolgus macaques.

  16. Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.

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    Iria Fernandez-Silva

    Full Text Available Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.

  17. Space science education based on the usage of microsatellites

    Science.gov (United States)

    Zaitzev, A.; Boyrchuk, K.; Panasuk, M.; Krasotkin, S.; Radchenko, V.; Fateev, V.; Tereshkov, A.

    Lomonosov Moscow State University, Institute of Terrestrial Magnetism, Ionosphere and Radio Wave Propagation and Mozhaisky Engineering Space Forces Academy together with collaborators are planning to launch two microsatellites - "Kompas-Tatyana" and "Universitetsky" in 2004. In the Skobeltsyn Institute of Nuclear Physics of Moscow University the team of educators and students was formed in order to develop and to test the space science education program. The program includes few directions. First, the curriculum materials which include all basic knowledge regarding the operation of satellites in outer space. There are cover the telecommunications, navigation, and physical conditions in outer space, the instruments and related subjects. Second stage of the program includes some practical works with real satellite data. When satellite telemetry received, the data must be processed and quick-look graphs constructed. The main task for students in the second stage is the approach to the analysis and the comparison with the data that already exist. They will solve the tasks how to infer some original results from raw data and how to the received data corresponds to the models of outer space. Third, after analysis the students are expected to prepare the written reports and display the results on the open lessons in the web-page formats. The practical realization of the educational program is planned for "Kompas-Tatyana" and "Universitetsky" satellites which will be launched in the end of 2004. It will carry out several scientific instruments with telemetry in the 137 Mhz open channel. Students will able to receive the "live" telemetry data. Such practice is rather exiting and motivates them to work hard with the program tasks. The simple receiving devices will allow to get some data in the high schools as well. Additional support for teachers and students will be provided via main server in the Internet. The pilot version of curriculum materials will be tested on the

  18. High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia.

    Science.gov (United States)

    Meglecz, Emese; Petenian, Frederic; Danchin, Etienne; D'Acier, Armelle Coeur; Rasplus, Jean-Yves; Faure, Eric

    2004-06-01

    Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing microsatellites or of microsatellites imbedded in minisatellite regions. The multiplication of microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous microsatellites can lead to the exchange of the flanking regions between microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.

  19. The Space Weather and Ultraviolet Solar Variability (SWUSV) Microsatellite Mission.

    Science.gov (United States)

    Damé, Luc

    2013-05-01

    We present the ambitions of the SWUSV (Space Weather and Ultraviolet Solar Variability) Microsatellite Mission that encompasses three major scientific objectives: (1) Space Weather including the prediction and detection of major eruptions and coronal mass ejections (Lyman-Alpha and Herzberg continuum imaging); (2) solar forcing on the climate through radiation and their interactions with the local stratosphere (UV spectral irradiance from 180 to 400 nm by bands of 20 nm, plus Lyman-Alpha and the CN bandhead); (3) simultaneous radiative budget of the Earth, UV to IR, with an accuracy better than 1% in differential. The paper briefly outlines the mission and describes the five proposed instruments of the model payload: SUAVE (Solar Ultraviolet Advanced Variability Experiment), an optimized telescope for FUV (Lyman-Alpha) and MUV (200-220 nm Herzberg continuum) imaging (sources of variability); UPR (Ultraviolet Passband Radiometers), with 64 UV filter radiometers; a vector magnetometer; thermal plasma measurements and Langmuir probes; and a total and spectral solar irradiance and Earth radiative budget ensemble (SERB, Solar irradiance & Earth Radiative Budget). SWUSV is proposed as a small mission to CNES and to ESA for a possible flight as early as 2017-2018.

  20. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes.

    Science.gov (United States)

    Gao, Huan; Cai, Shengli; Yan, Binlun; Chen, Baiyao; Yu, Fei

    2009-01-01

    To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia), rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  1. Germplasm of breeding Pseudosciaena crocea as revealed by microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    CHANG Yumei; DING Lei; LI Mingyun; XUE Liangyi; LIANG Liqun; HE Jianguo; LEI Qingquan

    2008-01-01

    The germplasm of breeding large yellow croaker(Pseudosciaena crocea Richardson)was revealed using 12 microsatellite markers.The results showed that the genetic diversities were on a mediated level in the bred Daiqu and Min-Yue stocks and two hybrid groups,as represented by 4.83 of the mean number of alleles and 0.561 of the average observed heterozygosity.The value of pair-wise differentiation coefficient(Fst)was only 13.1% between Daiqu and Min-Yue stocks,demonstrating the low level of differcn-tiation and a close relationship.However,STRUCTURE simulations and phylogenetie tree based on the UPGMA method supported that they are geographically different populations of the same species with distinct genetic structures.Examinations of individual ad-mixture showed that Min-Yue stock had been contaminated by alien individuals.Moreover,the genetic structures of the two hybridgroups resembled those of their parents,especially affected more by their female parents.Finally,the values of average observed beterozygasity between parents and their ascendants were compared and tested,as a result of no detectable differences(P>0.05).

  2. Development and characterization of genomic microsatellite markers in Prosopis cineraria

    Directory of Open Access Journals (Sweden)

    Shashi Shekhar Anand

    2017-06-01

    Full Text Available Characterization of genetic diversity is a must for exploring the genetic resources for plant development and improvement. Prosopis cineraria is ecologically imperative species known for its innumerable biological benefits. Since there is a lack of genetic resources for the species, so it is crucial to unravel the population dynamics which will be very effective in plant improvement and conservation strategies. Of the 41 genomic microsatellite markers designed from (AGn enriched library, 24 were subsequently employed for characterization on 30 genotypes of Indian arid region. A total of 93 alleles with an average 3.875 could be amplified by tested primer pairs. The average observed and expected heterozygosity was 0.5139 and 0.5786, respectively with 23 primer pairs showing significant deviations from Hardy-Weinberg equilibrium. Polymorphic information content average to 0.5102 and the overall polymorphism level was found to be 93.27%. STRUCTURE analysis and DARwin exhibited the presence of 4 clusters among 30 genotypes.

  3. Astrid-2, an advanced microsatellite for auroral research

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    G. T. Marklund

    Full Text Available The successful launch of the Swedish microsatellite Astrid-2 in December 1998 began a new era of auroral research, with advanced microprobes of 30 kg or less used as research tools. Innovative technologies and low-mass solutions were used for the sensors and deployment systems to allow a fairly complete set of scientific instruments within the 10 kg allocated for the scientific payload. A newly developed wire boom deployment system proved to function excellently. During its seven month lifetime Astrid-2 collected more than 26 Gbytes of high-quality data of auroral electric and magnetic fields, and auroral particle and plasma characteristics from approximately 3000 orbits at an inclination of 83° and an altitude of about 1000 km. Scientific results cover a broad range of topics, from the physics of energization of auroral particles to how the magnetosphere responds to the energy input from the solar wind and global magnetic field modelling. The fulfilment of both the technological and the scientific mission objectives has opened entirely new possibilities to carry out low-budget multipoint measurements in near-Earth space.

    Key words. Ionosphere (auroral ionosphere; instruments and techniques – Magnetospheric physics (auroral phenomena

  4. Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat

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    Huaigang Zhang

    2012-10-01

    Full Text Available Simple sequence repeats (SSRs, also known as microsatellites are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss. through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate.

  5. An improved technique for isolating codominant compound microsatellite markers.

    Science.gov (United States)

    Lian, Chunlan L; Abdul Wadud, Md; Geng, Qifang; Shimatani, Kenichiro; Hogetsu, Taizo

    2006-07-01

    An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.

  6. Infrequent microsatellite instability mutator phenotype in Chinese hepatocellular carcinomas

    Institute of Scientific and Technical Information of China (English)

    方丽; 房殿春; 汪荣泉; 杨仕明; 吴凯

    2003-01-01

    Objective:In order to elucidate the molecular mechanisms that might be responsible for hepatocarcinogenesis,we examined microsatellite instability(MSI),mismatch repair gene hMLH1 mutation and methylation in hepatocellular carcinoma.Methods:Fifty-two cases of surgically resected sporadic hepatocellular carcinoma(HCC)were studied.hMLH1 mutation was examined by two-dimensional electrophoresis and DNA sequencing; hMLH1 methylation was determined by methylation-specific PCR(MSP); and MSI at BAT26 was analyzed by PCR-based methods.Results:MSI at BAT26 was found in 3 of 52 cases(5.8%)of the tumors analyzed.No hMLH1 mutation or hypermethylation was found in these 52 cancerous tissues.No correlation existed between MSI and clinico-pathological characteristics of the patients.Conclusion:Our results suggest that MSI at BAT26 is rarely associated with carcinogenesis of chinese HCC.The genesis of sporadic HCC may occur in an alternative pathway that is probably different from MSI pathway.

  7. Development of novel polymorphic microsatellite markers in Siganus fuscescens.

    Science.gov (United States)

    Mao, X Q; Li, Z B; Ning, Y F; Shangguan, J B; Yuan, Y; Huang, Y S; Li, B B

    2016-07-29

    Rabbitfish, Siganus fuscescens, is widely distributed in the Indo-Pacific regions and eastern Mediterranean. Its dwelling place includes reef flats, coral reef regions, and seagrass meadows in tropical area and reef areas or shallow waters in locations at high latitudes. In the present study, 10 new polymorphic microsatellite markers were screened from 30 wild S. fuscescens individuals, using a method of fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. The number of polymorphic alleles per locus was 3 to 5 with a mean of 4.3, while the value of polymorphic information content ranged from 0.283 to 0.680. The values of the observed and expected heterozygosities were in the range 0.3333-0.8462 and 0.3011-0.7424, respectively. Deviation from Hardy-Weinberg equilibrium was not observed in this study. These polymorphic loci are expected to be effective in evaluating the genetic diversity, population structure, and gene flow and in determining the paternity in S. fuscescens, as well as for conservation management.

  8. Autonomous, agile micro-satellites and supporting technologies

    Energy Technology Data Exchange (ETDEWEB)

    Breitfeller, E; Dittman, M D; Gaughan, R J; Jones, M S; Kordas, J F; Ledebuhr, A G; Ng, L C; Whitehead, J C; Wilson, B

    1999-07-19

    This paper updates the on-going effort at Lawrence Livermore National Laboratory to develop autonomous, agile micro-satellites (MicroSats). The objective of this development effort is to develop MicroSats weighing only a few tens of kilograms, that are able to autonomously perform precision maneuvers and can be used telerobotically in a variety of mission modes. The required capabilities include satellite rendezvous, inspection, proximity-operations, docking, and servicing. The MicroSat carries an integrated proximity-operations sensor-suite incorporating advanced avionics. A new self-pressurizing propulsion system utilizing a miniaturized pump and non-toxic mono-propellant hydrogen peroxide was successfully tested. This system can provide a nominal 25 kg MicroSat with 200-300 m/s delta-v including a warm-gas attitude control system. The avionics is based on the latest PowerPC processor using a CompactPCI bus architecture, which is modular, high-performance and processor-independent. This leverages commercial-off-the-shelf (COTS) technologies and minimizes the effects of future changes in processors. The MicroSat software development environment uses the Vx-Works real-time operating system (RTOS) that provides a rapid development environment for integration of new software modules, allowing early integration and test. We will summarize results of recent integrated ground flight testing of our latest non-toxic pumped propulsion MicroSat testbed vehicle operated on our unique dynamic air-rail.

  9. Microsatellite Instability in Intestinal Metaplasia and Gastric Cancer

    Institute of Scientific and Technical Information of China (English)

    SHAOYun; ZHANGXiao-yong; LIUPing

    2004-01-01

    To investigate the changeable patterns of microsatellite instability(MSI)in intestinal metaplasia(IM)and gastric cancer(GC)and the role of MSI in gastric carcinogenesis. Methods: Silver staining single strand confornmtion polymorphism-polymeriase chain reaction(PCR-SSCP)wus used to screen MSI nmrkers at 5 loci in formalin-fixed, paraffin-embedded tissues of GC ( n = 30), IM ( n = 40) and corresponding normal gastric tissues. Resu/ts: The abnormal shifting of the single-strand DNA was identified in 7 (23.3%) out of GC and in 8 (20%) out of IM samples. Three ( 10 % ) tumors and one ( 2.5 % ) IM displayed high- frequency MSI ( two or more loci altered ). Low- frequencySI(one loci altered) was detected in 4( 13.3% )of the tmnors and in 7( 17.5% ) IM samples. GC with MSI was associated with distal location of the tumors but age,sex, differenl~ation, lymph nodes metastasis and TNM stage( P = 0.044).MSI was more likely detected in moderate-grade IM than in mild, grade IM tissues(34.8% versus 0; P = 0.013) ; and MSI had a tendency to be easily detected in female with IM. Conc/u,6~ : The progressive accmnulation of MSI in areas ofIM may contribute to GC development, represen~_g an importmlt molecular event in the multistep gastric ~~.

  10. Genetic characterization of the Bardigiano horse using microsatellite markers

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    Claudio Lisa

    2010-01-01

    Full Text Available The study was aimed at investigating the genetic structure of the Bardigiano horse and its relationships with the Haflinger, Maremmano and Arabian breeds using 11 microsatellite markers. A total of 94 alleles were detected across the breeds, with a mean of 8.5 alleles per locus and a mean observed heterozygosity of 0.69. Compared to the other breeds, the Bardigiano horse showed quite a high genetic variability, as indicated by the mean number of alleles (7.0 vs 6.1÷7.6 and by the observed heterozygosity (0.72 vs 0.66÷0.71. Moreover, the genotype distributions in the Bardigiano groups of different sex and age were not significantly different. The overall FST value showed that the genetic differences among breeds accounted for 7.8% (P=0.001 of the total variation, and the pairwise FST values were all significant. The assignment test allocated between 96.8 and 98.9% of the individuals to the population they were collected from, with a mean probability of assignment of about 97% for all breeds, except for the Arabian, where it approached 100%. The results have highlighted that the Bardigiano breed has a high within and between breed variability, which is considerably more than could be expected by looking at its evolution history. This justifies the need for the development of additional breeding strategies to preserve the existing genetic variability.

  11. Development of Sequence-Based Microsatellite Marker for Phalaenopsis Orchid

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    FATIMAH

    2011-06-01

    Full Text Available Phalaenopsis is one of the most interesting genera of orchids due to the members are often used as parents to produce hybrids. The establishment and development of highly reliable and discriminatory methods for identifying species and cultivars has become increasingly more important to plant breeders and members of the nursery industry. The aim of this research was to develop sequence-based microsatellite (eSSR markers for the Phalaenopsis orchid designed from the sequence of GenBank NCBI. Seventeen primers were designed and thirteen primers pairs could amplify the DNA giving the expected PCR product with polymorphism. A total of 51 alleles, with an average of 3 alleles per locus and polymorphism information content (PIC values at 0.674, were detected at the 16 SSR loci. Therefore, these markers could be used for identification of the Phalaenopsis orchid used in this study. Genetic similarity and principle coordinate analysis identified five major groups of Phalaenopsis sp. the first group consisted of P. amabilis, P. fuscata, P. javanica, and P. zebrine. The second group consisted of P. amabilis, P. amboinensis, P. bellina, P. floresens, and P. mannii. The third group consisted of P. bellina, P. cornucervi, P. cornucervi, P. violaceae sumatra, P. modesta. The forth group consisted of P. cornucervi and P. lueddemanniana, and the fifth group was P. amboinensis.

  12. Coding Microsatellite Frameshift Mutations Accumulate in Atherosclerotic Carotid Artery Lesions: Evaluation of 26 Cases and Literature Review.

    Science.gov (United States)

    Kurz, Carolin; Hakimi, Maani; Kloor, Matthias; Grond-Ginsbach, Caspar; Gross-Weissmann, Marie-Luise; Böckler, Dittmar; von Knebel Doeberitz, Magnus; Dihlmann, Susanne

    2015-06-09

    Somatic DNA alterations are known to occur in atherosclerotic carotid artery lesions; however, their significance is unknown. The accumulation of microsatellite mutations in coding DNA regions may reflect a deficiency of the DNA mismatch repair (MMR) system. Alternatively, accumulation of these coding microsatellite mutations may indicate that they contribute to the pathology. To discriminate between these two possibilities, we compared the mutation frequencies in coding microsatellites (likely functionally relevant) with those in noncoding microsatellites (likely neutral). Genomic DNA was isolated from carotid endarterectomy (CEA) specimens of 26 patients undergoing carotid surgery and from 15 nonatherosclerotic control arteries. Samples were analyzed by DNA fragment analysis for instability at three noncoding (BAT25, BAT26, CAT25) and five coding (AIM2, ACVR2, BAX, CASP5, TGFBR2) microsatellite loci, with proven validity for detection of microsatellite instability in neoplasms. We found an increased frequency of coding microsatellite mutations in CEA specimens compared with control specimens (34.6 versus 0%; p = 0.0013). Five CEA specimens exhibited more than one frameshift mutation, and ACVR2 and CASP5 were affected most frequently (5/26 and 6/26). Moreover, the rate of coding microsatellite alterations (15/130) differed significantly from that of noncoding alterations (0/78) in CEA specimens (p = 0.0013). In control arteries, no microsatellite alterations were observed, neither in coding nor in noncoding microsatellite loci. In conclusion, the specific accumulation of coding mutations suggests that these mutations play a role in the pathogenesis of atherosclerotic carotid lesions, since the absence of mutations in noncoding microsatellites argues against general microsatellite instability, reflecting MMR deficiency.

  13. Microsatellite markers in plants and insects part II: Databases and in silico tools for microsatellite mining and analyzing population genetic stratification

    Science.gov (United States)

    Nucleotide sequence information available in searchable sequence databases and the free in silico software with which to extract and analyze microsatellite data continues to grow at a rapid rate across eukaryote taxa. The sheer amount of information available means that a comprehensive or exhaustive...

  14. Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817).

    Science.gov (United States)

    Gravena, Waleska; Hrbek, Tomas; DA Silva, Vera M S; Astolfi-Filho, Spartaco; Farias, Izeni P

    2009-03-01

    We developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.

  15. Preliminary Study on Applicability of Microsatellite DNA Primers from Parasite Protozoa Trypanosoma cruzi in Free-living Protozoa

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wenjing; YU Yuhe; SHEN Yunfen; MIAO Wei; FENG Weisong

    2004-01-01

    In this paper, we took the lead in studying on specificity of the microsatellite DNA loci and applicability of microsatellite DNA primers in protozoa. In order to study characters of microsatellites in free-living protozoa, eight microsatellite loci primers developed from Trypanosoma cruzi (MCLE01, SCLE10, MCLE08, SCLE11, MCLF10, MCLG10,MCL03, MCL05) were employed to amplify microsatellite in four free-living protozoa, including Bodo designis, Euglena gracilis FACHB848, Paramecium bruzise and Tetrahymena thermophila BF1. In the amplification systems of P. bruzise, four loci (SCLE10, SCLE1 1, MCLF10, MCL03) were amplified successfully, and four amplification fragments were in proper size. In genome of E. gracilis FACHB848, five of eight primers brought five clear amplification bands. In B. designis, three (No.4, 5 and 7) of eight loci produced clear and sharp products without stutter bands, whereas no bands appeared in T.thermophila BF1. Further, eight 300-500bp amplification fragments were cloned and sequenced. Nevertheless, all sequenced products did not contain corresponding microsatellite sequence, although Bodo is in the same order and has the nearest phylogenetic relation with Trypanosoma among these four species. Thus, the microsatellite DNA primers can not be applied among order or more far taxa, and the specificity of microsatellite DNA is very high in protozoa. The results of this study will contribute to our understanding of microsatellite DNA in protozoa.

  16. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis

    Institute of Scientific and Technical Information of China (English)

    LI Li; GUO Ximing; ZHANG Guofan

    2009-01-01

    Microsatellites were screened in a backcross family of the Pacific oyster, Crassostrea gigas. Fifteen microsatellite loci were distinguishable and polymorphic with 6 types of allele-combinations. Null alleles were detected in 46.7% of loci, accounting for 11.7% of the total alleles. Four loci did not segregate in Mendelian Ratios. Three linkage groups were identified among 7 of the 15 segregating loci. Fluorescence-based automated capillary electrophoresis (ABI 310 Genetic Analyzer) that used to detect the microsatellite loci, has been proved a fast, precise, and reliable method in microsatellite genotyping.

  17. Preliminary study on applicability of microsatellite DNA primers from parasite protozoa Trypanosoma cruzi in free-living protozoa

    Science.gov (United States)

    Zhang, Wenjing; Yu, Yuhe; Shen, Yunfen; Miao, Wei; Feng, Weisong

    2004-04-01

    In this paper, we took the lead in studying on specificity of the microsatellite DNA loci and applicability of microsatellite DNA primers in protozoa. In order to study characters of microsatellites in free-living protozoa, eight microsatellite loci primers developed from Trypanosoma cruzi (MCLE01, SCLE10, MCLE08, SCLE11, MCLF10, MCLG10, MCL03, MCL05) were employed to amplify microsatellite in four free-living protozoa, including Bodo designis, Euglena gracilis FACHB848, Paramecium bruzise and Tetrahymena thermophila BF1. In the amplification systems of P. bruzise, four loci (SCLE10, SCLE11, MCLF10, MCL03) were amplified successfully, and four amplification fragments were in proper size. In genome of E. gracilis FACHB848, five of eight primers brought five clear amplification bands. In B. designis, three (No.4, 5 and 7) of eight loci produced clear and sharp products without stutter bands, whereas no bands appeared in T. thermophila BF1. Further, eight 300 500 bp amplification fragments were cloned and sequenced. Nevertheless, all sequenced products did not contain corresponding microsatellite sequence, although Bodo is in the same order and has the nearest phylogenetic relation with Trypanosoma among these four species. Thus, the microsatellite DNA primers can not be applied among order or more far taxa, and the specificity of microsatellite DNA is very high in protozoa. The results of this study will contribute to our understanding of microsatellite DNA in protozoa.

  18. Perspective on sequence evolution of microsatellite locus (CCGn in Rv0050 gene from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Jin Ruiliang

    2011-08-01

    Full Text Available Abstract Background The mycobacterial genome is inclined to polymerase slippage and a high mutation rate in microsatellite regions due to high GC content and absence of a mismatch repair system. However, the exact molecular mechanisms underlying microsatellite variation have not been fully elucidated. Here, we investigated mutation events in the hyper-variable trinucleotide microsatellite locus MML0050 located in the Rv0050 gene of W-Beijing and non-W-Beijing Mycobacterium tuberculosis strains in order to gain insight into the genomic structure and activity of repeated regions. Results Size analysis indicated the presence of five alleles that differed in length by three base pairs. Moreover, nucleotide gains occurred more frequently than loses in this trinucleotide microsatellite. Mutation frequency was not completely related with the total length, though the relative frequency in the longest allele was remarkably higher than that in the shortest. Sequence analysis was able to detect seven alleles and revealed that point mutations enhanced the level of locus variation. Introduction of an interruptive motif correlated with the total allele length and genetic lineage, rather than the length of the longest stretch of perfect repeats. Finally, the level of locus variation was drastically different between the two genetic lineages. Conclusion The Rv0050 locus encodes the bifunctional penicillin-binding protein ponA1 and is essential to mycobacterial survival. Our investigations of this particularly dynamic genomic region provide insights into the overall mode of microsatellite evolution. Specifically, replication slippage was implicated in the mutational process of this microsatellite and a sequence-based genetic analysis was necessary to determine that point mutation events acted to maintain microsatellite size integrity while providing genomic diversity.

  19. Heterogeneous topographic profiles of kinetic and cell cycle regulator microsatellites in atypical (dysplastic) melanocytic nevi.

    Science.gov (United States)

    Husain, Ehab A; Mein, Charles; Pozo, Lucia; Blanes, Alfredo; Diaz-Cano, Salvador J

    2011-04-01

    Atypical (dysplastic) melanocytic nevi are clinically heterogeneous malignant melanoma precursors, for which no topographic analysis of cell kinetic, cell cycle regulators and microsatellite profile is available. We selected low-grade atypical melanocytic nevi (92), high-grade atypical melanocytic nevi (41), melanocytic nevi (18 junctional, 25 compound) and malignant melanomas (16 radial growth phase and 27 vertical growth phase). TP53, CDKN2A, CDKN1A, and CDKN1B microsatellite patterns were topographically studied after microdissection; Ki-67, TP53, CDKN2A, CDKN1A, and CDKN1B expressions and DNA fragmentation by in situ end labeling for apoptosis were topographically scored. Results were statistically analyzed. A decreasing junctional-dermal marker expression gradient was observed, directly correlating with atypical melanocytic nevus grading. High-grade atypical melanocytic nevi revealed coexistent TP53-CDKN2A-CDKN1B microsatellite abnormalities, and significantly higher junctional Ki67-TP53 expression (inversely correlated with CDKN1A-CDKN1B expression and in situ end labeling). Malignant melanomas showed coexistent microsatellite abnormalities (CDKN2A-CDKN1B), no topographic gradient, and significantly decreased expression. Melanocytic nevi and low-grade atypical melanocytic nevi revealed sporadic junctional CDKN2A microsatellite abnormalities and no significant topographic kinetic differences. High-grade atypical melanocytic nevi accumulate junctional TP53-CDKN1A-CDKN1B microsatellite abnormalities, being progression TP53-independent and better assessed in the dermis. Melanocytic nevi and low-grade atypical melanocytic nevi show low incidence of microsatellite abnormalities, and kinetic features that make progression unlikely.

  20. Targeted oligonucleotide-mediated microsatellite identification (TOMMI from large-insert library clones

    Directory of Open Access Journals (Sweden)

    Ren Jun

    2005-11-01

    Full Text Available Abstract Background In the last few years, microsatellites have become the most popular molecular marker system and have intensively been applied in genome mapping, biodiversity and phylogeny studies of livestock. Compared to single nucleotide polymorphism (SNP as another popular marker system, microsatellites reveal obvious advantages. They are multi-allelic, possibly more polymorphic and cheaper to genotype. Calculations showed that a multi-allelic marker system always has more power to detect Linkage Disequilibrium (LD than does a di-allelic marker system 1. Traditional isolation methods using partial genomic libraries are time-consuming and cost-intensive. In order to directly generate microsatellites from large-insert libraries a sequencing approach with repeat-containing oligonucleotides is introduced. Results Seventeen porcine microsatellite markers were isolated from eleven PAC clones by targeted oligonucleotide-mediated microsatellite identification (TOMMI, an improved efficient and rapid flanking sequence-based approach for the isolation of STS-markers. With the application of TOMMI, an average of 1.55 (CA/GT microsatellites per PAC clone was identified. The number of alleles, allele size distribution, polymorphism information content (PIC, average heterozygosity (HT, and effective allele number (NE for the STS-markers were calculated using a sampling of 336 unrelated animals representing fifteen pig breeds (nine European and six Chinese breeds. Sixteen of the microsatellite markers proved to be polymorphic (2 to 22 alleles in this heterogeneous sampling. Most of the publicly available (porcine microsatellite amplicons range from approximately 80 bp to 200 bp. Here, we attempted to utilize as much sequence information as possible to develop STS-markers with larger amplicons. Indeed, fourteen of the seventeen STS-marker amplicons have minimal allele sizes of at least 200 bp. Thus, most of the generated STS-markers can easily be

  1. Improved Detection of Microsatellite Instability in Early Colorectal Lesions.

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    Jeffery W Bacher

    Full Text Available Microsatellite instability (MSI occurs in over 90% of Lynch syndrome cancers and is considered a hallmark of the disease. MSI is an early event in colon tumor development, but screening polyps for MSI remains controversial because of reduced sensitivity compared to more advanced neoplasms. To increase sensitivity, we investigated the use of a novel type of marker consisting of long mononucleotide repeat (LMR tracts. Adenomas from 160 patients, ranging in age from 29-55 years old, were screened for MSI using the new markers and compared with current marker panels and immunohistochemistry standards. Overall, 15 tumors were scored as MSI-High using the LMRs compared to 9 for the NCI panel and 8 for the MSI Analysis System (Promega. This difference represents at least a 1.7-fold increase in detection of MSI-High lesions over currently available markers. Moreover, the number of MSI-positive markers per sample and the size of allelic changes were significantly greater with the LMRs (p = 0.001, which increased confidence in MSI classification. The overall sensitivity and specificity of the LMR panel for detection of mismatch repair deficient lesions were 100% and 96%, respectively. In comparison, the sensitivity and specificity of the MSI Analysis System were 67% and 100%; and for the NCI panel, 75% and 97%. The difference in sensitivity between the LMR panel and the other panels was statistically significant (p<0.001. The increased sensitivity for detection of MSI-High phenotype in early colorectal lesions with the new LMR markers indicates that MSI screening for the early detection of Lynch syndrome might be feasible.

  2. Shape Distribution of Fragments from Microsatellite Impact Tests

    Science.gov (United States)

    Liou, J.C.; Hanada, T.

    2009-01-01

    Fragment shape is an important factor for conducting reliable orbital debris damage assessments for critical space assets, such as the International Space Station. To date, seven microsatellite impact tests have been completed as part of an ongoing collaboration between Kyushu University and the NASA Orbital Debris Program Office. The target satellites ranged in size from 15 cm 15 cm 15 cm to 20 cm 20 cm 20 cm. Each target satellite was equipped with fully functional electronics, including circuits, battery, and transmitter. Solar panels and multi-layer insulation (MLI) were added to the target satellites of the last two tests. The impact tests were carried out with projectiles of different sizes and impact speeds. All fragments down to about 2 mm in size were collected and analyzed based on their three orthogonal dimensions, x, y, and z, where x is the longest dimension, y is the longest dimension in the plane perpendicular to x, and z is the longest dimension perpendicular to both x and y. Each fragment was also photographed and classified by shape and material composition. This data set serves as the basis of our effort to develop a fragment shape distribution. Two distinct groups can be observed in the x/y versus y/z distribution of the fragments. Objects in the first group typically have large x/y values. Many of them are needle-like objects originating from the fragmentation of carbon fiber reinforced plastic materials used to construct the satellites. Objects in the second group tend to have small x/y values, and many of them are box-like or plate-like objects, depending on their y/z values. Each group forms the corresponding peak in the x/y distribution. However, only one peak can be observed in the y/z distribution. These distributions and how they vary with size, material type, and impact parameters will be described in detail within the paper.

  3. Technical Data Exchange Software Tools Adapted to Distributed Microsatellite Design

    Science.gov (United States)

    Pache, Charly

    2002-01-01

    One critical issue concerning distributed design of satellites, is the collaborative work it requires. In particular, the exchange of data between each group responsible for each subsystem can be complex and very time-consuming. The goal of this paper is to present a design collaborative tool, the SSETI Design Model (SDM), specifically developed for enabling satellite distributed design. SDM is actually used in the ongoing Student Space Exploration &Technology (SSETI) initiative (www.sseti.net). SSETI is lead by European Space Agency (ESA) outreach office (http://www.estec.esa.nl/outreach), involving student groups from all over Europe for design, construction and launch of a microsatellite. The first part of this paper presents the current version of the SDM tool, a collection of Microsoft Excel linked worksheets, one for each subsystem. An overview of the project framework/structure is given, explaining the different actors, the flows between them, as well as the different types of data and the links - formulas - between data sets. Unified Modeling Language (UML) diagrams give an overview of the different parts . Then the SDM's functionalities, developed in VBA scripts (Visual Basic for Application), are introduced, as well as the interactive features, user interfaces and administration tools. The second part discusses the capabilities and limitations of SDM current version. Taking into account these capabilities and limitations, the third part outlines the next version of SDM, a web-oriented, database-driven evolution of the current version. This new approach will enable real-time data exchange and processing between the different actors of the mission. Comprehensive UML diagrams will guide the audience through the entire modeling process of such a system. Tradeoffs simulation capabilities, security, reliability, hardware and software issues will also be thoroughly discussed.

  4. Microsatellite instability in gastric cancer and pre-cancerous lesions

    Institute of Scientific and Technical Information of China (English)

    Ping Liu; Xiao-Yong Zhang; Yun Shao; Dao-Fu Zhang

    2005-01-01

    AIM: To investigate the microsatellite instability (MSI) in cancer and pre-cancerous lesions of the stomach and its mechanisms underlying the development of gastric cancer.METHODS: Thirty-six gastric cancer samples were obtained from patients undergoing surgery. Forty-one gastric mucosa samples with dysplasia and 51 with intestinal metaplasia (IM) were obtained from patients with chronic gastritis undergoing gastro-endoscopy. Genomic DNA was extracted from the samples. Silver staining single strand conformation polymorphis-polymerize chain reaction (SSCP-PCR) was used to screen MSI markers at 5 loci (Bat-25, Bat-26, D5S346, D17S250, and D2S123)in fresh tissues and formalin-fixed, paraffin-embedded samples and their corresponding normal gastric mucosa.RESULTS: The abnormal shifting of the single-strand DNA (MSI) was identified in 21 out of 36 (58.3%) gastric cancers.Seven cases showed high-level MSI (two or more loci altered) and 14 showed low-level MSI (one locus altered).Gastric cancer with MSI had a tendency to be located in the distal stomach. MSI was also detected in 11 out of 41(26.8%) dysplasia samples and in 9 of 51 (17.6%) IM samples respectively. Three cases of dysplasia and one case of IM showed high-level MSI. Eight cases of dysplasia and 8 cases of IM displayed low-level MSI. MIS in IM was found only in moderate or severe-grade IM. No association was detected between MSI and dysplasia grade.CONCLUSION: Accumulation of MSI in dysplasia and intestinal metaplasia of gastric mucosa may be an early molecular event during gastric carcinogenesis and may contribute to the acquisition of transformed cell phenotype and the development of gastric cancer.

  5. Colorectal Tumour Microsatellite Instability Test Results: Perspectives from Patients

    Directory of Open Access Journals (Sweden)

    Lindor Noralane M

    2004-05-01

    Full Text Available Abstract Purpose To determine which individuals with colorectal cancer (CRC were interested in knowing the results of their tumour microsatellite instability (MSI and immunohistochemistry (IHC testing. We were also interested in the patients' reasons for choosing to learn their results and in the impact of those results on overall self-assessed quality of life. Patients and Methods CRCs from 414 individuals were assayed for MSI and IHC for DNA mismatch repair gene products (MLH1, MSH2, MSH6. Individuals were invited to learn their MSI/IHC results. They randomly received either brief or extended educational materials about the testing and a pretest survey to learn reasons for their interest and to assess their pretest quality of life. Results Of the 414 individuals, 307 (74% chose to learn their results. There was no significant difference in interest in knowing test results according to gender, age, educational level, or family history of colon cancer. The level of detail in the information piece received by the patients did not influence their desire to know their test results. Self-assessed quality of life was not altered by receiving results and was not correlated with the test outcome. Conclusions Individuals with colorectal cancer had a high level of interest in learning their individual MSI/IHC test results and did not seem deterred by the inherent complexity or ambiguity of this information. Regardless of test outcome, results did not significantly affect self-assessed quality of life. Further studies are needed to assess comprehension of results and behavioural changes resulting from the learning of MSI/IHC results.

  6. Microsatellite assessment of walrus (Odobenus rosmarus rosmarus stocks in Canada

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    Aaron BA Shafer

    2014-12-01

    Full Text Available Walruses in Canada are currently subdivided into seven stocks based on summering areas; Western Jones Sound (WJS, Baffin Bay (BB, Penny Strait-Lancaster Sound (PS-LS, North Foxe Basin (N-FB, Central Foxe Basin (C-FB, Hudson Bay Davis Strait (HB-DS and Southern and Eastern Hudson Bay (SE-HB. In this study, walrus were sampled from six of the seven stocks (SE-HB samples were not available and genotyped at 10 microsatellite loci. All stocks were genetically diverse (average heterozygosity of 0.58 with no evidence of inbreeding (average FIS of 0.03. We detected significant genetic differentiation among the stocks and a pattern of genetic spatial autocorrelation that suggests a moderate effect of geographic distance on gene flow among stocks. Bayesian clustering suggested the six recognized stocks were elements of two larger genetic clusters - a northern Arctic population (containing BB, WJS, and PS-LS stocks and a central Arctic population (containing C-FB, N-FB, and HB-DS stocks. These populations are moderately differentiated (FST = 0.07, but based on evidence of contemporary movement from assignment tests, are not completely isolated. There was support for maintaining the WJS stock and a combined BB+PS-LS stock, although the latter conclusion is based on a small sample size. Similarly, there was some evidence suggesting separation of the Foxe Basin stocks from the HB-DS but not the N-FB from the C-FB stock. However, given that there are morphological and chemical differences between N-FB and C-FB stocks, there is currently insufficient evidence to support a revision of the current stock designations.

  7. ARCADE small-scale docking mechanism for micro-satellites

    Science.gov (United States)

    Boesso, A.; Francesconi, A.

    2013-05-01

    The development of on-orbit autonomous rendezvous and docking (ARD) capabilities represents a key point for a number of appealing mission scenarios that include activities of on-orbit servicing, automated assembly of modular structures and active debris removal. As of today, especially in the field of micro-satellites ARD, many fundamental technologies are still missing or require further developments and micro-gravity testing. In this framework, the University of Padova, Centre of Studies and Activities for Space (CISAS), developed the Autonomous Rendezvous Control and Docking Experiment (ARCADE), a technology demonstrator intended to fly aboard a BEXUS stratospheric balloon. The goal was to design, build and test, in critical environment conditions, a proximity relative navigation system, a custom-made reaction wheel and a small-size docking mechanism. The ARCADE docking mechanism was designed against a comprehensive set of requirements and it can be classified as small-scale, central, gender mating and unpressurized. The large use of commercial components makes it low-cost and simple to be manufactured. Last, it features a good tolerance to off-nominal docking conditions and a by-design soft docking capability. The final design was extensively verified to be compliant with its requirements by means of numerical simulations and physical testing. In detail, the dynamic behaviour of the mechanism in both nominal and off-nominal conditions was assessed with the multibody dynamics analysis software MD ADAMS 2010 and functional tests were carried out within the fully integrated ARCADE experiment to ensure the docking system efficacy and to highlight possible issues. The most relevant results of the study will be presented and discussed in conclusion to this paper.

  8. Analysis of genetic diversity in Bolivian llama populations using microsatellites.

    Science.gov (United States)

    Barreta, J; Gutiérrez-Gil, B; Iñiguez, V; Romero, F; Saavedra, V; Chiri, R; Rodríguez, T; Arranz, J J

    2013-08-01

    South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.

  9. Historical metal pollution in natural gudgeon populations: Inferences from allozyme, microsatellite and condition factor analysis

    Energy Technology Data Exchange (ETDEWEB)

    Knapen, Dries, E-mail: dries.knapen@ua.ac.be [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); De Wolf, Hans [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Knaepkens, Guy [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Bervoets, Lieven [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Eens, Marcel [University of Antwerp, Department of Biology, Ethology Research Group, Universiteitsplein 1, 2610 Wilrijk (Belgium); Blust, Ronny [University of Antwerp, Department of Biology, Ecophysiology, Biochemistry and Toxicology Research Group, Groenenborgerlaan 171, 2020 Antwerpen (Belgium); Verheyen, Erik [Royal Belgian Institute of Natural Sciences, Department of Vertebrates, Molecular Laboratory, Vautierstraat 29, 1000 Brussel (Belgium)

    2009-10-19

    This study presents the results of a microsatellite and allozyme analysis on natural populations of the gudgeon (Gobio gobio) located in a pollution gradient of cadmium and zinc. Differences among contaminated and reference populations were observed at 2 allozyme loci, as well as a relationship between the fish condition factor and glucose-6-phosphate dehydrogenase genotypes, the locus that showed the largest difference in allele frequencies. The microsatellite data partly confirmed the differentiation pattern that was revealed by the allozyme survey. Our data further suggest that at least 2 microsatellite loci may be affected by natural selection. We thus illustrate that both microsatellite and allozyme loci do not necessarily behave as selectively neutral markers in polluted populations. Estimates of population differentiation can therefore be significantly different depending on which loci are being studied. Finally, these results are discussed in the light of the conservation unit concept, because microsatellites are often used to assess genetic variation in endangered natural populations and to propose measures for conservation or management.

  10. Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus species.

    Science.gov (United States)

    Lee, Gi-An; Song, Jae Young; Choi, Heh-Ran; Chung, Jong-Wook; Jeon, Young-Ah; Lee, Jung-Ro; Ma, Kyung-Ho; Lee, Myung-Chul

    2015-04-10

    The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3%) type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%). The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry). These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  11. Novel Microsatellite Markers Acquired from Rubus coreanus Miq. and Cross-Amplification in Other Rubus Species

    Directory of Open Access Journals (Sweden)

    Gi-An Lee

    2015-04-01

    Full Text Available The Rubus genus consists of more than 600 species that are distributed globally. Only a few Rubus species, including raspberries and blueberries, have been domesticated. Genetic diversity within and between Rubus species is an important resource for breeding programs. We developed genomic microsatellite markers using an SSR-enriched R. coreanus library to study the diversity of the Rubus species. Microsatellite motifs were discovered in 546 of 646 unique clones, and a dinucleotide repeat was the most frequent (75.3% type of repeat. From 97 microsatellite loci with reproducible amplicons, we acquired 29 polymorphic microsatellite markers in the Rubus coreanus collection. The transferability values ranged from 59.8% to 84% across six Rubus species, and Rubus parvifolius had the highest transferability value (84%. The average number of alleles and the polymorphism information content were 5.7 and 0.541, respectively, in the R. coreanus collection. The diversity index of R. coreanus was similar to the values reported for other Rubus species. A phylogenetic dendrogram based on SSR profiles revealed that seven Rubus species could be allocated to three groups, and that R. coreanus was genetically close to Rubus crataegifolius (mountain berry. These new microsatellite markers might prove useful in studies of the genetic diversity, population structure, and evolutionary relationships among Rubus species.

  12. Expression pattern and polymorphism of three microsatellite markers in the porcine CA3 gene

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    Zheng Rong

    2008-03-01

    Full Text Available Abstract Carbonic anhydrase III (CA3 is an abundant muscle protein characteristic of adult type-1, slow-twitch, muscle fibres. In order to further understand the functions of the porcine CA3 protein in muscle, the temporal and spatial distributions of its gene product were analysed and the association between the presence of specific polymorphisms and carcass traits in the pig was also examined. Real-time PCR revealed that the CA3 mRNA expression showed no differences with age in skeletal muscles from Yorkshire pigs at postnatal day-1, month-2, and month-4. We provide the first evidence that CA3 is differentially expressed in the skeletal muscle of Yorkshire and Meishan pig breeds. In addition, the whole pig genomic DNA sequence of CA3 was investigated and shown to contain seven exons and six introns. Comparative sequencing of the gene from three pig breeds revealed the existence of microsatellite SJ160 in intron 5 and microsatellite SJ158 and a novel microsatellite marker that includes a tandem repeat of (TCn in intron 4. We also determined the allele number and frequencies of the three loci in seven pig breeds and found that they are low polymorphic microsatellite markers. Statistical analysis showed that the CA3 microsatellite polymorphism was associated with dressing percentage, internal fat rate, carcass length, rib number and backfat thickness in the pig.

  13. Usefulness of microsatellite typing in population genetic studies of Trypanosoma cruzi

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    Macedo Andrea M

    2001-01-01

    Full Text Available Through microsatellite analysis of 53 monoclonal populations of Trypanosoma cruzi, we found a remarkable degree of genetic polymorphism with no single multilocus genotype being observed more than once. The microsatellite profile proved to be stable during 70 generations of the CL Brener clone in culture. The microsatellite profiling presented also high diagnostic sensitivity since DNA amplifications could be achieved with less than 100 fg DNA, corresponding to half parasite total DNA content. Based on these technical attributes the microsatellite assay turns out to be an important tool for direct typing T. cruzi in biological samples. By using this approach we were able to type T. cruzi in feces of artificially infected bugs and in single cells sorted by FACS. The microsatellites have shown to be excellent markers for T. cruzi phylogenetic reconstruction. We used maximum parsimony based on the minimum number of mutational steps to build an unrooted Wagner network, which confirms previous conclusions based on the analysis of the D7 domain of the LSU rDNA gene that T. cruzi is composed by two major groups. We also obtained evidence that strains belonging to rRNA group 2 are subdivided into two genetically distant clusters, and that one of these clusters is more related to rRNA group 1/2. These results suggest different origins for these strains.

  14. Morphological and microsatellite diversity associated with ecological factors in natural populations of Medicago laciniata Mill. (Fabaceae)

    Indian Academy of Sciences (India)

    Mounawer Badri; Adel Zitoun; Houcine Ilahi; Thierry Huguet; Mohamed Elarbi Aouani

    2008-12-01

    Genetic variability in 10 natural Tunisian populations of Medicago laciniata were analysed using 19 quantitative traits and 12 polymorphic microsatellite loci. A large degree of genetic variability within-populations and among-populations was detected for both quantitative characters and molecular markers. High genetic differentiation among populations for quantitative traits was seen, with $Q_{ST} = 0.47$, and $F_{ST} = 0.47$ for microsatellite markers. Several quantitative traits displayed no statistical difference in the levels of $Q_{ST}$ and $F_{ST}$. Further, significant correlations between quantitative traits and eco-geographical factors suggest that divergence in the traits among populations may track environmental differences. There was no significant correlation between genetic variability at quantitative traits and microsatellite markers within populations. The site-of-origin of eco-geographical factors explain between 18.13% and 23.40% of genetic variance among populations at quantitative traits and microsatellite markers, respectively. The environmental factors that most influence variation in measured traits among populations are assimilated phosphorus (P205) and mean annual rainfall, followed by climate and soil texture, altitude and organic matter. Significant associations between eco-geographical factors and gene diversity, $H_{e}$, were established in five-microsatellite loci suggesting that these simple sequence repeats (SSRs) are not necessarily biologically neutral.

  15. Map and analysis of microsatellites in the genome of Populus: The first sequenced perennial plant

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We mapped and analyzed the microsatellites throughout 284295605 base pairs of the unambiguously assembled sequence scaffolds along 19 chromosomes of the haploid poplar genome. Totally, we found 150985 SSRs with repeat unit lengths between 2 and 5 bp. The established microsatellite physical map demonstrated trat SSRs were distributed relatively evenly across the genome of Populus. On average, These SSRs occurred every 1883 bp within the poplar genome and the SSR densities in intergenic regions, introns, exons and UTRs were 85.4%, 10.7%, 2.7% and 1.2%, respectively. We took di-, tri-, tetra-and pentamers as the four classes of repeat units and found that the density of each class of SSRs decreased with the repeat unit lengths except for the tetranucleotide repeats. It was noteworthy that the length diversification of microsatellite sequences was negatively correlated with their repeat unit length and the SSRs with shorter repeat units gained repeats faster than the SSRs with longer repeat units. We also found that the GC content of poplar sequence significantly correlated with densities of SSRs with uneven repeat unit lengths (tri- and penta-), but had no significant correlation with densities of SSRs with even repeat unit lengths (di- and tetra-). In poplar genome, there were evidences that the occurrence of different microsatellites was under selection and the GC content in SSR sequences was found to significantly relate to the functional importance of microsatellites.

  16. Microsatellite analysis in the genome of Acanthaceae: An in silico approach

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    Priyadharsini Kaliswamy

    2015-01-01

    Full Text Available Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.

  17. Microsatellite abundance across the Anthozoa and Hydrozoa in the phylum Cnidaria.

    Science.gov (United States)

    Ruiz-Ramos, Dannise V; Baums, Iliana B

    2014-10-27

    Microsatellite loci have high mutation rates and thus are indicative of mutational processes within the genome. By concentrating on the symbiotic and aposymbiotic cnidarians, we investigated if microsatellite abundances follow a phylogenetic or ecological pattern. Individuals from eight species were shotgun sequenced using 454 GS-FLX Titanium technology. Sequences from the three available cnidarian genomes (Nematostella vectensis, Hydra magnipapillata and Acropora digitifera) were added to the analysis for a total of eleven species representing two classes, three subclasses and eight orders within the phylum Cnidaria. Trinucleotide and tetranucleotide repeats were the most abundant motifs, followed by hexa- and dinucleotides. Pentanucleotides were the least abundant motif in the data set. Hierarchical clustering and log likelihood ratio tests revealed a weak relationship between phylogeny and microsatellite content. Further, comparisons between cnidaria harboring intracellular dinoflagellates and those that do not, show microsatellite coverage is higher in the latter group. Our results support previous studies that found tri- and tetranucleotides to be the most abundant motifs in invertebrates. Differences in microsatellite coverage and composition between symbiotic and non-symbiotic cnidaria suggest the presence/absence of dinoflagellates might place restrictions on the host genome.

  18. Genetic Diversity of Three Spotted Seahorse, Hippocampus trimaculatus (Leach, 1814 in India Using Four Microsatellite Loci

    Directory of Open Access Journals (Sweden)

    Muthusamy THANGARAJ

    2012-11-01

    Full Text Available Seahorse populations are declining year by year not only in India but also throughout the world, because of over-fishing and increasing demand in Chinese market. The three spotted seahorse, Hippocampus trimaculatus is one of the dominant species and distributed all along the Indian coast. To study the genetic structure is very essential to conserve these species effectively. Hippocampus trimaculatus samples (n = 60/population were collected from Mullimunai in Palk Bay, Tuticorin in Gulf of Mannar and Vizhinjam in south Malabar in India as by-catch in small trawlnets. Microsatellites are being widely applied in animal genome mapping and phylogenetic analysis because of their co-dominant inheritance and high degree of polymorphism. The molecular polymorphism of microsatellite DNA has proved to be a potent tool in the analysis of several aspects of population genetics. In the present study, four microsatellite primers were used to investigate the genetic difference and structure of three selected populations of H. trimaculatus. The result showed the overall FST value (0.0989 of the microsatellite loci between Mullimunai and Vizhinjam was significantly different. The genetic distance between Mullimunai and Tuticorin was 0.183; between Tuticorin and Vizhinjam was 0.461; and Mullimunai and Vizhinjam was 0.837. There was no statistical evidence of recent severe bottlenecks in any of the three populations. Continuous monitoring of microsatellite variations within the populations of all the three locations was suggested to determine whether genetic variation within the populations is stabilized between year classes.

  19. Physical mapping of 49 microsatellite markers on chromosome 19 and correlation with the genetic linkage map

    Energy Technology Data Exchange (ETDEWEB)

    Reguigne-Arnould, I.; Mollicone, R.; Candelier, J.J. [INSERM, Villejuif (France)] [and others

    1996-03-05

    We have regionally localized 49 microsatellite markers developed by Genethon using a panel of previously characterized somatic cell hybrids that retain fragments from chromosome 19. The tight correlation observed between the physical and the genetic orders of the microsatellites provide cytogenetic anchorages to the genetic map data. We propose a position for the centromere just above D19S415, from the study of two hybrids, each of which retains one of the two derivatives of a balanced translocation t(1;19)(q11;q11). Microsatellites, which can be identified by a standard PCR protocol, are useful tools for the localization of disease genes and for the establishment of YAC or cosmid contigs. These markers can also judiciously be used for the characterization of new hybrid cell line panels. We report such a characterization of 11 clones, 8 of which were obtained by irradiation-fusion. Using the whole hybrid panel, we were able to define the order of 12 pairs of genetically colocalized microsatellites. As examples of gene mapping by the combined use of microsatellites and hybrid cell lines, we regionally assigned the PVS locus between the 19q13.2 markers D19S417 and D19S423 and confirmed the locations of fucosyltransferase loci FUT1, FUT2, and FUT5. 13 refs., 1 fig.

  20. Clinicopathological significance of loss of heterozygosity and microsatellite instability in hepatocellular carcinoma in China

    Institute of Scientific and Technical Information of China (English)

    Shu-Hui Zhang; Wen-Ming Cong; Zhi-Hong Xian; Meng-Chao Wu

    2005-01-01

    AIM: To determine the features of microsatellite alterations and their association with clinicopathological characteristics of hepatocellular carcinoma (HCC). METHODS: Loss of heterozygosity (LOH) and microsatellite instability (MSI) of 55 microsatellite loci were detected with PCR-based microsatellite polymorphism analyses in tumors and corresponding noncancerous liver tissues of 56 surgically resected HCCs using the MegaBACE 500 automatic DNA analysis system.RESULTS: LOH was found in 44 of 56 HCCs (78.6%) at one or several loci. Frequencies of LOH on 1p, 4q, 8p,16q, and 17p were 69.6% (39/56), 71.4% (40/56), 66.1% (37/56), 66.1% (37/56), and 64.3% (36/56), respectively. MSI was found in 18 of 56 HCCs (32.1%) at one or several loci. Ten of fifty-six (17.9%) HCCs had MSI-H. Serum HBV infection, alpha-fetoprotein concentration, tumor size, cirrhosis, histological grade, tumor capsule, as well as tumor intrahepatic metastasis, might be correlated with LOH on certain chromosome regions. CONCLUSION: Frequent microsatellite alterations exist in HCC. LOH, which represents a tumor suppressor gene pathway, plays a more important role in hepatocarcinogenesis. MSI, which represents a mismatch repair genepathway, is a rare event during liver carcinogenesis. Furthermore, LOH on certain chromosome regions may be correlated with clinicopathological characteristics in HCC.

  1. High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries.

    Science.gov (United States)

    Malausa, Thibaut; Gilles, André; Meglécz, Emese; Blanquart, Hélène; Duthoy, Stéphanie; Costedoat, Caroline; Dubut, Vincent; Pech, Nicolas; Castagnone-Sereno, Philippe; Délye, Christophe; Feau, Nicolas; Frey, Pascal; Gauthier, Philippe; Guillemaud, Thomas; Hazard, Laurent; Le Corre, Valérie; Lung-Escarmant, Brigitte; Malé, Pierre-Jean G; Ferreira, Stéphanie; Martin, Jean-François

    2011-07-01

    Microsatellites (or SSRs: simple sequence repeats) are among the most frequently used DNA markers in many areas of research. The use of microsatellite markers is limited by the difficulties involved in their de novo isolation from species for which no genomic resources are available. We describe here a high-throughput method for isolating microsatellite markers based on coupling multiplex microsatellite enrichment and next-generation sequencing on 454 GS-FLX Titanium platforms. The procedure was calibrated on a model species (Apis mellifera) and validated on 13 other species from various taxonomic groups (animals, plants and fungi), including taxa for which severe difficulties were previously encountered using traditional methods. We obtained from 11,497 to 34,483 sequences depending on the species and the number of detected microsatellite loci ranged from 199 to 5791. We thus demonstrated that this procedure can be readily and successfully applied to a large variety of taxonomic groups, at much lower cost than would have been possible with traditional protocols. This method is expected to speed up the acquisition of high-quality genetic markers for nonmodel organisms.

  2. Forecast of the Heterosis of Imported Meat Sheep by Genetic Polymorphism of Microsatellite DNA

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ying-jie; LIU Yue-qin; SUN Hong-xin; SUN Shao-hua; LI Yu

    2007-01-01

    Forecast of the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA was done in different sheep breeds. The gene frequency, the polymorphism information contents, the number of effective alleles, the heterozygosity, and the genetic distances were studied in four imported meat sheep and Small Tail Han sheep using five microsatellite loci. The crossing effects on the Small Tail Han sheep with four imported meat sheep were tested. The results indicate that there are genetic polymorphisms at five microsatellite loci in five sheep breeds. Five microsatellite loci can be used for genetic diversity evaluation in sheep breeds. The genetic variability of Dorset is the highest, and that of the Small Tail Han sheep is the lowest in the five sheep breeds. The order of heterosis from large to small in four imported meat sheep by the analysis of genetic relationship is White-Suffolk, Black-Suffolk,Dorset, and Texel. This accords with the testing results of actual heterosis. It is feasible to forecast the heterosis of Small Tail Han sheep crossed with imported meat sheep by genetic polymorphism of microsatellite DNA, which will have an important value for sheep breeding in the future.

  3. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    Science.gov (United States)

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  4. Isolation and Characterization of Microsatellite Loci in the Chinese Cobra Naja atra (Elapidae

    Directory of Open Access Journals (Sweden)

    Xiang Ji

    2011-07-01

    Full Text Available We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong’an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4–12 alleles per locus and heterozygosity (Ho ranged from 0.213–0.854 and He ranged from 0.301–0.838. Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001 proportion (16.0% of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low Nm (1.31 value in the two populations from mainland China. Thus, the Yong’an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs. The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.

  5. Isolation and characterization of microsatellite loci in the Chinese Cobra Naja atra (Elapidae).

    Science.gov (United States)

    Lin, Long-Hui; Mao, Lu-Xi; Luo, Xia; Qu, Yan-Fu; Ji, Xiang

    2011-01-01

    We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.

  6. Isolation and Characterization of Microsatellite Markers for Canavalia cathartica and C. lineata (Fabaceae

    Directory of Open Access Journals (Sweden)

    Asuka Yamashiro

    2013-01-01

    Full Text Available Premise of the study: Microsatellite markers were developed for the sea-dispersed legume Canavalia cathartica to investigate its genetic diversity and population structure. We also applied these microsatellite markers to the closely related species C. lineata. Methods and Results: Ten primer sets were developed for C. cathartica, and all of the primers were amplified in C. lineata. The number of alleles per locus ranged from two to 13 and one to 10 for C. cathartica and C. lineata, respectively. The expected heterozygosity ranged from 0.375 to 0.870 and from 0.071 to 0.877 for C. cathartica and C. lineata, respectively. Conclusions: The 10 microsatellite markers developed in this study can be used to analyze the population genetic structure of C. cathartica and other related taxa.

  7. High frequency of RPL22 mutations in microsatellite-unstable colorectal and endometrial tumors.

    Science.gov (United States)

    Ferreira, Ana M; Tuominen, Iina; van Dijk-Bos, Krista; Sanjabi, Bahram; van der Sluis, Tineke; van der Zee, Ate G; Hollema, Harry; Zazula, Monika; Sijmons, Rolf H; Aaltonen, Lauri A; Westers, Helga; Hofstra, Robert M W

    2014-12-01

    Ribosomal Protein L22 (RPL22) encodes a protein that is a component of the 60S subunit of the ribosome. Variants in this gene have recently been linked to cancer development. Mutations in an A8 repeat in exon 2 were found in a recent study in 52% of microsatellite-unstable endometrial tumors. These tumors are particularly prone to mutations in repeats due to mismatch repair deficiency. We screened this coding repeat in our collection of microsatellite-unstable endometrial tumors (EC) and colorectal tumors (CRC). We found 50% mutation frequency for EC and 77% mutation frequency for CRC. These results confirm the previous study on the involvement of RPL22 in EC and, more importantly, reports for the first time such high mutation frequency in this gene in colorectal cancer. Furthermore, considering the high mutation frequency found, our data point toward an important role for RPL22 in microsatellite instability carcinogenesis.

  8. Characterization of microsatellite markers in two exploited African trees, Entandrophragma candollei and E. utile (Meliaceae)1

    Science.gov (United States)

    Monthe, Franck S.; Duminil, Jérôme; Tosso, Félicien; Migliore, Jérémy; Hardy, Olivier J.

    2017-01-01

    Premise of the study: Multiplexes of nuclear microsatellite primers were developed to investigate population genetic structure and diversity in two exploited African rainforest trees: Entandrophragma candollei and E. utile (Meliaceae). Methods and Results: Microsatellite isolation was performed simultaneously on two nonenriched genomic libraries after next-generation sequencing. We developed 16 and 22 polymorphic markers for E. candollei and E. utile in three and four multiplexes, respectively. The number of alleles ranged from two to 17 for E. candollei and from three to 19 for E. utile. Mean expected and observed heterozygosity ranged between 0.75 ± 0.13 and 0.55 ± 0.23 for E. candollei and between 0.73 ± 0.10 and 0.49 ± 0.2 for E. utile. Conclusions: These sets of nuclear microsatellite markers constitute useful tools for exploring gene flow patterns in these two Entandrophragma species. PMID:28224058

  9. The relationship between serum vascular endothelial growth factor A and microsatellite instability in colorectal cancer

    DEFF Research Database (Denmark)

    Hansen, T F; Jensen, L H; Spindler, K-L G;

    2011-01-01

    AIM: It has been suggested that colorectal neoplasms with or without microsatellite instability (MSI) can stimulate angiogenesis in different ways. The vascular endothelial growth factor (VEGF) system is essential for the angiogenetic process and the growth of malignant tumours. The aim of this s......AIM: It has been suggested that colorectal neoplasms with or without microsatellite instability (MSI) can stimulate angiogenesis in different ways. The vascular endothelial growth factor (VEGF) system is essential for the angiogenetic process and the growth of malignant tumours. The aim...... lacking protein expression of any of the four mismatch repair genes (MLH1, PMS2, MSH2 or MSH6) were labelled as high MSI. The rest were considered to be microsatellite stable (MSS). The serum VEGF-A analyses were performed by ELISA. RESULTS: The tumours of 15 patients in the test cohort and 27...

  10. Development of new microsatellite markers from Mango (Mangifera indica) and cross-species amplification.

    Science.gov (United States)

    Ravishankar, Kundapura Venkataramana; Mani, Bellam Hanumantha-Reddy; Anand, Lalitha; Dinesh, Makki Ramachandra

    2011-04-01

    Microsatellite markers were developed and characterized to assess the genetic diversity among mango (Mangifera indica) cultivars and to test their amplification in closely related species. Thirty-six microsatellite (simple sequence repeats; SSR) loci were isolated by a microsatellite-enriched partial genomic library method. Primers designed for these loci were characterized using 30 diverse mango cultivars. The number of alleles ranged from 3 to 19 with an average of 9.2 alleles per locus. Polymorphic information content values ranged from 0.185 to 0.920 with a mean of 0.687. The total value for the probability of identity was 2.42 × 10(-31). The newly identified SSRs would be useful in genetic diversity studies, finger-printing, and mapping. Loci from five related species, M. odorata, M. anadamanica, M. zeylanica, M. camptosperma, and M. griffithii, were successfully amplified using these SSR primers, showing their potential utility across species.

  11. Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data

    DEFF Research Database (Denmark)

    Allentoft, Morten Erik; Schuster, Stephan C.; Holdaway, Richard N.

    2009-01-01

    Genetic variation in microsatellites is rarely examined in the field of ancient DNA (aDNA) due to the low quantity of nuclear DNA in the fossil record together with the lack of characterized nuclear markers in extinct species. 454 sequencing platforms provide a new high-throughput technology...... capable of generating up to 1 gigabases per run as short (200-400-bp) read lengths. 454 data were generated from the fossil bone of an extinct New Zealand moa (Aves: Dinornithiformes). We identified numerous short tandem repeat (STR) motifs, and here present the successful isolation and characterization...... of one polymorphic microsatellite (Moa_MS2). Primers designed to flank this locus amplified all three moa species tested here. The presented method proved to be a fast and efficient way of identifying microsatellite markers in ancient DNA templates and, depending on biomolecule preservation, has...

  12. Development and Characterization of Polymorphic Microsatellite Loci in Phellodendron amurense (Rutaceae

    Directory of Open Access Journals (Sweden)

    Jing-Hua Yu

    2013-03-01

    Full Text Available Premise of the study: Microsatellite markers were developed for the rare species Phellodendron amurense to assess the genetic diversity and population structure of this plant. Methods and Results: In total, 27 microsatellite markers were developed for P. amurense by using an enriched genomic library and hybridization; all of these primers successfully amplified DNA fragments in P. amurense. These markers were screened in 74 individuals from four populations in China; 15 loci were found to be polymorphic, with the number of alleles per locus ranging from one to nine. Conclusions: The microsatellite markers developed here represent a useful tool for studying the population genetic structure of P. amurense and to inform toward the development of effective conservation programs for this species.

  13. Characterization of Microsatellites for the Endangered Ruta oreojasme (Rutaceae and Cross-Amplification in Related Species

    Directory of Open Access Journals (Sweden)

    Marilena Meloni

    2013-04-01

    Full Text Available Premise of the study: Ruta oreojasme is an endangered species endemic to Gran Canaria (Canary Islands, Spain, where it occurs in small populations with disjunct distribution. Nothing is known about the genetic structure of these populations. Methods and Results: Using a microsatellite-enriched library method, 10 microsatellite markers have been developed from R. oreojasme, all of which showed polymorphism. The transferability of the 10 markers was tested in two other Canarian endemic species, R. microcarpa and R. pinnata, as well as in the widespread species R. montana. Conclusions: Our results demonstrate the value of these newly developed microsatellite markers to investigate the genetic structure in R. oreojasme and show their potential applicability for population genetic studies in other Ruta species.

  14. Isolation and characterization of eight polymorphic microsatellites for the spotted spiny lobster, Panulirus guttatus

    Directory of Open Access Journals (Sweden)

    Nathan Truelove

    2016-01-01

    Full Text Available Microsatellite sequences were isolated from enriched genomic libraries of the spotted spiny lobster, Panulirus guttatus using 454 pyrosequencing. Twenty-nine previously developed polymerase chain reaction primer pairs of Panulirus argus microsatellite loci were also tested for cross-species amplification in Panulirus guttatus. In total, eight consistently amplifying, and polymorphic loci were characterized for 57 individuals collected in the Florida Keys and Bermuda. The number of alleles per locus ranged from 8 to 20 and observed heterozygosities ranged from 0.409 to 0.958. Significant deviations from Hardy–Weinberg equilibrium were found in one locus from Florida and three loci from Bermuda. Quality control testing indicated that all loci were easy to score, highly polymorphic and showed no evidence of linkage disequilibrium. Null alleles were detected in three loci with moderate frequencies ranging from (20% to 22%. These eight microsatellites provide novel molecular markers for future conservation genetics research of P. guttatus.

  15. Characterization of nuclear microsatellite markers for Rumex bucephalophorus (Polygonaceae) using 454 sequencing1

    Science.gov (United States)

    Viruel, Juan; Ortiz, Pedro L.; Arista, Montserrat; Talavera, María

    2015-01-01

    Premise of the study: Nuclear microsatellite markers were developed in Rumex bucephalophorus subsp. canariensis (Polygonaceae) to investigate its genetic diversity and structure. Methods and Results: Sixteen polymorphic microsatellite markers were obtained using 454 next-generation sequencing with di-, tri-, and tetranucleotide repeats. The average number of alleles was 5.688 and 3.813 for R. bucephalophorus subsp. canariensis var. canariensis and var. fruticescens, respectively. Slightly higher levels of mean genetic diversity were found in var. canariensis (expected heterozygosity = 0.600) than in var. fruticescens (expected heterozygosity = 0.514). Cross-amplifications in related taxa within R. bucephalophorus showed good amplification and polymorphic patterns. Conclusions: These 16 novel nuclear microsatellite markers are the first in the genus Rumex and may serve as valuable tools to carry out studies on genetic diversity and structure as well as progeny studies. PMID:26697279

  16. Development of Polymorphic Microsatellite Markers for Phyllostachys edulis (Poaceae, an Important Bamboo Species in China

    Directory of Open Access Journals (Sweden)

    Wei-Xin Jiang

    2013-06-01

    Full Text Available Premise of the study: Polymorphic microsatellite markers were developed for Phyllostachys edulis (Poaceae, an ecologically and economically important bamboo species in China, to evaluate the genetic diversity and population genetic structure of P. edulis and other Phyllostachys species. Methods and Results: Twenty microsatellite markers were developed and their polymorphisms were tested on 71 samples from three geographically disparate populations. Each locus exhibited between two and 10 alleles with an average of five alleles. Excluding monomorphic loci, observed and expected heterozygosity ranged from zero to one and from 0.041 to 0.676, respectively. Conclusions: These 20 polymorphic microsatellite loci will be useful for studies on the molecular ecology, population genetics, and conservation of P. edulis.

  17. Polymorphic Microsatellite Markers for a Wind-Dispersed Tropical Tree Species, Triplaris cumingiana (Polygonaceae

    Directory of Open Access Journals (Sweden)

    Na Wei

    2014-09-01

    Full Text Available Premise of the study: Novel microsatellite markers were characterized in the wind-dispersed and dioecious neotropical tree Triplaris cumingiana (Polygonaceae for use in understanding the ecological processes and genetic impacts of pollen- and seed-mediated gene flow in tropical forests. Methods and Results: Sixty-two microsatellite primer pairs were screened, from which 12 markers showing five or more alleles per locus (range 5–17 were tested on 47 individuals. Observed and expected heterozygosities averaged 0.692 and 0.731, respectively. Polymorphism information content was between 0.417 and 0.874. Linkage disequilibrium was observed in one of the 66 pairwise comparisons between loci. Two loci showed deviation from Hardy–Weinberg equilibrium. An additional 14 markers exhibiting lower polymorphism were characterized on a smaller number of individuals. Conclusions: These microsatellite markers have high levels of polymorphism and reproducibility and will be useful in studying gene flow and population structure in T. cumingiana.

  18. Whole Genome Shotgun Sequences for Microsatellite Discovery and Application in Cultivated and Wild Macadamia (Proteaceae

    Directory of Open Access Journals (Sweden)

    Catherine J. Nock

    2014-03-01

    Full Text Available Premise of the study: Next-generation sequencing (NGS data are widely used for single-nucleotide polymorphism discovery and genetic marker development in species with limited available genome information. We developed microsatellite primers for the Proteaceae nut crop species Macadamia integrifolia and assessed cross-species transferability in all congeners to investigate genetic identification of cultivars and gene flow. Methods and Results: Primers were designed from both raw and assembled Illumina NGS paired-end reads. The final 12 microsatellite markers selected were polymorphic among wild individuals of all four Macadamia species—M. integrifolia, M. tetraphylla, M. ternifolia, and M. jansenii—and in commercial macadamia cultivars including hybrids. Conclusions: We demonstrate the utility of raw and assembled Illumina NGS reads from total genomic DNA for the rapid development of microsatellites in Macadamia. These primers will facilitate future studies of population structure, hybridization, parentage, and cultivar identification in cultivated and wild Macadamia populations.

  19. Isolation and characterization of 32 microsatellite loci for topmouth culter (Culter alburnus Basilewsky).

    Science.gov (United States)

    Liu, S-L; Gu, Z-M; Jia, Y-Y; Zhao, J-L; Jiang, W-P; Li, Q; Li, F

    2014-09-12

    The topmouth culter (Culter alburnus) is an economically important freshwater fish, which is widely distributed throughout large rivers, reservoirs, and lake areas of China. We report here the isolation and characterization of 32 new polymorphic microsatellite loci isolated from genomic DNA in this species enriched by (CA)12 and (GA)12 probes. The variability of these microsatellites was tested on 30 individuals cultured. The average allele number was 6.6 per locus, ranging from 3 to 12. The observed heterozygosity was from 0.4667 to 0.9000, and the expected heterozygosity was from 0.6163 to 0.9085. After using Bonferroni's correction for multiple tests, there was no evidence of linkage disequilibrium between pairs of loci, but deviations from Hardy-Weinberg equilibrium were found in 3 loci. These microsatellites can be used to study QTL of economic importance, population genetic diversity and the construction of genetic maps for C. alburnus in the future.

  20. Isolation and characterization of 19 polymorphic microsatellite loci from the topmouth gudgeon, Pseudorasbora parva.

    Science.gov (United States)

    Zeng, C; Gul, Y; Yang, K; Cui, L; Wang, W-M; Gao, Z-X

    2011-01-01

    The Asiatic topmouth gudgeon, Pseudorasbora parva, is recognized as one of the most invasive fish species in many countries outside of Asia. We isolated and characterized 19 microsatellite loci from P. parva. The polymorphism of these 19 loci was tested on 40 individuals of P. parva sampled from a wild population located in Ezhou, Hubei province of China. The loci had 5 to 11 alleles, with a mean of 7.7 at each locus; 11 loci conformed to Hardy-Weinberg equilibrium. The expected and observed heterozygosities ranged from 0.237 to 0.973 and from 0.647 to 0.914, respectively. All microsatellite loci were in linkage equilibrium. These microsatellite markers are potentially useful for the assessment of population genetic structure during invasion and dispersal of P. parva in new habitats.

  1. Characterization of polymorphic microsatellite markers in Pinus armandii (Pinaceae), an endemic conifer species to China1

    Science.gov (United States)

    Dong, Wan-Lin; Wang, Ruo-Nan; Yan, Xiao-Hao; Niu, Chuan; Gong, Lin-Lin; Li, Zhong-Hu

    2016-01-01

    Premise of the study: Pinus armandii (Pinaceae) is an important conifer tree species in central and southwestern China, and it plays a key role in the local forest ecosystems. To investigate its population genetics and design effective conservation strategies, we characterized 18 polymorphic microsatellite markers for this species. Methods and Results: Eighteen novel polymorphic and 16 monomorphic microsatellite loci of P. armandii were isolated using Illumina MiSeq technology. The number of alleles per locus ranged from two to five. The expected heterozygosity ranged from 0.061 to 0.609 with an average of 0.384, and the observed heterozygosity ranged from 0.063 to 0.947 with an average of 0.436. Seventeen loci could be successfully transferred to five related Pinus species (P. koraiensis, P. griffithii, P. sibirica, P. pumila, and P. bungeana). Conclusions: These novel microsatellites could potentially be used to investigate the population genetics of P. armandii and related species.

  2. Evidence of multiple paternity in Morelet's Crocodile (Crocodylus moreletii) in Belize, CA, inferred from microsatellite markers.

    Science.gov (United States)

    McVay, John D; Rodriguez, David; Rainwater, Thomas R; Dever, Jennifer A; Platt, Steven G; McMurry, Scott T; Forstner, Michael R J; Densmore, Llewellyn D

    2008-12-01

    Microsatellite data were generated from hatchlings collected from ten nests of Morelet's Crocodile (Crocodylus moreletii) from New River Lagoon and Gold Button Lagoon in Belize to test for evidence of multiple paternity. Nine microsatellite loci were genotyped for 188 individuals from the 10 nests, alongside 42 nonhatchlings from Gold Button Lagoon. Then mitochondrial control region sequences were generated for the nonhatchlings and for one individual from each nest to test for presence of C. acutus-like haplotypes. Analyses of five of the nine microsatellite loci revealed evidence that progeny from five of the ten nests were sired by at least two males. These data suggest the presence of multiple paternity as a mating strategy in the true crocodiles. This information may be useful in the application of conservation and management techniques to the 12 species in this genus, most of which are threatened or endangered.

  3. Development of Microsatellite Markers for the Neotropical Vine Dalechampia scandens (Euphorbiaceae

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    Mohsen Falahati-Anbaran

    2013-06-01

    Full Text Available Premise of the study: Microsatellite markers were developed to assess polymorphism and level of genetic diversity in four Mexican populations of the neotropical vine Dalechampia scandens (Euphorbiaceae. Methods and Results: Thirty-seven microsatellite markers representing bi-, tri-, tetra-, and pentanucleotide microsatellite repeats were developed. In total, 166 alleles were identified across 54 individuals. The number of alleles varied from one to 11 with an average of 4.49 alleles per locus. All loci except one were highly polymorphic between populations, whereas considerably less variation was detected within populations for most loci. The average observed and expected heterozygosities across study populations ranged from 0 to 0.63 and 0 to 0.59, respectively, for individual loci, and a deviation from Hardy–Weinberg equilibrium was observed for most loci. Conclusions: The developed markers may be useful for studying genetic structure, parentage analysis, mapping, phylogeography, and cross-amplification in other closely related species of Dalechampia.

  4. Development and Characterization of Microsatellite Markers for the Endangered Amazonian Tree Aniba rosaeodora (Lauraceae

    Directory of Open Access Journals (Sweden)

    Rafael C. Angrizani

    2013-09-01

    Full Text Available Premise of the study: Microsatellite loci were isolated and characterized for Brazilian rosewood (Aniba rosaeodora, an endangered neotropical hardwood tree, to investigate population and conservation genetics of this highly valuable nontimber forest resource. Methods and Results: We used an enriched genomic library method to isolate and characterize 11 nuclear microsatellite loci for A. rosaeodora, which exhibited an average of 9.6 and 8.7 alleles per locus in two populations from central Amazonia. Mean observed and expected heterozygosities over the 11 loci were 0.604 and 0.687, and 0.807 and 0.828, respectively, in the two populations. Conclusions: The polymorphic microsatellite loci developed for A. rosaeodora showed highly informative content and can be used as a powerful tool in genetic diversity and population structure, gene flow, and mating system studies for conservation purposes.

  5. Development and characterization of new microsatellites for Eugenia dysenterica DC (Myrtaceae).

    Science.gov (United States)

    Telles, M P C; Silva, J B; Resende, L V; Vianello, R P; Chaves, L J; Soares, T N; Collevatti, R G

    2013-02-06

    Microsatellite markers were developed for population genetic analyses of the Neotropical tree Eugenia dysenterica DC (Myrtaceae), after construction of a shotgun genomic library for microsatellite discovery. Nine primers were designed, of which 5 yielded amplified product. These primers were polymorphic for 97 individuals collected in 3 distinct localities. The number of alleles per locus (primer) ranged from 3 to 11 and expected heterozygosities varied from 0.309 to 0.884. The probability of locus identity was ~1.88 x 10(-4) and the probability of paternity exclusion was ~0.9367. The 5 microsatellite primer pairs may be suitable for population genetic studies such as parentage and fine-scale genetic analyses of this species.

  6. The same but different: monomorphic microsatellite markers as a new tool for genetic analysis.

    Science.gov (United States)

    Nazareno, Alison G; dos Reis, Mauricio S

    2011-10-01

    The nucleotide variation at a microsatellite locus lacking length polymorphisms among its alleles was assessed to generate an informative tool for genetic analysis. From a set of microsatellite markers, a monomorphic microsatellite locus developed for the palm species Butia eriospatha was used to elucidate whether there are polymorphic sites in its flanking regions. DNA sequences ≈133 bp long were obtained. Aligned sequences show variation at 17 polymorphic sites with both insertions and nucleotide substitutions. Fourteen distinct sequences (alleles) among 22 individuals were identified. The percent sequence difference varied from 0.0 to 5%, indicating that there is significant variation among sequences. Due to significant levels of information and sequence diversity on a simple sequence repeat (SSR) locus of identical size, our study highlights that this molecular marker class can be a useful tool for population genetics and evolutionary studies for many plant species.

  7. Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

    Science.gov (United States)

    Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

  8. New Microsatellite Markers for Tricyrtis macrantha (Convallariaceae and Cross-Amplification in Closely Related Species

    Directory of Open Access Journals (Sweden)

    Noriko Ohki

    2013-05-01

    Full Text Available Premise of the study: Microsatellite markers were characterized in Tricyrtis macrantha (sect. Brachycyrtis, Convallariaceae, a vulnerable species endemic to Japan, to investigate its genetic diversity and population structure. Methods and Results: Eleven microsatellite markers were developed. The number of alleles per locus ranged from one to seven, and genetic diversity per locus ranged from 0.142 to 0.812. Four markers were successfully amplified in other species of sect. Brachycyrtis (T. ishiiana, T. ishiiana var. surugensis, and T. macranthopsis. Conclusions: The microsatellite markers can be used to investigate the genetic diversity and population structure of the vulnerable and endangered species of Tricyrtis sect. Brachycyrtis, to aid in the development of conservation strategies for each species.

  9. Development of microsatellite markers using next-generation sequencing for the columnar cactus Echinopsis chiloensis (Cactaceae).

    Science.gov (United States)

    Ossa, Carmen G; Larridon, Isabel; Peralta, Gioconda; Asselman, Pieter; Pérez, Fernanda

    2016-12-01

    The aim of this study was to develop microsatellite markers as a tool to study population structure, genetic diversity and effective population size of Echinopsis chiloensis, an endemic cactus from arid and semiarid regions of Central Chile. We developed 12 polymorphic microsatellite markers for E. chiloensis using next-generation sequencing and tested them in 60 individuals from six sites, covering all the latitudinal range of this species. The number of alleles per locus ranged from 3 to 8, while the observed (Ho) and expected (He) heterozygosity ranged from 0.0 to 0.80 and from 0.10 to 0.76, respectively. We also detected significant differences between sites, with FST values ranging from 0.05 to 0.29. Microsatellite markers will enable us to estimate genetic diversity and population structure of E. chiloensis in future ecological and phylogeographic studies.

  10. Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa

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    Costa Vânia

    2012-09-01

    Full Text Available Abstract Background The wild boar (Sus scrofa is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. Findings A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999, low probability of identity (2.0E-13 – 2.5E-9 and a parentage assignment of 100%. Conclusions Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.

  11. Development of the First Chloroplast Microsatellite Loci in Ginkgo biloba (Ginkgoaceae

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    Chun-Xiang Xie

    2013-07-01

    Full Text Available Premise of the study: To investigate population genetics, phylogeography, and cultivar origin of Ginkgo biloba, chloroplast microsatellite primers were developed. Methods and Results: Twenty-one chloroplast microsatellite markers were identified referring to the two published chloroplast genomes of G. biloba. Polymorphisms were assessed on four natural populations from the two refugia in China. Eight loci were detected to be polymorphic in these populations. The number of alleles per locus ranged from three to seven, and the unbiased haploid diversity per locus varied from 0.441 to 0.807. Conclusions: For the first time, we developed 21 chloroplast microsatellite markers for G. biloba, including 13 monomorphic and eight polymorphic ones within the assessed natural populations. These markers should provide a powerful tool for the study of genetic variation of both natural and cultivated populations of G. biloba, as well as cultivars.

  12. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

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    Jaehyuk Choi

    2013-12-01

    Full Text Available Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980’s. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

  13. Development of microsatellite markers using Illumina MiSeq sequencing to characterize Ephedra gerardiana (Ephedraceae)1

    Science.gov (United States)

    De, Ji; Zhu, Weidong; Liu, Tianmeng; Wang, Zhe; Zhong, Yang

    2017-01-01

    Premise of the study: Ephedra gerardiana (Ephedraceae), occurring in the Himalayan ranges, is an important plant species used in Tibetan medicine. Due to the lack of molecular markers to characterize genetic diversity, knowledge for conservation and uses of E. gerardiana resources is limited; we therefore developed microsatellite markers for use in this species. Methods and Results: Using Illumina MiSeq sequencing technology, we developed 29 polymorphic microsatellite loci suitable for E. gerardiana, of which 15 loci also showed polymorphisms in two related Ephedra species, E. saxatilis and E. monosperma. The average number of effective alleles per locus ranged from two to six. The observed and expected heterozygosity ranged from 0.23 to 0.83 and 0.44 to 0.86, respectively, in E. gerardiana populations. Conclusions: The developed 29 microsatellite markers are effective for the study of genetic structure and genetic diversity of E. gerardiana, and 15 of these markers are suitable for related Ephedra species. PMID:28337389

  14. Isolation and Characterization of Microsatellite Markers for the Cleistogamous Species Lamium amplexicaule (Lamiaceae

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    Bojana Stojanova

    2013-02-01

    Full Text Available Premise of the study: Lamium amplexicaule is a cleistogamous plant that produces both closed flowers (obligately self-pollinated and open flowers (potentially outcrossed. The conditions for the maintenance of such a mating system depend on the outcrossing rate of the open flowers, which can be estimated using neutral microsatellite markers. Methods and Results: Forty primer pairs corresponding to microsatellite motifs obtained by coupling multiplex microsatellite enrichment and next-generation sequencing were tested. Thirteen primers amplified with satisfying results. The polymorphism of these markers was studied in four French populations. Allele number varied from one to eight per locus and per population. Heterozygosity levels were significantly lower than those expected under Hardy-Weinberg equilibrium. Conclusions: Our results are consistent with a partial self-fertilization pattern. These markers will be used to estimate the outcrossing rate as well as population differentiation in L. amplexicaule.

  15. Characterization of microsatellite loci in the lichen-forming fungus Cetraria aculeata (Parmeliaceae, Ascomycota).

    Science.gov (United States)

    Lutsak, Tetiana; Fernández-Mendoza, Fernando; Greshake, Bastian; Dal Grande, Francesco; Ebersberger, Ingo; Ott, Sieglinde; Printzen, Christian

    2016-09-01

    Polymorphic microsatellite markers were developed for the lichen species Cetraria aculeata (Parmeliaceae) to study fine-scale population diversity and phylogeographic structure. Using Illumina HiSeq and MiSeq, 15 fungus-specific microsatellite markers were developed and tested on 81 specimens from four populations from Spain. The number of alleles ranged from four to 13 alleles per locus with a mean of 7.9, and average gene diversities varied from 0.40 to 0.73 over four populations. The amplification rates of 10 markers (CA01-CA10) in populations of C. aculeata exceeded 85%. The markers also amplified across a range of closely related species, except for locus CA05, which did not amplify in C. australiensis and C. "panamericana," and locus CA10 which did not amplify in C. australiensis. The identified microsatellite markers will be used to study the genetic diversity and phylogeographic structure in populations of C. aculeata in western Eurasia.

  16. Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage.

    Science.gov (United States)

    Li, Fay-Wei; Rushworth, Catherine A; Beck, James B; Windham, Michael D

    2017-01-01

    Boechera (Brassicaceae) has many features to recommend it as a model genus for ecological and evolutionary research, including species richness, ecological diversity, experimental tractability and close phylogenetic proximity to Arabidopsis . However, efforts to realize the full potential of this model system have been thwarted by the frequent inability of researchers to identify their samples and place them in a broader evolutionary context. Here we present the Boechera Microsatellite Website (BMW), a portal that archives over 55 000 microsatellite allele calls from 4471 specimens (including 133 nomenclatural types). The portal includes analytical tools that utilize data from 15 microsatellite loci as a highly effective DNA barcoding system. The BMW facilitates the accurate identification of Boechera samples and the investigation of reticulate evolution among the ±83 sexual diploid taxa in the genus, thereby greatly enhancing Boechera 's potential as a model system.

  17. Isolation and Characterization of Sixteen Polymorphic Microsatellite Loci in the Golden Apple Snail Pomacea canaliculata

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    Yan Liu

    2011-09-01

    Full Text Available We report the characterization of 16 polymorphic microsatellite markers in the golden apple snail, Pomacea canaliculata, a pest registered in the list of “100 of the world’s worst invasive alien species”. The fast isolation by AFLP (Amplified Fragment Length Polymorphism of sequences containing repeats (FIASCO method was used to isolate microsatellite loci, and polymorphism was explored with 29 individuals collected in an invasive region from China. These primers showed a number of alleles per locus ranging from three to 13. The ranges of observed and expected heterozygosity were 0.310–0.966 and 0.523–0.898, respectively. These microsatellite markers described here will be useful for population genetic studies of P. canaliculata.

  18. Isolation of microsatellite primers for Melampyrum sylvaticum (Orobanchaceae), an endangered plant in the United Kingdom.

    Science.gov (United States)

    Crichton, Rhiannon J; Squirrell, Jane; Woodin, Sarah J; Dalrymple, Sarah E; Hollingsworth, Peter M

    2012-11-01

    Microsatellite markers were developed for the hemiparasitic plant Melampyrum sylvaticum to investigate the breeding system, genetic diversity, and structure of populations in the United Kingdom, Sweden, and Norway. Microsatellites were isolated from genomic DNA using an enrichment protocol. Twenty-nine loci were characterized in two individuals from each of 15 geographically disparate populations ("global"). Seven polymorphic loci were further characterized in one population ("local"). The number of alleles per locus ranged from two to 12 in the global sample and one to seven in the local sample. The expected heterozygosity ranged from 0-0.75, the observed heterozygosity from 0-0.1, and the inbreeding coefficient from 0.84-1 in the local sample. The results show the utility of these novel polymorphic microsatellite markers for further conservation genetic analyses. The strong deficit of heterozygosity across all loci in the local sample suggests the species may be inbreeding.

  19. Prognostic value of BRAF and KRAS mutation status in stage II and III microsatellite instable colon cancers

    NARCIS (Netherlands)

    de Cuba, E. M. V.; Snaebjornsson, P.; Heideman, D. A. M.; van Grieken, N. C. T.; Bosch, L.J.W.; Fijneman, R. J. A.; Belt, E.; Bril, H.; Stockmann, H. B. A. C.; Hooijberg, E.; Punt, C. J. A.; Koopman, M.; Nagtegaal, I. D.; Coupe, V. H. M.; Carvalho, B.; Meijer, G. A.

    2016-01-01

    Microsatellite instability (MSI) has been associated with favourable survival in early stage colorectal cancer (CRC) compared to microsatellite stable (MSS) CRC. The BRAF V600E mutation has been associated with worse survival in MSS CRC. This mutation occurs in 40% of MSI CRC and it is unclear wheth

  20. Development of new VNTR markers for pike and assessment of variability at di- and tetranucleotide repeat microsatellite loci

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Taggart, J.B.; Meldrup, Dorte

    1999-01-01

    -0.57), though one highly variable microsatellite (13 alleles; expected heterozygosity 0.79) was identified. In combination with previously published microsatellites a set consisting of nine polymorphic loci appeared to be useful for discriminating populations, as determined by assignment tests. (C) 1999...

  1. Localization and Characterization of 170 BAC-derived clones and mapping of Ninety-Four Microsatellites in the Hessian Fly

    Science.gov (United States)

    Ninety-four microsatellites from enriched genomic libraries of Hessian fly (Mayetiola destructor (Say)) were localized to 170 cognate clones in a Hessian fly bacterial artificial chromosome (BAC) library. These microsatellite-positive BAC clones were physically mapped to polytene chromosomes by fl...

  2. Development of an affordable typing method for Meyerozyma guilliermondii using microsatellite markers.

    Science.gov (United States)

    Wrent, Petra; Rivas, Eva-María; Peinado, José M; de Silóniz, María-Isabel

    2016-01-18

    Despite previously published methods, there is still a lack of rapid and affordable methods for genotyping the Meyerozyma guilliermondii yeast species. The development of microsatellite markers is a useful genotyping method in several yeast species. Using the Tandem Repeat Finder Software, a total of 19 microsatellite motifs (di-, tri-, and tetra- repetition) were found in silico in seven of the nine scaffolds published so far. Primer pairs were designed for all of them, although only four were used in this work. All microsatellite amplifications showed size polymorphism, and the results were identical when repeated. The combination of three microsatellite markers (sc15F/R, sc32 F/R and sc72 F/R) produced a different pattern for each of the Type Culture Collection strains of M. guilliermondii used to optimize the method. The three primer pairs can be used in the same PCR reaction, which reduces costs, in tandem with the fluorescent labeling of only the forward primer in each primer pair. Microsatellite typing was applied on 40 more M. guilliermondii strains. The results showed that no pattern is repeated between the different environmental niches. Four M. guilliermondii strains were only amplified with primer pair sc32 F/R, and subsequently identified as Meyerozyma caribbica by Taq I-RFLP of the 5.8S ITS rDNA. Most out-group species gave negative results even for physiologically similarly species such as Debaryomyces hansenii. The microsatellite markers used in this work were stable over time, which enables their use as a traceability tool.

  3. Microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence

    Institute of Scientific and Technical Information of China (English)

    Jian-Chun Cai; Di Liu; Kai-Hua Liu; Hai-Ping Zhang; Shan Zhong; Ning-Sao Xia

    2008-01-01

    AIM: To investigate the microsatellite alterations in phenotypically normal esophageal squamous epithelium and metaplasia-dysplasia-adenocarcinoma sequence.METHODS: Forty-one specimens were obtained from esophageal cancer (EC) patients. Histopathological assessment identified 23 squamous cell carcinomas (SCC) and 18 adenocarcinomas (ADC), including only 8 ADC with Barrett esophageal columnar epithelium (metaplasia) and dysplasia adjacent to ADC. Paraffinembedded normal squamous epithelium, Barrett esophageal columnar epithelium (metaplasia), dysplasia and esophageal tumor tissues were dissected from the surrounding tissues under microscopic guidance. DNA was extracted using proteinase K digestion buffer, and DNA was diluted at 1:100, 1:1000, 1:5000, 1:10000 and 1:50000, respectively. Seven microsatellite markers (D2S123, D3S1616, D3S1300, D5S346, D17S787, D18S58 and BATRII loci) were used in this study. Un-dilution and dilution polymerase chain reactions (PCR) were performed, and microsatellite analysis was carried out.RESULTS: No statistically significant difference was found in microsatellite instability (MSI) and loss of heterozygosity (LOH) of un-diluted DNA between SCC and ADC. The levels of MSI and LOH were high in the metaplasia-dysplasia-adenocarcinoma sequence of diluted DNA. The more the diluted DNA was, the higher the rates of MSI and LOH were at the above 7 loci, especially at D3S1616, D5S346, D2S123, D3S1300 and D18S58 loci.CONCLUSION: The sequence of metaplasia-dysplasia-adenocarcinoma is associated with microsatellite alterations, including MSI and LOH. The MSI and LOH may be the early genetic events during esophageal carcinogenesis, and genetic alterations at the D3S1616, D5S346 and D3S123 loci may play a role in the progress of microsatellite alterations.

  4. Resistance of Asian Cryptococcus neoformans serotype A is confined to few microsatellite genotypes.

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    Weihua Pan

    Full Text Available BACKGROUND: Cryptococcus neoformans is a pathogenic yeast that causes cryptococcosis, a life threatening disease. The prevalence of cryptococcosis in Asia has been rising after the onset of the AIDS epidemic and estimates indicate more than 120 cases per 1,000 HIV-infected individuals per year. Almost all cryptococcal disease cases in both immunocompromised and immunocompetent patients in Asia are caused by C. neoformans var. grubii. Epidemiological studies on C. neoformans in pan-Asia have not been reported. The present work studies the genetic diversity of the fungus by microsatellite typing and susceptibility analysis of approximately 500 isolates from seven Asian countries. METHODOLOGY/PRINCIPAL FINDINGS: Genetic diversity of Asian isolates of C. neoformans was determined using microsatellite analysis with nine microsatellite markers. The analysis revealed eight microsatellite complexes (MCs which showed different distributions among geographically defined populations. A correlation between MCs and HIV-status was observed. Microsatellite complex 2 was mainly associated with isolates from HIV-negative patients, whereas MC8 was associated with those from HIV-positive patients. Most isolates were susceptible to amphotericin B, itraconazole, voriconazole, posaconazole, and isavuconazole, but 17 (3.4% and 10 (2% were found to be resistant to 5-flucytosine and fluconazole, respectively. Importantly, five Indonesian isolates (approximately 12.5% from all Indonesian isolates investigated and 1% from the total studied isolates were resistant to both antifungals. The majority of 5-flucytosine resistant isolates belonged to MC17. CONCLUSIONS: The findings showed a different distribution of genotypes of C. neoformans var. grubii isolates from various countries in Asia, as well as a correlation of the microsatellite genotypes with the original source of the strains and resistance to 5-flucytosine.

  5. Genetic variation in BoLA microsatellite loci in Portuguese cattle breeds.

    Science.gov (United States)

    Bastos-Silveira, C; Luís, C; Ginja, C; Gama, L T; Oom, M M

    2009-02-01

    Major histocompatibility complex (MHC) typing based on microsatellites can be a valuable approach to understanding the selective processes occurring at linked or physically close MHC genes and can provide important information on variability and relationships of populations. Using microsatellites within or in close proximity with bovine lymphocyte antigen (BoLA) genes, we investigated the polymorphisms in the bovine MHC, known as the BoLA, in eight Portuguese cattle breeds. Additional data from non-BoLA microsatellite loci were also used to compare the variability between these regions. Diversity was higher in BoLA than in non-BoLA microsatellites, as could be observed by the number of alleles, allelic richness and observed heterozygosity. Brava de Lide, a breed selected for aggressiveness and nobility, presented the lowest values of observed heterozygosity and allelic richness in both markers. Results from neutrality tests showed few statistically significant differences between the observed Hardy-Weinberg homozygosity (F) and the expected homozygosity (F(E)), indicating the apparent neutrality of the BoLA microsatellites within the analysed breeds. Nevertheless, we detected a trend of lower values of observed homozygosity compared with the expected one. We also detected some differences in the levels of allelic variability among the four BoLA microsatellites. Our data showed a higher number of alleles at the BoLA-DRB3 locus than at the BoLA-DRBP1 locus. These differences could be related to their physical position in the chromosome and may reflect functional requirements for diversity.

  6. Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

    Science.gov (United States)

    Pandey, Madhav; Richards, Matt; Sharma, Jyotsna

    2015-12-01

    We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

  7. Development of microsatellite markers in the tetraploid fern Ceratopteris thalictroides (Parkeriaceae) using RAD tag sequencing.

    Science.gov (United States)

    Yang, X Y; Long, Z C; Gichira, A W; Guo, Y H; Wang, Q F; Chen, J M

    2016-02-19

    To understand the genetic variability of the tetraploid fern Ceratopteris thalictroides (Parkeriaceae), we described 30 polymorphic microsatellite markers obtained using the restriction site-associated DNA (RAD) tag sequencing technique. A total of 26 individuals were genotyped for each marker. The number of alleles per locus ranged from 4 to 10, and the expected heterozygosity and the Shannon-Wiener index ranged from 0.264 to 0.852 and 0.676 to 2.032, respectively. Because these 30 microsatellite markers exhibit high degrees of genetic variation, they will be useful tools for studying the adaptive genetic variation and sustainable conservation of C. thalictroides.

  8. Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

    Directory of Open Access Journals (Sweden)

    Guohong Cai

    Full Text Available High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats. Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach. However, constraints of this approach include: 1 many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2 difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps, with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%. After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6% were successfully amplified and 214 (90.7% produced single PCR products. Twenty-three (9.7% were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins

  9. Development of microsatellite loci for the invasive weed Wedelia trilobata (Asteraceae).

    Science.gov (United States)

    Wu, Wei; Zhou, Ren-Chao; Huang, Hui-Run; Ge, Xue-Jun

    2010-11-01

    Microsatellite markers were developed to help elucidate the population genetics of the invasive species Wedelia trilobata. • Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) repeats protocol, 23 sets of primers for amplifying microsatellite loci were identified in W. trilobata, 10 of which showed polymorphism (two to five alleles per locus) in samples of two populations of W. trilobata, one from China and one from Peru. Six of these loci were successfully amplified from samples of the native congener W. chinensis, with expected sizes. • These markers may be useful for further investigation of population genetics of Wedelia trilobata and other congener species.

  10. Isolation and characterization of polymorphic microsatellite loci in the green leafhopper Empoasca vitis Goethe (Homoptera).

    Science.gov (United States)

    Papura, D; Giresse, X; Chauvin, B; Caron, H; Delmotte, F; VAN Helden, M

    2009-05-01

    Eight dinucleotide microsatellite loci were isolated and characterized within the green leafhopper Empoasca vitis (Goethe) using an enrichment cloning procedure. Primers were tested on 171 individuals collected in the southwest of France from the vine plants. The identified loci were polymorphic, with allelic diversity ranging from two to 18 alleles per locus. Observed heterozygosities were from 0.021 to 0.760. These microsatellite markers should prove to be a useful tool for estimating the population genetic structure, host-plant specialization and migration capacity of this insect.

  11. Microsatellite Markers in the Western Prairie Fringed Orchid, Platanthera praeclara (Orchidaceae

    Directory of Open Access Journals (Sweden)

    Andrew A. Ross

    2013-04-01

    Full Text Available Premise of the study: Primers for 31 microsatellite-containing loci were developed for the threatened orchid Platanthera praeclara to enable characterization of the population genetics of this tallgrass prairie native. Methods and Results: Sixteen polymorphic microsatellite loci were identified from four populations. Six of these loci were not in linkage disequilibrium. The average number of alleles per locus per population ranged from 6.4 to 8.9. Conclusions: The results indicate that six of the polymorphic loci will be useful in future studies of population structure, gene flow, and genetic diversity.

  12. Genome-wide microsatellite identification in the fungus Anisogramma anomala using Illumina sequencing and genome assembly.

    Science.gov (United States)

    Cai, Guohong; Leadbetter, Clayton W; Muehlbauer, Megan F; Molnar, Thomas J; Hillman, Bradley I

    2013-01-01

    High-throughput sequencing has been dramatically accelerating the discovery of microsatellite markers (also known as Simple Sequence Repeats). Both 454 and Illumina reads have been used directly in microsatellite discovery and primer design (the "Seq-to-SSR" approach). However, constraints of this approach include: 1) many microsatellite-containing reads do not have sufficient flanking sequences to allow primer design, and 2) difficulties in removing microsatellite loci residing in longer, repetitive regions. In the current study, we applied the novel "Seq-Assembly-SSR" approach to overcome these constraints in Anisogramma anomala. In our approach, Illumina reads were first assembled into a draft genome, and the latter was then used in microsatellite discovery. A. anomala is an obligate biotrophic ascomycete that causes eastern filbert blight disease of commercial European hazelnut. Little is known about its population structure or diversity. Approximately 26 M 146 bp Illumina reads were generated from a paired-end library of a fungal strain from Oregon. The reads were assembled into a draft genome of 333 Mb (excluding gaps), with contig N50 of 10,384 bp and scaffold N50 of 32,987 bp. A bioinformatics pipeline identified 46,677 microsatellite motifs at 44,247 loci, including 2,430 compound loci. Primers were successfully designed for 42,923 loci (97%). After removing 2,886 loci close to assembly gaps and 676 loci in repetitive regions, a genome-wide microsatellite database of 39,361 loci was generated for the fungus. In experimental screening of 236 loci using four geographically representative strains, 228 (96.6%) were successfully amplified and 214 (90.7%) produced single PCR products. Twenty-three (9.7%) were found to be perfect polymorphic loci. A small-scale population study using 11 polymorphic loci revealed considerable gene diversity. Clustering analysis grouped isolates of this fungus into two clades in accordance with their geographic origins. Thus, the

  13. Genetic structure of Apis mellifera macedonica in the Balkan Peninsula based on microsatellite DNA polymorphism

    DEFF Research Database (Denmark)

    Uzunov, Aleksandar; Meixner, Marina D; Kiprijanovska, Hrisula;

    2014-01-01

    The genetic variability of honey bees (Apis mellifera L.) from south eastern Europe was investigated using microsatellite analyses of 107 samples from Albania, the Republic of Macedonia, Greece and Bulgaria together with 42 reference samples (Apis mellifera carnica) from Slovenia. Genetic structure...... and spatial analyses of the microsatellite data showed a clear distinction between the Slovenian bees and all other populations, and confirmed the existence of Apis mellifera macedonica as an indigenous honey bee population in the regions that were sampled. In most areas however, varying degrees...

  14. Microsatellite marker isolation and development for the giant Pacific Octopus (Enteroctopus dofleini)

    Science.gov (United States)

    Toussaint, Rebecca K.; Sage, G. Kevin; Talbot, Sandra L.; Scheel, David

    2012-01-01

    We isolated and developed 18 novel microsatellite markers for the giant Pacific octopus (Enteroctopus dofleini) and examined them for 31 individuals from Prince William Sound (PWS), Alaska. These loci displayed moderate levels of allelic diversity (averaging 11 alleles per locus) and heterozygosity (averaging 65%). Seven loci deviated from Hardy–Weinberg Equilibrium (HWE) due to heterozygote deficiency for the PWS population, although deviations were not observed for all these loci in other populations, suggesting the PWS population is not in mutation-drift equilibrium. These novel microsatellite loci yielded sufficient genetic diversity for potential use in population genetics, individual identification, and parentage studies.

  15. Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

    Science.gov (United States)

    Ramirez-Macias, D.; Shaw, K.; Ward, R.; Galvan-Magana, F.; Vazquez-Juarez, R.

    2009-01-01

    In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy–Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.

  16. Current Hypotheses on How Microsatellite Instability Leads to Enhanced Survival of Lynch Syndrome Patients

    Directory of Open Access Journals (Sweden)

    Kristen M. Drescher

    2010-01-01

    Full Text Available High levels of microsatellite instability (MSI-high are a cardinal feature of colorectal tumors from patients with Lynch Syndrome. Other key characteristics of Lynch Syndrome are that these patients experience fewer metastases and have enhanced survival when compared to patients diagnosed with microsatellite stable (MSS colorectal cancer. Many of the characteristics associated with Lynch Syndrome including enhanced survival are also observed in patients with sporadic MSI-high colorectal cancer. In this review we will present the current state of knowledge regarding the mechanisms that are utilized by the host to control colorectal cancer in Lynch Syndrome and why these same mechanisms fail in MSS colorectal cancers.

  17. Isolation and characterization of microsatellite loci from the tick Amblyomma aureolatum (Acari: Ixodidae).

    Science.gov (United States)

    Ogrzewalska, M; Bajay, M M; Schwarcz, K; Bajay, S K; Telles, M P C; Pinheiro, J B; Zucchi, M I; Pinter, A; Labruna, M B

    2014-11-14

    Amblyomma aureolatum (Pallas) is the main vector of the bacterium Rickettsia rickettsii, the etiological agent of Brazilian spotted fever. This disease is the most lethal human spotted fever rickettsiosis in the world. Microsatellite loci were isolated from a dinucleotide-enriched library produced from A. aureolatum sampled in Southeastern Brazil. Eight polymorphic microsatellites were further characterized among 38 individuals sampled from São Paulo metropolitan region. The number of observed alleles ranged from 2 to 9, observed heterozygosity was 0.184-0.647, and expected heterozygosity was 0.251-0.747. Cross-species amplifications suggested that these loci will be useful for other Amblyomma species.

  18. Characterization of 11 novel microsatellite markers for the vagabond butterflyfish, Chaetodon vagabundus

    KAUST Repository

    Saenz Agudelo, Pablo

    2015-02-21

    Microsatellite markers were developed for the coral reef fish Chaetodon vagabundus using shotgun pyrosequencing. As threats to coral reefs intensify, information on larval connectivity is of increasing value for efficient conservation planning. Here, 11 novel microsatellites were characterized for 192 individuals from Papua New Guinea. The number of alleles per locus ranged from 7 to 32, while observed and expected heterozygosity values varied from 0.214 to 0.903. These markers will be used to study population structure and larval connectivity of this iconic coral reef fish in coral reefs across the Indo-Pacific.

  19. Development and characterization of novel microsatellite loci for Lusitanian toadfish, Halobatrachus didactylus

    Directory of Open Access Journals (Sweden)

    Carla Sousa-Santos

    2015-01-01

    Full Text Available The Lusitanian toadfish Halobatrachus didactylus is an eastern Atlantic polygynous species showing male paternal care. In this paper we describe 5 novel microsatellite loci obtained by 454 GS-FLX Titanium pyrosequencing of a microsatellite-enriched library. The number of alleles per polymorphic locus varied between 2 and 4, and the observed heterozygosity ranged from 0.082 to 0.600. No significant deviation from Hardy–Weinberg equilibrium was found and there was no evidence for linkage disequilibrium. These markers will be of great value for paternity studies and population genetics of this species.

  20. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood

    DEFF Research Database (Denmark)

    van Tilborg, Angela A G; Kompier, Lucie C; Lurkin, Irene

    2012-01-01

    . Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers...... with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined...

  1. Population structure and genetic diversity of Brazilian popcorn germplasm inferred by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Tereza Aparecida da Silva

    2015-05-01

    Conclusions: The analysis allowed to identify microsatellite loci with high levels of heterozygosity (UMC1549 and UMC1072. These loci can be indicated as promising for detecting polymorphisms in popcorn accessions and in the monitoring of genetic improvement programs. Moreover, allowed to identify heterozygous accessions (BOZM 260, this accession showed allelic variation at all analyzed microsatellite loci and can be recommended for crosses with plants that have desirable agronomic characteristics, with a view to the broadening of the genetic base of popcorn accessions and developing new cultivars.

  2. Microsatellite markers for Dayaoshania cotinifolia (Gesneriaceae), a critically endangered perennial herb.

    Science.gov (United States)

    Zhang, Bing; Wang, Hong-Wei; Cheng, Yue-Qin; Ye, Yong-Zhong; Wang, Zhao-Shan

    2011-09-01

    Microsatellite primers were developed for the critically endangered species Dayaoshania cotinifolia (Gesneriaceae) to evaluate population genetic diversity and detect population history. • In our study, 15 primer sets were developed using an enriched genomic library. These are the first microsatellite loci developed for this genus. Genetic diversity was measured using 40 individuals. The number of alleles per locus ranged from one to six, and the incidence of observed heterozygosities was 0.365 and 0.410 in two populations. • The described markers will be useful in future population genetics studies of this critically endangered species.

  3. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    Science.gov (United States)

    Pajuelo, Mónica J.; Eguiluz, María; Dahlstrom, Eric; Requena, David; Guzmán, Frank; Ramirez, Manuel; Sheen, Patricia; Frace, Michael; Sammons, Scott; Cama, Vitaliano; Anzick, Sarah; Bruno, Dan; Mahanty, Siddhartha; Wilkins, Patricia; Nash, Theodore; Gonzalez, Armando; García, Héctor H.; Gilman, Robert H.; Porcella, Steve; Zimic, Mirko

    2015-01-01

    Background Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen. Methods For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples. Results The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites. Conclusions/Significance The availability of draft

  4. Nine novel, polymorphic microsatellite markers for the study of threatened Caribbean acroporid corals.

    Science.gov (United States)

    Baums, I B; Devlin-Durante, M K; Brown, L; Pinzón, J H

    2009-07-01

    Caribbean reef-building corals in the genus Acropora have been declining dramatically since the 1980s and are now listed as threatened. The study of their complex reproductive system (mixed asexual and sexual) and their population structure requires highly polymorphic nuclear genetic markers. Of eight previously developed microsatellite loci for A. palmata, only five behaved in a Mendelian fashion and only four reliably amplified the sister species, A. cervicornis. Here, nine novel microsatellite markers are presented that dramatically increase the power to distinguish between asexual and sexual reproductive events and may help to refine population boundaries and gene flow across their ranges.

  5. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.

    Directory of Open Access Journals (Sweden)

    Mónica J Pajuelo

    2015-12-01

    Full Text Available Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.The predicted size of the hybrid (proglottid genome combined with cyst genome T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.The availability of draft genomes for T. solium represents a

  6. Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis)

    Science.gov (United States)

    Ramey, A.; Graziano, S.L.; Nielsen, J.L.

    2008-01-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco. ?? 2007 Blackwell Publishing Ltd.

  7. PERMANENT GENETIC RESOURCES: Isolation and characterization of microsatellite loci from the Arctic cisco (Coregonus autumnalis).

    Science.gov (United States)

    Ramey, A; Graziano, S L; Nielsen, J L

    2008-03-01

    Eight polymorphic microsatellite loci were isolated and characterized for the Arctic cisco, Coregonus autumnalis. Loci were evaluated in 21 samples from the Colville River subsistence fishery. The number of alleles per locus ranged from two to 18. Observed heterozygosity of loci varied from 0.10 to 1.00, and expected heterozygosity ranged from 0.09 to 0.92. All eight microsatellite markers were in Hardy-Weinberg equilibrium. The loci presented here will be useful in describing population structure and exploring populations of origin for Arctic cisco.

  8. Utility of immunohistochemistry in predicting microsatellite instability in endometrial carcinoma.

    Science.gov (United States)

    Modica, Ippolito; Soslow, Robert A; Black, Destin; Tornos, Carmen; Kauff, Noah; Shia, Jinru

    2007-05-01

    Identification of the microsatellite instability (MSI) phenotype in endometrial carcinoma is important given that such tumors are the most common noncolorectal tumors to occur in hereditary nonpolyposis colorectal cancer syndrome, and may bear prognostic relevance. The objective of this study was to assess the utility of immunohistochemistry (IHC), a simple and fast technique, in detecting MSI in endometrial carcinoma. The study subjects consisted of 90 endometrial carcinoma patients with equal representation of MSI-high (MSI-H) and non-MSI-H tumors. MSI was tested using the standard polymerase chain reaction-based method and the 5 NCI-recommended markers. Overall, IHC with MLH1 and MSH2 antibodies detected 69% of MSI-H tumors with a specificity of 100%. Adding PMS2 and MSH6 to the antibody panel increased the sensitivity to 91% but decreased the specificity to 83%. The most common IHC abnormality in MSI tumors was concurrent loss of MLH1/PMS2. Assessment of staining was straightforward in most cases but not in all. Staining inadequacies existed. Five stains (4 MLH1 and 1 MSH6) were not interpretable because of the lack of any internal positive control. Two percent to 10% of the cases (depending on the antibody assessed) had only focal weak staining; the highest frequency (10%) occurred with MLH1 antibody. PMS2 staining detected 7 MLH1-staining present MSI-H cases, thus partly accounting for the increased sensitivity with the 4-antibody panel. MSH6 staining identified 9 cases with loss of MSH6 alone, 6 of 9 were non-MSI-H, thus partly accounting for the decreased specificity with the 4-antibody panel. In conclusion, our results suggest that IHC is useful in detecting MSI in endometrial carcinoma. Although IHC has a lower sensitivity with more apparent staining inadequacies in detecting MSI in endometrial carcinoma than it does in colorectal carcinoma, its use in endometrial carcinoma may be an important adjunct when screening for hereditary cases. In the future, as

  9. High-level microsatellite instability in appendiceal carcinomas.

    Science.gov (United States)

    Taggart, Melissa W; Galbincea, John; Mansfield, Paul F; Fournier, Keith F; Royal, Richard E; Overman, Michael J; Rashid, Asif; Abraham, Susan C

    2013-08-01

    High-level microsatellite instability (MSI-high) is found in approximately 15% of all colorectal adenocarcinomas (CRCs) and in at least 20% of right-sided cancers. It is most commonly due to somatic hypermethylation of the MLH1 gene promoter region, with familial cases (Lynch syndrome) representing only 2% to 3% of CRCs overall. In contrast to CRC, MSI-high in appendiceal adenocarcinomas is rare. Only 4 MSI-high appendiceal carcinomas and 1 MSI-high appendiceal serrated adenoma have been previously reported, and the prevalence of MSI in the appendix is unknown. We identified 108 appendiceal carcinomas from MD Anderson Cancer Center in which MSI status had been assessed by immunohistochemistry for the DNA mismatch-repair proteins MLH1, MSH2, MSH6, and PMS2 (n=83), polymerase chain reaction (n=7), or both (n=18). Three cases (2.8%) were MSI-high, and 1 was MSI-low. The 3 MSI-high cases included: (1) a poorly differentiated nonmucinous adenocarcinoma with loss of MLH1/PMS2 expression, lack of MLH1 promoter methylation, and lack of BRAF gene mutation, but no detected germline mutation in MLH1 from a 39-year-old man; (2) an undifferentiated carcinoma with loss of MSH2/MSH6, but no detected germline mutation in MSH2 or TACSTD1, from a 59-year-old woman; and (3) a moderately differentiated mucinous adenocarcinoma arising in a villous adenoma with loss of MSH2/MSH6 expression, in a 38-year-old man with a strong family history of CRC who declined germline testing. When the overall group of appendiceal carcinomas was classified according to histologic features and precursor lesions, the frequencies of MSI-high were: 3 of 108 (2.8%) invasive carcinomas, 3 of 96 (3.1%) invasive carcinomas that did not arise from a background of goblet cell carcinoid tumors, and 0 of 12 (0%) signet ring and mucinous carcinomas arising in goblet cell carcinoid tumors. These findings, in conjunction with the previously reported MSI-high appendiceal carcinomas, highlight the low prevalence of MSI

  10. Application of a double-enrichment procedure for microsatellite isolation and the use of tailed primers for high throughput genotyping

    Directory of Open Access Journals (Sweden)

    Fábio Mendonça Diniz

    2007-03-01

    Full Text Available The number of microsatellite loci and their allelic diversity contribute to increase accuracy and informativity of genetic estimates, however, the isolation of microsatellite loci is not only laborious but also quite expensive. We used (GATAn and (GACAn tetranucleotide probes and single- and double-enrichment hybridization to construct and screen a genomic library with an increased proportion of DNA fragments containing repeat motifs. Repeats were found using both types of hybridization but the double-enrichment procedure recovered sequences of which 100% contained (GATAn and (GACAn motifs. Microsatellite loci primers were then designed with an M13R-tail or CAG-tag to produce scorable PCR products with minimal stutter. The approach used in this study suggests that double-enrichment is a worthwhile strategy when isolating repeat motifs from eukaryotic genomes. Moreover, the use of tailed microsatellite primers provides increased resolution for compound microsatellite loci, with a significant decrease in costs.

  11. Microsatellites for Oenothera gayleana and O. hartwegii subsp. filifolia (Onagraceae), and their utility in section Calylophus1

    Science.gov (United States)

    Lewis, Emily M.; Fant, Jeremie B.; Moore, Michael J.; Hastings, Amy P.; Larson, Erica L.; Agrawal, Anurag A.; Skogen, Krissa A.

    2016-01-01

    Premise of the study: Eleven nuclear and four plastid microsatellite markers were screened for two gypsum endemic species, Oenothera gayleana and O. hartwegii subsp. filifolia, and tested for cross-amplification in the remaining 11 taxa within Oenothera sect. Calylophus (Onagraceae). Methods and Results: Microsatellite markers were tested in two to three populations spanning the ranges of both O. gayleana and O. hartwegii subsp. filifolia. The nuclear microsatellite loci consisted of both di- and trinucleotide repeats with one to 17 alleles per population. Several loci showed significant deviation from Hardy–Weinberg equilibrium, which may be evidence of chromosomal rings. The plastid microsatellite markers identified one to seven haplotypes per population. The transferability of these markers was confirmed in all 11 taxa within Oenothera sect. Calylophus. Conclusions: The microsatellite loci characterized here are the first developed and tested in Oenothera sect. Calylophus. These markers will be used to assess whether pollinator foraging distance influences population genetic parameters in predictable ways. PMID:26949578

  12. Detection and Selection of Microsatellites in the Genome of Paracoccidioides brasiliensis as Molecular Markers for Clinical and Epidemiological Studies

    Science.gov (United States)

    Nascimento, Érika; Martinez, Roberto; Rodrigues Lopes, André; de Souza Bernardes, Luciano Angelo; Pomponio Barco, Carolina; Goldman, Maria Helena S.; Taylor, John W.; McEwen, Juan G.; Pasetto Nobrega, Marina; Nobrega, Francisco G.; Goldman, Gustavo H.

    2004-01-01

    Paracoccidioides brasiliensis, a thermodimorphic fungus, is the causative agent of the prevalent systemic mycosis in Latin America, paracoccidioidomycosis (PCM). Here, we describe the microsatellite patterns observed in a collection of P. brasiliensis random sequence tags. We identified 1,117 microsatellite patterns in about 3.8 Mb of unique sequences (0.47% of the total DNA used in the analysis). The majority of these microsatellites (87.5%) are found in noncoding sequences. We used two polymorphic microsatellites located on noncoding and coding sequences, as well as two microsatellites located on introns, as molecular markers to discriminate P. brasiliensis isolates, to look for relationships between the genetic background of the strains and the types of human disease they cause. We did not observe any correlation between the clinical form of human PCM and four simple sequence repeat patterns analyzed. PMID:15528688

  13. Microsatellite Markers of Willow Species and Characterization of 11 Polymorphic Microsatellites for Salix eriocephala (Salicaceae), a Potential Native Species for Biomass Production in Canada.

    Science.gov (United States)

    Lauron-Moreau, Aurélien; Pitre, Frédéric E; Brouillet, Luc; Labrecque, Michel

    2013-03-27

    Biomass produced from dedicated plantations constitutes a source of renewable energy and is expected to play an important role in several countries in the coming decades. The cultivation of woody crops such as willows therefore raises several environmental issues. In North America, several native willows are potentially interesting for biomass producers. Willow trees are diverse but few species used for environmental applications have been the object of molecular genetic studies. Based on the sequenced poplar genome, 24 microsatellite markers were assayed on five native North American willow species: Salix amygdaloides, S. discolor, S. eriocephala, S. interior and S. nigra. Polymorphic microsatellite markers were used to characterize the allele data on the shrub Salix eriocephala, a North American species with economic potential. Eleven markers amplified and confirmed the potential of this species. Analysis of samples from six populations in eastern Canada showed that all markers were variable as well as polymorphic in at least one population. The number of alleles per locus ranged from 1 to 9 (mean 2.95) and showed that these microsatellite markers can be used to assess genetic diversity of North American willow species.

  14. Microsatellite instability in tumor and nonneoplastic colorectal cells from hereditary non-polyposis colorectal cancer and sporadic high microsatellite-instable tumor patients.

    Science.gov (United States)

    Dietmaier, W; Gänsbauer, S; Beyser, K; Renke, B; Hartmann, A; Rümmele, P; Jauch, K W; Hofstädter, F; Rüschoff, J

    2000-01-01

    Genetic alterations such as loss of heterozygosity (LOH) and microsatellite instability (MSI) have been frequently studied in various tumor types. Genetic heterogeneity of nonneoplastic cells has not yet been sufficiently investigated. However, genomic instability in normal cells could be a potentially important issue, in particular when these cells are used as reference in LOH and MSI analyses of tumor samples. In order to investigate possible genetic abnormalities in normal colorectal cells of tumor patients, MSI analyses of normal colonic mucosa were performed. Up to 15 different laser-microdissected normal regions containing 50-150 cells were investigated in each of 15 individual microsatellite-stable, sporadic high microsatellite-instable (MSI-H) and hereditary non-polyposis coli cancer (HNPCC) colorectal cancer patients. Frequent MSI and heterogeneity in the MSI pattern were found both in normal and tumor cells from 10 HNPCC and sporadic MSI-H tumor patients whose tumors had defect mismatch repair protein expressions. This observation shows that MSI can also occur in nonneoplastic cells which has to be considered in MSI analyses for molecular HNPCC screening. In addition, considerable genetic heterogeneity was detected in all MSI-H (sporadic and HNPCC) tumors when analyzing five different regions with less than 150 cells, respectively. These differences were not detectable in larger tumor regions containing about 10,000 cells. Thus, heterogeneity of the MSI pattern (e.g. intratumoral MSI) is an important feature of tumors with the MSI-H phenotype.

  15. Microsatellite Markers of Willow Species and Characterization of 11 Polymorphic Microsatellites for Salix eriocephala (Salicaceae, a Potential Native Species for Biomass Production in Canada

    Directory of Open Access Journals (Sweden)

    Aurélien Lauron-Moreau

    2013-03-01

    Full Text Available Biomass produced from dedicated plantations constitutes a source of renewable energy and is expected to play an important role in several countries in the coming decades. The cultivation of woody crops such as willows therefore raises several environmental issues. In North America, several native willows are potentially interesting for biomass producers. Willow trees are diverse but few species used for environmental applications have been the object of molecular genetic studies. Based on the sequenced poplar genome, 24 microsatellite markers were assayed on five native North American willow species: Salix amygdaloides, S. discolor, S. eriocephala, S. interior and S. nigra. Polymorphic microsatellite markers were used to characterize the allele data on the shrub Salix eriocephala, a North American species with economic potential. Eleven markers amplified and confirmed the potential of this species. Analysis of samples from six populations in eastern Canada showed that all markers were variable as well as polymorphic in at least one population. The number of alleles per locus ranged from 1 to 9 (mean 2.95 and showed that these microsatellite markers can be used to assess genetic diversity of North American willow species.

  16. Polymorphic microsatellites developed by cross-species amplifications in common pheasant breeds

    NARCIS (Netherlands)

    Baratti, M.; Alberti, A.; Groenen, M.A.M.; Veenendaal, T.; Fulgheri, F.D.

    2001-01-01

    Genetic variability was analysed in two common breeds of pheasant (Phasianus colchicus L. 1758) by means of cross-species amplifications of microsatellite loci: 154 chicken, Gallus gallus and 32 turkey, Meleagris gallopavo, primers were tested for amplification of pheasant DNA. Thirty-six primers (2

  17. Mutability of Y-chromosomal microsatellites: Rates, characteristics, molecular bases, and rorensic implications

    NARCIS (Netherlands)

    K. Ballantyne (Kaye); M.A. Goedbloed (Miriam); R.N. Fang (Rixun); O. Schaap (Onno); O. Lao Grueso (Oscar); A. Wollstein (Andreas); Y. Choi (Ying); K. van Duijn (Kate); M. Vermeulen (Mark); S. Brauer (Silke); R. Decorte (Ronny); M. Poetsch (Micaela); N. von Wurmb-Schwark (Nicole); P. de Knijff (Peter); D. Labuda (Damian); H. Vézina (Hélne); H. Knoblauch (Hans); R. Lessig (Rüdiger); L. Roewer (Lutz); R. Ploski (Rafal); T. Dobosz (Tadeusz); J. Henke (Jürgen); M.R. Furtado (Manohar); M.H. Kayser (Manfred)

    2010-01-01

    textabstractNonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data ar

  18. The reproductive biology of Polytrichum formosum : clonal structure and paternity revealed by microsatellites

    NARCIS (Netherlands)

    Van der Velde, M; During, HJ; Van de Zande, L; Bijlsma, R

    2001-01-01

    Using highly polymorphic microsatellite markers, we assessed clonal structure and paternity in a population of the bryophyte species Polytrichum formosum. Identical multilocus genotypes of individual shoots were almost never observed in spatially separated cushions, but were found to be highly clust

  19. Long-tailed Duck (Clangula hyemalis) Microsatellite DNA Data; Alaska, Canada, Russia, 1994-2002

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This data set describes nuclear microsatellite genotypes derived from twelve autosomal loci (6AB, Aph02, Aph08, Aph19, Aph23, Bca10, Bca11, Hhi5, Sfi11, Smo07,...

  20. Discrimination of American cranberry cultivars and assessment of clonal heterogeneity using microsatellite markers

    Science.gov (United States)

    Cranberries (Vaccinium macrocarpon Ait.) are an economically important fruit crop derived from a North American native species. We report the application of 12 simple sequence repeats (SSR) or microsatellite markers to assess the genetic diversity of cranberry cultivars. We studied 164 samples of 21...

  1. Microsatellite Markers in and around Rice Genes: Applications in Variety Identification and DUS Testing

    NARCIS (Netherlands)

    Bonow, S.; Pinho, Von E.V.R.; Vieira, M.G.C.; Vosman, B.

    2009-01-01

    In Brazil, rice (Oryza sativa L.) varieties adapted to different ecological regions are available on the market. However, these varieties exhibit highly similar morphologies, which makes their identification difficult. In this study we identified microsatellites in and around genes that are useful f

  2. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants.

    Science.gov (United States)

    George, Biju; Bhatt, Bhavin S; Awasthi, Mayur; George, Binu; Singh, Achuit K

    2015-11-01

    Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been  shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR(2-6)(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR(2-6). However, GC content strongly showed negative correlation with relative density (R (2) = 0.5, P plants possesses relatively more genomic diversity compared to higher plants.

  3. Chromosomal distribution of microsatellite repeats in Amazon cichlids genome (Pisces, Cichlidae)

    Science.gov (United States)

    Schneider, Carlos Henrique; Gross, Maria Claudia; Terencio, Maria Leandra; de Tavares, Édika Sabrina Girão Mitozo; Martins, Cesar; Feldberg, Eliana

    2015-01-01

    Abstract Fish of the family Cichlidae are recognized as an excellent model for evolutionary studies because of their morphological and behavioral adaptations to a wide diversity of explored ecological niches. In addition, the family has a dynamic genome with variable structure, composition and karyotype organization. Microsatellites represent the most dynamic genomic component and a better understanding of their organization may help clarify the role of repetitive DNA elements in the mechanisms of chromosomal evolution. Thus, in this study, microsatellite sequences were mapped in the chromosomes of Cichla monoculus Agassiz, 1831, Pterophyllum scalare Schultze, 1823, and Symphysodon discus Heckel, 1840. Four microsatellites demonstrated positive results in the genome of Cichla monoculus and Symphysodon discus, and five demonstrated positive results in the genome of Pterophyllum scalare. In most cases, the microsatellite was dispersed in the chromosome with conspicuous markings in the centromeric or telomeric regions, which suggests that sequences contribute to chromosome structure and may have played a role in the evolution of this fish family. The comparative genome mapping data presented here provide novel information on the structure and organization of the repetitive DNA region of the cichlid genome and contribute to a better understanding of this fish family’s genome. PMID:26753076

  4. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood

    NARCIS (Netherlands)

    A.A.G. van Tilborg (Angela); L.C. Kompier (Lucie); I. Lurkin (Irene); R. Poort (Ricardo); S. El Bouazzaoui (Samira); K.A. van der Keur (Kirstin); T.C.M. Zuiverloon (Tahlita); L. Dyrskjot (Lars); T.F. Orntoft (Torben); M.J. Roobol-Bouts (Monique); E.C. Zwarthoff (Ellen)

    2012-01-01

    textabstractMicrosatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in

  5. New polymorphic tetranucleotide microsatellites improve scoring accuracy in the bottlenose dolphin Tursiops aduncus

    NARCIS (Netherlands)

    Nater, Alexander; Kopps, Anna M.; Kruetzen, Michael

    2009-01-01

    We isolated and characterized 19 novel tetranucleotide microsatellite markers in the Indo-Pacific bottlenose dolphin (Tursiops aduncus) in order to improve genotyping accuracy in applications like large-scale population-wide paternity and relatedness assessments. One hundred T. aduncus from Shark Ba

  6. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

    Directory of Open Access Journals (Sweden)

    Angela A G van Tilborg

    Full Text Available Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance.

  7. Development of microsatellite markers for six Tetranychus species by transfer from Tetranychus urticae genome.

    Science.gov (United States)

    Zhang, Jia; Sun, Jing-Tao; Jin, Peng-Yu; Hong, Xiao-Yue

    2016-09-01

    Microsatellite markers are frequently used to explore the population genetic structure of organisms. Spider mites (genus Tetranychus) are important agricultural pests. Several markers have been developed for T. urticae, but for other spider mites, few such markers are available, hampering studies of their population genetics. In this study, we developed and characterized microsatellite markers for six non-model spider mite species (T. truncatus, T. kanzawai, T. ludeni, T. piercei, T. phaselus and T. pueraricola) by cross-species amplification of markers in the T. urticae genome, in order to better understand the population structure of Tetranychus species. Among 228 screened loci, many were polymorphic, including 13 loci in T. urticae, 11 loci in T. truncatus, 15 loci in T. pueraricola, 23 loci in T. kanzawai, 19 loci in T. piercei, 11 loci in T. phaselus and 9 loci in T. ludeni. Sequence analysis determined that the fragment length variations of the transferred microsatellites were mainly due to the variations of the numbers of repeats. These new microsatellite markers should be useful for studying the population genetics of the seven Tetranychus species.

  8. Characterization of thirteen microsatellite loci from the Ghanian antimalarial plant Cryptolepis sanguinolenta

    Science.gov (United States)

    Cryptolepis sanguinolenta (Lindl.) Schlechter (Periplocaceae) is an herbaceous plant used in traditional medicine to treat malaria and populations of the species are diminishing due to overharvesting and lack of conservation. Co-dominant microsatellite markers that can be used to characterize geneti...

  9. Isolation and characterization of 108 novel microsatellite loci for Atlantic coastal killifish (Fundulus heteroclitus)

    Science.gov (United States)

    We characterized 108 polymorphic microsatellite loci for the mummichog (Fundulus heteroclitus), an Atlantic coastal killifish. Allelic diversity among 26 individuals ranged between 2 and 15 alleles per locus, while expected heterozygosity ranged from 0.075 to 0.904. Significant ...

  10. Male prairie voles with different avpr1a microsatellite lengths do not differ in courtship behaviour.

    Science.gov (United States)

    Graham, Brittney M; Solomon, Nancy G; Noe, Douglas A; Keane, Brian

    2016-07-01

    Females are generally expected to be selective when choosing their social and sexual partners. In a previous laboratory study, female prairie voles (Microtus ochrogaster) showed significant social and sexual preferences for males with longer microsatellite DNA within the avpr1a gene encoding the vasopressin 1a receptor, as predicted if females select mates whose parental behaviour should increase female reproductive success. We tested the hypothesis that males with short versus long avpr1a microsatellite alleles exhibit differences in courtship behaviour, which could act as cues for female mate preference. The only behavioural difference we detected between males with short versus long avpr1a microsatellite alleles in mate preference trials was that males with short avpr1a microsatellite alleles sniffed the anogenital region of females more frequently during the first two days of the trials. Our results did not strongly support the hypothesis that a male's avpr1a genotype predicts the courtship behaviours we measured and suggests that other courtship behaviours or traits, such as odour and vocalizations, may be more important to female prairie voles when choosing mates. Additional studies using a wider array of species are needed to assess the degree to which male mammal courtship behaviour provides information on mate quality to females.

  11. Isolation and characterization of twelve microsatellite loci for the Japanese Devilray (Mobula japanica)

    NARCIS (Netherlands)

    Poortvliet, Marloes; Galvan-Magana, Felipe; Bernardi, Giacomo; Croll, Donald A.; Olsen, Jeanine L.

    2011-01-01

    Twelve polymorphic microsatellites loci were characterized for Mobula japanica (Japanese Devilray) using an enrichment protocol. All but two loci were in Hardy-Weinberg equilibrium with no evidence of linkage disequilibrium or null-alleles for a sample of 40 individuals from two populations. The num

  12. De novo genome assembly of Cercospora beticola for microsatellite marker development and validation

    Science.gov (United States)

    Cercospora leaf spot caused by Cercospora beticola is a significant threat to the production of sugar and table beet worldwide. A de novo genome assembly of C. beticola was used to develop eight polymorphic and reproducible microsatellite markers for population genetic analyses. These markers were u...

  13. Genetic monitoring of supportive breeding in brown trout ( Salmo trutta L.), using microsatellite DNA markers

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Eg Nielsen, Einar; Ruzzante, D.E.;

    2000-01-01

    Stocking with offspring of local wild fish, so-called supportive breeding, is often advocated as an alternative to stocking domesticated fish. However, it is important to ensure that supportive breeding does not result in inbreeding and loss of genetic variability. We analysed eight microsatellite...

  14. Isolation and characterization of microsatellite loci in Sisyrinchium (Iridaceae) and cross amplification in other genera.

    Science.gov (United States)

    Miz, R B; Tacuatiá, L O; Cidade, F W; de Souza, A P; Bered, F; Eggers, L; de Souza-Chies, T T

    2016-09-16

    Recent phylogenetic studies on Sisyrinchium strongly suggest that species classified in section Hydastylus and section Viperella belong to a single group of plants in recent adaptive radiation (Clade IV). These species neither present clear morphological differentiation among them nor show clear identification using DNA barcode markers. Thus, the main goal of this study was to develop a set of polymorphic microsatellite markers compatible for representative species of both sections to ensure variability that could be revealed by SSR markers. Therefore, microsatellite primers were isolated and characterized for Sisyrinchium palmifolium and S. marchioides. In addition, transferability of the developed primers was tested in Iridoideae, primarily in closely related species of Sisyrinchium. Sixteen microsatellite loci were developed from enriched genomic libraries, of which ten were polymorphic. GST values indicated higher differentiation among subpopulations of S. palmifolium than those from S. marchioides. Major transferability was obtained using primers isolated from S. marchioides. All primers exhibited higher rates of cross-amplification for species belonging to Clade IV of Sisyrinchium, as well as to the genera Calydorea and Herbertia. These developed microsatellite markers can be used as an efficient tool for characterization of genetic variability in species belonging to Iridoideae, as well as for studies on population dynamics, genetic structure, and mating system in other Sisyrinchium species.

  15. Development of microsatellite markers for Fusicladium effusum, the causal agent of pecan scab

    Science.gov (United States)

    Pecan scab (caused by F. effusum) is the most important diseases of pecan in the southeastern U.S. Microsatellite (simple sequence repeat, SSR) motifs were mined from the genome of Fusicladium effusum assembled from 454 pyrosequencing and Illumina Miseq reads. A total of 278 SSR primers were designe...

  16. Characterization of polymorphic microsatellite DNA markers in the black-tailed godwit (Limosa limosa : Aves)

    NARCIS (Netherlands)

    Verkuil, Yvonne I.; Trimbos, Krijn; Haddrath, Oliver; Baker, Allan J.; Piersma, Theunis

    2009-01-01

    We isolated and tested 16 microsatellite loci in black-tailed godwits from the Netherlands (Limosa limosa limosa), and from Australasia (subspecies melanuroides). One locus was monomorphic, two loci had null-alleles and one was significantly heterozygote deficient. The remaining 12 polymorphic loci

  17. Chromosomal distribution of microsatellite repeats in Amazon cichlids genome (Pisces, Cichlidae).

    Science.gov (United States)

    Schneider, Carlos Henrique; Gross, Maria Claudia; Terencio, Maria Leandra; de Tavares, Édika Sabrina Girão Mitozo; Martins, Cesar; Feldberg, Eliana

    2015-01-01

    Fish of the family Cichlidae are recognized as an excellent model for evolutionary studies because of their morphological and behavioral adaptations to a wide diversity of explored ecological niches. In addition, the family has a dynamic genome with variable structure, composition and karyotype organization. Microsatellites represent the most dynamic genomic component and a better understanding of their organization may help clarify the role of repetitive DNA elements in the mechanisms of chromosomal evolution. Thus, in this study, microsatellite sequences were mapped in the chromosomes of Cichla monoculus Agassiz, 1831, Pterophyllum scalare Schultze, 1823, and Symphysodon discus Heckel, 1840. Four microsatellites demonstrated positive results in the genome of Cichla monoculus and Symphysodon discus, and five demonstrated positive results in the genome of Pterophyllum scalare. In most cases, the microsatellite was dispersed in the chromosome with conspicuous markings in the centromeric or telomeric regions, which suggests that sequences contribute to chromosome structure and may have played a role in the evolution of this fish family. The comparative genome mapping data presented here provide novel information on the structure and organization of the repetitive DNA region of the cichlid genome and contribute to a better understanding of this fish family's genome.

  18. CHARACTERIZATION OF SEVEN POLYMORPHIC MICROSATELLITE LOCI IN THE COMMON LOON (GAVIA IMMER)

    Science.gov (United States)

    We describe polymerase chain reaction (PCR) primers and conditions to amplify seven microsatellite DNA loci isolated from the Common Loon (Gavia immer). The PCR primers were tested on 83 individuals from ten locations in North America, including breeding, migration stopover, and...

  19. Status of the fast mission: Micro-satellite formation flying for technology, science and education

    NARCIS (Netherlands)

    Guo, J.; Maessen, D.C.; Gill, E.K.A.; Moon, S.G.; Zheng, G.

    2009-01-01

    FAST (Formation for Atmospheric Science and Technology demonstration) is a cooperative Dutch Chinese formation flying mission led by Delft University of Technology (TU Delft) in the Netherlands and Tsinghua University in China. It is expected to be the first international micro-satellite formation f

  20. Chromosomal structural changes and microsatellite variations in newly synthesized hexaploid wheat mediated by unreduced gametes

    Indian Academy of Sciences (India)

    HAO LI; YAJUAN WANG; XIAOXUE GUO; YINPENG DU; CHANGYOU WANG; WANQUAN JI

    2016-12-01

    Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0–S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newlysynthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheatpopulation NA0928, which would be valuable resistance resources for wheat improvement.

  1. Novel microsatellite marker development from the unassembled genome sequence data of the marbled flounder Pseudopleuronectes yokohamae.

    Science.gov (United States)

    Minegishi, Yuki; Ikeda, Minoru; Kijima, Akihiro

    2015-12-01

    Various genome-scale data have been increasingly published in diverged species, but they can be reused for other purposes by re-analyzing in other ways. As a case study to utilize the published genome data, we developed microsatellite markers from the genome sequence data (assembled contigs and unassembled reads) of the marbled flounder Pseudopleuronectes yokohamae. No microsatellites were identified in the contig sequences, whereas the computer software found 781,773 sequences containing microsatellites with di- to hexa-nucleotide motif in the unassembled reads. For 86,732 unique sequences among them, a total of 331,368 primer pairs were designed. Screening based on PCR amplification, polymorphisms and accurate genotyping resulted in sixteen primer sets, which were later characterized using 45 samples collected in Onagawa Bay, Miyagi, Japan. The presence of null alleles was suggested at four loci in the studied population but no evidence of allelic dropout was found. The observed number of alleles and heterozygosity was 2-20 and 0-0.88889, respectively, indicating polymorphisms and usefulness for population genetic analyses of this species. In addition, a large number of the microsatellite primers developed in this study are potentially applicable also for kinship estimation, individual fingerprint and linkage map construction.

  2. Research, Design and Manufacture of Functional Components of the Microsatellite's Components "Republica Moldova"

    Science.gov (United States)

    Bostan, Ion; Canter, Valeriu; Secrieru, Nicolae; Bodean, Ghenadie; Blaja, Valeriu

    2012-06-01

    This paper deals with the main current results of investigation , designing and manufacturing of functional components of microsatellite, obtained in the State investigation programm, "Valoristaion of renewable energy in the Republic of Moldova and development of Moldavian Satellite". The satellite will have a mass of 12.5 kg. The paper contains 8 chapters, 11 figures, 11 bibliographical references.

  3. Microsatellite analysis of serum DNA in patients with oral squamous cell carcinoma.

    Science.gov (United States)

    Kakimoto, Yoshidou; Yamamoto, Nobuharu; Shibahara, Takahiko

    2008-11-01

    The purpose of this study was to assess the possibility of prognosis of oral squamous cell carcinoma by microsatellite blood assay. Altered microsatellite DNA in the blood of cancer patients may provide a novel method for tumor detection. DNA from normal and tumor tissues and serum obtained at two time-points (preoperatively and postoperatively) in 20 patients with oral squamous cell carcinoma was examined at 9 microsatellite loci on chromosomes 2, 3, and 21 by polymerase chain reaction (PCR)-based analysis of loss of heterozygosity (LOH). Eighteen patients (90%) showed microsatellite alterations in serum DNA identical to those in the corresponding tumor DNA. Among those showing allelic imbalance preoperatively (18 patients, 90%), 8 patients (44%) showed no evidence of allelic imbalance in serum postoperatively, and these showed no recurrence or distant metastasis. In 10 patients, allelic imbalance was detected postoperatively in serum. Seven (70%) out of these 10 patients showed an allelic imbalance at both time-points (preoperatively and postoperatively), and these patients had a poor prognosis. In conclusion, this study suggests that blood testing for circulating tumor genetic markers may provide valuable prognostic information and a guide for future therapy.

  4. Development and characterization of microsatellite markers in the sexual-apomictic complex Taraxacum officinale (dandelion)

    NARCIS (Netherlands)

    Falque, M.; Keurentjes, J.J.B.; Bakx-Schotman, J.M.T.; Van Dijk, P.J.

    1998-01-01

    Microsatellite markers were developed in Taraxacum officinale to study gene flow between sexual and apomictic plants and to identify clones. Twenty five thousand genomic DNA clones were hybridized with a (CT)(12)D probe. The density of (GA/CT)(n) repeats was estimated at one every 61 kb in the T.

  5. Development and characterization of nine new microsatellite markers in Taraxacum (Asteraceae).

    NARCIS (Netherlands)

    Vasut, R.; Dijk, P.J.; Falque, M.; Trávnicek, B.; Jong, de J.H.S.G.M.

    2004-01-01

    This study aims at developing and characterizing new microsatellite primer pairs in Taraxacum officinale auct. to produce polymorphic markers for genetical and evolutionary studies on apomixis in this sexual-apomictic complex. A total of 24 diploid plants were tested for allelic polymorphism and

  6. Microsatellite Attitude Determination and Control Subsystem Design and Implementation: Software-in-the-Loop Approach

    Directory of Open Access Journals (Sweden)

    Ho-Nien Shou

    2014-01-01

    Full Text Available The paper describes the development of a microsatellite attitude determination and control subsystem (ADCS and verification of its functionality by software-in-the-loop (SIL method. The role of ADCS is to provide attitude control functions, including the de-tumbling and stabilizing the satellite angular velocity, and as well as estimating the orbit and attitude information during the satellite operation. In Taiwan, Air Force Institute of Technology (AFIT, dedicating for students to design experimental low earth orbit micro-satellite, called AFITsat. For AFITsat, the operation of the ADCS consists of three modes which are initialization mode, detumbling mode, and normal mode, respectively. During the initialization mode, ADCS collects the early orbit measurement data from various sensors so that the data can be downlinked to the ground station for further analysis. As particularly emphasized in this paper, during the detumbling mode, ADCS implements the thrusters in plus-wide modulation control method to decrease the satellite angular velocity. ADCS provides the attitude determination function for the estimation of the satellite state, during normal mode. The three modes of microsatellite adopted Kalman filter algorithm estimate microsatellite attitude. This paper will discuss using the SIL validation ADCS function and verify its feasibility.

  7. Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.)

    NARCIS (Netherlands)

    Liebhard, R.; Gianfranceschi, L.; Koller, B.; Ryder, C.D.; Tarchini, R.; Weg, van de W.E.; Gessler, C.

    2002-01-01

    The availability of suitable genetic markers is essential to efficiently select and breed apple varieties of high quality and with multiple disease resistances. Microsatellites (simple sequence repeats, SSR) are very useful in this respect since they are codominant, highly polymorphic, abundant and

  8. Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids

    NARCIS (Netherlands)

    Dijk, van T.; Noordijk, Y.; Dubos, T.; Bink, M.C.A.M.; Visser, R.G.F.; Weg, van de W.E.

    2012-01-01

    BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles fo

  9. Development of Multiplex Microsatellite PCR Panels for the Seagrass Thalassia hemprichii (Hydrocharitaceae

    Directory of Open Access Journals (Sweden)

    Kor-jent van Dijk

    2014-11-01

    Full Text Available Premise of the study: New microsatellites were developed for the seagrass Thalassia hemprichii (Hydrocharitaceae, a long-lived seagrass species that is found throughout the shallow waters of tropical and subtropical Indo-West Pacific. Three multiplex PCR panels were designed utilizing new and previously developed markers, resulting in a toolkit for generating a 16-locus genotype. Methods and Results: Through the use of microsatellite enrichment and next-generation sequencing, 16 new, validated, polymorphic microsatellite markers were isolated. Diversity was between two and four alleles per locus totaling 36 alleles. These markers, plus previously developed microsatellite markers for T. hemprichii and T. testudinum, were tested for suitability in multiplex PCR panels. Conclusions: The generation of an easily replicated suite of multiplex panels of codominant molecular markers will allow for high-resolution and detailed genetic structure analysis and clonality assessment with minimal genotyping costs. We suggest the establishment of a T. hemprichii primer convention for the unification of future data sets.

  10. Mapping of panda plumage color locus on the microsatellite linkage map of the Japanese quail

    Directory of Open Access Journals (Sweden)

    Mizutani Makoto

    2006-01-01

    Full Text Available Abstract Background Panda (s is an autosomal recessive mutation, which displays overall white plumage color with spots of wild-type plumage in the Japanese quail (Coturnix japonica. In a previous study, the s locus was included in the same linkage group as serum albumin (Alb and vitamin-D binding protein (GC which are mapped on chicken (Gallus gallus chromosome 4 (GGA4. In this study, we mapped the s locus on the microsatellite linkage map of the Japanese quail by linkage analysis. Results Segregation data on the s locus were obtained from three-generation families (n = 106. Two microsatellite markers derived from the Japanese quail chromosome 4 (CJA04 and three microsatellite markers derived from GGA4 were genotyped in the three-generation families. We mapped the s locus between GUJ0026 and ABR0544 on CJA04. By comparative mapping with chicken, this locus was mapped between 10.0 Mb and 14.5 Mb region on GGA4. In this region, the endothelin receptor B subtype 2 gene (EDNRB2, an avian-specific paralog of the mammalian endothelin receptor B gene (EDNRB, is located. Because EDNRB is responsible for aganglionic megacolon and spot coat color in mouse, rat and equine, EDNRB2 is suggested to be a candidate gene for the s locus. Conclusion The s locus and the five microsatellite markers were mapped on CJA04 of the Japanese quail. EDNRB2 was suggested to be a candidate gene for the s locus.

  11. Construction and testing of a microsatellite database containing more than 500 tomato varieties

    NARCIS (Netherlands)

    Bredemeijer, G.M.M.; Cooke, R.J.; Ganal, M.W.; Peeters, R.; Isaac, P.; Noordijk, Y.; Rendell, S.

    2002-01-01

    The aim of this study was to evaluate the suitability of sequence tagged microsatellite site (STMS) markers for varietal identification and discrimination in tomato. For this purpose, a set of 20 STMS primer pairs was used to construct a database containing the molecular description of the most comm

  12. Isolation, characterization, and multiplexing of novel microsatellite markers for the tropical scalloped spiny lobster (Panulirus homarus).

    Science.gov (United States)

    Delghandi, M; Goddard, S; Jerry, D R; Dao, H T; Afzal, H; Al-Jardani, S S

    2015-12-29

    Of the various spiny lobster species in the tropical and subtropical Indo-West Pacific region, the tropical scalloped spiny lobster (Panulirus homarus) supports one of the most commercially valuable fishery resources in many coastal African and Asian countries. The last decade has witnessed a serious decline in the wild populations of this species. Knowledge of the genetic basis of spiny lobster population structure is a prerequisite to achieve a sustainable fisheries management for this species. Here, we describe 13 novel polymorphic microsatellite markers developed for P. homarus, using a cross-species primer design strategy based on P. ornatus Roche 454 shot-gun generated sequencing. Microsatellite polymorphisms were assessed in 96 unrelated P. homarus individuals of a natural population, with the number of alleles per locus varying from 2 to 14, the observed and expected heterozygosity from 0.00 to 0.78 and from 0.03 to 0.79, respectively, and with only four loci (Pho-G27, Pho-G32, Pho-G36, and Pho-G58) deviating from Hardy- Weinberg equilibrium. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between loci Pho-G22 - Pho-G30, and Pho-G30 - Pho-G35. The successful cross amplification of these microsatellites highlights the potential of the developed microsatellites for future population genetic research within the different Panulirus species.

  13. Characterization of microsatellite loci in the marine seaweeds, Fucus serratus and F-evanescens (Heterokontophyta; Fucaceae)

    NARCIS (Netherlands)

    Coyer, JA; Veldsink, JH; Jones, K; Stam, WT; Olsen, JL

    2002-01-01

    Fucus serratus and F. evanescens commonly occur on Northern European shores. Nine microsatellite loci were developed for F. serratus (8-22 alleles, observed heterozygosities = 0.367-0.850) and one for F. evanescens (seven alleles, observed heterozygosity = 0.804). Cross-amplification was apparent, a

  14. Frequent non-reciprocal exchange in microsatellite-containing-DNA-regions of vertebrates

    DEFF Research Database (Denmark)

    Ziegler, J.O.; Wälther, M.; Linzer, T.R.

    2009-01-01

    Microsatellites are DNA-fragments containing short repetitive motifs with 2-10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the rep...

  15. Status of the fast mission: Micro-satellite formation flying for technology, science and education

    NARCIS (Netherlands)

    Guo, J.; Maessen, D.C.; Gill, E.K.A.; Moon, S.G.; Zheng, G.

    2009-01-01

    FAST (Formation for Atmospheric Science and Technology demonstration) is a cooperative Dutch Chinese formation flying mission led by Delft University of Technology (TU Delft) in the Netherlands and Tsinghua University in China. It is expected to be the first international micro-satellite formation

  16. Characterization and cross-amplification of microsatellite markers in four species of anemonefish (Pomacentridae, Amphiprion spp.)

    KAUST Repository

    Bonin, Mary C.

    2015-04-09

    Anemonefish are iconic symbols of coral reefs and have become model systems for research on larval dispersal and population connectivity in coral reef fishes. Here we present 24 novel microsatellite markers across four species of anemonefish and also test 35 previously published markers for cross-amplification on two anemonefish species in order to facilitate further research on their population genetics and phylogenetics. Novel loci were isolated from sequences derived from microsatellite-enriched or 454 GS-FLX shotgun sequence libraries developed using congeneric DNA. Primer testing successfully identified 15 new microsatellite loci for A. percula, 4 for A. melanopus, 3 for A. akindynos, and 2 for A. omanensis. These novel microsatellite loci were polymorphic with a mean of 10 ± 1.6 SE (standard error) alleles per locus and an average observed heterozygosity of 0.647 ± 0.032 SE. Reliable cross-amplification of 12 and 26 of the 35 previously published Amphiprion markers was achieved for A. melanopus and A. akindynos, respectively, suggesting that the use of markers developed from the DNA of congeners can provide a quick and cost-effective alternative to the isolation of new loci. Together, the markers presented here provide an important resource for ecological, evolutionary, and conservation genetic research on anemonefishes that will inform broader conservation and management actions for coral reef fishes. © 2015 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg

  17. Isolation of polymorphic microsatellite loci from the flea beetle Phyllotreta nemorum L. (Coleoptera: Chrysomelidae)

    NARCIS (Netherlands)

    Verbaarschot, P.G.H.; Calvo, D.; Esselink, G.D.; Molina, J.M.; Vrieling, K.; Jong, de P.W.

    2007-01-01

    Ten microsatellite markers for the flea beetle Phyllotreta nemorum were developed using di- and trinucleotide repeat-enriched libraries. Each of these primer pairs were characterized on 96 individuals. Expected heterozygosities ranged between 0.11 and 0.84 and the number of alleles ranged between tw

  18. What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

    Science.gov (United States)

    Sixty-five microsatellite alleles from three Simple Sequence Repeat (SSR) loci (cAGG9, CCT01 and GT03) of various Citrus, Fortunella or Poncirus accessions were cloned and sequenced to determine their mode of evolution. This data was used to assess sequence variation by calculating the average numb...

  19. New polymorphic tetranucleotide microsatellites improve scoring accuracy in the bottlenose dolphin Tursiops aduncus

    NARCIS (Netherlands)

    Nater, Alexander; Kopps, Anna M.; Kruetzen, Michael

    We isolated and characterized 19 novel tetranucleotide microsatellite markers in the Indo-Pacific bottlenose dolphin (Tursiops aduncus) in order to improve genotyping accuracy in applications like large-scale population-wide paternity and relatedness assessments. One hundred T. aduncus from Shark

  20. Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel Perna viridis.

    Science.gov (United States)

    Ong, C C; Teh, C H; Tan, S G; Yusoff, K; Yap, C K

    2008-04-01

    We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species.

  1. Allelic discrimination in naturalized ovine from Pantanal Sul-Matogrossense by means of microsatellite markers

    Directory of Open Access Journals (Sweden)

    Crispim Bruno do Amaral

    2012-08-01

    Full Text Available The molecular biology techniques that are used in allelic discrimination for individual and sheep breeds characterization are important tools in breeding programs and conservation of genetic resources. The use of microsatellite markers allows allelic differentiation, which in turn allows us to infer the genetic variability of sample populations. The study aimed to test the sensitivity and efficiency of fluorescent capillary electrophoresis, using microsatellite primers, for allelic discrimination of the Crioulo breed from Pantanal sul-matogrossense, as well as verify the possibility of using the products of sequencing in genetic variability analysis. For this test, were used blood samples from Pantaneira breed sheep. The allelic discrimination of eight microsatellites was determined by capillary electrophoresis in automatic sequencer and the results analyses were performed on the programs CERVUS and Dendro-UPGMA. The results indicated the possibility of using this technique for the individual genotyping of all loci tested in electrophoretic analysis and its potential to allelic discrimination even in case of difference between two pairs of bases between the alleles. The resulting dendrogram based on the distance matrix by the UPGMA assembly method, indicated medium similarity coefficient of 0.72 in the group of animals. It was concluded that there is the viability and efficiency of the microsatellite molecular markers technique using capillary electrophoresis for allelic discrimination and the utility of results for studies of genetic variability, paternity diagnosis and characterization of the Crioulo sheep herd from Pantanal sul-matogrossense.

  2. Isolation and characterization of microsatellite loci from the yellow-eyed penguin (Megadyptes antipodes).

    Science.gov (United States)

    Boessenkool, S; King, T M; Seddon, P J; Waters, J M

    2008-09-01

    Twelve microsatellite loci were isolated and characterized in the endangered yellow-eyed penguin (Megadyptes antipodes) using enriched genomic libraries. Polymorphic loci revealed two to eight alleles per locus and observed heterozygosity ranged from 0.21 to 0.77. These loci will be suitable for assessing current and historical patterns of genetic variability in yellow-eyed penguins.

  3. Status of the fast mission: Micro-satellite formation flying for technology, science and education

    NARCIS (Netherlands)

    Guo, J.; Maessen, D.C.; Gill, E.K.A.; Moon, S.G.; Zheng, G.

    2009-01-01

    FAST (Formation for Atmospheric Science and Technology demonstration) is a cooperative Dutch Chinese formation flying mission led by Delft University of Technology (TU Delft) in the Netherlands and Tsinghua University in China. It is expected to be the first international micro-satellite formation f

  4. Mission Design of the Dutch-Chinese FAST Micro-Satellite Mission

    NARCIS (Netherlands)

    Maessen, D.C.; Guo, J.; Gill, E.; Laan, E.; Moon, S.; Zheng, G.T.

    2009-01-01

    The paper treats the mission design for the Dutch-Chinese FAST (Formation for Atmospheric Science and Technology demonstration) mission. The space segment of the 2.5 year mission consists out of two formation flying micro-satellites. During the mission, new technologies will be demonstrated and, usi

  5. THE USE OF MICROSATELLITE MARKERS TO STUDY GENETIC DIVERSITY IN INDONESIAN SHEEP

    Directory of Open Access Journals (Sweden)

    Jakaria

    2012-03-01

    Full Text Available The purpose of this research was to study genetic diversity in Indonesian sheep population using microsatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep. Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci data were analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from 17 microsatellite loci, while average number of alleles was 6.10 alleles (6 to 18 alleles from five Indonesian sheep populations (garut sheep of fighting type, garut sheep of meat type, purbalingga sheep, batur sheep and jember sheep population. The average of observed heterozygosity (Ho and expected heterozygosity (He values were 0.5749 and 0.6896, respectively, while the genetic differentiation for inbreeding among population (FIS, within population (FIT and average genetic differentiation (FST were 0.1006, 0.1647 and 0.0712, respectively. Genetic distance and genetic tree showed that Indonesian sheep population was distinct from garut sheep of fighting and meat types, purbalingga sheep, batur sheep and jember sheep population. Based on this results were needed a strategy for conservation and breeding programs in each Indonesian sheep population.

  6. Multicenter collaborative study for standardization of Candida albicans genotyping using a polymorphic microsatellite marker.

    Science.gov (United States)

    Garcia-Hermoso, Dea; MacCallum, Donna M; Lott, Timothy J; Sampaio, Paula; Serna, Maria-José Buitrago; Grenouillet, Fréderic; Klaassen, Corné H W; Bretagne, Stéphane

    2010-07-01

    Microsatellite-based genotyping for Candida albicans can give discrepant results between laboratories when expressed in fragment sizes, because their determination depends on electrophoretic conditions. The interlaboratory reproducibility was assessed in six laboratories provided with an allelic ladder. Despite variations in size determinations, alleles were correctly assigned, making data transportable between laboratories.

  7. Temporal genetic variation as revealed by a microsatellite analysis of European sardine ( Sardina pilchardus) archived samples

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2012-01-01

    The Adriatic stock of European sardine ( Sardina pilchardus) has experienced large interannual demographic fluctuations over the last 30 years, with a severe decline beginning in 1991 and continuing until 1997. In the present study, six microsatellite loci were used on a time series collection of...

  8. Microsatellite Loci for Orthophytum ophiuroides (Bromelioideae, Bromeliaceae Species Adapted to Neotropical Rock Outcrops

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    Felipe Aoki-Gonçalves

    2014-03-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Orthophytum ophiuroides, a rupicolous bromeliad species endemic to neotropical rocky fields. These microsatellite loci will be used to investigate population differentiation and species cohesion in such fragmented environments. The loci were tested for cross-amplification in related bromeliad species. Methods and Results: Eleven polymorphic microsatellite markers were isolated and characterized from an enriched library of O. ophiuroides. The loci were tested on 42 individuals from two populations of this species. The number of alleles per locus ranged from three to nine and the expected and observed heterozygosities ranged from 0.167 to 0.870 and from 0.369 to 0.958, respectively. Seven loci successfully amplified in other related bromeliad species. Conclusions: Our results suggest that the microsatellite loci developed here will be useful to assess genetic diversity and gene flow in O. ophiuroides for the investigation of population differentiation and species cohesion in neotropical mountainous habitats.

  9. Development and characterization of microsatellite markers in the sexual-apomictic complex Taraxacum officinale (dandelion)

    NARCIS (Netherlands)

    Falque, M.; Keurentjes, J.J.B.; Bakx-Schotman, J.M.T.; Van Dijk, P.J.

    1998-01-01

    Microsatellite markers were developed in Taraxacum officinale to study gene flow between sexual and apomictic plants and to identify clones. Twenty five thousand genomic DNA clones were hybridized with a (CT)(12)D probe. The density of (GA/CT)(n) repeats was estimated at one every 61 kb in the T. of

  10. Development and characterization of nine new microsatellite markers in Taraxacum (Asteraceae)

    NARCIS (Netherlands)

    Vašut, R.J.; van Dijk, P.J.; Falque, M.; Trávnícek, B.; Jong, J.P.

    2004-01-01

    This study aims at developing and characterizing new microsatellite primer pairs in Taraxacum officinale auct. to produce polymorphic markers for genetical and evolutionary studies on apomixis in this sexual-apomictic complex. A total of 24 diploid plants were tested for allelic polymorphism and het

  11. Development and characterization of nine new microsatellite markers in Taraxacum (Asteraceae).

    NARCIS (Netherlands)

    Vasut, R.; Dijk, P.J.; Falque, M.; Trávnicek, B.; Jong, de J.H.S.G.M.

    2004-01-01

    This study aims at developing and characterizing new microsatellite primer pairs in Taraxacum officinale auct. to produce polymorphic markers for genetical and evolutionary studies on apomixis in this sexual-apomictic complex. A total of 24 diploid plants were tested for allelic polymorphism and het

  12. RNA-binding proteins in microsatellite expansion disorders: mediators of RNA toxicity.

    Science.gov (United States)

    Echeverria, Gloria V; Cooper, Thomas A

    2012-06-26

    Although protein-mediated toxicity in neurological disease has been extensively characterized, RNA-mediated toxicity is an emerging mechanism of pathogenesis. In microsatellite expansion disorders, expansion of repeated sequences in noncoding regions gives rise to RNA that produces a toxic gain of function, while expansions in coding regions can disrupt protein function as well as produce toxic RNA. The toxic RNA typically aggregates into nuclear foci and contributes to disease pathogenesis. In many cases, toxicity of the RNA is caused by the disrupted functions of RNA-binding proteins. We will discuss evidence for RNA-mediated toxicity in microsatellite expansion disorders. Different microsatellite expansion disorders are linked with alterations in the same as well as disease-specific RNA-binding proteins. Recent studies have shown that microsatellite expansions can encode multiple repeat-containing toxic RNAs through bidirectional transcription and protein species through repeat-associated non-ATG translation. We will discuss approaches that have characterized the toxic contributions of these various factors.

  13. Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management

    Science.gov (United States)

    The International Cocoa Genebank, Trinidad (ICG,T) is the largest public domain field gene bank collection of cacao and the correct identity of each tree is crucial for germplasm movement, evaluation and phenotypic characterization. Nine microsatellite loci were used to assess the identity of 1480 t...

  14. Microsatellite markers for the human nematode parasite Ascaris lumbricoides: development and assessment of utility.

    Science.gov (United States)

    Criscione, Charles D; Anderson, Joel D; Raby, Kyle; Sudimack, Dan; Subedi, Janardan; Rai, Dev R; Upadhayay, Ram P; Jha, Bharat; Williams-Blangero, Sarah; Anderson, Timothy J C

    2007-06-01

    We describe 35 microsatellite markers from the human parasitic nematode Ascaris lumbricoides. We found 7 sex-linked markers and demonstrate that 26 autosomal loci can be scored reliably. These markers have high genetic variability and provide the tools to address multiple questions concerning the epidemiology, fine-scale genetic structure, host specificity, and mating systems of this parasite.

  15. Empirical evaluation reveals best fit of a logistic mutation model for human Y-chromosomal microsatellites.

    Science.gov (United States)

    Jochens, Arne; Caliebe, Amke; Rösler, Uwe; Krawczak, Michael

    2011-12-01

    The rate of microsatellite mutation is dependent upon both the allele length and the repeat motif, but the exact nature of this relationship is still unknown. We analyzed data on the inheritance of human Y-chromosomal microsatellites in father-son duos, taken from 24 published reports and comprising 15,285 directly observable meioses. At the six microsatellites analyzed (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393), a total of 162 mutations were observed. For each locus, we employed a maximum-likelihood approach to evaluate one of several single-step mutation models on the basis of the data. For five of the six loci considered, a novel logistic mutation model was found to provide the best fit according to Akaike's information criterion. This implies that the mutation probability at the loci increases (nonlinearly) with allele length at a rate that differs between upward and downward mutations. For DYS392, the best fit was provided by a linear model in which upward and downward mutation probabilities increase equally with allele length. This is the first study to empirically compare different microsatellite mutation models in a locus-specific fashion.

  16. Characterization of microsatellite loci in the marine seaweed Ascophyllum nodosum (Phaeophyceae; Fucales)

    NARCIS (Netherlands)

    Olsen, JL; Sadowski, G; Stam, WT; Veldsink, JH; Jones, K

    Ascophyllum nodosum L. dominates rocky intertidal shores throughout the temperate North Atlantic. Six microsatellite loci were developed for A. nodosum using enriched libraries. The number of alleles ranged from 9 to 24 and heterozygosities from 0.2213 to 0.7785. Ascophyllum is monotypic. There was

  17. Characterization of microsatellite loci in the marine seaweeds, Fucus serratus and F-evanescens (Heterokontophyta; Fucaceae)

    NARCIS (Netherlands)

    Coyer, J.A.; Veldsink, J.H.; Jones, K.; Stam, W.T.; Olsen, J.L.

    Fucus serratus and F. evanescens commonly occur on Northern European shores. Nine microsatellite loci were developed for F. serratus (8-22 alleles, observed heterozygosities = 0.367-0.850) and one for F. evanescens (seven alleles, observed heterozygosity = 0.804). Cross-amplification was apparent,

  18. Characterization of Microsatellite Markers for Pinedrops, Pterospora andromedea (Ericaceae, from Illumina MiSeq sequencing

    Directory of Open Access Journals (Sweden)

    Lisa C. Grubisha

    2014-10-01

    Full Text Available Premise of the study: Pterospora andromedea (Ericaceae is a mycoheterotrophic plant endemic to North America with a disjunct distribution. Eastern populations are in decline compared to western populations. Microsatellite loci will allow comparison of genetic diversity in endangered to nonthreatened populations. Methods and Results: Illumina MiSeq sequencing resulted in development of 12 polymorphic microsatellite loci from 63 perfect microsatellite loci tested. One polymorphic locus was obtained from a traditional enrichment method. These 13 loci were screened across two western and two eastern populations. For western and eastern populations, respectively, number of alleles ranged from one to 10 and one to four, and observed heterozygosity ranged from 0.000 to 0.389 and 0.000 to 0.143. Conclusions: These are the first microsatellite loci developed for Pterospora. They will be useful in conservation efforts of the eastern populations and for examination of population genetic parameters at different geographic scales and comparison with mycorrhizal fungal hosts.

  19. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes.

    Science.gov (United States)

    Ruiz-Ruano, Francisco J; Cuadrado, Ángeles; Montiel, Eugenia E; Camacho, Juan Pedro M; López-León, María Dolores

    2015-06-01

    Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.

  20. Dinucleotide microsatellite DNA loci from the ant Myrmica scabrinodis

    DEFF Research Database (Denmark)

    Zeisset, Inga; Ebsen, Jon R.; Boomsma, Jacobus Jan

    2005-01-01

    We describe the isolation and characterization of five dinucleotide microsatellite loci in the ant Myrmica scabrinodis, which were obtained using a magnetic bead hybridization selection protocol. The PCR primers were tested on nine to 11 individuals. The number of alleles ranged from two to 13, a...