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Sample records for microsatellite dna analysis

  1. DNA microsatellite analysis for tomato genetic differentiation

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    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.

  2. 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.

  3. Microsatellite DNA analysis proves nucleus of interspecies reconstructed blastocyst coming from that of donor giant panda

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A method for DNA isolation from early development of blastocyst and further analysis of nuclear and mitochondrial DNA was developed in present study. Total DNA was prepared from interspecies reconstructed blastocyst and a giant panda specific microsatellite locus g010 was successfully amplified. DNA sequencing of the PCR product showed that two sequences of reconstructed blastocysts are the same as that of positive control giant panda. Our results prove that the nucleus of interspecies reconstructed blastocyst comes from somatic nucleus of donor giant panda.

  4. Microsatellite-based parentage analysis of Aedes aegypti (Diptera: Culicidae) using nonlethal DNA sampling.

    Science.gov (United States)

    Wong, Jacklyn; Chu, Yui Yin; Stoddard, Steven T; Lee, Yoosook; Morrison, Amy C; Scott, Thomas W

    2012-01-01

    To track Aedes aegypti (L.) egg-laying behavior in the field in Iquitos, Peru, we developed methods for 1) sampling DNA from live mosquitoes and 2) high through-put parentage analysis using microsatellite markers. We were able to amplify DNA extracted from a single hind leg, but not from the pupal exuvia. Removal of a leg from teneral females caused no significant changes in female behavioral or life history traits (e.g., longevity, blood feeding frequency, fecundity, egg hatch rate, gonotrophic cycle length, or oviposition behavior). Using a panel of nine microsatellite markers and an exclusion-based software program, we matched offspring to parental pairs in 10 Ae. aegypti test families in which parents originated from natural development sites in Iquitos. By mating known individuals in the laboratory, retaining the male, sampling the female's DNA before release, and collecting offspring in the field, the technique we developed can be used to genotype large numbers of Ae. aegypti, reconstruct family relationships, and track the egg-laying behavior of individual Ae. aegypti in nature.

  5. Genetic linkage analysis of familial amyotrophic lateral sclerosis using human chromosome 21 microsatellite DNA markers

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, D.R.; Sapp, P.; O`Regan, J.; McKenna-Yasek, D.; Schlumpf, K.S.; Haines, J.L.; Gusella, J.F.; Horvitz, H.R.; Brown, R.H. Jr. [Massachusetts Institute of Technology, Cambridge, MA (United States)

    1994-05-15

    Amyotrophic lateral sclerosis (ALS; Lou Gehrig`s Disease) is a lethal neurodegenerative disease of upper and lower motorneurons in the brain and spinal cord. We previously reported linkage of a gene for familial ALS (FALS) to human chromosome 21 using 4 restriction fragment length polymorphism DNA markers and identified disease-associated mutations in the superoxide dismutase (SOD)-1 gene in some ALS families. We report here the genetic linkage data that led us to examine the SOD-1 gene for mutations. We also report a new microsatellite DNA marker for D21S63, derived from the cosmid PW517. Ten microsatellite DNA markers, including the new marker D21S63, were used to reinvestigate linkage of FALS to chromosome 21. Genetic linkage analysis performed with 13 ALS familes for these 10 DNA markers confirmed the presence of a FALS gene on chromosome 21. The highest total 2-point LOD score for all families was 4.33, obtained at a distance of 10 cM from the marker D21S223. For 5 ALS families linked to chromosome 21, a peak 2-point LOD score of 5.94 was obtained at the DNA marker D21S223. A multipoint score of 6.50 was obtained with the markers D21S213, D21S223, D21S167, and FALS for 5 chromosome 21-linked ALS families. The haplotypes of these families for the 10 DNA markers reveal recombination events that further refined the location of the FALS gene to a segment of approximately 5 megabases (Mb) between D21S213 and D21S219. The only characterized gene within this segment was SOD-1, the structural gene for Cu, Zn SOD. 30 refs., 4 figs., 4 tabs.

  6. Analysis of microsatellite instability in stool DNA of patients with colorectal cancer using denaturing high performance liquid chromatography

    Institute of Scientific and Technical Information of China (English)

    Seok-Byung Lim; Yong Shin; Sang-Geun Jang; Jae-Hyun Park; Jae-Gahb Park; Seung-Yong Jeong; Il-Jin Kim; Dae Yong Kim; Kyung Hae Jung; Hee Jin Chang; Hyo Seong Choi; Dae Kyung Sohn; Hio Chung Kang

    2006-01-01

    AIM: To evaluate the usefulness of denaturing high performance liquid chromatography (DHPLC) for analyzing microsatellite instability (MSI) status in stool DNA of patients with colorectal cancer.METHODS: A total of 80 cancer tissues from patients with primary sporadic colorectal tumor (proximal cancer:27, distal cancer: 53) and matched stool (which were employed for comparison with the tissues) were analyzed for MSI status in BAT 26. DNA samples extracted from stool were evaluated by nested polymerase chain reaction (PCR) and DHPLC for MSI analysis.RESULTS: Six cases (7.5%) of MSI were identified in BAT 26 from 80 cancer tissues. All the stool DNA samples from patients whose cancer tissue showed MSI also displayed MSI in BAT 26.CONCLUSION: As MSI is one of the established fecal DNA markers to screen colorectal cancer, we propose to use DHPLC for the MSI analysis in fecal DNA.

  7. [Analysis of Microsatellite DNA in Rodents from Eastern Urals Radioactive Trace Zone and Contiguous Territories].

    Science.gov (United States)

    Rakitin, S B; Grigorkina, E B; Olenev, G V

    2016-04-01

    The variability of four microsatellite loci of rodents, caught from the head part of Eastern Urals Radioactive Trace (EURT), along with the rodents inhabiting contiguous zone with background radiation level and distant-reference territory, was analyzed forthe first time. Differences in the parameters of genetic diversity between northern red-backed voles from the EURT zone and from the reference population were detected. An increase in some indices of genetic diversity in animals from a contiguous to the EURT zone was found; this is probably associated with animal migration and configuration of the area of pollution. A transfer of radiation-induced effects to the contiguous territories and a decrease in the possibility of fixation of adaptations in a series of generations of mobile rodent species in the area of local radioactive pollution are consequences of migrations. The results of the study make it possible to recommend microsatellite markers for the analysis of radiation-induced effects in rodents as model objects of radioecological monitoring.

  8. DNA fingerprinting and diversity analysis in Aus genotypes using microsatellite markers

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    MD. MONIRUL ISLAM

    2015-08-01

    Full Text Available DNA fingerprinting and genetic diversity of 94 Aus (6 BRRI released Aus variety and 88 local Aus landraces genotypes were carried out to protect the Aus landraces from biopiracy. A total of 91 microsatellite markers were tested for screening the genotypes. Among 91 amplified products, 56% have polymorphic bands giving 195 alleles. The number of alleles per locus ranged from four (RM25 and RM147 to twenty seven (RM519, where average allele number was 9.76. The Polymorphism Information Contents (PIC lied between 0.455 (RM5 to 0.934 (RM519. Most robust marker was found RM519 since it provided the highest PIC value (0.934. Pair-wise genetic dissimilarity co-efficient showed the lowest genetic dissimilarity was found BRRI dhan42 and BRRI dhan43 and the highest genetic dissimilarity was found local landraces each other. Here it is shown that most Aus landraces is recognized to have broad genetic base. Thus it is recommended to use these landraces for future breeding program or include new and untouched local landraces to incorporate new genes and broaden genetic base.

  9. Microsatellite DNA Analysis on the Polyandry of Green Sea Turtle Chelonia mydas

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    Dewi Purnama

    2013-12-01

    Full Text Available Green turtle (Cheloniamydas; Testudines is included in the group of polyandryanimals, which is single female mated with many male. DNA polymorphism method generally considered to have a high degree of accuracy as compared to other methods to elucidate polyandry phenomena on many animals. In this research, three microsatellite loci were used to identify the number and frequency of genotypes per locus, the number and frequency alleles per locus, and genotypes and number of alleles in the nest. The purpose of this research was to study the reproductive pattern of Cheloniamydas and compensation eggs of males from hatchling’s population in turtle conservation area of Pangumbahan Coastal Park, West Java. The result showed that from 10 nests, we could find 37 genotypes with 11 alleles for D108 locus, 21 genotypes with 9 alleles for B103 locus, and 27 genotypes with 9 alleles for C102 locus. The alleles number of each nest was more than 5 alleles for 5 nests, and more than 4 alleles for the remaining nests. Based on the probabilities of alleles contribution of each parent, the green turtle was polyandry animals.

  10. 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.

  11. 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

  12. 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.

  13. Development of novel microsatellite DNA markers by cross-amplification and analysis of genetic variation in gerbils.

    Science.gov (United States)

    Du, Xiaoyan; Chen, Zhenwen; Li, Wei; Tan, Yuanqing; Lu, Jing; Zhu, Xiangdong; Zhao, Taiyun; Dong, Gang; Zeng, Lin

    2010-01-01

    The objectives of this study are to establish microsatellite loci for the Mongolian gerbil based on mouse microsatellite DNA sequences and to investigate genetic variation in the laboratory gerbil (Capital Medical University, CMU) and 2 wild gerbil populations (from Yin Chuan city [YIN] and the Hohehot Municipality [HOH]). In total, 536 mouse microsatellite markers were chosen to identify polymorphic dinucleotide repeat loci in the gerbil by cross-amplification. Of these markers, 313 (58.39%) have been discretely amplified from the CMU laboratory gerbil and been sequenced. Of the 313 sequenced markers, 130 were confirmed as simple sequence repeat (SSR) loci in the gerbil. In total, 6 of those newly identified loci plus 6 identified in previous reports were used to estimate the genetic polymorphism for 30 laboratory gerbils and 54 wild gerbils (27 each of the HOH and YIN groups). A total of 29 alleles were observed in the 3 populations, and 11 of 12 loci (91.67%) are polymorphic markers. Nei's standard genetic distances of 0.0592 (CMU vs. HOH) and 0.1033 (CMU vs. YIN) were observed. The averages of observed versus expected heterozygosity are 0.5231/0.4008, 0.5051/0.3882, and 0.4825/0.3665 for the YIN, HOH, and CMU populations, respectively. These results show that cross-amplification using mouse microsatellite primers is an efficient way to identify gerbil SSR loci. By using these 12 selected markers, we have demonstrated that genetic variation level within the CMU population is higher than that has been reported previously and are comparable with the levels found in 2 wild populations.

  14. Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Bekkevold, Dorte; Jensen, L.F.;

    2006-01-01

    -admixed individuals nevertheless remained in the wild-caught samples. In addition, two resident populations in isolated tributaries were found to be indigenous. The indigenous anadromous individuals from the Skjern River were unlikely to have been recruited from either the isolated tributary populations......1. Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population...... of the Skjern River, Denmark, by identifying remaining non-admixed individuals to be used for supportive breeding. 2. We analysed microsatellite DNA markers in historical (1940-50s) and contemporary (1992-2004) samples from the Skjern River system, from the strain of domesticated trout previously used...

  15. A combined DNA-microsatellite and isozyme analysis of the population structure of the harbour porpoise in Danish waters and west Greenland

    DEFF Research Database (Denmark)

    Andersen, L W; Holm, L E; Siegismund, Hans Redlef;

    1997-01-01

    One hundred and twenty-four specimens of the harbour porpoise, Phocoena phocoena, occurring in inner Danish waters (IDW), the North Sea and West Greenland were analysed to study subdivision into genetically differentiated subpopulations using PCR-amplified DNA-microsatellites and isozyme markers...... or nonrandom mating. The analysis of the genetical population structure showed that harbour porpoises from West Greenland, the North Sea and IDW were three geographically, genetically differentiated populations even though connected through some degree of gene flow. A tendency for females to be more stationary...... than males was suggested. Furthermore, the population structure suggested a closer relationship between IDW and the North Sea....

  16. Analysis of microsatellite markers D18S70 and d20S116 in DNA isolated from dentin: Use in forensic medicine

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    Puzović Dragana

    2009-01-01

    Full Text Available Introduction. Short tandem repeats and more specifically microsatellites represent a powerful tool in forensic medicine. In the past years, they have been extensively used in human identification and paternity testing. Objective The aim of the present study was to analyze two microsatellite markers in the Serbian population, i.e. to determine the number of alleles and the relevant forensic parameters. Methods. DNA was isolated from teeth samples using standard proteinase K digestion and phenol/chloroform alcohol extraction. PCR products were analyzed on polyacrilamide gels and visualized by AgNO3 staining. Forensic parameters were calculated using the Cervus software. Results. The loci D18S70 and D20S116 were analyzed on a sample of 70 unrelated, healthy adult individuals from Serbia. The number of alleles was determined and Hardy Weinberg equilibrium was confirmed for both loci. D18S70 and D20S116 demonstrated 6 and 8 alleles, respectively. The power of discrimination (PD and the power of exclusion (PE for the tested STR loci, D18S70 and D20S116 were 0.92 (PD, 0.41 (PE and 0.95 (PD, 0.480 (PE, respectively. Conclusion. According to the presented data, D18S70 and D20S116 are most informative markers. Based on allelic frequencies and statistical parameters for forensic testing, it may be suggested that these two microsatellites represent useful markers for individual identification and parentage analysis in the Serbian population.

  17. Genetic Diversity and Differentiation of the Orange-Spotted Grouper (Epinephelus coioides Between and Within Cultured Stocks and Wild Populations Inferred from Microsatellite DNA Analysis

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    Haoran Lin

    2011-07-01

    Full Text Available In the present study, we employed microsatellite DNA markers to analyze the genetic diversity and differentiation between and within cultured stocks and wild populations of the orange-spotted grouper originating from the South China Sea and Southeast Asia. Compared to wild populations, genetic changes including reduced genetic diversity and significant differentiation have taken place in cultured grouper stocks, as shown by allele richness and heterozygosity studies, pairwise Fst, structure, molecular variance analysis, as well as multidimensional scaling analysis. Although two geographically adjacent orange-spotted grouper populations in China showed negligible genetic divergence, significant population differentiation was observed in wild grouper populations distributed in a wide geographical area from China, through Malaysia to Indonesia. However, the Mantel test rejected the isolation-by-distance model of genetic structure, which indicated the genetic differentiation among the populations could result from the co-effects of various factors, such as historical dispersal, local environment, ocean currents, river flows and island blocks. Our results demonstrated that microsatellite markers could be suitable not only for genetic monitoring cultured stocks but also for revealing the population structuring of wild orange-spotted grouper populations. Meanwhile, our study provided important information for breeding programs, management of cultured stocks and conservation of wild populations of the orange-spotted grouper.

  18. Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L. as revealed by microsatellite DNA analysis

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    D. LOUKOVITIS

    2015-01-01

    Full Text Available Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

  19. Haplotype analysis of DNA microsatellites tightly linked to the locus of Usher syndrome type I on chromosome 11q

    Energy Technology Data Exchange (ETDEWEB)

    Korostishevsky, M.; Kalinsky, H.; Seroussi, E. [Sackler Faculty of Medicine, Ramat-Aviv (Israel)] [and other

    1994-09-01

    Usher syndrome type I (USHI), an autosomal recessive disorder associated with congenital sensorineural deafness and progressive visual loss, is closely linked to the D11S533 locus. The availability of 7 other polymorphic markers within few centimorgans spanning the disease locus allowed us to identify a unique and single haplotype among all carriers of USHI gene in the Samaritan kindred. Occurrence of recombination in this small chromosomal interval is rare, hindering the detection of the mitotic recombination events needed for analysis by traditional linkage methods. Attempts to order the eight loci by linkage disequilibrium models proved to be problematic. However, our haplotype analysis implied that recombinations which had arisen in past generations may be utilized in fine mapping of the USHI gene and in resolving the conflicting linkage maps previously obtained for this region. We have developed a simple algorithm for predicting the order of the microsatellites on the basis of haplotype resemblance. The following chromosomal map in which the USHI gene is closest to D11S533 (location score of 31.0 by multipoint analysis) is suggested: D11S916, GARP, D11S527, D11S533, OMP, D11S906, D11S911, D11S937. Physical mapping efforts are currently directed to verify and to detail the map of this chromosomal region.

  20. Genetic Monitoring of PLCε Knockout Mice by Microsatellite DNA Analysis%PLCε基因敲除小鼠微卫星DNA遗传监测分析

    Institute of Scientific and Technical Information of China (English)

    崔智; 李晓娟; 白云峰; 侯俊; 戴广海; 李瑞生

    2012-01-01

    Objective To determine the genetic characteristics of PLCe knockout mice by polymorphic microsatellite DNA loci analysis. Methods Genome DNA of 28 PLCe gene knockout mice were amplified by PCR using screening 15 microsatellite DNA loci, and population genetic diversity was identified by gene fragments. Results Among 13 microsatellite DNA loci (DlMit365, D3Mit51 , D4Mit235 , D6MM02, D7Mit281 , D8Mitll3, D9Mit23 , D10MM80, D13Mit88,D16Mitl45,D17Mit36,D18Mit94,D19Mit97),each locus of electrophoresis distance of DNA fragments in the 28 PLCe gene knockout mice kept consistent and presented monomorphism , indicating the genetic stability. However the two loci Dq (knock genotype) and Dy (wild-type) were used to discriminate 28 PLCe gene knockout mice by PCR amplification. Among them, 6 mice were of gene knock mice, 7 mice were of wild-type mice, and 15 mice were of heterozygous type. Conclusions The method of microsatellite marker analysis can be used to monitor population genetic quality and accurately distinguish different genotypes of mice , providing a feasible method for the detection of genetic quality%目的 利用多态性微卫星DNA位点分析PLCε基因敲除小鼠的遗传特性.方法 用所筛选的15个微卫星DNA位点对28只PLCε基因敲除小鼠的DNA进行了PCR扩增,通过基因片段大小来分析群体的遗传多样性.结果 13个微卫星DNA位点中(D1Mit365、D3Mit51、D4Mit235、D6Mit102、D7Mit281、D8Mit113、D9Mit23、D10Mit180、D13Mit88、D16Mit145、D17Mit36、D18Mit94、D19Mit97)每个位点的28只小鼠DNA片段泳动距离一致,呈现单态性,表明该群体符合近交系的遗传特性;而利用Dq(敲基因型)和Dy(野生型)两个位点对28只小鼠的PCR扩增结果进行了鉴别分析,其中敲除基因型小鼠为6只;野生型为7只;杂合型为15只.结论 利用微卫星标记技术可以对群体进行遗传质量监测,并能有效地鉴别不同的基因型,为小鼠的遗传质量监测提供了一种可行的方法.

  1. 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.

  2. 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.

  3. Genetic diversity within and among four South European native horse breeds based on microsatellite DNA analysis: implications for conservation.

    Science.gov (United States)

    Solis, A; Jugo, B M; Mériaux, J C; Iriondo, M; Mazón, L I; Aguirre, A I; Vicario, A; Estomba, A

    2005-01-01

    In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Pottoka, but appeared to stand in an intermediate position between this and the meat breeds. Assuming that Pottoka is the breed less affected by admixture, the others gradually distanced themselves from it through varying influences from outside breeds, among other factors. In a comparative study with other breeds, the French breeds Ardanais, Comtois, and Breton were the closest to the four native breeds. Three different approaches for evaluating the distribution of genetic diversity were applied. The high intrabreed variability of Euskal Herriko Mendiko Zaldia (EHMZ) was pointed out in these analyses. In our opinion, cultural, economic, and scientific factors should also be considered in the management of these horse breeds.

  4. Genetic diversity and differentiation of masu salmon (Oncorhynchus masou masou) between and within cultured populations inferred from microsatellite DNA analysis

    Institute of Scientific and Technical Information of China (English)

    Zhiying JIA; Yuyong ZHANG; Shuqiang CHEN; Lianyu SHI

    2012-01-01

    Masu salmon,Oncorhynchus masou masou,is one of the most valuable fishery species that has been introduced to China,though to date no studies on the genetic diversity and genetic relationship among hatchery populations has been performed with molecular markers.We undertook such a study and sampled 120 individuals from three hatchery stocks and analyzed 20 microsatellite loci.All loci were polymorphic and a total of 91 alleles were detected.A relatively low level of genetic diversity was revealed with effective number of allele of 3.1094,3.3299 and 3.1894 and expected heterozygosity of 0.6600,0.6648 and 0.6638 in the three stocks,respectively.Deviations from Hardy-Weinberg equilibrium were found due to heterozygote deficit.Accordingly,evidence of genetic bottlenecks were found in the three stocks.An individual assignment test demonstrated that 85% of individuals were correctly assigned into their original stocks.Pairwise Fst revealed that significant differentiation occurred between these three stocks.The results of the study indicated that disequilibrium of genetic structure and differentiation has occurred in all three stocks.This information collectively provides a basis for measures to avoid of loss of genetic diversity and introgression in Chinese aquaculture.

  5. 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.

  6. 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.

  7. Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar.

    Science.gov (United States)

    Meerow, Alan W; Wisser, Randall J; Brown, J Steven; Kuhn, David N; Schnell, Raymond J; Broschat, Timothy K

    2003-02-01

    Using 15 simple sequence repeat (SSR) microsatellite DNA loci, we analyzed genetic variation within Cocos nucifera germplasm collections at two locations in south Florida, representing eight cultivars. The loci were also used in a parentage analysis of progeny of the 'Fiji Dwarf' variety at both locations. A total of 67 alleles were detected, with eight the highest number at any one locus. These loci identified 83 of the 110 individual palms. Gene diversity of the 15 loci ranged from 0.778 to 0.223, with a mean of 0.574. 'Fiji Dwarf', 'Malayan Dwarf', 'Green Niño' and 'Red Spicata' cultivars resolve as distinct clusters in a neighbor joining tree using modified Rogers distance, while the tall varieties form two aggregates. The highest gene diversity was found in the tall cultivars (H = 0.583 cumulatively), and the lowest in the 'Malayan Dwarf' (H = 0.202). After the tall coconuts, the 'Fiji Dwarf' was most genetically diverse (H = 0.436), and had the largest number of unique alleles. Genetic identity is highest among the 'Malayan Dwarf' phenotypes, and between the tall varieties. The 'Red Malayan Dwarf' is genetically distinct from the 'Green' and 'Yellow Malayan Dwarf' phenotypes, which cannot be distinguished with the SSR loci used. Off-type 'Malayan Dwarf' phenotypes (putative hybrids with talls) can be identified genotypically. Parentage analyses of 30 'Fiji Dwarf' progeny propagated from five adults surrounded by other cultivars estimate that only 20% of the progeny were out-crossed to the other varieties, while 40-46% were possible selfs. This suggests that a seed-production orchard of the variety maintained at reasonable distance from other varieties, will likely yield only 'Fiji Dwarf' genotypes. Our data are discussed in the context of hypotheses of coconut dissemination around the world.

  8. Postglacial recolonization patterns and genetic relationships among whitefish ( Coregonus sp.) populations in Denmark, inferred from mitochondrial DNA and microsatellite markers

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons; Berg, Søren

    1999-01-01

    The genetic relationships among morphologically and geographically divergent populations of whitefish (genus: Coregonus) from Denmark and the Baltic Sea region were studied by analysis of microsatellites and polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) analysis...... the Baltic Sea. Instead, the data suggested a recent common origin of all Danish whitefish populations, including North Sea houting, probably by recolonization via the postglacial Elbe River system. Estimates of genetic differentiation among populations based on mtDNA and microsatellites were qualitatively...

  9. 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...

  10. 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.

  11. 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.

  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. 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.

  14. DNA copy-number alterations underlie gene expression differences between microsatellite stable and unstable colorectal cancers

    DEFF Research Database (Denmark)

    Jorissen, Robert N; Lipton, Lara; Gibbs, Peter

    2008-01-01

    Purpose: About 15% of colorectal cancers harbor microsatellite instability (MSI). MSI-associated gene expression changes have been identified in colorectal cancers, but little overlap exists between signatures hindering an assessment of overall consistency. Little is known about the causes...... and downstream effects of differential gene expression. Experimental Design: DNA microarray data on 89 MSI and 140 microsatellite-stable (MSS) colorectal cancers from this study and 58 MSI and 77 MSS cases from three published reports were randomly divided into test and training sets. MSI-associated gene...... expression changes were assessed for cross-study consistency using training samples and validated as MSI classifier using test samples. Differences in biological pathways were identified by functional category analysis. Causation of differential gene expression was investigated by comparison to DNA copy...

  15. DNA marker mining of ILSTS035 microsatellite locus on chromosome 6 of Hanwoo cattle

    Indian Academy of Sciences (India)

    Jung-Sou Yeo; Jea-Young Lee; Jae-Woo Kim

    2004-12-01

    We describe tests for detecting and locating quantitative trait loci (QTL) for traits in Hanwoo cattle. From results of a permutation test to detect QTL for marbling, we selected the microsatellite locus ILSTS035 on chromosome 6 for further analysis. -means clustering analysis applied to five traits and nine DNA markers in ILSTS035 resulted in three cluster groups. Finally we employed the bootstrap test method to calculate confidence intervals using the resampling method to find major DNA markers. We conclude that the major markers of ILSTS035 locus on chromosome 6 of Hanwoo cattle are markers 235 bp and 266 bp.

  16. DNA Slippage Occurs at Microsatellite Loci without Minimal Threshold Length in Humans: A Comparative Genomic Approach

    Science.gov (United States)

    Leclercq, Sébastien; Rivals, Eric; Jarne, Philippe

    2010-01-01

    The dynamics of microsatellite, or short tandem repeats (STRs), is well documented for long, polymorphic loci, but much less is known for shorter ones. For example, the issue of a minimum threshold length for DNA slippage remains contentious. Model-fitting methods have generally concluded that slippage only occurs over a threshold length of about eight nucleotides, in contradiction with some direct observations of tandem duplications at shorter repeated sites. Using a comparative analysis of the human and chimpanzee genomes, we examined the mutation patterns at microsatellite loci with lengths as short as one period plus one nucleotide. We found that the rates of tandem insertions and deletions at microsatellite loci strongly deviated from background rates in other parts of the human genome and followed an exponential increase with STR size. More importantly, we detected no lower threshold length for slippage. The rate of tandem duplications at unrepeated sites was higher than expected from random insertions, providing evidence for genome-wide action of indel slippage (an alternative mechanism generating tandem repeats). The rate of point mutations adjacent to STRs did not differ from that estimated elsewhere in the genome, except around dinucleotide loci. Our results suggest that the emergence of STR depends on DNA slippage, indel slippage, and point mutations. We also found that the dynamics of tandem insertions and deletions differed in both rates and size at which these mutations take place. We discuss these results in both evolutionary and mechanistic terms. PMID:20624737

  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. CTAB methods for DNA extraction of sweetpotato for microsatellite analysis Métodos CTAB de extração de DNA para a análise de microssatélites em batata-doce

    Directory of Open Access Journals (Sweden)

    Aline Borges

    2009-08-01

    Full Text Available Microsatellite markers have proved to be useful in genetic diversity assessments of sweetpotato (Ipomoea batatas but practical DNA extraction methods to ensure good quality and quantity DNA for these studies are yet to be established. This study compares the efficiency of three modified methodologies for DNA extraction of six sweetpotato landraces using the CTAB extraction buffer in regard to quantity and purity of DNA quantification and microsatellite band patterns. All methodologies yielded satisfactory results, but the method based in leaf tissue macerated in liquid nitrogen was deemed more adequate because of its simplicity and lower cost. However, the method based in dry leaf tissue was considered more advantageous, first because elicits practicability in the plant acquisition and drying process, especially when the collection is performed in situ, and also because its simplicity makes possible the cold storage of the dry, ground samples for future DNA extractions.Os marcadores microssatélites são úteis para a análise da diversidade genética de variedades tradicionais de batata-doce (Ipomoea batatas. Para estes estudos, métodos práticos de extração de DNA precisam ser estabelecidos para assegurar uma boa qualidade e quantidade de DNA extraído. Assim, foi comparada a eficiência de três metodologias para extração de DNA usando o tampão de extração CTAB, todas com modificações. Para verificar a quantidade e pureza na quantificação de DNA, bem como o padrão de bandas de microssatélites para as três metodologias utilizaram-se seis etnovariedades de batata-doce. Os testes mostraram que as três metodologias apresentaram resultados satisfatórios. Uma das metodologias baseada em tecido foliar macerado em nitrogênio líquido mostrou-se a mais adequada devido à simplicidade e menor custo. Entretanto, o método baseado em tecido foliar seco foi o mais vantajoso devido à praticidade na aquisição da planta e no processo de

  19. 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...

  20. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs

    OpenAIRE

    2010-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of t...

  1. Microsatellite DNA polymorphism in selectively controlled Apis mellifera carnica and Apis mellifera caucasica populations from Poland

    Directory of Open Access Journals (Sweden)

    Nikolova Stanimila R.

    2015-01-01

    Full Text Available Genetic polymorphism in selectively controlled honeybee populations of A. m. carnica and A. m. caucasica in Poland, was characterized by microsatellite DNA analysis. All honeybee samples were analyzed for nine microsatellite loci: Ac011; A024; A043; A088; Ap226; Ap238; Ap243; Ap249 and Ap256, which were found to be polymorphic in both populations. The mean number of alleles per locus was 6.222 for A. m. carnica and 4.556 for A. m. caucasica. Average observed and expected heterozygosity values were calculated as 0.976 and 0.734 in A. m. carnica and as 0.933 and 0.603 in A. m. caucasica, respectively. For the nine microsatellite loci, a total of 76 alleles were found in both populations. Thirty-five private alleles were observed in A. m. carnica and 20 in A. m. caucasica. Information about allele frequencies, FST values and genotypic differentiation is given. Nei’s genetic distance between studied populations of A. m. carnica and A. m. caucasica was calculated as 0.384.

  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. 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.

  4. SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

  5. 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.

  6. 大口黑鲈微卫星DNA指纹图谱的构建和遗传结构分析%ESTABLISHMENT OF DNA FINGERPRINTING AND ANALYSIS ON GENETIC STRUCTURE OF LARGEMOUTH BASS WITH MICROSATELLITE

    Institute of Scientific and Technical Information of China (English)

    樊佳佳; 白俊杰; 李胜杰; 任坤; 叶星

    2012-01-01

    以国内目前养殖的大口黑鲈[ Micropterus salmoides (Lacépède)]群体(CH)、2009年引进的佛罗里达亚种(FL-09)、2010年引进的佛罗里达亚种(FL-10)、2010年引进的北方亚种(NT-10)为实验材料,应用43个微卫星DNA标记对这4个大口黑鲈群体进行遗传检测,构建了各群体的微卫星DNA指纹图谱,并对其遗传结构进行分析.结果显示:CH、FL-09、FL-10和NT-10群体的平均等位基因数(A)分别为2.58、3.74、3.70和4.21,平均期望杂合度(He)分别为0.4549、0.4896、0.5010和0.6138,平均多态信息量(PIC)分别为0.3786、0.4443、0.4566和0.5546,表明国内目前养殖的大口黑鲈群体遗传多样性水平远远低于国外新引进的大口黑鲈群体.利用UPGMA法对4个群体进行聚类,结果FL-09和FL-10聚为一支,遗传距离为0.0506; NT-10和CH聚为另一支,遗传距离为0.4244,推测FL-09和FL-10两个佛罗里达亚种属于相同的群体,而NT-10和CH两个北方亚种来自不同的群体,甚至不同的水系.同时从指纹图谱中,筛选到5个特异的微卫星标记(JZL114、MiSaTPW11、Lma120、Mdo6和Msa121),可以鉴别FL、NT-10和CH群体,其中MiSaTPW11和Msa121这两个标记组合可以完全鉴别这3个群体.将5个特异性微卫星标记的图谱数据转化成计算机可以识别的数码指纹,可以方便应用于大口黑鲈不同群体及其杂交种的鉴定.研究结果可以为我国大口黑鲈种质资源保存、品种鉴定和良种选育提供理论依据.%DNA fingerprinting offers great potential in aquaculture and in fisheries as a tool for identification of individuals, construction of pedigrees and population genetic analysis. Microsatellites, also called simple sequence repeats (SSR), are widely dispersed along and among chromosomes, and each locus is characterized by a known DNA sequence. Due to a tendency for hypervariability and because only small amounts of tissue are required for typing, microsatellites have supplanted

  7. Microsatellite DNA typing for assessment of genetic variability in Marwari breed of Indian goat

    Directory of Open Access Journals (Sweden)

    Anoop Singh Yadav

    2015-07-01

    Full Text Available Aim: To estimate existing within-breed genetic variability in Marwari goats under field conditions and the generated data that can be used to determine genetic relationships with other breed of goats. Materials and Methods: A total of 146 blood samples of goats of Marwari breed were randomly collected from genetically unrelated animals from different villages of Bikaner Districts of Rajasthan, India. Genomic DNA was extracted from whole blood using proteinase K-digestion followed by standard phenol–chloroform extraction procedure at room temperature and confirmed through horizontal electrophoresis on 0.8% agarose gel containing ethidium bromide. Fifteen caprine microsatellite markers were used to estimate genetic variability among the goats of Marwari breed in terms of allelic and genotype frequencies, heterozygosities and polymorphism information content (PIC value. Results: A total of 74 alleles were contributed by Marwari goat across all 15 microsatellite loci. The number of alleles per locus varied from two (ILSTS-087 to 9 (ILSTS-058 alleles, with a mean of 4.93 whereas the effective number of allele varied from 1.35 (ILSTS-005 to 3.129 (ILSTS011 with a mean of 2.36. The effective number of allele is lesser than observed number at all the loci. Allelic sizes ranged from 125 bp (ILSTS-028 and ILSTS-033 to 650 bp (ILSTS-011 and ILSTS-019. The expected heterozygosity ranged from 0.240 (locus ILSTS-005 to 0.681 (locus ILSTS-011, with an average value of 0.544. The observed heterozygosity (Ho ranged from 0.1428 (locus ILSTS-087 to 0.9285 (locus ILSTS-034, with an average value of 0.5485 indicates substantial and very good number of heterozygotes, in the population. The highest PIC value (1.1886 was observed at ILSTS-044 locus and least (0.0768 at ILSTS-065 locus for Marwari goat. Conclusion: Microsatellite analysis revealed a high level of polymorphism across studied microsatellite markers and informativeness of the markers for genetic

  8. 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...

  9. Newborn genetic identification: a protocol using microsatellite DNA as an alternative to footprinting.

    Science.gov (United States)

    de Pancorbo, M M; Rodríguez-Alarcón, J; Castro, A; Fernández-Fernández, I; Melchor, J C; Linares, A; García-Orad, A; Fernández-Llebrez del Rey, L; Aranguren, G; Santillana, L

    1997-07-04

    Newborn identification by foot- or finger-printing presents serious drawbacks. This study proposes an alternative method based on DNA analysis of blood-spots taken from the newborn child. CSF1PO, TPOX and TH01 microsatellite loci were chosen to develop a fast and reliable protocol to be applied in cases where it is suspected that newborn children have been exchanged. The advantage of these loci is that one can simultaneously amplify them by PCR multiplex reaction and determine their alleles, thereby reducing the time needed for identification tests. Moreover, the amplification products of these loci are very small (< 350 bp) and so can be analyzed in samples with degraded DNA. We have been able to prove that it is possible to obtain results in blood-spots taken from newborns up to 13 years before and kept at room temperature. Thus the protocol proposed here can be applied in long-term post-natal identification cases.

  10. 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.

  11. Stocking impact and temporal stability of genetic composition in a brackish northern pike population ( Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Larsen, Peter Foged; Hansen, Michael Møller; Eg Nielsen, Einar;

    2005-01-01

    During the last decade, brackish northern pike populations in Denmark have been subject to stocking programmes, using nonindigenous pike from freshwater lakes, in order to compensate for drastic population declines. The present study was designed to investigate the genetic impact of stocking...... freshwater pike into a brackish pike population in Stege Nor, Denmark. We analysed polymorphism at eight microsatellite loci in samples representing the indigenous Stege Nor population prior to stocking (ie from 1956 to 1957), along with a sample of the contemporary Stege Nor population and samples from...

  12. Exome-wide somatic microsatellite variation is altered in cells with DNA repair deficiencies.

    Directory of Open Access Journals (Sweden)

    Zalman Vaksman

    Full Text Available Microsatellites (MST, tandem repeats of 1-6 nucleotide motifs, are mutational hot-spots with a bias for insertions and deletions (INDELs rather than single nucleotide polymorphisms (SNPs. The majority of MST instability studies are limited to a small number of loci, the Bethesda markers, which are only informative for a subset of colorectal cancers. In this paper we evaluate non-haplotype alleles present within next-gen sequencing data to evaluate somatic MST variation (SMV within DNA repair proficient and DNA repair defective cell lines. We confirm that alleles present within next-gen data that do not contribute to the haplotype can be reliably quantified and utilized to evaluate the SMV without requiring comparisons of matched samples. We observed that SMV patterns found in DNA repair proficient cell lines without DNA repair defects, MCF10A, HEK293 and PD20 RV:D2, had consistent patterns among samples. Further, we were able to confirm that changes in SMV patterns in cell lines lacking functional BRCA2, FANCD2 and mismatch repair were consistent with the different pathways perturbed. Using this new exome sequencing analysis approach we show that DNA instability can be identified in a sample and that patterns of instability vary depending on the impaired DNA repair mechanism, and that genes harboring minor alleles are strongly associated with cancer pathways. The MST Minor Allele Caller used for this study is available at https://github.com/zalmanv/MST_minor_allele_caller.

  13. 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.

  14. Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis.

    Science.gov (United States)

    Zhang, Futie; Tan, Deqing

    2010-01-01

    Largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry 1874), one of the endemic fish species in the upper reaches of the Yangtze River in China, is a benthic and potamodromous fish that is typically found in rivers with torrential flow. Three dams in the Yangtze River, Ertan Dam, Three Gorges Dam and Gezhouba Dam, may have had vital impacts on the habitat and spawning behaviors of largemouth bronze gudgeon, and could ultimately threaten the survival of this fish. We studied the population genetic diversity of C. guichenoti samples collected at seven sites (JH, GLP, BX, HJ, MD, SDP and XB) within the Yangtze River and one of its tributaries, the Yalong River. Genetic diversity patterns were determined by analyzing genetic data from 11 polymorphic microsatellite loci. A high genetic diversity among these largemouth bronze gudgeon populations was indicated by the number of microsatellite alleles (A) and the expected heterozygosity (HE). No significant population variation occurred among GLP, BX, HJ and MD populations, but dramatic population differentiation was observed among JH and XB, two dam-blocked populations, versus other populations. Tests for bottlenecks did not indicate recent dramatic population declines and concurrent losses of genetic diversity in any largemouth bronze gudgeon populations. To the contrary, we found that dams accelerated the population differentiation of this fish.

  15. 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...

  16. Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos genome and cross-amplification in other birds

    Directory of Open Access Journals (Sweden)

    Xu Ke

    2005-07-01

    Full Text Available Abstract In order to study duck microsatellites, we constructed a library enriched for (CAn, (CAGn, (GCCn and (TTTCn. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97 was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04 at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%. The polymorphism information content (PIC of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose.

  17. 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...

  18. Genetic divergence in popcorn genotypes using microsatellites in bulk genomic DNA

    Directory of Open Access Journals (Sweden)

    Tereza Aparecida da Silva

    2009-01-01

    Full Text Available The genetic diversity of 25 popcorn genotypes was estimated based on DNA bulks from 78 plants of eachvariety. The procedure involved 23 microsatellite loci distributed on 9 maize chromosomes. Clustering analysis according tothe Tocher method and the hierarchical clustering procedures (nearest neighbor, furthest neighbor and Unweighted Pair-Group Method Using Arithmetic Averages - UPGMA were performed. The cophenetic correlation coefficients indicated theUPGMA method as adequate to distinguish the varieties. The clusters suggested by the molecular analysis generally groupedgenotypes with the same genealogy together. The genetic dissimilarity of the varieties Argentina, Chile, PA-091 and PR-023was higher than of the others. Therefore, higher heterozygosity is expected in progenies from crosses with the other genotypes.

  19. 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.

  20. Paternity testing using microsatellite DNA markers in captive Adélie penguins (Pygoscelis adeliae).

    Science.gov (United States)

    Sakaoka, Ken; Suzuki, Isao; Kasugai, Naeko; Fukumoto, Yohei

    2014-01-01

    We investigated the paternity of 39 Adélie penguins (Pygoscelis adeliae) hatched at the Port of Nagoya Public Aquarium between 1995 and 2005 breeding seasons using microsatellite DNA markers. Among the 13 microsatellite marker loci tested in this study, eight markers amplified and were found to be polymorphic in the colony's founders of the captive population (n = 26). Multiple marker analysis confirmed that all the hatchlings shared alleles with their social fathers and that none of them were sired by any male (all males ≥4 years old in the exhibit tank during each reproductive season; n = 9-15) other than the one carrying out parental duties, except in the case of two inbred hatchlings whose half-sibling parents shared the same father. These results demonstrated that extra-pair paternity (EPP) did not occur in this captive population and that even if EPP has been detected among them, the probability of excluding all other possible fathers in the exhibit tank is extremely high based on paternity exclusion probabilities across the investigated loci. The paternity exclusion probabilities were almost the same between 1994 and 2005. The probability of identity across the investigated loci declined between the two time points, but was still high. These results are reflected in a very short history of breeding in this captive population. In other words, the parentage analyses using a suite of microsatellite markers will be less effective as generations change in small closed populations, such as zoo and aquarium populations. © 2014 Wiley Periodicals, Inc.

  1. Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region.

    Science.gov (United States)

    Liao, Yuying; Mo, Guodong; Sun, Junli; Wei, Fengying; Liao, Dezhong Joshua

    2016-05-01

    The domestic chicken (Gallus gallus domesticus) is an excellent model for genetic studies of phenotypic diversity. The Guangxi Region of China possesses several native chicken breeds displaying a broad range of phenotypes well adapted to the extreme hot-and-wet environments in the region. We thus evaluated the genetic diversity and relationships among six native chicken populations of the Guangxi region and also evaluated two commercial breeds (Arbor Acres and Roman chickens). We analyzed the sequences of the D-loop region of the mitochondrial DNA (mtDNA) and 18 microsatellite loci of 280 blood samples from six Guangxi native chicken breeds and from Arbor Acres and Roman chickens, and used the neighbor-joining method to construct the phylogenetic tree of these eight breeds. Our results showed that the genetic diversity of Guangxi native breeds was relatively rich. The phylogenetic tree using the unweighed pair-group method with arithmetic means (UPGAM) on microsatellite marks revealed two main clusters. Arbor Acres chicken and Roman chicken were in one cluster, while the Guangxi breeds were in the other cluster. Moreover, the UPGAM tree of Guangxi native breeds based on microsatellite loci was more consistent with the genesis, breeding history, differentiation and location than the mtDNA D-loop region. STRUCTURE analysis further confirmed the genetic structure of Guangxi native breeds in the Neighbor-Net dendrogram. The nomenclature of mtDNA sequence polymorphisms suggests that the Guangxi native chickens are distributed across four clades, but most of them are clustered in two main clades (B and E), with the other haplotypes within the clades A and C. The Guangxi native breeds revealed abundant genetic diversity not only on microsatellite loci but also on mtDNA D-loop region, and contained multiple maternal lineages, including one from China and another from Europe or the Middle East.

  2. 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...

  3. Genetic variation of Anastrepha suspensa (Diptera: Tephritidae) in Florida and the Caribbean using microsatellite DNA markers.

    Science.gov (United States)

    Boykin, Laura M; Shatters, Robert G; Hall, David G; Dean, David; Beerli, Peter

    2010-12-01

    Anastrepha suspensa (Loew) (Diptera: Tephritidae), the Caribbean fruit fly, is indigenous to Florida and the Greater Antilles where it causes economic losses in fruit crops, including citrus. Because of the geographic separation of many of its native locations and anecdotal descriptions of regional differences in host preferences, there have been questions about the population structure of A. suspensa. Seven DNA microsatellite markers were used to characterize the population genetic structure of A. suspensa, in Florida and the Caribbean from a variety of hosts, including citrus. We genotyped 729 A. suspensa individuals from Florida, Puerto Rico, Cayman Island, Dominican Republic, and Jamaica. The investigated seven loci displayed from 5 to 19 alleles, with expected heterozygosities ranging from 0.05 to 0.83. There were five unique alleles in Florida and three unique alleles in the Caribbean samples; however, no microsatellite alleles were specific to a single host plant. Genetic diversity was analyzed using F(ST) and analysis of molecular variance and revealed low genetic diversity between Florida and Caribbean samples and also between citrus and noncitrus samples. Analyses using migrate revealed there is continuous gene flow between sampling sites in Florida and the Caribbean and among different hosts. These results support previous comparisons based on the mitochondrial cytochrome oxidase I locus indicating there is no genetic differentiation among locations in Florida and the Caribbean and that there is no separation into host races.

  4. Population Structure of the Raccoon Dog on the Grounds of the Imperial Palace, Tokyo, Revealed by Microsatellite Analysis of Fecal DNA.

    Science.gov (United States)

    Saito, Wataru; Amaike, Yosuke; Sako, Takako; Kaneko, Yayoi; Masuda, Ryuichi

    2016-10-01

    The raccoon dog (Nyctereutes procyonoides, Canidae, Carnivora) is highly adaptable to urban environments. Populations of carnivorans inhabiting urban areas sometimes differ ecologically and genetically from those in rural areas. However, there is little information on urban raccoon dogs. This study focused on raccoon dog populations in Tokyo, one of the most highly urbanized cities in the world. We examined the genotypes of 10 microsatellites for 101 fecal samples from raccoon dogs inhabiting the grounds of the Imperial Palace, a green space in central Tokyo. We successfully genotyped 58 samples originating from 31 individuals. We also analyzed muscle tissue samples from raccoon dogs from the grounds of the Imperial Palace, the Akasaka Imperial Grounds (a green space close to the Imperial Palace), and the surrounding urban area, and then investigated the genetic structure and diversity of these populations, and the genetic differentiation among them. The population on the grounds of the Imperial Palace was genetically differentiated from that in the Akasaka Imperial Grounds, suggesting that the roads and buildings act as barriers to gene flow. In addition, the population on the grounds of the Imperial Palace showed greater genetic difference from that in the surrounding area than that in the Akasaka Imperial Grounds. We speculate that the moats around the Imperial Palace restrict individual ranges within the palace grounds and limit migration and gene flow to other areas.

  5. 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.

  6. 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.

  7. 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.

  8. Genetic differentiation in pointing dog breeds inferred from microsatellites and mitochondrial DNA sequence.

    Science.gov (United States)

    Parra, D; Méndez, S; Cañón, J; Dunner, S

    2008-02-01

    Recent studies presenting genetic analysis of dog breeds do not focus specifically on genetic relationships among pointing dog breeds, although hunting was among the first traits of interest when dogs were domesticated. This report compares histories with genetic relationships among five modern breeds of pointing dogs (English Setter, English Pointer, Epagneul Breton, Deutsch Drahthaar and German Shorthaired Pointer) collected in Spain using mitochondrial, autosomal and Y-chromosome information. We identified 236 alleles in autosomal microsatellites, four Y-chromosome haplotypes and 18 mitochondrial haplotypes. Average F(ST) values were 11.2, 14.4 and 13.1 for autosomal, Y-chromosome microsatellite markers and mtDNA sequence respectively, reflecting relatively high genetic differentiation among breeds. The high gene diversity observed in the pointing breeds (61.7-68.2) suggests contributions from genetically different individuals, but that these individuals originated from the same ancestors. The modern English Setter, thought to have arisen from the Old Spanish Pointer, was the first breed to cluster independently when using autosomal markers and seems to share a common maternal origin with the English Pointer and German Shorthaired Pointer, either via common domestic breed females in the British Isles or through the Old Spanish Pointer females taken to the British Isles in the 14th and 16th centuries. Analysis of mitochondrial DNA sequence indicates the isolation of the Epagneul Breton, which has been formally documented, and shows Deutsch Drahthaar as the result of crossing the German Shorthaired Pointer with other breeds. Our molecular data are consistent with historical documents.

  9. Characteristic Analysis of Microsatellite DNA in the Genome of Gobiidae%虾虎鱼科(Gobiidae)基因组微卫星 DNA 的分布特征

    Institute of Scientific and Technical Information of China (English)

    白翠翠; 柳淑芳; 庄志猛

    2016-01-01

    The family Gobiidae is one of the largest fish families consisting of more than 200 genera and 2000 species. This family was found in near shore seawater, brackish water, and freshwater in the temperate and tropical areas all over the world. In this study we applied microsatellite DNA (short sequence repeat, SSR) to characterize the genetic structure of Gobiidae. We analyzed 153 SSR sequences amplified in our laboratory and 535 SSR sequences downloaded and screened from GenBank. The 686 sequences originated from 19 different species of Gobiidae. The total length of these sequences was about 295062 bp, in which 473 microsatellite repeat loci were found by using the bio-software Tandem Repeats Finder. The length of the repeat sequences was 33370 bp. We found that 361 dinucleotide repeat sequences accounted for the majority (76.32%) of the 473 repeat loci. Moreover, the AC repeat sequences were the most common (94.18) in the dinucleotide repeat sequences, whereas AT and GC repeat sequences were not observed. The number of the trinucleotide repeat sequences was 35 (7.4%), including 12 ACT repeat sequences that were the majority (34.29%). There were 68 tetranuleotide repeat sequences including 31 CTAT that was the dominant (14.38%). The numbers of both petranucleotide and hexanucleotide repeat sequences were 2 (0.42%) and 7 (1.48%) respectively. Intriguingly repeats of single nucleotide sequences were absent. Our results about the distribution of microsatellite contributed to a better understanding of the genomic structure of goby fish, and might provide important information for the development and application of goby fish microsatellite markers.%为了解虾虎鱼科(Gobiidae)鱼类基因组遗传结构特征,本研究自主开发矛尾复虾虎鱼(Synechogobius hasta)微卫星序列153条,结合从 GenBank 中筛选出的虾虎鱼科微卫星序列535条,合计686条微卫星序列,隶属于19种虾虎鱼,序列总长度为295062 bp,包含473个微卫星

  10. 利用微卫星DNA标记分析贵州3个地方猪种的遗传多样性%Genetic Diversity Analysis of Three Guizhou Local Pig Breeds Using Microsatellite DNA Markers

    Institute of Scientific and Technical Information of China (English)

    郭宏宇; 林家栋

    2009-01-01

    [Objective] The research aimed to provide the genetic basis for the protection, development and utilization of Guizhou local pig breeds. [Method] From 27 pairs of porcine microsatellite primers recommended by Food and Agriculture Organization of the United Nations (FAO) and International Society for Animal Genetics (ISAG), six pairs (S0155, SW240, IGF1, SW951, SW857, SW24) were selected for microsatellite DNA detection of three Guizhou local pig breeds, including Nuogu Pig, Kele Pig and Guanling Pig. Subsequently, their genetic diversities were analyzed. [Result] The three pig breeds were high polymorphic at the six microsatellite loci (PIC>0.5). The Neis standard genetic distance of them was 0.206 3-0.481 5. The genetic distance between Nuogu Pig and Kele Pig was the closest, and that between Nuogu Pig and Guanling Pig was the furthest. [Conclusion] The three Guizhou local pig breeds are in high genetic diversities. Nuogu Pig is a special type of Kele Pig, an excellent Chinese local pig breed.

  11. [Mutation in microsatellite repeats of DNA and embryonal death in humans].

    Science.gov (United States)

    Nikitina, T V; Nazarenko, S A

    2000-07-01

    In the analysis of tetranucleotide DNA repeats inheritance carried out in 55 families with a history of spontaneous miscarriages and normal karyotypes in respect to 21 loci located on seven autosomes, 8 embryos (14.5%) demonstrating 12 cases of the presence of alleles absent in both parents were described. The study of chromosome segregation using other DNA markers permitted highly probable exclusion of false paternity as well as uniparental disomy as the reasons for parent/child allele mismatches. The high probability of paternity together with the presence of a "new" allele at any offspring locus points to the mutation having occurred during game-togenesis in one of the parents. Examination of mutation in spontaneous abortuses revealed an increased number of tandem repeat units at microsatellite loci in three cases and an decreased number of these repeats in six cases. In two abortuses, a third allele absent in both parents, which resulted from a somatic mutation that occurred during embryonic development, was observed. The prevalence of the male germline mutations, revealed during investigation of the mutation origin, was probably associated with an increased number of DNA replication cycles in sperm compared to the oocytes. In spontaneous abortuses, the mean mutation rate of the tetranucleotide repeat complexes analyzed was 9.8 x 10(-3) per locus per gamete per generation. This was about five times higher than the spontaneous mutation rate of these STR loci. It can be suggested that genome instability detected at the level of repeated DNA sequences can involve not only genetically neutral loci but also active genomic regions crucial for embryonic viability. This results in cell death and termination of embryonic development. Our findings indicate that the death of embryos with normal karyotypes in most cases is associated with an increased frequency of germline and somatic microsatellite mutations. The data of the present study also provide a practical tool for

  12. 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.

  13. Are we narrowing genetic variability in seed orchards? An attempt to answer, based on the analysis of microsatellite DNA of grafts growing in Scots pine (Pinus sylvestris L. seed orchard in the Forest District Susz

    Directory of Open Access Journals (Sweden)

    Przybylski Paweł

    2015-09-01

    Full Text Available Scots pine (Pinus sylvestris L. is the most common species in Poland’s forest stands. The mode of pine stands renovation requires that silviculture practitioners have continuous access to seed banks. Orchard-grown seeds are predicted to constitute an increasingly larger part of the average demand for pine seeds in Poland. Seed orchards, due to a limited number of maternal trees as well as the irregularity of their blooming and pollination, enhance the risk of genetic diversity reduction in planted forest stands. This is of particular importance in the context of dynamic climate change. Markers based on microsatellite DNA fragments are effective tools for monitoring genetic variability. In the present study, three different microsatellite DNA fragments were used: SPAC 12.5, SPAG 7.14 and SPAC 11.4. The main objective of this research was to study genetic variability in one of the biggest seed orchards in Poland, located in the Forest District Susz. The obtained results indicated heterozygosity loss within the orchard, proving the existence of specimen selection effects on genetic variability. Hence, it seems quite important to take account of molecular genetic variability of maternal trees in future breeding strategies.

  14. Genetic Divergence in Domestic Japanese Quail Inferred from Mitochondrial DNA D-Loop and Microsatellite Markers

    Science.gov (United States)

    Nakano, Mikiharu; Tadano, Ryo; Kawahara-Miki, Ryoka; Kono, Tomohiro; Takahashi, Shinji; Kawashima, Takaharu; Fujiwara, Akira; Nirasawa, Keijiro; Mizutani, Makoto; Matsuda, Yoichi

    2017-01-01

    To assess the genetic diversity of domestic Japanese quail (Coturnix japonica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources—the pre-war and post-war populations—which is well supported by their breeding histories. PMID

  15. STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.

    Science.gov (United States)

    Kraemer, Lars; Beszteri, Bánk; Gäbler-Schwarz, Steffi; Held, Christoph; Leese, Florian; Mayer, Christoph; Pöhlmann, Kevin; Frickenhaus, Stephan

    2009-01-30

    Microsatellites (MSs) are DNA markers with high analytical power, which are widely used in population genetics, genetic mapping, and forensic studies. Currently available software solutions for high-throughput MS design (i) have shortcomings in detecting and distinguishing imperfect and perfect MSs, (ii) lack often necessary interactive design steps, and (iii) do not allow for the development of primers for multiplex amplifications. We present a set of new tools implemented as extensions to the STADEN package, which provides the backbone functionality for flexible sequence analysis workflows. The possibility to assemble overlapping reads into unique contigs (provided by the base functionality of the STADEN package) is important to avoid developing redundant markers, a feature missing from most other similar tools. Our extensions to the STADEN package provide the following functionality to facilitate microsatellite (and also minisatellite) marker design: The new modules (i) integrate the state-of-the-art tandem repeat detection and analysis software PHOBOS into workflows, (ii) provide two separate repeat detection steps - with different search criteria - one for masking repetitive regions during assembly of sequencing reads and the other for designing repeat-flanking primers for MS candidate loci, (iii) incorporate the widely used primer design program PRIMER3 into STADEN workflows, enabling the interactive design and visualization of flanking primers for microsatellites, and (iv) provide the functionality to find optimal locus- and primer pair combinations for multiplex primer design. Furthermore, our extensions include a module for storing analysis results in an SQLite database, providing a transparent solution for data access from within as well as from outside of the STADEN Package. The STADEN package is enhanced by our modules into a highly flexible, high-throughput, interactive tool for conventional and multiplex microsatellite marker design. It gives the user

  16. Chloroplast and microsatellite DNA diversities reveal the introduction history of Brazilian peppertree (Schinus terebinthifolius) in Florida.

    Science.gov (United States)

    Williams, Dean A; Overholt, William A; Cuda, James P; Hughes, Colin R

    2005-10-01

    Brazilian peppertree (Schinus terebinthifolius) is a woody perennial that has invaded much of Florida. This native of northeastern Argentina, Paraguay, and Brazil was brought as an ornamental to both the west and east coasts of Florida at the end of the 19th century. It was recorded as an invader of natural areas in the 1950s, and has since extended its range to cover over 280 000 ha. Our goals were to understand the history of this invasion, as one step toward understanding why this exotic was so successful, and ultimately to improve development of biological control agents. We sampled plants from the native and exotic ranges, particularly Florida, and genotyped these individuals at nuclear and chloroplast loci. Nuclear microsatellite and cpDNA loci reveal strong genetic population structure consistent with limited dispersal in the introduced and native ranges. Bayesian clustering of microsatellite data separates the east and west coast plants in Florida into distinct populations. The two chloroplast haplotypes found in Florida are also concordant with this separation: one predominates on the east coast, the other on the west coast. Analysis of samples collected in South America shows that haplotypes as distinct as the two in Florida are unlikely to have come from a single source population. We conclude that the genetic evidence supports two introductions of Brazilian peppertree into Florida and extensive hybridization between them. The west coast genotype likely came from coastal Brazil at about 27 degrees south, whereas the east coast genotype probably originated from another, as yet unidentified site. As a result of hybridization, the Florida population does not exhibit low genetic variation compared to populations in the native range, possibly increasing its ability to adapt to novel environments. Hybridization also has important consequences for the selection of biocontrol agents since it will not be possible to identify closely co-adapted natural enemies in

  17. 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.

  18. MITOCHONDRIAL AND MICROSATELLITE DNA ANALYSES OF AUSTROPOTAMOBIUS PALLIPES POPULATIONS IN SOUTH TYROL (ITALY AND TYROL (AUSTRIA

    Directory of Open Access Journals (Sweden)

    BARIC S.

    2005-07-01

    Full Text Available Historical data show that the native white-clawed crayfish, Austropotamobius pallipes, was once widespread throughout South Tyrol (northern Italy, whereas recent studies identified only half a dozen remaining populations. In order to implement conservation strategies based on knowledge of genetic diversity, each of the six remaining populations in South Tyrol and one population in Tyrol (Austria were investigated by (i sequencing segments of two mitochondrial DNA genes, 16S rRNA and cytochrome c oxidase subunit I, and (ii by analysing four microsatellite DNA loci. Extremely low degrees of genetic differentiation within and among the South Tyrolean populations of A. pallipes were found with mitochondrial DNA sequences. In contrast, microsatellite data displayed not only substantial genetic structure among populations, but also moderate genetic variability within four out of six populations in South Tyrol. The two remaining populations revealed a complete absence of genetic variability. Moreover, both of these populations as well as the population from Austria were fixed for single alleles at three of the four investigated microsatellite loci. Our data have important conservation implications and also show that mitochondrial DNA is not always a sufficient tool to study crayfish populations on a small geographical scale.

  19. Estimating the long-term effects of stocking domesticated trout into wild brown trout ( Salmo trutta ) populations : an approach using microsatellite DNA analysis of historical and contemporary samples

    DEFF Research Database (Denmark)

    Hansen, Michael Møller

    2002-01-01

    . The study was based on analysis of two historical samples (194556), represented by old scale collections, and seven contemporary samples (1986-2000). In one population historical and contemporary samples were remarkably genetically similar despite more than a decade of intense stocking. Estimation...... equal survival and reproductive performance of wild and domesticated trout. This demonstrates poor performance and low fitness of domesticated trout in the wild. In another population there was a strong genetic contribution from domesticated trout (between 57% and 88% in different samples), both...... in samples from a broodstock thought to represent the indigenous population and in a sample of wild spawners. Survival of domesticated trout and admixture with indigenous fish in the broodstock and subsequent stocking into the river, combined with a low population size of native trout relative to the number...

  20. Characterization of 14 microsatellite DNA markers for the tropical forest tree Virola surinamensis (Rol.) Warb. (Myristicaceae).

    Science.gov (United States)

    Draheim, Hope; Cui, Melissa; Dick, Christopher W

    2009-09-01

    Fourteen microsatellite DNA markers were developed for studies of gene flow in the Neotropical rain forest tree Virola surinamensis. The loci were unlinked and polymorphic in a sample of 21 individuals, with two to 10 alleles per locus and observed heterozygosity ranging from 0.14 to 0.76. The overall exclusion probability (0.997) indicates high resolution for parentage-based analyses of gene flow.

  1. Genetic Diversity and Population Structure for the Conservation of Giant Spiny Frog (Quasipaa spinosa) Using Microsatellite Loci and Mitochondrial DNA

    Institute of Scientific and Technical Information of China (English)

    Danna YU; Rongquan ZHENG; Qinfang LU; Guang YANG; Yao FU; Yun ZHANG

    2016-01-01

    The giant spiny frog (Quasipaa spinosa) is an endangered species with a relatively small distribution limited to southern China and Northern Vietnam. This species is becoming increasingly threatened because of over-exploitation and habitat degradation. This study provides data on the genetic diversity and population genetic structure of the giant spiny frog to facilitate the further development of effective conservation recommendations for this economically important but threatened species. We examined 10 species-specific microsatellite loci and Cyt b genes (562 bp) collected from 13 wild populations across the entire range of this species. Results of 10 microsatellite loci analysis showed a generally high level of genetic diversity. Moreover, the genetic differentiation among all 12 populations was moderate to large (overall FST= 0.1057). A total of 51 haplotypes were identified for Cyt b, which suggests high haplotype nucleotide diversities. Phylogeographic and population structure analyses using both DNA markers suggested that the wild giant spiny frog can be divided into four distinct major clades, i.e., Northern Vietnam, Western China, Central China, and Eastern China. The clades with significant genetic divergence are reproductively isolated, as evidenced by a high number of private alleles and strong incidence of failed amplification in microsatellite loci. Our research, coupled with other studies, suggests that Q. spinosa might be a species complex within which no detectable morphological variation has been revealed. The four phylogenetic clades and some subclades with distinct geographical distribution should be regarded as independent management units for conservation purposes.

  2. Effective DNA fragmentation technique for simple sequence repeat detection with a microsatellite-enriched library and high-throughput sequencing.

    Science.gov (United States)

    Tanaka, Keisuke; Ohtake, Rumi; Yoshida, Saki; Shinohara, Takashi

    2017-04-01

    Two different techniques for genomic DNA fragmentation before microsatellite-enriched library construction-restriction enzyme (NlaIII and MseI) digestion and sonication-were compared to examine their effects on simple sequence repeat (SSR) detection using high-throughput sequencing. Tens of thousands of SSR regions from 5 species of the plant family Myrtaceae were detected when the output of individual samples was >1 million paired-end reads. Comparison of the two DNA fragmentation techniques showed that restriction enzyme digestion was superior to sonication for identification of heterozygous genotypes, whereas sonication was superior for detection of various SSR flanking regions with both species-specific and common characteristics. Therefore, choosing the most suitable DNA fragmentation method depends on the type of analysis that is planned.

  3. Intraspecific polymorphism of microsatellite DNA of russian sturgeon (Acipenser gueldenstaedtii, Brandt

    Directory of Open Access Journals (Sweden)

    O. Malysheva

    2016-12-01

    Full Text Available Purpose. Determination of the peculiarities of intraspecific genetic polymorphism of Russian sturgeon based on microsatellite DNA markers. Methodology. The polymerase chain reaction (PCR with the detection of results based on capillary electrophoresis was used for the determination of intraspecific polymorphism of microsatellite DNA Russian sturgeon. Findings. On microsatellite DNA markers was investigated genetic polymorphism of Russian sturgeon (Acipenser gueldenstaedtii Brandt Black Sea and Dnieper population. It was identified of 56 allelic variants of such DNA-markers investigated as LS-19, LS-68, LS-39, Aox-27, LS-54 and Aox-45. On locus LS-19 allelic variants have been identified, the locus LS-68 was the most polymorphic and consisted of 21 alleles, 11 allelic variants have been identified by the LS-39 locus, and 16 allelic variants have been identified for the LS-54 locus. Aox-27 locus was the least polymorphic microsatellite markers among the study and consisted of 7 allelic variants. For Aox-45 locus 16 allelic variants have been identified. A study of the genetic structure of the Russian Black Sea-Dnieper sturgeon population is not currently been carried out in full and reduced only to the evaluation of the number of identified allelic variants and relative frequency of alleles. Calculations of heterozygosity parameters for Russian sturgeon became complicated definition tetraploid genetic structure of this species on the studied DNA markers. Such studies are an important component in the further work on the conservation of genetic diversity of sturgeon, which will provide an opportunity to carry out the state control over reproduction and preservation of valuable and endangered species under increased anthropogenic impact on natural populations. Originality. For the first time, new data of the peculiarities of the intraspecific genetic polymorphism of Russian sturgeon was obtained using species-specific microsatellite DNA markers

  4. Detection of coding microsatellite frameshift mutations in DNA mismatch repair-deficient mouse intestinal tumors.

    Science.gov (United States)

    Woerner, Stefan M; Tosti, Elena; Yuan, Yan P; Kloor, Matthias; Bork, Peer; Edelmann, Winfried; Gebert, Johannes

    2015-11-01

    Different DNA mismatch repair (MMR)-deficient mouse strains have been developed as models for the inherited cancer predisposing Lynch syndrome. It is completely unresolved, whether coding mononucleotide repeat (cMNR) gene mutations in these mice can contribute to intestinal tumorigenesis and whether MMR-deficient mice are a suitable molecular model of human microsatellite instability (MSI)-associated intestinal tumorigenesis. A proof-of-principle study was performed to identify mouse cMNR-harboring genes affected by insertion/deletion mutations in MSI murine intestinal tumors. Bioinformatic algorithms were developed to establish a database of mouse cMNR-harboring genes. A panel of five mouse noncoding mononucleotide markers was used for MSI classification of intestinal matched normal/tumor tissues from MMR-deficient (Mlh1(-/-) , Msh2(-/-) , Msh2(LoxP/LoxP) ) mice. cMNR frameshift mutations of candidate genes were determined by DNA fragment analysis. Murine MSI intestinal tumors but not normal tissues from MMR-deficient mice showed cMNR frameshift mutations in six candidate genes (Elavl3, Tmem107, Glis2, Sdccag1, Senp6, Rfc3). cMNRs of mouse Rfc3 and Elavl3 are conserved in type and length in their human orthologs that are known to be mutated in human MSI colorectal, endometrial and gastric cancer. We provide evidence for the utility of a mononucleotide marker panel for detection of MSI in murine tumors, the existence of cMNR instability in MSI murine tumors, the utility of mouse subspecies DNA for identification of polymorphic repeats, and repeat conservation among some orthologous human/mouse genes, two of them showing instability in human and mouse MSI intestinal tumors. MMR-deficient mice hence are a useful molecular model system for analyzing MSI intestinal carcinogenesis.

  5. Polymorphic microsatellite DNA markers for the Florida manatee (Trichechus manatus latirostris)

    Science.gov (United States)

    Pause, K.C.; Nourisson, C.; Clark, A.; Kellogg, M.E.; Bonde, R.K.; McGuire, P.M.

    2007-01-01

    Florida manatees (Trichechus manatus latirostris) are marine mammals that inhabit the coastal waters and rivers of the southeastern USA, primarily Florida. Previous studies have shown that Florida manatees have low mitochondrial DNA variability, suggesting that nuclear DNA loci are necessary for discriminatory analyses. Here we report 10 polymorphic microsatellite loci with an average of 4.2 alleles per locus, and average heterozygosity of 50.1%. These loci have been developed for use in population studies, parentage assignment, and individual identification. ?? 2007 Blackwell Publishing Ltd.

  6. Estimating black bear population density and genetic diversity at Tensas River, Louisiana using microsatellite DNA markers

    Science.gov (United States)

    Boersen, Mark R.; Clark, Joseph D.; King, Tim L.

    2003-01-01

    The Recovery Plan for the federally threatened Louisiana black bear (Ursus americanus luteolus) mandates that remnant populations be estimated and monitored. In 1999 we obtained genetic material with barbed-wire hair traps to estimate bear population size and genetic diversity at the 329-km2 Tensas River Tract, Louisiana. We constructed and monitored 122 hair traps, which produced 1,939 hair samples. Of those, we randomly selected 116 subsamples for genetic analysis and used up to 12 microsatellite DNA markers to obtain multilocus genotypes for 58 individuals. We used Program CAPTURE to compute estimates of population size using multiple mark-recapture models. The area of study was almost entirely circumscribed by agricultural land, thus the population was geographically closed. Also, study-area boundaries were biologically discreet, enabling us to accurately estimate population density. Using model Chao Mh to account for possible effects of individual heterogeneity in capture probabilities, we estimated the population size to be 119 (SE=29.4) bears, or 0.36 bears/km2. We were forced to examine a substantial number of loci to differentiate between some individuals because of low genetic variation. Despite the probable introduction of genes from Minnesota bears in the 1960s, the isolated population at Tensas exhibited characteristics consistent with inbreeding and genetic drift. Consequently, the effective population size at Tensas may be as few as 32, which warrants continued monitoring or possibly genetic augmentation.

  7. Microsatellite data analysis for population genetics

    Science.gov (United States)

    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 ...

  8. [Analysis of genetic variations in different goose breeds using microsatellite markers].

    Science.gov (United States)

    Liu, Shuang; Li, Peng; Song, Yi; Li, Shi-Ze; Wei, Chun-Bo; Yang, Huan-Min

    2006-11-01

    The genetic diversity of six goose breeds (White Goose, Zi Goose, Huoyan Goose, Wanxi Goose, Rhin, Landoise) was analyzed using microsatellite markers. Heterozygosity(H), polymorphism information content (PIC) and genetic distances were calculated for each breed based on the allele frequency. Results showed that 7 microsatellite sites were highly polymorphic, and could be used as effective markers for analysis of genetic relationship among different goose breeds. The mean heterozygosityies of were between 0.6617 (Rhin) and 0.8814 (Zi goose), among six goose breeds, the lowest was Rhin goose (0.6617) and the highest was Zi goose (0.8814). The range of mean PIC was between 0.6145 and 0.7814, which was in the similar range as the mean heterozygosities. Based on the UPGMA cluster analysis results, six goose breeds were grouped into classes, White, Zi, Huoyan and Wanxi Goose in one class, and the foreign breeds of Rhin and Landoise goose in another class. These results indicated that the dendrogram obtain from genetic distance could be used to correctly reflect the phylogenetic relationship among the six goose breeds, suggesting that microsatellite DNA marker is a useful tool to determine the genetic diversity in closely related breeds.

  9. Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

    Science.gov (United States)

    Gladden; Ferguson; Friesen; Clayton

    1999-03-01

    Beluga whales (Delphinapterus leucas) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples (n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.

  10. THE GENETIC STRUCTURE OF FOUR POPULATIONS OF OREOCHROMIS AUREUS BY MICROSATELLITE DNA ANALYSIS%四个奥利亚罗非鱼群体的微卫星分析

    Institute of Scientific and Technical Information of China (English)

    张庭; 卢迈新; 叶星; 全迎春; 高风英; 黄樟翰; 白俊杰

    2009-01-01

    Genetic diversity and phylogenetic relationships among four breed varieties of Oreochromis aureus (83), O. au-reus (02) , O. aureus (05) and red O. aureus were studied using microsatellite analysis technology. 19 pairs of microsatel-lite DNA primers of Oreochromis niloticu registered in GenBank which were selected and proved to amplify successfully on Oreochromis aureus by pre-experiment were used. The PCR reaction condition especially concentration of Mg2+ and annealing temperature were adjusted for each pair of primers. Amplified PCR products were electrophoresed in PAGE and stained according to the silver stain procedures and then imagined by Alphalmager. A total of 82 alleles were obtained from the four populations. The number of alleles for each locus ranged from 2-8, and the average alleles was 4.3 each locus, Average observed heterozygosity and average expected heterozygosity were calculated by POPGENE3.2 software. The results showed that the observed value of average heterozy-gosity of the four O. aureus populations ranged from 0.154 to 0.391. The expected value of average heterozygosity ranged from 0.181 to 0.428, and the average polymorphism information contents ranged from 0.1513 to 0.3882, respectively. The lowest genetic diversity level was found in the O. aureus (02). The highest genetic similarity index (0.9422) and the lowest genetic distance (0.0596) were found between O. aureus (05) and O. aureus (83), which indicated a closer phy-logenetic relationship between these two populations. On the other hand, the lowest genetic similarity index (0.6977) and the highest genetic distance (0.3599) existed between O. aureus (83) and red O. aureus, which suggested a farthest phy-logenetic relationship between these two populations. The evaluation results of the genetic deviation index D revealed that there were loci departed from Hardy-Weinberg equilibrium in all the four O. aureus populations. Results of null allele anal-ysis by MicroChecker showed that

  11. Genetic Diversity and Population Structure of the Critically Endangered Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis as Revealed by Mitochondrial and Microsatellite DNA

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    Minmin Chen

    2014-06-01

    Full Text Available Ecological surveys have indicated that the population of the critically endangered Yangtze finless porpoise (YFP, Neophocaena asiaeorientalis asiaeorientalis is becoming increasingly small and fragmented, and will be at high risk of extinction in the near future. Genetic conservation of this population will be an important component of the long-term conservation effort. We used a 597 base pair mitochondrial DNA (mtDNA control region and 11 microsatellite loci to analyze the genetic diversity and population structure of the YFP. The analysis of both mtDNA and microsatellite loci suggested that the genetic diversity of the YFP will possibly decrease in the future if the population keeps declining at a rapid rate, even though these two types of markers revealed different levels of genetic diversity. In addition, mtDNA revealed strong genetic differentiation between one local population, Xingchang–Shishou (XCSS, and the other five downstream local populations; furthermore, microsatellite DNA unveiled fine but significant genetic differentiation between three of the local populations (not only XCSS but also Poyang Lake (PY and Tongling (TL and the other local populations. With an increasing number of distribution gaps appearing in the Yangtze main steam, the genetic differentiation of local populations will likely intensify in the future. The YFP is becoming a genetically fragmented population. Therefore, we recommend attention should be paid to the genetic conservation of the YFP.

  12. cpDNA Microsatellite Markers for Lemna minor (Araceae: Phylogeographic Implications

    Directory of Open Access Journals (Sweden)

    Gowher A. Wani

    2014-07-01

    Full Text Available Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation.

  13. 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.

  14. Variation on DNA microsatellite of Holstein-Friesian dairy cows in Baturaden Dairy Cattle Breeding Center

    Directory of Open Access Journals (Sweden)

    C Sumantri

    2007-06-01

    Full Text Available Eight microsatellite loci of which the locations were three on chromosome 6 (BTA6 namely CSN 3, BM 143 and BM 415; two on chromosome 9 (BTA9 namely ETH 225 and BM 4208; and three on chromosome 10 (BTA10 namely BP 31, BM 1237 and BM 888 were used to investigate genotypic variation of Holstein-Friesian (HF dairy cows in Baturraden Dairy Cattle Breeding Centre. Research activities were carried out through some steps involving blood collection, DNA isolation, amplification on DNA fragments by polymerase chain reaction (PCR and separation by electrophoresis with silver staining. Frequency and heterozygosity of genes under consideration were calculated. The results showed that the eight microsatellite loci exhibited a total number of 33 alleles. Locations of those alleles were five in BM 143 and BM 4208 loci; four in BM 415, CSN 3, ETH 225, BM 1237, BM 888 loci; and three in BP 31 locus. A number of 14 out of 33 alleles might be specific alleles for HF dairy cattle in Baturraden Dairy Cattle Breeding Centre. The lowest heterozygosity per locus (ĥ was 0.6151 for BM 415 whilst the highest one was 0.7301 for BM 888. Additionally, the average heterozygosity for all loci (Ĥ detected in this study was 0.6768. The genotype BB on locus BM 143 and AC on locus CSN-3 significantly affected (P<0.05 the estimated breeding value of milk yield of HF cows in this location.

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

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    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.

  16. Identification of DNA-microsatellite markers for the characterization of somatic embryos in Quercus suber.

    Science.gov (United States)

    Gómez-Garay, Arancha; Bueno, Angeles; Pintos, Beatriz

    2013-01-01

    Nuclear DNA-microsatellite markers led the possibility to characterize individually both Quercus suber trees and somatic embryos. The genotype inferred by SSR markers opens the possibility to obtain a fingerprint for clonal lines identification. Furthermore, allow to infer the origin of somatic embryos from haploid cells (microspores) or from diploid tissues. Using few SSR markers from other Quercus species and an automatic system based in fluorescence, it is possible to obtain a high discrimination power between genotypes. This method is sufficient to assign tissues to an individual tree with high statistical certainty. Nevertheless, it is necessary to take care to select the adequate DNA extraction method to avoid PCR inhibitors present in diverse Q. suber tissues.

  17. Genetic variation of Chinese and Japanese wild Pacific abalone (Haliotis discus hannai) measured by microsatellite DNA markers

    Institute of Scientific and Technical Information of China (English)

    LI Qi; KIJIMA Akihiro

    2006-01-01

    Population differentiation and relationships among three wild populations of the Pacific abalone Haliotis discus hannai collected from coastal seas around China and Japan were estimated using microsatellite DNA analysis. The results obtained with six microsatellite loci showed a high genetic diversity for China and Japan populations. The mean number of alleles per locus ranged from 11.7 to 23.0, and the average of observed and expected heterozygosity ranged from 0.656 to 0.721, and from 0.721 to 0.793, respectively. The observed genotype frequencies at each locus were mostly in agreement with Hardy-Weinberg expectations with five exceptions. Significant differences were detected between Chinese and Japanese H. discus hannai populations [Weir and Cocker-ham's fixation index(Fst) range: 0.020~0.023; Slatkin's fixation index (Rst) range: 0.016~0.044], and no obvious difference was detected between the samples of Japanese H. discus hannai populations (Fst=0.002; Rst = 0.007). The level of differentiation among populations is further evidenced by the nNeighbor-joining tree topology on which the Japanese samples were closely clustered, and the Chinese population formed a separate cluster. These results suggest that care should be taken in future management of different populations.

  18. Analysis of genital Candida albicans infection by rapid microsatellite markers genotyping

    Institute of Scientific and Technical Information of China (English)

    SHI Wei-min; MEI Xing-yu; GAO Fei; HUO Ke-ke; SHEN Liang-liang; QIN Hai-hong; WU Zhou-wei; ZHENG Jie

    2007-01-01

    Background Candida albicans (C. albicans) infection, often occurring in genital candidiasis, has increased dramatically recently. Developing an efficient C. albicans typing method may contribute to understanding its epidemiological characteristics and guiding efficient treatment. We used rapid microsatellite genotyping assay for interstrain differentiation of C. albicans isolates and explored some characteristics of its spread.Methods DNA was extracted from C. albicans isolates from gentalia, recta and mouths of 39 female cases and 27 male cases of genital candidiasis. Three fluorescent primers for the microsatellite markers in conserved genes (CDC3, EF3and HIS3) of C. albicans were used to amplify the isolates DNA by PCR. Fluorescent signals were read with an automatic sequencer and analyzed with GeneScan software.Results Analysis of the three microsatellites markers showed 18 gene allelic associations in genital C. albicans infected patients: 10 allelic associations in female and 11 allelic associations in male, of which 3 allelic associations shared by both genders covered 71% of infections. The most dominant allele association of pathogenic strains for both genders was 116:124, 122:131,160:200 that covered about 50% of infection. Gentalia and recta shared the same strains in 80%of female patients, but in only 3.8% of male patients. There were 2.7% female patients, but no males, with same strain in both gentalia and mouths. Five of seven genital C. albicans infected couples had the same allelic associations of which 4were the dominant pathogenic C. albicans susceptible for both genders.Conclusions The predominant allelic association of the pathogenic strain in genital C. albicans infection is 116:124,122:131, 160:200. Vaginal pathogenic strains are probably maintained from the rectal reservoir. Pathogenic strains of male patients are probably from frequent sexual intercourse. The aggressiveness of some strains varies with gender.

  19. Genetic relationships of Kampung, Pelung, Sentul and Black Kedu Chicken using Microsatellite DNA Markers: I. Lingkage group of macro chromosome

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    Tike Sartika

    2009-05-01

    Full Text Available Genetic relationships of Kampung, Pelung, Sentul and Black Kedu chickens were studied on the basis of microsatellite DNA polymorphism. DNA samples were analyzed using nine microsatellite markers which chosen from linkage group of macrochromosome (chromosome 1-8 such as, locus ABR 258, ABR359, ABR 297, ABR 339, ABR 75, ABR 209, ABR 28, ABR 419 and ABR 604. Analyses of amplified DNA fragments were performed using Gene Mapper 2.0 software (PE, Applied Biosystems. The allele frequencies in each breed estimated by direct counting. Since all nine microsatellite markers were polymorphic, genetic distance between the breeds could be calculated based on the frequencies of alleles of the microsatellite. Genetic relationships between the breeds could be constructed. The results indicated that a total of 73 allele were detected while typing all the four breeds of local chicken and one breed of White Leghorn as outgroup breed acrossed nine loci. The number of alleles was observed in all of the breed ranged 3-17 alleles according to the microsatellite under scrutiny. Highest observed number of alleles was found in Kampung Chicken 60 alleles (82.2%. The UPGMA method for dendogram based on Nei genetic distances indicated that the local chickens have the same of ancestor, while Kampung and Sentul chicken have the same cluster followed by Black Kedu and Pelung Chicken.

  20. Species diversity and geographic distribution of Gymnotus (Pisces: Gymnotiformes by nuclear (GGACn microsatellite analysis

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    Fernandes-Matioli F.M.C.

    2000-01-01

    Full Text Available Patterns of amplified DNA fragments flanked by (GGACn microsatellites, obtained by single primer amplification reaction (SPAR, from 198 Gymnotus specimens (Pisces: Gymnotiformes sampled from 8 southeastern Brazilian river basins were analyzed. The species studied were Gymnotus carapo, G. pantherinus, G. inaequilabiatus, and G. sylvius. The indirectly obtained patterns reflected the distribution of simple sequence repeats in the nuclear genome of the specimens. Species-specific patterns of DNA amplification were found and were useful for the analysis of the geographic distribution of Gymnotus species. Monomorphic patterns were found in G. carapo, G. pantherinus, and G. inaequilabiatus. Three polymorphic patterns were found in G. sylvius populations. The SPAR technique could be a useful molecular tool in conservation programs involving communities of neotropical freshwater fish.

  1. Mutation rates of TGFBR2 and ACVR2 coding microsatellites in human cells with defective DNA mismatch repair.

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    Heekyung Chung

    Full Text Available Microsatellite instability promotes colonic tumorigenesis through generating frameshift mutations at coding microsatellites of tumor suppressor genes, such as TGFBR2 and ACVR2. As a consequence, signaling through these TGFbeta family receptors is abrogated in DNA Mismatch repair (MMR-deficient tumors. How these mutations occur in real time and mutational rates of these human coding sequences have not previously been studied. We utilized cell lines with different MMR deficiencies (hMLH1-/-, hMSH6-/-, hMSH3-/-, and MMR-proficient to determine mutation rates. Plasmids were constructed in which exon 3 of TGFBR2 and exon 10 of ACVR2 were cloned +1 bp out of frame, immediately after the translation initiation codon of an enhanced GFP (EGFP gene, allowing a -1 bp frameshift mutation to drive EGFP expression. Mutation-resistant plasmids were constructed by interrupting the coding microsatellite sequences, preventing frameshift mutation. Stable cell lines were established containing portions of TGFBR2 and ACVR2, and nonfluorescent cells were sorted, cultured for 7-35 days, and harvested for flow cytometric mutation detection and DNA sequencing at specific time points. DNA sequencing revealed a -1 bp frameshift mutation (A9 in TGFBR2 and A7 in ACVR2 in the fluorescent cells. Two distinct fluorescent populations, M1 (dim, representing heteroduplexes and M2 (bright, representing full mutants were identified, with the M2 fraction accumulating over time. hMLH1 deficiency revealed 11 (5.91 x 10(-4 and 15 (2.18 x 10(-4 times higher mutation rates for the TGFBR2 and ACVR2 microsatellites compared to hMSH6 deficiency, respectively. The mutation rate of the TGFBR2 microsatellite was approximately 3 times higher in both hMLH1 and hMSH6 deficiencies than the ACVR2 microsatellite. The -1 bp frameshift mutation rates of TGFBR2 and ACVR2 microsatellite sequences are dependent upon the human MMR background.

  2. 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.

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

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    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.

  4. Microsatellite DNA markers for delineating population structure and kinship among the endangered Kirtland’s warbler (Dendroica kirtlandii)

    Science.gov (United States)

    TIM L. KING; MICHAEL S. EACKLES; ANNE P. HENDERSON; CAROL I. BOCETTI; DAVE CURRIE; JR WUNDERLE

    2005-01-01

    We document the isolation and characterization of 23 microsatellite DNA markers for the endangered Kirtland’s warbler (Dendroica kirtlandii), a Nearctic/Neotropical migrant passerine. This suite of markers revealed moderate to high levels of allelic diversity (averaging 7.7 alleles per locus) and heterozygosity (averaging 72%). Genotypic frequencies at 22 of 23 (95%)...

  5. Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin (Pontoporia blainvillei).

    Science.gov (United States)

    Gariboldi, María Constanza; Túnez, Juan Ignacio; Failla, Mauricio; Hevia, Marta; Panebianco, María Victoria; Paso Viola, María Natalia; Vitullo, Alfredo Daniel; Cappozzo, Humberto Luis

    2016-12-01

    The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F-statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex-biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long-term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.

  6. 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.

  7. Pollen dispersal analysis using DNA markers

    OpenAIRE

    Wei Zhou; Hong Wang

    2014-01-01

    Modes of pollen dispersal are important for plant ecology, conservation, and evolutionary biology as pollen-mediated gene flow connects one generation of sexually-reproducing plants to the next. With the development of DNA molecular techniques, molecular markers (especially microsatellite markers) have replaced traditional physical markers for pollen flow analysis. Methods of paternity assignment with maximum likelihood and Bayesian inference have greatly improved the estimation of pollen flo...

  8. Genetic variation and phylogeographic structure of the cotton aphid, Aphis gossypii, based on mitochondrial DNA and microsatellite markers.

    Science.gov (United States)

    Wang, Xing-Ya; Yang, Xian-Ming; Lu, Bin; Zhou, Li-Hong; Wu, Kong-Ming

    2017-05-15

    Aphis gossypii, one of the most important agricultural pests in the world, can cause serious economic losses in the main crop-producing areas. To clarify issues such as the genetic differentiation, genetic structure, and demographic history of A. gossypii populations, we used 10 nuclear microsatellite loci (SSR) and two mitochondrial gene sequences (COI and Cytb) to investigate genetic diversity and population structure of A. gossypii populations that were collected from 33 sampling sites in China from different climatic zones. SSR and mtDNA data suggested low to moderate levels of genetic diversity. A star-shaped network of mtDNA haplotypes indicated that the maternal ancestor of China cotton aphids likely originated in Xinjiang. The POPTREE, STRUCTURE and principal coordinate analysis (PCoA) revealed two genetic clusters: an eastern and a western region group. Isolation by distance (IBD) results showed a positive correlation between geographic distance and genetic distance in the vast eastern region but not in the western region. Neutrality testing and mismatch distribution analysis provided strong evidence for a recent rapid expansion in most populations. Genetic bottleneck was not detected in A. gossypii populations of China. The present work can help us to develop strategies for managing this pest.

  9. [The diagnostic value of microsatellite LOH analysis and the prognostic relevance of angiogenic gene expression in urinary bladder cancer].

    Science.gov (United States)

    Szarvas, Tibor

    2009-12-01

    Bladder cancer is the second most common malignancy affecting the urinary system. Currently, histology is the only tool that determines therapy and patients' prognosis. As the treatment of non-invasive (Ta/T1) and muscle invasive (T2-T4) bladder tumors are completely different, correct staging is important, although it is often hampered by disturbing factors. Molecular methods offer new prospects for early disease detection, confirmation of unclear histological findings and prognostication. Applying molecular biological methods, the present study is searching for answers to current diagnostic and prognostic problems in bladder carcinoma. We analyzed tumor, blood and/or urine samples of 334 bladder cancer patients and 117 control individuals. Genetic alterations were analyzed in urine samples of patients and controls, both by PCR-based microsatellite loss of heterozigosity (LOH) analysis using 12 fluorescently labeled primers and by DNA hybridization based UroVysion FISH technique using 4 probes, to assess the diagnostic values of these methods. Whole genome microsatellite analysis (with 400 markers) was performed in tumor and blood specimens of bladder cancer patients to find chromosomal regions, the loss of which may be associated with tumor stage. Furthermore, we assessed the prognostic value of Tie2, VEGF, Angiopoietin-1 and -2. We concluded that DNA analysis of voided urine samples by microsatellite analysis and FISH are sensitive and non-invasive methods to detect bladder cancer. Furthermore, we established a panel of microsatellite markers that could differentiate between non-invasive and invasive bladder cancer. However, further analyses in a larger cohort of patients are needed to assess their specificity and sensitivity. Finally, we identified high Ang-2 and low Tie2 gene expression as significant and independent risk factors of tumor recurrence and cancer related survival.

  10. 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.

  11. 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.

  12. 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.

  13. Genetic variability in spotted seatrout (Cynoscion nebulosus), determined with microsatellite DNA markers

    Science.gov (United States)

    Ward, R.; Bowers, K.; Hensley, R.; Mobley, B.; Belouski, E.

    2007-01-01

    Variation in the allele frequencies of five microsatellite loci was surveyed in 1256 individual spotted seatrout (Cynoscion nebulosus) obtained from 12 bays and estuaries from Laguna Madre, Texas, to Charlotte Harbor, Florida, to St. John's River on the Florida Atlantic Coast. Texas and Louisiana collection sites were resampled each year for two to four years (1998-2001). Genetic differentiation was observed. Spotted seatrout from Florida waters were strongly differentiated from spotted seatrout collected in Louisiana and Texas. The greatest genetic discontinuity was observed between Tampa Bay and Charlotte Harbor, and Charlotte Harbor seatrout were most similar to Atlantic Coast spotted seatrout. Texas and Louisiana samples were not strongly structured within the northwestern Gulf of Mexico and there was little evidence of temporal differentiation within bays. These findings are contrary to those of earlier analyses with allozymes and mitochondrial DNA (mtDNA) where evidence of spatial differentiation was found for spotted seatrout resident on the Texas coast. The differences in genetic structure observed among these markers may reflect differences in response to selective pressure, or may be due to differences in underlying genetic processes.

  14. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

    Science.gov (United States)

    Jan, Catherine

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

  15. 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.

  16. 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.

  17. The historical demography and genetic variation of the endangered Cycas multipinnata (Cycadaceae in the red river region, examined by chloroplast DNA sequences and microsatellite markers.

    Directory of Open Access Journals (Sweden)

    Yi-Qing Gong

    Full Text Available Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU. In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.

  18. The Historical Demography and Genetic Variation of the Endangered Cycas multipinnata (Cycadaceae) in the Red River Region, Examined by Chloroplast DNA Sequences and Microsatellite Markers

    Science.gov (United States)

    Gong, Yi-Qing; Zhan, Qing-Qing; Nguyen, Khang Sinh; Nguyen, Hiep Tien; Wang, Yue-Hua; Gong, Xun

    2015-01-01

    Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species. PMID:25689828

  19. 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....

  20. 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.

  1. 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.

  2. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords

    DEFF Research Database (Denmark)

    Glover, Kevin A.; Skaala, Øystein; Limborg, Morten;

    2011-01-01

    Glover, K. A., Skaala, Ø., Limborg, M., Kvamme, C., and Torstensen, E. Microsatellite DNA reveals population genetic differentiation among sprat (Sprattus sprattus) sampled throughout the Northeast Atlantic, including Norwegian fjords. – ICES Journal of Marine Science, 68: 2145–2151. Sprat...... (Sprattus sprattus), small pelagic shoaling fish, were sampled from the Celtic, North, and Baltic seas, and 10 Norwegian fjords. Significant overall genetic differentiation was observed among samples when analysed with eight microsatellite DNA loci (Global FST = 0.0065, p ... differences were observed between the Baltic and all other samples (largest pairwise FST = 0.043, p sample from the Celtic Sea (CEL) and the North Sea (NSEA; FST = 0.001, p = 0.16), but variable levels of genetic differentiation were...

  3. Microsatellite and mitochondrial DNA polymorphism reveals life history dependent interbreeding between hatchery and wild brown trout ( Salmo trutta L.)

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Ruzzante, D.E.; Eg Nielsen, Einar

    2000-01-01

    The effects of stocking hatchery trout into wild populations were studied in a Danish river, using microsatellite and mitochondrial DNA (mtDNA) markers. Baseline samples were taken from hatchery trout and wild trout assumed to be unaffected by previous stocking. Also, samples were taken from...... resident and sea trout from a stocked section of the river. Genetic differentiation between the hatchery strain and the local wild population was modest (microsatellite F-ST = 0.06). Using assignment tests, more than 90% of individuals from the baseline samples were classified correctly. Assignment tests...... to the hatchery strain suggested that interbreeding took place between hatchery and wild trout. The latter result also indicated that male hatchery trout contributed more to interbreeding than females. We suggest that stronger selection acts against stocked hatchery trout that become anadromous compared...

  4. Microsatellite DNA polymorphisms and the relation with body weight in sea cucumber Apostichopus japonicus

    Institute of Scientific and Technical Information of China (English)

    WANG Xiuli; SHAN Xue; QIU Xuemei; MENG Xiangying; CHANG Yaqing

    2009-01-01

    The relationship between microsatellite polymorphism and body weight of captive bred Chinese sea cucumber Apostichopus japonicus was investigated in two local populations in Dalian.Among ten loci discovered, nine show changes except for A J07 loci. Seven loci were found highly polymorphic in both populations. For each locus in two populations, the average number of alleles is 6.428 6 and 6.285 7, the average observed heterozygosity at 0.225 7 and 0.245 9, the expected heterozygosity at 0.776 8 and 0.748 8, the polymorphism information content (PIC) at 0.709 2 and 0.674 6, respectively. Further analysis show significant correlation between A. japonicus body weight and occurrence markers AJ02 and AJ04. The findings of the relation may be helpful for molecular breeding,as well as the marker-assisted selection of sea cucumbers.

  5. Mid-Holocene decline in African buffalos inferred from Bayesian coalescence-based analyses of microsatellites and mitochondrial DNA

    DEFF Research Database (Denmark)

    Heller, Rasmus; Lorenzen, Eline D.; Okello, J.B.A

    2008-01-01

    pandemic in the late 1800s, but little is known about the earlier demographic history of the species. We analysed genetic variation at 17 microsatellite loci and a 302-bp fragment of the mitochondrial DNA control region to infer past demographic changes in buffalo populations from East Africa. Two Bayesian......-Holocene aridification of East Africa caused a major decline in the effective population size of the buffalo, a species reliant on moist savannah habitat for its existence....

  6. 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.

  7. 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...

  8. Population structure of Purple Sandpipers (Calidris maritima) as revealed by mitochondrial DNA and microsatellites.

    Science.gov (United States)

    LeBlanc, Nathalie M; Stewart, Donald T; Pálsson, Snaebjörn; Elderkin, Mark F; Mittelhauser, Glen; Mockford, Stephen; Paquet, Julie; Robertson, Gregory J; Summers, Ron W; Tudor, Lindsay; Mallory, Mark L

    2017-05-01

    The Purple Sandpiper (Calidris maritima) is a medium-sized shorebird that breeds in the Arctic and winters along northern Atlantic coastlines. Migration routes and affiliations between breeding grounds and wintering grounds are incompletely understood. Some populations appear to be declining, and future management policies for this species will benefit from understanding their migration patterns. This study used two mitochondrial DNA markers and 10 microsatellite loci to analyze current population structure and historical demographic trends. Samples were obtained from breeding locations in Nunavut (Canada), Iceland, and Svalbard (Norway) and from wintering locations along the coast of Maine (USA), Nova Scotia, New Brunswick, and Newfoundland (Canada), and Scotland (UK). Mitochondrial haplotypes displayed low genetic diversity, and a shallow phylogeny indicating recent divergence. With the exception of the two Canadian breeding populations from Nunavut, there was significant genetic differentiation among samples from all breeding locations; however, none of the breeding populations was a monophyletic group. We also found differentiation between both Iceland and Svalbard breeding populations and North American wintering populations. This pattern of divergence is consistent with a previously proposed migratory pathway between Canadian breeding locations and wintering grounds in the United Kingdom, but argues against migration between breeding grounds in Iceland and Svalbard and wintering grounds in North America. Breeding birds from Svalbard also showed a genetic signature intermediate between Canadian breeders and Icelandic breeders. Our results extend current knowledge of Purple Sandpiper population genetic structure and present new information regarding migration routes to wintering grounds in North America.

  9. Microsatellite instability analysis in hereditary non-polyposis colon cancer using the Bethesda consensus panel of microsatellite markers in the absence of proband normal tissue

    Directory of Open Access Journals (Sweden)

    Dourisboure Ricardo J

    2006-01-01

    Full Text Available Abstract Background Hereditary non-polyposis colon cancer (HNPCC is an autosomal dominant syndrome predisposing to the early development of various cancers including those of colon, rectum, endometrium, ovarium, small bowel, stomach and urinary tract. HNPCC is caused by germline mutations in the DNA mismatch repair genes, mostly hMSH2 or hMLH1. In this study, we report the analysis for genetic counseling of three first-degree relatives (the mother and two sisters of a male who died of colorectal adenocarcinoma at the age of 23. The family fulfilled strict Amsterdam-I criteria (AC-I with the presence of extracolonic tumors in the extended pedigree. We overcame the difficulty of having a proband post-mortem non-tumor tissue sample for MSI testing by studying the alleles carried by his progenitors. Methods Tumor MSI testing is described as initial screening in both primary and metastasis tumor tissue blocks, using the reference panel of 5 microsatellite markers standardized by the National Cancer Institute (NCI for the screening of HNPCC (BAT-25, BAT-26, D2S123, D5S346 and D17S250. Subsequent mutation analysis of the hMLH1 and hMSH2 genes was performed. Results Three of five microsatellite markers (BAT-25, BAT-26 and D5S346 presented different alleles in the proband's tumor as compared to those inherited from his parents. The tumor was classified as high frequency microsatellite instability (MSI-H. We identified in the HNPCC family a novel germline missense (c.1864C>A mutation in exon 12 of hMSH2 gene, leading to a proline 622 to threonine (p.Pro622Thr amino acid substitution. Conclusion This approach allowed us to establish the tumor MSI status using the NCI recommended panel in the absence of proband's non-tumor tissue and before sequencing the obligate carrier. According to the Human Gene Mutation Database (HGMD and the International Society for Gastrointestinal Hereditary Tumors (InSiGHT Database this is the first report of this mutation.

  10. Rapid isolation of microsatellite DNAs and identification of polymorphic mitochondrial DNA regions in the fish rotan (Perccottus glenii) invading European Russia

    Science.gov (United States)

    King, Timothy L.; Eackles, Michael S.; Reshetnikov, Andrey N.

    2015-01-01

    Human-mediated translocations and subsequent large-scale colonization by the invasive fish rotan (Perccottus glenii Dybowski, 1877; Perciformes, Odontobutidae), also known as Amur or Chinese sleeper, has resulted in dramatic transformations of small lentic ecosystems. However, no detailed genetic information exists on population structure, levels of effective movement, or relatedness among geographic populations of P. glenii within the European part of the range. We used massively parallel genomic DNA shotgun sequencing on the semiconductor-based Ion Torrent Personal Genome Machine (PGM) sequencing platform to identify nuclear microsatellite and mitochondrial DNA sequences in P. glenii from European Russia. Here we describe the characterization of nine nuclear microsatellite loci, ascertain levels of allelic diversity, heterozygosity, and demographic status of P. glenii collected from Ilev, Russia, one of several initial introduction points in European Russia. In addition, we mapped sequence reads to the complete P. glenii mitochondrial DNA sequence to identify polymorphic regions. Nuclear microsatellite markers developed for P. glenii yielded sufficient genetic diversity to: (1) produce unique multilocus genotypes; (2) elucidate structure among geographic populations; and (3) provide unique perspectives for analysis of population sizes and historical demographics. Among 4.9 million filtered P. glenii Ion Torrent PGM sequence reads, 11,304 mapped to the mitochondrial genome (NC_020350). This resulted in 100 % coverage of this genome to a mean coverage depth of 102X. A total of 130 variable sites were observed between the publicly available genome from China and the studied composite mitochondrial genome. Among these, 82 were diagnostic and monomorphic between the mitochondrial genomes and distributed among 15 genome regions. The polymorphic sites (N = 48) were distributed among 11 mitochondrial genome regions. Our results also indicate that sequence reads generated

  11. Mitochondrial and microsatellite DNA markers reveal a Balkan origin for the highly invasive horse-chestnut leaf miner Cameraria ohridella (Lepidoptera, Gracillariidae).

    Science.gov (United States)

    Valade, R; Kenis, M; Hernandez-Lopez, A; Augustin, S; Mari Mena, N; Magnoux, E; Rougerie, R; Lakatos, F; Roques, A; Lopez-Vaamonde, C

    2009-08-01

    Biological invasions usually start with a small number of founder individuals. These founders are likely to represent a small fraction of the total genetic diversity found in the source population. Our study set out to trace genetically the geographical origin of the horse-chestnut leafminer, Cameraria ohridella, an invasive microlepidopteran whose area of origin is still unkown. Since its discovery in Macedonia 25 years ago, this insect has experienced an explosive westward range expansion, progressively colonizing all of Central and Western Europe. We used cytochrome oxidase I sequences (DNA barcode fragment) and a set of six polymorphic microsatellites to assess the genetic variability of C. ohridella populations, and to test the hypothesis that C. ohridella derives from the southern Balkans (Albania, Macedonia and Greece). Analysis of mtDNA of 486 individuals from 88 localities allowed us to identify 25 geographically structured haplotypes. In addition, 480 individuals from 16 populations from Europe and the southern Balkans were genotyped for 6 polymorphic microsatellite loci. High haplotype diversity and low measures of nucleotide diversities including a significantly negative Tajima's D indicate that C. ohridella has experienced rapid population expansion during its dispersal across Europe. Both mtDNA and microsatellites show a reduction in genetic diversity of C. ohridella populations sampled from artificial habitats (e.g. planted trees in public parks, gardens, along roads in urban or sub-urban areas) across Europe compared with C. ohridella sampled in natural stands of horse-chestnuts in the southern Balkans. These findings suggest that European populations of C. ohridella may indeed derive from the southern Balkans.

  12. Application of plant DNA markers in forensic botany: genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.

    Science.gov (United States)

    Craft, Kathleen J; Owens, Jeffrey D; Ashley, Mary V

    2007-01-05

    As highly polymorphic DNA markers become increasingly available for a wide range of plant and animal species, there will be increasing opportunities for applications to forensic investigations. To date, however, relatively few studies have reported using DNA profiles of non-human species to place suspects at or near crime scenes. Here we describe an investigation of a double homicide of a female and her near-term fetus. Leaf material taken from a suspect's vehicle was identified to be that of sand live oak, Quercus geminata, the same tree species that occurred near a shallow grave where the victims were found. Quercus-specific DNA microsatellites were used to genotype both dried and fresh material from trees located near the burial site and from the material taken from the suspect's car. Samples from the local population of Q. geminata were also collected and genotyped in order to demonstrate that genetic variation at four microsatellite loci was sufficient to assign leaves to an individual tree with high statistical certainty. The cumulative average probability of identity for these four loci was 2.06x10(-6). DNA was successfully obtained from the dried leaf material although PCR amplification was more difficult than amplification of DNA from fresh leaves. The DNA profiles of the dried leaves from the suspect's car did not match those of the trees near the crime scene. Although this investigation did not provide evidence that could be used against the suspect, it does demonstrate the potential for plant microsatellite markers providing physical evidence that links plant materials to live plants at or near crime scenes.

  13. 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.

  14. Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from fecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae).

    Science.gov (United States)

    Oliveira, M L; Duarte, J M B

    2013-01-16

    We tried to amplify mitochondrial, microsatellite and amelogenin loci in DNA from fecal samples of a wild Mazama americana population. Fifty-two deer fecal samples were collected from a 600-ha seasonal semideciduous forest fragment in a subtropical region of Brazil (21°20'S, 47°17'W), with the help of a detection dog; then, stored in ethanol and georeferenced. Among these samples 16 were classified as "fresh" and 36 as "non-fresh". DNA was extracted using the QIAamp(®) DNA Stool Mini Kit. Mitochondrial loci were amplified in 49 of the 52 samples. Five microsatellite loci were amplified by PCR; success in amplification varied according to locus size and sample age. Successful amplifications were achieved in 10/16 of the fresh and in 13/36 of the non-fresh samples; a negative correlation (R = -0.82) was found between successful amplification and locus size. Amplification of the amelogenin locus was successful in 22 of the 52 samples. The difficulty of amplifying nuclear loci in DNA samples extracted from feces collected in the field was evident. Some methodological improvements, including collecting fresh samples, selecting primers for shorter loci and quantifying the extracted DNA by real-time PCR, are suggested to increase amplification success in future studies.

  15. SSR_pipeline--computer software for the identification of microsatellite sequences from paired-end Illumina high-throughput DNA sequence data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (SSRs; for example, microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains three analysis modules along with a fourth control module that can be used to automate analyses of large volumes of data. The modules are used to (1) identify the subset of paired-end sequences that pass quality standards, (2) align paired-end reads into a single composite DNA sequence, and (3) identify sequences that possess microsatellites conforming to user specified parameters. Each of the three separate analysis modules also can be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc). All modules are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, Windows). The program suite relies on a compiled Python extension module to perform paired-end alignments. Instructions for compiling the extension from source code are provided in the documentation. Users who do not have Python installed on their computers or who do not have the ability to compile software also may choose to download packaged executable files. These files include all Python scripts, a copy of the compiled extension module, and a minimal installation of Python in a single binary executable. See program documentation for more information.

  16. Autophagy is upregulated during colorectal carcinogenesis, and in DNA microsatellite stable carcinomas.

    Science.gov (United States)

    Sena, Paola; Mariani, Francesco; Mancini, Stefano; Benincasa, Marta; Magnani, Giulia; Pedroni, Monica; Palumbo, Carla; Roncucci, Luca

    2015-12-01

    Cancer cells are exposed to a wide range of stress sources, such as nutrient deprivation and hypoxia, as well as cytotoxic chemotherapy and radiotherapy. Certain forms of stress can also promote survival activating the metabolic autophagy pathway in cancer cells. Autophagy is dramatically increased in cancer cells. In these conditions, it is becoming evident that autophagy protects cells, by providing an alternative energy source and by eliminating dysfunctional organelles or proteins. Its role in tumorigenesis is more controversial and both the presence and the absence of autophagy have been implicated. Autophagy is known to be associated with the poor outcome of patients with various types of cancers, and its effectiveness as a prognostic marker in colorectal cancer was demonstrated by several studies. The inhibition of autophagy may be a potential therapeutic target in colorectal cancer. In vitro experiments have shown that the inhibition of autophagy increases 5-FU-induced apoptosis. There are two trials currently investigating the addition of chloroquine to 5-FU-based chemotherapy and bevacizumab. In the present study, we evaluated the expression of LC3B-II in samples of human colorectal microadenomas (i.e., dysplastic aberrant crypt foci) and carcinomas compared to normal mucosa. Furthermore, the expression pattern of LC3B-II was assessed in carcinomas classified as DNA microsatellite stable (MSS) and unstable (MSI). Thus, immunofluorescence techniques coupled with confocal microscopy and immunoblot experiments were performed. The results clearly showed a significant increase in expression of the autophagic key factor in microadenomas and carcinomas with respect to normal mucosa. In MSS carcinomas, the level of LC3B-II expression was higher than that in the MSI carcinomas.

  17. Congruence of microsatellite and mitochondrial DNA variation in acrobat ants (Crematogaster subgenus Decacrema, Formicidae: Myrmicinae) inhabiting Macaranga (Euphorbiaceae) myrmecophytes.

    Science.gov (United States)

    Ueda, Shouhei; Nagano, Yusuke; Kataoka, Yowsuke; Komatsu, Takashi; Itioka, Takao; Shimizu-Kaya, Usun; Inui, Yoko; Itino, Takao

    2015-01-01

    A previously reported mitochondrial DNA (mtDNA) phylogeny of Crematogaster (subgenus Decacrema) ants inhabiting Macaranga myrmecophytes indicated that the partners diversified synchronously and their specific association has been maintained for 20 million years. However, the mtDNA clades did not exactly match morphological species, probably owing to introgressive hybridization among younger species. In this study, we determined the congruence between nuclear simple sequence repeat (SSR, also called microsatellite) genotyping and mtDNA phylogeny to confirm the suitability of the mtDNA phylogeny for inferring the evolutionary history of Decacrema ants. Analyses of ant samples from Lambir Hills National park, northeastern Borneo, showed overall congruence between the SSR and mtDNA groupings, indicating that mtDNA markers are useful for delimiting species, at least at the local level. We also found overall high host-plant specificity of the SSR genotypes of Decacrema ants, consistent with the specificity based on the mtDNA phylogeny. Further, we detected cryptic genetic assemblages exhibiting high specificity toward particular plant species within a single mtDNA clade. This finding, which may be evidence for rapid ecological and genetic differentiation following a host shift, is a new insight into the previously suggested long-term codiversification of Decacrema ants and Macaranga plants.

  18. Congruence of microsatellite and mitochondrial DNA variation in acrobat ants (Crematogaster subgenus Decacrema, Formicidae: Myrmicinae inhabiting Macaranga (Euphorbiaceae myrmecophytes.

    Directory of Open Access Journals (Sweden)

    Shouhei Ueda

    Full Text Available A previously reported mitochondrial DNA (mtDNA phylogeny of Crematogaster (subgenus Decacrema ants inhabiting Macaranga myrmecophytes indicated that the partners diversified synchronously and their specific association has been maintained for 20 million years. However, the mtDNA clades did not exactly match morphological species, probably owing to introgressive hybridization among younger species. In this study, we determined the congruence between nuclear simple sequence repeat (SSR, also called microsatellite genotyping and mtDNA phylogeny to confirm the suitability of the mtDNA phylogeny for inferring the evolutionary history of Decacrema ants. Analyses of ant samples from Lambir Hills National park, northeastern Borneo, showed overall congruence between the SSR and mtDNA groupings, indicating that mtDNA markers are useful for delimiting species, at least at the local level. We also found overall high host-plant specificity of the SSR genotypes of Decacrema ants, consistent with the specificity based on the mtDNA phylogeny. Further, we detected cryptic genetic assemblages exhibiting high specificity toward particular plant species within a single mtDNA clade. This finding, which may be evidence for rapid ecological and genetic differentiation following a host shift, is a new insight into the previously suggested long-term codiversification of Decacrema ants and Macaranga plants.

  19. 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.

  20. Microsatellite analysis in the genome of Acanthaceae: An in silico approach

    Directory of Open Access Journals (Sweden)

    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.

  1. Microsatellite DNA mutations in double-crested cormorants (Phalacrocorax auritus) associated with exposure to PAH-containing industrial air pollution.

    Science.gov (United States)

    King, L E; de Solla, S R; Small, J M; Sverko, E; Quinn, J S

    2014-10-01

    Hamilton Harbour, Ontario, Canada is one of the most polluted sites on the Great Lakes, and is subject to substantial airborne pollution due to emissions from both heavy industry and intense vehicle traffic. Mutagenic Polycyclic aromatic hydrocarbons (PAHs) are present at very high concentrations in the air and sediment of Hamilton Harbour. We used five variable DNA microsatellites to screen for mutations in 97 families of Double-crested Cormorants (Phalacrocorax auritus) from three wild colonies, two in Hamilton Harbour and one in cleaner northeastern Lake Erie. Mutations were identified in all five microsatellites at low frequencies, with the majority of mutations found in chicks from the Hamilton Harbour site closest to industrial sources of PAH contamination. Microsatellite mutation rates were 6-fold higher at the Hamilton Harbour site closest to the industrial sources of PAH contamination than the other Hamilton Harbour site, and both were higher than the reference colony. A Phase I metabolite of the PAH benzo[a]pyrene identified by LC-MS/MS in bile and liver from Hamilton Harbour cormorant chicks suggests that these cormorants are exposed to and metabolizing PAHs, highlighting their potential to have caused the observed mutations.

  2. Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

    Science.gov (United States)

    Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

    2017-02-01

    There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

  3. Comparative Analysis of the Korean Population of Magnaporthe oryzae by Multilocus Microsatellite Typing

    Directory of Open Access Journals (Sweden)

    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.

  4. Gene flow among Anopheles albimanus populations in Central America, South America, and the Caribbean assessed by microsatellites and mitochondrial DNA.

    Science.gov (United States)

    Molina-Cruz, Alvaro; de Mérida, Ana María P; Mills, Katherine; Rodríguez, Fernando; Schoua, Carolina; Yurrita, María Marta; Molina, Eduviges; Palmieri, Margarita; Black, William C

    2004-09-01

    Gene flow was examined among Anopheles albimanus populations from Cuba, Mexico, Guatemala, El Salvador, Nicaragua, Costa Rica, Panama, Colombia, and Venezuela by examining variation at four microsatellite (MS) loci and a mitochondrial DNA (mtDNA) marker. There was little variation among Central American populations and weak isolation by distance was only observed with the MS loci. There was moderate to large variation between Central and South American populations, suggesting a barrier to gene flow between Central and South America. However, Panamanian and Pacific Costa Rican populations differed with respect to western Central America, suggesting that there may be another barrier within Central America. There was small to moderate variation among Caribbean and continental populations. Phylogenetic and diversity analyses of mtDNA indicate that more ancestral and diverse haplotypes were present in the Caribbean population, suggesting that current continental An. albimanus populations may have originated from the Caribbean.

  5. Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci: high variation but low differentiation

    DEFF Research Database (Denmark)

    Simonsen, Bo Thisted; Siegismund, H R; Arctander, P

    1998-01-01

    The African buffalo (Syncerus caffer) is widespread throughout sub-Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed...... of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male-biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic...

  6. 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...

  7. Microsatellite Analysis of the Population Genetic Structure of Anolis carolinensis Introduced to the Ogasawara Islands.

    Science.gov (United States)

    Sugawara, Hirotaka; Takahashi, Hiroo; Hayashi, Fumio

    2015-01-01

    DNA analysis can reveal the origins and dispersal patterns of invasive species. The green anole Anolis carolinensis is one such alien animal, which has been dispersed widely by humans from its native North America to many Pacific Ocean islands. In the Ogasawara (Bonin) Islands, this anole was recorded from Chichi-jima at the end of the 1960s, and then from Haha-jima in the early 1980s. These two islands are inhabited. In 2013, it was also found on the uninhabited Ani-jima, close to Chichi-jima. Humans are thought to have introduced the anole to Haha-jima, while the mode of introduction to Ani-jima is unknown. To clarify its dispersal patterns within and among these three islands, we assessed the fine-scale population genetic structure using five microsatellite loci. The results show a homogeneous genetic structure within islands, but different genetic structures among islands, suggesting that limited gene flow occurs between islands. The recently established Ani-jima population may have originated from several individuals simultaneously, or by repeated immigration from Chichi-jima. We must consider frequent incursions among these islands to control these invasive lizard populations and prevent their negative impact on native biodiversity.

  8. Correlation Analysis of Microsatellite DNA Markers Related to Muscular Quality Traits in Mirror Common Carp(Cyprinus carpio L.)%镜鲤肌肉品质性状的微卫星标记分析

    Institute of Scientific and Technical Information of China (English)

    吴景; 郑先虎; 匡友谊; 吕伟华; 曹顶臣; 孙效文

    2013-01-01

    A total of 233 microsatellite markers were used to analyze the genotypes in the reference panel contained 107 individuals obtained from mirror common carp(Cyprinus carpio L.) strain, and two muscle quality traits including fat content and protein content were tested using GLM (General Linear Model) single marker of the regression. The determination of the threshold values by 10000 Permutation test revealed that 17 markers had significant correlation (P < 0.05) with the two traits, in which HLJ030, HLJ2560, HLJ3633 and HLJ3554 had very significant correlation with muscle protein content(P<0.01). In addition, the genotypes of these cor-relative loci captured were determined by Daucan’s in SPSS 17.0 software. These functional markers and genotypes related to the traits may provide the efficient evidence for improving muscle quality trait in the common carp.%利用233个微卫星标记检测镜鲤(Cyprinus carpio L.)一个家系的107尾个体的基因型,采用GLM方法对肌肉脂肪含量和蛋白质含量4种经济性状进行单标记回归分析。 Permutation检验结果显示:有17个标记分别与肌肉脂肪和蛋白质含量具有显著相关性(P<0.05),其中,有4个标记(HLJ030、HLJ2560、HLJ3633,和HLJ3554)与肌肉蛋白质含量呈极显著相关(P<0.01),表明这些标记与性状间可能存在连锁关系。对同一标记不同基因型之间进行了多重比较,找到了与这两种性状相关的优势基因型,为鲤的肌肉品质性状选育提供了有效的依据。

  9. Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites.

    Science.gov (United States)

    Godoy, J A; Jordano, P

    2001-09-01

    A long-standing challenge in studies of seed dispersal by animal frugivores has been the characterization of the spatial relationships between dispersed seeds and the maternal plants, i.e. the seed shadow. The difficulties to track unambiguously the origin of frugivore-dispersed seeds in natural communities has been considered an unavoidable limitation of the research field and precluded a robust analysis of the direct consequences of zoochory. Here we report that the multilocus genotype at simple sequence repeat (SSR; microsatellite) loci of the woody endocarp, a tissue of maternal origin, provides an unequivocal genetic fingerprint of the source tree. By comparing the endocarp genotype against the complete set of genotypes of reproductive trees in the population, we could unambiguously identify the source tree for 82.1% of the seeds collected in seed traps and hypothesize that the remaining 17.9% of sampled seeds come from other populations. Identification of the source tree for Prunus mahaleb seeds dispersed by frugivores revealed a marked heterogeneity in the genetic composition of the seed rain in different microhabitats, with a range of 1-5 distinct maternal trees contributing seeds to a particular landscape patch. Within-population dispersal distances ranged between 0 and 316 m, with up to 62% of the seeds delivered within 15 m of the source trees. Long distance dispersal events, detected by the exclusion of all reproductive trees in the population, accounted for up to 17.9% of the seeds sampled. Our results indicate strong distance limitation of seed delivery combined with infrequent long-distance dispersal events, extreme heterogeneity in the landscape pattern of genetic makeup, and a marked mosaic of multiple parentage for the seeds delivered to a particular patch.

  10. 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,...

  11. 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...

  12. 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

  13. 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.

  14. 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...

  15. Microsatellite analysis of the genetic relationships between wild and cultivated giant grouper in the South China Sea

    Indian Academy of Sciences (India)

    QING WANG; XIANG WANG; ZHENZHEN XIE; YIQ ILI; LING XIAO; CHENG PENG; HAIFA ZHANG; SHUISHENG LI; YONG ZHANG; HAORAN LIN

    2016-06-01

    The giant grouper (Epinephelus lanceolatus) is a coral fish with high commercial value in Southeast Asia. In the present study, we isolated 11 microsatellite DNA markers, and analysed the genetic diversity and differentiation between cultured stocks and wild populations of the giant grouper originating from the South China Sea. A total of 390 alleles at 11 microsatellite loci were detected in 130 individuals from five different populations. The expected heterozygosity varied from 0.131 to 0.855 with a mean value of 0.623 and the observed heterozygosity varied from 0.145 to 0.869 with a mean value of 0.379. The allelic richness and heterozygosity studies revealed that the genetic diversity of the cultured population was significantly reduced when compared with that of the wild population. The Fis,pairwise Fst values, analysis of molecular variance (AMOVA), three- dimensional factorial correspondence analysis and structure analysis revealed significant population differentiation between the cultured stocks and the wild populations, among the three cultured populations and between the two wild populations. These differences may be caused by random genetic drift, the effects of artificial selection and founder effects. Our results will be useful in the management of cultured stocks and conservation of wild populations of the giant group

  16. 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

  17. 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

  18. Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

    Science.gov (United States)

    Lukoschek, V; Waycott, M; Keogh, J S

    2008-07-01

    Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

  19. Microsatellite DNA markers: evaluating their potential for estimating the proportion of hatchery-reared offspring in a stock enhancement programme.

    Science.gov (United States)

    Bravington, M V; Ward, R D

    2004-05-01

    We describe a statistical method for estimating the effectiveness of a stock enhancement programme using nuclear DNA loci. It is based on knowing the population allele frequencies and the genotypes of the hatchery parents (mother only, or mother and father), and on determining the probability that a wild-born animal will by chance have a genotype consistent with hatchery origin. We show how to estimate the proportion of released animals in the wild population, and its standard error. The method is applied to a data set of eight microsatellite loci in brown tiger prawns (Penaeus esculentus), prior to the start of a possible enhancement programme. We conclude that, for this particular data set, the effectiveness of such an enhancement programme could be quantified accurately if both maternal and paternal genotypes are known, but not if maternal genotypes only are known. Full paternal genotyping would require offspring genotyping and thus would be expensive, but a partly typed paternal genotype from a mass homogenate of offspring would be almost as effective and much cheaper. The experiment would become feasible based on maternal genotypes alone, if a further three typical microsatellite loci could be found to add to the existing panel of eight. The methods detailed should be of interest to any enhancement project that relies on nuclear DNA markers to provide tags.

  20. High variation and very low differentiation in wide ranging plains zebra (Equus quagga): insights from mtDNA and microsatellites

    DEFF Research Database (Denmark)

    Lorenzen, Eline D; Arctander, Peter; Siegismund, Hans R

    2008-01-01

    Patterns of genetic differentiation in the plains zebra (Equus quagga) were analysed using mitochondrial DNA control region variation and seven microsatellites. The six morphologically defined subspecies of plains zebra lacked the population genetic structure indicative of distinct evolutionary...... units. Both marker sets showed high levels of genetic variation and very low levels of differentiation. There was no geographical structuring of mitochondrial DNA haplotypes in the phylogenetic tree, and the plains zebra showed the lowest overall differentiation recorded in any African ungulate studied...... so far. Arid-adapted African ungulates have shown significant regional genetic structuring in support of the Pleistocene refuge theory. This was not the case in the zebra, and the data are discussed in relation to the impact of Pleistocene climate change on a nonbovid member of the savannah ungulate...

  1. Linkage analysis of five Chinese families with arrhythmogenic right ventricular cardiomyopathy using microsatellite genetic markers

    Institute of Scientific and Technical Information of China (English)

    黄峻; 杨春梅; 马立隽; 单其俊; 许迪; 华子春; 曹克将

    2003-01-01

    Objective To explore the linkage relationship between specific genetic markers and arrhythmogenic right ventricular cardiomyopathy (ARVC) in Chinese pedigrees.Methods The microsatellite genetic markers D2S152, D14S252, and D10S1664 were studied for their linkages to ARVC in five Chinese ARVC pedigrees and a normal population of 121 Chinese individuals. Genomic DNA of the pedigrees and normal population was amplified using PCR techniques. Denaturing polyacrylamide sequencing gel (4%) electrophoresis was used to detect microsatellite repeat polymorphisms. Gels were silver-stained. A classical linkage analysis program was used assuming models of autosomal dominance and recession. Results The logarithm of the odds (LOD) scores of D2S152 with ARVC in LW, WD, DS, LC and TY pedigrees were 2.174, -0.589, -∞, - (indicating that linkage is not supported in this mode), and -∞ respectively in autosomal dominant model (recombination fraction=0.000 respectively)and were -∞, -∞, -∞, -∞, and 0.182 respectively in the autosomal recessive model. The LOD scores of D14S252 with ARVC in LW, WD, DS, LC and TY pedigrees were -, -, -∞, -, and 0 respectively in autosomal dominant model, and were -∞, -0.812, -∞, -∞, and 0.087 respectively in autosomal recessive model. The LOD scores of D2S152 with ARVC in LW, WD, DS, LC and TY pedigrees were -, -0.539, -, and 0.602 respectively in autosomal dominant model and were -, -∞, -∞, -∞, and -∞ respectively in autosomal recessive model. Conclusions The LOD score for D2S152 in the LW pedigree was 2.174, indicating that the chance of linkage is about 150∶ 1. This suggests that there is a possible ARVC-related gene near this marker. There were no clear linkage relationships between ARVC and D10S1664 and D14S252 in this family, and no linkages between ARVC and any of the three genetic markers in the other four families. These results also suggest that there is genetic heterogeneity in LW and in the other pedigrees.

  2. 结直肠癌线粒体基因组的微卫星不稳定性%Mitochondrial DNA microsatellite instability in colorectal cancer

    Institute of Scientific and Technical Information of China (English)

    崔海宏; 黄平; 赵婷; 张振华; 徐伟; 王小鹏; 韩英

    2012-01-01

    目的:探讨结直肠癌(colorectal cancer,CRC)线粒体DNA(mitochondrial DNA,mtDNA)非编码区及编码区的微卫星不稳定.方法:选取50例新鲜CRC及相应癌旁组织标本,提取基因组DNA.利用荧光标记聚合酶链反应及短重复序列位点扫描的方法,对线粒体DNA编码区及非编码区微卫星不稳定进行比较分析.结果:共检出19例线粒体微卫星不稳定(mitochondrial microsatellite instability,mtMSl),发生率为38%(19/50),线粒体非编码区微卫星与编码区微卫星不稳定有显著相关性(重要数据列出来P<0.05).结论:结直肠癌患者肠黏膜细胞mtDNA中存在较高频率的微卫星不稳定,在一些结直肠癌的发生中可能起一定作用.%AIM: To investigate microsatellite instability in the non-coding region and coding regions of mitochondrial DNA in colorectal cancer. METHODS: Mitochondrial DNA was extracted from 50 cases of fresh CRC samples and matched tumor-adjacent noncancerous tissue. Fluorescence polymerase chain reaction and short tandem repeat locus scanning were conducted to analyze microsatellite instability. RESULTS: Mitochondrial DNA microsatellite instability was detected in 19 of 50 (38%) patients with CRC. The microsatellite instability in the non-coding region and coding region of mitochondrial DNA had a significant correlation (X2 = 4.929, P = 0.026). CONCLUSION: There is a high frequency of microsatellite instability in mitochondrial DNA of CRC patients, and mitochondrial DNA micro-satellite instability may play a role in the occurrence of colorectal cancer.

  3. Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers

    Directory of Open Access Journals (Sweden)

    Wallace Richard

    2007-06-01

    Full Text Available Abstract Background The eastern oyster, Crassostrea virginica (Gmelin 1791, is an economically important species cultured in many areas in North America. It is also ecologically important because of the impact of its filter feeding behaviour on water quality. Populations of C. virginica have been threatened by overfishing, habitat degradation, and diseases. Through genome research, strategies are being developed to reverse its population decline. However, large-scale expressed sequence tag (EST resources have been lacking for this species. Efficient generation of EST resources from this species has been hindered by a high redundancy of transcripts. The objectives of this study were to construct a normalized cDNA library for efficient EST analysis, to generate thousands of ESTs, and to analyze the ESTs for microsatellites and potential single nucleotide polymorphisms (SNPs. Results A normalized and subtracted C. virginica cDNA library was constructed from pooled RNA isolated from hemocytes, mantle, gill, gonad and digestive tract, muscle, and a whole juvenile oyster. A total of 6,528 clones were sequenced from this library generating 5,542 high-quality EST sequences. Cluster analysis indicated the presence of 635 contigs and 4,053 singletons, generating a total of 4,688 unique sequences. About 46% (2,174 of the unique ESTs had significant hits (E-value ≤ 1e-05 to the non-redundant protein database; 1,104 of which were annotated using Gene Ontology (GO terms. A total of 35 microsatellites were identified from the ESTs, with 18 having sufficient flanking sequences for primer design. A total of 6,533 putative SNPs were also identified using all existing and the newly generated EST resources of the eastern oysters. Conclusion A high quality normalized cDNA library was constructed. A total of 5,542 ESTs were generated representing 4,688 unique sequences. Putative microsatellite and SNP markers were identified. These genome resources provide the

  4. Establishment of microsatellite-based triplex PCR for parentage analysis of Chinese shrimp Fenneropenaeus chinensis

    Institute of Scientific and Technical Information of China (English)

    GAO Huan; KONG Jie; LIU Ping; MENG Xianhong; LUAN Sheng; ZHANG Tianshi

    2007-01-01

    Through exploring the microsatellite primers from the random genome sequences of Chinese shrimp (Fenneropenaeus chinensis), some microsatellite primers were obtained with rich polymorphic genetic information, and a triplex PCR was established using three primers (RS1101, RS0683 and H081 primers). By adjusting the final concentration of Mg2+, dNTP and primers, and using a touch-town PCR program, the optimum amplification parameters of PCR system were obtained, which could successfully amplify the three primers in a PCR reaction. In the denatured PAGE gel, the amplified DNA fragments of three primers RS1 101,RS0683 and H081 could be easily identified each other. For the triplex PCR system, the PPE (probabilities of paternity exclusion) is 0.967 9,and the DP (discrimination power) is 0.999 327.Using the triplex PCR to test ten individuals of a parentage and their parents, an individual was excluded from the parentage in all of the three microsatellite loci, which might be mixed into the parentage for some unknown reason such as factitious misplay. The triplex PCR will be of great practical value in identifying the parentages of F. chinensis.

  5. 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.

  6. Isolation and genetic diversity analysis of microsatellite DNA in Macrobrachium nipponense%日本沼虾微卫星引物筛选及群体遗传多样性分析

    Institute of Scientific and Technical Information of China (English)

    冯建彬; 马克异; 李家乐; 华雪铭; 丁怀宇

    2010-01-01

    采用(CI)15、(CA)15两种生物素标记及磁珠富集法构建了太湖日本沼虾基因组微卫星富集文库.120个微卫星克隆中83个位点的核心序列重复在10个以上,长度介于191~580 bp,平均为311 bp;重复类型中,(CA/GT)n及(AG/TC)n分别占59.09%及20.45%,还检测到(GC)n(AAG)n、(ACAA)n和(GGCAGA)n等17种类型,包括25.75%完美型,20.45%非完美型和53.80%复合性.用其中12条微卫星引物扩增吴江、滨湖、宜兴和吴兴4个群体240个个体的基因组DNA,各位点表现出较高的遗传多样性,除Mni86、Mni103和Mni114外,其它群体位点大都表现出显著的杂合子缺失,4个群体的遗传分化为低度分化(FST<0.05),4个群体中97.58%遗传变异存在于群体内,仅有2.42%的遗传变异来自于群体之间;吴江和吴兴群体亲缘关系最近,与宜兴和滨湖群体亲缘关系渐远.

  7. Isolation and characterization of microsatellite DNA loci in the threatened flat-spired three-toothed land snail Triodopsis platysayoides

    Science.gov (United States)

    King, Timothy L.; Eackles, Michael S.; Garner, B. A.; van Tuinen, M.; Arbogast, B. S.

    2015-01-01

    The hermaphroditic flat-spired three-tooth land snail (Triodopsis platysayoides) is endemic to a 21-km stretch of the Cheat River Gorge of northeastern West Virginia, USA. We document isolation and characterization of ten microsatellite DNA markers in this at-risk species. The markers displayed a moderate level of allelic diversity (averaging 7.1 alleles/locus) and heterozygosity (averaging 58.6 %). Allelic diversity at seven loci was sufficient to produce unique multilocus genotypes; no indication of selfing was detected in this cosexual species. Minimal deviations from Hardy–Weinberg equilibrium and no linkage disequilibrium were observed within subpopulations. All loci deviated from Hardy–Weinberg expectations when individuals from subpopulations were pooled. Microsatellite markers developed for T. platysayoides yielded sufficient genetic diversity to (1) distinguish all individuals sampled and the level of selfing; (2) be appropriate for addressing fine-scale population structuring; (3) provide novel demographic insights for the species; and (4) cross-amplify and detect allelic diversity in the congeneric T. juxtidens.

  8. Population genetic patterns revealed by microsatellite data challenge the mitochondrial DNA based taxonomy of Astyanax in Mexico (Characidae, Teleostei).

    Science.gov (United States)

    Hausdorf, Bernhard; Wilkens, Horst; Strecker, Ulrike

    2011-07-01

    Astyanax has become an important model system for evolutionary studies of cave animals. We investigated correlations of population genetic patterns revealed by microsatellite data and phylogeographic patterns shown by mitochondrial DNA sequences in Mexican cave and surface fish of the genus Astyanax (Characidae, Teleostei) to improve the understanding of the colonization history of this neotropical fish in Central and North America and to assess a recent taxonomic classification. The distribution of nuclear genotypes is not congruent with that of the mitochondrial clades. Admixture analyses suggest there has been nuclear gene flow between populations defined by different mitochondrial clades. The microsatellite data indicate that there was mitochondrial capture of a cave population from adjacent populations. Furthermore, gene flow also occurred between populations belonging to different nuclear genotypic clusters. This indicates that neither the nuclear genotypic clusters nor the mitochondrial clades represent independent evolutionary units, although the mitochondrial divergences are high and in a range usually characteristic for different fish species. This conclusion is supported by the presence of morphologically intermediate forms. Our analyses show that the Trans-Mexican Volcanic Belt limited gene flow, but has been crossed by Astyanax several times. In Yucatán, where obvious geographic barriers are missing, the incongruence between the distribution of nuclear and mitochondrial markers reflects random colonization events caused by inundations or marine transgressions resulting in random phylogeographic breaks. Thus, conclusions about the phylogeographic history and even more about the delimitation of species should not be based on single genetic markers.

  9. 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

  10. Restricted gene flow at the micro- and macro-geographical scale in marble trout based on mtDNA and microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Patarnello Tomaso

    2011-04-01

    Full Text Available Abstract Background The genetic structure of the marble trout Salmo trutta marmoratus, an endemic salmonid of northern Italy and the Balkan peninsula, was explored at the macro- and micro-scale level using a combination of mitochondrial DNA (mtDNA and microsatellite data. Results Sequence variation in the mitochondrial control region showed the presence of nonindigenous haplotypes indicative of introgression from brown trout into marble trout. This was confirmed using microsatellite markers, which showed a higher introgression at nuclear level. Microsatellite loci revealed a strong genetic differentiation across the geographical range of marble trout, which suggests restricted gene flow both at the micro-geographic (within rivers and macro-geographic (among river systems scale. A pattern of Isolation-by-Distance was found, in which genetic samples were correlated with hydrographic distances. A general West-to-East partition of the microsatellite polymorphism was observed, which was supported by the geographic distribution of mitochondrial haplotypes. Conclusion While introgression at both mitochondrial and nuclear level is unlikely to result from natural migration and might be the consequence of current restocking practices, the pattern of genetic substructuring found at microsatellites has been likely shaped by historical colonization patterns determined by the geological evolution of the hydrographic networks.

  11. Population structure and gene flow of the Atlantic walrus ( Odobenus rosmarus rosmarus ) in the eastern Atlantic Arctic based on mitochondrial DNA and microsatellite variation

    DEFF Research Database (Denmark)

    Andersen, L.W.; Born, E.W.; Gjertz, I.;

    1998-01-01

    The population structure of the Atlantic walrus, Odobenus rosmarus rosmarus, was studied using 11 polymorphic microsatellites and restriction fragment length polymorphism detected in the NADH-dehydrogenase ND1, ND2 and ND3/4 segments in mtDNA. A total of 105 walrus samples were analysed from nort...

  12. Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

    Directory of Open Access Journals (Sweden)

    Emma C. Wallace

    2017-05-01

    Full Text Available Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92% produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.

  13. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata.

    Science.gov (United States)

    Jamsari, Amirul Firdaus Jamaluddin; Min-Pau, Tan; Siti-Azizah, Mohd Nor

    2011-04-01

    Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae), a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07) was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.

  14. Isolation and multiplex genotyping of polymorphic microsatellite DNA markers in the snakehead murrel, Channa striata

    Directory of Open Access Journals (Sweden)

    Amirul Firdaus Jamaluddin Jamsari

    2011-01-01

    Full Text Available Seven polymorphic microsatellite loci were isolated and characterized for the snakehead murrel, Channa striata (Channidae, a valuable tropical freshwater fish species. Among 25 specimens collected from Kedah state in Malaysia, the number of alleles per locus ranged from 2 to 7. Observed and expected heterozygosities ranged from 0.120 to 0.880 and 0.117 to 0.698, respectively. A single locus (CS1-C07 was significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction. These novel markers would be useful for population genetic studies of the C. striata.

  15. Forensic species identification of large macaws using DNA barcodes and microsatellite profiles.

    Science.gov (United States)

    Abe, Hideaki; Hayano, Azusa; Inoue-Murayama, Miho

    2012-01-01

    Using mitochondrial and nuclear markers species identification was conducted in the case of seized feathers. Earlier, we had sequenced cytochrome c oxidase subunit I (COI) both from 10 seized specimens and 43 validation specimens from captive macaws belonging to 4 Ara species (A. macao, A. chloropterus, A. ararauna, and A. ambiguus) and identified 19 haplotypes based on COI sequences. Species-level identification using Barcode of Life Data Systems showed that seized feathers shared the highest similarity with scarlet macaws (A. macao), and this result was supported by the tree-base identification with high bootstrap values. Moreover, microsatellite profiles in AgGT17 locus showed that patterns of allelic distribution in the seized feathers were apparently distinct from those of red-and-green macaw (A. chloropterus), but were overlapped with those of A. macao, suggesting that all of seized feathers were derived from several individuals of A. macao. We also determined the parentage of hybrid macaws by the combination of COI barcodes and microsatellite profiles. The technique presented here will contribute to forensic identification and future conservation of large macaws that have been lost due to deforestation.

  16. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.

    Science.gov (United States)

    Cornuet, Jean-Marie; Pudlo, Pierre; Veyssier, Julien; Dehne-Garcia, Alexandre; Gautier, Mathieu; Leblois, Raphaël; Marin, Jean-Michel; Estoup, Arnaud

    2014-04-15

    DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X. Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc CONTACT: estoup@supagro.inra.fr Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Microsatellite Analysis of Genetic Diversity Between Loach with Different Levels of Ploidy

    Institute of Scientific and Technical Information of China (English)

    Li Ya-juan; Qi Hong-rui; Ma Hai-yan; Zhou He; Xu Wen; Sui Yi; Li Jia-qi

    2014-01-01

    We used microsatellite markers to investigate the genetic parameters of three different polyploidy populations ofMisgurnus anguillicaudatus from Honghu City, Hubei Province. Polyacrylamide gel electrophoresis banding patterns of diploid (2n), triploid (3n) and tetraploid loaches (4n) were analyzed with PopGen software. A total of 68 alleles were obtained from seven microsatellite loci and the polymorphism information content (PIC) indices were all above 0.5. The average expected mean heterozygosity values (He) were 0.8420, 0.7186 and 0.8521; the average observed mean heterozygosity values (Ho) were 0.9674, 0.9785 and 0.8928; and the Hardy-WeinbergP values were 0.3078, 0.3151 and 0.3762, for diploid, triploid and tetraploid individuals, respectively. The results indicated that the three populations were highly polymorphic, with no deviations from Hardy-Weinberg equilibrium observed at all the seven microsatellite loci. This indicated a high level of genetic diversity within the populations. A cluster analysis diagram showed that the shortest genetic distance was between diploid and tetraploid loaches and they shared a close phylogenetic relationship. The triploid and tetraploid individuals had the most distant phylogenetic relationship.

  18. Identification of geographically distributed sub-populations of Leishmania (Leishmania major by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Schwenkenbecher Jan

    2008-06-01

    Full Text Available Abstract Background Leishmania (Leishmania major, one of the agents causing cutaneous leishmaniasis (CL in humans, is widely distributed in the Old World where different species of wild rodent and phlebotomine sand fly serve as animal reservoir hosts and vectors, respectively. Despite this, strains of L. (L. major isolated from many different sources over many years have proved to be relatively uniform. To investigate the population structure of the species highly polymorphic microsatellite markers were employed for greater discrimination among it's otherwise closely related strains, an approach applied successfully to other species of Leishmania. Results Multilocus Microsatellite Typing (MLMT based on 10 different microsatellite markers was applied to 106 strains of L. (L. major from different regions where it is endemic. On applying a Bayesian model-based approach, three main populations were identified, corresponding to three separate geographical regions: Central Asia (CA; the Middle East (ME; and Africa (AF. This was congruent with phylogenetic reconstructions based on genetic distances. Re-analysis separated each of the populations into two sub-populations. The two African sub-populations did not correlate well with strains' geographical origin. Strains falling into the sub-populations CA and ME did mostly group according to their place of isolation although some anomalies were seen, probably, owing to human migration. Conclusion The model- and distance-based analyses of the microsatellite data exposed three main populations of L. (L. major, Central Asia, the Middle East and Africa, each of which separated into two sub-populations. This probably correlates with the different species of rodent host.

  19. Genetic characterization of Kenai brown bears (Ursus arctos): Microsatellite and mitochondrial DNA control region variation in brown bears of the Kenai Peninsula, south central Alaska

    Science.gov (United States)

    Jackson, J.V.; Talbot, S.L.; Farley, S.

    2008-01-01

    We collected data from 20 biparentally inherited microsatellite loci, and nucleotide sequence from the maternally inherited mitochondrial DNA (mtDNA) control region, to determine levels of genetic variation of the brown bears (Ursus arctos L., 1758) of the Kenai Peninsula, south central Alaska. Nuclear genetic variation was similar to that observed in other Alaskan peninsular populations. We detected no significant inbreeding and found no evidence of population substructuring on the Kenai Peninsula. We observed a genetic signature of a bottleneck under the infinite alleles model (IAM), but not under the stepwise mutation model (SMM) or the two-phase model (TPM) of microsatellite mutation. Kenai brown bears have lower levels of mtDNA haplotypic diversity relative to most other brown bear populations in Alaska. ?? 2008 NRC.

  20. Complementary analysis of microsatellite tumor profile and mismatch repair defects in colorectal carcinomas

    Institute of Scientific and Technical Information of China (English)

    Alfredo Blanes; Salvador J Diaz-Cano

    2006-01-01

    Microsatellite instability (MSI) is a prognostic factor and a marker of deficient mismatch repair (MMR) in colorectal adenocarcinomas (CRC). However, a proper application of this marker requires understanding the following: (1)The MSI concept: The PCR approach must amplify the correct locus and accurately identify the microsatellite pattern in the patient's normal tissue. MSI is demonstrated when the length of DNA sequences in a tumor differs from that of nontumor tissue. Any anomalous expansion or reduction of tandem repeats results in extra-bands normally located in the expected size range (100 bp,above or below the expected product), differ from the germline pattern by some multiple of the repeating unit,and must show appropriate stutter. (2) MSI mechanisms:MMR gene inactivation (by either mutation or protein down-regulation as frequently present in deep CRC compartments) leads to mutation accumulation in a cell with every cellular division, resulting in malignant transformation. These mechanisms can express tumor progression and result in a decreased prevalence of aneuploid cells and loss of the physiologic cell kinetic correlations in the deep CRC compartments. MSI molecular mechanisms are not necessarily independent from chromosomal instability and may coexist in a given CRC. (3) Because of intratumoural heterogeneity, at least two samples from each CRC should be screened, preferably from the superficial (tumor cells above the muscularis propria) and deep (tumor cells infiltrating the muscularis propria) CRC compartments to cover the topographic tumor heterogeneity. (4) Pathologists play a critical role in identifying microsatellite-unstable CRC, such as occur in young patients with synchronous or metachronous tumors or with tumors showing classic histologic features. In these cases, MSI testing and/or MMR immunohistochemistry are advisable, along with gene sequencing and genetic counseling if appropriate. MSI is an excellent functional and prognostically

  1. Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0

    Directory of Open Access Journals (Sweden)

    Estoup Arnaud

    2010-07-01

    Full Text Available Abstract Background Approximate Bayesian computation (ABC is a recent flexible class of Monte-Carlo algorithms increasingly used to make model-based inference on complex evolutionary scenarios that have acted on natural populations. The software DIYABC offers a user-friendly interface allowing non-expert users to consider population histories involving any combination of population divergences, admixtures and population size changes. We here describe and illustrate new developments of this software that mainly include (i inference from DNA sequence data in addition or separately to microsatellite data, (ii the possibility to analyze five categories of loci considering balanced or non balanced sex ratios: autosomal diploid, autosomal haploid, X-linked, Y-linked and mitochondrial, and (iii the possibility to perform model checking computation to assess the "goodness-of-fit" of a model, a feature of ABC analysis that has been so far neglected. Results We used controlled simulated data sets generated under evolutionary scenarios involving various divergence and admixture events to evaluate the effect of mixing autosomal microsatellite, mtDNA and/or nuclear autosomal DNA sequence data on inferences. This evaluation included the comparison of competing scenarios and the quantification of their relative support, and the estimation of parameter posterior distributions under a given scenario. We also considered a set of scenarios often compared when making ABC inferences on the routes of introduction of invasive species to illustrate the interest of the new model checking option of DIYABC to assess model misfit. Conclusions Our new developments of the integrated software DIYABC should be particularly useful to make inference on complex evolutionary scenarios involving both recent and ancient historical events and using various types of molecular markers in diploid or haploid organisms. They offer a handy way for non-expert users to achieve model checking

  2. Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness.

    Science.gov (United States)

    Telfer, Emily J; Stovold, Grahame T; Li, Yongjun; Silva-Junior, Orzenil B; Grattapaglia, Dario G; Dungey, Heidi S

    2015-01-01

    Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource

  3. Chromosomal locations of four minor rDNA loci and a marker microsatellite sequence in barley

    DEFF Research Database (Denmark)

    Pedersen, C.; Linde-Laursen, I.

    1994-01-01

    is located about 54% out on the short arm of chromosome 4 and it has not previously been reported in barley. We have designated the new locus Nor-I6. rDNA loci on homoeologous group 4 chromosomes have not yet been reported in other Triticeae species. The origin of these 4 minor rDNA loci is discussed...

  4. Microsatellite DNA markers applied to detection of multiple paternity in Caiman latirostris in Santa Fe, Argentina.

    Science.gov (United States)

    Amavet, Patricia; Rosso, Esteban; Markariani, Rosa; Piña, Carlos Ignacio

    2008-12-01

    Detecting multiple paternity in wild populations of the broad-snouted caiman (Caiman latirostris) has important implications for conservation efforts. We have applied microsatellite markers to examine genetic variation in C. latirostris and also have provided the first data concerning detection of multiple paternity in wild populations of this species. Blood samples from four nest-guarding C. latirostris females and their hatchlings were obtained from Santa Fe Province, Argentina. Amplified products were analyzed by electrophoresis on 10% polyacrylamide gels and visualized with silver staining. Four out of the eight markers tested reliably amplified and yielded useful data. Using polyacrylamide gels with silver staining provides high enough resolution to obtain individual genotypes. In order to assess the presence or absence of more than two parents in each nest, we used the single locus Minimum Method, and applied Cervus 3.0 and Gerud 2.0 software in parentage analyses. Our results indicate more than one father in at least two families. This behavior could be the consequence of high habitat variability in the area where our population was sampled. The ability to understand mating systems is important for maintaining viable populations of exploited taxa like C. latirostris.

  5. Nuclear and mitochondrial DNA microsatellite instability in hepatocellular carcinoma in Chinese

    Institute of Scientific and Technical Information of China (English)

    Dian-Chun Fang; Li Fang; Rong-Quan Wang; Shi-Ming Yang

    2004-01-01

    AIM: To study the nuclear microsatellite instability (nMSI)at BAT26 and mitochondral microsalellite instability (mtMSI)in the occurrence and development of hepatocellular carcinoma and the relationship between nMSI and mtMSI.METHODS: nMSI was observed with PCR and mtMSI with PCR-SSCP in 52 cases of hepatocellular carcinoma.RESULTS: mtMSI was detected in 11 out of the 52 cases of hepatocellular carcinoma (21.2%). Among the 11 cases of hepatocellular carcinoma with mtMSI, 7 occured in one locus and 4 in 2 loci. The frequency of mtMSI in the 52 cases of hepatocellular careinoma showed no correlation to sex, age,infection of hepatitis B, liver cirrhosis as well as positive AFP of the patients (P>0.05). In addition, nMSI was detected in 3 out of 52 cases of hepatocellular carcinoma (5.8%) and there was no correlation of the incidence of mtMSI to that CONCLUSION: mtMSI may be involved in the coccurrence and development of hepatocellular carcinoma and it is independent of nMSI.

  6. 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.

  7. Inferring Genetic Variation and Demographic History of Michelia yunnanensis Franch. (Magnoliaceae from Chloroplast DNA Sequences and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Shikang Shen

    2017-04-01

    Full Text Available Michelia yunnanensis Franch., is a traditional ornamental, aromatic, and medicinal shrub that endemic to Yunnan Province in southwest China. Although the species has a large distribution pattern and is abundant in Yunnan Province, the populations are dramatically declining because of overexploitation and habitat destruction. Studies on the genetic variation and demography of endemic species are necessary to develop effective conservation and management strategies. To generate such knowledge, we used 3 pairs of universal cpDNA markers and 10 pairs of microsatellite markers to assess the genetic diversity, genetic structure, and demographic history of 7 M. yunnanensis populations. We calculated a total of 88 alleles for 10 polymorphic loci and 10 haplotypes for a combined 2,089 bp of cpDNA. M. yunnanensis populations showed high genetic diversity (Ho = 0.551 for nuclear markers and Hd = 0.471 for cpDNA markers and low genetic differentiation (FST = 0.058. Geographical structure was not found among M. yunnanensis populations. Genetic distance and geographic distance were not correlated (P > 0.05, which indicated that geographic isolation is not the primary cause of the low genetic differentiation of M. yunnanensis. Additionally, M. yunnanensis populations contracted ~20,000–30,000 years ago, and no recent expansion occurred in current populations. Results indicated that the high genetic diversity of the species and within its populations holds promise for effective genetic resource management and sustainable utilization. Thus, we suggest that the conservation and management of M. yunnanensis should address exotic overexploitation and habitat destruction.

  8. Genetic relationships of grizzly bears (Ursus arctos) in the Prudhoe Bay region of Alaska: inference from microsatellite DNA, mitochondrial DNA, and field observations.

    Science.gov (United States)

    Cronin, M; Shideler, R; Hechtel, J; Strobeck, C; Paetkau, D

    1999-01-01

    Grizzly bears are abundant in the region of the Prudhoe Bay oil fields in northern Alaska. We used field observations and molecular genetic data to identify parent-offspring and sibling relationships among bears in this region. We determined genotypes at 14 microsatellite DNA loci and the cytochrome b gene of mitochondrial DNA (mtDNA) for 36 bears. We identified 17 possible mother-offspring pairs and 8 possible father-offspring pairs. This includes verification of the relationships of 14 mother-offspring pairs identified from field observations. Three additional mother-offspring pairs and all eight father-offspring pairs were determined from genetic and age data. Relatedness coefficients based on numbers of shared alleles between individuals were as expected: approximately 0.50 for parent-offspring and sibling pairs and approximately 0.75 for a father-offspring pair resulting from a father-daughter mating. The level of genetic variation (mean number of alleles per locus = 6.6, mean heterozygosity = 70%) and allele frequencies in grizzly bears in the Prudhoe Bay region are similar to those in other parts of the species' range.

  9. Genetic diversity and differentiation of sea trout (Salmo trutta) populations in Lithuanian rivers assessed by microsatellite DNA variation.

    Science.gov (United States)

    Samuiloviene, Aurelija; Kontautas, Antanas; Gross, Riho

    2009-11-01

    The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F (ST) values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.

  10. Independent clonal origin of multiple uterine leiomyomas that was determined by X chromosome inactivation and microsatellite analysis

    DEFF Research Database (Denmark)

    Canevari, Renata A; Pontes, Anaglória; Rosa, Fabíola E;

    2005-01-01

    OBJECTIVE: In an attempt to clarify the clonality and genetic relationships that are involved in the tumorigenesis of uterine leiomyomas, we used a total of 43 multiple leiomyomas from 14 patients and analyzed the allelic status with 15 microsatellite markers and X chromosome inactivation analysis....... STUDY DESIGN: We have used a set of 15 microsatellite polymorphism markers mapped on 3q, 7p, 11, and 15q by automated analysis. The X chromosome inactivation was evaluated by the methylation status of the X-linked androgen receptor gene. RESULTS: Loss of heterozygosity analysis showed a different...... pattern in 7 of the 8 cases with allelic loss for at least 1 of 15 microsatellite markers that were analyzed. A similar loss of heterozygosity findings at 7p22-15 was detected in 3 samples from the same patient. X chromosome inactivation analysis demonstrated the same inactivated allele in all tumors...

  11. Heterozygosity analysis of Bionda Piemontese and Bianca di Saluzzo chicken breeds by microsatellites markers: a preliminary study

    Directory of Open Access Journals (Sweden)

    M. Longeri

    2010-04-01

    Full Text Available Conservation of genetic variability is one of the main goals in animal production science and the analysis of breeds genetic asset can supply objective basis for effective conservation programs and selection strategies. Bionda Piemontese (PIB and Bianca di Saluzzo (SAB chicken breeds originated in Piemonte region. Breeds conservation programmes started in 1999 in Verzuolo (CN aiming to preserve the breeds and to improve their diffusion being particularly adapted to free range rearing systems thanks to their resistance. PIB and SAB are both suggested for traditional recipes and production (e.g. Morozzo capon and are Slow Food presidia. A total of 76 birds were analysed: PIB (n=36, SAB (n=40. Genomic DNA was extracted from blood samples. All birds were genotyped at eight microsatellite loci. Each marker was subjected to PCR and the products were separated by electrophoresis in 4.2% denaturing polyacrylamide gels on ABI Prism 377 DNA Sequencer equipped with Genescan and Genotyper software. The results of this preliminary study highlight the genetic differences occurring between PIB and SAB populations

  12. 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

  13. Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA.

    Science.gov (United States)

    Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

    2014-11-01

    There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids.

  14. Microsatellite (SSR amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands

    Directory of Open Access Journals (Sweden)

    Abasalt Hossienzadeh-Colagar

    2016-09-01

    Full Text Available Microsatellites or simple sequence repeats (SSRs are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP; but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced ‘stutter products’ differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as ‘stutter bands’. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered.

  15. Microsatellite-centromere mapping in Japanese scallop ( Patinopecten yessoensis) through half-tetrad analysis in gynogenetic diploid families

    Science.gov (United States)

    Li, Qi; Qi, Mingjun; Nie, Hongtao; Kong, Lingfeng; Yu, Hong

    2016-06-01

    Gene-centromere mapping is an essential prerequisite for understanding the composition and structure of genomes. Half-tetrad analysis is a powerful tool for mapping genes and understanding chromosomal behavior during meiosis. The Japanese scallop ( Patinopecten yessoensis), a cold-tolerant species inhabiting the northwestern Pacific coast, is a commercially important marine bivalve in Asian countries. In this study, inheritance of 32 informative microsatellite loci was examined in 70-h D-shaped larvae of three induced meiogynogenetic diploid families of P. yessoensis for centromere mapping using half-tetrad analysis. The ratio of gynogenetic diploids was proven to be 100%, 100% and 96% in the three families, respectively. Inheritance analysis in the control crosses showed that 51 of the 53 genotypic ratios observed were in accordance with Mendelian expectations at the 5% level after Bonferroni correction. Seven of the 32 microsatellite loci showed the existence of null alleles in control crosses. The second division segregation frequency ( y) of the microsatellite loci ranged from 0.07 to 0.85 with a mean of 0.38, suggesting the existence of positive interference after a single chiasma formation in some chromosomes in the scallop. Microsatellite-centromere distances ranged from 4 cM to 42 cM under the assumption of complete interference. Information on the positions of centromeres in relation to the microsatellite loci will represent a contribution towards the assembly of genetic maps in the commercially important scallop species.

  16. High frequency of extrapair fertilization in a plural breeding bird, the Mexican jay, revealed by DNA microsatellites.

    Science.gov (United States)

    Li; Brown

    2000-12-01

    We used tetra-nucleotide microsatellite DNA typing to estimate the frequency of extrapair fertilization (EPF) in a plural breeding species, the Mexican jay, Aphelocoma ultramarina, in Arizona. We found EPF in 32 of 51 complete broods (63%) and 55 of 139 nestlings (40%) for which the putative father had been identified (one of the highest rates of EPF known for birds). At least 96.1% of EPF fathers came from within the group. This is by far the highest known within-group EPF rate among socially monogamous, communally rearing species. Most (70%) males of breeding age (3+ years) had no genetic paternity in a given year. Social fathers (i.e. those with nests and mated females) rarely obtained EPFs; of 25 social fathers, 23 had young in only one nest and only two had young in two nests by virtue of EPF. Of the 27 males known to be EPF fathers without a nest of their own, none had young in more than one nest. Only 7% of EPF fathers had their own broods reaching banding age (day 14), compared with 29.7% of social fathers. The proportion of EPF young was significantly larger in smaller broods. Breeding females in all age classes were equally likely to have EPF young. Copyright 2000 The Association for the Study of Animal Behaviour.

  17. Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers.

    Science.gov (United States)

    Hama-Ali, Emad Omer; Alwee, Sharifah Shahrul Rabiah Syed; Tan, Soon Guan; Panandam, Jothi Malar; Ling, Ho Chai; Namasivayam, Parameswari; Peng, Hoh Boon

    2015-05-01

    Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method.

  18. A novel microsatellite DNA marker at locus D7S1870 detects hemizygosity in 75% of patients with Williams syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert-Dussardier, B. [Hopital des Enfants-Malades, Paris (France)]|[Hopital Dupuytren, Limoges (France); Bonneau, D. [Hopital des Enfants-Malades, Paris (France)]|[Hopital Jean Bernard, Poitiers (France); Gigarel, N.; Le Merrer, M.; Bonnet, D.; Lyonnet, S.; Munnich, A. [Hopital des Enfants-Malades, Paris (France); Philip, N.; Mattei, M.G. [Hopital de La Timone, Marseille (France)] [and others

    1995-02-01

    Williams syndrome (WS) is a predominantly sporadic developmental disorder characterized by dysmorphic facial features, infantile hypercalcemia, premature aging of skin, mental retardation and gregarious personality. Supravalvular aortic stenosis (SVAS) and other vascular diseases caused by the narrowing of large elastic arteries are present in almost 80% of cases. Recently, hemizygosity at the elastin locus has been shown in sporadic WS, suggesting that this disease is caused by deletions encompassing the elastin gene on chromosome 7q11.23. Taking advantage of a large series of sporadic WS (27 cases), we have explored the potential application of novel microsatellite DNA markers in the rapid detection of hemizygosity in WS. We report here a highly informative marker at locus D7S1870, which detected failure of parental inheritance in almost 75% of cases of WS in our series. This marker can be regarded therefore as a reliable and useful diagnostic tool in suspected cases of WS as well as in complicated forms of supravalvular aortic stenosis. 10 refs., 2 figs.

  19. Microsatellite DNA fingerprints and genetic diversity of sugarcane cultivars (clones) from Guizhou Province

    Science.gov (United States)

    Twelve sugarcane genotypes (three cultivars and nine clones involved in regional tests) from Guizhou Province, China were analyzed using SSR-capillary electrophoresis/fluorescence detection (SSR-CE/FD) technology to construct the SSR fingerprints and assess the genetic diversity. A total of 131 DNA ...

  20. Development and characterization of highly polymorphic long TC repeat microsatellite markers for genetic analysis of peanut

    Directory of Open Access Journals (Sweden)

    Macedo Selma E

    2012-02-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is a crop of economic and social importance, mainly in tropical areas, and developing countries. Its molecular breeding has been hindered by a shortage of polymorphic genetic markers due to a very narrow genetic base. Microsatellites (SSRs are markers of choice in peanut because they are co-dominant, highly transferrable between species and easily applicable in the allotetraploid genome. In spite of substantial effort over the last few years by a number of research groups, the number of SSRs that are polymorphic for A. hypogaea is still limiting for routine application, creating the demand for the discovery of more markers polymorphic within cultivated germplasm. Findings A plasmid genomic library enriched for TC/AG repeats was constructed and 1401 clones sequenced. From the sequences obtained 146 primer pairs flanking mostly TC microsatellites were developed. The average number of repeat motifs amplified was 23. These 146 markers were characterized on 22 genotypes of cultivated peanut. In total 78 of the markers were polymorphic within cultivated germplasm. Most of those 78 markers were highly informative with an average of 5.4 alleles per locus being amplified. Average gene diversity index (GD was 0.6, and 66 markers showed a GD of more than 0.5. Genetic relationship analysis was performed and corroborated the current taxonomical classification of A. hypogaea subspecies and varieties. Conclusions The microsatellite markers described here are a useful resource for genetics and genomics in Arachis. In particular, the 66 markers that are highly polymorphic in cultivated peanut are a significant step towards routine genetic mapping and marker-assisted selection for the crop.

  1. Population Genetics of Overwintering Monarch Butterflies, Danaus plexippus (Linnaeus), from Central Mexico Inferred from Mitochondrial DNA and Microsatellite Markers

    Science.gov (United States)

    Pfeiler, Edward; Nazario-Yepiz, Nestor O.; Pérez-Gálvez, Fernan; Chávez-Mora, Cristina Alejandra; Laclette, Mariana Ramírez Loustalot; Rendón-Salinas, Eduardo

    2017-01-01

    Abstract Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and 7 microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from 4 overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the 2 behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the 2 groups, possibly owing to the number of significant deviations from Hardy–Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35000–40000 years before present) followed by a stable effective female population size (Nef) of about 6 million over the last 10000 years. PMID:28003372

  2. Population Genetics of Overwintering Monarch Butterflies, Danaus plexippus (Linnaeus), from Central Mexico Inferred from Mitochondrial DNA and Microsatellite Markers.

    Science.gov (United States)

    Pfeiler, Edward; Nazario-Yepiz, Nestor O; Pérez-Gálvez, Fernan; Chávez-Mora, Cristina Alejandra; Laclette, Mariana Ramírez Loustalot; Rendón-Salinas, Eduardo; Markow, Therese Ann

    2017-03-01

    Population genetic variation and demographic history in Danaus plexippus (L.), from Mexico were assessed based on analyses of mitochondrial cytochrome c oxidase subunit I (COI; 658 bp) and subunit II (COII; 503 bp) gene segments and 7 microsatellite loci. The sample of 133 individuals included both migratory monarchs, mainly from 4 overwintering sites within the Monarch Butterfly Biosphere Reserve (MBBR) in central Mexico (states of Michoacán and México), and a nonmigratory population from Irapuato, Guanajuato. Haplotype (h) and nucleotide (π) diversities were relatively low, averaging 0.466 and 0.00073, respectively, for COI, and 0.629 and 0.00245 for COII. Analysis of molecular variance of the COI data set, which included additional GenBank sequences from a nonmigratory Costa Rican population, showed significant population structure between Mexican migratory monarchs and nonmigratory monarchs from both Mexico and Costa Rica, suggesting limited gene flow between the 2 behaviorally distinct groups. Interestingly, while the COI haplotype frequencies of the nonmigratory populations differed from the migratory, they were similar to each other, despite the great physical distance between them. Microsatellite analyses, however, suggested a lack of structure between the 2 groups, possibly owing to the number of significant deviations from Hardy-Weinberg equilibrium resulting from heterzoygote deficiencies found for most of the loci. Estimates of demographic history of the combined migratory MBBR monarch population, based on the mismatch distribution and Bayesian skyline analyses of the concatenated COI and COII data set (n = 89) suggested a population expansion dating to the late Pleistocene (~35000-40000 years before present) followed by a stable effective female population size (Nef) of about 6 million over the last 10000 years. © The American Genetic Association 2016.

  3. Genetic diversity in four populations of Nguni (Zulu sheep assessed by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    Nokuthula W. Kunene

    2014-02-01

    Full Text Available Zulu sheep are found mainly in the rural KwaZulu-Natal province and the numbers are declining due to indiscriminate inbreeding. There is thus a need for phenotypic and genetic characterisation as a first phase for planning conservation strategies. Zulu sheep populations sampled were from Makhathini research station (MS (n=33, University of Zululand (UZ (n=21, a community at KwaMthethwa (KM (n=32 and from Msinga (EM (n=33. One European breed Appen - ninica (AP was used as out group. Microsatellite analysis using 29 microsatellite loci was used in this study. Among the Zulu sheep, the mean number of alleles per locus was the lowest (3.86 in UZ and the highest (6.24 was realised in EM. The mean values of observed and expected heterozygosity were 0.57 and 0.61, respectively. Neighbour-joining tree showed two main Zulu sheep clusters: the UZ, KM and MS sheep populations clustered together and the second cluster included only representatives from the EM population. The STRUCTURE analysis showed that KM, AP and EM were founded in separate clusters, whereas UZ and MS clustered together. The study demonstrated that there was a common origin of the population from the research stations (MS and UZ populations. It also demonstrated that the EM had a different history for the other three populations. This work suggests that exchange of rams could be useful in reducing inbreeding when considering conservation breeding programmes.

  4. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

    Directory of Open Access Journals (Sweden)

    Islam Md-Sajedul

    2012-03-01

    Full Text Available Abstract Background Huanglongbing (HLB is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida, Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a

  5. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide

    Science.gov (United States)

    2012-01-01

    Background Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. Results A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Conclusions Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources

  6. Multilocus microsatellite analysis of 'Candidatus Liberibacter asiaticus' associated with citrus Huanglongbing worldwide.

    Science.gov (United States)

    Islam, Md-Sajedul; Glynn, Jonathan M; Bai, Yang; Duan, Yong-Ping; Coletta-Filho, Helvecio D; Kuruba, Gopal; Civerolo, Edwin L; Lin, Hong

    2012-03-20

    Huanglongbing (HLB) is one of the most destructive citrus diseases in the world. The disease is associated with the presence of a fastidious, phloem-limited α- proteobacterium, 'Candidatus Liberibacter asiaticus', 'Ca. Liberibacter africanus' or 'Ca. Liberibacter americanus'. HLB-associated Liberibacters have spread to North America and South America in recent years. While the causal agents of HLB have been putatively identified, information regarding the worldwide population structure and epidemiological relationships for 'Ca. L. asiaticus' is limited. The availability of the 'Ca. L. asiaticus' genome sequence has facilitated development of molecular markers from this bacterium. The objectives of this study were to develop microsatellite markers and conduct genetic analyses of 'Ca. L. asiaticus' from a worldwide collection. Two hundred eighty seven isolates from USA (Florida), Brazil, China, India, Cambodia, Vietnam, Taiwan, Thailand, and Japan were analyzed. A panel of seven polymorphic microsatellite markers was developed for 'Ca. L. asiaticus'. Microsatellite analyses across the samples showed that the genetic diversity of 'Ca. L. asiaticus' is higher in Asia than Americas. UPGMA and STRUCTURE analyses identified three major genetic groups worldwide. Isolates from India were genetically distinct. East-southeast Asian and Brazilian isolates were generally included in the same group; a few members of this group were found in Florida, but the majority of the isolates from Florida were clustered separately. eBURST analysis predicted three founder haplotypes, which may have given rise to three groups worldwide. Our results identified three major genetic groups of 'Ca. L. asiaticus' worldwide. Isolates from Brazil showed similar genetic makeup with east-southeast Asian dominant group, suggesting the possibility of a common origin. However, most of the isolates recovered from Florida were clustered in a separate group. While the sources of the dominant 'Ca. L

  7. GENETIC STRUCTURE AND ALLEL DIVERSITY OF THREE BALINESE GENERATIONS BASED ON FIVE AUTOSOMAL MICROSATELLITE DNA LOCI

    Directory of Open Access Journals (Sweden)

    Ayu Saka Laksmita

    2015-09-01

    Full Text Available This research was aimed to find out the genetic structures of three generations of Balinese population, in order to determine the best loci used for paternity testing among this population, and observed the mutation rate of these loci. The DNA samples were taken from the epithelium cell of 25 families which were collected from the children, father, mother, grandfather and grandmother of the children, from both mother and father sides (family with three generations. The DNA was extracted in Phenol-Chloroform method with modifications. DNA amplification was conducted in PCR method using pairs of primer 5, namely: FGA, D18S51, D2S1338, TPOX, and D16S539, and its products were electrophoresed and visualized in 10% of PAGE, stained in silver nitrate. The genetic structures of the three family generations showed 30 variants with different frequencies in each locus. The highest heterozygosity value was detected in FGA (8 alleles, then followed by D18S51 (7 alleles, TPOX (6 alleles, D16S539 (5 alleles, and the lowest was in D2S1338 (4 alleles. The highest value of heterozigosity and Power of Discrimination were found in FGA, followed by TPOX, D18S51, D2S1338, and the lowest was in D16S539. Therefore, it can be concluded that out of five loci tested, 4 of them can be recommended to be used for paternity testing of Balinese population, except D16S539

  8. 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.

  9. Searching for a stock structure in Sardina pilchardus from the Adriatic and Ionian seas using a microsatellite DNA-based approach

    DEFF Research Database (Denmark)

    Ruggeri, Paolo; Splendiani, Andrea; Bonanomi, Sara;

    2013-01-01

    In the present study the genetic variability of European sardine from Adriatic and Ionian seas was investigated in order to detect the occurrence of genetic structure within and between these basins. In several samples the analysis of genetic variability at eight microsatellite loci showed a numb...

  10. 微卫星DNA多态性分析在常用近交系小鼠遗传监测中的应用研究%Microsatellite DNA Polymorphisms in Inbred Strain Mice and Selection as Genetic Monitoring Markers

    Institute of Scientific and Technical Information of China (English)

    欧阳兆和; 陈振文; 李瑞生; 战大伟

    2003-01-01

    The aim of genetic monitoring is to checking the genetic contamination within inbred starains, which insures that the strains according with the require of colony . At present the methods based on allozyme biochemistry are the National Standard instructed. methods that using microsatellite DNA would be more useful for genetic monitoring than methods based on allozyme biochemistry because the genome itself is being tested rather than a protein product and a larger portion of the genome can be sampled, and easy to distinguish. methods that using microsatellite DNA had abundant microsatellite loci(over 7300, before 1999) can be identified. Applying enough microsatellite loci will present abundant straps and well polymorphism, which can reflection inherit and variation of roundly genene. In addition, this novel approach allows the rapid, sensitive, convenientand accuracy, even individual identificaton. So we should select microsatellite DNA which is polymorphisms as genetic monitoring markers to determining the strains' origin and genetic background of inbred mice.Untill now Only feasibility has been reported, and in which microsatellite DNA loci have not enough polymorphisms to distinguish genetic differences. Articles on standards and practicality have not been founded in our country. With the optimization of components of reaction buffer and amplificaton parameter, PCR for amplification microsatellite DNA was finally set up. Using the techniques microsatellite DNA can amplified efficaciously. The final concentrations of Mg2+ was 1 . 5-3.0 mmol/L, annealing temperature was 50 ℃-65 ℃. The condition for the PCR amplify were , 94 ℃ for 3min, 30cycles of 94℃ for 30s, 50℃-65℃ for 30s,72℃ for 1min,finally at 72℃ for 1min,then store at 4℃.

  11. Microsatellite marker-based genetic analysis of relatedness between commercial and heritage turkeys (Meleagris gallopavo).

    Science.gov (United States)

    Kamara, D; Gyenai, K B; Geng, T; Hammade, H; Smith, E J

    2007-01-01

    The turkey is second only to the chicken in importance as an agriculturally important poultry species. Unlike the chicken, however, genetic studies of the turkey continue to be limited. For example, to date, many genomic investigations have been conducted to characterize genetic relationships between commercial (CO) and non-CO chicken breeds, whereas the nature of the genetic relatedness between CO and heritage turkeys remains unknown. The objective of the current research was to use microsatellites to analyze the genetic relatedness between CO and heritage domestic turkeys including Narragansett, Bourbon Red, Blue Slate, Spanish Black, and Royal Palm. Primer pairs specific for 10 previously described turkey microsatellite markers were used. The phylogenetic analysis showed that the Blue Slate, Bourbon Red, and Narragansett were genetically closely related to the CO strain, with a Nei distance of 0.30, and the Royal Palm and Spanish Black were the least related to the CO strain, with Nei distances of 0.41 and 0.40, respectively. The present work provides a foundation for the basis of using heritage turkeys to genetically improve CO populations by introgression.

  12. Parentage assignment and parental contribution analysis in large yellow croaker Larimichthys crocea using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Xiande LIU; Guangtai ZHAO; Zhiyong WANG; Mingyi CAI; Hua YE; Qiurong WANG

    2012-01-01

    The large yellow croaker Larimichthys crocea is one of the most important fish species in China.To estimate the reproductive success of breeders,three independent full-factorial crosses were created and the fins of breeders and progenies were sampled for microsatellite analysis.Out of 959 offspring from three sets,99.6% were assigned to their parents using 6-7 microsatellite markers.In all crosses,some parent pairs produced a large number of offspring and some parent pairs did not produce any offspring.The contributions of male or female parents were unequal,ranging from 1.0-89.3% across the three sets.The loss of putative Ne was 69.6% in set 1,31.2% in set 2 and 57.6% in set 3.These results suggest that the unequal contribution of parents is universal in artificial breeding ofL.crocea,especially in a small population,and this should be taken into account in hatcheries or when releasing animals for resource enhancement [Current Zoology 58 (2):244-249,2012].

  13. Outcrossing and paternity analysis of Pinus densiflora (Japanese red pine) by microsatellite polymorphism.

    Science.gov (United States)

    Lian, C; Miwa, M; Hogetsu, T

    2001-07-01

    This study employed microsatellite loci to analyse outcrossing rate and pollen dispersal in Japanese red pine (Pinus densiflora) in an isolated stand. The average offspring outcrossing rate for 29 cones was 0.955. Significant differences in outcrossing rates between offspring groups on individual branches that extended in different directions at different heights were not detected. Male parents of 874 offspring collected from the maternal tree were assessed by exclusion using polymorphisms at three microsatellite loci. Paternity analysis indicated that at least 31% of the offspring were fertilized by pollen from trees outside the stand. The average distance of pollen migration within the study stand was 68 m, with a maximum value of 325 m. There was excess mating with nearby P. densiflora trees, of which only a few were predominant pollen donors. In addition, a weakly directional bias in P. densiflora pollination was also detected in the study stand, suggesting that female strobili on a branch of the maternal tree were more easily fertilized by pollen from trees in that direction.

  14. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    Science.gov (United States)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  15. Analysis of olive fly invasion in California based on microsatellite markers.

    Science.gov (United States)

    Zygouridis, N E; Augustinos, A A; Zalom, F G; Mathiopoulos, K D

    2009-04-01

    The olive fruit fly, Bactrocera oleae, is the main pest of the olive fruit and its expansion is exclusively restricted to the cultivation zone of the olive tree. Even though olive production has a century-old history in California, the olive fly was first detected in the Los Angeles area in 1998. Within 5 years of the first observation, the insect was reported from all olive cultivation areas of the state. Field-collected flies from five locations in California and another from Israel were analyzed on the basis of microsatellite polymorphisms in 10 microsatellite loci. These results were integrated with those of a previous study of olive fly populations around the European part of the Mediterranean basin. The analysis pointed to the eastern part of the Mediterranean as the putative source of the observed invasion. Moreover, samples from California were quite different from Mediterranean samples implying the participation of phenomena such as genetic drift during the invasion and expansion of the olive fly in California.

  16. Analysis of genetic diversity and population structure of Chinese yak breeds (Bos grunniens) using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Guixiang Zhang; Weisheng Chen; Ming Xue; Zhigang Wang; Hong Chang; Xu Han; Xinjun Liao; Donglei Wang

    2008-01-01

    Nine Chinese yak breeds (Maiwa,Tianzhu White,Qinghai Plateau,Sibu,Zhongdian,Pall,Tibetan High Mountain,Jiulong,and Xin-jiang) and Gayal were analyzed by means of 16 microsatellite markers to determine the level of genetic variation within populations,genetic relationship between populations,and population structure for each breed.A total of 206 microsatellite alleles were observed.Mean F-statistics (0.056) for 9 yak breeds indicated that 94.4% of the genetic variation was observed within yak breeds and 5.6% of the genetic variation existed amongst breeds.The Neighbor-Joining phylogenetic free was constructed based on Nei's standard genetic dis-tances and two clusters were obtained.The Gayal separated from the yaks far away and formed one cluster and 9 yak breeds were grouped together.The analysis of population structure for 9 yak breeds and the Gayal showed that they resulted in four clusters; one clus-ter includes yaks from Tibet Autonomous Region and Qinghai Province,one cluster combines Zhongdian,Maiwa,and Tianzhu White,and Jiulong and Xinjiang come into the third cluster.Pali was mainly in the first cluster (90%),Jiulong was mainly in the second cluster (87.1%),Zhongdian was primarily in the third cluster (83%),and the other yak breeds were distributed in two to three clusters.The Gayal was positively left in the fourth cluster (99.3%).

  17. Geographic Structure of Plasmodium vivax: Microsatellite Analysis of Parasite Populations from Sri Lanka, Myanmar, and Ethiopia

    Science.gov (United States)

    Gunawardena, Sharmini; Karunaweera, Nadira D.; Ferreira, Marcelo U.; Phone-Kyaw, Myatt; Pollack, Richard J.; Alifrangis, Michael; Rajakaruna, Rupika S.; Konradsen, Flemming; Amerasinghe, Priyanie H.; Schousboe, Mette L.; Galappaththy, Gawrie N. L.; Abeyasinghe, Rabindra R.; Hartl, Daniel L.; Wirth, Dyann F.

    2010-01-01

    Genetic diversity and population structure of Plasmodium vivax parasites can predict the origin and spread of novel variants within a population enabling population specific malaria control measures. We analyzed the genetic diversity and population structure of 425 P. vivax isolates from Sri Lanka, 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 (HE) was 0.7517 in Ethiopia, 0.8450 in Myanmar, and 0.8610 in Sri Lanka. Significant linkage disequilibrium was maintained. Population structure showed two clusters (Asian and African) according to geography and ancestry. Strong clustering of outbreak isolates from Sri Lanka and Ethiopia was observed. Predictive power of ancestry using two-thirds of the isolates 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. PMID:20133999

  18. 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.

  19. Organellar genome, nuclear ribosomal DNA repeat unit, and microsatellites isolated from a small-scale of 454 GS FLX sequencing on two mosses.

    Science.gov (United States)

    Liu, Yang; Forrest, Laura L; Bainard, Jillian D; Budke, Jessica M; Goffinet, Bernard

    2013-03-01

    Recent innovations in high-throughput DNA sequencing methodology (next generation sequencing technologies [NGS]) allow for the generation of large amounts of high quality data that may be particularly critical for resolving ambiguous relationships such as those resulting from rapid radiations. Application of NGS technology to bryology is limited to assembling entire nuclear or organellar genomes of selected exemplars of major lineages (e.g., classes). Here we outline how organellar genomes and the entire nuclear ribosomal DNA repeat can be obtained from minimal amounts of moss tissue via small-scale 454 GS FLX sequencing. We sampled two Funariaceae species, Funaria hygrometrica and Entosthodon obtusus, and assembled nearly complete organellar genomes and the whole nuclear ribosomal DNA repeat unit (18S-ITS1-5.8S-ITS2-26S-IGS1-5S-IGS2) for both taxa. Sequence data from these species were compared to sequences from another Funariaceae species, Physcomitrella patens, revealing low overall degrees of divergence of the organellar genomes and nrDNA genes with substitutions spread rather evenly across their length, and high divergence within the external spacers of the nrDNA repeat. Furthermore, we detected numerous microsatellites among the 454 assemblies. This study demonstrates that NGS methodology can be applied to mosses to target large genomic regions and identify microsatellites.

  20. Polymorphic microsatellite loci from two enriched genomic libraries for the genetic analysis of the miiuy croaker, Miichthys miiuy (Sciaenidae).

    Science.gov (United States)

    Wang, R X; Xu, T J; Sun, Y N; He, G Y

    2010-05-18

    Twelve polymorphic microsatellites from the (AG)(13) and (CA)(13) enriched genomic libraries of Miichthys miiuy were isolated and characterized in a test population; the number of alleles ranged from two to nine. The observed and expected heterozygosities ranged from 0.1923 to 1.0000 and from 0.2633 to 0.8337, respectively. Three loci deviated from Hardy-Weinberg equilibrium, and linkage disequilibrium between five pairs of loci was significant. These polymorphic microsatellite loci can be used for genetic diversity analysis and molecular-assisted breeding of M. miiuy.

  1. Comparison of microsatellite length polymorphism and multilocus sequence typing for DNA-Based typing of Candida albicans.

    Science.gov (United States)

    Garcia-Hermoso, Dea; Cabaret, Odile; Lecellier, Gael; Desnos-Ollivier, Marie; Hoinard, Damien; Raoux, Dorothée; Costa, Jean-Marc; Dromer, Françoise; Bretagne, Stéphane

    2007-12-01

    For genotyping Candida albicans isolates, two PCR-based methods have recently emerged: multilocus sequence typing (MLST), based on the sequence of selected genes, and microsatellite length polymorphism (MLP), based on the length of PCR products containing variable numbers of short DNA repeats. To compare the two methods in their abilities to differentiate and group C. albicans isolates, we selected 50 independent isolates collected at the National Reference Center for Mycoses and Antifungals. MLST typing was performed using sequencing of seven loci as described at (http://test1.mlst.net). The MLP method consisted of a single multiplex PCR testing three different loci. Dendrograms were constructed by the unweighted pair group cluster method with Euclidean metric for both methods. The correlation between the distance matrices was performed with a Mantel test tested with 1,000 random permutations. The sensitivity and specificity of the MLP typing system were determined after allocating MLST groups for the greater number of isolates of each distinct MLP group. The discriminatory power index was >0.99, and the distances between the isolates were highly correlated with both systems. The Mantel coefficient and the Pearson product-moment correlation coefficient were 35,699 and 0.32, respectively (P < or = 1.2 x 10(-6)). Using MLP, the average specificity and sensitivity of clustering compared to MLST were 83% and 73%, respectively, when the singletons were excluded. The two methods are similarly discriminatory and can be interchangeable depending on the objectives. MLP is less expensive and faster than MLST. However, MLST is currently more accurate and additional standardization is needed for MLP.

  2. Combined microsatellite and FGFR3 mutation analysis enables a highly sensitive detection of urothelial cell carcinoma in voided urine

    NARCIS (Netherlands)

    B.W. van Rhijn (Bas); I. Lurkin (Irene); D.K. Chopin; W.J. Kirkels (Wim); J.P. Thiery (Joachim); Th.H. van der Kwast (Theo); F. Radvanyi (Franois); E.C. Zwarthoff (Ellen)

    2003-01-01

    textabstractPURPOSE: Fibroblast growth factor receptor 3 (FGFR3) mutations were reported recently at a high frequency in low-grade urothelial cell carcinoma (UCC). We investigated the feasibility of combining microsatellite analysis (MA) and the FGFR3 status for the detection of UC

  3. Validation of microsatellite multiplexes for parentage analysis in a coral reef fish (Lutjanus carponotatus, Lutjanidae)

    KAUST Repository

    Harrison, Hugo B.

    2014-05-25

    Parentage analysis is an important tool for identifying connectivity patterns in coral reef fishes, but often requires numerous highly polymorphic markers. We isolated 21 polymorphic microsatellite markers from the stripey snapper, Lutjanus carponotatus and describe their integration into three multiplex PCRs. All markers were highly polymorphic with a mean of 24.9 ± 1.8 SE alleles per locus and an average observed heterozygosity of 0.797 ± 0.038 SE across 285 genotyped individuals. Using a simulated dataset, we conclude that the complete marker set provides sufficient resolution to resolve parent–offspring relationships in natural populations with 99.6 ± 0.1 % accuracy in parentage assignments. This multiplex assay provides an effective means of investigating larval dispersal and population connectivity in this fishery-targeted coral reef fish species and informing the design of marine protected area networks for biodiversity conservation and fisheries management.

  4. Separation and relationships of seven Euglena strains based on microsatellite DNA finger-printing%七株眼虫基于微卫星DNA指纹图谱的区分和关系分析

    Institute of Scientific and Technical Information of China (English)

    张文静; 余育和; 沈韫芬; 颜庆云

    2006-01-01

    尽管以前对眼虫进行过大量的形态发育研究和基于核糖体RNA基因的系统发育分析,但对于株系之间的关系仍然知之甚少.因其形态特征有限并且易变,很难鉴定眼虫的相似种和同种内不同的株.作者利用微卫星DNA指纹图谱,在七株眼虫中扩增了七个微卫星DNA位点,成功扩增的六个微卫星引物都得到了四到八个条带.从微卫星DNA指纹图谱计算得到的相似性系数范围从0.000到0,957.根据相似性系数得到的树状结构,七株眼虫在距离为0.9346处分为三支:E.mutabilis,E.intermedia和E.gracilis.其中,五株E.gracilis分为两组:来自日本的和美国的.不同地区的株得到不同的基因型,并初步分析了它们之间的关系.研究表明七株眼虫根据微卫星DNA指纹图谱被明显区分开.微卫星DNA指纹图谱具有很高的分辨率,是鉴定和区分原生动物相似种和同种内不同株的一种有用的新方法.%The genetic relationships among Euglena strains remain poorly understood, despite a rich history of morphological examination and an extensive phylogenetic analysis of the ribosomal RNA genes. It is difficult to identify related species of the genus Euglena and to separate different strains of the same species because the morphological characters are variable and limited. We address this question using microsatellite DNA fingerprinting. Seven microsatellite loci were amplified from 7 Euglena strains. A total of 4 - 8 bands were successfully amplified for each of 6microsatellite primer pairs. Microsatellite DNA fingerprinting and similarity values ranging from 0.000 to 0.957 a-mong the seven strains were obtained, which were used to construct a similarity tree among them. According to the tree, at the linkage distance of 0.9346 seven strains were separated into three clusters: E. mutabilis, E. intermedia and E. gracilis consisting of Japanese and USA groups. Further, in the cluster E. gracilis, different genotypes

  5. Genetic Structure and Preliminary Findings of Cryptic Diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae Inferred from Mitochondrial DNA and Microsatellite Analyses

    Directory of Open Access Journals (Sweden)

    Yuzine Esa

    2013-01-01

    Full Text Available This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8*, possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8* in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed “genetic species” of mahseer.

  6. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

    Science.gov (United States)

    Eggert, Lori S; Rasner, Caylor A; Woodruff, David S

    2002-10-07

    Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.

  7. Seed dispersal by animals: exact identification of source trees with endocarp DNA microsatellites

    OpenAIRE

    Godoy, José A.; Jordano, Pedro

    2001-01-01

    A long-standing challenge in studies of seed dispersal by animal frugivores has been the characterization of the spatial relationships between dispersed seeds and the maternal plants, i.e. the seed shadow. The difficulties to track unambiguously the origin of frugivore- dispersed seeds in natural communities has been considered an unavoidable limitation of the research field and precluded a robust analysis of the direct consequences of zoochory. Here we report that the multilocus genotype at ...

  8. DNA typing and genetic relations among European hazelnut (Corylus avellana L.) cultivars using microsatellite markers.

    Science.gov (United States)

    Boccacci, P; Akkak, A; Botta, R

    2006-06-01

    In this work, 78 hazelnut (Corylus avellana L.) cultivars from various germplasm repositories were studied at 16 simple sequence repeat (SSR) loci in order to identify the genotypes and investigate their genetic relations. Polymorphism at SSR loci was evaluated on the basis of number of alleles (mean: 9.4), expected heterozygosity (mean: 0.78), and power of discrimination (mean: 0.91). Several synonyms reported in the literature were confirmed, and new cases of synonymy were identified. The parentage of North American cultivars 'Butler', 'Ennis', and 'Royal', the French selection 'Fercoril-Corabel', and 'Impératrice Eugenie' was investigated on the basis of the alleles present at 16 loci and analysis at 8 additional loci. A dendrogram generated from cluster analysis using the unweighted pair group method with arithmetic mean grouped cultivars according to their pedigrees or geographical origins. There was an evident differentiation of the northern European cultivars from the southern European ones and from the Turkish cultivars. The latter clustered close to but separate from the Italian and Spanish clusters. It is very likely that exchanges of cultivars occurred between the central and western Mediterranean basin as a result of human migration and trade. A database containing the SSR profiles of the most important hazelnut cultivars will be useful for identification of cultivars and synonyms, legal protection, and parentage analysis.

  9. Loss of genetic variability in a hatchery strain of Senegalese sole (Solea senegalensis revealed by sequence data of the mitochondrial DNA control region and microsatellite markers

    Directory of Open Access Journals (Sweden)

    Pablo Sánchez

    2012-06-01

    Full Text Available Comparisons of the levels of genetic variation within and between a hatchery F1 (FAR, n=116 of Senegalese sole, Solea senegalensis, and its wild donor population (ATL, n = 26, both native to the SW Atlantic coast of the Iberian peninsula, as well as between the wild donor population and a wild western Mediterranean sample (MED, n=18, were carried out by characterizing 412 base pairs of the nucleotide sequence of the mitochondrial DNA control region I, and six polymorphic microsatellite loci. FAR showed a substantial loss of genetic variability (haplotypic diversity, h=0.49±0.066; nucleotide diversity, π=0.006±0.004; private allelic richness, pAg=0.28 to its donor population ATL (h=0.69±0.114; π=0.009±0.006; pAg=1.21. Pairwise FST values of microsatellite data were highly significant (P < 0.0001 between FAR and ATL (0.053 and FAR and MED (0.055. The comparison of wild samples revealed higher values of genetic variability in MED than in ATL, but only with mtDNA CR-I sequence data (h=0.948±0.033; π=0.030±0.016. However, pairwise ΦST and FST values between ATL and MED were highly significant (P < 0.0001 with mtDNA CR-I (0.228 and with microsatellite data (0.095, respectively. While loss of genetic variability in FAR could be associated with the sampling error when the broodstock was established, the results of parental and sibship inference suggest that most of these losses can be attributed to a high variance in reproductive success among members of the broodstock, particularly among females.

  10. New polymorphic microsatellite markers derived from hemocyte cDNA library of Manila clam Ruditapes philippinarum challenged by the protozoan parasite Perkinsus olseni

    Science.gov (United States)

    Kang, Hyun-Sil; Hong, Hyun-Ki; Park, Kyung-Il; Cho, Moonjae; Youn, Seok-Hyun; Choi, Kwang-Sik

    2017-02-01

    Manila clam Ruditapes philippinarum is one of the most important benthic animals in the coastal north Pacific region, where clam populations have been mixed genetically through trade and aquaculture activities. Accordingly, identification of the genetically different clam populations has become one of the most important issues to manage interbreeding of the local and introduced clam populations. To identify genetically different populations of clam populations, we developed 11 expressed sequence tag (EST)-microsatellite loci (i.e., simple sequence repeat, SSR) from 1,128 clam hemocyte cDNA clones challenged by the protozoan parasite Perkinsus olseni. Genotype analysis using the markers developed in this study demonstrated that clams from a tidal flat on the west coast contained 6 to 19 alleles per locus, and a population from Jeju Island had 4 to 20 alleles per locus. The expected heterozygosity of the 2 clam populations ranged from 0.472 to 0.919 for clams from the west coast, and 0.494 to 0.919 for clams from Jeju Island, respectively. Among the 11 loci discovered in this study, 7 loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction. The 5 loci developed in this study also successfully amplified the SSRs of R. variegatus, a clam species taxonomically very close to R. philippinarum, from Hong Kong and Jeju Island. We believe that the 11 novel polymorphic SSR developed in this study can be utilized successfully in Manila clam genetic diversity analysis, as well as in genetic discrimination of different clam populations.

  11. New polymorphic microsatellite markers derived from hemocyte cDNA library of Manila clam Ruditapes philippinarum challenged by the protozoan parasite Perkinsus olseni

    Science.gov (United States)

    Kang, Hyun-Sil; Hong, Hyun-Ki; Park, Kyung-Il; Cho, Moonjae; Youn, Seok-Hyun; Choi, Kwang-Sik

    2017-03-01

    Manila clam Ruditapes philippinarum is one of the most important benthic animals in the coastal north Pacific region, where clam populations have been mixed genetically through trade and aquaculture activities. Accordingly, identification of the genetically different clam populations has become one of the most important issues to manage interbreeding of the local and introduced clam populations. To identify genetically different populations of clam populations, we developed 11 expressed sequence tag (EST)-microsatellite loci (i.e., simple sequence repeat, SSR) from 1,128 clam hemocyte cDNA clones challenged by the protozoan parasite Perkinsus olseni. Genotype analysis using the markers developed in this study demonstrated that clams from a tidal flat on the west coast contained 6 to 19 alleles per locus, and a population from Jeju Island had 4 to 20 alleles per locus. The expected heterozygosity of the 2 clam populations ranged from 0.472 to 0.919 for clams from the west coast, and 0.494 to 0.919 for clams from Jeju Island, respectively. Among the 11 loci discovered in this study, 7 loci significantly deviated from the Hardy-Weinberg equilibrium after Bonferroni correction. The 5 loci developed in this study also successfully amplified the SSRs of R. variegatus, a clam species taxonomically very close to R. philippinarum, from Hong Kong and Jeju Island. We believe that the 11 novel polymorphic SSR developed in this study can be utilized successfully in Manila clam genetic diversity analysis, as well as in genetic discrimination of different clam populations.

  12. Population structure of plaice ( Pleuronectes platessa L.) in northern Europe: a comparison of resolving power between microsatellites and mitochondrial DNA data

    Science.gov (United States)

    Hoarau, G.; Piquet, A. M.-T.; van der Veer, H. W.; Rijnsdorp, A. D.; Stam, W. T.; Olsen, J. L.

    2004-05-01

    We used Single Strand Conformation Polymorphism (SSCP) of mtDNA control region to assess the population structure of the flatfish Pleuronectes platessa (plaice), to compare these data with a previous study based on microsatellite loci, and to test for possible sex-biased dispersal. From 461 individuals, 163 haplotypes were identified across 11 locations. Diversity was higher with mtDNA ( h =0.776 to 0.981; π = 0.0178 to 0.0298) as compared to microsatellite loci using the same samples ( He = 0.721 to 0.77). Genetic diversity was lower in samples from Iceland and Faroe, as compared to the continental shelf samples. Although both classes of markers revealed a relatively strong differentiation between shelf and off-shelf populations ( θ = 0.1015 and θ = 0.0351, respectively), only the mtDNA data were able to detect differentiation within the continental shelf, i.e., a North Sea-Irish Sea group which was weakly distinguishable from Norway ( θ = 0.0046), the Baltic ( θ = 0.0136) and the Bay of Biscay ( θ = 0.0162). No evidence was obtained for isolation by distance, nor for sex-biased dispersal. This study demonstrates the importance of using more than one class of markers, especially for species such as plaice, with large populations, high dispersal and recent colonisation histories.

  13. Microsatellite analysis of Damask rose (Rosa damascena Mill. accessions from various regions in Iran reveals multiple genotypes

    Directory of Open Access Journals (Sweden)

    Naghavi Mohammad

    2007-03-01

    Full Text Available Abstract Background Damask roses (Rosa damascena Mill. are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran. Results All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus. Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions. It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran. Conclusion This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding.

  14. Population genetic structure of Siniperca chuatsi in the middle reach of the Yangtze River inferred from mitochondrial DNA and microsatellite loci.

    Science.gov (United States)

    Tian, Changxu; Yang, Min; Liang, Xu-Fang; Cao, Liang; Zheng, Hezi; Zhao, Cheng; Zhu, Kecheng; Yuan, Yongchao

    2015-02-01

    The Chinese mandarin fish (Siniperca chuatsi) is currently one of the most important economic freshwater fish in China, whereas the wild resource has declined dramatically in recent years. In this study, we examined the genetic structure and diversity of five populations from the middle reach of the Yangtze River using mitochondrial cytochrome b sequences and microsatellite markers. This research revealed high genetic diversity and low genetic differentiation of S. chuatsi from these regions. The pairwise Fst values of the two markers showed low and no-significant differentiation among populations. AMOVA analysis of two markers and the haplotype genealogy of the Cytb gene confirmed these results. The STRUCTURE analysis of the microsatellite marker implied that the dam upon the tributary of the Yangtze River blocked the gene flow among those regions. This research will be useful in breeding programs and conservation management of this species.

  15. Genetic diversity analysis in blackgram (Vigna mungo (L.) Hepper) using AFLP and transferable microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi).

    Science.gov (United States)

    Gupta, S K; Gopalakrishna, T

    2009-02-01

    Genetic diversity in 20 elite blackgram (Vigna mungo (L.) Hepper) genotypes was studied using microsatellite and AFLP markers. Thirty-six microsatellite markers from azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) were successfully amplified across the 20 blackgram genotypes and 33 microsatellite markers showed polymorphism. A total of 137 microsatellite alleles were generated with an average of 4.1 alleles per locus. The number of alleles ranged from two to nine and the polymorphic information content value for the microsatellite markers varied from 0.10 to 0.87 with an average of 0.49. Microsatellite markers were highly informative and a combination of only three microsatellite markers (CEDG264, CEDG173, and CEDG044) was sufficient to discriminate all 20 blackgram genotypes. In the case of AFLP, 11 primer pairs generated 324 polymorphic marker fragments. The polymorphic information content values for AFLP primer combinations ranged from 0.21 to 0.34 with an average of 0.29. Similarity measures and clustering analyses were made using microsatellite and AFLP data separately. The resulting dendrograms distributed the 20 blackgram genotypes into five main clusters. The dendrograms were comparable with each other with the Mantel test between the cophenetic matrices of microsatellite data and AFLP data showing moderate correlation (r = 0.64). The results of the principal components analysis were well congruent with the dendrograms. In the dendrograms as well as in the principal components analyses, genotype Trombay wild (Vigna mungo var. silvestris) was placed separately from rest of the genotypes. This study demonstrated that the azuki bean microsatellite markers are highly polymorphic and informative and can be successfully used for genome analysis in blackgram. Results indicate that sufficient variability is present in the blackgram genotypes and would be helpful in the selection of suitable parents for breeding purposes and gene mapping studies.

  16. Pollen dispersal analysis using DNA markers

    Directory of Open Access Journals (Sweden)

    Wei Zhou

    2014-01-01

    Full Text Available Modes of pollen dispersal are important for plant ecology, conservation, and evolutionary biology as pollen-mediated gene flow connects one generation of sexually-reproducing plants to the next. With the development of DNA molecular techniques, molecular markers (especially microsatellite markers have replaced traditional physical markers for pollen flow analysis. Methods of paternity assignment with maximum likelihood and Bayesian inference have greatly improved the estimation of pollen flow characteristics with regard to direction, distance, and strength. Pollen dispersal curves have been characterized by single parameter, two-parameter, multi-parameter, and two-component composite models to better evaluate the shape of dispersal distributions. These innovative techniques and methods have been successfully applied to assess pollination patterns in studies of plant sexual polymorphism, population connectivity, and natural hybridization, which, in turn, have provided important insights into basic theories of evolution, ecology, and conservation. In the coming years, high-throughput sequencing technologies are expected to accelerate the application of molecular marker-based pollen flow analysis across a wide range of plant taxa.

  17. Microsatellite analysis of genetic diversity and population structure of Arabian horse populations.

    Science.gov (United States)

    Khanshour, Anas; Conant, Eleanore; Juras, Rytis; Cothran, Ernest Gus

    2013-01-01

    The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here, we explore 7 different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya Arabian and Polish Arabian) and in America (American Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, analysis of molecular variance, factorial correspondence analysis, and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source among population variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.

  18. Microsatellite instability analysis using BAT-26 marker in patients with gastric or colorectal cancer diagnosed at Hospital Universitario de Santander.

    Directory of Open Access Journals (Sweden)

    Wilmer Cárdenas

    2009-11-01

    Full Text Available Introduction: The path of microsatellite instability has mainly been found in cancers of digestive tracts, of which 90% of cases are hereditary cancer patients and 15% are patients with sporadic cancer. That instability produces a phenotype called Microsatellite instability (IMI+ or phenotype by replication mistake (RER+ that leads to the accumulation of mutations in higher rates to normal. Objectives: To identify the presence of IMI+ phenotype in patients analyzed and evaluated its relationship with the differentiation histopathologic tumor, because which together have been associated with a better prognosis and improved response to treatment given to the patient. Methodology: DNA was extracted from blood samples (normal cells and biopsy of the tumor (tumor cells of the 23 patients who were included in the study and through the amplification by PCR and subsequent capillary electrophoresis was typified the microsatellite mononucleotidic BAT-26, who was employed by his sensitivity to detect IMI+ phenotype (95%. Finally, we made a statistical correlation between the microsatellite instability phenotype, the presence (IMI+ or the absence (IMI-, with histopathological findings using Fisher’s exact test. Results: In 17% of cases (4 patients had IMI+: 3 of them with colorectal cancer (CRC -2 cases possibly with hereditary cancer- and one with gastric cancer (GC. There was no association between phenotype IMI+ with the pathological diagnosis, age, sex and differentiation histopathologic tumor. Conclusion: We found the phenotype IMI + in 17% of cases without association with the degree of differentiation histopathologic tumor, possibly by the reduced number of samples analyzed, making it essential to review the methods of fixation, paraffin and storage tissue because current techniques hinder digestion of proteinase k and PCR.

  19. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers.

    Science.gov (United States)

    Seo, Dongwon; Bhuiyan, Md Shamsul Alam; Sultana, Hasina; Heo, Jung Min; Lee, Jun Heon

    2016-04-01

    Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  20. Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Dongwon Seo

    2016-04-01

    Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

  1. An Extensive Analysis of Y-Chromosomal Microsatellite Haplotypes in Globally Dispersed Human Populations

    Science.gov (United States)

    Kayser, Manfred; Krawczak, Michael; Excoffier, Laurent; Dieltjes, Patrick; Corach, Daniel; Pascali, Vincente; Gehrig, Christian; Bernini, Luigi F.; Jespersen, Jørgen; Bakker, Egbert; Roewer, Lutz; de Knijff, Peter

    2001-01-01

    The genetic variance at seven Y-chromosomal microsatellite loci (or short tandem repeats [STRs]) was studied among 986 male individuals from 20 globally dispersed human populations. A total of 598 different haplotypes were observed, of which 437 (73.1%) were each found in a single male only. Population-specific haplotype-diversity values were .86–.99. Analyses of haplotype diversity and population-specific haplotypes revealed marked population-structure differences between more-isolated indigenous populations (e.g., Central African Pygmies or Greenland Inuit) and more-admixed populations (e.g., Europeans or Surinamese). Furthermore, male individuals from isolated indigenous populations shared haplotypes mainly with male individuals from their own population. By analysis of molecular variance, we found that 76.8% of the total genetic variance present among these male individuals could be attributed to genetic differences between male individuals who were members of the same population. Haplotype sharing between populations, ΦST statistics, and phylogenetic analysis identified close genetic affinities among European populations and among New Guinean populations. Our data illustrate that Y-chromosomal STR haplotypes are an ideal tool for the study of the genetic affinities between groups of male subjects and for detection of population structure. PMID:11254455

  2. Genetic potential analysis of German mirror carp (Cyprinus carpio L.) using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    Ning HOU; Xiaoshu HOU; Yong LI; Dayu LI; Fujun LIU; Ruixin MAO; Xiaowen SUN

    2008-01-01

    Using 30 microsatellite markers and combin-ing quantifiable characteristics such as body weight, body length and body width, we evaluated the genetic potential of 3 German mirror carp (Cyprinus carpio L.) popula-tions. Number of effective alleles (Ae), observed (Ho) and expected (He) heterozygosity values and polymorphic information contents (PIC) were all calculated. Two hun-dred and eighty-seven alleles and 559 genotypes were detected. The DNA fragment length was 109-400 bp. The Hardy-Weinberg Equilibrium was checked and the phenomenon of some disequilibrium was studied accord-ing to the χ2test. The results showed that the level of genetic variability was moderate, but genetic potential of Shuanglai population was much lower than that of Huanxin and Songpu breeding populations. PIC of the three populations of German mirror carp were between 0.08787 and 0.5377, both highly and moderately poly-morphic markers were 13. The number of the Ae was between 1.1014 and 6.4665. The Ho and He heterozygos-ity values were 0.0968-0.9892 and 0.0926-0.8554, respect-ively. The linkage correlation was analyzed using the data of body weight, body length and body width, and 30 loci. The result showed that there existed 2 loci, HLJ319 and HLJ693, associated with body length. The HLJ693 locus was significantly correlated with body weight trait. The HLJ677 locus was linked with body width. And then the result was verified in Recombinant Inbred Lines (RIL) of common carp. It showed that the HLJ319 locus was sig-nificantly linked with body length, the same as the result of quantitative trait loci (QTL) location for common carp.

  3. 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.

  4. Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

    Directory of Open Access Journals (Sweden)

    J. F. Vázquez-Armijo

    2017-06-01

    Full Text Available The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

  5. Microsatellite analysis reveals strong but differential impact of a social parasite on its two host species.

    Science.gov (United States)

    Fischer-Blass, Birgit; Heinze, Jürgen; Foitzik, Susanne

    2006-03-01

    The speed and the dynamics of the co-evolutionary process strongly depend on the relative strengths of reciprocal selection pressures exerted by the interacting species. Here, we investigate the influence of an obligate social parasite, the slave-making ant Harpagoxenus sublaevis, on populations of the two main host species Leptothorax acervorum and Leptothorax muscorum from a German ant community. A combination of genetic and demographic data allowed us to analyse the consequences of raiding pressure on the hosts' life history and possible host preferences of the parasite. We can demonstrate that slave raids during which the social parasite pillages brood from neighbouring host colonies are both frequent and extremely destructive for both host species. Microsatellite analysis showed that, on average, a single slave-maker colony conducts more than three raids per year and that host colonies mostly perish in the aftermath of these parasite attacks. Only in few cases, surviving nests of previously raided host colonies were found in the surroundings of slave-maker colonies. As a consequence of the high prevalence of parasites and their recurrent and devastating slave raids on host colonies, the life expectancy of host colonies was severely reduced. Combining our results on host-specific parasitic colony founding and raiding frequencies with the post-raid survival rate, we can demonstrate an overall higher mortality rate for the smaller host species L. muscorum. This might be caused by a preference of H. sublaevis for this secondary host species as demographic data on host species usage indicate.

  6. The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

    OpenAIRE

    Eggert, Lori S.; Rasner, Caylor A; Woodruff, David S.

    2002-01-01

    Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central...

  7. Molecular Characterization of Lates niloticus (Perciformes, Latidae Populations from three Nigerian Waterbodies using Random Amplified Polymorphic DNA and Microsatellite Markers

    Directory of Open Access Journals (Sweden)

    Ogbuebunu K. E.

    2017-02-01

    Full Text Available Thirty Lates niloticus (Linnaeus, 1758 from three Nigerian waterbodies were genotyped on six RAPD primers and five microsatellites loci. RAPD revealed that effective number of alleles (AE at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN across populations equals 2.000. Characterization on five microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of differentiation (FST within populations was 0.236. Overall gene flow (Nm among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fish species, especially L. niloticus. Thus, it can be concluded that L. niloticus in the three (3 sampled Nigerian waterbodies is undergoing evolution.

  8. 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.

  9. 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.

  10. Phenetic analysis of Trifolium resupinatum L. (Persian clover and Trifolium fragiferum L. (strawberry clover using new microsatellite loci

    Directory of Open Access Journals (Sweden)

    Maryam Haerinasab

    2013-06-01

    Full Text Available Trifolium resupinatum and T. fragiferum are two important crop species among the legumes. T. fragiferum is considered as one of the gene pools of T. resupinatum. In this study, the transferability of SSR markers from T. pratense and T. repens to genotypes of these two species was evaluated and new microsatellite loci for these species were obtained. Their genomic similarity was studied using the SSR markers and phenetic analysis. The results of this study indicated a high level of transferability and polymorphism for microsatellites from T. pratense and T. repens to genotype of T. resupinatum and T. fragiferum. Studies also showed that the genetic diversity was high among the populations and the studied populations were grouped in the low levels of similarity. Also, T. resupinatum and T. fragiferum were grouped in clusters with very low similarity that indicated genomic differences between them in tested SSR loci. This study showed that microsatellites can be useful tools to evaluate genetic variation in these species. The results suggested that as long as specific SSR primers for these two species were not designed, SSR primers of T. pratense and T. repens could be used with high reliability for genomic analysis of these species.

  11. Monomorphic Analysis of Microsatellite Loci at BAT-26%微卫星BAT-26位点单态性的分析

    Institute of Scientific and Technical Information of China (English)

    狄金明; 张一楚; 陈蕾; 顾琴龙

    2001-01-01

    Objective MSI plays an important role in carainogenesis of manttumors.Most MS loci show polymorphism in normal tissues.It has been reported that BAT-26 was quasi-monomorphic,showing only minor size variathions.To analysis monomorphism at BAT-26 loci,60 normal colorectal tissues were examined.Methods Genomic DNA extracted from tissues was PCR amplified.PCR products were run on 6% denaturing polyacrylamide gel and stained with silver.Results All specimens showed no variation in the length of MS DNA at BAT-26 loci.Conclusion BAT-26 has much monomorphism in human genome.%目的 微卫星不稳定性(MicrosatelliteInstability,MSI)在许多肿瘤的发生中具很重要的作用,大多数微卫星(Microsatellite,MS)位点在正常人群中多态性明显,有报道表明BAT-26位点单态性很好,据此我们分析了60例正常肠粘膜标本中BAT-26位点MSDNA的情况,以便了解BAT-26位点单态性情况。方法 组织DNA提取后PCR扩增,扩增产物行6%变性聚丙烯酰胺凝胶电泳,最后银染。结果 所有标本在BAT-26位点MSDNA长度无明显改变。结论 BAT-26具有较好的单态性。

  12. 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.

  13. Novel Tetra-nucleotide Microsatellite DNA Markers for Assessing the Evolutionary Genetics and Demographics of Northern Snakehead (Channa argus) Invading North America

    Science.gov (United States)

    King, Timothy L.; Johnson, R.L.

    2011-01-01

    We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity (averaging 6.8 alleles/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection has not achieved mutation-drift equilibrium. These results were consistent with instances of deviations from Hardy-Weinberg equilibrium and the presence of some linkage disequilibrium. A comparison of individual pair-wise distances suggested the presence of multiple differentiated groups of related individuals. Results of all analyses are consistent with a pattern of multiple, recent introductions. The microsatellite markers developed for C. argus yielded sufficient genetic diversity to potentially: (1) delineate kinship; (2) elucidate fine-scale population structure; (3) define management (eradication) units; (4) estimate dispersal rates; (5) estimate population sizes; and (6) provide unique demographic perspectives of control or eradication effectiveness

  14. Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster.

    Science.gov (United States)

    Miller, Adam D; Good, Robert T; Coleman, Rhys A; Lancaster, Melanie L; Weeks, Andrew R

    2013-01-01

    A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus = 2.79; mean expected heterozygosity = 0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced.

  15. 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...

  16. 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

  17. Analysis of Inactivation of hMLH1 by Promoter Hypermethylation and Microsatellite Instability in Gastric Carcinogenesis

    Institute of Scientific and Technical Information of China (English)

    Dong Wang; Yao Xu; Xin Geng; Weiming Zhang

    2006-01-01

    BJECTIVE To study the microsatellite instability (MSI) and methylation state of the hMLH1 gene promoter and their mechanisms underlying the development of gastric cancer.METHODS Forty-one gastric cancer samples were obtained from patients undergoing surgery and 46 chronic atrophic gastritis tissues with dysplasia or intestinal metaplasia (IM) were obtained from patients undergoing gastro-endoscopy. Fourteen normal gastric mucosal samples were used as controls. Genomic DNA was extracted from the samples and 5 microsatellite markers were used to measure MSI. Methylationspecific PCR (MSP) was used to screen the methylation state of the samples. DNA sequencing and immunohistochemistry were performed to verify the results.RESULTS MSI was identified in 22 out of the 41 (53.7%) gastric cancers,of which 8 cases showed high-level MSI (2 or more loci altered) and 14showed low-level MSI (1 locus altered). MSI was also detected in 12 out of 46 (26.1%) pre-cancerous lesions of the stomach, whereas it was not seen in the normal tissue. Moreover, hMLH1 hypermethylation was detected in 17 out of the 41 (41.5%) gastric cancers, 9 out of the 46 (19.6%)pre-cancerous lesions and O out of the 14 normal tissue. Significant differences in frequency of MSI and hMLH1 promoter methylation were observed among gastric cancers, precancerous lesions and normal gastric tissue. Gastric samples with MSI had a tendency to be hypermethylated in the hMLH1 promoter. DNA sequencing and immunohistochemistry results also confirmed that hMLH1 promoter methylation could lead to loss of the hMLH1 protein and gene silence which sequentely resulted in gene mismatch and MSI.CONCLUSION Accumulation of MSI and hMLH1 promoter methylation may be important early molecular events during gastric carcinogenesis and may contribute to the acquisition of a transformed cell phenotype and the development of gastric cancer.

  18. Population Genetics of European Anchovy (Engraulis encrasicolus L. in the Seas of Turkey Based on Microsatellite DNA

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    Fevzi Bardakci

    2014-06-01

    Results: In this study, 13 microsatellite loci in 541 samples were analysed for determination of genetic structure of anchovy along Turkish coasts. The genetic variability was high among population, the average alleles numbers per locus per population ranged from 11.0 to 22.8. Observed heterozygosity per population was ranged from 0.612 (Mersin to 0.733 (İstanbul while expected heterozygosity was ranged from 0.774 (Mersin to 0.823 (Perşembe. The highest genetic distance was found between Antalya and Trabzon populations (FST=0.06949, the lowest between Antalya and İskenderun populations (0,00010. Analyses of 13 microsatellite loci were showed that there was low population structuring among all anchovy population (Fst: 0,024; SE 0,005. Although high genetic diversities was detected, for most loci with most populations were showed Hardy-Weinberg disequilibrium. Genetic distance analyses showed up Mediterranean specimens were highly distinct from Aegean and Black sea populations. Aegean populations were closer to Black sea populations because of higher gene flow between them rather than Mediterranean. A STRUCTURE computer program was indicated the presence of four possible genetic groups in Turkish territorial waters. Conclusions: Data to obtained from this study has found useful for the identification of genetic structuring of European anchovy distributed along the coasts of Turkish Seas. Results are also useful for planning of fishery management of anchovies in Turkey.

  19. Biotype status and genetic polymorphism of the whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) in Greece: mitochondrial DNA and microsatellites.

    Science.gov (United States)

    Tsagkarakou, A; Tsigenopoulos, C S; Gorman, K; Lagnel, J; Bedford, I D

    2007-02-01

    The genetic polymorphism and the biotype identity of the tobacco whitefly Bemisia tabaci (Gennadius) have been studied in population samples taken from different localities within Greece from cultivated plants growing in greenhouses or in open environments and from non-cultivated plants. Two different approaches were used: sequencing of the mitochondrial cytochrome oxidase I (mtCOI) gene and genotyping using microsatellite markers. Analyses of the mtCOI sequences revealed a high homogeneity between the Greek samples which clustered together with Q biotype samples that had been collected from other countries. When genetic polymorphism was examined using six microsatellite markers, the Greek samples, which were all characterized as Q biotype were significantly differentiated from each other and clustered into at least two distinct genetic populations. Moreover, based on the fixed differences revealed by the mtCOI comparison of known B. tabaci biotype sequences, two diagnostic tests for discriminating between Q and B and non-Q/non-B biotypes were developed. Implementation of these diagnostic tools allowed an absence of the B biotype and presence of the Q biotype in the Greek samples to be determined.

  20. MICROSATELLITES ANALISIS FOR THE STUDY OF BIODIVERSITY AND TRACEABILITY OF THE PIG

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    IUDITH IPATE

    2013-07-01

    Full Text Available Traceability of animals and animal products has a priority for governments of the European countries. The great development reached by the molecular genetic in last decades, has determined a high knowledge of the genome of the different species. The Deoxyribonucleic Acid (DNA of each animal is different (with the exceptions of monozygotic twins and clones. Since the genome of each animal contains approximately three billion DNA units, the range for variation among the DNA sequences of animals is enormous, consequently DNA markers analysis allows assuring a traceability of 100% in the meat industry. A methodology using 17 ISAG (International Society for Animal Genetics DNA microsatellite markers is proposed for meat traceability. Principal methods used to reveal DNA polymorphism are described as their applicability in species identification and meat traceability. The objective it was analysis the DNA profile of pig with 10 microsatellite markers and results of meat identity control.

  1. Determination of microsatellite repeats in the human thyroid peroxidase (TPOX) gene using an automated gene analysis system with nanoscale engineered biomagnetite.

    Science.gov (United States)

    Nakagawa, Takahito; Maruyama, Kohei; Takeyama, Haruko; Matsunaga, Tadashi

    2007-04-15

    The number of repeat in the microsatellite region (AATG)(5-14) of the human thyroid peroxidase gene (TOPX) was determined using an automated DNA analysis system with nano-scale engineered biomagnetite. Thermal melting curve analysis of DNA duplexes on biomagnetite indicated that shorter repeat sequences (less than 9 repeats) were easily discriminated. However, it was difficult to determine the number of repeats at more than nine. In order to improve the selectivity of this method for the longer repeats, a "double probe hybridization assay" was performed in which an intermediate probe was used to replace a target repeat sequence having more than 9 repeats with a shorter sequence possessing less than 9 repeats. Thermal probe melting curve analyses and Tm determination confirmed that the target with 10 repeats was converted to 5 repeats, 11 repeats converted to 4 and 12 to 3, respectively. Furthermore, rapid determination of repeat numbers was possible by measuring fluorescence intensities obtained by probe dissociation at 56 and 66 degrees C, and 40, 60 and 80 degrees C for signal normalization.

  2. Comparative analysis of the within-population genetic structure in wild cherry (Prunus avium L.) at the self-incompatibility locus and nuclear microsatellites.

    Science.gov (United States)

    Schueler, Silvio; Tusch, Alexandra; Scholz, Florian

    2006-10-01

    Gametophytic self-incompatibility (SI) systems in plants exhibit high polymorphism at the SI controlling S-locus because individuals with rare alleles have a higher probability to successfully pollinate other plants than individuals with more frequent alleles. This process, referred to as frequency-dependent selection, is expected to shape number, frequency distribution, and spatial distribution of self-incompatibility alleles in natural populations. We investigated the genetic diversity and the spatial genetic structure within a Prunus avium population at two contrasting gene loci: nuclear microsatellites and the S-locus. The S-locus revealed a higher diversity (15 alleles) than the eight microsatellites (4-12 alleles). Although the frequency distribution of S-alleles differed significantly from the expected equal distribution, the S-locus showed a higher evenness than the microsatellites (Shannon's evenness index for the S-locus: E = 0.91; for the microsatellites: E = 0.48-0.83). Also, highly significant deviations from neutrality were found for the S-locus whereas only minor deviations were found for two of eight microsatellites. A comparison of the frequency distribution of S-alleles in three age-cohorts revealed no significant differences, suggesting that different levels of selection acting on the S-locus or on S-linked sites might also affect the distribution and dynamics of S-alleles. Autocorrelation analysis revealed a weak but significant spatial genetic structure for the multilocus average of the microsatellites and for the S-locus, but could not ascertain differences in the extent of spatial genetic structure between these locus types. An indirect estimate of gene dispersal, which was obtained to explain this spatial genetic pattern, indicated high levels of gene dispersal within our population (sigma(g) = 106 m). This high gene dispersal, which may be partly due to the self-incompatibility system itself, aids the effective gene flow of the

  3. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L..

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    Bin Han

    Full Text Available Microsatellites or simple sequence repeats (SSRs are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR; 70,564 (23.9% were found to be monomorphic and 224,703 (76.1% were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3% amplified one locus, 8 (17.8% amplified multiple identical loci, and 13 (28.9% did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising

  4. Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

    Science.gov (United States)

    2010-01-01

    Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections. PMID:21637613

  5. Analysis of Two Chinese Yak(Bos grunniens) Population Using Bovine Microsatellite Primers

    Institute of Scientific and Technical Information of China (English)

    Wang Minqiang; S.Weigend; A.Barre-Dirie; J.W.Carnwath; Lou Zhonglin; H.Niemann

    2005-01-01

    Two Chinese domestic yak populations representing the Plateau type and the Huanhu Alpine type were analysed with 12 bovine microsatellite primers. All primer pairs functioned in the yak genome and polymorphism was found at all loci. The allele size ranges and frequencies of the two yak populations were similar and there was considerable overlap with the allele size ranges observed in cattle. Data for European cattle breeds was obtained from the Cattle Diversity Database(CaDBase)to interpret the heterozygosity and genetic distance estimates in yak populations. Heterozygosity estimated for the two yak populations was comparable to that of European cattle while Nei's Genetic Distance DA between the two yak populations was less than distances between the most closely related German cattle breeds. Bovine microsatellite primers proved to be a valuable tool for characterization of yak populations.

  6. Genetic diversity analysis in the section Caulorrhizae (genus Arachis using microsatellite markers

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    Darío A. Palmieri

    2010-01-01

    Full Text Available Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections.

  7. 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

  8. Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

    OpenAIRE

    Mónica J Pajuelo; María Eguiluz; Eric Dahlstrom; David Requena; Frank Guzmán; Manuel Ramirez; Patricia Sheen; Michael Frace; Scott Sammons; Vitaliano Cama; Sarah Anzick; Dan Bruno; Siddhartha Mahanty; Patricia Wilkins; Theodore Nash

    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 patho...

  9. Analysis on Frequency and Density of Microsatellites in Coding Sequences of Several Eukaryotic Genomes

    Institute of Scientific and Technical Information of China (English)

    Bin Li; Qingyou Xia; Cheng Lu; Zeyang Zhou; Zhonghuai Xiang

    2004-01-01

    Microsatellites or simple sequence repeats (SSRs) have been found in most organisms during the last decade. Since large-scale sequences are being generated, especially those that can be used to search for microsatellites, the development of these markers is getting more convenient. Keeping SSRs in viewing the importance of the application, available CDS (coding sequences) or ESTs (expressed sequence tags) of some eukaryotic species were used to study the frequency and density of various types of microsatellites. On the basis of surveying CDS or EST sequences amounting to 66.6 Mb in silkworm, 37.2 Mb in fly, 20.8 Mb in mosquito, 60.0 Mb in mouse, 34.9 Mb in zebrafish and 33.5 Mb in Caenorhabditis elegans, the frequency of SSRs was 1/1.00 Kb in silkworm, 1/0.77 Kb in fly, 1/1.03 Kb in mosquito, 1/1.21 Kb in mousey 1/1.25 Kb in zebrafish and 1/1.38 Kb in C. Elegans. The overall average SSR frequency of these species is 1/1.07 Kb. Hexanucleotide repeats (64.5%-76.6%) are the most abundant class of SSR in the investigated species, followed by trimeric, dimeric, tetrameric, monomeric and pentameric repeats. Furthermore, the A-rich repeats are predominant in each type of SSRs, whereas G-rich repeats are rare in the coding regions.

  10. Analysis of microsatellite instability in CRISPR/Cas9 editing mice.

    Science.gov (United States)

    Huo, Xueyun; Du, Yating; Lu, Jing; Guo, Meng; Li, Zhenkun; Zhang, Shuangyue; Li, Xiaohong; Chen, Zhenwen; Du, Xiaoyan

    2017-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR- associated (Cas) protein 9 system is a novel and powerful tool which is widely used for genome editing. CRISPR/Cas9 is RNA-guided and can lead to desired genomic modifications. However, whether the CRISPR/Cas9-mediated genome editing causes genomic alterations and genomic instability, such as microsatellite instability (MSI), is still unknown. Here we detected MSI in 21 CRISPR/Cas9 mouse strains using a panel of 42 microsatellite loci which were selected from our previous studies. Surprisingly, MSI occurrence was common in CRISPR/Cas9 modified genome, and most of the strains (19/21, 90.5%) examined showed MSI. Of 42 loci examined, 8 loci (8/42, 19.05%) exhibited MSI in the Cas9 editing mice. The Ttll9 (4/42, 9.5%) were the most unstable strains, and D10Mit3 and D10Mit198 (9/21, 42.9%) were considered to be the most "hot" loci in the Cas9 strains we tested. Through analyzing the mutation of microsatellite loci, we provide new insights into the genomic alterations of CRISPR/Cas9 models and it will help us for a better understanding of this powerful technology. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. 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.

  12. Diagnostic value of a microsatellite DNA marker for copper toxicosis in West-European Bedlington terriers and incidence of the disease.

    Science.gov (United States)

    Rothuizen, J; Ubbink, G J; van Zon, P; Teske, E; van den Ingh, T S; Yuzbasiyan-Gurkan, V

    1999-06-01

    Recently, linkage of a DNA microsatellite marker to inherited copper toxicosis has been reported in American Bedlington terrier families. Due to the fact that there is little exchange of breeding stock between the USA and Europe, it remains to be investigated whether in Europe the marker is informative and is linked with the disease. We have therefore examined the diagnostic value of the microsatellite marker in the European Bedlington. In 130 dogs at least one year of age (62 from The Netherlands, 35 from Belgium, and 33 from Germany) histo- or cytochemical staining of copper was done in liver biopsies. Based on liver histo- or cytochemistry, 51 dogs were obligate carriers, and 25 dogs had copper toxicosis. The inferred genotypes of these 76 dogs were compared with the marker genotypes. All dogs with the disease were homozygous for the 167 bp marker allele. All obligate carriers were heterozygotes with the 167 bp and a 163-bp alleles. All phenotypically healthy dogs were either homozygous for the 163 bp allele or heterozygous. Thus, the marker was in complete linkage disequilibrium with the putative copper toxicosis gene with the 167 bp allele in phase with the disease allele. The frequencies of the 167 bp and the 163 bp allele, respectively, were 0.33 and 0.67 in Dutch dogs, 0.31 and 0.69 in German dogs, and 0.57 and 0.43 in Belgian dogs. We have confirmed the utility of this marker for diagnosis of inherited copper toxicosis in European Bedlington terriers.

  13. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  14. Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data.

    Science.gov (United States)

    Aketarawong, Nidchaya; Isasawin, Siriwan; Sojikul, Punchapat; Thanaphum, Sujinda

    2015-01-01

    The Carambola fruit fly, Bactrocera carambolae, is an invasive pest in Southeast Asia. It has been introduced into areas in South America such as Suriname and Brazil. Bactrocera carambolae belongs to the Bactrocera dorsalis species complex, and seems to be separated from Bactrocera dorsalis based on morphological and multilocus phylogenetic studies. Even though the Carambola fruit fly is an important quarantine species and has an impact on international trade, knowledge of the molecular ecology of Bactrocera carambolae, concerning species status and pest management aspects, is lacking. Seven populations sampled from the known geographical areas of Bactrocera carambolae including Southeast Asia (i.e., Indonesia, Malaysia, Thailand) and South America (i.e., Suriname), were genotyped using eight microsatellite DNA markers. Genetic variation, genetic structure, and genetic network among populations illustrated that the Suriname samples were genetically differentiated from Southeast Asian populations. The genetic network revealed that samples from West Sumatra (Pekanbaru, PK) and Java (Jakarta, JK) were presumably the source populations of Bactrocera carambolae in Suriname, which was congruent with human migration records between the two continents. Additionally, three populations of Bactrocera dorsalis were included to better understand the species boundary. The genetic structure between the two species was significantly separated and approximately 11% of total individuals were detected as admixed (0.100 ≤ Q ≤ 0.900). The genetic network showed connections between Bactrocera carambolae and Bactrocera dorsalis groups throughout Depok (DP), JK, and Nakhon Sri Thammarat (NT) populations. These data supported the hypothesis that the reproductive isolation between the two species may be leaky. Although the morphology and monophyly of nuclear and mitochondrial DNA sequences in previous studies showed discrete entities, the hypothesis of semipermeable boundaries may not

  15. 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.

  16. MICROSATELLITE ANALYSIS OF THE SLOVAK CARNIOLAN HONEY BEE (APIS MELLIFERA CARNICA

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    Dušan Paál

    2013-02-01

    Full Text Available The aim of this study was the selection and testing of suitable microsatellite markers for evaluation of the Slovak carniolan honey bee, particularly the population structure, genetic diversity, breed assignment and paternity testing of honey bee queens in Slovakia. Fourteen microsatellite markers running in two multiplex PCR reactions have been tested on 40 randomly selected workers and queens and further verified by PIC index, expected heterozygosity (HE and observed heterozygosity (HO. Chi-squared test of goodness of fit (α = 0,05 was used to check the Hardy-Weinberg equilibrium (HWE of genotype for each marker. For the comparison tests the workers of A. mellifera mellifera x ligurica, A. mellifera macedonica and A. mellifera iberica were analyzed, using the same set of markers. We identified a total of 123 alleles in the Slovak carniolan honey bee samples, with the mean value of 8,78 allele per locus. Eleven markers showed the PIC value greater than 0,5 and thus were highly informative. The mean value of expected heterozygosity HE for all loci was 0,705 ± 0,15, the mean value of observed heterozygosity HO was 0,704 ± 0,18. The frequencies of genotypes for most tested markers were in The aim of this study was the selection and testing of suitable microsatellite markers for evaluation of the Slovak carniolan honey bee, particularly the population structure, genetic diversity, breed assignment and paternity testing of honey bee queens in Slovakia. Fourteen microsatellite markers running in two multiplex PCR reactions have been tested on 40 randomly selected workers and queens and further verified by PIC index, expected heterozygosity (HE and observed heterozygosity (HO. Chi-squared test of goodness of fit (α = 0,05 was used to check the Hardy-Weinberg equilibrium (HWE of genotype for each marker. For the comparison tests the workers of A. mellifera mellifera x ligurica, A. mellifera macedonica and A. mellifera iberica were analyzed, using

  17. A SUBLOCUS OF THE MULTICOPY MICROSATELLITE MARKER CMS1 MAPS PROXIMAL TO SPINAL MUSCULAR-ATROPHY (SMA) AS SHOWN BY RECOMBINANT ANALYSIS

    NARCIS (Netherlands)

    VANDERSTEEGE, G; COBBEN, JM; OSINGA, J; SCHEFFER, H; VANOMMEN, GJB; BUYS, CHCM

    1995-01-01

    The critical region containing the spinal muscular atrophy (SMA) gene is flanked by the 5q11-q13 markers, D5S435 and D5S557, as determined by linkage analysis. Here we present the results of an analysis of a Dutch SMA family with the multicopy microsatellite marker CMS1. A crossover is revealed in

  18. Microsatellite isolation and marker development in carrot - genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae

    Directory of Open Access Journals (Sweden)

    Yildiz Mehtap

    2011-08-01

    Full Text Available Abstract Background The Apiaceae family includes several vegetable and spice crop species among which carrot is the most economically important member, with ~21 million tons produced yearly worldwide. Despite its importance, molecular resources in this species are relatively underdeveloped. The availability of informative, polymorphic, and robust PCR-based markers, such as microsatellites (or SSRs, will facilitate genetics and breeding of carrot and other Apiaceae, including integration of linkage maps, tagging of phenotypic traits and assisting positional gene cloning. Thus, with the purpose of isolating carrot microsatellites, two different strategies were used; a hybridization-based library enrichment for SSRs, and bioinformatic mining of SSRs in BAC-end sequence and EST sequence databases. This work reports on the development of 300 carrot SSR markers and their characterization at various levels. Results Evaluation of microsatellites isolated from both DNA sources in subsets of 7 carrot F2 mapping populations revealed that SSRs from the hybridization-based method were longer, had more repeat units and were more polymorphic than SSRs isolated by sequence search. Overall, 196 SSRs (65.1% were polymorphic in at least one mapping population, and the percentage of polymophic SSRs across F2 populations ranged from 17.8 to 24.7. Polymorphic markers in one family were evaluated in the entire F2, allowing the genetic mapping of 55 SSRs (38 codominant onto the carrot reference map. The SSR loci were distributed throughout all 9 carrot linkage groups (LGs, with 2 to 9 SSRs/LG. In addition, SSR evaluations in carrot-related taxa indicated that a significant fraction of the carrot SSRs transfer successfully across Apiaceae, with heterologous amplification success rate decreasing with the target-species evolutionary distance from carrot. SSR diversity evaluated in a collection of 65 D. carota accessions revealed a high level of polymorphism for these

  19. Polymorphism analysis of microsatellites and construction of linkage map in part regions of four chromosomes in chicken

    Institute of Scientific and Technical Information of China (English)

    WANG Shouzhi; LI Hui; LI Ning; GAO Yu; DU Zhiqiang; GU Zhiliang; WANG Qigui; LI Zhihui; WANG Ying

    2007-01-01

    Based on chicken' consensus map issued in 2000, 17 microsatellites near 4 candidate genes such as IGF2, OBR, GDFS and APOA1 in 4 chromosomes (chromosome 5, 7, 8 and 24) were chosen for polymorphism analysis and construction of linkage map. Combining the technique of PCR and the fluorescent semi-automated detection, genome scanning was performed for 440 chickens, which was derived from China Agricultural University chicken resource families within three generations. The individuals of this resource families were genotyped. The results showed that the number of alleles ranged from 4 to 14; heterozygosity (H) of markers was between 0.3116 and 0.9148. Polymorphic information content (PIC) varied from 0.2672 to 0.8679. Microsatellites along with above-mentioned 4 candidate genes doing as general markers were used to construct linkage map. The spans of 4 linkage maps constructed in the part region of chromosome 5, 7, 8 and 24 were 263.5, 79.9, 206.2 and 104.2 cM, respectively. The order of markers was consistent with that of counterpart of reported consensus map. However, The spans of linkage map were larger than that of consensus map. The constructed linkage maps laid the foundation for mapping quantitative trait loci (QTL) responsible for economically important traits in chicken.

  20. The population structure of Trypanosoma cruzi: expanded analysis of 54 strains using eight polymorphic CA-repeat microsatellites

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    Riva P Oliveira

    1999-09-01

    Full Text Available Recently we cloned and sequenced the first eight Trypanosoma cruzi polymorphic microsatellite loci and studied 31 clones and strains to obtain valuable information about the population structure of the parasite. We have now studied 23 further strains, increasing from 11 to 31 the number of strains obtained from patients with chronic Chagas disease. This expanded set of 54 strains and clones analyzed with the eight microsatellites markers confirmed the previously observed diploidy, clonal population organization and very high polymorphism of T. cruzi. Moreover, this new study disclosed two new features of the population genetic structure of T. cruzi. The first was the discovery that, similarly to what we had previously shown for strains isolated from insect vectors, mammals and humans with acute disease, isolates from patients in the chronic phase of Chagas disease could also be multiclonal, albeit at a reduced proportion. Second, when we used parsimony to display the genetic relationship among the clonal lineages in an unrooted Wagner network we observed, like before, a good correlation of the tree topography with the classification in three clusters on the basis of single locus analysis of the ribosomal RNA genes. However, a significant new finding was that now the strains belonging to cluster 2 split in two distant sub-clusters. This observation suggests that the evolutionary history of T. cruzi may be more complex than we previously thought.

  1. Paternity Analysis of the Olive Variety “Istrska Belica” and Identification of Pollen Donors by Microsatellite Markers

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    Alenka Baruca Arbeiter

    2014-01-01

    Full Text Available The leading olive variety in Slovenia is “Istrska belica” (Olea europaea L., which currently represents 70% of all olive trees in productive orchards. Paternity analysis based on microsatellite markers was used for genotyping and identification of the potential pollen donors of “Istrska belica” and for assessing the proportion of self-fertilization in monovarietal olive orchards in the Slovene Istria. Seven microsatellite loci were used for genotyping thirty-one olive embryos from “Istrska belica” trees and for all potential pollen donor varieties, which are grown in the region and could participate as pollinators. Genotyping results and allele identification were performed using the FaMoz software. The most probable pollen donor was assigned to 39% of all analyzed embryos. Among all analyzed embryos no single case of self-fertilization was confirmed. According to the present results, the variety “Istrska belica” was in all cases fertilized by foreign pollen. The results will contribute to defining the new guidelines for farmers regarding the proper management and growing practice in monovarietal olive groves.

  2. The analysis of genetic diversity and differentiation of six Chinese cattle populations using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A total of 321 individuals from six cattle populations of four species in a bovine subfamily in China were studied using 12 pairs of microsatellite markers. The genetic diversities within and between populations were calculated. The phylogenetic trees were constructed by(δμ)2 and DA distances, and the divergence times between populations were estimated by (δμ)2. Altogether, 144 microsatellite alleles were detected including 24 private alleles and nine shared alleles. Chinese Holstein had the largest number of private alleles (10), whereas,Bohai black and Buffalo had the smallest number of private alleles (2). Chinese Holstein showed the highest genetic variability. Its observed number of alleles (Na), mean effective number of alleles (MNA), and mean heterozygosity (He) were 7.7500, 4.9722, and 0.7719,respectively, whereas, the Buffalo and Yak showed low genetic variability. In the phylogenetic trees, Luxi and Holstein grouped first,followed by Bohai and Minnan. Yak branched next and buffalo emerged as the most divergent population from other cattle populations.Luxi and Bohai were estimated to have diverged 0.039-0.105 million years ago (MYA), however, buffalo and Holstein diverged 0.501-1.337 MYA. The divergence time of Yak versus Minnan, Holstein and buffalo was 0.136-0.363, 0.273-0.729, and 0.326-0.600MYA, respectively.

  3. Comparative analysis of microsatellite variability in five macaw species (Psittaciformes, Psittacidae: application for conservation

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    Flavia T. Presti

    2011-01-01

    Full Text Available Cross-amplification was tested and variability in microsatellite primers (designed for Neotropical parrots compared, in five macaw species, viz., three endangered blue macaws (Cyanopsitta spixii [extinct in the wild], Anodorhynchus leari [endangered] and Anodorhynchus hyacinthinus [vulnerable], and two unthreatened red macaws (Ara chloropterus and Ara macao. Among the primers tested, 84.6% successfully amplified products in C. spixii, 83.3% in A. leari, 76.4% in A. hyacinthinus, 78.6% in A. chloropterus and 71.4% in A. macao. The mean expected heterozygosity estimated for each species, and based on loci analyzed in all the five, ranged from 0.33 (A. hyacinthinus to 0.85 (A. macao. As expected, the results revealed lower levels of genetic variability in threatened macaw species than in unthreatened. The low combined probability of genetic identity and the moderate to high potential for paternity exclusion, indicate the utility of the microsatellite loci set selected for each macaw species in kinship and population studies, thus constituting an aid in planning in-situ and ex-situ conservation.

  4. Genetic diversity analysis among pigeonpea genotypes adapted to South American regions based on microsatellite markers

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    Adna Cristina Barbosa de Sousa

    2011-08-01

    Full Text Available The pigeonpea [Cajanus cajan (L Millspaugh] is one of the most important perennial legume crops utilized in the food, fodder, soil conservation, crop-livestock integrated systems, reclaiming of degraded pastures and symbiotic nitrogen fixation. Microsatellite markers were used to estimate the genetic diversity of 77 pigeonpea genotypes selected from the germplasm collections at Embrapa Cattle-Southeast and, to evaluate their transferability to Phaseolus vulgaris and Vigna unguiculata species. The number of alleles per locus ranged from 2 to12, with an average of 5.1 alleles. The PIC values ranged from 0.11 to 0.80 (average 0.49 and the D values from 0.23 to 0.91 (average 0.58. The averages of observed and expected heterozygosity were 0.25 and 0.47, respectively, showing a deficit in heterozygosity. A model-based Bayesian approach implemented in the software STRUCTURE was used to assign genotypes into clusters. A dendrogram was constructed based on the modified Roger's genetic distances using a neighbor-joining method (NJ. A total of four clusters were assembled by STRUCTURE and a strong tendency of correspondence between the Bayesian clusters in the NJ tree was observed. The genetic distance ranged from 0.09 to 0.62 (average 0.37, showing a low genetic diversity in the pigeonpea genotypes. Transferability of pigeonpea-specific microsatellites revealed a cross-amplification and the presence of polymorphic alleles in P. vulgaris and V. unguiculata.

  5. Use of microsatellite markers in molecular analysis of segregating populations of papaya (Carica papaya L.) derived from backcrossing.

    Science.gov (United States)

    Pinto, F O; Pereira, M G; Luz, L N; Cardozo, D L; Ramos, H C C; Macedo, C M P

    2013-07-08

    Brazil is the world leader in papaya production. However, only a small number of cultivars are registered for commercial planting, mainly owing to delays in obtaining cultivars and the high costs of the field phase of breeding programs. These costs can be reduced when molecular tools are combined with conventional breeding methods. In the present study, we conducted a molecular analysis of a self-fertilized population of a first backcrossing generation of BC1S1 papaya plants via microsatellite markers both to monitor the level of homozygosity and the gene/allele transfer that confers the Golden trait (fruit color) and to assess the parental genomic proportion in the genotypes studied. Based on the analysis of 20 polymorphic microsatellite loci, 19 genotypes with the Golden trait belonging to BC1S1 were evaluated in addition to the parental genotypes. Genetic distance was estimated through weighted index. The genotypes were then grouped using the hierarchical nearest neighbor method, and the analysis of principal coordinates was used to measure the proportion of parental genomes in the segregating genotypes. The mean value of the inbreeding coefficient was 0.36. The analysis of the principal coordinates revealed that on average, 64% of the recurrent parent genome was present in the population. Together, the analyses allowed the selection of 3 individuals for the next backcross cycle (33BC1S1-18, 34BC1S1-16, and 37BC1S1-10). These individuals had a higher proportion of the recurrent parent and were grouped close to the recurrent parent in the cluster analysis.

  6. Genome-wide survey and analysis of microsatellites in nematodes, with a focus on the plant-parasitic species Meloidogyne incognita

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    Guillemaud Thomas

    2010-10-01

    Full Text Available Abstract Background Microsatellites are the most popular source of molecular markers for studying population genetic variation in eukaryotes. However, few data are currently available about their genomic distribution and abundance across the phylum Nematoda. The recent completion of the genomes of several nematode species, including Meloidogyne incognita, a major agricultural pest worldwide, now opens the way for a comparative survey and analysis of microsatellites in these organisms. Results Using MsatFinder, the total numbers of 1-6 bp perfect microsatellites detected in the complete genomes of five nematode species (Brugia malayi, Caenorhabditis elegans, M. hapla, M. incognita, Pristionchus pacificus ranged from 2,842 to 61,547, and covered from 0.09 to 1.20% of the nematode genomes. Under our search criteria, the most common repeat motifs for each length class varied according to the different nematode species considered, with no obvious relation to the AT-richness of their genomes. Overall, (ATn, (AGn and (CTn were the three most frequent dinucleotide microsatellite motifs found in the five genomes considered. Except for two motifs in P. pacificus, all the most frequent trinucleotide motifs were AT-rich, with (AATn and (ATTn being the only common to the five nematode species. A particular attention was paid to the microsatellite content of the plant-parasitic species M. incognita. In this species, a repertoire of 4,880 microsatellite loci was identified, from which 2,183 appeared suitable to design markers for population genetic studies. Interestingly, 1,094 microsatellites were identified in 801 predicted protein-coding regions, 99% of them being trinucleotides. When compared against the InterPro domain database, 497 of these CDS were successfully annotated, and further assigned to Gene Ontology terms. Conclusions Contrasted patterns of microsatellite abundance and diversity were characterized in five nematode genomes, even in the case of

  7. 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

    重复类型,占总数的53.86%;其次为两碱基核心重复类型,占总数的43.36%;而四、五、六碱基重复类型以及复合型的SSR数量均较少,且数量差异不大,共占EST-SSR总数的2.78%。柑橘全爪螨EST-SSR核心重复次数主要集中在5—10次。【结论】采用磁珠富集法,并将酶切、接头连接一步化,可提高个体微小的螨类及微小昆虫SSR的富集效率。柑橘全爪螨gSSR核心重复次数要远多于从转录组数据库获得的EST-SSR。总体而言,gSSR和EST-SSR中的三碱基重复SSR具有更好的优化率。此外,柑橘全爪螨gSSR具有微卫星家族现象。%Objective] The objective of this study is to construct the microsatellite-enriched libraries, and identify genomic- microsatellite (gSSR) from the genome of the citrus red mite,Panonychus citri. Meanwhile, a large number of gene-microsatellite (EST-SSR) markers were also indentified from the transcriptome database ofP. citri. Based on these SSR sequences, the selected SSR primer pairs were validated.[Method]On the basis of isolating high quality genomic DNA ofP. citri, enriched microsatellite libraries were constructed by streptavidin-coated magnetic beads utilizing methodologies that exploit the strong affinity between biotin and the protein streptavidin. A fast and easy protocol was proposed through a combination of two different published methods. Briefly, genomic DNA was digested by the restriction enzyme and then ligated to designed adaptors. Microsatellite-containing DNA fragments were captured by streptavidin-coated magnetic beads. The beads affinity capture of microsatellite repeats using biotinylated oligonucleotide probes. Subsequently, PCR was used to amplify the captured molecules for transferring single strand DNA to double strand DNA. The PCR products were then ligated to pGEM-T Easy vector and transformed into Trans5α competent cells. Then, clones from these libraries were screened for microsatellite content. Meanwhile

  8. Does tumorigenesis select for or against mutations of the DNA repair-associated genes BRCA2 and MRE11?: Considerations from somatic mutations in microsatellite unstable (MSI gastrointestinal cancers

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    Elghalbzouri-Maghrani Elhaam

    2006-01-01

    Full Text Available Abstract Background The BRCA2 and MRE11 proteins participate in the repair of double-strand DNA breaks by homologous recombination. Germline BRCA2 mutations predispose to ovarian, breast and pancreatic cancer, while a germline MRE11 mutation is associated with an ataxia telangiectasia-like disorder. Somatic mutations of BRCA2 are rare in typical sporadic cancers. In tumors having microsatellite instability (MSI, somatic truncating mutations in a poly [A] tract of BRCA2 are reported on occasion. Results We analyzed gastrointestinal MSI cancers by whole gene BRCA2 sequencing, finding heterozygous truncating mutations in seven (47% of 15 patients. There was no cellular functional defect in RAD51 focus-formation in three heterozygously mutated lines studied, although other potential functions of the BRCA2 protein could still be affected. A prior report of mutations in primary MSI tumors affecting the IVS5-(5–15 poly [T] tract of the MRE11 gene was confirmed and extended by analysis of the genomic sequence and protein expression in MSI cancer cell lines. Statistical analysis of the published MRE11 mutation rate in MSI tumors did not provide evidence for a selective pressure favoring biallelic mutations at this repeat. Conclusion Perhaps conflicting with common suspicions, the data are not compatible with selective pressures during tumorigenesis promoting the functional loss of BRCA2 and MRE11 in MSI tumors. Instead, these data fit closely with an absence of selective pressures acting on BRCA2 and MRE11 gene status during tumorigenesis.

  9. 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.

  10. Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago

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    Sávio P. Reis

    2008-01-01

    Full Text Available In this study, 15 microsatellite DNA loci used in comparative tests by the International Society for Animal Genetics were applied to the evaluation of genetic diversity and management, and the efficiency of paternity testing in Marajoara horses and Puruca ponies from the Marajó Archipelago. Based on the genotyping of 93 animals, mean allelic diversity was estimated as 9.14 and 7.00 for the Marajoara and Puruca breeds, respectively. While these values are similar to those recorded in most European breeds, mean levels of heterozygosity were much lower (Marajoara 49%, Puruca 40%, probably as a result of high levels of inbreeding in the Marajó populations. The mean informative polymorphic content of this 15-marker system was over 50% in both breeds, and was slightly higher in the Marajoara horses. The discriminative power and exclusion probabilities derived from this system were over 99% for both populations, emphasizing the efficacy of these markers for paternity testing and genetic management in the two breeds.

  11. [Aspirin suppresses microsatellite instability].

    Science.gov (United States)

    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.

  12. Information Analysis of DNA Sequences

    CERN Document Server

    Mohammed, Riyazuddin

    2010-01-01

    The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they do not seem to participate in the process of transcription of amino-acids, they have been termed "junk DNA." Although it is believed that the non-coding regions in genomes have no role in cell growth and evolution, demonstration that these regions carry useful information would tend to falsify this belief. In this paper, we consider entropy as a measure of information by modifying the entropy expression to take into account the varying length of these sequences. Exons are usually much shorter in length than introns; therefore the comparison of the entropy values needs to be normalized. A length correction strategy was employed using randomly generated nucleonic base strings built out of the alphabet of the same size as the exons under question. Our analysis shows that intron...

  13. Demographic estimates from Y chromosome microsatellite polymorphisms: Analysis of a worldwide sample

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    Macpherson J

    2004-08-01

    Full Text Available Abstract Polymorphisms in microsatellites on the human Y chromosome have been used to estimate important demographic parameters of human history. We compare two coalescent-based statistical methods that give estimates for a number of demographic parameters using the seven Y chromosome polymorphisms in the HGDP-CEPH Cell Line Panel, a collection of samples from 52 worldwide populations. The estimates for the time to the most recent common ancestor vary according to the method used and the assumptions about the prior distributions of model parameters, but are generally consistent with other global Y chromosome studies. We explore the sensitivity of these results to assumptions about the prior distributions and the evolutionary models themselves.

  14. Cytomolecular discrimination of the A(m) chromosomes of Triticum monococcum and the A chromosomes of Triticum aestivum using microsatellite DNA repeats.

    Science.gov (United States)

    Megyeri, Mária; Mikó, Péter; Farkas, András; Molnár-Láng, Márta; Molnár, István

    2017-02-01

    The cytomolecular discrimination of the A(m)- and A-genome chromosomes facilitates the selection of wheat-Triticum monococcum introgression lines. Fluorescence in situ hybridisation (FISH) with the commonly used DNA probes Afa family, 18S rDNA and pSc119.2 showed that the more complex hybridisation pattern obtained in T. monococcum relative to bread wheat made it possible to differentiate the A(m) and A chromosomes within homoeologous groups 1, 4 and 5. In order to provide additional chromosomal landmarks to discriminate the A(m) and A chromosomes, the microsatellite repeats (GAA)n, (CAG)n, (CAC)n, (AAC)n, (AGG)n and (ACT)n were tested as FISH probes. These showed that T. monococcum chromosomes have fewer, generally weaker, simple sequence repeat (SSR) signals than the A-genome chromosomes of hexaploid wheat. A differential hybridisation pattern was observed on 6A(m) and 6A chromosomes with all the SSR probes tested except for the (ACT)n probe. The 2A(m) and 2A chromosomes were differentiated by the signals given by the (GAA)n, (CAG)n and (AAC)n repeats, while only (GAA)n discriminated the chromosomes 3A(m) and 3A. Chromosomes 7A(m) and 7A could be differentiated by the lack of (GAA)n and (AGG)n signals on 7A. As potential landmarks for identifying the A(m) chromosomes, SSR repeats will facilitate the introgression of T. monococcum chromatin into wheat.

  15. Sequence Divergence of Microsatellites and Phylogeny Analysis in Tetraploid Cotton Species and Their Putative Diploid Ancestors

    Institute of Scientific and Technical Information of China (English)

    Wang-Zhen GUO; Dong FANG; Wen-Duo YU; Tian-Zhen ZHANG

    2005-01-01

    To determine the level of microsatellite sequence differences and to use the information to construct a phylogenetic relationship for cultivated tetraploid cotton (Gossypium spp.) species and their putative diploid ancestors, 10 genome-derived microsatellite primer pairs were used to amplify eight species,including two tetraploid and six diploid species, in Gossypium. A total of 92 unique amplicons were resolved using polyacrylamide gel electrophoresis. Each amplicon was cloned, sequenced, and analyzed using standard phylogenetic software. Allelic diversities were caused mostly by changes in the number of simple sequence repeat (SSR) motif repeats and only a small proportion resulted from interruption of the SSR motif within the locus for the same genome. The frequency of base substitutions was 0.5%-1.0% in different genomes, with only few indels found. Based on the combined 10 SSR flanking sequence data, the homology of A-genome diploid species averaged 98.9%, even though most of the amplicons were of the same size, and the sequence homology between G. gossypioides (Ulbr.) Standl. and three other D-genome species (G.raimondii Ulbr., G. davidsonii Kell., and G. thurberi Tod.) was 98.5%, 98.6%, and 98.5%, respectively.Phylogenetic trees of the two allotetraploid species and their putative diploid progenitors showed that homoelogous sequences from the A- and D-subgenome were still present in the polyploid subgenomes and they evolved independently. Meanwhile, homoelogous sequence interaction that duplicated loci in the polyploid subgenomes became phylogenetic sisters was also found in the evolutionary history of tetraploid cotton species. The results of the present study suggest that evaluation of SSR variation at the sequence level can be effective in exploring the evolutionary relationships among Gossypuim species.

  16. Competing risks analysis of microsatellite instability as a prognostic factor in colorectal cancer.

    Science.gov (United States)

    Toh, J; Chapuis, P H; Bokey, L; Chan, C; Spring, K J; Dent, O F

    2017-08-01

    Despite an extensive literature suggesting that high microsatellite instability (MSI-H) enhances survival and protects against recurrence after colorectal cancer resection, such effects remain controversial as many studies show only a weak bivariate association or no multivariable association with outcome. This study examined the relationship between MSI status and colorectal cancer outcomes with adjustment for death from other causes as a competing risk. A hospital database of patients following colorectal cancer resection was interrogated for clinical, operative, pathology, adjuvant therapy and follow-up information. MSI-H status was determined by immunohistochemistry for mismatch repair protein deficiency. The cumulative incidence of recurrence and colorectal cancer-specific death was evaluated by competing risks methods. Among 1009 patients who had a resection between August 2002 and December 2008, and were followed to at least December 2013, there were 114 (11·3 per cent) with MSI-H (72·8 per cent aged at least 70 years; 63·2 per cent women). After potentially curative resection, with adjustment for non-colorectal cancer death as a competing risk and adjustment for 22 clinical, operative and pathological variables, there was no association between MSI-H and recurrence (hazard ratio (HR) 0·81, 95 per cent c.i. 0·42 to 1·57) or colorectal cancer-specific death (HR 0·73, 0·39 to 1·35) in this patient population. For palliative resections, there was no association between MSI-H and colorectal cancer-specific death (HR 0·65, 0·21 to 2·04). MSI-H was associated with non-colorectal cancer death after both curative (HR 1·55, 1·04 to 2·30) and palliative (HR 3·80, 1·32 to 11·00) resections. Microsatellite instability status was not an independent prognostic variable in these patients. © 2017 BJS Society Ltd Published by John Wiley & Sons Ltd.

  17. A comparative analysis of distribution and conservation of microsatellites in the transcripts of sequenced Fusarium species and development of genic-SSR markers for polymorphism analysis.

    Science.gov (United States)

    Mahfooz, Sahil; Srivastava, Arpita; Srivastava, Alok K; Arora, Dilip K

    2015-09-01

    We used an in silico approach to survey and compare microsatellites in transcript sequences of four sequenced members of genus Fusarium. G + C content of transcripts was found to be positively correlated with the frequency of SSRs. Our analysis revealed that, in all the four transcript sequences studied, the occurrence, relative abundance and density of microsatellites varied and was not influenced by transcript sizes. No correlation between relative abundance and transcript sizes was observed. The relative abundance and density of microsatellites were highest in the transcripts of Fusarium solani when compared with F. graminearum, F. verticillioides and F. oxysporum. The maximum frequency of SSRs among all four sequence sets was of trinucleotide repeats (67.8%), whereas the dinucleotide repeat represents Fusarium species. In order to study polymorphism within Fusarium isolates, 11 polymorphic genic-SSR markers were developed. Of the 11 markers, 5 were from F. oxysporum and remaining 6 belongs to F. solani. SSR markers from F. oxysporum were found to be more polymorphic (38%) as compared to F. solani (26%). Eleven polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Fusarium. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

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    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.

  19. 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.

  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. Analysis of the genetic diversity between Gentile di Puglia, Sopravissana and Sarda sheep breeds using microsatellite markers

    Directory of Open Access Journals (Sweden)

    Gennaro Catillo

    2010-01-01

    Full Text Available Two Italian sheep breeds – Gentile di Puglia and Sopravissana – have undergone a consistent decline in numbers and have been widely substituted by the Sarda breed, which gives higher milk yield. With the aim to provide a basis for con- servation decisions, the genetic variability of the three breeds was investigated in this study. DNA of 60 animals was PCR amplified at the following microsatellite loci: CSSM43, CSSM47, CSSM60, TGLA110, TGLA122, TGLA126, TGLA377, ETH3, ETH10, ETH225, NRAMP1, OARCP20 and SPS115. Allele frequencies, gene diversity and genetic distances were calculat- ed. The highest differences in allele frequencies were found at the following loci: TGLA377, TGLA122, NRAMP1, OARCP20 and ETH3, while at the other loci the most frequent alleles were the same. The average inbreeding rate was 0.156 in the Gentile di Puglia, 0.158 in the Sopravissana and 0.137 in the Sarda. Average gene diversity of the analysed microsatel- lites was 0.59. Genetic distance between Gentile di Puglia and Sopravissana (0.081 indicates moderate differentiation; distances between the Sarda and the endangered breeds – 0.111 from the Gentile di Puglia and 0.107 from the Sopravissana - indicate a medium-high differentiation rate. The disappearance of the two less productive breeds would entail a consistent loss of genetic diversity. The inbreeding values are low enough to allow the implementation of sound conservation programmes.

  2. High frequency of submicroscopic chromosomal imbalances in patients with syndromic craniosynostosis detected by a combined approach of microsatellite segregation analysis, multiplex ligation-dependent probe amplification and array-based comparative genome hybridisation.

    NARCIS (Netherlands)

    Jehee, F.S.; Krepischi-Santos, A.C.; Rocha, K.M.; Cavalcanti, D.P.; Kim, C.A.; Bertola, D.R.; Alonso, L.G.; D'Angelo, C.S.; Mazzeu, J.F.; Froyen, G.; Lugtenberg, D.; Vianna-Morgante, A.M.; Rosenberg, C.; Passos-Bueno, M.R.

    2008-01-01

    We present the first comprehensive study, to our knowledge, on genomic chromosomal analysis in syndromic craniosynostosis. In total, 45 patients with craniosynostotic disorders were screened with a variety of methods including conventional karyotype, microsatellite segregation analysis, subtelomeric

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. Population genetic analysis of the Brahman cattle (Bos indicus) in Colombia with microsatellite markers.

    Science.gov (United States)

    Novoa, M A; Usaquén, W

    2010-04-01

    The Brahman is one of the most popular breeds for meat production in the Neotropics. However, genetic studies of the breed in Latin American countries have only recently begun. In total, 178 animals of the Brahman breed from 20 Colombian provinces were genotyped at 11 microsatellite markers with the aim of studying the genetic diversity of this population and its genetic relationships with zebuine and taurine breeds. The outcomes of multivariate analyses, Bayesian inferences and inter-individual genetic distances suggested that there is no genetic sub-structure in the population, because of the high rate of animal migration among provinces. The population shows a high degree of heterozygosity and allelic diversity compared with other breeds, reflecting its multibreed origin. The study of the genetic relationships among the breeds reveals that the Brahman breed belongs to the zebuine group. However, it is the population nearest to taurine breeds with high frequencies of taurine alleles. Intensive artificial selection may have favoured the taurine alleles after the breed was formed. There has also been some degree of mixture with local taurine breeds while the Brahman breed has evolved in Colombia.

  6. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment.

    Science.gov (United States)

    Rai, Shalini; Kashyap, Prem Lal; Kumar, Sudheer; Srivastava, Alok Kumar; Ramteke, Pramod W

    2016-01-01

    Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2%) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

  7. Population genetic analysis and conservation strategies for redtail shrimp Fenneropenaeus penicillatus using ten microsatellite markers.

    Science.gov (United States)

    Cao, Y Y; Shangguan, J B; Li, Z B

    2017-03-15

    Fenneropenaeus penicillatus, which is on the Red List of Endangered Species for China, is an important shrimp species. However, there is not enough genetic information on F. penicillatus for conservation and management purposes. Ten microsatellite markers were used to analyze the genetic diversity, genetic differentiation, and population structure of F. penicillatus to provide scientific information for the conservation of the species. Low genetic diversity and moderate genetic differentiation were found among 12 putative populations [Beihai, Dongshan (DS), Hainan (HN), Lianjiang, Nanao (NA), Ningde (ND), Putian, Quanzhou (QZ), Xiamen (XM), Shenzhen, Zhanjiang, and Zhangpu] along the southeast coast of China. QZ, XM, and DS exhibited the highest genetic diversity, while NA and ND had the lowest genetic diversity. Genetic differentiation among all populations, except HN, was low compared to the genetic differentiation between HN and the other 11 putative populations. These 12 putative populations were divided into two subgroups. One group consisted of XM, DS, and QZ. The other group consisted of the other eight putative populations with the exception of HN. The HN Island population requires further study due to its large genetic distance from the other 11 putative populations. Problems with the current conservation strategy are pointed out and suggestions given based on genetic information.

  8. A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States.

    Science.gov (United States)

    Conant, E K; Juras, R; Cothran, E G

    2012-02-01

    The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear.

  9. Population genetic analysis among five Indian population groups using six microsatellite markers.

    Science.gov (United States)

    Ghosh, Anu; Das, Birajalaxmi; Seshadri, M

    2003-04-01

    Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

  10. Post-bottleneck genetic diversity of elephant populations in South Africa, revealed using microsatellite analysis.

    Science.gov (United States)

    Whitehouse, A M; Harley, E H

    2001-09-01

    Widespread hunting had fragmented and severely reduced elephant populations in South Africa by 1900. Elephant numbers increased during the 1900s, although rates of recovery of individual populations varied. The Kruger National Park elephant population increased rapidly, to more than 6000 by 1967, with recruitment boosted by immigration from Mozambique. The Addo Elephant National Park population was reduced to 11 elephants in 1931 and remains relatively small (n = 325). Loss of genetic variation is expected to occur whenever a population goes through a bottleneck, especially when post-bottleneck recovery is slow. Variation at nine polymorphic microsatellite loci was analysed for Kruger and Addo elephants, as well as museum specimens of Addo elephants shot prior to the population bottleneck. Significantly reduced genetic variation and heterozygosity were observed in Addo in comparison to Kruger (mean alleles/locus and H(E): Addo 1.89, 0.18; Kruger 3.89, 0.44). Two alleles not present in the current Addo population were observed in the museum specimens. Addo elephants represent a genetic subset of the Kruger population, with high levels of genetic differentiation resulting from rapid genetic drift. The Kruger population is low in genetic diversity in comparison to East African elephants, confirming this population also suffered an appreciable bottleneck.

  11. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae).

    Science.gov (United States)

    Harrison, Hugo B; Feldheim, Kevin A; Jones, Geoffrey P; Ma, Kayan; Mansour, Hicham; Perumal, Sadhasivam; Williamson, David H; Berumen, Michael L

    2014-06-01

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species.

  12. Validation of microsatellite multiplexes for parentage analysis and species discrimination in two hybridizing species of coral reef fish (Plectropomus spp., Serranidae)

    KAUST Repository

    Harrison, H.B.

    2014-04-24

    Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus (Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

  13. Population structure of the African savannah elephant inferred from mitochondrial control region sequences and nuclear microsatellite loci

    DEFF Research Database (Denmark)

    Nyakaana, S; Arctander, P; Siegismund, H R

    2002-01-01

    Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern...... populations and 44 alleles in the total sample were found. The gene diversity ranged from 0.51 to 0.72 in the localities studied. An analysis of molecular variance showed significant genetic differentiation between populations within regions and also between regions. The extent of subdivision between...... populations at the mtDNA control region was approximately twice as high as shown by the microsatellite loci (mtDNA F(ST) = 0.59; microsatellite R(ST) = 0.31). We discuss our results in the light of Pleistocene refugia and attribute the observed pattern to population divergence in allopatry accompanied...

  14. Intracavity DNA melting analysis with optofluidic lasers.

    Science.gov (United States)

    Lee, Wonsuk; Fan, Xudong

    2012-11-01

    DNA melting analysis holds great promise for simple and fast DNA sequence discrimination. However, conventional fluorescence-based methods suffer from a small differential signal and demanding melting curve analysis, both of which make it difficult to distinguish the target DNA from the mismatched one. Herein, we propose and demonstrate a highly specific intracavity DNA melting analysis scheme utilizing an optofluidic laser. The laser optically amplifies the small yet intrinsic thermal dynamic difference between the target and the single-base-mismatched DNA, resulting in a differential signal that is orders of magnitude greater than with fluorescence-based methods. In particular, the existence of a phase transition between the stimulated laser emission and fluorescence (i.e., spontaneous emission) enables accurate determination of the DNA transition temperature difference. Furthermore, the high differential signal in the intracavity detection allows for scanning of the laser excitation at a fixed temperature to distinguish two DNA sequences, which provides another means for rapid DNA analysis. In this paper, we first theoretically investigate DNA melting analysis using an optofluidic laser and then experimentally explore this scheme with a high-quality optofluidic ring resonator. Distinction of two DNA sequences of up to 100 bases long is demonstrated. The intracavity detection developed here will lead to novel optofluidic devices that enable rapid and simple analysis of DNAs with very long sequences.

  15. Construction and identification of DNA libraries enriched for microsatellite repeat sequences of Chinese hamster%中国地鼠基因组微卫星富集文库的构建与分析

    Institute of Scientific and Technical Information of China (English)

    宋国华; 耿佳宁; 贾若愚; 岳文斌; 刘田福; 胡松年

    2011-01-01

    目的 筛选中国地鼠微卫星位点,为中国地鼠种质资源的分类、进化等遗传研究奠定基础.方法中国地鼠基因组DNA经超声打碎,用2%琼脂糖凝胶电泳回收500~1000 bp的DNA片段,与SNX连接头连接,连接产物与生物素标记的14种微卫星探针变性及退火,再通过链亲和素偶联磁珠亲和捕捉,经吸附、洗涤及洗脱,然后以洗脱产物为模板,通过PCR扩增,与pGEM-T载体连接,转化大肠杆菌DH10B,构建中国地鼠微卫星DNA富集文库.结果 测序结果发现,微卫星DNA序列的阳性克隆占70.3%.结论 中国地鼠微卫星文库的建立和微卫星的筛选将为下一步进行中国地鼠遗传连锁图谱的构建、分子进化和系统发育研究提供大量的微卫星标记.%Objective To screen the microsatellite loci of Chinese hamster DNA to serve the genetic studies of germplasm resources, classification and evolution of Chinese hamsters. Methods Genomic DNAs from Chinese hamster was fragmented by ultrasonication. The fragments in size from 500 bp to 1000 bp were recovered by 2% agarose gel electro-phoresis and ligated to SNX linkers with T4 DNA ligase, then denatured and hybridized to 14 biotinylated oligonucleotides. The biotinylated hybrids were retained on magnetic beads according to the strong afinity between biotin and streptavidin. The products was amplified by PCR and cloned into pGEM-T plasmid vector, and then transformed into Escherichia coli DH10B to construct DNA libraries enriched for microsatellite repeat sequences of Chinese hamster. Results The results of sequencing showed that sequences contained microsatellites indicating a high degree of microsatellite enrichment. Conclusions The new polymorphic microsatellite markers identified and characterized in this study may serve the Chinese hamster genetic linkage mapping, molecular evolution and phylogenetic studies.

  16. Analysis of beta-catenin, Ki-ras, and microsatellite stability in azoxymethane-induced colon tumors of BDIX/Orl Ico rats.

    Science.gov (United States)

    Sørensen, Nanna Møller; Kobaek-Larsen, Morten; Bonne, Anita; van Zutphen, Bert; Fenger, Claus; Kristiansen, Karsten; Ritskes-Hoitinga, Merel

    2003-12-01

    The aim of the study reported here was to investigate whether the azoxymethane (AOM)-induced colon cancer rat model mimics the human situation with regard to microsatellite stability, changes in expression of beta-catenin, and/or changes in the sequence of the proto-oncogene Ki-ras. Colon cancer was induced by administration of four weekly doses of AOM (15 mg/kg of body weight per week) separated by a one-week break between the second and third injections. As the histopathologic characteristics of this model resemble those of the human counterpart, further characterization of the genetic changes was undertaken. The animals were euthanized 28 to 29 weeks after the first AOM injection, and tumor specimens were taken for histologic and DNA analyses. Since microsatellite variation was found in only a few (< 2%) specimens, the model can be considered as having stable microsatellites. This result is in accordance with those of similar studies in other rat models and with most human colorectal cancers. Immunohistochemical analyses of beta-catenin did not reveal loss of gene activity, nor did the sequencing of Ki-ras reveal mutations. These results are in contrast to most findings in comparable rat studies. The deviations may be due to differences in exposure to the carcinogen or difference in strain and/or age. The lack of beta-catenin and Ki-ras alterations in this colon cancer model is unlike human sporadic colorectal cancers where these genetic changes are common findings.

  17. Rapid radiation in spiny lobsters (Palinurus spp as revealed by classic and ABC methods using mtDNA and microsatellite data

    Directory of Open Access Journals (Sweden)

    Macpherson Enrique

    2009-11-01

    Full Text Available Abstract Background Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene and/or more recent (Pleistocene oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae. In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC methods. Results Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our

  18. Analysis of the genetic relationships and diversity among 11 populations of Xanthoceras sorbifolia using phenotypic and microsatellite marker data

    Directory of Open Access Journals (Sweden)

    Zhan Shen

    2017-03-01

    Conclusions: Microsatellite markers can be used to efficiently distinguish X. sorbifolia populations and assess their genetic diversity. The information we have provided will contribute to the conservation and management of this important plant genetic resource.

  19. Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites

    Directory of Open Access Journals (Sweden)

    Rensing Stefan A

    2006-05-01

    Full Text Available Abstract Background The moss Physcomitrella patens is an emerging model in comparative plant science. At present, the Physcomitrella genome is sequenced at the Joint Genome Institute (USA. In this study we present our results on the development of expressed sequence tag-derived microsatellite markers for Physcomitrella patens, their classification and applicability as genetic markers on the intra- as well as on the interspecies level. We experienced severe restrictions to compare our results on Physcomitrella with earlier studies for other plant species due to varying microsatellite search criteria and a limited selection of analysed species. As a consequence, we performed a side by side analysis of expressed sequence tag-derived microsatellites among 24 plant species covering a broad phylogenetic range and present our results on the observed frequencies. Results We identified 3,723 microsatellites using the software MISA in a non-redundant Physcomitrella expressed sequence tag database comprising more than 37 megabases of nucleotide information. For 2,951 microsatellites appendant primer sequences have been derived. PCR of 376 microsatellites yielded 88 % successful amplicons and over 30 % polymorphisms between two Physcomitrella accessions. The polymorphism information content of 64 microsatellites based on 21 different Physcomitrella accessions was comparably high with a mean of 0.47 +/- 0.17. Of the 64 Physcomitrella microsatellite markers, 34 % respectively 79.7 % revealed cross-species applicability in two closely related moss species. In our survey of two green algae, two mosses, a fern, a fern palm, the ginkgo tree, two conifers, ten dicots and five monocots we detected an up to sevenfold variation in the overall frequency with a minimum of 37 up to maximal 258 microsatellites per megabase and a high variability among the different microsatellite class and motif frequencies. Numerous species-specific microsatellite frequencies became

  20. Genetic variation in time and space : Microsatellite analysis of extinct and extant populations of Atlantic salmon

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Hansen, Michael Møller; Loeschcke, V.

    1999-01-01

    Information on genetic composition of past and present populations may be obtained by analyzing DNA from archival samples. A study is presented on the genetic population structure of extant and extinct local populations of Atlantic salmon from 1913 to 1989 using dried scales as a source of DNA...... to establish in several recent studies. The discrepancy may be due to impact of human activities on the genetic structure of present populations, whereas old samples represent populations in a more unaffected state. However, other explanations related to differences in the sampling of past and present...

  1. Antibody-based screening for hereditary nonpolyposis colorectal carcinoma compared with microsatellite analysis and sequencing

    DEFF Research Database (Denmark)

    Christensen, Mariann; Katballe, Niels; Wikman, Friedrik;

    2002-01-01

    BACKGROUND: Germline mutations in the DNA mismatch repair genes, MSH2, MLH1, and others are associated with hereditary nonpolyposis colorectal cancer (HNPCC). Due to the high costs of sequencing, cheaper screening methods are needed to identify HNPCC cases. Ideally, these methods should have a hi...

  2. The Use of DNA Microsatellite Markers for Genetic Diversity Identifi cation of Soybean (Glycine max (L Meriil. as a Supplementary Method in Reference Collections Management

    Directory of Open Access Journals (Sweden)

    Nina Agusti Widaningsih

    2016-02-01

    Full Text Available Large number of new soybean varieties are mostly derived from crosses of elite genotypes resulted ina narrowing of both the genetic diversity and the phylogenetic relationship between soybean varieties. Thus,discrimination among soybean varieties is becoming more diffi cult, especially when morphological traits wereapplied. In Plant Variety Protection (PVP system, new varieties of soybeans including granted PVP right, localand breeding varieties registered in PVP offi ce were frequently increased, implicate on increasingly the numberof soybean varieties collections. To assist the management of varieties collections, a standard fi ngerprinting datais further needed. In comparison to the management of plant collection in the fi eld, molecular marker systemswhich are rapid, reliable, informative and relatively simple are continually sought for practical applications ingermplasm conservation, management and enhancement. This study aimed to identify the genetic diversity andphylogenetic relationship of soybean varieties that have earned PVP Right as well as local varieties and breedingvarieties registered in the PVP offi ce using microsatellite or simple sequence repeats (SSR markers.This study was conducted in Molecular Biology laboratory, Indonesian Center for Agricultural Biotechnologyand Genetic Resources Research and Development (ICABIOGRAD Bogor, from February to May 2013. The datawere analyzed using the genetic analysis package NTSYSpc 2.02i and PowerMarker V3.25. The result showed arelatively narrow genetic diversity among 45 varieties of soybean analyzed in present study which were indicatedby the small number of genotypes and total number of alleles (NA, and the low value of gene diversity and PICvalues (<0.75. Cluster analysis showed that the grouping varieties are not related to morphological characters butrelated to phylogeny relationship between varieties. Despite the group of varieties were not clustered in accordancewith morphological

  3. Example of the application the microsatellite DNA fragments in the study of farmed European catfish (Silurus glanis, L. broodstock

    Directory of Open Access Journals (Sweden)

    Kuciñski Marcin

    2015-06-01

    Full Text Available European catfish, Silurus glanis L., is the second largest freshwater fish in Europe. The species is very popular among the farmers, as it is one of the most promising European aquaculture species. Despite the growing importance of European catfish in freshwater aquaculture, the genetic data available on this species are still limited. The main purpose of the present study was to develop a reliable, feasible genetic protocol for future studies on European catfish populations and broodstocks in Poland. The genetic characteristics of the tested fish group were based on genetic parameters such as the polymorphism information content (PIC, the effective population size (Ne, the inbreeding coefficient (Fis, and the Garza-Williamson index (M, among others. Additionally, the potential effects of a genetic bottleneck on the genetic variation of the broodstock were examined. The genetic analysis protocol described in this study can be used to establish genetic-based records for European catfish broodstocks, including for sperm cryobanking. This approach will be useful for elaborating the selection procedures that allow for optimal assemblages of spawning pairs in artificial reproduction. The application of the genetic analysis protocol in practice will permit maintaining high quality in European catfish broodstocks.

  4. Electrochemical measurement for analysis of DNA sequence

    Energy Technology Data Exchange (ETDEWEB)

    Cho, S.B.; Hong, J.S.; Pak, J.H. [Korea University, Seoul (Korea); Kim, Y.M. [National Institute of Health, Seoul (Korea)

    2002-02-01

    One of the important roles of a DNA chip is the capability of detecting genetic diseases and mutations by analyzing DNA sequence. For a successful electrochemical genotyping, several aspects should be considered including the chemical treatment of electrode surface, DNA immobilization on electrode, hybridization, choice of an intercalator to be selectively bound to double standed DNA, and an equipment for detecting and analyzing the output singal. Au was used as the electrode material, 2-mercaptoethanol was used for linking DNA to Au electrode, and methylene blue was used as an indicator that can be bound to a double stranded DNA selectively. From the analysis of reductive current of this indicator that was bound to a double stranded DNA on an electrode, a normal double stranded DNA was able to be distinguished from a single stranded DNA in just a few seconds. Also, it was found that the peak reduction current of indicator is proportional to the concentration of target DNA to be hybridized with probe DNA. Therefore, it is possible to realize a simple and cheap DNA sensor using the electrochemical measurement for genotyping. (author). 20 refs., 8 figs., 1 tab.

  5. 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.

  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. 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

  8. The utility of microsatellite DNA markers for the evaluation of area-wide integrated pest management using SIT for the fruit fly, Bactrocera dorsalis (Hendel), control programs in Thailand.

    Science.gov (United States)

    Aketarawong, Nidchaya; Chinvinijkul, Suksom; Orankanok, Watchreeporn; Guglielmino, Carmela Rosalba; Franz, Gerald; Malacrida, Anna Rodolfa; Thanaphum, Sujinda

    2011-01-01

    The oriental fruit fly, Bactrocera dorsalis (Hendel), is a key pest that causes reduction of the crop yield within the international fruit market. Fruit flies have been suppressed by two Area-Wide Integrated Pest Management programs in Thailand using Sterile Insect Technique (AW-IPM-SIT) since the late 1980s and the early 2000s. The projects' planning and evaluation usually rely on information from pest status, distribution, and fruit infestation. However, the collected data sometimes does not provide enough detail to answer management queries and public concerns, such as the long term sterilization efficacy of the released fruit fly, skepticism about insect migration or gene flow across the buffer zone, and the re-colonisation possibility of the fruit fly population within the core area. Established microsatellite DNA markers were used to generate population genetic data for the analysis of the fruit fly sampling from several control areas, and non-target areas, as well as the mass-rearing facility. The results suggested limited gene flow (m flies in the control areas and flies captured outside. In addition, no genetic admixture was revealed from the mass-reared colony flies from the flies within the control area, which supports the effectiveness of SIT. The control pests were suppressed to low density and showed weak bottleneck footprints although they still acquired a high degree of genetic variation. Potential pest resurgence from fragmented micro-habitats in mixed fruit orchards rather than pest incursion across the buffer zone has been proposed. Therefore, a suitable pest control effort, such as the SIT program, should concentrate on the hidden refuges within the target area.

  9. Detailed deletion mapping of loss of heterozygosity on 9p13-23 in laryngeal squamous cell carcinoma by microsatellite analysis

    Institute of Scientific and Technical Information of China (English)

    徐先发; 高燕宁; 程书鈞

    2004-01-01

    Background This study was designed to investigate the hot spots of microsatellite loss of heterozygosity (LOH) on 9p13-23 in laryngeal squamous cell carcinoma and to find out the correlation between the incidence of microsatellite LOH and the clinicopathological parameters.Methods Tumor tissues were obtained from paraffin embedded sections with microdissection. Genomic DNA was extracted from tumor tissues and peripheral blood lymphocytes with the phenol-chloroform. Polymerase chain reaction (PCR) amplification and denaturing gel electrophoresis were carried out in a set of 42 squamous cell carcinoma (SCC) of larynx and corresponding peripheral blood lymphocytes using 13 highly polymorphic microsatellite markers on 9p13-23. The correlation was analyzed between microsatellite LOH at the high frequency on 9p13-23 and clinicopathological parameters in the patients with squamous cell carcinoma of larynx.Results Of the 42 laryngeal cancers, 41 (97.6%) showed LOH in at least one of the microsatellite markers tested on 9p13-23. The most frequently deleted marker was D9S162 in 17 of the 19 (89.5%) informative samples. The marker D9S171, which is located on 9p21, had LOH detected in 12 of the 15 informative cases (80.0%). LOH at the D9S1748 marker (closest to the p16 gene locus) was detected in 18 of the 36 informative cases (50.0%). Allelic deletion mapping revealed two minimal regions of LOH encompassing markers D9S161-D9S171 on 9p21 and IFNA-D9S162 on 9p22-23. Multiple LOH (≥4) on 9p21-23 was found more frequently in the patients under 60 years, with supraglottic SCC or cervical lymph node metastasis than those over 60 years, with glottic SCC or without cervical lymph node metastasis (P<0.01 or 0.01, 0.05, respectively). On the contrary, there was no correlation between T stages or pathologic classification and the frequency of LOH on 9p21-23 in 42 SCC of Larynx.Conclusions These findings imply the presence of at least two putative tumor suppressor genes on 9p13-23 in

  10. 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.

  11. 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

  12. LINKAGE ANALYSIS BY 2-DIMENSIONAL DNA TYPING

    NARCIS (Netherlands)

    MEERMAN, GJT; MULLAART, E; VANDERMEULEN, MA; DENDAAS, JHG; MOROLLI, B; UITTERLINDEN, AG; VIJG, J

    1993-01-01

    In two-dimensional (2-D) DNA typing, genomic DNA fragments are separated, first according to size by electrophoresis in a neutral polyacrylamide gel and second according to sequence by denaturing gradient gel electrophoresis, followed by hybridization analysis using micro- and minisatellite core pro

  13. Bovine and equine forensic DNA analysis

    NARCIS (Netherlands)

    van de Goor, L.H.P.

    2011-01-01

    Animal forensic DNA analysis is being used for human criminal investigations (e.g traces from cats and dogs), wildlife management, breeding and food safety. The most common DNA markers used for such forensic casework are short tandem repeats (STR). Rules and guidelines concerning quality assurance (

  14. Detection of parasitizing coccidia and determination of host crane species, sex and genotype by faecal DNA analysis.

    Science.gov (United States)

    Honma, H; Suyama, Y; Nakai, Y

    2011-11-01

    In Japan, the three main crane species are the endangered red-crowned crane (Grus japonensis) inhabiting Hokkaido, the northernmost island of Japan; the vulnerable hooded crane (Grus monacha); and the vulnerable white-naped crane (Grus vipio). Both the hooded and white-naped cranes migrate in winter to Izumi in Kyushu, the southern island of Japan. In this study, we investigated the cranes and their coccidian parasites, through a targeted molecular approach using faecal DNA to develop a noninvasive method for infectious disease research. To determine the origin of noninvasively collected faecal samples, host species were identified by sequencing a region of approximately 470 bp of the mitochondrial 16S ribosomal RNA gene in the faecal DNA. Furthermore, to avoid sample redundancy, individual determination was performed by fragment analysis using microsatellite and sex-linked markers. For microsatellite genotyping, previously reported markers and markers isolated in this study were examined, and seven loci for red-crowned cranes, eight for hooded cranes and six for white-naped cranes displayed polymorphisms. A low error rate was demonstrated by comparing microsatellite data generated from faecal DNA samples with that generated from feather DNA samples, indicating a high reliability. Polymerase chain reaction-based capillary electrophoresis (PCR-CE), employing genetic markers in the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA, was employed to detect crane coccidia. The sensitivity of detection of PCR-CE using faecal DNA was inferior to that with traditional microscopy; however, our results suggest that PCR-CE can depict crane coccidia diversity with higher resolution and it is a useful tool to characterize community composition of coccidia in detail.

  15. 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.

  16. Nanopore sensors for DNA analysis

    DEFF Research Database (Denmark)

    Solovyeva, Vita; Venkatesan, B.M.; Shim, Jeong

    2012-01-01

    Solid-state nanopore sensors are promising devices for single DNA molecule detection and sequencing. This paper presents a review of our work on solid-state nanopores performed over the last decade. In particular, here we discuss atomic-layer-deposited (ALD)-based, graphene-based, and functionali......Solid-state nanopore sensors are promising devices for single DNA molecule detection and sequencing. This paper presents a review of our work on solid-state nanopores performed over the last decade. In particular, here we discuss atomic-layer-deposited (ALD)-based, graphene...

  17. 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.

  18. 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.

  19. Expression pattern and polymorphism of three microsatellite markers in the porcine CA3 gene

    Directory of Open Access Journals (Sweden)

    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.

  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. Isolation and Characterization of Microsatellite Loci in the Chinese Cobra Naja atra (Elapidae

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    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.

  2. 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.

  3. Analysis of genetic relationships of pearl millet (Pennisetum glaucum L.) landraces from Zimbabwe, using microsatellites

    CSIR Research Space (South Africa)

    Chakauya, E

    2008-01-01

    Full Text Available and indigenous farmer given names. Analysis was done by PAGE stained with ethidium bromide. Simple matching coefficients were compared and the genetic relationships between genotypes were clarified on dendrograms by unweighted pair-group averages (UPGMA). Two...

  4. Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

    Science.gov (United States)

    Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

    2014-11-01

    Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

  5. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection.

    Science.gov (United States)

    Gichira, Andrew W; Li, Zhizhong; Saina, Josphat K; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W; Wang, Qingfeng; Chen, Jinming

    2017-01-01

    Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica's chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  6. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae: structural comparative analysis, gene content and microsatellite detection

    Directory of Open Access Journals (Sweden)

    Andrew W. Gichira

    2017-01-01

    Full Text Available Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp, with a pair of Inverted Repeats (IR 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp and a small single copy (SSC, 18,696. H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  7. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    Institute of Scientific and Technical Information of China (English)

    SHAN Tifeng; PANG Shaojun; LIU Feng; XU Na; ZHAO Xiaobo; GAO Suqin

    2012-01-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation.To better understand the genetic relationships of different gametophyte cultures isolated from different sources,20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U.pinnatifida isolated from wild sporophytes in Vladivostok,Russia and from cultivated sporophytes from Dalian and Qingdao,China.One locus was abandoned because of poor amplification.At the sex-linked locus of Up-AC-2A8,3 alleles were detected in 25 female gametophyte clones,with sizes ranging from 307 to 316 bp.At other loci,3 to 7 alleles were detected with an average of 4.5 alleles per locus.The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones,respectively.The average gene diversity for Russian,Chinese,and for the combined total of gametophyte clones was 0.1,0.4,and 0.5,respectively.Russian gametophyte clones had unique alleles at 7 out of the 19 loci.In cluster analysis,Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance.Overall,high genetic diversity was detected in gametophyte clones isolated from the two countries.These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  8. Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease

    Science.gov (United States)

    Llewellyn, Martin S.; Lewis, Michael D.; Acosta, Nidia; Yeo, Matthew; Carrasco, Hernan J.; Segovia, Maikell; Vargas, Jorge; Torrico, Faustino; Miles, Michael A.; Gaunt, Michael W.

    2009-01-01

    Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe. PMID:19721699

  9. Trypanosoma cruzi IIc: phylogenetic and phylogeographic insights from sequence and microsatellite analysis and potential impact on emergent Chagas disease.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    Full Text Available Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe.

  10. The complete chloroplast genome sequence of an endemic monotypic genus Hagenia (Rosaceae): structural comparative analysis, gene content and microsatellite detection

    Science.gov (United States)

    Saina, Josphat K.; Long, Zhicheng; Hu, Guangwan; Gituru, Robert W.

    2017-01-01

    Hagenia is an endangered monotypic genus endemic to the topical mountains of Africa. The only species, Hagenia abyssinica (Bruce) J.F. Gmel, is an important medicinal plant producing bioactive compounds that have been traditionally used by African communities as a remedy for gastrointestinal ailments in both humans and animals. Complete chloroplast genomes have been applied in resolving phylogenetic relationships within plant families. We employed high-throughput sequencing technologies to determine the complete chloroplast genome sequence of H. abyssinica. The genome is a circular molecule of 154,961 base pairs (bp), with a pair of Inverted Repeats (IR) 25,971 bp each, separated by two single copies; a large (LSC, 84,320 bp) and a small single copy (SSC, 18,696). H. abyssinica’s chloroplast genome has a 37.1% GC content and encodes 112 unique genes, 78 of which code for proteins, 30 are tRNA genes and four are rRNA genes. A comparative analysis with twenty other species, sequenced to-date from the family Rosaceae, revealed similarities in structural organization, gene content and arrangement. The observed size differences are attributed to the contraction/expansion of the inverted repeats. The translational initiation factor gene (infA) which had been previously reported in other chloroplast genomes was conspicuously missing in H. abyssinica. A total of 172 microsatellites and 49 large repeat sequences were detected in the chloroplast genome. A Maximum Likelihood analyses of 71 protein-coding genes placed Hagenia in Rosoideae. The availability of a complete chloroplast genome, the first in the Sanguisorbeae tribe, is beneficial for further molecular studies on taxonomic and phylogenomic resolution within the Rosaceae family.

  11. Inheritance mode of microsatellite loci and their use for kinship analysis in the Pacific oyster (Crassostrea gigas)

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Five full-sib families of the Pacific oyster (Crassostrea gigas) larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.

  12. Microsatellite markers from the 'South American fruit fly' Anastrepha fraterculus: a valuable tool for population genetic analysis and SIT applications

    Science.gov (United States)

    2014-01-01

    Background Anastrepha fraterculus Wiedemann is a horticultural pest which causes significant economic losses in the fruit-producing areas of the American continent and limits the access of products to international markets. The use of environmentally friendly control strategies against this pest is constrained due to the limited knowledge of its population structure. Results We developed microsatellite markers for A. fraterculus from four genomic libraries, which were enriched in CA, CAA, GA and CAT microsatellite motifs. Fifty microsatellite regions were evaluated and 14 loci were selected for population genetics studies. Genotypes of 122 individuals sampled from four A. fraterculus populations were analyzed. The level of polymorphism ranged from three to 13 alleles per locus and the mean expected heterozygosity ranged from 0.60 to 0.64. Comparison between allelic and genotypic frequencies showed significant differences among all pairs of populations. Conclusions This novel set of microsatellite markers provides valuable information for the description of genetic variability and population structure of wild populations and laboratory strains of A. fraterculus. This information will be used to identify and characterize candidate strains suitable to implement effective pest control strategies and might represent a first step towards having a more comprehensive knowledge about the genetics of this pest. PMID:25471285

  13. Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes

    NARCIS (Netherlands)

    Babaei, A.; Tabaei-Aghdaei, S.R.; Khosh-Khui, M.; Omidbaigi, R.; Naghavi, M.R.; Esselink, G.D.; Smulders, M.J.M.

    2007-01-01

    Background - Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 a

  14. Inheritance Pattern of Microsatellite Loci and Their Use for Kinship Analysis m the Japanese Scallop Patinopecten yessoensis

    Institute of Scientific and Technical Information of China (English)

    XU Kefeng; LI Qi

    2009-01-01

    The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four con-trolled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four fami-lies were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.

  15. An Integrated Workflow for DNA Methylation Analysis

    Institute of Scientific and Technical Information of China (English)

    Pingchuan Li; Feray Demirci; Gayathri Mahalingam; Caghan Demirci; Mayumi Nakano; Blake C.Meyers

    2013-01-01

    The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our "Next-Gen Sequence" websites (http://mpss.udel.edu),along with small RNA,RNA-seq and other data types.

  16. Pyrosequencing Analysis for Breast Cancer DNA Methylome.

    Science.gov (United States)

    Kuscu, Cem; Kuscu, Canan

    2016-01-01

    Unraveling DNA methylation profile of tumor is important for the diagnosis and treatment of cancer patients. Because of the heterogeneity of clinical samples, it is very difficult to get methylation profile of only tumor cells. Laser capture Microdissection (LCM) is giving us a chance to isolate the DNA only from the tumor cells without any stroma cell's DNA contamination. Once we capture the breast tumor cells, we can isolate the genomic DNA which is followed by the bisulfite treatment in which unmethylated cytosines of the CG pairs are converted into uracil; however, methylated cytosine does not go into any chemical change during this reaction. Next, bisulfite treated DNA is used in the regular PCR reaction to get a single band PCR amplicon which will be used as a template for the pyrosequencing. Pyrosequencing is a powerful method to make a quantitative methylation analysis for each specific CG pair.

  17. Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

    Science.gov (United States)

    Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

    2017-08-08

    Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Ancient DNA analysis - An established technique in charting the evolution of tuberculosis and leprosy.

    Science.gov (United States)

    Donoghue, Helen D; Spigelman, Mark; O'Grady, Justin; Szikossy, Ildikó; Pap, Ildikó; Lee, Oona Y-C; Wu, Houdini H T; Besra, Gurdyal S; Minnikin, David E

    2015-06-01

    Many tuberculosis and leprosy infections are latent or paucibacillary, suggesting a long time-scale for host and pathogen co-existence. Palaeopathology enables recognition of archaeological cases and PCR detects pathogen ancient DNA (aDNA). Mycobacterium tuberculosis and Mycobacterium leprae cell wall lipids are more stable than aDNA and restrict permeability, thereby possibly aiding long-term persistence of pathogen aDNA. Amplification of aDNA, using specific PCR primers designed for short fragments and linked to fluorescent probes, gives good results, especially when designed to target multi-copy loci. Such studies have confirmed tuberculosis and leprosy, including co-infections. Many tuberculosis cases have non-specific or no visible skeletal pathology, consistent with the natural history of this disease. M. tuberculosis and M. leprae are obligate parasites, closely associated with their human host following recent clonal distribution. Therefore genotyping based on single nucleotide polymorphisms (SNPs) can indicate their origins, spread and phylogeny. Knowledge of extant genetic lineages at particular times in past human populations can be obtained from well-preserved specimens where molecular typing is possible, using deletion analysis, microsatellite analysis and whole genome sequencing. Such studies have identified non-bovine tuberculosis from a Pleistocene bison from 17,500 years BP, human tuberculosis from 9000 years ago and leprosy from over 2000 years ago.

  19. DNA analysis of natural fiber rope.

    Science.gov (United States)

    Dunbar, Mignon; Murphy, Terence M

    2009-01-01

    When rope is found at a crime scene, the type of fiber is currently identified through its microscopic characteristics. However, these characteristics may not always unambiguously distinguish some types of rope from others. If rope samples contain cells from the plants of origin, then DNA analysis may prove to be a better way to identify the type of rope obtained from a crime scene. The objective of this project was to develop techniques of DNA analysis that can be used to differentiate between ropes made from Cannabis sativa L. (hemp), Agave sisalana Perrine (sisal), Musa textilis Née (abaca, "Manila hemp"), Linum usitatissimum L. (flax), and Corchorus olitorus L. (jute). The procedures included extracting the DNA from the rope, performing polymerase chain reaction (PCR) using the extracted DNA as a template, and analyzing the DNA products. A primer pair for PCR, chosen from within a chloroplast gene for the large subunit of ribulose bisphosphate carboxylase/oxygenase, was designed to be specific for plant DNA and complementary to the genes from all five plants. The resulting PCR fragments were approximately 771 base pairs long. The PCR fragments, distinguished through base sequence analysis or restriction enzyme analysis, could be used to identify the five different rope types. The procedure provides a useful addition to visual methods of comparing rope samples.

  20. Molecular characterization and genetic diversity analysis of different rice cultivars by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Allhgholipour Mehrzad

    2014-01-01

    Full Text Available A total of 52 rice SSR markers well distributed on 12 chromosomes were used to characterize and assess the genetic diversity among ninety four rice genotypes. The total number of polymorphic alleles was 361 alleles with the average of 5.86 alleles per SSR locus. The study revealed that some markers such as RM276 and RM5642 on chromosome 6 and RM14 and RM1 on chromosome 1 have more than 9 observed alleles compared to other primers like RM16, RM207, RM208 and RM317 with 3-4 alleles. The highest and lowest PIC values were observed for primers RM276 (0.892 and RM208 (0.423 respectively. Using Shannon´s diversity index, a mean genetic diversity of 1.641 was obtained from the analysis, indicating a high level of genetic variation among these cultivars. Cluster analysis using the complete linkage method based on jaccard similarity coefficient revealed that all genotypes were classified to nine clusters at genetic similarity level of 0.010.75, which contained 12, 16, 2, 18, 3, 6, 16, 10 and 11 varieties, respectively. Results of discriminant analysis showed that the nine cluster groups were confirmed at high levels of correct percent (96.8 and revealed true differences among these clusters. As a final result from this study, we selected eight cultivars from different cluster including Daylamani, Tarom mohali (landrace rice cultivars, RI1843046, Back cross line, RI184472, RI184421 (promising cultivars, Line 23 and IR50 (IRRI lines as parents. All of the selected cultivars will be arranged in complete diallel design to obtain combining abilities, gene effects and heterosis for each important morphology and physico-chemical characters.

  1. Electrochemical biosensing strategies for DNA methylation analysis.

    Science.gov (United States)

    Hossain, Tanvir; Mahmudunnabi, Golam; Masud, Mostafa Kamal; Islam, Md Nazmul; Ooi, Lezanne; Konstantinov, Konstantin; Hossain, Md Shahriar Al; Martinac, Boris; Alici, Gursel; Nguyen, Nam-Trung; Shiddiky, Muhammad J A

    2017-02-17

    DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.

  2. Identification and Analysis of Genetic Diversity Structure Within Pisum Genus Based on Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    ZONG Xu-xiao; Rebecca Ford; Robert R Redden; GUAN Jian-ping; WANG Shu-min

    2009-01-01

    To assesse the genetic diversity among wild and cultivated accessions of 8 taxonomic groups in 2 species, and 5 subspecies under Pisum genus, and to analyze population structure and their genetic relationships among various groups of taxonomy,the study tried to verify the fitness of traditionally botanical taxonomic system under Pisum genus and to provide essential information for the exploration and utilization of wild relatives of pea genetic resources. 197 Pisum accessions from 62 counties of 5 continents were employed for SSR analysis using 21 polymorphic primer pairs in this study. Except for cultivated field pea Pisum sativum ssp. sativum vat. sativum (94 genotypes), also included were wild relative genotypes that were classified as belonging to P. fulvum, P. sativum ssp.abyssinicum, P. sativum ssp. asiaticum, P. sativum ssp. transcaucasicum, P. sativum ssp. elatius vat. elatius, P. sativum ssp. elatius vat. pumilio and P. sativum ssp.sativum vat. arvense (103 genotypes). The PCA analyses and 3-dimension PCA graphs were conducted and drawn by NTSYSpe 2.2d statistical package. Nei78 genetic distances among groups of genetic resources were calculated, and cluster analysis using UPGMA method was carried out by using Popgene V1.32 statistical package, the dendrogram was drawn by MEGA3.1 statistical package. Allelie statistics were carried out by Popgene V1.32. The significance test between groups of genotypes was carried out by Fstat V2.9.3.2 statistical package. 104 polymorphic bands were amplified using 21 SSR primer pairs with unambiguous unique polymorphic bands. 4.95 alleles were detected by each SSR primer pair in average, of which 65.56% were effective alleles for diversity. PSAD270, PSAC58, PSAA18, PSAC75, PSAA175 and PSAB72 were the most effective SSR pairs. SSR alleles were uniformly distributed among botanical taxon units under Pisum genus, but significant difference appeared in most pairwise comparisons for genetic diversity between taxon unit based

  3. Forensic analysis of polymorphism and regional stratification of Y-chromosomal microsatellites in Belarus.

    Science.gov (United States)

    Rebała, Krzysztof; Tsybovsky, Iosif S; Bogacheva, Anna V; Kotova, Svetlana A; Mikulich, Alexei I; Szczerkowska, Zofia

    2011-01-01

    Nine loci defining minimal haplotypes and four other Y-chromosomal short tandem repeats (Y-STRs) DYS437, DYS438, DYS439 and GATA H4.1 were analysed in 414 unrelated males residing in four regions of Belarus. Haplotypes of 328 males were further extended by 7 additional Y-STRs: DYS388, DYS426, DYS448, DYS456, DYS458, DYS460 and DYS635. The 13-locus haplotype diversity was 0.9978 and discrimination capacity was 78.7%, indicating presence of identical haplotypes among unrelated males. Seven additional Y-STRs enabled almost complete discrimination of undifferentiated 13-locus haplotypes, increasing haplotype diversity to 0.9998 and discrimination capacity to 97.9%. Analysis of molecular variance of minimal haplotypes excluded the use of a Y-STR database for Belarusians residing in northeastern Poland as representative for the Belarusian population in forensic practice, and revealed regional stratification within the country. However, four additional markers (DYS437, DYS438, DYS439 and GATA H4.1) were shown to eliminate the observed geographical substructure among Belarusian males. The results imply that in case of minimal and PowerPlex Y haplotypes, a separate frequency database should be used for northern Belarus to estimate Y-STR profile frequencies in forensic casework. In case of Yfiler haplotypes, regional stratification within Belarus may be neglected.

  4. Construction of heteroduplex DNA and in vitro model for functional analysis of mismatch repair

    Institute of Scientific and Technical Information of China (English)

    WANG Yi; Clark Alan; WANG Jiaxun; SUN Menghong; SHI Daren

    2004-01-01

    Functional deficiency of mismatch repair (MMR) system is one of the mechanisms of tumorigenesis. With the development of the investigation and the requirement from the clinical diagnosis and treatment it is necessary to build up a method to evaluate the functional status of the whole MMR system in the concerned tumors. The original ssDNA and dsDNA from wild type (wt) bacteriophage M13mp2 and its three derivates with mutation points in the lacZα Gene have been used to construct two kinds of heteroduplex DNA molecules. One named del(2) has two bases deleted in the negative strand, the other has a G·G mismatch base pair in the negative strand too. Introducing this heteroduplex DNA into E. Coli NR9162 (mutS-) without the MMR ability on the indicator plate with x-gal and IPTG, there are three kinds of plaques, mixture plaque as the characteristic phenotype of heteroduplex DNA, blue and clear plaques. If the cell extract is mismatch repair competent the percentage of the mixture plaque will decrease after incubation with these heteroduplex DNA, the repair efficiency is expressed in percentage as 100× (1 minus the ratio of percentages of mixture plaque obtained from the extract-treated sample and untreated samples), which can imply the functional status of MMR system of certain samples. After large T-antigen-dependent SV-40 DNA replication assay cell extract from TK6, a human lymphoblastoid B-cell lymphoma cell line with MMR ability, and Lovo, a human colonic carcinoma cell line with MMR deficiency have incubated with these heteroduplex DNA. The repair efficiency of TK6 to del(2) is more than 60%, to G·G is more than 50%. The Lovo efficiency to del(2) is less than 10%, to G·G is less than 20%. Therefore, in this in vitro model used for functional analysis of mismatch repair of heteroduplex DNA as the repair target, TK6 can serve as the control for MMR proficiency and Lovo as the control for MMR deficiency. Using this model the tumor tissue from a case of hereditary

  5. New technologies for DNA analysis

    DEFF Research Database (Denmark)

    McGinn, Steven; Bauer, David; Brefort, Thomas

    2016-01-01

    The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 4 1/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and d...

  6. 黑斑狗鱼部分基因组文库构建和微卫星位点的筛选%Construction Fractional Genomic Libraries and Screening Microsatellites DNA of Esox reieherti Dybowski

    Institute of Scientific and Technical Information of China (English)

    王洪哲; 殷倩茜; 冯志纲; 李大宇; 孙效文; 李婵

    2008-01-01

    采用磁珠富集与放射性杂交相结合的方法开发黑斑狗鱼(Esox reieherti Dybowski)基因组微卫星资源.基因组DNA经Sau 3A Ⅰ限制性内切酶消化后,选取400-900bp的片段进行PCR全基因组扩增,并利用生物素标记的(CA)12、 (GA)12探针进行微卫星片段的富集.将得到的片段与pGEM-T载体连接后转入DH5α大肠杆菌中,然后利用γ-32P标记的放射性同位素探针进行第二次杂交.结果,共获得微卫星基因组文库1600个菌,杂交前菌落PCR检测阳性克隆率为90.91%;杂交后得到的阳性克隆为1300个,占87.25%.从中挑出196个进行测序,192(97.96%)个含有微卫星序列.在得到的微卫星序列中,重复单元除CA/GT、 GA/CT外,还观察到单碱基、四碱基、五碱基重复单元.根据侧翼序列应用引物设计软件Primer Premier 5.0设计引物70对,选择合成32对,通过优化PCR反应条件,结果有28对引物可扩增出清晰可重复的目的条带.本研究旨在对黑斑狗鱼基因组资源的开发利用起到一定的促进作用,并为黑斑狗鱼养殖品系的优化、遗传多样性的检测及遗传图谱的构建等奠定基础.%Esox reieherti Dybowsk genomic microsatellites were developed by using enrichment protocols combined with radioactive hybridization protocol. Four hundred to nine hundred base pair fragments were selected for the whole genome. DNA PCR amplification after digestion with restriction endonuclease Sau 3A Ⅰ, and (CA)12, (GA)12 probes marked with biotin were used for microsatellite DNA enrichment. The product fragments were connected with carrier pGEM-T and transferred into DHSα Escherichia coli competent cells, and radioactive isotope probes marked with γ-32 P were used for the second hybridization. As a result, a total of 1600 bacteria were obtained in the microsatellite genomic libraries, positive clones accounted for 90.91% before hybridization and 81.25% after hybridization, amounting to 1300. One hundred and

  7. Tools for assessing kinship, population structure, phylogeography, and interspecific hybridization in Asian carps invasive to the Mississippi River, USA: isolation and characterization of novel tetranucleotide microsatellite DNA loci in silver carp Hypophthalmichthys molitrix

    Science.gov (United States)

    King, T.L.; Eackles, M.S.; Chapman, D.C.

    2011-01-01

    We document the isolation and characterization of novel tetranucleotide microsatellite DNA markers for the invasive silver carp Hypophthalmichthys molitrix and provide the results of cross-species amplification for three additional invasive carp species: bighead (H. nobilis), grass (Ctenopharyngodon idella) and black (Mylopharyngodon piceus). In the target species these markers yielded levels of allelic diversity (average 4.4 alleles/locus) and heterozygosity (average 54.7%) sufficient to: (1) provide unique multilocus genotypes; (2) delineate kinship relationships; (3) differentiate populations/species; (4) estimate effective population sizes; and (5) provide unique demographic perspectives for control or eradication. Currently these markers are being utilized to determine the degree of introgressive hybridization between H. molitrix and H. nobilis, to quantify gene flow between different sub-basins established in the central United States, and to assess the demographic status of sub-basin groups. This information will be critically important in the management/control of these invasive species.

  8. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae cloned by serendipity can be useful in genetic analysis of polyploids

    Directory of Open Access Journals (Sweden)

    Luis Boto

    2011-01-01

    Full Text Available A new microsatellite locus (SAS1 for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose.

  9. A polymorphic microsatellite from the Squalius alburnoides complex (Osteichthyes, Cyprinidae) cloned by serendipity can be useful in genetic analysis of polyploids.

    Science.gov (United States)

    Boto, Luis; Cunha, Carina; Doadrio, Ignacio

    2011-07-01

    A new microsatellite locus (SAS1) for Squalius alburnoides was obtained through cloning by serendipity. The possible usefulness of this new species-specific microsatellite in genetic studies of this hybrid-species complex, was explored. The polymorphism exhibited by SAS1 microsatellite is an important addition to the set of microsatellites previously used in genetic studies in S. alburnoides complex, that mostly relied in markers described for other species. Moreover, the SAS1 microsatellite could be used to identify the parental genomes of the complex, complementing other methods recently described for the same purpose..

  10. Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii.

    Science.gov (United States)

    Cipollaro, M; Di Bernado, G; Forte, A; Galano, G; De Masi, L; Galderisi, U; Guarino, F M; Angelini, F; Cascino, A

    1999-09-01

    Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption.

  11. Superimposed Code Theorectic Analysis of DNA Codes and DNA Computing

    Science.gov (United States)

    2010-03-01

    Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences ”, 2008 IEEE Proceedings of International Symposium on Information Theory, pp. 2292...5, June 2008, pp. 525-34. 32 28. A. Macula, et al., “Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences ”, 2008...combinatorial method of bio-memory design and detection that encodes item or process information as numerical sequences represented in DNA. ComDMem is a

  12. Analyzsis of population genetic structure of laboratory orange tabby cat by microsatellite DNA markers%微卫星DNA标记技术对试验用虎皮猫群体遗传结构的分析

    Institute of Scientific and Technical Information of China (English)

    衣帅; 谢姗珊; 刘继峰; 杜小燕; 齐飞虎; 李益琛; 任文陟; 刘殿峰; 陈振文

    2013-01-01

    用筛选优化出的24个具有丰富多态性的微卫星位点对华北制药厂的34只虎皮猫基因组DNA进行PCR扩增,对扩增产物进行琼脂糖凝胶电泳和STR扫描,运用popgene3.2软件对试验用虎皮猫群体进行群体遗传结构分析.结果显示,虎皮猫群体平均观测等位基因数为4.083 3,平均有效等位基因数为2.632 3,平均有效杂合度为0.610 8,平均香隆指数为1.078 6.结果表明,微卫星DNA标记技术适于猫群体遗传结构分析;该试验用虎皮猫群体符合封闭群的遗传特性.%To evaluate the genetic structure of the laboratory orange tabby cat population. Twenty four refined polymorphic microsatellite loci were applied to amplify the genomic DNA from 34 orange tabby cats in Huabei Pharmaceutical factory by PCR. The PCR products were analyze by agarose gel electrophoresis,and short tandem repeat(STR) scanning. Software popgene 3. 2 was used to analyze the genetic structure. For the orange tabby cat population, the observed average number of alleles is 4. 083 3;the average effective number of alleles is 2. 632 3; the mean effective heterozygosity is 0. 610 8;the mean Shannon's information index is 1. 078 6. The microsatellite DNA markers are suitable for analyzing the genetic structure of cats and the laboratory orange tabby cat population has the characters of closed colony.

  13. Microsatellite DNA typing for assessment of genetic variability in Tharparkar breed of Indian zebu (Bos indicus) cattle, a major breed of Rajasthan

    Indian Academy of Sciences (India)

    M. Sodhi; M. Mukesh; B. Prakash; S. P. S. Ahlawat; R. C. Sobti

    2006-12-01

    The present study estimates genetic variability with a set of 25 microsatellite markers in a random sample of 50 animals of Tharparkar breed of Indian zebu (Bos indicus) cattle. Tharparkar is a dual-purpose breed, valued for its milk as well as draught utility, and is adapted to the inhospitable Thar desert conditions of Rajasthan typified by summer temperature hovering above 50°C, sparse rainfall and vegetation, and scarcity of even drinking water. The observed number of alleles ranged from 4 (ETH3, ILSTS030, INRA5, INRA63 and MM8) to 11 (HEL9 and ILSTS034), with allelic diversity (average number of observed alleles per locus) of 6.20. Observed and expected heterozygosity ranged from 0.25 (INRA63) to 0.77 (ETH10), and from 0.51 (HEL5 and HAUT27) to 0.88 (HEL9) respectively. Wide range of genetic variability supported the utility of these microsatellite loci in measurement of genetic diversity indices in other Indian cattle breeds too. Various average genetic variability measures, namely allele diversity (6.20), observed heterozygosity (0.57), expected heterozygosity (0.67) and mean polymorphism information content (0.60) values showed substantial within-breed genetic variability in this major breed of Rajasthan, despite accumulated inbreeding as reflected by high average inbreeding coefficient $(F_{\\text{IS}} = 0.39)$. The Tharparkar population has not experienced a bottleneck in the recent past.

  14. 随机人群与精神分裂症患者微卫星DNA vWA多态性的关联性分析%Polymorphism of microsatellite DNA vWA in random population and schizophrenic patients

    Institute of Scientific and Technical Information of China (English)

    刘辉; 于卫建; 方芳; 王学滨; 杨光; 刘奔; 梁晓华; 周杰

    2005-01-01

    于随机人群(19.5%),差异有显著性(RR=1.866,P=0.043);其他各等位基因检出率差异无显著性(P>0.05).结论:精神分裂症患者vWA-14的检出率显著低于随机人群,提示vWA-14在精神分裂症时可能会因某种原因而被负选择,其附近可能存在抵抗精神分裂症发病的基因.精神分裂症患者vWA-17的检出率显著高于随机人群,表明vWA-17与精神分裂症相关联,其附近可能存在精神分裂症易感基因.%BACKGROUND: Schizophrenia is substantially heritable, but specific susceptibility genes remain difficult to be identified. Therefore, it is necessary to explore hereditary markers first.OBJECTIVE: To investigate the relationship between schizophrenia and related vWA allele genes based on the analysis of microsatellite DNA vWA polymorphism.DESIGN: A case-controlled study with schizophrenic patients and randomly selected population as subjects.SETTING: Ward of Dalian Seventh People's Hospital and Molecular Biological Laboratory of Dalian Medical University.between March and July 2002 at Dalian Seventh People's Hospital which specializes in schizophrenia. Schizophrenia was diagnosed according to the diagnostic standard of the third edition of "the American Diagnostic Statistical Manual for Schizophrenic Diseases", and their clinical manifestations were predominantly negative signs. Altogether 123 normal blood samples were collected from random population at the Blood Center of Dalian Red Cross. They all denied psychological ailments and severe systematic diseases, and they had no kinship with each other.METHODS: Heparin anti-coagulation blood samples were collected and PCR compound amplification was carried out with the aid of PE Profiler plus system. Then the products were subjected to electrophoresis and gene detection with ABI310 type gene analysis system so as to calculate the frequency of allele genes; Hardy-Weinberg equation law was used to make coincidence test and linkage analysis of the theoretical frequency

  15. 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.

  16. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    Science.gov (United States)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2017-05-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed ( H o) and expected ( H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  17. Inbreeding and genetic diversity analysis in a hatchery release population and clones of Rhopilema esculentum based on microsatellite markers

    Science.gov (United States)

    Tian, Tao; Chen, Zaizhong; Wang, Mosang; Hu, Yulong; Wang, Weiji

    2016-07-01

    Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye (Scyphozoa: Rhizostomatidae). A total of 85 alleles were detected in 600 individuals. Within-population levels of observed (H o) and expected (H e) heterozygosity ranged from 0.152 to 0.839 (mean=0.464) and from 0.235 to 0.821 (mean=0.618), respectively. The polymorphism information content (PIC) of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability of ten loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.

  18. Mitochondrial DNA analysis in Parkinson's disease.

    Science.gov (United States)

    Schapira, A H; Holt, I J; Sweeney, M; Harding, A E; Jenner, P; Marsden, C D

    1990-01-01

    The reduced form of nicotinamide adenine dinucleotide coenzyme Q reductase (complex I) activity has recently been shown to be deficient in the substantia nigra of patients dying with Parkinson's disease. This biochemical defect is identical to that produced by the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), which also produces parkinsonism in humans. Complex I comprises 25 polypeptides, seven of which are encoded by mitochondrial DNA. Restriction fragment analysis of substantia nigra DNA from six patients with Parkinson's disease did not show any major deletion. In two cases, there were different novel polymorphisms that were not observed in control brain (n = 6) or blood (n = 34) samples.

  19. Structural analysis of the dnaA and dnaN genes of Escherichia coli.

    Science.gov (United States)

    Ohmori, H; Kimura, M; Nagata, T; Sakakibara, Y

    1984-05-01

    The nucleotide sequence of the entire region containing the Escherichia coli dnaA and dnaN genes was determined. Base substitutions by such mutations as dnaA46, dnaA167, dnaN59, and dnaN806 were also identified. Analyses of coding frames, the mutational base substitutions, and other data indicate that dnaN follows dnaA, both have the same orientation, and are separated by only 4 bp. The deduced amino acid sequence specifies Mrs and isoelectric points consistent with those of the previously identified gene products. The transcriptional initiation site of the dnaA gene was assigned by analysis of in vitro RNA products. Examination of the intercistronic sequence and analysis of in vitro transcription supported the notion that the dnaA and dnaN genes constitute a single operon.

  20. RNA and DNA aptamers in cytomics analysis.

    Science.gov (United States)

    Ulrich, Henning; Martins, Antonio Henrique B; Pesquero, João Bosco

    2005-08-01

    Using systematic evolution of ligands by exponential enrichment (SELEX), RNA or DNA molecules are selected from a combinatorial oligonucleotide library by their ability to bind their targets, i.e., cell surface antigens, with affinity and specificity similar to that of monoclonal antibodies. The generation of these high-affinity binders, also denominated aptamers, is carried out in vitro and does not involve animals. Therefore, aptamers can be developed against almost every molecule of biological importance, including toxins and nonimmunogenic targets, against which antibodies cannot be raised. The incorporation of modified pyrimidines resulting in nuclease-resistant RNA aptamers makes them promising candidates for studying protein interactions in vitro and in vivo. DNA aptamers do not need modifications for most applications. The protocols in this unit can be used for the development of fluorescent-tagged RNA or DNA aptamers for any cell surface protein in cytomics analysis.

  1. 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.

  2. 黑斑原(鱼兆)微卫星DNA 富集文库构建与鉴定%CONSTRUCTION AND IDENTIFICATION OF DNA LIBRARIES ENRICHED FOR MICROSATELLITE REPEAT SEQUENCES OF GLYPTOSTERNUM MACULATUM

    Institute of Scientific and Technical Information of China (English)

    郭宝英; 谢从新; 祁鹏志; 吴常文; 邓一兵

    2011-01-01

    采用磁珠富集法,利用生物素标记的(CA)12 寡核苷酸探针从黑斑原(鱼兆)基因组DNA MboI 酶切的400-1000 bp 片段中筛选CA/GT 微卫星位点,洗脱的杂交片段克隆到pMD18-T 载体上构建富集微卫星基因组文库后,通过PCR 筛选检测出720 个阳性克隆,占所有克隆的89.2%,从阳性克隆中随机选取139 个进行测序,序列分析发现,124 个克隆含有7 个以上的重复序列,其中完全的为80 个(64.5%),不完全的为40 个(32.3%),复合的为15 个(3.2%),重复次数范围为7-165 次,平均为52 次.在124 条序列中共59 条可以设计引物.%Microsatellite marker (SSR) has been widely used in population genetics and genetic map construction. In order to determine the genetic diversity of G. Maculatum, this study was undertaken to develop and characterize the micro satellite sequence firstly for further to develop the micro satellite markers. Genomic DNA was extracted from muscle tissue using a traditional proteinase K digestion and phenol-chloroform extraction procedure with RNA removed by Rnase. Approximately 2 u.g of total genomic DNA was digested with Mbo\\, then ligated to the adapters (Linker A and Linker B). The treated DNA sample was then pooled and fragments were separated on a 1.5% agarose gel prior to size selection. The resulting fragments (400-1000 bp) were extracted from the gel matrix using a column and amplified 20 cycles with Linker B primers. The amplified DNA was hybridized with 5μL of 5'-biotinylated (CA)12repeat oligos in a total volume of 100 μL of 6x SSC and 0.1% SDS. The mixture was incubated at 95℃ for 5min, followed by anneal at 65℃ for 60min and cooled to room temperature. During this hybridization, the 100 μL (per treatment) of Streptavidin coated beads was resuspended in 300 μL l× hybridization buffer (6x SSC + 0.1% SDS) and washed three times. The hybridization mixture was added to the washed beads and incubated for 30 min at room temperature. The beads were

  3. Extrapair paternity and maternity in the three-toed woodpecker, Picoides tridactylus: insights from microsatellite-based parentage analysis.

    Directory of Open Access Journals (Sweden)

    Meng-Hua Li

    Full Text Available Molecular techniques have revealed that avian mating systems are more diverse and complex than previously thought. We used microsatellite markers to determine genetic parentage, the prevalence of extrapair paternity and quasi-parasitism (i.e. situations where a male's extrapair mate lay in his nest in a socially monogamous population of three-toed woodpeckers (Picoides tridactylus in southern Finland. A total of 129 adults and nestlings, representing 5-9 families annually from 2004-2007, were genotyped at up to ten microsatellite loci. The results of genetic assignment tests confirmed that monogamous parentage characterized the majority (84.6%, 22/26 of broods, and that most (93.8%, 75/80 nestlings were the offspring of their social parents. Two of 80 nestlings (2.5% in two of 26 broods (7.7% were sired by extrapair males and quasi-parasitism occurred in 3.8% (3/80 of nestlings and 7.7% (2/26 of broods. Hence, the levels of extrapair parentage were low, possibly because both genetic polygyny and polyandry are constrained by the high paternal effort required for parental care. The co-occurrence of low levels of extrapair paternity and quasi-parasitism are discussed in light of ecological and behavioural factors characterizing the species biology.

  4. Discrimination of patients with microsatellite instability colon cancer using 1H HR MAS MR spectroscopy and chemometric analysis.

    Science.gov (United States)

    Tessem, May-Britt; Selnaes, Kirsten M; Sjursen, Wenche; Tranø, Gerd; Giskeødegård, Guro F; Bathen, Tone F; Gribbestad, Ingrid S; Hofsli, Eva

    2010-07-02

    The primary aim of this study was to analyze human colon cancer and normal adjacent tissue using (1)H HR MAS MR spectroscopy and chemometric analyses, evaluating possible biomarkers for colon cancer. The secondary aim was to investigate metabolic profiles of tissue samples (n = 63, 31 patients) with microsatellite instability (MSI-H) compared to microsatellite stable (MSS) colon tissue. Our hypothesis was that this method may provide an alternative to MSI genotyping. Cancer samples were clearly separated from normal adjacent mucosa by 100% accuracy. Several metabolites such as lactate, taurine, glycine, myo-inositol, scyllo-inositol, phosphocholine (PC), glycerophosphocholine (GPC), creatine, and glucose were identified as potential biomarkers for cancer detection. Adenomas (n = 4) were also separated from cancer and normal samples mainly based on higher GPC and PC levels. Interestingly, metabolic differences in normal colon mucosa between MSI-H and MSS patients were observed. MSI status was validated with 80% accuracy with a sensitivity and specificity of 79% and 82%, respectively, including both cancer and normal samples The metabolic differences between MSI-H and MSS may be very interesting in the early detection of cancer development and of high clinical importance in the work of improving diagnosis and characterization of colon cancer.

  5. 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.

  6. Taxonomy of pasteurella anatipestifer. 1. DNA base composition and DNA-DNA hybridization analysis.

    Science.gov (United States)

    Bangun, A; Johnson, J L; Tripathy, D N

    1987-01-01

    DNA was isolated from 15 strains of Pasteurella anatipestifer and from one strain each of Moraxella nonliquefaciens, M. bovis, Pasteurella multocida, P. haemolytica, P. gallinarum, P. pneumotropica, and P. ureae. The guanine-plus-cytosine contents of P. anatipestifer ranged from 32 to 35 mole %, whereas those of Moraxella and Pasteurella spp. were much higher, ranging from 40 to 45 mole %. DNA-DNA hybridization analysis revealed that homology of nine P. anatipestifer strains to strains ATCC 11845 and PA 15 was 52 to 100%, whereas homology of Moraxella and Pasteurella strains to these strains was only 3 to 17%. Similarly, homology of P. anatipestifer strains, Moraxella, and Pasteurella species other than P. multocida to P. multocida reference strain P-2192 was low. These results strongly suggest that P. anatipestifer is genetically unrelated to either Pasteurella or Moraxella.

  7. 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).

  8. Integrated microfluidic systems for DNA analysis.

    Science.gov (United States)

    Njoroge, Samuel K; Chen, Hui-Wen; Witek, Małgorzata A; Soper, Steven A

    2011-01-01

    microfluidic systems that are composed of two or more microdevices directed toward DNA analyses. Our discussions will primarily be focused on the integration of various processing steps with microcapillary electrophoresis (μCE) or microarrays. The advantages afforded by fully integrated microfluidic systems to enable challenging applications, such as single-copy DNA sequencing, single-cell gene expression analysis, pathogen detection, and forensic DNA analysis in formats that provide high throughput and point-of-analysis capabilities will be discussed as well.

  9. 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.

  10. Analysis of microsatellite markers and single nucleotide polymorphisms in candidate genes for susceptibility to bipolar affective disorder in the chromosome 12Q24.31 region.

    Science.gov (United States)

    Shink, Eric; Harvey, Mario; Tremblay, Monique; Gagné, Bernard; Belleau, Pascal; Raymond, Catherine; Labbé, Michel; Dubé, Marie-Pierre; Lafrenière, Ronald G; Barden, Nicholas

    2005-05-05

    Previous results from our genetic analyses using pedigrees from a French Canadian population suggested that the interval delimited by markers D12S86 and D12S378 on chromosome 12 was the most probable genomic region to contain a susceptibility gene for affective disorders. Here we present a more detailed genetic analysis of a 7.7 Mb genomic region located on 12q24.31. This region was saturated with 20 microsatellite markers to refine the candidate region and linkage analysis performed in 41 families from the Saguenay-Lac-St-Jean (SLSJ) region of Quebec. The results of two point parametric analysis using MFLINK supported the presence of a susceptibility locus on chromosome 12q24.31. Association studies with microsatellite markers using a case/control sample from the same population (n = 401) and analyzed with CLUMP revealed significant allelic associations between the bipolar phenotype and markers NBG6 (P = 0.008) and NBG12 (P < 10(-3)). According to these results, we investigated candidate genes in the NBG12 area. We analyzed 32 genes for the presence of polymorphisms in coding sequences and intron/exon junctions and genotyped 22 non-synonymous SNPs in the SLSJ case/control sample. Two uncommon polymorphisms (minor allele frequency < or = 0.03) found in KIAA1595 and FLJ22471 genes, gave P-values below 0.05 with the T1 statistic. Moreover, using haplotype analysis, a nearly significant haplotypic association was observed at the HM74 gene. These results do not give strong support for a role in the susceptibility to bipolar disorder of any of these genes analyzed. However, the significance of rare polymorphisms should be explored by further analyses. Copyright 2005 Wiley-Liss, Inc.

  11. Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources.

    Science.gov (United States)

    Paiva, Samuel Rezende; Mariante, Arthur da Silva; Blackburn, Harvey D

    2011-01-01

    Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs.

  12. Analysis of Genomic Microsatellite Sequence and Development of SSR Markers in Metasequoia glyptostroboides%水杉基因组微卫星分析及标记开发

    Institute of Scientific and Technical Information of China (English)

    张新叶; 张亚东; 彭婵; 宋丛文; 杨彦伶

    2013-01-01

    In this paper, the partial genome of Metasequoia glyptostroboides, a rare plant, was sequenced by using the ROCHE-454 GLX high-throughput sequencing platform. Through sequence assembly and microsatellite finding, 1 965 microsatellite loci were obtained in the sequence and the repeat unit length was 2 - 5 base pairs, by which 921 pairs of primer were designed with the Primer 3 Plus software. Analysis of these microsatellite sequences showed that tetranucleotide microsatellite was the most abundant, accounting for 38.8% of the total repeat sequences, followed by dinucleotide (31.8%), trinucleotide (22%) and pentanucleotide (7.4%) in the M. glyptostroboides genome. Among the dinucleotide repeat types, AG type was the most, accounting for 13.9% of total repeats and 43.8% of dinucleotide repeats. In the eight trinucleotide repeat types, AAG type accounted for 8.3% of total repeats and 37.7% of trinucleotide repeats, followed by ATG (23.1%), AAC (16.%) and AAT (13.0%). The analysis of different lengths of the microsatellite repeat unit showed that the most abundant variants were dinucleotide microsatellite and there were 23 different types of repeat lengths, followed by the tetranucleotide repeat (10 types), trinucleotide repeat (8 types) and pentanucleotide repeat (3 types). The validation of SSR markers showed that, 87 pairs brought about clear products and 46 pairs had polymorphic products, accounting for 62. 14% and 32.86% out of the 140 primer pairs,respectively.

  13. DNA Analysis of PCR-Inhibitory Forensic Samples

    OpenAIRE

    Hedman, Johannes

    2011-01-01

    DNA evidence, linking perpetrators to crime scenes, is central to many legal proceedings. However, crime scene samples often contain extraneous substances that may interfere with the PCR-based forensic analysis, resulting in partial or negative DNA profiles. Extensive DNA purification may remove inhibitors, but involves the risk of DNA loss. In this work, pre-PCR processing was applied to improve the success rate of forensic DNA analysis of “dirty” samples without interfering with the comp...

  14. A New World Monkey microsatellite (AP74 higly conserved in Primates

    Directory of Open Access Journals (Sweden)

    Oklander Luciana Inés

    2012-04-01

    Full Text Available Given their great variability, microsatellites or STRPs became the most commonly used genetic markers over the last 15 years. The analysis of these markers requires minimum quantities of DNA, allowing the use of non invasive samples, such as feces or hair. We amplified the microsatellite Ap74 in blood and hair samples in order to analyze the levels of genomic conservation among a wide range of primates including: Lemur catta, Alouatta caraya, Ateles belzebuth, Ateles chamek, Pan troglodytes, Papio sp., and Homo sapiens. In all cases we obtained amplification products that exhibited similar size both in monkeys and human (oscillating between 126 and 176 bp, except in the lemur where the detected fragment presented a size of approximately 1000 bp. The analysis of the nucleotide sequences permitted the evaluation of the molecular modifications experienced during the evolutionary process in primates.

  15. 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....

  16. 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

  17. Meat speciation by restriction fragment length polymorphism analysis using an α-actin cDNA probe.

    Science.gov (United States)

    Fairbrother, K S; Hopwood, A J; Lockley, A K; Bardsley, R G

    1998-09-01

    Classical DNA fingerprinting is based on separation of DNA restriction fragments by electrophoresis and hybridisation to nucleic acid probes containing repetitive nucleotide sequences. The use of such mini- or micro-satellite probes tends to yield patterns specific to an individual rather than to a species, hence their value in forensic analysis but general unsuitability for meat speciation. In the present study, a cDNA probe based on conserved sequences contained in members of the actin multigene family has been evaluated for potential application in meat speciation. Genomic DNA was extracted from muscle and digested with BamHI before electrophoresis and hybridisation to a murine α-actin cDNA probe. Beef, pork, lamb, horse, chicken and fish DNA restriction fragments formed characteristic 'fingerprints' which were reproducible and varied sufficiently to allow discrimination even between closely-related species. However no major differences were seen between individuals of the same breed or between different breeds within a species. When DNA obtained from fresh tissue and also from meat heated at 120 °C was analysed, the gel patterns were essentially the same. An attractive feature of this approach is that it employs a single cross-reacting probe and set of conditions, and gives different patterns with all species so far studied. This simplicity suggests applications in meat speciation or related areas of biology.

  18. Performance Analysis of Anti-Interference Wireless Packet Networks for LEO Micro-Satellite with Adaptive Nulling Antenna Array

    Institute of Scientific and Technical Information of China (English)

    LIU Hai-tao; HAN Fang-jing; WAN Jian-wei

    2006-01-01

    Information integrity is key to successful operations in intricacy environments in the future, especially when strong interferences exist. This paper presents the design of a novel wireless packet network receiver system for Low Earth Orbit (LEO) micro-satellites with adaptive nulling antenna arrays. It uses three types of interference suppression in cascade: namely spread spectrum, adaptive array nulling, and transform domain filtering. This paper proposes a pilot channel-aided method in order to make full advantage of this arrangement, and analyzes its throughput and delay performance using the Markov chain model. Our results show that this method can achieve excellent delay and throughput performance: When the number of array antenna is 8, its throughput increase relative to the standard Slot-ALOHA protocol is 125 %.

  19. Analysis of Genetic Diversity and Relationships in a Tunisian Fig (Ficus carica) Germplasm Collection by Random Amplified Microsatellite Polymorphisms

    Institute of Scientific and Technical Information of China (English)

    Khaled Chatti; Olfa Saddoud; Amel Salhi-Hannachi; Messaoud Mars; Mohamed Marrakchi; Mokhtar Trifi

    2007-01-01

    The random amplified mirosatellite polymorphism method was performed in a set of Tunisian fig landraces using eighteen primer combinations. Atotal of sixty three random amplified microsatellite polymorphism (RAMPO) markers were scored and used either to assess the genetic diversity in these cultivars or to detect cases of mislabeling. Opportunely, data proved that the designed procedure constitutes an attractive and fast method with low costs and prevents radio exposure. As a result, we have identified the primer combinations that are the most efficient to detect genetic polymorphism in this crop. Therefore, the derived unweighted pair-group method with arithmetic averages (UPGMA) dendrogram illustrates the genetic divergence among the landraces studied and exhibits a typically continuous variation. Moreover, no evident correlation between the sexes of trees was observed. In addition, using these markers, discrimination between landraces has been achieved. Thus, random amplified mirosatellite polymorphism is proved to be powerful for characterizing the local fig germplasm.

  20. Analysis of microsatellite polymorphisms within the GLC1F locus in Japanese patients with normal tension glaucoma

    Science.gov (United States)

    Murakami, Kaori; Ota, Masao; Shiota, Tomoko; Nomura, Naoko; Kashiwagi, Kenji; Mabuchi, Fumihiko; Iijima, Hiroyuki; Kawase, Kazuhide; Yamamoto, Tetsuya; Nakamura, Makoto; Negi, Akira; Sagara, Takeshi; Nishida, Teruo; Inatani, Masaru; Tanihara, Hidenobu; Aihara, Makoto; Araie, Makoto; Fukuchi, Takeo; Abe, Haruki; Higashide, Tomomi; Sugiyama, Kazuhisa; Kanamoto, Takashi; Kiuchi, Yoshiaki; Iwase, Aiko; Ohno, Shigeaki; Inoko, Hidetoshi; Mizuki, Nobuhisa

    2010-01-01

    Purpose To investigate whether the GLC1F locus is associated with normal tension glaucoma (NTG) in Japanese patients. Methods We recruited 242 unrelated Japanese subjects, including, 141 NTG patients and 101 healthy controls. The patients exhibiting a comparatively early onset were selected as they suggest that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 11 highly polymorphic microsatellite markers in and around the GLC1F locus. Results Individuals carrying the 163 allele of D7S1277i had a statistically significant increased risk of NTG (p=0.0013, pc=0.016, OR=2.47, 95%CI=1.42–4.30). None of the other markers identified significant loci (pc>0.05) after Bonferroni’s correction. Conclusions These findings suggested that the genes in the GLC1F locus may be associated with the pathogenesis of NTG. PMID:20309402

  1. Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs.

    Science.gov (United States)

    Jin, S B; Zhang, X F; Lu, J G; Fu, H T; Jia, Z Y; Sun, X W

    2015-04-17

    A group of 107 F1 hybrid common carp was used to construct a linkage map using JoinMap 4.0. A total of 4877 microsatellite and single nucleotide polymorphism (SNP) markers isolated from a genomic library (978 microsatellite and 3899 SNP markers) were assigned to construct the genetic map, which comprised 50 linkage groups. The total length of the linkage map for the common carp was 4775.90 cM with an average distance between markers of 0.98 cM. Ten quantitative trait loci (QTL) were associated with eye diameter, corresponding to 10.5-57.2% of the total phenotypic variation. Twenty QTL were related to eye cross, contributing to 10.8-36.9% of the total phenotypic variation. Two QTL for eye diameter and four QTL for eye cross each accounted for more than 20% of the total phenotypic variation and were considered to be major QTL. One growth factor related to eye diameter was observed on LG10 of the common carp genome, and three growth factors related to eye cross were observed on LG10, LG35, and LG44 of the common carp genome. The significant positive relationship of eye cross and eye diameter with other commercial traits suggests that eye diameter and eye cross can be used to assist in indirect selection for many commercial traits, particularly body weight. Thus, the growth factor for eye cross may also contribute to the growth of body weight, implying that aggregate breeding could have multiple effects. These findings provide information for future genetic studies and breeding of common carp.

  2. Microsatellite DNA Variation of the Gametophyte Clones Isolated from Introduced Laminaria japonica (Phaeophyta) and L. Iongissima of China and Varieties Derived from them

    Institute of Scientific and Technical Information of China (English)

    Bing-Jun Li; Yuan-Yuan Shi; Guan-Pin Yang; Shi Che; Xiao-Jie Li; Yi-Zhou Cong

    2008-01-01

    The variation of 90 Laminaria gametophyte clones representing the introduced Laminariajaponica (Group 1) and Laminaria Iongissima (Group 2), the varieties of L. japonica (Group 3) and the varieties derived from interspecific hybrids (Group 4) was determined with 10 microsatellite markers. The allelic diversity and Nei's gene diversity of Group 1 were significantly higher than those of Group 2 (2.9 vs. 1.8 and 0.414 vs. 0.161, respectively), demonstrating that the variation of the introduced L. japonica is richer than that of L. Iongiesima. Both allelic diversity and Nei's gene diversity of Group 3 were lower than those of Group 1, indicating that only a portion of variation of L. japonica was incorporated into the varieties of L. japonica. Significant genetic differentiation was detected between four groups and between female (Population 1) and male (Population 2) gametophyte clones in each group. The variation among groups accounted for 39.95%, while that among populations accounted for 21.65% of the total. The genetic distance between Group 1 and Group 4 was obviously longer than that between Group 2 and Group 4 (0.686 vs. 0.291), Indicating that maternal gametophyte clone contributed more variation to the hybrids than the paternal gametophyte clone did.

  3. Good news for conservation: mitochondrial and microsatellite DNA data detect limited genetic signatures of inter-basin fish transfer in Thymallus thymallus (Salmonidae from the Upper Drava River

    Directory of Open Access Journals (Sweden)

    Meraner A.

    2013-06-01

    Full Text Available In the last few decades, numerous populations of European grayling, Thymallus thymallus, have been suffering from stocking-induced genetic admixture of foreign strains into wild populations. Concordantly, genetic introgression was also reportedfor grayling stocks inhabiting the Upper Drava River, but all published genetic data based on specimens caught at least a decade ago, when stocking load was strong. Here, we applied mitochondrial control region sequencing and nuclear microsatellite genotyping to Upper Drava grayling fry collections and reference samples to update patterns and extent of human-mediated introgression. In contrast to previous data, we highlighted an almost genetic integrity of Drava grayling, evidencing limited genetic signatures of trans-basin stocking for grayling of Northern Alpine Danubian origin. Recent hybridisation was detected only twice among sixty-nine samples, while several cases of later-generation hybrids were disclosed by linking mitochondrial sequence to nuclear genetic data. The observed past, but very limited recent genetic introgression in grayling from Upper Drava seems to reflect shifting stocking trends, changing from massive introduction of trans-basin fish to more conservation-oriented strategies during the last 27 years. In a conservation context, we encourage pursuing the use of local wild grayling for supportive- and captive-breeding, but underline the need for genetic approaches in brood-stock selection programs. Finally, our integrated results from sibship reconstruction validate our strictly fry-based sampling scheme, thus offering a reasonable alternative also for other rheophilic fish species with similar life-history characteristics.

  4. DNA hybridization sensing for cytogenetic analysis

    DEFF Research Database (Denmark)

    Kwasny, Dorota; Dapra, Johannes; Brøgger, Anna Line;

    2013-01-01

    Cytogenetic analysis focuses on studying the cell structure, mainly in respect to chromosome content and their structure. Chromosome abnormalities, such as translocations may cause various genetic disorders, but are also associated with heametological malignancies. Chromosome translocations...... for cheaper detection a label-free approach has been investigated using electrochemical impedance spectroscopy as a sensing method. We present here our recent results in regards to DNA sensing on metallic and conductive polymer electrodes for translocation detection. Our sensors are inexpensive and can...... be successfully applied in cytogenetic analysis as a replacement of standard techniques....

  5. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  6. 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.

  7. Genetic analysis of CRHRA1 and CRHRA2 microsatellites and their association with rheumatoid arthritis in South Asian and Caucasian populations of the East Midlands, UK.

    Directory of Open Access Journals (Sweden)

    Anant Ghelani

    2012-06-01

    Full Text Available Two microsatellites from corticotropin releasing hormone (CRH gene locus (CRHRA1 and CRHRA2 were reported to be associated with rheumatoid arthritis (RA in Caucasians. This study aims to replicate the association in a South Asian (SA and Caucasian RA sample from the East Midlands, UK. DNA from 281 South Asians (111 patients, 43 siblings, 127 controls and 287 Caucasians (116 patients, 64 siblings, 107 controls were genotyped. The Odds Ratio for carrying at least one copy of the CRHRA1*10 risk allele was 1.32 (Confidence Interval, CI=0.77-2.28 in Caucasians and 1.55 (CI=0.92-2.63 in South Asians, indicative of a trend for association. The risk allele CRHRA2*14 was lower in South Asians compared to Caucasians (5.5%-8.6% vs. 17.7-18.2 %; P<0.005. Significant linkage disequilibrium was observed between CRHRA1 and CRHRA2 in both cohorts. CRHRA1*10 was the frequently transmitted allele in SA patients. A non-significant association was observed with CRHRA1*10 allele in both RA populations.

  8. Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family

    Institute of Scientific and Technical Information of China (English)

    Yan Zhang; Liqun Liang; Peng Jiang; Dayu Li; Cuiyun Lu; Xiaowen Sun

    2008-01-01

    Genome evolution arises from two main ways of duplication and reduction. Fish specific genome duplication (FSGD) may have oc curred before the radiation of the teleosts. Common carp {Cyprinus carpio L.) has been considered to be a tetraploid species, because of its chromosome numbers (2n=100) and its high DNA content. Using 69 microsatellite primer pairs, the variations were studied to better understand the genome evolution (genome duplication and diploidization) of common carp from a gynogenetic family. About 48% of primer pairs were estimated to amplify duplicates based on the number of PCR amplification per individual. Segregation patterns in the family suggested a partially duplicated genome structure and disomic inheritance. This indicates that the common carp is tetraploid and polyploidy occurred by allotetraploidy. Two primer pairs (HLJ021 and HLJ332) were estimated to amplify reduction based on the number of PCR amplification per individual. One allele in HLJ002 locus and HLJ332 locus was clearly lost in the gynogenetic family and the same as in six wild populations. Segregation patterns in the family suggested a partially diplodization genome structure. A hypothesis transition (dynamic) and equilibrium (static) were proposed to explain the common carp genome evolution between genome duplication and diploidization.

  9. Investigation of the association between the GLC3A locus and normal tension glaucoma in Japanese patients by microsatellite analysis

    Directory of Open Access Journals (Sweden)

    M Kamio

    2009-01-01

    (NTG in Japanese patients.Materials and Methods: One hundred forty-two Japanese patients with NTG and 101 Japanese healthy controls were recruited. Patients exhibiting a comparatively early onset were selected as this suggests that genetic factors may show stronger involvement. Genotyping and assessment of allelic diversity was performed on 13 highly polymorphic microsatellite markers in and around the GLC3A locus.Results: There were decreased frequencies of the 444 allele of D2S0416i and the 258 allele of D2S0425i in cases compared to controls (P = 0.022 and P = 0.034, respectively. However, this statistical significance disappeared when corrected (Pc > 0.05. We did not find any significant association between the remaining 11 microsatellite markers, including D2S177, which may be associated with CYP1B1, and NTG (P > 0.05.Conclusions: Our study showed no association between the GLCA3 locus and NTG, suggesting that the CYP1B1 gene, which is reportedly involved in a range of glaucoma phenotypes, may not be an associated factor in the pathogenesis of NTG.Keywords: GLCA3, microsatellite, normal tension glaucoma, polymorphism

  10. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

    This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

  11. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

    This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

  12. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in bottle gourd (Lagenaria siceraria (Mol.) Standl.).

    Science.gov (United States)

    Bhawna; Abdin, M Z; Arya, L; Verma, M

    2015-02-01

    Improved breeding for developing fruit quality in bottle gourd (Lagenaria siceraria (Mol.) Standl.) necessitates knowledge regarding its genetic diversity. To achieve this, a set of 108 locus-specific SSR markers has been developed in bottle gourd by cross-species transferability from 995 mapped Cucumis sativus SSR markers. During screening, 280 primer pairs amplified in the bottle gourd germplasm, which were further evaluated in a diverse set of 42 lines, resulting in 19 polymorphic, 89 monomorphic, 15 with multiple bands, and the rest 157 showed no or very non-specific amplification. The 19 polymorphic primer pairs produced a total of 54 alleles. Gene diversity, Shannon's information index, and Nei's coefficient of differentiation were calculated suggesting a moderate genetic variation at the species level. A model-based population structure analysis divided these germplasm into two subpopulations. This marker set will be applicable for evaluating the genetic structure for association mapping, DNA fingerprinting, and mounting linkage maps and will be a practical tool set for further genetics. This study provides one of the first quantitative views of population genetic variation in bottle gourd.

  13. Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA

    NARCIS (Netherlands)

    S. Vives (Sergi); M.T. Gilbert (Thomas); C. Arenas (Conchita); E. Gigli (Elena); O. Lao Grueso (Oscar); C. Lalueza-Fox (Carles)

    2008-01-01

    textabstractBackground. We have analysed the distribution of post mortem DNA damage derived miscoding lesions from the datasets of seven published Neandertal specimens that have extensive cloned sequence coverage over the mitochondrial DNA (mtDNA) hypervariable region 1 (HVS1). The analysis was rest

  14. Scanometric analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles.

    Science.gov (United States)

    Cho, Hyunmin; Jung, Juyeon; Chung, Bong Hyun

    2012-08-07

    We introduce a scanometric detection method for the analysis of DNA microarrays using DNA intercalator-conjugated gold nanoparticles that can be analyzed with the naked eye or with an optical scanner after the enhancement of the AuNPs. Moreover, we successfully detected a hemagglutinin-subtyping DNA array using this method.

  15. Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species.

    Science.gov (United States)

    Santos, Jean C S; Barreto, Mariana A; Oliveira, Fernanda A; Vigna, Bianca B Z; Souza, Anete P

    2015-03-15

    Urochloa humidicola is a warm-season grass commonly used as forage in the tropics and is recognized for its tolerance to seasonal flooding. This grass is an important forage species for the Cerrado and Amazon regions of Brazil. U. humidicola is a polyploid species with variable ploidy (6X-9X) and facultative apomixis with high phenotypic plasticity. However, this apomixis and ploidy, as well as the limited knowledge of the genetic basis of the germplasm collection, have constrained genetic breeding activities, yet microsatellite markers may enable a better understanding of the species' genetic composition. This study aimed to develop and characterize new polymorphic microsatellite molecular markers in U. humidicola and to evaluate their transferability to other Urochloa species. A set of microsatellite markers for U. humidicola was identified from two new enriched genomic DNA libraries: the first library was constructed from a single sexual genotype and the second from a pool of eight apomictic genotypes selected on the basis of previous results. Of the 114 loci developed, 72 primer pairs presented a good amplification product, and 64 were polymorphic among the 34 genotypes tested. The number of bands per simple sequence repeat (SSR) locus ranged from 1 to 29, with a mean of 9.6 bands per locus. The mean polymorphism information content (PIC) of all loci was 0.77, and the mean discrimination power (DP) was 0.87. STRUCTURE analysis revealed differences among U. humidicola accessions, hybrids, and other Urochloa accessions. The transferability of these microsatellites was evaluated in four species of the genus, U. brizantha, U. decumbens, U. ruziziensis, and U. dictyoneura, and the percentage of transferability ranged from 58.33% to 69.44% depending on the species. This work reports new polymorphic microsatellite markers for U. humidicola that can be used for breeding programs of this and other Urochloa species, including genetic linkage mapping, quantitative trait

  16. 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

  17. LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.

    Directory of Open Access Journals (Sweden)

    Marcos R H Estécio

    Full Text Available BACKGROUND: Alterations in DNA methylation in cancer include global hypomethylation and gene-specific hypermethylation. It is not clear whether these two epigenetic errors are mechanistically linked or occur independently. This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer. METHODOLOGY/PRINCIPAL FINDINGS: We examined 61 cancer cell lines and 60 colorectal carcinomas and their adjacent tissues using LINE-1 bisulfite-PCR as a surrogate for global demethylation. Colorectal carcinomas with sporadic microsatellite instability (MSI, most of which are due to a CpG island methylation phenotype (CIMP and associated MLH1 promoter methylation, showed in average no difference in LINE-1 methylation between normal adjacent and cancer tissues. Interestingly, some tumor samples in this group showed increase in LINE-1 methylation. In contrast, MSI-showed a significant decrease in LINE-1 methylation between normal adjacent and cancer tissues (P<0.001. Microarray analysis of repetitive element methylation confirmed this observation and showed a high degree of variability in hypomethylation between samples. Additionally, unsupervised hierarchical clustering identified a group of highly hypomethylated tumors, composed mostly of tumors without microsatellite instability. We extended LINE-1 analysis to cancer cell lines from different tissues and found that 50/61 were hypomethylated compared to peripheral blood lymphocytes and normal colon mucosa. Interestingly, these cancer cell lines also exhibited a large variation in demethylation, which was tissue-specific and thus unlikely to be resultant from a stochastic process. CONCLUSION/SIGNIFICANCE: Global hypomethylation is partially reversed in cancers with microsatellite instability and also shows high variability in cancer, which may reflect alternative progression pathways in cancer.

  18. 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

  19. DNA Methylation: Bisulphite Modification and Analysis

    OpenAIRE

    Patterson, Kate; Molloy, Laura; Qu, Wenjia; Clark, Susan

    2011-01-01

    Epigenetics describes the heritable changes in gene function that occur independently to the DNA sequence. The molecular basis of epigenetic gene regulation is complex, but essentially involves modifications to the DNA itself or the proteins with which DNA associates. The predominant epigenetic modification of DNA in mammalian genomes is methylation of cytosine nucleotides (5-MeC). DNA methylation provides instruction to gene expression machinery as to where and when the gene should be expres...

  20. 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

  1. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties.

    Science.gov (United States)

    Rusanov, K; Kovacheva, N; Vosman, B; Zhang, L; Rajapakse, S; Atanassov, A; Atanassov, I

    2005-08-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultivation is based on a very narrow genepool and that oil rose collections contain many genetically identical accessions. The study of long-term vegetative propagation of the Damask roses also reveals high somatic stability for the microsatellite loci analyzed.

  2. 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.

  3. 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.

  4. 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.

  5. Evaluating the interaction of faecal pellet deposition rates and DNA degradation rates to optimize sampling design for DNA-based mark-recapture analysis of Sonoran pronghorn.

    Science.gov (United States)

    Woodruff, S P; Johnson, T R; Waits, L P

    2015-07-01

    Knowledge of population demographics is important for species management but can be challenging in low-density, wide-ranging species. Population monitoring of the endangered Sonoran pronghorn (Antilocapra americana sonoriensis) is critical for assessing the success of recovery efforts, and noninvasive DNA sampling (NDS) could be more cost-effective and less intrusive than traditional methods. We evaluated faecal pellet deposition rates and faecal DNA degradation rates to maximize sampling efficiency for DNA-based mark-recapture analyses. Deposition data were collected at five watering holes using sampling intervals of 1-7 days and averaged one pellet pile per pronghorn per day. To evaluate nuclear DNA (nDNA) degradation, 20 faecal samples were exposed to local environmental conditions and sampled at eight time points from one to 124 days. Average amplification success rates for six nDNA microsatellite loci were 81% for samples on day one, 63% by day seven, 2% by day 14 and 0% by day 60. We evaluated the efficiency of different sampling intervals (1-10 days) by estimating the number of successful samples, success rate of individual identification and laboratory costs per successful sample. Cost per successful sample increased and success and efficiency declined as the sampling interval increased. Results indicate NDS of faecal pellets is a feasible method for individual identification, population estimation and demographic monitoring of Sonoran pronghorn. We recommend collecting samples sampling interval of four to seven days in summer conditions (i.e., extreme heat and exposure to UV light) will achieve desired sample sizes for mark-recapture analysis while also maximizing efficiency [Corrected]. © 2014 John Wiley & Sons Ltd.

  6. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

    Energy Technology Data Exchange (ETDEWEB)

    Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

    2011-01-01

    It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

  7. Molecular phylogenetics and microsatellite analysis reveal cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon's Great Basin.

    Science.gov (United States)

    Hoekzema, Kendra; Sidlauskas, Brian L

    2014-08-01

    Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs throughout western North America and is the most commonly occurring fish in Oregon. Because of the high genetic and morphological variation in this species across its range, it has been referred to as a species complex; however, no revision to its taxonomy has occurred since 1984. Here, the phylogenetics and population genetics of speckled dace are examined throughout Oregon's Great Basin to describe genetic variation and infer the geographic boundaries between distinct taxonomic entities and populations. We tested the validity of a putative subspecies, Foskett Spring speckled dace, that occurs in a single spring within Warner Valley in Southeast Oregon and is listed Federally as threatened. Dace were collected from Foskett Spring and all surrounding basins containing speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur), created phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data, and genotyped eight microsatellite loci for population-level analyses. Three highly divergent clades warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins combined. Although Foskett Spring dace were not monophyletic, substantial population structure occurs at the basin-level and separates Foskett Spring dace from other dace in the surrounding Warner Valley. Thus, we recommend ESU status for the isolated population of speckled dace in Foskett Spring. The high, previously unrecognized, taxonomic diversity within this region indicates a need for a range-wide phylogeographic study of speckled dace and an investigation of the morphological distinctiveness of the putative new species.

  8. Mitochondrial DNA depletion analysis by pseudogene ratioing.

    Science.gov (United States)

    Swerdlow, Russell H; Redpath, Gerard T; Binder, Daniel R; Davis, John N; VandenBerg, Scott R

    2006-01-30

    The mitochondrial DNA (mtDNA) depletion status of rho(0) cell lines is typically assessed by hybridization or polymerase chain reaction (PCR) experiments, in which the failure to hybridize mtDNA or amplify mtDNA using mtDNA-directed primers suggests thorough mitochondrial genome removal. Here, we report the use of an mtDNA pseudogene ratioing technique for the additional confirmation of rho0 status. Total genomic DNA from a U251 human glioma cell line treated with ethidium bromide was amplified using primers designed to anneal either mtDNA or a previously described nuclear DNA-embedded mtDNA pseudogene (mtDNApsi). The resultant PCR product was used to generate plasmid clones. Sixty-two plasmid clones were genotyped, and all arose from mtDNApsi template. These data allowed us to determine with 95% confidence that the resultant mtDNA-depleted cell line contains less than one copy of mtDNA per 10 cells. Unlike previous hybridization or PCR-based analyses of mtDNA depletion, this mtDNApsi ratioing technique does not rely on interpretation of a negative result, and may prove useful as an adjunct for the determination of rho0 status or mtDNA copy number.

  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. Knowledge on DNA Success Rates to Optimize the DNA Analysis Process: From Crime Scene to Laboratory.

    Science.gov (United States)

    Mapes, Anna A; Kloosterman, Ate D; van Marion, Vincent; de Poot, Christianne J

    2016-07-01

    DNA analysis has become an essential intelligence tool in the criminal justice system for the identification of possible offenders. However, it appears that about half of the processed DNA samples contains too little DNA for analysis. This study looks at DNA success rates within 28 different categories of trace exhibits and relates the DNA concentration to the characteristics of the DNA profile. Data from 2260 analyzed crime samples show that cigarettes, bloodstains, and headwear have relatively high success rates. Cartridge cases, crowbars, and tie-wraps are on the other end of the spectrum. These objective data can assist forensics in their selection process.The DNA success probability shows a positive relation with the DNA concentration. This finding enables the laboratory to set an evidence-based threshold value in the DNA analysis process. For instance, 958 DNA extracts had a concentration value of 6 pg/μL or less. Only 46 of the 958 low-level extracts provided meaningful DNA profiling data.

  11. 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.

  12. 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.

  13. Microsatellite analysis of Rosa damascena Mill. accessions reveals genetic similarity between genotypes used for rose oil production and old Damask rose varieties

    OpenAIRE

    Rusanov, K.; Kovacheva, N.; Vosman, B.J.; Zhang, L.; Rajapakse, S; Atanassov, A.; Atanassov, I.

    2005-01-01

    Damask roses are grown in several European and Asiatic countries for rose oil production. Twenty-six oil-bearing Rosa damascena Mill. accessions and 13 garden Damask roses were assayed by molecular markers. Microsatellite genotyping demonstrated that R. damascena Mill. accessions from Bulgaria, Iran, and India and old European Damask rose varieties possess identical microsatellite profiles, suggesting a common origin. At the same time, the data indicated that modern industrial oil rose cultiv...

  14. 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.

  15. 玉米丝黑穗病菌基因组SSR的信息分析%Information Analysis on Microsatellites in the Genome of Sporisorium reilianum

    Institute of Scientific and Technical Information of China (English)

    王士臻; 张作刚; 李新凤; 高俊明; 王建明

    2012-01-01

    A total of genome of publicly available DNA sequence in Sporisorium reilianum was researched for dinucleotide to hexanucleotide simple sequence repeat (SSR) to determine the type, size and frequency. A total of 888 SSRs were observed in the first three chromosomes. Total length of SSRs was 3. 512 kb, about 0. 068% of these chromosomes. The SSRs occur on average about once every 3. 512 kb for dinucleotide to hexanucleotide in the first three chromosomes. The most abundant microsatellites were trinucleotide repeats with the number of 329, followed by hexanucleotide and pentanucleotide repeats, and the number of these SSRs was 185 and 155, respectively. The least abundant was tetranucleotide repeat, only 101 were found.%利用已经公布的玉米丝黑穗病菌基因组测序的结果,对该基因组中基序为2~6碱基的微卫星(SSR)序列进行了系统的分析.结果表明,在已经公布的23条基因组中选择前3条染色体进行分析,共有888个SSR,其总长度为3.512 kb,占这3条基因组染色体碱基数的0.068%,平均6.50 kb中就分布有一个长度大于15 bp的SSR序列.其中,数量最多的为三碱基重复序列,共有SSR数量329个,其次为六碱基重复序列,数量达185个.五碱基重复序列的SSR数量为155个,数量最少的是四碱基重复序列,只有101个.

  16. Mapping QTLs Affecting Economic Traits on BTA3 in Chinese Holstein with Microsatellite Markers

    Institute of Scientific and Technical Information of China (English)

    QIN Chun-hua; CHU Qin; CHU Gui-yan; ZHANG Yi; ZHANG Qin; ZHANG Sheng-li; SUN Dong-xiao

    2014-01-01

    It had been demonstrated that the strong and highly signiifcantquantitative trait locus (QTL) can affect protein percentage on Bos Taurus Autosome 3 (BTA3) at the position 52 cM, near the microsatelliteDIK4353, with the 95% conifdence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of ifne mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markersBMS2904 andMB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis (LA) and linkage-disequilibrium (LD) analysis (LA/LD) was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly signiifcant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identiifed at 42 and 46 cM, respectively. These ifndings provided a general idea for the ifne mapping of the causal mutation for milk production and functional traits on BTA3 in the future.

  17. Characterization of 12 polymorphic microsatellite markers in the Chinese tree shrew (Tupaia belangeri chinensis)

    Institute of Scientific and Technical Information of China (English)

    Xiao-Hong LIU; Yong-Gang YAO

    2013-01-01

    The Chinese tree shrew (Tupaia belangeri chinensis) is a small experimental animal with a close affinity to primates.This species has long been proposed to be an alternative experimental animal to primates in biomedical research.Despite decades of study,there is no pure breed for this animal,and the overall genetic diversity of wild tree shrews remains largely unknown.In order to obtain a set of genetic markers for evaluating the genetic diversity of tree shrew wild populations and tracing the lineages in inbreeding populations,we developed 12 polymorphic microsatellite markers from the genomic DNA of the tree shrew.An analysis of a wild population of 117 individuals collected from the suburb of Kunming,China,showed that these loci exhibited a highly expected heterozygosity (0.616).These 12 microsatellites were sufficient for individual identification and parentage analysis.The microsatellite markers developed in this study will be of use in evaluating genetic diversity and lineage tracing for the tree shrew.

  18. 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.

  19. 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.

  20. The future of forensic DNA analysis

    Science.gov (United States)

    Butler, John M.

    2015-01-01

    The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of ‘faster, higher, stronger’, forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles. PMID:26101278

  1. Molecular Analysis of Microsatellite Mutagenesis in Soybean (Glycine max)%大豆微卫星诱发突变的分子分析

    Institute of Scientific and Technical Information of China (English)

    朱保葛; 孙勇如

    2004-01-01

    Microsatellite or SSR marker is an efficient tool for plant genotype identification, molecular mapping and marker-assisted selection. Objective of this study is to analyze the mutagenized microsatellite variations in soybean genome and reveal nature of these mutations. In the present study, mutations at fifteen microsatellite loci were detected in genomic DNAs of soybean mutant E182 induced by EMS (ethyne metyl sulfate) using PCR amplification of 485 pairs of SSR primers. These fifteen mutagenized microsatellite loci with repeat number variation were Satt005, Satt117, Satt185, Satt282, Satt290, Satt420, Satt452, Satt483, Satt569, Satt579, Satt600, Satt602, Sat_086, Sat_107 and Sat_135, respectively. Sequencing results of these fifteen loci indicated that microsatellite sequences at Satt282, Satt483, Satt579, Satt600 and Satt602 loci were respectively deleted 1-, 3-, 8-, 20- and 1-trinucleotide (all [ATT]1-20 except for [CAA]8[TAA]12 at Satt600 locus) repeats, which made allele sizes at these five loci decrease 3, 9, 24, 60 and 3 bp, respectively. And while microsatellite sequences at the other ten mutated loci, Satt005, Satt117, Satt185, Satt290, Satt420, Satt452, Satt569 and Sat_086, Sat_107, Sat_135, were respectively inserted 1-, 6-, 6-, 3-, 4-, 3-, 8-trinucleotide repeats (ATT)1-8 and 12-, 6-, 16-dinucleotide repeats (AT)6-16, making allele sizes at these ten loci increase 3, 18, 18, 9, 12, 9, 24, 24, 12, 32 bp, respectively. On the other hand, eleven events of base mutations were detected in flanking regions at seven (Sat-107, Satt185, Satt282, Satt420, Satt569, Satt579 and Satt600) of fifteen mutated microsatellite loci. These base mutations consisted of 6 transitions (4T→C and 2 A→G), 2 transvertions (A→T and T→A), 1 insertion (T) and 2 deletions (A and T). The experimental results proved that EMS mutagenesis could cause different types of mutations at microsatellite multilocus in soybean genome, including repeat number variations in microsatellite

  2. 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).

  3. Relationship between microsatellite instability and deficiency of DNA mismatch repair system in lung carcinoma%肺癌微卫星不稳定性与错配修复基因缺陷的相关性研究

    Institute of Scientific and Technical Information of China (English)

    李曼; 喻喆; 李英华; 张晶

    2011-01-01

    Objectiye To investigate the relationship between microsatellite instability (MSI) and mismatch repair gene (MMR) in lung carcinoma,and to analyze its action in lung carcinogenesis.Methods DNA was extracted from 50 cases of lung carcinoma and adjacent normal tissue.SSCP was used to detect MSI.Immunohistochemistry was performed to measure the expression of hMLH1 and hMSH2 protein in lung carcinoma.Results Of the 50 cases of lung carcinoma,14 with high MSI,21 with low MSI,and 15 with microsatellite stability,0 with MSI in normal group (P = 0.000).Lack of hMLH1 and hMLH2 staining was found in 37 of 50 (74 %) and 16 of 50 (32 %) lung carcinoma tissues with MSI,respectively; but both of hMLH1 and hMSH2 positive staining was found in the lung carcinoma tissues with MSS.Conclusion MSI appears to be associated with lung carcinogenesis,and inactivation of either hMLH1 or hMSH2 may be responsible for MSI,suggesting that MSI may become one of diagnosis indexes of lung carcinoma.%目的 通过对肺癌微卫星不稳定性(MSI)的分析与错配修复基因蛋白表达的检测,探讨肺癌发病的分子机制.方法 从50例肺癌患者的正常肺组织、癌组织中提取DNA;SSCP法检测标本中MSI发生情况;免疫组织化学法检测错配修复基因hMLH1及hMSH2在肺癌中的表达情况.结果 50例肺癌中微卫星高度不稳定(MSI-H)14例,低度不稳定(MSI-I)21例,稳定(MSS)15例,正常组织中未出现MSI,两者之间差异有统计学意义(P=0.000);免疫组化结果显示hMLH1在MSI肺癌组织中常为缺失表达,表达率为74%(37/50);hMSH2在MSI肺癌组织中也呈缺失表达,表达率为32%(16/50);而在MSS肺癌组织中均显示hMLH1、hMSH2基因蛋白表达阳性.结论 肺癌的发生可能存在MSI途径,而hMLH1、hMSH2的表达失活则可能导致MSI的发生,因此,MSI可作为肺癌诊断的指标之一.

  4. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians and its application in size-related QTL analysis.

    Directory of Open Access Journals (Sweden)

    Hongjun Li

    Full Text Available Bay scallop (Argopecten irradians is one of the most economically important aquaculture species in China. In this study, we constructed a consensus microsatellite-based genetic linkage map with a mapping panel containing two hybrid backcross-like families involving two subspecies of bay scallop, A. i. irradians and A. i. concentricus. One hundred sixty-one microsatellite and one phenotypic (shell color markers were mapped to 16 linkage groups (LGs, which corresponds to the haploid chromosome number of bay scallop. The sex-specific map was 779.2 cM and 781.6 cM long in female and male, respectively, whereas the sex-averaged map spanned 849.3 cM. The average resolution of integrated map was 5.9 cM/locus and the estimated coverage was 81.3%. The proportion of distorted markers occurred more in the hybrid parents, suggesting that the segregation distortion was possibly resulted from heterospecific interaction between genomes of two subspecies of bay scallop. The overall female-to-male recombination rate was 1.13:1 across all linked markers in common to both parents, and considerable differences in recombination also existed among different parents in both families. Four size-related traits, including shell length (SL, shell height (SH, shell width (SW and total weight (TW were measured for quantitative trait loci (QTL analysis. Three significant and six suggestive QTL were detected on five LGs. Among the three significant QTL, two (qSW-10 and qTW-10, controlling SW and TW, respectively were mapped on the same region near marker AiAD121 on LG10 and explained 20.5% and 27.7% of the phenotypic variance, while the third (qSH-7, controlling SH was located on LG7 and accounted for 15.8% of the phenotypic variance. Six suggestive QTL were detected on four different LGs. The linkage map and size-related QTL obtained in this study may facilitate marker-assisted selection (MAS in bay scallop.

  5. 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...

  6. Comparative Analysis of Eubacterial DNA Polymerase Ⅲ Alpha Subunits

    Institute of Scientific and Technical Information of China (English)

    Xiao-Qian Zhao; Jian-Fei Hu; Jun Yu

    2006-01-01

    DNA polymerase Ⅲ is one of the five eubacterial DNA polymerases that is responsible for the replication of DNA duplex. Among the ten subunits of the DNA polymerase Ⅲ core enzyme, the alpha subunit catalyzes the reaction for polymerizing both DNA strands. In this study, we extracted genomic sequences of the alpha subunit from 159 sequenced eubacterial genomes, and carried out sequencebased phylogenetic and structural analyses. We found that all eubacterial genomes have one or more alpha subunits, which form either homodimers or heterodimers.Phylogenetic and domain structural analyses as well as copy number variations of the alpha subunit in each bacterium indicate the classification of alpha subunit into four basic groups: polC, dnaE1, dnaE2, and dnaE3. This classification is of essence in genome composition analysis. We also consolidated the naming convention to avoid further confusion in gene annotations.

  7. Analysis of Translesion DNA Synthesis by the Mitochondrial DNA Polymerase γ.

    Science.gov (United States)

    Copeland, William C; Kasiviswanathan, Rajesh; Longley, Matthew J

    2016-01-01

    Mitochondrial DNA is replicated by the nuclear-encoded DNA polymerase γ (pol γ) which is composed of a single 140 kDa catalytic subunit and a dimeric 55 kDa accessory subunit. Mitochondrial DNA is vulnerable to various forms of damage, including several types of oxidative lesions, UV-induced photoproducts, chemical adducts from environmental sources, as well as alkylation and inter-strand cross-links from chemotherapy agents. Although many of these lesions block DNA replication, pol γ can bypass some lesions by nucleotide incorporation opposite a template lesion and further extension of the DNA primer past the lesion. This process of translesion synthesis (TLS) by pol γ can occur in either an error-free or an error-prone manner. Assessment of TLS requires extensive analysis of oligonucleotide substrates and replication products by denaturing polyacrylamide sequencing gels. This chapter presents protocols for the analysis of translesion DNA synthesis.

  8. Analysis of Translesion DNA Synthesis by the Mitochondrial DNA Polymerase γ

    Science.gov (United States)

    Copeland, William C.; Kasiviswanathan, Rajesh; Longley, Matthew J.

    2016-01-01

    Summary Mitochondrial DNA is replicated by the nuclear encoded DNA polymerase γ (pol γ) which is composed of a single 140 kDa catalytic subunit and a dimeric 55 kDa accessory subunit. Mitochondrial DNA is vulnerable to various forms of damage, including several types of oxidative lesions, UV-induced photoproducts, chemical adducts from environmental sources, as well as alkylation and inter-strand crosslinks from chemotherapy agents. Although many of these lesions block DNA replication, Pol γ can bypass some lesions by nucleotide incorporation opposite a template lesion and further extension of the DNA primer past the lesion. This process of translesion synthesis (TLS) by Pol γ can occur in either an error-free or an error-prone manner. Assessment of TLS requires extensive analysis of oligonucleotide substrates and replication products by denaturing polyacrylamide sequencing gels. This chapter presents protocols for the analysis of translesion DNA synthesis. PMID:26530671

  9. Urban DNA: Morphogenetic Analysis of Urban Pattern

    Directory of Open Access Journals (Sweden)

    H. Serdar Kaya

    2017-06-01

    Full Text Available Urban pattern is the result of a dynamic transformation process, which can follow two different trajectories: planned interventions generally produces clear geometrical patterns in large areas, however, unplanned transformation process needs more time and has relatively smaller and partial effects on the urban pattern but creates more complex urban patterns. Highly complex spatial structure of urban pattern governed by local and global forces should be analyzed via advanced methods that corresponds the complexity of the pattern. Analyses of the dynamic structure of the multidimensional urban system shows the necessity of using advanced methods and several parameters together. The aim of this paper is developing a new method to analyze and represent highly complex urban pattern via evaluating geometrical, topological, and mathematical parameters to evaluate essential characteristics of cities. Physical space is analyzed by ‘geometrical parameters’, ‘topological parameters’, ‘parameters related to use and perception’ and ‘parameters related to complexity’. Calculation results gives two main information about urban structure: Firstly, values gives information about spatial characteristics and diversity of urban pattern. Secondly, the spatial distribution map of changing urban pattern reflects the unique structure of settlements, which resembles DNA of living creatures. In this paper, Istanbul was selected as case study area because of the rich historical background and dynamic urban growth process resulting various types of settlements including historical settlements, old villages, unplanned development, squatter areas and gated communities with different densities. As the proposed model shows essential morphological characteristics of urban pattern as a morphological DNA, outputs of this model has a potential to be used in different areas such as comparative analysis of geometrically different cities, analyzing irregularities in

  10. 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...

  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. 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.

  14. Extracting DNA from submerged pine wood.

    Science.gov (United States)

    Reynolds, M Megan; Williams, Claire G

    2004-10-01

    A DNA extraction protocol for submerged pine logs was developed with the following properties: (i) high molecular weight DNA, (ii) PCR amplification of chloroplast and nuclear sequences, and (iii) high sequence homology to voucher pine specimens. The DNA extraction protocol was modified from a cetyltrimehtylammonium bromide (CTAB) protocol by adding stringent electrophoretic purification, proteinase K, RNAse, polyvinyl pyrrolidone (PVP), and Gene Releaser. Chloroplast rbcL (ribulose-1,5-bisphosphate carboxylase) could be amplified. Nuclear ribosomal sequences had >95% homology to Pinus taeda and Pinus palustris. Microsatellite polymorphism for PtTX2082 matched 2 of 14 known P. taeda alleles. Our results show DNA analysis for submerged conifer wood is feasible.

  15. Polymorphic microsatellites of analysis in cultivars of taro Análise polimórfica por microssatélites em cultivares de taro

    Directory of Open Access Journals (Sweden)

    Raquel SC Nunes

    2012-03-01

    Full Text Available Taro (Colocasia esculenta is a tuberous plant belonging to the Araceae family whose tuber is the 14th most consumed food crop in the world. Characterized as an unconventional vegetable, taro is grown in Brazil as a subsistence crop, but in recent years began to gain commercial importance, especially in the states of Espirito Santo, Minas Gerais and Rio de Janeiro. To avoid loss of genetic diversity of the local varieties traditionally grown in Brazil a core collection for taro germplasm has been developed by the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper. The aim of this study was to perform a molecular characterization of the seven regional core collections. Genetic diversity of the cultivars was investigated by using SSR (Simple Sequence Repeats polymorphisms, in seven loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 and Xuqtem110. Genetic diversity of the cultivars, based on the seven microsatellite alleles, was evaluated by using the software GelCompar II, showed that the loci Xuqtem73, Xuqtem88 and Xuqtem110 were the most informative, featuring 7, 10 and 8 alleles, respectively, a percentage of cultivars with polymorphic alleles of 85, 57 and 100% and identical PIC of 0.91. Based on Xuqtem110 locus analysis, the seven cultivars were grouped in two clusters. Chinês Regional Incaper cultivar was originated from Chinês cultivar which originated the São Bento cultivar, corroborating previous results. Macaquinho and Chinês cultivars were shown to be the primitive ones originating the allelic collections found in the states of Mato Grosso do Sul and Espirito Santo.O taro (Colocasia esculenta é uma hortaliça da família Araceae cujo rizoma é o décimo quarto alimento vegetal mais consumido no mundo. Caracterizado como uma hortaliça não convencional, o taro é cultivado no Brasil como uma cultura de subsistência, mas nos últimos anos começou a ser

  16. 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.

  17. Analysis of the Framework of Microsoft DNA

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Microsoft DNA(Distributed interNet Application) has p rovided a effective framework of combination PC with the Internet perfectly; In addition, this open framework hase also given the integration of multilingual co mponents a strong managing platform. This article has deeply analysed the main technologys of Microsoft DNA, involve COM basic technology, framework of DNA, Microfost UDA(Universal Data Access),com ponent management with COM+, asynchronous communication with MSMQ(M icrosoft Message Queue). In...

  18. Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA.

    Science.gov (United States)

    Atanesyan, Lilit; Steenkamer, Maryvonne J; Horstman, Anja; Moelans, Cathy B; Schouten, Jan P; Savola, Suvi P

    2017-01-01

    Molecular genetic analysis of formalin-fixed, paraffin-embedded (FFPE) tissues is of great importance both for research and diagnostics. Multiplex ligation-dependent probe amplification (MLPA) is a widely used technique for gene copy number determination, and it has been successfully used for FFPE tissue-extracted DNA analysis. However, there have been no studies addressing the effect of tissue fixation procedures and DNA extraction methods on MLPA. This study therefore focuses on selecting optimal preanalytic conditions such as FFPE tissue preparation conditions and DNA extraction methods. Healthy tissues were fixed in buffered or nonbuffered formalin for 1 hour, 12 to 24 hours, or 48 to 60 hours at 4 °C or at room temperature. DNA extracted from differently fixed and subsequently paraffin-embedded tissues was used for MLPA. Four commercial DNA extraction kits and one in-house method were compared. Tissues fixed for 12 to 24 hours in buffered formalin at room temperature produced DNA with the most optimal quality for MLPA. The in-house FFPE DNA extraction method was shown to perform as efficient as or even superior to other methods in terms of suitability for MLPA, time and cost-efficiency, and ease of performance. FFPE-extracted DNA is well suitable for MLPA analysis, given that optimal tissue fixation and DNA extraction methods are chosen.

  19. DNA analysis by single molecule stretching in nanofluidic biochips

    DEFF Research Database (Denmark)

    Abad, E.; Juarros, A.; Retolaza, A.

    2011-01-01

    Stretching single DNA molecules by confinement in nanofluidic channels has attracted a great interest during the last few years as a DNA analysis tool. We have designed and fabricated a sealed micro/nanofluidic device for DNA stretching applications, based on the use of the high throughput Nano......-DNA stained with the fluorescent dye YOYO-1 were stretched in the nanochannel array and the experimental results were analysed to determine the extension factor of the DNA in the chip and the geometrical average of the nanochannel inner diameter. The determination of the extension ratio of the chip provides...

  20. 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...

  1. 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...

  2. Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The archaeological site of Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. 14C analysis showed that this cemetery was used from 217 B.C. to 283 A.D.Ancient DNA was analyzed by 364 bp of the mitochondrial DNA hypervariable region Ⅰ (mtDNA HVR-Ⅰ), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.

  3. Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

    Directory of Open Access Journals (Sweden)

    Biswas-Fiss Esther E

    2012-06-01

    Full Text Available Abstract Background Single-stranded DNA binding proteins (SSB are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. Results We have cloned and purified SSB from Bacillus anthracis (SSBBA. In the absence of DNA, at concentrations ≤100 μg/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. Conclusions Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.

  4. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing.

    Science.gov (United States)

    Kim, Keun-Sik; Noh, Choong Hwan; Moon, Shin-Joo; Han, Seung-Hee; Bang, In-Chul

    2016-06-01

    Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus).

    Science.gov (United States)

    Jaeger, Collin P; Duvall, Melvin R; Swanson, Bradley J; Phillips, Christopher A; Dreslik, Michael J; Baker, Sarah J; King, Richard B

    2016-06-01

    Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.

  7. 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.

  8. 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.

  9. 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.

  10. The value of DNA paternity identification in beef cattle: examples from Nevada's free-range ranches.

    Science.gov (United States)

    Gomez-Raya, L; Priest, K; Rauw, W M; Okomo-Adhiambo, M; Thain, D; Bruce, B; Rink, A; Torell, R; Grellman, L; Narayanan, R; Beattie, C W

    2008-01-01

    The feasibility and economic value of DNA paternity identification were investigated and illustrated using Nevada beef cattle operations. A panel of 15 microsatellites was genotyped in 2,196 animals from 8 ranches with a total of 31,571 genotypes. Probabilities of exclusion for each marker within ranch and across ranches were computed. Joint probabilities of exclusion for the 15 microsatellites were also determined, resulting in values over 0.99 for any individual ranch and across ranches. Dropping 1 or 2 microsatellites with the lowest probabilities of exclusion resulted in joint probabilities greater than 0.99 and with marginal reduction compared with the probabilities with 15 microsatellites. Formulas for benefit-cost analysis for a DNA paternity identification program in beef cattle were derived. Genotyping 15 microsatellites with 20 calves per sire resulted in benefits of $1.71 and $2.44 per dollar invested at bull culling rates of 0.20 and 0.30, respectively. The breakpoints for the program to be profitable occurred when the ratio of the price of 1 kg of calf liveweight over the cost of genotyping 1 microsatellite was greater than 1.1 for a bull culling rate of 0.30. Benefit-cost analysis was also derived under incomplete DNA paternity identification using a lower number of DNA markers than necessary to achieve joint probabilities of exclusion of 0.99. Approximately a 20% increase in the benefit-cost ratio was achieved using 10 vs. 12 microsatellites with incomplete paternity identification. The greater the number of bulls in the operation, the lower the benefit-cost ratio of the paternity testing program. Low probabilities of exclusion and a high number of bulls in the beef operation reduced the benefit-cost ratio dramatically. The DNA paternity identification programs are feasible and may be profitable for free-range beef cattle operations.

  11. 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