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Sample records for rapd multilocus phenotypes

  1. RAPD

    African Journals Online (AJOL)

    ufuoma

    2013-09-11

    Sep 11, 2013 ... column of individual fish with the aid of hypodermal needle. The drawn blood were ... Abbreviations: RAPD-DNA, Random amplified polymorphic deoxyribonucleic acid-polymerase chain reaction; PIC, polymorphic information content; RMS ..... lignin degrading Bacteria from the soil. J. Appl. Sci. Res.

  2. RAPD

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-18

    Aug 18, 2009 ... Full Length Research Paper. Differentiation of Lactobacillus-probiotic strains by ... Key words: Lactobacillus, RAPD analysis, differentiation. INTRODUCTION. The random amplified polymorphic DNA ..... co-efficient, follow by cluster analysis of the pairwise distance matrix among molecular profiles using the ...

  3. Delineation of the species Haemophilus influenzae by phenotype, multilocus sequence phylogeny, and detection of marker genes

    DEFF Research Database (Denmark)

    Nørskov-Lauritsen, Niels; Overballe, MD; Kilian, Mogens

    2009-01-01

    branching cluster, intermingled with strains of "H. intermedius" and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make...... genospecies biotype IV, and the never formally validated species "Haemophilus intermedius". Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene...

  4. Genetic variation of some hawthorn species based on phenotypic characteristics and RAPD marker

    Directory of Open Access Journals (Sweden)

    Javad Erfani-Moghadam

    2016-03-01

    Full Text Available Hawthorn (Crataegus spp. is an important forest fruit species in Iran. Genetic variability among some genotypes of hawthorn was investigated using morphological traits and random amplified polymorphic DNA (RAPD marker. The collected genotypes belonged to four species of Crataegus genus. High variability among genotypes was found for most of the traits. Results from the principal component analysis (PCA indicated that 85.05% of the observed variability was accounted by the first five components. The first two components explained about 55.24% of the total achieved variability. In PCA, fruit weight, fruit length, fruit diameter, fruit moisture, fruit dry matter, leaf length, leaf area, leaf width, number of leaves per node, seed weight and seed length were predominant in the first two components, indicating that they were useful for the assessment of hawthorn germplasm characterization. A total of 58 polymorphic bands were produced with 10 RAPD primers. The bands' sizes ranged from 180 to 2700 bp. The number of the observed polymorphic bands for each primer ranged from 4 to 8, with an average of 5.8 alleles per locus. The polymorphism information content was observed to be the highest (0.79 in the Oligo_32 locus, whereas the Oligo_339 locus had the lowest value of 0.64, with an average of 0.72, among the RAPD primers. The Jaccard's genetic similarity coefficient ranged from 0.12 to 0.95 among the genotypes. At a similarity coefficient of 0.46, the unweighted pair group method with arithmetic mean (UPGMA cluster analysis divided the genotypes into three major groups.

  5. Phenotypic characterization and random amplified polymorphic DNA (RAPD) analysis of Pasteurella multocida isolated from Korean pigs.

    Science.gov (United States)

    Lee, Ki-Eun; Jeoung, Hye-Young; Lee, Ji-Youn; Lee, Myoung-Heon; Choi, Hwan-Won; Chang, Kyung-Soo; Oh, Young-Hee; An, Dong-Jun

    2012-05-01

    Pasteurella multocida causes various respiratory disease symptoms in pigs, including atrophic rhinitis and pneumonia. In the present study, 69 strains of P. multocida were isolated from 443 pigs with respiratory clinical symptoms at 182 farms located throughout South Korea from 2009 to 2010. A multiplex capsular PCR typing assay revealed that 69 strains of P. multocida isolated in this study had the biosynthetic locus of the capsules of either serogroup A (47 strains, 68.1%) or serogroup D (22 strains, 31.9%). The 22 strains positive for serogroup D-specific primers were divided into four clusters and the 47 strains positive for serogroup A-specific primers were divided into 12 clusters according to the results of Random Amplified Polymorphic DNA (RAPD) analysis. P. multocida strains in the present study were susceptible to most of the antimicrobial agents used. An analysis of antimicrobial resistance and virulence gene pattern combined with RAPD indicated that a certain P. multocida strain appeared to be genetically identical, implying the persistence of the strain within a single farm.

  6. (RAPD) markers

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... Biotechnol. Biotechnol. Equip.14: 16-18. Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I. (2003). Comparative study of the discriminating capacity of RAPD,. AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736-744 ...

  7. Random amplified polymorphic DNA (RAPD) and simple sequence ...

    African Journals Online (AJOL)

    Administrator

    2011-06-06

    Jun 6, 2011 ... of polymorphic bands, average number of alleles per locus, effective .... Materials for DNA isolation were obtained from a set of 5 to 7 plants ..... Among factors that might have contributed to ... Inheritance of RAPDs in F1 hybrids of corn. ... by using cluster analysis of RAPD molecular marker, phenotype and.

  8. EM Adaptive LASSO – A Multilocus Modeling Strategy for Detecting SNPs Associated With Zero-inflated Count Phenotypes

    Directory of Open Access Journals (Sweden)

    Himel eMallick

    2016-03-01

    Full Text Available Count data are increasingly ubiquitous in genetic association studies, where it is possible to observe excess zero counts as compared to what is expected based on standard assumptions. For instance, in rheumatology, data are usually collected in multiple joints within a person or multiple sub-regions of a joint, and it is not uncommon that the phenotypes contain enormous number of zeroes due to the presence of excessive zero counts in majority of patients. Most existing statistical methods assume that the count phenotypes follow one of these four distributions with appropriate dispersion-handling mechanisms: Poisson, Zero-inflated Poisson (ZIP, Negative Binomial, and Zero-inflated Negative Binomial (ZINB. However, little is known about their implications in genetic association studies. Also, there is a relative paucity of literature on their usefulness with respect to model misspecification and variable selection. In this article, we have investigated the performance of several state-of-the-art approaches for handling zero-inflated count data along with a novel penalized regression approach with an adaptive LASSO penalty, by simulating data under a variety of disease models and linkage disequilibrium patterns. By taking into account data-adaptive weights in the estimation procedure, the proposed method provides greater flexibility in multi-SNP modeling of zero-inflated count phenotypes. A fast coordinate descent algorithm nested within an EM (expectation-maximization algorithm is implemented for estimating the model parameters and conducting variable selection simultaneously. Results show that the proposed method has optimal performance in the presence of multicollinearity, as measured by both prediction accuracy and empirical power, which is especially apparent as the sample size increases. Moreover, the Type I error rates become more or less uncontrollable for the competing methods when a model is misspecified, a phenomenon routinely

  9. PCR, RAPD and ARDRA analyses

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... The rhizobia, Sinorhizobium meliloti and Rhizobium sullae, which fix nitrogen in root nodules of alfalfa. (Medicago sativa L.) and sulla (Hedysarum sp.) forage legumes, respectively, were isolated from root nodules and soils from Morocco. We used three PCR-based techniques namely, rep-PCR, RAPD and.

  10. Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens

    Directory of Open Access Journals (Sweden)

    Weronica eEk

    2012-03-01

    Full Text Available Most biological traits are regulated by a complex interplay between genetic and environmental factors. By intercrossing divergent lines, it is possible to identify individual and interacting QTL involved in the genetic architecture of these traits. When the loci have been mapped, alternative strategies are needed for fine-mapping and studying the individual and interactive effects of the QTL in detail. We have previously identified, replicated and fine-mapped a four-locus QTL network that determines nearly half of the eight-fold difference in body-weight at 56 days of age between two divergently selected chicken lines. Here, we describe, to our knowledge, the first generation of a three-locus QTL introgression line in chickens to further study the effect of three of the interacting loci in this network on metabolic phenotypes. Recurrent marker assisted backcrossing was used to simultaneously transfer QTL alleles from the low-weight selected line into the high-weight selected line. Three generations of backcrossing and one generation of intercrossing resulted in an introgression line where all three introgressed QTL and several unlinked and linked control-loci were segregating at nearly expected allele frequencies. We show that marker-based sexing is an efficient method for sexing breeding populations and how intensive selection can be applied using artificial insemination to generate large half-sib families. Based on our empirical observations, we provide recommendations for future introgression-line breeding experiments. In the future, use of this confirmed introgression line will facilitate detailed studies of the effects of genetic interactions on complex traits.

  11. Genetic Diversity Study Among Six Genera of Amaranth Family Found in Malang Based on RAPD Marker

    Directory of Open Access Journals (Sweden)

    Arik Arubil Fatinah

    2012-12-01

    Full Text Available Genera of amaranth family tend to have phenotypic variation partly caused by environmental factor. Phenotypic variation was the result of interaction between genetic and environmental factors. One of molecular markers that is widely used for detecting genetic variation is RAPD. RAPD is used for polymorphism detections and is now possible for identifiying a large number of loci and ascribes unambiguous taxonomic and genetic relationships among different taxa. Members of amaranth family found in Indonesia are Amaranthus, Celosia, Aerva, Alternanthera, Achyranthes, Gomphrena, Salsola, and Iresine. Six genera of which (Amaranthus, Celosia, Aerva, Alternanthera, Achyranthes, and Gomphrena were observed in this study. DNA was extracted from fresh young leaves using Doyle and Doyle’s method with modification in the extraction buffer used. RAPD analyses were carried out with 20 decamer primers from Kit A of Operon Technology. DNA was amplified using master cycler gradient Eppendorf with 35 cycles. RAPD products were separated on 1,5 % agarose gels and detected by staining with ethidium bromide. There were 374 bands generated in 18 random primers. The number of monomorphic bands, polymorphic bands, and the percentage of polymorphism were 21 bands, 353 bands, and 94,38 % respectively. The high number and percentage of polymorphic bands revealed genomic DNA variation. This variation is in accordance with phenotypic variation detected in this experiment. Therefore, it can be concluded that, based on DNA polymorphism detected by RAPD, Amaranth family can be classified into two sub families namely Amaranthoideae and Gomphrenoideae.

  12. RAPD

    African Journals Online (AJOL)

    user

    2011-02-07

    Feb 7, 2011 ... albicans isolates obtained from oral cavity of patients was carried out using random amplified polymorphic DNA ... the skin and mucosal surfaces of the genital and intest- inal tracts as well as the .... isoamyl alcohol (24:24:1).

  13. RAPD

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... The cultures used in the study were obtained from cyanobacterial culture collection of CAS in Botany, University of Madras. Eight strains of non heterocystous, filamentous Oscillatoria spp. and four strains of Lyngbya spp. were used. The details of the cultures used as sources of DNA are presented in Table ...

  14. Characterization of specific random amplified polymorphic (RAPD ...

    African Journals Online (AJOL)

    CAGATCCTTTGCCACACTGA-3') and Udtg4 (5'- CGTACCTGCCAA CATA ACAG - 3') were successfully designed and could be applied as a diagnostic marker in detection of catechin content production of gambier plant. Keywords: Gambier, RAPD, specific ...

  15. The reproducibility of random amplified polymorphic DNA (RAPD ...

    African Journals Online (AJOL)

    RAPD) profiles of Streptococcus thermophilus strains by using the polymerase chain reaction (PCR). Several factors can cause the amplification of false and non reproducible bands in the RAPD profiles. We tested three primers, OPI-02 MOD, ...

  16. Genetic structure of populations of Mugil cephalus using RAPD ...

    African Journals Online (AJOL)

    , Andhra Pradesh and Tamil Nadu in India was studied using randomly amplified polymorphic DNA (RAPD) markers. Five selective primers provided distinct and consistent RAPD profiles in all the four populations. The bands in the range 400 ...

  17. A Novel Multivariate Approach to Phenotyping and Association Mapping of Multi-Locus Gametophytic Self-Incompatibility Reveals S, Z, and Other Loci in a Perennial Ryegrass (Poaceae Population

    Directory of Open Access Journals (Sweden)

    Daniel Thorogood

    2017-08-01

    Full Text Available Self-incompatibility (SI is a mechanism that many flowering plants employ to prevent fertilisation by self- and self-like pollen ensuring heterozygosity and hybrid vigour. Although a number of single locus mechanisms have been characterised in detail, no multi-locus systems have been fully elucidated. Historically, examples of the genetic analysis of multi-locus SI, to make analysis tractable, are either made on the progeny of bi-parental crosses, where the number of alleles at each locus is restricted, or on crosses prepared in such a way that only one of the SI loci segregates. Perennial ryegrass (Lolium perenne L. possesses a well-documented two locus (S and Z gametophytic incompatibility system. A more universal, realistic proof of principle study was conducted in a perennial ryegrass population in which allelic and non-allelic diversity was not artificially restricted. A complex pattern of pollinations from a diallel cross was revealed which could not possibly be interpreted easily per se, even with an already established genetic model. Instead, pollination scores were distilled into principal component scores described as Compatibility Components (CC1-CC3. These were then subjected to a conventional genome-wide association analysis. CC1 associated with markers on linkage groups (LGs 1, 2, 3, and 6, CC2 exclusively with markers in a genomic region on LG 2, and CC3 with markers on LG 1. BLAST alignment with the Brachypodium physical map revealed highly significantly associated markers with peak associations with genes adjacent and four genes away from the chromosomal locations of candidate SI genes, S- and Z-DUF247, respectively. Further significant associations were found in a Brachypodium distachyon chromosome 3 region, having shared synteny with Lolium LG 1, suggesting further SI loci linked to S or extensive micro-re-arrangement of the genome between B. distachyon and L. perenne. Significant associations with gene sequences aligning with

  18. Multilocus DNA barcoding - Species Identification with Multilocus Data.

    Science.gov (United States)

    Liu, Junning; Jiang, Jiamei; Song, Shuli; Tornabene, Luke; Chabarria, Ryan; Naylor, Gavin J P; Li, Chenhong

    2017-11-30

    Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.

  19. Efficiency of random amplified polymorphic DNA (RAPD) and inter ...

    African Journals Online (AJOL)

    Genetic diversity evaluations among 10 canola (Brassica napus) genotypes were determined using RAPD and ISSR markers. The RAPD and ISSR primers with the highest degree of polymorphism were selected. A total of 67 bands of polymorphic RAPD bands were detected out of 77 bands, with an average of 13.4 ...

  20. Application of random amplified polymorphic DNA (RAPD) markers ...

    African Journals Online (AJOL)

    SAM

    2014-06-11

    Jun 11, 2014 ... The random amplified polymorphic DNA (RAPD) technique has been widely applied to identify different varieties of plants for molecular breeding. However, application of RAPD markers to identify parthenogenesis in plants has not been reported. In this investigation, we used pedigree and RAPD markers ...

  1. Application of random amplified polymorphic DNA (RAPD) markers ...

    African Journals Online (AJOL)

    The random amplified polymorphic DNA (RAPD) technique has been widely applied to identify different varieties of plants for molecular breeding. However, application of RAPD markers to identify parthenogenesis in plants has not been reported. In this investigation, we used pedigree and RAPD markers to differentiate ...

  2. RAPD-SCAR marker and genetic relationship analysis of three Demodex species (Acari: Demodicidae).

    Science.gov (United States)

    Zhao, Ya-E; Wu, Li-Ping

    2012-06-01

    For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis.

  3. RAPD profile variation amongst provenances of neem.

    Science.gov (United States)

    Farooqui, N; Ranade, S A; Sane, P V

    1998-08-01

    Neem, described as a tree for solving global problems, is an evergreen, long-lived, multipurpose tree of the tropics with a wide distribution range in India. It is believed to be highly cross-pollinated. Inter-provenance variations have been reported in neem in case of morphological and physiological characters. Yet no reports about the genetic determinism for these variations are available to our knowledge. In order to have an idea about the extent and/or nature of genetic (DNA) variation in neem, the powerful RAPD technique has been employed. RAPD profiles of 34 accessions/provenances of neem were generated with 200 decamer random primers, of which the data from the 49 primers, that resulted in reproducible amplification products, were considered for analysis. Based on the presence/absence of bands, a similarity matrix was computed. Dendrogram was constructed by UPGMA method based on the pairwise similarities amongst the RAPD profiles. The similarities in RAPD profiles amongst the different DNAs was more than that expected due to the cross-pollinated nature of the tree and furthermore, these more-than-expected similarities were not due to random chance. These results suggest that neem may have a narrow genetic base.

  4. RAPD markers demonstrate genetic diversity in Pterocarpus ...

    African Journals Online (AJOL)

    RAPD markers demonstrate genetic diversity in Pterocarpus angolensis from Zimbabwe and Zambia. E Chisha-Kasumu, S Woodward, A Price. Abstract. Understanding the availability, extent and apportionment of genetic variability in natural populations of the southern African savanna tree Pterocarpus angolensis can ...

  5. Random amplified polymorphic DNA (RAPD) marker associated ...

    African Journals Online (AJOL)

    Jane

    2011-06-29

    Jun 29, 2011 ... between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth. INTRODUCTION. Salinity is the major factor limiting plants growth, widely spread and has more ...

  6. Random amplified polymorphic DNA (RAPD) marker associated ...

    African Journals Online (AJOL)

    Jane

    2011-06-29

    Jun 29, 2011 ... bands detected were polymorphic for the provenances of A. senegal and the dissimilarity indices between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth ...

  7. Application of randomly amplified polymorphic DNA (RAPD ...

    African Journals Online (AJOL)

    Jane

    2011-10-10

    Oct 10, 2011 ... Both RAPD markers and PPO genes data were scored as binary system where 1 and 0 indicated the presence or absence of a particular band respectively. Data were analyzed using NT-SYS-pc. (Numerical taxonomy and multivariate analysis system) program. Both AFLP and protein gels were scored as ...

  8. Genetic Diversity and Differentiation of Colletotrichum spp. Isolates Associated with Leguminosae Using Multigene Loci, RAPD and ISSR

    Directory of Open Access Journals (Sweden)

    Farshid Mahmodi

    2014-03-01

    Full Text Available Genetic diversity and differentiation of 50 Colletotrichum spp. isolates from legume crops studied through multigene loci, RAPD and ISSR analysis. DNA sequence comparisons by six genes (ITS, ACT, Tub2, CHS-1, GAPDH, and HIS3 verified species identity of C. truncatum, C. dematium and C. gloeosporiodes and identity C. capsici as a synonym of C. truncatum. Based on the matrix distance analysis of multigene sequences, the Colletotrichum species showed diverse degrees of intera and interspecific divergence (0.0 to 1.4% and (15.5–19.9, respectively. A multilocus molecular phylogenetic analysis clustered Colletotrichum spp. isolates into 3 well-defined clades, representing three distinct species; C. truncatum, C. dematium and C. gloeosporioides. The ISSR and RAPD and cluster analysis exhibited a high degree of variability among different isolates and permitted the grouping of isolates of Colletotrichum spp. into three distinct clusters. Distinct populations of Colletotrichum spp. isolates were genetically in accordance with host specificity and inconsistent with geographical origins. The large population of C. truncatum showed greater amounts of genetic diversity than smaller populations of C. dematium and C. gloeosporioides species. Results of ISSR and RAPD markers were congruent, but the effective maker ratio and the number of private alleles were greater in ISSR markers.

  9. Phenotype and genotype differentiation between flathead grey ...

    African Journals Online (AJOL)

    This study aimed to study the phenotype and genotype differentiation and to compare the amount of differences in phenotype based on morphometric character indices and meristic counts with the amount of differences in genotype based on random amplified polymorphic DNA (RAPD) fingerprinting between two Mugilidae, ...

  10. RAPD analysis reveals genetic variation in different populations of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-09-15

    Sep 15, 2009 ... ginseng (Um et al., 2001). Naugzemys et al. (2007) analyzed Lonicera caerulea germplasm accessions using. RAPD markers and found that RAPD analysis is efficient for genotyping of accessions. DNA polymorphism signifi- cantly exceeds the morphological diversity of the sam- ples. A total of 105 bands ...

  11. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    [Panwar P., Nath M., Yadav V. K. and Kumar A. 2010 Comparative evaluation of genetic diversity using RAPD, SSR and cytochome P450 gene based markers ... sity analysis, the present study aimed to evaluate the relative usefulness of RAPD .... primer ranged from 3 to 15, and size of the products ranged from 300 bp to ...

  12. Identification of sugarcane interspecies hybrids with RAPDs | Zhang ...

    African Journals Online (AJOL)

    Identification of “Saccharum officinarum × Erianthus fulvus” F1 hybrids was performed with random amplified polymorphic DNA (RAPD) analysis. Of 280 RAPD primers used, two primers, OPA-19 and OPN-11, were found to be the most suitable for identification of the hybrids. And the hybrids facticitycheck-out rate was 70.6 ...

  13. DNA Sequences of RAPD Fragments in the Egyptian cotton ...

    African Journals Online (AJOL)

    Random Amplified Polymorphic DNAs (RAPDs) is a DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence. Despite the fact that the RAPD technique has become a very powerful tool and has found use in numerous applications, yet, the nature of ...

  14. The reproducibility of RAPD profiles: Effects of PCR components on RAPD analysis of four centaurium species

    Directory of Open Access Journals (Sweden)

    Skorić Marijana

    2012-01-01

    Full Text Available Random amplified polymorphic DNA (RAPD analysis is a simple and reliable method used to detect DNA polymorphism. Several factors can affect the amplification profiles, thereby causing false bands and non-reproducibility of the assay. In this study, we analyzed the effects of different concentrations of primer, magnesium chloride, template DNA and Taq DNA polymerase to develop and standardize a RAPD protocol for Centaurium species. The optimized PCR reaction mixture included: 50 ng of DNA extracted using a CTbased protocol, 2.5 mM MgCl2, 7.5 pmol primer and 2 U of Taq polymerase in a final volume of 25 μl. Each of the five primers used in experiments (OPB11, OPB15, OPB18, OPF05 and OPH02 generated reproducible and distinguishable fingerprinting patterns of four Centaurium species. The obtained optimized RAPD protocol and the selected primers are useful for our further work in the genetic diversity studies of Centaurium species.

  15. Characterization of Grain Amaranth (Amaranthus spp. Germplasm in South West Nigeria Using Morphological, Nutritional, and Random Amplified Polymorphic DNA (RAPD Analysis

    Directory of Open Access Journals (Sweden)

    Pamela E. Akin-Idowu

    2016-01-01

    Full Text Available Efficient utilization of plant genetic resources for nutrition and crop improvement requires systematic understanding of the important traits. Amaranthus species are distributed worldwide with an interesting diversity of landraces and cultivars whose leaves and seeds are consumed. Despite their potential to enhance food security and economic livelihoods, grain amaranth breeding to improve nutritional quality and adoption by farmers in sub-Saharan Africa is scanty. This study assessed the variation among 29 grain amaranth accessions using 27 phenotypic (10 morphological and 17 nutritional characters and 16 random amplified polymorphic DNA (RAPD primers. Multivariate analysis of phenotypic characters showed the first four principal components contributing 57.53% of observed variability, while cluster analysis yielded five groups at 87.5% similarity coefficient. RAPD primers generated a total of 193 amplicons with an average of 12.06 amplicons per primer, 81% of which were polymorphic. Genetic similarities based on Jaccard’s coefficient ranged from 0.61 to 0.88. The RAPD-based unweighted pair group method with arithmetic mean dendrogram grouped the accessions into nine clusters, with the same species clustering together. RAPD primers distinguished the accessions more effectively than phenotypic markers. Accessions in the different clusters as obtained can be exploited for heterotic gain in desired nutritional traits.

  16. Development and significance of RAPD-SCAR markers for the identification of Litchi chinensis Sonn. by improved RAPD amplification and molecular cloning

    Directory of Open Access Journals (Sweden)

    Jingliang Cheng

    2015-01-01

    Conclusions: This study developed stable SCAR markers for the identification of L. chinensis by the cloning of the improved RAPD fragments. Combining RAPD and SCAR markers provides a simple and reliable tool for the genetic characterization of plant species.

  17. [Molecular characters of Centella asiatica found with RAPD technology].

    Science.gov (United States)

    Ruan, Yuan; Mo, Rong-Hao; Li, Min; Huang, Liu-Qing; Luo, Yu; Li, Xiong-Ying; Zhou, Juan; Wu, Yao-Sheng

    2008-07-01

    To analyze the DNA molecular characters of Centella asiatica with RAPD technology. With the genomic DNA as templates extracted from various source of Centella asiatica samples, optimized RAPD PCR reaction systems had been used. The random promers had been screened to amplify the specific molecular fragments of Centella asiatica. The specific genetic bands of Centella asiatica species from various habitats were established which were highly stable and repeatable and obviously different from those of other families, genuses of plants such as Gynostemma pentaphylum, Tobacco, Cayratia japonica. The developed method of RAPD analysis for the genetic character bands of Centella asiatica could be applied to identify real Centella asiatica from its spurious breed plants. The genetic character bands of Centella asiatica amplified with the RAPD method show high homogeneous in several samples from different habitats.

  18. Conversion of the random amplified polymorphic DNA (RAPD ...

    African Journals Online (AJOL)

    Conversion of the random amplified polymorphic DNA (RAPD) marker UBC#116 linked to Fusarium crown and root rot resistance gene (Frl) into a co-dominant sequence characterized amplified region (SCAR) marker for marker-assisted selection of tomato.

  19. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    Analogy of ISSR and RAPD markers for comparative analysis of genetic diversity among different Jatropha curcas genotypes. S Gupta, M Srivastava, GP Mishra, PK Naik, RS Chauhan, SK Tiwari, M Kumar, R Singh ...

  20. Comparative evaluation of genetic diversity using RAPD, SSR and ...

    Indian Academy of Sciences (India)

    A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt ...

  1. Identification of SSR and RAPD markers associated with QTLs of ...

    African Journals Online (AJOL)

    SERVER

    2008-04-03

    Apr 3, 2008 ... 5′-GAC AGG CCA A-3′. RAPD. 8. 650. 5′-AGT ATG CAG C-3′. RAPD. 9. The alleles of identified QTLs of studied traits trans- mitted to F2 plants and F3 families are from both parents based on their negative and positive additive effects. All of identified QTLs had small additive effects and other.

  2. ( rkers i willow amplif RAPD) n gene (Salix fication )

    African Journals Online (AJOL)

    SAM

    than more marke. Conc. In this g technique sh values. n effective mu that for SSR for RAPD ers. clusion s study, we m howing relations ultiplex ratio. R (4.588) and. (0.876) tha may conclude. Singh et ships between is more for R d similarly ma an that for that molecula al. 3225. 94 Salix. RAPD (6.246 arker index i. SSR (0.751.

  3. Genetic diversity of Palestine landraces of faba bean (Vicia faba) based on RAPD markers.

    Science.gov (United States)

    Basheer-Salimia, R; Shtaya, M; Awad, M; Abdallah, J; Hamdan, Y

    2013-09-03

    Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine.

  4. Avaliação por RAPD de plantas de abacaxizeiro cultivar Smooth Cayenne derivadas do seccionamento do talo e cultura de tecidos Evaluation of pineapple plants cultivar Smooth Cayenne from peduncle division and tissue culture by RAPD

    Directory of Open Access Journals (Sweden)

    MARIA VITÓRIA CECCHETTI GOTTARDI

    2002-04-01

    Full Text Available Foram coletadas, em área comercial da fazenda Córrego dos Bois, município de Canápolis -- MG, plantas de abacaxizeiro cultivar Smooth Cayenne, para serem avaliadas quanto à propagação pelo método do seccionamento do talo e cultura de tecidos, bem como análise por RAPD das mudas decorrentes destes dois processos de propagação. A propagação pelo seccionamento do talo foi eficiente na produção de mudas, tanto em quantidade como em qualidade, em um curto espaço de tempo, além de apresentar a mesma característica genotípica (análise por RAPD das plantas-matrizes de origem. Já no processo de produção de mudas por cultura de tecidos, não foi obtida uma quantidade suficiente de mudas que comprovasse a utilização de uma metodologia mais sofisticada. Além da perda por contaminação em laboratório de 70% do material em estudo, foi necessária a utilização de um longo período, aproximadamente 18 meses, para a obtenção das mudas. Na análise por RAPD das plantas decorrentes deste processo de propagação, foram observados padrões de bandas diferentes em algumas amostras, as quais podem estar relacionadas com uma possível variação somaclonal.Plants of pineapple Smooth Cayenne cultivar were collected from a commercial area, Córrego dos Bois farm, in Canápolis, state of Minas Gerais, to evaluate two different processes of propagation, peduncle division and tissue culture. These same plants were characterized by RAPD analysis. According to the two propagation method, the peduncle division was efficient in seedlings propagation, in quantity as well as in quality, at a short period of time, resulting the same phenotype and genetic characteristics (RAPD analysis from the matrix descent plants. In the tissue culture method, the quantity of seedlings obtained were not good enough that could prove the use of a sophisticated methodology. Besides loosing 70% of the material, it was necessary to expend a long period of time, at

  5. Comparing FTIR and RAPD techniques in the typing of C. albicans in a clinical set-up

    Science.gov (United States)

    Sandt, Christophe L.; Sockalingum, Ganesh D.; Toubas, Dominique; Aubert, Dominique; Lepan, Herve; Lepouse, Claire; Jaussaud, Maryse; Leon, Alain; Pinon, Jean-Michel; Manfait, Michel

    2002-03-01

    Candida albicans is an opportunistic pathogen, generally though to be of endogenous origin, with however reported outbreaks. Epidemilogy of C. albicans has been studied so far by genotypic methods mainly, including the classical RAPD analysis. Albeit powerful, genotypic techniques are expensive, time consuming and complex to implement. FTIR spectroscopy is simple, rapid, inexpensive and an increasingly used technique for the identification of microorganisms. As a phenotypic method, it provides rapid whole cells 'fingerprinting' using few consumables and can detect very subtle differences between strains of the same species. In this study, C. albicans strains isolated from 50 patients from six hospital units were collected and studied by FTIR spectroscopy and RAPD-PCR. Discrimination of strains was computed using classification algorithms on selected features of the spectral data. Results from 10 patients, for whom iterative sampling was possible, are presented and discussed. Emphasis was laid on the reproducibility of dat for strain-level identification. FTIR analysis shows that (a) the C. albicans spectra were different from one patient to another, (b) seven patients exhibit each a homogeneous group while three patients display each two groups of strains. RAPD-PCR and FTIR analyses correlate quite well showing that FTIR spectroscopy could be a potential epidemiological tool in the control of nosocomial fungal infections.

  6. RAPD Analysis for Determination of Components in Herbal Medicine

    Directory of Open Access Journals (Sweden)

    V. M. Shinde

    2007-01-01

    Full Text Available In this study, the RAPD (Random Amplified Polymorphic DNA technique was employed for determination of the components in an Ayurvedic herbal prescription, Rasayana Churna. One-hundred-and-twenty decamer oligonucleotide primers were screened in the RAPD analysis to identify three Ayurvedic medicines, dried stem of Tinospora cordifolia, dried fruit of Emblica officinalis and dried fruit of Tribulus terestris, the Ayurvedic prescription. Primer OPC-6 simultaneously generated three distinct amplicons, each specific to one component. The marker with 600 bp is specific to Tinospora cordifolia; the marker 500 bp is specific to Emblica officinalis and the remaining marker >1000 bp was present in Tribulus terestris. Presence of three herbal medicines was determined when RAPD reaction with OPC-6 was performed. The technique was proved to contribute to the identification of components in Ayurvedic herbal preparation and thus helping to serve as a complementary tool for quality control.

  7. Screening of rapd primer for teak (Tectona grandis

    Directory of Open Access Journals (Sweden)

    Imas Cintamulya

    2016-04-01

    Full Text Available Identification of DNA polymorphisms in teak is important. It is a first step to determine the presence of genetic varia-tion in teak. The information of genetic variation is needed for teak breeding development. RAPD is one of method which can be used for identification of DNA polymorphism. This study aim to get the RAPD primer which can detect the DNA polymorphism in teak. Benefits of this study are provide information about primer which can detect the DNA polymorphism in teak, DNA polymorphism data can be used for genetic variation analysis which needed for teak breeding development. The primers which used in this study shown the DNA polymorphism in teak. The primer are OPF6 (5'-GGGAATTCGG-3 ', OPF8 (5'-GGGATATCGC-3', and OPF11 (5'-TTGGTACCCC-3 '. The highest DNA poly-morphism is shown in DNA which amplified with OPF-8 primer. Keywords: RAPD, Primer, Polymorphism, DNA, Tectona grandis

  8. DGGE-RAPD analysis as a useful tool for cultivar identification ...

    African Journals Online (AJOL)

    DGGE-RAPD) was used to overcome the main drawbacks of RAPD (i.e., the low levels of reproducibility and polymorphism). As a model, six barley cultivars of known origin were tested for RAPD markers using DGGE methodology with 29 ...

  9. Caracterización de tilapia roja (Oreochromis sp. con marcadores moleculares RAPD Characterization of the red tilapia Oreochromis sp. through molecular markers RAPD

    Directory of Open Access Journals (Sweden)

    Julieta Torres Jaramillo

    2010-04-01

    Full Text Available Se utilizó la técnica RAPD (amplificación al azar de ADN polimórfico para el estudio de la diversidad genética de Oreochromis sp. (tilapia roja en cinco piscícolas del Valle del Cauca (Colombia y en la determinación del nivel de introgresión de las especies parentales Oreochromis mosambicus, O. niloticus y O. aureus. Se evaluaron 25 cebadores, ocho fueron polimórficos y se obtuvieron 109 bandas. Los valores de heterocigosidad esperada (0.196 a 0.256 y la estructura genética (Gst = 0.22 para Oreochromis sp. indicaron un elevado grado de polimorfismo y alta estructuración genética. Estos resultados fueron consistente con el Fst = 0.268 (P Random amplified polymorphic DNA (RAPD markers were used to study genetic diversity on red Tilapia (Oreochromis sp. species collected from five fish farms located in the Valle del Cauca, Colombia and to determine the level of introgression from three parental species O. mosambicus, O. niloticus and O. aureus into local Oreochromis populations. from the 25 RAPD primers evaluated, eight were polymorphic and 109 banding patterns were observed, any of them were specific. The expected levels of heterozygosis (0.1964 to 0.2561 and genetic structure (Gst = 0.22 funded for Oreochrosmis sp. indicate high grade of polymorphism and genetic structuring. This results were observed following the analysis of molecular variance [AMOVA] (Fst = 0.268 (P <0.0001 and Multiple correspondence analysis (Gst = 0.040. The values of genetic similarity, the analysis of group, the analysis of multiple correspondence and the level of introgression, indicated that the differences in the introgression levels(P=0.0001 were significant. The low level of observed genetic differentiation among populations, could be the result of fish with the same genetic origin, whereas the high variation within populations can be displayed by handling practices and the pressure of selection to favor commercial phenotypes. The level of introgression

  10. Analysis of DNA polymorphism (RAPD-PCR) and reciprocal effects of geese crossbreeds.

    Science.gov (United States)

    Lisowski, Mirosław; Slawinska, Anna; Dluzniewska, Paulina; Mazanowski, Adam; Bednarczyk, Marek

    2008-01-01

    Commercial geese breeding in Poland is based on two strains of White Italian geese (W11 and W33). The crossbreeds W33 (paternal line) and W11 (maternal line) are distributed in Poland under the commercial brand of White Kołuda goose. However, there are several breeds which are covered by the animal genetic resources conservation program and kept as conservative flocks. These breeds proved invaluable to commercial geese breeding to stabilize body weight, improve muscling and decrease the amount of fat in the carcass of the crossbreeds. Therefore, this study analyzed the reciprocal crossbreeds of White Kołuda geese with the individuals from conservative flocks. DNA polymorphism (RAPD-PCR) of the crossbreeds as well as the phenotypic effect of crossbreeding was evaluated. PCR amplification of five RAPD markers resulted in obtaining 14.25 band/crossbreed group. The genetic similarity of the crossbreeds expressed as band sharing frequency (BS) ranged from 0.44 to 0.97. The direction of crossing of the W33 goose with one of the individuals from the conservative flock strongly affected the genetic similarity estimates. The body weight in the 17th or 24th week of life and the percentage of leg muscle weight in the 24th week of life differed significantly depending on the crossbreed genotype. A similar relationship was demonstrated for egg fertilization and number of nestlings per goose. As the lines were differentiated only by origin of the Z chromosome, the background of the differences in genetic polymorphism and the phenotypic records is hypothesized as (i) the linkage of some production traits with sex chromosomes; (ii) the impact of selection on W33 individuals resulting in lower performance of geese with a W33-derived Z chromosome; (iii) genetic imprinting displayed as the effect of either maternal or paternal origin of the Z chromosome.

  11. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-03

    Dec 3, 2008 ... (PCR) technology has offered new marker systems for diagnosis of genetic diversity in large scale studies (Saiki et al., 1988). Over the last 15 years, polymerase chain reaction technology has led to the development of two simple and quick techniques called random amplified polymorphic DNA (RAPD) and ...

  12. Genetic variation in hawthorn ( Crataegus spp.) using RAPD markers

    African Journals Online (AJOL)

    In this study, we report the use of random amplified polymorphic DNA (RAPD) to determine genetic relationships in the genus Crataegus. Five species, including Crataegus monogyna, Crataegus meyeri, Crataegus aronia, Crataegus pentagyna and Crataegus pontica were chosen from northwest forests of Iran and ...

  13. Screening and characterization a RAPD marker of tobacco brown ...

    African Journals Online (AJOL)

    RAPD) methods were used to analyze F2 individuals of 82-3041 × Yunyan 84 to screen and characterize the molecular marker linked to brown-spot resistant gene. A total of 800 arbitrary decamer oligonucleotide primers were used for RAPD ...

  14. Optimization of DNA isolation and PCR protocol for RAPD analysis ...

    African Journals Online (AJOL)

    Genetic analysis of plants relies on high yields of pure DNA samples. Here we present the optimization of DNA isolation and PCR conditions for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular India containing high levels of polysaccharides, polyphenols and secondary ...

  15. Molecular Characterization of Cultivated Pawpaw (Asimina triloba) Using RAPD Markers

    Science.gov (United States)

    Hongwen Huang; Desmond R. Layne; Thomas L. Kubisiak

    2003-01-01

    Thirty-four extant pawpaw [Asimina triloba (L.) Dunal] cultivars and advanced selections representing a large portion of the gene pool of cultivated pawpaws were investigated using 71 randomly amplified polymorphic DNA (RAPD) markers to establish genetic identities and evaluate genetic relatedness. All 34 cultivated pawpaws were uniquely...

  16. Phylogenetic Relationships in Actinidia as Revealed by RAPD Analysis

    Science.gov (United States)

    Hongwen Huang; Zuozhou Li; Jianqiang Li; Thomas L. Kubiisiak; Desmond R. Lavne

    2002-01-01

    Phylogenetic relationships within the Actinidia were investigated using randomly amplified polymorphic DNA (RAPD) markers. DNAs from 10 taxa, including31 species encompassing all four sections and four series of the traditional subdivisions within the genus, were amplified using 22 preselected 10-mer oligonucieotide primers. A total 204 DNA bands...

  17. Random amplified polymorphic DNA (RAPD) markers reveal genetic ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2013-10-16

    Oct 16, 2013 ... 1Indian Agricultural Research Institute- Regional Station, Kalimpong, West Bengal, India- 734 301. 2Central Agricultural Research Institute, Port .... List of selected informative RAPD primers, their sequence and some information about generated bands in this study. DNA marker. Marker sequence. (5' to 3').

  18. Identification of RAPD marker for the White Backed Plant Hopper ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-03-08

    Mar 8, 2010 ... The experimental material consisted of two parents Gurjari (white backed plant hopper resistant) and. Jaya (white backed plant hopper susceptible) and their F2 progeny. The purpose of the study was the identification of RAPD (Random Amplified Polymorphic DNA) marker for white backed plant hopper.

  19. RAPD-based detection of genomic instability in cucumber plants ...

    African Journals Online (AJOL)

    Random amplified polymorphic DNA (RAPD) markers were used to evaluate genetic stability of regenerants of cucumber plants obtained through somatic embryogenesis. Somatic embryo plants and plants of F1 hybrids, from which they were derived, were compared during weaning, early growth, flowering, fruiting and at ...

  20. ( Quercus spp. ) using random amplified polymorphic DNA (RAPD)

    African Journals Online (AJOL)

    Five species, including: Quercus robur, Quercus macranthera, Quercus infectoria, Quercus magnosquamata and Quercus libani were collected from Northwest forests of Iran and analyzed. Each tree was judged as a genuine type of each species according to the morphological structures. 10 RAPD primers reproducibly and ...

  1. Identification of RAPD markers linked to pubescent trait in cassava ...

    African Journals Online (AJOL)

    The presence of pubescence on the leaves of cassava confers resistance to mealybug, an important pest of cassava in Africa. We therefore, investigated RAPD markers linked to the pubescent trait in four descendants of cassava clone TMS 4(2)1425, namely, diploid (2X) 4(2)1425 pubescent, diploid (2X) 4(2)1425 ...

  2. (Quercus spp.) using random amplified polymorphic DNA (RAPD)

    African Journals Online (AJOL)

    ajl10

    2012-06-05

    Jun 5, 2012 ... Quercus is one of the most important woody genera of the Northern hemisphere and considered as one of the main forest tree species in Iran. In this study, genetic relationships in the genus Quercus, using random amplified polymorphic DNA (RAPD) was examined. Five species, including: Quercus robur,.

  3. Mapping of randomly amplified polymorphic DNA primer (RAPD) on ...

    African Journals Online (AJOL)

    Genet & Botany only

    2012-08-14

    Aug 14, 2012 ... RAPD primers GLC-07 and GLB-11. PCR amplification using primer GLC-07 produced single band of ... PCR amplification profile of the two genetic stocks of common wheat,. NT2A2B and NT1D1B using .... Isolation of recombinants involving barley arms 3HL and 6HL. Theor. Appl. Genet. 83:489-494.

  4. Genetic diversity in rhizobial isolates determined by RAPDs

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Nine soil rhizobia isolated from different field locations were subjected to RAPD analysis to study the diversity. It was found that Rhizobium isolates from Agricultural Research Station - Aliyar Nagar (ALN 7),. Department of Agricultural Microbiology (SOB 1), isolates from TNAU Eastern block field No.36 (EB ...

  5. Genetic diversity in rhizobial isolates determined by RAPDs ...

    African Journals Online (AJOL)

    Nine soil rhizobia isolated from different field locations were subjected to RAPD analysis to study the diversity. It was found that Rhizobium isolates from Agricultural Research Station - Aliyar Nagar (ALN 7), Department of Agricultural Microbiology (SOB 1), isolates from TNAU Eastern block field No.36 (EB 36) and Millet ...

  6. Random amplified polymorphic DNA (RAPD) markers reveal genetic ...

    African Journals Online (AJOL)

    The present study evaluated genetic variability of superior bael genotypes collected from different parts of Andaman Islands, India using fruit characters and random amplified polymorphic DNA (RAPD) markers. Genomic DNA extracted from leaf material using cetyl trimethyl ammonium bromide (CTAB) method was ...

  7. Identification of RAPD markers linked to salinity tolerance in wheat

    African Journals Online (AJOL)

    armghan_shehzad

    tolerance in wheat. Waqas Manzoor Bhutta* and Muhammad Hanif. Department of Botany, Government College University Faisalabad, 38040-Pakistan. Accepted 24 August, 2009 ... Key words: Marker, RAPD, root length, salinity, wheat. INTRODUCTION. Salinity is a ..... to leaf rust resistance in barley. Theor. Appl. Genet.

  8. Optimization of DNA isolation and PCR protocol for RAPD analysis ...

    African Journals Online (AJOL)

    hope&shola

    of DNA isolation and PCR conditions for RAPD analysis of selected medicinal and aromatic plants of conservation concern from Peninsular ... The technique is ideal for isolation of DNA from different plant species and the DNA isolated was used for ..... showed a reading of between 1.6 to 1.7 after calculating the 260/280 nm ...

  9. Identification of random amplified polymorphic DNA (RAPD) marker ...

    African Journals Online (AJOL)

    ... the most effective method for disease control. The application of molecular markers is an efficient way to identify host resistance for breeding programs. In this study, bulked segregant analysis (BSA) was used to search for random amplified polymorphic DNA (RAPD) markers linked to the late blight resistance gene Ph-3, ...

  10. RAPD-based detection of genomic instability in cucumber plants ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-07-20

    Jul 20, 2009 ... RAPD-based detection of genomic instability in cucumber plants derived from somatic embryogenesis. Khaled M. Suliman Elmeer1*, Thomas F. Gallagher2 and Michael J. Hennerty2. 1Plant Tissue Culture Laboratory. Department of Water Research and Agriculture Doha-Qatar. 2School of biology and ...

  11. RAPD analysis of colchicine induced variation of the Dendrobium ...

    African Journals Online (AJOL)

    The highest variation was obtained in regenerates treated with 25 mg/L colchicine, which also exhibited reduced regeneration rates from plbs and mean plantlet fresh weight. RAPD analysis also showed high polymorphism between the mutated regenerant DSB V, and 13 species of the Dendrobium genera, and 13 orchids ...

  12. Marcadores RAPD para detecção de resistência à ferrugem-asiática-da-soja RAPD markers for detection soybean rust resistance

    Directory of Open Access Journals (Sweden)

    Marcelo Marchi Costa

    2008-12-01

    Full Text Available Os objetivos deste trabalho foram confirmar a herança da resistência da PI 459025 (Rpp4 à ferrugem-asiática-da-soja e identificar marcadores moleculares do tipo RAPD, ligados a este gene de resistência, em populações de soja. Pelo cruzamento dos genitores contrastantes PI 459025 x Coodetec 208 obteve-se uma população, cujas populações das gerações F2 e F2:3 foram artificialmente infectadas e avaliadas quanto à reação ao fungo Phakopsora pachyrhizi, pelo tipo de lesão (RB - resistente e TAN - suscetível. Com os resultados da avaliação fenotípica, dois "bulks" foram obtidos com DNA de plantas homozigóticas resistentes e suscetíveis, respectivamente, pela análise de "bulks" segregantes. De 600 iniciadores RAPD aleatórios, foram identificados três com fragmentos polimórficos entre os "bulks" e parentais contrastantes quanto à resistência. Pela análise do qui-quadrado, confirmaram-se: a herança monogênica, com dominância completa quanto à resistência ao patógeno, e a segregação 3:1 para a presença de banda dos três marcadores. Os três marcadores são ligados respectivamente a 5,1, 6,3 e 14,7 cM de distância do loco de resistência, em fase de repulsão no grupo de ligação G, o que foi confirmado pela utilização do marcador microssatélite Satt288. Estes marcadores são promissores na seleção assistida para resistência à ferrugem-asiática-da-soja.The objectives of this work were to confirm the PI 459025 inheritance of resistance (Rpp4 to Asian soybean rust pathogen and to detect RAPD markers linked to this resistance gene in soybean populations. Through the cross of the distint parental lines PI 459025 x Coodetec 208, a population was obtained, whose F2 and F2:3 generations had their populations artificially infected and evaluated for the reaction to Phakopsora pachyrhizi, by lesion type classification (RB - resistant and TAN - susceptible. Using the phenotypic results, the bulked segregant analysis

  13. Multilocus enzyme electrophoresis study of Bacillus sphaericus

    Directory of Open Access Journals (Sweden)

    Viviane Zahner

    1995-02-01

    Full Text Available Multilocus enzyme electrophoresis (MLEE has been used in the study of some Bacillus species. In this work we applied MLEE and numerical analysis in the study of the Bacillus sphaericus group. B. sphaericus can be distinguished from other entomopathogenic Bacillus by a unique allele (NP-4. Within the species, all insect pathogens were recovered in the same phenetic cluster and all of these strains have the same band position (electrophoresis migration on the agarose gel (ADH-2. The entomopathogenic group of B. sphaericus seems to be a clonal population, having two widespread frequent genotypes (zymovar 59 and zymovar 119.

  14. RAPD-based genetic relationships in different Bougainvillea cultivars

    Directory of Open Access Journals (Sweden)

    Richa Srivastava

    2009-01-01

    Full Text Available The present study deals with authenticating existing knowledge about 21 Bougainvillea cultivars comprisingof 9 hybrids and their parents through RAPD analysis. The 19 degenerate primer sets generated 234 bands from which 158(67.5% were polymorphic. The UPGMA based dendrogram divided 21 cultivars into two major groups with Jaccard’ssimilarity coefficient ranging from 0.51 to 0.942. Group A had three cultivars namely Trinidad, Formosa and Dr. H. B. Singhin which Dr. H.B. Singh was confirmed as a hybrid of other two cultivars. Group B was sub divided into 8 clusters. Theparentages of 7 out of 8 hybirds have been confirmed based on clusters. The study concluded that the RAPD technique issuitable for confirmation of parent-hybrid relationship.

  15. Selection processes in a citrus hybrid population using RAPD markers

    Directory of Open Access Journals (Sweden)

    Oliveira Roberto Pedroso de

    2003-01-01

    Full Text Available The objective of this work was to evaluate the processes of selection in a citrus hybrid population using segregation analysis of RAPD markers. The segregation of 123 RAPD markers between 'Cravo' mandarin (Citrus reticulata Blanco and 'Pêra' sweet orange (C. sinensis (L. Osbeck was analysed in a F1 progeny of 94 hybrids. Genetic composition, diversity, heterozygosity, differences in chromosomal structure and the presence of deleterious recessive genes are discussed based on the segregation ratios obtained. A high percentage of markers had a skeweness of the 1:1 expected segregation ratio in the F1 population. Many markers showed a 3:1 segregation ratio in both varieties and 1:3 in 'Pêra' sweet orange, probably due to directional selection processes. The distribution analysis of the frequencies of the segregant markers in a hybrid population is a simple method which allows a better understanding of the genetics of citrus group.

  16. How to test for a relative afferent pupillary defect (RAPD)

    OpenAIRE

    David C Broadway

    2016-01-01

    The 'swinging light test' is used to detect a relative afferent pupil defect (RAPD): a means of detecting differences between the two eyes in how they respond to a light shone in one eye at a time. The test can be very useful for detecting unilateral or asymmetrical disease of the retina or optic nerve (but only optic nerve disease that occurs in front of the optic chiasm).

  17. How to test for a relative afferent pupillary defect (RAPD

    Directory of Open Access Journals (Sweden)

    David C Broadway

    2012-01-01

    Full Text Available The 'swinging light test' is used to detect a relative afferent pupil defect (RAPD: a means of detecting differences between the two eyes in how they respond to a light shone in one eye at a time. The test can be very useful for detecting unilateral or asymmetrical disease of the retina or optic nerve (but only optic nerve disease that occurs in front of the optic chiasm.

  18. Phylogenetic analysis of burkholderia species by multilocus sequence analysis.

    Science.gov (United States)

    Estrada-de los Santos, Paulina; Vinuesa, Pablo; Martínez-Aguilar, Lourdes; Hirsch, Ann M; Caballero-Mellado, Jesús

    2013-07-01

    Burkholderia comprises more than 60 species of environmental, clinical, and agro-biotechnological relevance. Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, lepA, and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia. The two large groups were named A and B, whereas the B. rhizoxinica/B. endofungorum, and B. andropogonis groups consisted of two and one species, respectively. The group A encompasses several plant-associated and saprophytic bacterial species. The group B comprises the B. cepacia complex (opportunistic human pathogens), the B. pseudomallei subgroup, which includes both human and animal pathogens, and an assemblage of plant pathogenic species. The distinct lineages present in Burkholderia suggest that each group might represent a different genus. However, it will be necessary to analyze the full set of Burkholderia species and explore whether enough phenotypic features exist among the different clusters to propose that these groups should be considered separate genera.

  19. Genetic analysis of Aralia cordata Thunb by RAPD.

    Science.gov (United States)

    Qu, Fan; Zhou, Jue; Zhou, Zhou; Li, Huiyu; Burrows, Elizabeth

    2008-10-25

    In the research, genetic analysis of Aralia cordata Thunb. (Araliaceae) was conducted using randomly amplified polymorphism DNA (RAPD). 161 loci were detected with 12 RAPD primers. Percentage of Polymorphic Band (PPB) varied from 34.78% to 63.35%. All the samples were respectively collected from the eight provinces richest in Aralia cordata Thunb resources in China, including Hunan, Yunnan, Zhejiang, Sichuan, Jiangxi, Anhui, Shanxi and Gansu. The results showed that Hunan Province enjoyed the highest level of genetic differentiation and Gansu was the lowest. The total genetic diversity (H(T)) of RAPD, intraspecific genetic diversity (H(S)) and genetic diversity (D(ST)) of the various places was respectively 26.33%, 11.14%, and 49.36%. The differentiation among the species accounted for 98.76% of total genetic diversity (G(ST)). Based on the cluster results of genetic distance, the 8 samples were classified into three groups. It is concluded that Hunan Province enjoyed the highest level of genetic differentiation of Aralia cordata Thunb and Gansu was the lowest, which provides a basis for the taxonomic identification and germplasm resource research of Aralia cordata Thunb in the future.

  20. Serotyping and RAPD profiles of Salmonella enterica isolates from Mauritius.

    Science.gov (United States)

    Khoodoo, M H R; Issack, M I; Jaufeerally-Fakim, Y

    2002-01-01

    The genus Salmonella is a common agent of gastroenteritis in Mauritius, generating more cases of the disease during summer than during winter. The aims of this study were to assess the genetic diversity of isolates of Salmonella enterica by RAPD fingerprinting, and to establish the relationship between human and chicken isolates. Twenty-six isolates were obtained from hospital laboratories and commercial poultry producers locally. The RAPD profiles, biochemical and serological analyses showed that two of the chicken isolates were mistakenly identified as Salmonella. The genetic diversity of the remaining 24 isolates (five chicken and 19 human), confirmed as Salmonella, was analysed using four arbitrary primers, OPA-10, OPR-03, OPI-06 and OPJ-09, chosen from an initial set of 10 decamers. Seventy RAPD markers were generated in four individual DNA profiles. Cluster analysis (UPGMA) performed using the NTSYS-pc V 1.8 computer software, confirmed that some strains of Salmonella isolated from chicken were genetically similar to those isolated from humans. Furthermore, a 1 kbp band amplified using primer OPA-10 was specific for the Salmonella genus as it was not amplified in any of the control bacteria.

  1. Genetic Variability of the Tomato Leaf Miner (Tuta absoluta Meirick; Lepidoptera: Gelechiidae, in Tunisia, Inferred from RAPD-PCR Variabilidad Genética del Minador de Hojas de Tomate (Tuta absoluta Meyrick; Lepidoptera: Gelechiidae en Túnez desde RAPD-PCR

    Directory of Open Access Journals (Sweden)

    Asma Bettaibi

    2012-06-01

    Full Text Available The tomato leaf miner Tuta absoluta Meyrick has invaded tomato (Solanum lycopersicum L. crop in Tunisia since 2008 and is representing today a major threat to the production of this crop. In this study, we used the Randomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR technology to assess the genetic variability within and among seven populations of T. absoluta, collected on tomato from different regions in Tunisia. Using five RAPD-PCR primers and 108 individuals, 140 polymorphic fragments were recorded. From 335 different RAPD phenotypes generated, 71 were redundant and 264 unique to a specific population. The genetic structure of T. absoluta was investigated using analysis of molecular variance (AMOVA, genetic distances (Fst and multidimensional scaling (MDS. We detected a high genetic diversity within and among populations in conjunction with a significant differentiation between populations, suggesting that different founder genotypes would have been responsible of the introduction of T. absoluta in Tunisia. The presence of overlapping phenotypes probably indicates migration events between populations, mainly through infested plant material carried by humans.El minador de hojas de tomate Tuta absoluta Meyrick ha invadido el cultivo del tomate (Solanum lycopersicum L. en Túnez desde 2008 y actualmente representa una importante amenaza para su producción. En este estudio usamos la tecnología de ADN polimórfico amplificado al azar-reacción de cadena polimerasa (RAPD-PCR para evaluar la variabilidad genética dentro y entre siete poblaciones de T. absoluta, colectadas desde tomate en diferentes regiones de Túnez. Usando cinco primers RAPD-PCR y 108 individuos, se registraron 140 fragmentos polimórficos. Se generaron 335 fenotipos RAPD diferentes, entre los cuales 71 fueron redundantes y 264 únicos para una población específica. La estructura genética de T. absoluta se investigó usando análisis de varianza molecular

  2. Genetic variation in a population of Bipolaris oryzae based on RAPD ...

    African Journals Online (AJOL)

    Isolates of Bipolaris oryzae were analysed by RAPD techniques to determine the amount of intraspecific genetic variability. In order to do RAPD-PCR, seven primers were applied. At first, DNA of all isolates was isolated, and then DNA was amplified in thermocycler by using seven primers at a thermal program. As the result ...

  3. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  4. Varietal identification of coffee seeds by RAPD technique

    OpenAIRE

    Maria Lúcia Crochemore; Liliane Moreira Nunes; Giselly Aparecida Andrade; Hugo Bruno Correa Molinari; Maria Elizabeth Vasconcellos

    2004-01-01

    This study aimed the identification of cultivars and/or lines of Coffea arabica of commercial interest, using PCR-RAPD markers. The DNA of ground seeds lots of 12 cultivars and/or lines were evaluated with five primers (Operon OPA 01, OPA 04, OPG 11, OPY 16, and OPX 09) were obtained from a selection of 56 primers. The electrophoretic profiles allowed distinction among eight cultivars and/or lines as well as heterogeneity between and within lots of IAPAR59.Classicamente, a identificação de cu...

  5. Empirical Statistical Power for Testing Multilocus Genotypic Effects under Unbalanced Designs Using a Gibbs Sampler

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    Chaeyoung Lee

    2012-11-01

    Full Text Available Epistasis that may explain a large portion of the phenotypic variation for complex economic traits of animals has been ignored in many genetic association studies. A Baysian method was introduced to draw inferences about multilocus genotypic effects based on their marginal posterior distributions by a Gibbs sampler. A simulation study was conducted to provide statistical powers under various unbalanced designs by using this method. Data were simulated by combined designs of number of loci, within genotype variance, and sample size in unbalanced designs with or without null combined genotype cells. Mean empirical statistical power was estimated for testing posterior mean estimate of combined genotype effect. A practical example for obtaining empirical statistical power estimates with a given sample size was provided under unbalanced designs. The empirical statistical powers would be useful for determining an optimal design when interactive associations of multiple loci with complex phenotypes were examined.

  6. Reevaluation of RAPD markers involved in a case of stingray misidentification (Dasyatidae: Dasyatis).

    Science.gov (United States)

    Faria, V V; Rolim, L S; Vaz, L A L; Furtado-Neto, M A A

    2012-10-25

    We investigated a reported case of stingray Dasyatis americana misidentification not detected in a published study using the random amplified polymorphic DNA (RAPD) technique. If the referred specimen (landed by fisheries in Ceará, northeastern Brazil) was misidentified (as Dasyatis centroura) in the field, why did its RAPD data fail to clarify the mistake? Was it due to limitations of RAPD markers or perhaps to a taxonomic issue? Contrary to our initial expectations, neither of these hindered the detection of the misidentification. After reanalyzing the primary genetic data associated with the misidentified specimen (PCR gel photographs and/or matrices of presence/absence of markers for six RAPD primers), we found that the RAPD markers were sufficient to correctly assign the misidentified specimen to its proper species identity. In the original study, the specimen misidentification was neither noticed by the authors nor apparent in the published article due to how their results were interpreted and presented.

  7. Genetic diversity of worldwide Jerusalem artichoke (Helianthus tuberosus) germplasm as revealed by RAPD markers.

    Science.gov (United States)

    Wangsomnuk, P P; Khampa, S; Wangsomnuk, P; Jogloy, S; Mornkham, T; Ruttawat, B; Patanothai, A; Fu, Y B

    2011-12-12

    Jerusalem artichoke (Helianthus tuberosus) is a wild relative of the cultivated sunflower (H. annuus); it is an old tuber crop that has recently received renewed interest. We used RAPD markers to characterize 147 Jerusalem artichoke accessions from nine countries. Thirty RAPD primers were screened; 13 of them detected 357 reproducible RAPD bands, of which 337 were polymorphic. Various diversity analyses revealed several different patterns of RAPD variation. More than 93% of the RAPD variation was found within accessions of a country. Weak genetic differentiation was observed between wild and cultivated accessions. Six groups were detected in this germplasm set. Four ancestral groups were found for the Canadian germplasm. The most genetically distinct accessions were identified. These findings provide useful diversity information for understanding the Jerusalem artichoke gene pool, for conserving Jerusalem artichoke germplasm, and for choosing germplasm for genetic improvement.

  8. Multilocus sequence typing of Staphylococcus aureus with DNA array technology

    NARCIS (Netherlands)

    W.B. van Leeuwen (Willem); C. Jay (Corinne); S.V. Snijders (Susan); N. Durin (Nathalia); B. Lacroix (Bruno); H.A. Verbrugh (Henri); M.C. Enright (Mark); A. Troesch (Alain); A.F. van Belkum (Alex)

    2003-01-01

    textabstractA newly developed oligonucleotide array suited for multilocus sequence typing (MLST) of Staphylococcus aureus strains was analyzed with two strain collections in a two-center study. MLST allele identification for the first strain collection fully agreed with

  9. Multilocus genetics to reconstruct aeromonad evolution

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    Roger Frédéric

    2012-04-01

    Full Text Available Abstract Background Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes. Results The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas. Conclusions Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or “disease specialized” while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been

  10. Genetic Variability in Nicotianatabacum and Nicotiana Species as Revealed by RAPD Markers: 1. Development of the RAPD Procedure

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    del Piano L

    2014-12-01

    Full Text Available At present there is no information about the level of genetic variability in N. tabacum and in the Nicotiana genus as revealed by random amplified polymorphic DNA (RAPD. Such knowledge could be useful for taxonomic and breeding purposes. The aim of this paper is to assess the potential application of the DNA polymorphisms generated by RAPD markers within this genus and in tobacco. As rigorously standardized reaction conditions are required to obtain a reproducible RAPD marker, four rapid DNA extraction methods were compared and several parameters of the reaction conditions for the random polymorphic DNA amplification were analysed and optimized. The DNA of six-week-old leaves of N. tabacum var. Samsun was obtained with the following methods differing in the strategy of purification: the cetyltrimethylammonium bromide (CTAB method, that of Edwards, nucleon phytopure system and the method of Goring. Reproducible amplification profiles were obtained with all the methods except for Edwards'. As regards amplification conditions, the effects of primer-template annealing temperature, of a final extension step, of the number of cycles and of the length of extension time in each cycle were analysed. Moreover, the effects on amplification reaction of the DNA amount, of MgCl2, primer and deoxynucleotide triphosphate (dNTP concentration were evaluated. Then DNA of 12 Nicotiana species and Nicotianatabacum was amplified with primers OPA-01 and OPA-13 which revealed a considerable polymorphism. The same primers used to analyse 36 var. of N. tabacum belonging to different types, showed identical amplification profiles. Further amplification experiments were carried out with only 12 of the tobacco lines; three primers among the 12 assayed revealed one polymorphic fragment each.

  11. Multilocus sequence analysis of Treponema denticola strains of diverse origin

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    Mo Sisu

    2013-02-01

    Full Text Available Abstract Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA to 8.9% (dnaN. Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic

  12. Caracterização molecular de butiazeiro por marcadores RAPD Molecular characterization of Pindo palm by RAPD markers

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    Adrise Medeiros Nunes

    2008-09-01

    Full Text Available O grupo botânico Arecaceae é de extremo interesse por compreender plantas em extinção e por apresentar um grande potencial de exploração econômica. O butiazeiro (Butia capitata (Mart. Becc. ocorre naturalmente no Sul do Brasil. Sua caracterização molecular é de extremo interesse para futuros trabalhos de melhoramento genético. Assim sendo, verificou-se a variabilidade genética existente entre vinte e dois genótipos de butiazeiro da espécie (Butia capitata, pertencentes ao BAG (Banco Ativo de Germoplasma de frutíferas nativas do Centro Agropecuário da Palma - UFPel. Esses genótipos foram analisados usando marcadores do tipo RAPD (Random Amplified Polymorphic DNA. Um total de 136 fragmentos foram obtidos, sendo 77 polimórficos. O primer OPA11 apresentou maior polimorfismo, produzindo 9 perfis diferentes. A análise de agrupamento, realizada pelo método UPGMA, produziu um dendrograma que permitiu a clara separação dos genótipos em dois grupos principais. Verificou-se que, com a técnica de marcadores de RAPD, foi possível obter um perfil molecular único e uma estimativa da variabilidade existente entre os genótipos de butiazeiro avaliados.The study of the botanical group Arecaceae is of extreme interest for evolving several endangered species of plants and for presenting a great potential of economical exploration. The Pindo palm (or wine palm, jelly palm (Butia capitata (Mart. Becc. is natural from the south of Brazil. Its molecular characterization is of extreme interest for future researches of genetic improvement. Since little is known about the variability of the species, the existent genetic variability was verified among twenty-two genotypes of Pindo palm (or wine palm, jelly palm, from BAG (Germoplasm Assets Bank of fruit trees native from the Agricultural Center of the Palma - UFPEL, which were analyzed using markers RAPD (Random Amplified Polymorphic DNA with Operon Technologies' decamers primers. With 21 primers

  13. Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex

    Science.gov (United States)

    Ramachandran, Padmini; Lacher, David W.; Pfeiler, Erika A.

    2013-01-01

    Members of the Lactobacillus acidophilus complex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of the L. acidophilus complex (L. acidophilus, L. amylovorus, L. crispatus, L. gallinarum, L. gasseri, and L. johnsonii) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of the hsp60 gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genes fusA, gpmA, gyrA, gyrB, lepA, pyrG, and recA, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of the L. acidophilus complex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection of Lactobacillus species. PMID:24038697

  14. Population genetic variation in sainfoin (Fabaceae revealed by RAPD markers

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    Houshang NOSRATI

    2012-05-01

    Full Text Available Studies on plants show that populations growing on the stressful environments indicate higher levels of genetic diversity, and that in outcrossing species majority of total genetic variation allocated to within population rather than between populations. We compared the level of genetic variation between populations growing in stressful and normal environments, and measured levels of within- and between population genetic variations in Onobrychis viciifolia L. (Sainfoin, Fabaceae based on RAPDs. Our results show that populations growing on he stressful environment i.e. saline soils indicated either the lowest 0.2466 or highest (0.3186 within-population genetic variation based on Nei’s diversity. That disagrees with Niche-Width Variation Theory, which expects highest genetic diversity within stressful populations. Partitioning the total genetic variation by analysis of molecular variance (AMOVA showed that 89.03% of total genetic diversity allocated to within populations while 10.97% of this variation dedicated to among populations, indicating predominantly outcrossing mode of pollination in sainfoin. The two population pairs growing under similar environmental stresses (cold climate and saline soil showed higher genetic similarity. This may suggest that RAPDs patterns reflex selection rather than random drift.

  15. Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids.

    Science.gov (United States)

    Zheng, Chaozhi; Voorrips, Roeland E; Jansen, Johannes; Hackett, Christine A; Ho, Julie; Bink, Marco C A M

    2016-05-01

    For both plant (e.g., potato) and animal (e.g., salmon) species, unveiling the genetic architecture of complex traits is key to the genetic improvement of polyploids in agriculture. F1 progenies of a biparental cross are often used for quantitative trait loci (QTL) mapping in outcrossing polyploids, where haplotype reconstruction by identifying the parental origins of marker alleles is necessary. In this paper, we build a novel and integrated statistical framework for multilocus haplotype reconstruction in a full-sib tetraploid family from biallelic marker dosage data collected from single-nucleotide polymorphism (SNP) arrays or next-generation sequencing technology given a genetic linkage map. Compared to diploids, in tetraploids, additional complexity needs to be addressed, including double reduction and possible preferential pairing of chromosomes. We divide haplotype reconstruction into two stages: parental linkage phasing for reconstructing the most probable parental haplotypes and ancestral inference for probabilistically reconstructing the offspring haplotypes conditional on the reconstructed parental haplotypes. The simulation studies and the application to real data from potato show that the parental linkage phasing is robust to, and that the subsequent ancestral inference is accurate for, complex chromosome pairing behaviors during meiosis, various marker segregation types, erroneous genetic maps except for long-range disturbances of marker ordering, various amounts of offspring dosage errors (up to ∼20%), and various fractions of missing data in parents and offspring dosages. Copyright © 2016 by the Genetics Society of America.

  16. Can multilocus heterozygosity reveal inbreeding depression?

    Science.gov (United States)

    Syukri, F; Nakajima, T; Nakajima, M

    2016-07-01

    Inbred lines of fish have been widely exploited as model organisms to determine the effect of inbreeding, which is often closely related to fitness such as endurance and productivity compared to morphological traits. Until now, much is unknown about the effects of inbreeding to fish. In the present study, inbred lines of guppies were used to examine the inbreeding effect on morphological traits corresponding to genotype variation. Two strains, called AY and NA1, were selected from the closed culture system. Both strains showed different levels of inbreeding coefficients when compared to microsatellite markers. The AY strain was less inbred as compared to NA1 strain. However, correlation between the standard lengths with multilocus heterozygosity (MLH) at the individual level was observed in the AY, but not in the NA1 strain. This indicated that highly inbred animals have higher similarity in morphological traits as compared to less inbred ones. The inbreeding process showed the importance of heterozygosity, even in laboratory-reared animals. This experiment illustrated the effects of inbreeding towards morphological and genetic changes. ?

  17. Development of RAPD-SCAR markers for different Ganoderma species authentication by improved RAPD amplification and molecular cloning.

    Science.gov (United States)

    Fu, J J; Mei, Z Q; Tania, M; Yang, L Q; Cheng, J L; Khan, M A

    2015-05-25

    The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species.

  18. Multilocus genotyping of Giardia duodenalis in Malaysia.

    Science.gov (United States)

    Huey, Choy Seow; Mahdy, Mohammed A K; Al-Mekhlafi, Hesham M; Nasr, Nabil A; Lim, Yvonne A L; Mahmud, Rohela; Surin, Johari

    2013-07-01

    Giardia duodenalis is considered the most common intestinal parasite in humans worldwide. In Malaysia, many studies have been conducted on the epidemiology of giardiasis. However, there is a scarcity of information on the genetic diversity and the dynamics of transmission of G. duodenalis. The present study was conducted to identify G. duodenalis assemblages and sub-assemblages based on multilocus analysis of the glutamate dehydrogenase (gdh), beta-giardin (bg) and triose phosphate isomerase (tpi) genes. Faecal specimens were collected from 484 Orang Asli children with a mean age of 7 years and examined using light microscopy. Specimens positive for Giardia were subjected to PCR analysis of the three genes and subsequent sequencing in both directions. Sequences were edited and analysed by phylogenetic analysis. G. duodenalis was detected in 17% (84 of 484) of the examined specimens. Among them, 71 were successfully sequenced using at least one locus. Genotyping results showed that 30 (42%) of the isolates belonged to assemblage A, 32 (45%) belonged to assemblage B, while discordant genotype results were observed in 9 specimens. Mixed infections were detected in 43 specimens using a tpi-based assemblage specific protocol. At the sub-assemblages level, isolates belonged to assemblage A were AII. High nucleotide variation found in isolates of assemblage B made subtyping difficult to achieve. The finding of assemblage B and the anthroponotic genotype AII implicates human-to-human transmission as the most possible mode of transmission among Malaysian aborigines. The high polymorphism found in isolates of assemblage B warrants a more defining tool to discriminate assemblage B at the sub-assemblage level. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Genetic structure and variation in the relict populations of Alsophila spinulosa from southern China based on RAPD markers and cpDNA atpB-rbcL sequence data.

    Science.gov (United States)

    Wang, Ting; Su, Ying-juan; Li, Xue-Yan; Zheng, Bo; Chen, Guo-Pei; Zeng, Qing-Lu

    2004-01-01

    RAPD markers and sequences of chloroplast DNA (cpDNA) atpB-rbcL intergenic spacers were used to characterize the pattern of genetic variation and the phylogenetic relationships of the relict populations of Alsophila spinulosa located in Jian Feng Ling (JFL) and Diao Luo Shan (DLS), Hainan, and Tang Lang Shan (TLS), Ding Hu Shan (DHS), and Da Xi Shan (DXS), Guangdong, of southern China. 28 random primers generated 118 bands, out of which 26 (22.03%) were polymorphic loci, distinguishing 17 different RAPD phenotypes. Percentage of polymorphic loci, Shannon phenotypic diversity and Nei's gene diversity comprehensively indicated that JFL possessed the highest diversity, TLS and DHS in intermediate and DLS or DXS the least; the corresponding values of the population appeared correlated with the population size. Differentiation was detected among populations of A. spinulosa (1-Hpop/Hsp=0.7453, GST=0.7763, and phist=0.8145). AMOVA showed that 47.44% of the variance was partitioned among regions (Hainan and Guangdong), 34.01% attributed among populations within regions, whereas only 18.55% occurring within populations. Low level of intra-specific diversity was maintained in A. spinulosa with Shannon diversity and gene diversity merely 0.0560 and 0.0590, repectively. Sequence length of atpB-rbcL intergenic spacer varied from 724 bp to 730 bp. Base composition was with A+T content between 63.17% and 63.70%. 13 haplotypes of atpB-rbcL noncoding spacers were identified. UPGMA dendrogram of RAPD phenotypes, principal components analysis based on RAPD patterns, minimum spanning network and neighbour-joining (NJ) tree established on atpB-rbcL haplotypes consistently suggested the geographical subdivision of populations of A. spinulosa between Hainan and Guangdong. Breeding system and conservation strategy of A. spinulosa was discussed based on the information of population genetic structure and variation.

  20. Invasion and spreading of Cabomba caroliniana revealed by RAPD markers

    Science.gov (United States)

    Jin, Xiaofeng; Ding, Bingyang; Gao, Shuqin; Jiang, Weimei

    2005-12-01

    Applying randomly amplified polymorphic DNA (RAPD), the genetic variation of Cabomba caroliniana Gray (cabomba or fanwort), a new alien plant in China, was analyzed in this paper. Total 143 bands, including 47 polymorphic bands, were amplified from 23 primers in 20 samples. The sampling distance was large, but its genetic diversity was low. The main results were that: (1) Cabomba, which grew and dispersed mainly in fragment, was an abundant and dominant species in freshwater, and its main dispersal mechanism was vegetative reproduction (2) Cabomba was originally introduced into China as an aquarium submerged plant. Somehow, those discarded cabomba became invasive species in the areas of Hangzhou, Shanghai, and Meicheng, and other places. (3) Although the level of genetic diversity in cabomba was low, their rapid dispersion and propagation could seriously harm to local aquatic community. Therefore, specific measure should be used to control cabomba from uncontrolled spreading and damage to local vegetation communities.

  1. Multilocus sequence analysis of the family Halomonadaceae.

    Science.gov (United States)

    de la Haba, Rafael R; Márquez, M Carmen; Papke, R Thane; Ventosa, Antonio

    2012-03-01

    Multilocus sequence analysis (MLSA) protocols have been developed for species circumscription for many taxa. However, at present, no studies based on MLSA have been performed within any moderately halophilic bacterial group. To test the usefulness of MLSA with these kinds of micro-organisms, the family Halomonadaceae, which includes mainly halophilic bacteria, was chosen as a model. This family comprises ten genera with validly published names and 85 species of environmental, biotechnological and clinical interest. In some cases, the phylogenetic relationships between members of this family, based on 16S rRNA gene sequence comparisons, are not clear and a deep phylogenetic analysis using several housekeeping genes seemed appropriate. Here, MLSA was applied using the 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA genes for species of the family Halomonadaceae. Phylogenetic trees based on the individual and concatenated gene sequences revealed that the family Halomonadaceae formed a monophyletic group of micro-organisms within the order Oceanospirillales. With the exception of the genera Halomonas and Modicisalibacter, all other genera within this family were phylogenetically coherent. Five of the six studied genes (16S rRNA, 23S rRNA, gyrB, rpoD and secA) showed a consistent evolutionary history. However, the results obtained with the atpA gene were different; thus, this gene may not be considered useful as an individual gene phylogenetic marker within this family. The phylogenetic methods produced variable results, with those generated from the maximum-likelihood and neighbour-joining algorithms being more similar than those obtained by maximum-parsimony methods. Horizontal gene transfer (HGT) plays an important evolutionary role in the family Halomonadaceae; however, the impact of recombination events in the phylogenetic analysis was minimized by concatenating the six loci, which agreed with the current taxonomic scheme for this family. Finally, the findings of

  2. Molecular characterization of Aspergillus infections in an Iranian educational hospital using RAPD-PCR method

    Directory of Open Access Journals (Sweden)

    Kambiz Diba

    2014-09-01

    Conclusion: The hospital sources for the Aspergillus clinical isolates included air condition and walls. RAPD-PCR analysis can play a trivial role to find the hospital sources of Aspergillus clinical isolates.

  3. Analysis of genetic relationships of Central American and Mexican pines using RAPD markers that distinguish species

    OpenAIRE

    Furman, Burford J.; Grattapaglia, Dario; Dvorak, William S.; O'Malley, David M.

    1997-01-01

    Phylogenetic relationships were inferred for six Central American and Mexican pine species by analysing RAPD marker differences among pooled DNA samples. This population level pooling strategy discounts low-frequency allelic variation within taxa, thus obtaining a ‘cumulative genotype’ to compare among taxa. We used the morphologically based taxonomy of pines as the basis for inference concerning molecular marker divergence. Only RAPD polymorphisms that were repeatable and inte...

  4. Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE) using RAPD Markers

    OpenAIRE

    Luciana do Valle Rego Oliveira; Ricardo Tadeu de Faria; Claudete de Fátima Ruas; Paulo Maurício Ruas; Melissa de Oliveira Santos; Carvalho,Valdemar P.

    2010-01-01

    In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intra...

  5. Risk assessment of cadmium-contaminated soil on plant DNA damage using RAPD and physiological indices.

    Science.gov (United States)

    Liu, Wan; Yang, Y S; Li, P J; Zhou, Q X; Xie, L J; Han, Y P

    2009-01-30

    Impact assessment of contaminants in soil is an important issue in environmental quality study and remediation of contaminated land. A random amplified polymorphic DNA (RAPD) 'fingerprinting' technique was exhibited to detect genotoxin-induced DNA damage of plants from heavy metal contaminated soil. This study compared the effects occurring at molecular and population levels in barley seedlings exposed to cadmium (Cd) contamination in soil. Results indicate that reduction of root growth and increase of total soluble protein level in the root tips of barley seedlings occurred with the ascending Cd concentrations. For the RAPD analyses, nine 10-base pair (bp) random RAPD primers (decamers) with 60-70% GC content were found to produce unique polymorphic band patterns and subsequently were used to produce a total of 129 RAPD fragments of 144-2639 base pair in molecular size in the root tips of control seedlings. Results produced from nine primers indicate that the changes occurring in RAPD profiles of the root tips following Cd treatment included alterations in band intensity as well as gain or loss of bands compared with the control seedlings. New amplified fragments at molecular size from approximately 154 to 2245 bp appeared almost for 10, 20 and 40 mg L(-1) Cd with 9 primers (one-four new polymerase chain reaction, (PCR) products), and the number of missing bands enhanced with the increasing Cd concentration for nine primers. These results suggest that genomic template stability reflecting changes in RAPD profiles were significantly affected and it compared favourably with the traditional indices such as growth and soluble protein level at the above Cd concentrations. The DNA polymorphisms detected by RAPD can be applied as a suitable biomarker assay for detection of the genotoxic effects of Cd stress in soil on plants. As a tool in risk assessment the RAPD assay can be used in characterisation of Cd hazard in soil.

  6. Identification of Some Date Palm (Phoenix dactylifera L.) Cultivars in Saudi Arabia Using RAPD Fingerprints

    OpenAIRE

    A.M. AI-Moshileh; M.I. Motawei; A. AI-Wasel; T. Abdel-Latif

    2004-01-01

    The suitability of randomly amplified polymorphic DNA (RAPD) fingerprints as genetic markers in date palms was tested. Five date palm cultivars (Barbi, Nabtet Ali. Rothanah, Ajwa, and Sokkari) from Saudi well- known dates were subject to DNA fingerprint analysis. From 20 primers tested, only 12 were selected as reproducible, giving 64 bands. The RAPD profiles obtained were successfully used to differentiate the genotypes. Based on the pair-wise comparison of amplification products, the geneti...

  7. Variability analysis of Sukun durian plant (Durio zibethinus) based on RAPD marker

    OpenAIRE

    PARJANTO; SUPRIYADI; ISMI PUJI RUWAIDA

    2009-01-01

    Ruwaida IP, Supriyadi, Parjanto. 2009. Variability analysis of Sukun durian plant (Durio zibethinus) based on RAPD marker. Nusantara Bioscience 1: 84-91.The purpose of the study is to assess the diversity of the durian varieties of Sukun, Sunan, Kani, Monthong, and Petruk; and Sukun durian variety grown in different regions based on RAPD markers. Materials research is durian leaves of Sukun, Sunan, Kani, Monthong and Petruk from Ranukutri Garden Seeds, Karanganyar, and also Sukun durian leaf ...

  8. Genetic diversity analysis of rice (Oryza sativa L.) landraces through RAPD markers

    OpenAIRE

    Alam, M.S.

    2014-01-01

    The molecular marker is a useful tool for assessing genetic variations and resolving cultivar identities. Information on genetic diversity and relationships among rice landraces from Bangladesh is currently very limited. Thirty-five rice genotypes including 33 landraces and 01 HYV of Bangladesh and 1 Indian landrace of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD) technique. For molecular characterization, RAPD markers viz., OPC 03...

  9. Isozyme and RAPD studies in Prosopis glandulosa and P. Velutina (Leguminosae, Mimosoideae

    Directory of Open Access Journals (Sweden)

    Bessega Cecilia

    2000-01-01

    Full Text Available Allozyme and random amplified polymorphic DNA (RAPD techniques have been compared for their usefulness for genetic and taxonomic studies in Prosopis glandulosa and P. velutina populations. Isozymes and RAPDs yielded similarly high estimates of genetic variability. Genetic structure and differentiation were analyzed through non-hierarchical Wright's F DT. For all populations considered, both markers produced low gene flow (Nm 1, in agreement with that expected for conspecific populations. However, in RAPD data the expected reduction in F DT and the increase in Nm were not observed. Correlation between F DT and geographical distance matrices (Mantel test for all populations was significant (P = 0.02 when based on isozymes, but not so (P = 0.33 when based on RAPDs. No significant associations among genetic and geographical or climatic variables were observed. Two isoenzyme systems (GOT and PRX enabled us to distinguish between P. glandulosa and P. velutina, but no diagnostic band for recognition of populations or species studied here were detected by RAPD. However, RAPD markers showed higher values for genetic differentiation among conspecific populations of P. glandulosa and a lower coefficient of variation than those obtained from isozymes.

  10. Detection of genetic variation in Ocimum species using RAPD and ISSR markers.

    Science.gov (United States)

    Patel, Hardik K; Fougat, Ranbir S; Kumar, Sushil; Mistry, Jigar G; Kumar, Mukesh

    2015-10-01

    There is a lack of information on the molecular characterization of Ocimum species and hence, efforts have been made under the present study to characterize 17 Ocimum genotypes belonging to 5 different species (O. basilicum, O. americanum, O. sanctum, O. gratissimum and O. Polystachyon) through random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers. PCR amplification using 20 RAPD primers generated a total of 506 loci, of which 490 (96.47 %) loci were found polymorphic. The PIC value for RAPD ranged from 0.907 (OPF 14) to 0.954 (OPC 11) with an average of 0.937. The ISSR primers generated a total of 238 loci, of them 234 (98.17 %) loci were polymorphic. The PIC value ranged from 0.892 (UBC 808) to 0.943 (ISSR A12) with an average of 0.923. The average Jaccard's similarity coefficient based on RAPD and ISSR analysis was 0.58 and 0.52, respectively. Clustering pattern of dendrogram generated using the pooled RAPD and ISSR data showed all Ocimum genotypes in their respective species groups at a cutoff value of 0.49 and 0.42, respectively. Many unique species-specific alleles were amplified by RAPD and ISSR markers. In both marker systems, a maximum number of unique alleles were observed in O. sanctum. The results of the present investigation provided valid guidelines for collection, conservation and characterization of Ocimum genetic resources.

  11. Comparative assessment of genetic diversity among Indian bamboo genotypes using RAPD and ISSR markers.

    Science.gov (United States)

    Desai, Parth; Gajera, Bhavesh; Mankad, Mounil; Shah, Shikha; Patel, Armi; Patil, Ghanshyam; Narayanan, Subhash; Kumar, Nitish

    2015-08-01

    Bamboo is one of the important plant for pulp, paper and charcoal industries. After China, India is the second largest bamboo reserve in Asia. Around the globe, wide genetic diversity of bamboo is present which serves as the base for selection and improvement. DNA based molecular markers appears to be a striking substitute for systematic assessment of the genetic diversity in conservation and genetic improvement of plants. DNA based molecular markers such as RAPD and ISSR were used to assess the genetic diversity in 13 bamboo genotypes. Total 120 RAPD and 63 ISSR primers were tested, of which only 42 polymorphic primers (30 RAPD and 12 ISSR), gave reproducible amplification profile and were used in this study. 30 RAPD primers yielded total 645 amplified fragments, of which 623 were polymorphic, and 20.76 polymorphic bands per primer were observed across 13 genotypes. 12 ISSR primers produced 246 amplified fragments, of which 241 were polymorphic, and 20.08 polymorphic bands per primer was observed across 13 different genotypes. The Jaccard's coefficient of RAPD, ISSR and pooled RAPD and ISSR dendrograms ranged from 0.26 to 0.83, 0.23 to 0.86 and 0.26 to 0.84 respectively. The present study found the large genetic diversity present between different elite genotypes of bamboo. Such investigation can deliver a well understanding of the available genotypes, which might be further exploited for the paper industry.

  12. Studi Epidemiologi Agen Zoonosis Escherichia coli O157:H7 melalui Analisis Random Amplification of Polymorphic DNA (RAPD

    Directory of Open Access Journals (Sweden)

    I Wayan Suardana

    2012-11-01

    Full Text Available Epidemiological studies of zoonotic agent Escherichia coli O157:H7 have been analyzed pheneticallyand or phylogenetically. In a phenetic classification, micoorganisms are arranged into groups (phena onthe basis of high overall similarity using both phenotypic and genotypic methods without judgementaspect of its ancestry or evolutionary. Due to its importance to epidemiological aspect, the study of geneticvariation of isolates origin from some sources need to be conducted in order to trace the routes of infection.A total of 20 samples obtained from some sources i.e clinically human feces, non-clinically human feces,cattle feces, chicken feces, and beef feces were used in this study. The study was started by confirming allof the isolates using O157 latex agglutination test and H7 antiserum test, followed by genomic DNAanalysis by random amplification of polymorphic DNA /RAPD methods. RAPD results were analyzed using a simple matching coeficient (Ssm and alogorhythm unweighted pair group method using arithmeticaverages (UPGMA programe. Results showed there were range of genetic DNA from local isolates (75.1–99,6% which was almost similar to ATCC 43894 control isolate. The highest similarity (99.6% to ATCC43894 control was showed by SM-7(1 isolate obtained from cattle fecal and KL-68(1, isolate obtainedfrom clinically human fecal. In addition, KL-52(7 obtained from clinically human fecal had high similarity(99.6% to MK-35 isolate obtained from chicken fecal. On the other hand, DS-21(4 and DS-16(2 isolatesthat were obtained from beef had high similarity (84.9% to other isolates including ATCC 43894 controlisolate. The highest similarity of E. coli O157:H7 isolates that were obtained from cattle feces, beef, andchicken feces to human feces isolate indicated that there were both cattle and chicken were potentialreservoirs of the zoonotic agen which can be transmitted to human.

  13. A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

    NARCIS (Netherlands)

    Udayanga, D.; Liu, X.; Crous, P.W.; McKenzie, E.H.C.; Chukeatirote, E.; Hyde, K.D.

    2012-01-01

    The genus Diaporthe (Phomopsis) includes important plant pathogenic fungi with wide host ranges and geographic distributions. In the present study, phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS, and partial

  14. Multilocus analysis of Phoma sclerotioides isolates from Minnesota

    Science.gov (United States)

    Phoma sclerotioides causes brown root rot in alfalfa which reduces winter survival. Regional genotypes occur, but local population structures have not been characterized. The population genetic structure and gene flow within alfalfa fields in Minnesota was inferred using multilocus analysis. Portion...

  15. Comparison of multi-locus enzyme and protein gel electrophoresis ...

    African Journals Online (AJOL)

    Comparison of multi-locus enzyme and protein gel electrophoresis in the discrimination of five Fusarium species isolated from Egyptian cottons. ... resolution in organizing all isolates in their respective species-specific clusters. A low correlations was detected between geographical origin of isolates and genetic diversity.

  16. Sam Karlin and multi-locus population genetics.

    Science.gov (United States)

    Feldman, Marcus W

    2009-06-01

    Between 1967 and 1982, Sam Karlin made fundamental contributions to many areas of deterministic population genetic theory. This remembrance focuses on his work in multi-locus population genetics, primarily on the interaction between genotypic selection and the rate of recombination.

  17. Identification of RAPD markers linked to salinity tolerance in wheat ...

    African Journals Online (AJOL)

    Genetic diversity can be measured by a number of ways, including pedigree, phenotype and allelic diversity at loci controlling phenotypes of interest. A DNA marker for root length in wheat (Triticum aestivum L.) was identified. The individual plants from F2 population segregation for salinity tolerance and the parents (S-24 ...

  18. Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    YUYU SURYASARI POERBA

    2010-07-01

    Full Text Available Poerba YS, Ahmad F (2010 Genetic variability among 18 cultivars of cooking bananas and plantains by RAPD and ISSR markers. Biodiversitas 11: 118-123. This study was done to assess the molecular diversity of 36 accessions (18 cultivars of the plantain and cooking bananas (Musa acuminata x M. balbisiana, AAB, ABB subgroups based on Random amplified polymorphic DNA (RAPD and and Inter Simple Sequence Repeats (ISSR markers and to determine genetic relationships in the bananas. RAPD and ISSR fingerprinting of these banana varieties was carried out by five primers of RAPDs and two primers of ISSRs. RAPD primers produced 63 amplified fragments varying from 250 to 2500 bp in size. 96.82% of the amplification bands were polymorphic. ISSR primers produced 26 amplified fragments varying from 350 bp to 2000 bp in size. The results showed that 92.86% of the amplification bands were polymorphic. The range of genetic distance of 18 cultivars was from 0.06-0.67.

  19. Identification and differentiation of Trichophyton rubrum clinical isolates using PCR-RFLP and RAPD methods.

    Science.gov (United States)

    Hryncewicz-Gwóźdź, A; Jagielski, T; Dobrowolska, A; Szepietowski, J C; Baran, E

    2011-06-01

    Trichophyton rubrum represents the most frequently isolated causative agent of superficial dermatophyte infections. Several genotyping methods have recently been introduced to improve the delineation between pathogenic fungi at both the species and the strain levels. The purpose of this study was to apply selected DNA fingerprinting methods to the identification and strain discrimination of T. rubrum clinical isolates. Fifty-seven isolates from as many tinea patients were subjected to species identification by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis and strain differentiation using a randomly amplified polymorphic DNA (RAPD) method, with two primers designated 1 and 6. Using PCR-RFLP, 55 of the isolates studied were confirmed to be T. rubrum. Among those, a total of 40 and five distinct profiles were obtained by RAPD with primers 1 and 6, respectively. The combination of profiles from both RAPD assays resulted in 47 genotypes and an overall genotypic diversity rate of 85.4%. A dendrogram analysis performed on the profiles generated by RAPD with primer 1 showed most of the isolates (87.3%) to be genetically related. PCR-RFLP serves as a rapid and reliable method for the identification of T. rubrum species, while the RAPD analysis is rather a disadvantageous tool for T. rubrum strain typing.

  20. Strong genetic differentiation among east Atlantic populations of the sword razor shell ( Ensis siliqua) assessed with mtDNA and RAPD markers

    Science.gov (United States)

    Arias, Alberto; Fernández-Moreno, Mercedes; Fernández-Tajes, Juan; Gaspar, Miguel B.; Méndez, Josefina

    2011-03-01

    The sword razor shell Ensis siliqua (Linnaeus, 1758) is a bivalve with a high commercial value being appreciated in fresh and processed markets. However, the genetic studies carried out in populations of E. siliqua are scarce. In this work, the genetic variability and differentiation of the sword razor shell was assessed using PCR-RFLPs of a fragment of the 16S rRNA mitochondrial gene and random amplified polymorphic loci (RAPD) in nine localities from Ireland, Spain, and Portugal. In the 314 individuals examined for the mitochondrial fragment, 12 composite haplotypes were observed; meanwhile, a unique phenotype was observed for each of the 242 individuals analyzed with 61 RAPD loci. Two of the mitochondrial composite haplotypes accounted for the majority of individuals (89.81%) and showed a remarkably disjoint distribution between Irish and Iberian samples, with the exception of Aveiro which exhibited as the most frequent haplotype the same found in Ireland. The level of variability observed for each sample was generally correlated with both types of markers and the results obtained suggest the existence of a strong population differentiation between Irish and Iberian localities, except for the Portuguese sample from Aveiro which is surprisingly closer to Irish individuals, although it is probably highly differentiated.

  1. Diversidade genética de pitayas nativas do cerrado com base em marcadores RAPD Genetic diversity of native pitaya native from brazilian savannas with basis on RAPD markers

    Directory of Open Access Journals (Sweden)

    Keize Pereira Junqueira

    2010-09-01

    naturally vegetate on solid rocky sandstone or quartzite, tree trunks and on rocky fields sand soils at Minas Gerais, Goiás, Distrito Federal, Tocantins, Rio de Janeiro and Bahia, with strong evidences that Brazil central region is the biggest pitayas dispersion center, because of wide phenotypic diversity observed in collected accesses. We had the objective to realize genetic diversity study of 13 pitaya accesses maintained at Embrapa Cerrados germoplasm collection through RAPD (Random Amplified Polymorphic DNA molecular markers. Each access genomic DNA were extracted and fourteen decamer initiators were used to obtain RAPD molecular markers, that were converted in a binary data matrix, from where we estimate genetic distances between accesses and realize grouping and graphic dispersion analysis. 162 RAPD markers were obtained, making 11,57 markers medium per primer. From markers total, 154 (95,06% were polymorphic. Genetic distances varied within 0,088 and 0,848, biggest values observed refer to distance between Unaí, MG access and Seleção Embrapa Cerrados access. The most different access was "Unaí, MG", that showed 0,675 of genetic distance avarege in relation to others accessions. The high genetic distance verified is due to the fact that the referred accesses do not belong to the same species. Pitaya accesses groups had little relation to their geographic origin. The genetic diversity found at brazilian savannas allow to include this biome at pitaya species diversity center, showing good perspectives to studies about this fruit potential.

  2. Identification of metalliferous ecotypes of Cistus ladanifer L. using RAPD markers

    Energy Technology Data Exchange (ETDEWEB)

    Quintela-Sabaris, C.; Fraga, M.I. [Dept. of Botany, Univ. of Santiago de Compostela (Spain); Kidd, P.S. [Dept. of Soil Science and Chemical Agronomy, Univ. of Santiago de Compostela (Spain)

    2005-04-01

    The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures. (orig.)

  3. Identification of metalliferous ecotypes of Cistus ladanifer L. using RAPD markers.

    Science.gov (United States)

    Quintela-Sabarís, Celestino; Kidd, Petra S; Fraga, María Isabel

    2005-01-01

    The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures.

  4. RAPD Analysis and Antibiotic Susceptibility for Mycobacterium tuberculosis Strains Isolated from Different Locations in Egypt

    Directory of Open Access Journals (Sweden)

    Ali, A. M.

    2011-01-01

    Full Text Available The routine identification of mycobacterial strains isolated from patients in different locations in Egypt was confirmed by specific DNA fragment amplification. The susceptibilities of 72 Mycobacterium tuberculosis strains against the four antibiotics used in tuberculosis treatment (Isoniazid, INH; Rifampicin, Rif; Streptomycin, St and Ethambutol, E were examined. Our results indicated that, multi drug resistant tuberculosis (MDR-TB represents about 19.5% of the tested strains, whereas sensitive strains represented 26.4%. The genetic polymorphism of the tested strains was examined using RAPD analysis. Six selected strains represent the different antibiotic susceptibility groups were examined using RAPD fingerprinting. No difference between the strains was recorded using the RFLP analysis of amplified specific fragment. The discrimination power of RAPD analysis was inadequate to clarify the genetic correlation between the tested strains. MDR-TB was approximately double time in 2008 compared with the value in 2007. Most of the new MDRTB was correlated with resident dense population regions.

  5. Genetic diversity characterization of cassava cultivars (Manihot esculenta Crantz.: I RAPD markers

    Directory of Open Access Journals (Sweden)

    Colombo Carlos

    1998-01-01

    Full Text Available RAPD markers were used to investigate the genetic diversity of 31 Brazilian cassava clones. The results were compared with the genetic diversity revealed by botanical descriptors. Both sets of variates revealed identical relationships among the cultivars. Multivariate analysis of genetic similarities placed genotypes destinated for consumption "in nature" in one group, and cultivars useful for flour production in another. Brazil?s abundance of landraces presents a broad dispersion and is consequently an important resource of genetic variability. The botanical descriptors were not able to differentiate thirteen pairs of cultivars compared two-by-two, while only one was not differentiated by RAPD markers. These results showed the power of RAPD markers over botanical descriptors in studying genetic diversity, identifying duplicates, as well as validating, or improving a core collection. The latter is particularly important in this vegetatively propagated crop.

  6. Molecular Characterization of Some Turkish Olive Cultivars Using Random Amplified Polymorphic DNA (RAPD Markers

    Directory of Open Access Journals (Sweden)

    Ergün KAYA

    2015-03-01

    Full Text Available Olive (Olea europea L. is one of the oldest cultivated plants characteristic in the Mediterranean area, where it is the most important oilproducing crop. The cultivated olive (O. europaea L. var. europaea is propagated by cutting or grafting, whereas wild olive (O. europaea L. var. sylvestris is reproduced from seeds. These two olive types are interfertile and have led to a large number of varieties. Morphological descriptions are not entirely reliable, due to numerous synonyms and homonyms in designations, labelling mistakes, the presence of varietal clones, and the uncertain identification methods thus far applied. Molecular markers, as random amplified polymorphic DNA (RAPD markers, are environment-independent and efficient to identify olive varieties and to detect synonymous and homonymous. In this study, fifteen selected RAPD markers are used for determination of relationships among twenty individuals belonging to four important Turkish olive cultivars. Our results showed that RAPD markers can be used to differentiate olive cultivars

  7. Molecular characterization of shiitake medicinal mushroom, Lentinus edodes strains (higher Basidiomycetes) using RAPD and ITS sequencing.

    Science.gov (United States)

    Sharma, Shivani; Khanna, Pardeep Kumar; Kapoor, Shammi

    2014-01-01

    The molecular phylogeny in seven strains of Lentinus edodes was studied based on RAPD and their internal transcribed spacers (ITS) regions. The strains were analyzed by RAPD with 20 arbitrary primers. Fifteen primers were found efficient for the amplification of the genomic DNA. The size of the polymorphic bands were in the range of 100-1000 bp. However, the size of ITS1-2 and ITS1-4 regions varied among the strains from 278 to 575 bp and from 410 to 616 bp, respectively. The higher alignment score of the ITS 1-2 region indicated more variability in the ITS 1-4 region. Thus, on the basis of RAPD-PCR and ITS sequencing it was found that strains LeC and LeI showed a high degree of divergence from all other strains.

  8. Genotoxicity Evaluation of an Urban River on Freshwater Planarian by RAPD Assay.

    Science.gov (United States)

    Zhang, He-Cai; Liu, Tong-Yi; Shi, Chang-Ying; Chen, Guang-Wen; Liu, De-Zeng

    2017-04-01

    The aim of this study was to evaluate the genotoxic potential of an urban river - the Wei River in Xinxiang, China using randomly amplified polymorphic DNA (RAPD) assay in planarians. The results showed that the total number of polymorphic bands and varied bands in RAPD patterns of treated planarians decreased with the water sample site far away from the sewage outlet of a factory. In addition, the genome template stability of treated groups decreased and the degree of the decline was negatively related to the distance between the sample site and the sewage outlet, suggesting that the Wei River water had genotoxicity effects on planarians and strengthening the management of the Wei River was necessary. Furthermore, this work also indicated that RAPD assay in planarians was a very promising test for environmental monitoring studies.

  9. [Genetic monitoring of populations of Matthiola fragrans (Bunge) using RAPD and AFLP analysis].

    Science.gov (United States)

    Khadeeva, N V; Goriunova, S V; Kochumova, A A; Iakovleva, E Iu; Mel'nikova, N V; Zholobova, O O; Korotkov, O I; Kudriavtsev, A M

    2011-01-01

    The possibility of using RAPD and AFLP methods for genetic monitoring of populations of Matthiola fragrans (Bunge), a species included in the Red Book of the USSR, was shown for the first time. An analysis of inter- and intrapopulation and interspecies genome polymorphism was performed. Differences in the genetic structure of Matthiola populations from various geographical collection points were revealed. A simple method of performing RAPD analysis and the great number of unique markers found in each population compared with the AFLP analysis, as well as the good division of populations under statistical treatment, allow us to draw the conclusion that using the RAPD method in genetic monitoring of rare and insufficiently studied species is well founded.

  10. Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India.

    Science.gov (United States)

    Ashraf, Kamran; Ahmad, Altaf; Chaudhary, Anis; Mujeeb, Mohd; Ahmad, Sayeed; Amir, Mohd; Mallick, N

    2014-04-01

    The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard's similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program.

  11. Preparation of genomic DNA for RAPD analysis from thick-walled dormant teliospores of Tilletia species.

    Science.gov (United States)

    Gang, D R; Weber, D J

    1995-07-01

    We describe a method for isolating genomic DNA from teliospores of Tilletia caries (DC) Tul., T. controversa Kuhn and T. foetida (T. laevis) (Wallr.) Liro. for random-amplified polymorphic DNA (RAPD) analysis. DNA analysis of teliospores of covered smut or bunt has been difficult because of the thick wall and the high lipid content of the spores. This method overcomes these problems and yields sufficient quantities of DNA from the three species' teliospores for RAPDs. DNA quality appears to be good with very little degradation. RAPD amplifications of the extracted DNAs are reproducible and produce numerous large molecular weight bands from each individual. This procedure should permit the use of DNA analysis techniques to study species and races of Tilletia as well as fungi with similar spore structure.

  12. Major clades of Agaricales: a multilocus phylogenetic overview.

    Science.gov (United States)

    P. Brandon Matheny; Judd M. Curtis; Valerie Hofstetter; M. Catherine Aime; Jean-Marc Moncalvo; Zai-Wei Ge; Zhu-Liang Yang; Joseph F. Ammirati; Timothy J. Baroni; Neale L. Bougher; Karen W. Lodge Hughes; Richard W. Kerrigan; Michelle T. Seidl; Aanen; Matthew Duur K. DeNitis; Graciela M. Daniele; Dennis E. Desjardin; Bradley R. Kropp; Lorelei L. Norvell; Andrew Parker; Else C. Vellinga; Rytas Vilgalys; David S. Hibbett

    2006-01-01

    An overview of the phylogeny of the Agaricales is presented based on a multilocus analysis of a six-gene region supermatrix. Bayesian analyses of 5611 nucleotide characters of rpb1, rpb1-intron 2, rpb2 and 18S, 25S, and 5.8S ribosomal RNA genes recovered six major clades, which are recognized informally and labeled the Agaricoid, Tricholomatoid, Marasmioid, Pluteoid,...

  13. Genetic similarity among strawberry cultivars assessed by RAPD and ISSR markers

    Directory of Open Access Journals (Sweden)

    Rafael Gustavo Ferreira Morales

    2011-12-01

    Full Text Available Most strawberry (Fragaria × ananassa Duchesne cultivars used in Brazil are developed in other countries, it became clear the need to start the strawberry breeding program in the country. To start a breeding program is necessary the genetic characterization of the germplasm available. Molecular markers are important tools that can be used for this purpose. The objectives of the present study were to assess the genetic similarity among 11 strawberry cultivars using RAPD and ISSR molecular markers and to indicate the possible promising crosses. The DNA of the eleven strawberry cultivars was extracted and amplified by PCR with RAPD and ISSR primers. The DNA fragments were separated in agarose gel for the RAPD markers and in polyacrylamide gel for the ISSR markers. The genetic similarity matrix was estimated by the Jaccard coefficient. Based on this matrix, the cultivars were grouped using the UPGMA method. The dendogram generated by the RAPD markers distributed the cultivars in three groups while the ISSR markers generated two groups. There was no direct relationship between the marker groups when the two types of markers were compared. The grouping proposed by the ISSR markers was more coherent with the origin and the genealogy of the cultivars than that proposed by the RAPD markers, and it can be considered the most efficient method for the study of genetic divergence in strawberry. The most promising crosses, based on the genetic divergence estimated from the RAPD and ISSR molecular data were between the Tudla and Ventana and the Oso Grande and Ventana cultivars, respectively.

  14. Multilocus inference of species trees and DNA barcoding.

    Science.gov (United States)

    Mallo, Diego; Posada, David

    2016-09-05

    The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree-gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

  15. Random amplified polymorphic DNA (RAPD) fingerprints for identification of red meat animal species.

    Science.gov (United States)

    Koh, M C; Lim, C H; Chua, S B; Chew, S T; Phang, S T

    1998-03-01

    The random amplified polymorphic DNA (RAPD) method was used to generate fingerprint patterns for 10 meat species: wild boar, pig, horse, buffalo, beef, venison, dog, cat, rabbit and kangaroo. A total of 29 10-nucleotide primers, with GC contents ranging from 50-80%, were evaluated for their specificity and efficiency. The fingerprint patterns that were generated were found in some cases to be species-specific, i.e. one species could be differentiated from another. The advantages and disadvantages of using RAPD-PCR for the identification of red meat species are also discussed.

  16. Extraction of total DNA and optimization of the RAPD reaction system in Dioscorea opposita Thunb.

    Science.gov (United States)

    Wen, G Q; Li, J; Liu, X H; Zhang, Y S; Wen, S S

    2014-02-28

    Dioscorea opposita Thunb. has been used as health food and herbal medicinal ingredients in traditional Chinese medicine. In this study, the total DNA of D. opposita Thunb. was extracted using an improved cetyltrimethylammonium bromide (CTAB) method, and the extracted DNA was further used for random amplified polymorphic DNA (RAPD) reaction system by design of the L16 (4(4)) orthogonal diagram. The results showed that the improved CTAB method can be used to isolate high-quality and high-concentration DNA, and the optimized protocol can overcome the instability of RAPD reaction system. The knowledge stated here can be used to study the genetic diversity of D. opposita Thunb.

  17. GENETSKA RAZNOLIKOST DIVLJIH I UZGAJANIH RIBA (Labeo calbasu, Hamilton, 1822) S RAPD ANALIZOM GENOMSKE DNA

    OpenAIRE

    Mostafa, M. G.; Ishtiaq Ahmed, A. S.; M. G. Mustafa; M.G. Rabbane; Islam, M. N.; Rafiquzzaman, S. M.

    2009-01-01

    Genetska raznolikost dvaju divljih kalibausa, Labeo calbasu, i jedne mrjestilišne populacije proučavana je pomoću random amplified polymorphic DNA (RAPD) metode. Tri 10–mer nasumična primera (OPA01, OPB02 and OPC03) postigla su ukupno 26 ponovljivih i dosljedno prebrojivih RAPD traka, od kojih je 15 (57,69%) bilo polimorfično (P95), upućujući na visoku razinu genetske varijacije u svim proučavanim populacijama. Od triju populacija, Padma populacija je pokazala relativno nižu razinu genetske r...

  18. RAPD discloses high molecular diversity of Mycobacterium tuberculosis from Michoacan, Mexico.

    Science.gov (United States)

    Guill N-Nepita, A L; Vazquez-Marrufo, G; Blanco-Guillot, F T; Figueroa-Aguilar, G A; Vazquez-Garciduenas, M S

    2013-10-01

    Random amplified polymorphism DNA (RAPD) is an easy, inexpensive technique for the characterization of pathogens in low-income countries. In this study we used RAPD to assess the genetic diversity of a small collection of isolates of mycobacteria from the Mexican state of Michoacan. In contrast with the low annual tuberculosis incidence in Michoacan relative to the national average, we found a high molecular diversity value suggesting high population diversity of M. tuberculosis in the studied region. Our findings justify further typing efforts with other molecular tools such as MIRU-VNTR and spoligotyping.

  19. Analysis of genetic diversity of certain species of Piper using RAPD-based molecular markers.

    Science.gov (United States)

    Chowdhury, Utpal; Tanti, Bhaben; Rethy, Parakkal; Gajurel, Padma Raj

    2014-09-01

    The utility of RAPD markers in assessing genetic diversity and phenetic relationships of six different species of Piper from Northeast India was investigated. Polymerase chain reaction (PCR) with four arbitrary 10-mer oligonucleotide primers applied to the six species produced a total of 195 marker bands, of which, 159 were polymorphic. On average, six RAPD fragments were amplified per reaction. In the UPGMA phenetic dendrogram based on Jaccard's coefficient, the different accessions of Piper showed a high level of genetic variation. This study may be useful in identifying diverse genetic stocks of Piper, which may then be conserved on a priority basis.

  20. Coupling- and repulsion-phase RAPDs for marker-assisted selection of PI 181996 rust resistance in common bean.

    Science.gov (United States)

    Johnson, E; Miklas, P N; Stavely, J R; Martinez-Cruzado, J C

    1995-04-01

    The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20490 tightly linked (no recombinants) in coupling phase and OAE19890 linked in repulsion phase (at 6.2±2.8 cM) to PI 181996 rust resistance. These RAPDs, generated by single decamer primers in the polymerase chain reaction, were identified in near-isogenic bulks of non-segregating resistant and susceptible BC4F2 (NX-040*4/PI 181996) lines. Linkage of the RAPD markers was confirmed by screening 19 BC4F2 and 57 BC4F3 individuals segregating for PI 181996 resistance. Utility of the RAPDs OAC20490 and OAE19890 was investigated in a diverse group of common bean cultivars and lines. All cultivars into which the PI 181996 resistance was introgressed had the RAPD OAC20490. A RAPD similar in size to OAC20490, observed in some susceptible common bean lines, was confirmed by Southern blotting to be homologous to the RAPD OAC20490. Use of the RAPDs OAC20490 and OAE19890 in marker-assisted selection (MAS) is proposed. The coupling-phase RAPD is most useful for MAS of resistant BCnF1individuals during traditional backcross breeding. The repulsion-phase RAPD has greatest utility in MAS of homozygous-resistant individuals in F2 or later-segregating generations.

  1. Evaluation of some walnut genotypes in the west of Iran using fruit characteristics and RAPD marker

    Directory of Open Access Journals (Sweden)

    Nassim Zare-rashnoodi

    2017-11-01

    Full Text Available Persian walnut (Juglans regia L. belongs to the family Juglandaceae is one of the most important nut crops in Iran. In this research, morphometric and genetic variations among some genotypes of Persian walnut collected from different parts of west Iran were evaluated based on nut characteristics and RAPD markers. In the first experiment, 29 traits related to nut and kernel were used to evaluate genetic potential of 119 walnut genotypes. The primary results of fruit morphometric characteristics showed that there is high variability in the some evaluated traits such as fruit shape, nut diameter and Kernel removal from nut in studied genotypes. Also, in the second experiment, the genetic diversity among 50 genotypes of walnut was evaluated using 13 RAPD markers. A total of 87 alleles were produced in the 13 RAPD markers with their sizes ranging from 140 to 2500 bp. The number of observed alleles for each locus ranged from 4 (OPA-18 and OPA-13 to 11 (OPA-09, with an average of 6.46 alleles per locus. Shannon's information index (I value was observed to be highest (3.20 in the OPA-09 locus, while the OPA-13 locus had the lowest value (0.70 with an average of 1.66 among RAPD locus. The Jaccards’ genetic similarity coefficient ranged from 0.08 to 0.79 among genotypes. Finally, our results demonstrate some of these genotypes have been desirable traits and must be conserved as valuable genetic resources, from the perspective of breeding.

  2. Genetic diversity and relationships in mulberry (genus Morus as revealed by RAPD and ISSR marker assays

    Directory of Open Access Journals (Sweden)

    Thangavelu K

    2004-01-01

    Full Text Available Abstract Background The genus Morus, known as mulberry, is a dioecious and cross-pollinating plant that is the sole food for the domesticated silkworm, Bombyx mori. Traditional methods using morphological traits for classification are largely unsuccessful in establishing the diversity and relationships among different mulberry species because of environmental influence on traits of interest. As a more robust alternative, PCR based marker assays including RAPD and ISSR were employed to study the genetic diversity and interrelationships among twelve domesticated and three wild mulberry species. Results RAPD analysis using 19 random primers generated 128 discrete markers ranging from 500–3000 bp in size. One-hundred-nineteen of these were polymorphic (92%, with an average of 6.26 markers per primer. Among these were a few putative species-specific amplification products which could be useful for germplasm classification and introgression studies. The ISSR analysis employed six anchored primers, 4 of which generated 93 polymorphic markers with an average of 23.25 markers per primer. Cluster analysis of RAPD and ISSR data using the WINBOOT package to calculate the Dice coefficient resulted into two clusters, one comprising polyploid wild species and the other with domesticated (mostly diploid species. Conclusion These results suggest that RAPD and ISSR markers are useful for mulberry genetic diversity analysis and germplasm characterization, and that putative species-specific markers may be obtained which can be converted to SCARs after further studies.

  3. Evaluation of RAPD-PCR and protein profile analysis to differentiate ...

    Indian Academy of Sciences (India)

    vibriosis in hatchery reared and commercially farmed pe- naeid shrimps resulting in severe economic losses to shrimp industry in Asia (Lavilla-Pitogo et al. ..... with amplicon sizes ranging from 0.2 to 4.0 kb. Cluster analysis of primers CRA25 and PM3 generated RAPD pro- files separated the isolates at an average similarity ...

  4. Use of the RAPD-PCR fingerprinting and API system for clustering ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... clustering lactic acid bacteria isolated from traditional ... shaped isolates formed five clusters based on numerical analysis of the RAPD-PCR profiles. ..... these isolates are of value in improving the nutritive con- tents and controlling the growth of spoilage and pathogen in diary industry. REFERENCES.

  5. Genetic diversity in natural populations of Jacaranda decurrens Cham. determined using RAPD and AFLP markers

    Directory of Open Access Journals (Sweden)

    Bianca W. Bertoni

    2010-01-01

    Full Text Available Jacaranda decurrens (Bignoniaceae is an endemic species of the Cerrado with validated antitumoral activity. The genetic diversity of six populations of J. decurrens located in the State of São Paulo was determined in this study by using molecular markers for randomly amplified polymorphic DNA (RAPD and amplified fragment length polymorphism (AFLP. Following optimization of the amplification reaction, 10 selected primers generated 78 reproducible RAPD fragments that were mostly (69.2% polymorphic. Two hundred and five reproducible AFLP fragments were generated by using four selected primer combinations; 46.3% of these fragments were polymorphic, indicating a considerable level of genetic diversity. Analysis of molecular variance (AMOVA using these two groups of markers indicated that variability was strongly structured amongst populations. The unweighted pair group method with arithmatic mean (UPGMA and Pearson's correlation coefficient (RAPD -0.16, p = 0.2082; AFLP 0.37, p = 0.1006 between genetic matrices and geographic distances suggested that the population structure followed an island model in which a single population of infinite size gave rise to the current populations of J. decurrens, independently of their spatial position. The results of this study indicate that RAPD and AFLP markers were similarly efficient in measuring the genetic variability amongst natural populations of J. decurrens. These data may be useful for developing strategies for the preservation of this medicinal species in the Cerrado.

  6. Comparison of Manzanilla and wild type olives by RAPD-PCR ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-02-15

    Feb 15, 2010 ... (Aegean Union of Olive and Olive Oil Exporters, 2007). Turkey also has a significant position among countries cultivating olives. The total number of ..... Collins G, Sedgley MA (2004). Molecular linkage map of olive. (Olea europea L.) based on RAPD, microsatellites and SCAR markers. Genome, 47: 26-35.

  7. Cucumber (Cucumis sativus L. relationship analysis using RAPD-PCR and isozyme methods

    Directory of Open Access Journals (Sweden)

    ARIFIN NOOR SUGIHARTO

    2008-04-01

    Full Text Available RAPD-PCR method and isozyme analysis were used to obtain information of genetic relationship among cucumber varieties. Such information is urgently utilized to support plant breeding program of cucumber. Research was done at the Biotechnology Laboratory of Plant Pest and Diseases, Faculty of Agriculture of Brawijaya University, Malang and Molecular Biology Laboratory, Faculty of Matemathic and Natural Sciences of Brawijaya University, Malang. DNA isolation was done using CTAB method by additional NaCl modification. Sixteen primers from operon were employed to amplify DNA genome by RAPD-PCR. Two enzymes, Esterase and AAT were chosen for isozyme analysis. Clad 97 Program was used for analyzing the data and results in data grouping based on proximity value. Cluster analysis based on isozyme data indicated that there was an adequate lower genetic variation in cucumber, where seven of nine tested varieties showed proximity value of 1.00. Eleven of sixteen primers in RAPD-PCR analysis produced DNA bands. Relativity analysis by using RAPD-PCR method showed high enough of genetic variation. Relativity analysis by using both methods showed that variety 07 was the furthermost. The proximity value between varieties 01 and 02 was 0.916667, these varieties have the higest proximity value among all varieties.

  8. RAPD-PCR analysis of cultured type olives in Turkey | Sesli | African ...

    African Journals Online (AJOL)

    The aim of this study was to detect genetic similarities and distances among cultured type olive trees by RAPD-PCR technique. Olives are raised in a high range from the Aegean, Mediterranean, Marmara and Black Sea to Southeast Anatolia regions of Turkey. Olive breeding had a rapid increase in Turkey during recent ...

  9. Genetic analysis of Penthorum chinense Pursh by improved RAPD and ISSR in China

    Directory of Open Access Journals (Sweden)

    Zhiqiang Mei

    2017-11-01

    Conclusions: This study indicated that improved RAPD and ISSR methods are useful tools for evaluating the genetic diversity and characterizing P. chinense. Our findings can provide the theoretical basis for cultivar identification, standardization, and molecular-assisted breeding of P. chinense for medicinal use.

  10. Assessment of genetic diversity in lettuce (Lactuca sativaL.) germplasm using RAPD markers.

    Science.gov (United States)

    Sharma, Shubhangi; Kumar, Pankaj; Gambhir, Geetika; Kumar, Ramesh; Srivastava, D K

    2018-01-01

    The importance of germplasm characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programmes. In the present study, genetic variability and relationships among 25 Lactuca sativa L. genotypes were tested using random amplified polymorphic DNA (RAPD) molecular markers. A total of 45 random decamer oligonucleotide primers were examined to generate RAPD profiles, out of these reproducible patterns were obtained with 22 primers. A total of 87 amplicon were obtained, out of which all were polymorphic and 7 were unique bands. The level of polymorphism across genotypes was 100% as revealed by RAPD. Genetic similarity matrix, based on Jaccard's coefficients ranged from 13.7 to 84.10% indicating a wide genetic base. Dendrogram was constructed by unweighted pair group method with arithmetic averages method. RAPD technology could be useful for identification of different accessions as well as assessing the genetic similarity among different genotypes of lettuce. The study reveals the limited genetic base and the needs to diversify using new sources from the germplasm.

  11. Molecular Analysis of Synedrela Nodiflora (L. Gaertn. Resistance Against Fomesafen using RAPD Markers

    Directory of Open Access Journals (Sweden)

    Murni Dwiati

    2015-01-01

    Based on the RAPD markers used in this study, it can be concluded that genetic distance between susceptible and resistant S. nodiflora is higher than that within susceptible samples supporting our previous morphological and protein data, although genetic variation among susceptible individuals seems to be significantly high.

  12. The PCR based technique RAPD is popular not only because it ...

    African Journals Online (AJOL)

    renu.bhatnagar

    2015-04-01

    Apr 1, 2015 ... markers were employed (1) to detect the genetic diversity and polymorphism among different isolates of. Pseudomonas collected from rhizospheric soil of different locations and (2) to estimate the relative efficiencies of both RAPD and ISSR markers. MATERIALS AND METHODS. Bacterial isolates and ...

  13. RAPD-PCR analysis of cultured type olives in Turkey | Sesli | African ...

    African Journals Online (AJOL)

    In this study, samples were obtained from the Olive Production Research Institute (Manzanilla, Domat, Gemlik and Memecik) and sapling producers in Manisa, Akhisar (Uslu, Edremit). Genomic DNA's were extracted from young leaves and PCR was used generate RAPD bands. Sixty random primers obtained from Operon ...

  14. Genetic relationships in Lens species and parentage determination of their interspecific hybrids using RAPD markers.

    Science.gov (United States)

    Ahmad, M; McNeil, D L; Fautrier, A G; Armstrong, K F; Paterson, A M

    1996-06-01

    Broadening of the genetic base and systematic exploitation of heterosis in cultivated lentils requires reliable information on genetic diversity in the germplasm. The ability of random amplified polymorphic DNA (RAPD) to distinguish among different taxa of Lens was evaluated for several geographically dispersed accessions/cultivars of four diploid Lens species. This study was carried out to assess whether RAPD data can provide additional evidence about the origin of the cultivated lentil and to measure genetic variability in lentil germplasm. Three cultivars of Lens culinaris ssp. culinaris, including one microsperma, and two macrosperma types, and four wild species (L. culinaris ssp. orientalis, L. odemensis and L. nigricans) were evaluated for genetic variability using a set of 1 11-mer and 14 random 10-mer primers. One hundred and fifty-eight reproducible and scorable DNA bands were observed from these primers. Genetic distances between each of the accessions were calculated from simple matching coefficients. Split decomposition analysis of the RAPD data allowed construction of an unrooted tree. This study revealed that (1) the level of intraspecific genetic variation in cultivated lentils is narrower than that in some wild species. (2) L. culinaris ssp. orientalis is the most likely candidate as a progenitor of the cultivated species, (3) L. nigricans accession W6 3222 (unknown) and L. c. ssp. orientalis W6 3244 (Turkey) can be reclassified as species of L. odemensis and (4) transmission of genetic material in Lens interspecific hybrids is genotypically specific, as identified by the RAPD markers in our study.

  15. Marcadores moleculares RAPD e descritores morfológicos na avaliação da diversidade genética de goiabeiras (Psidium guajava L. = RAPD molecular markers and morphological descriptors in the evaluation of genetic diversity of guava (Psidium guajava L.

    Directory of Open Access Journals (Sweden)

    Aroldo Gomes Filho

    2010-10-01

    Full Text Available O conhecimento da variabilidade genética e fenotípica entre diferentes acessos de goiabeiras é importante para se apoiar programas de melhoramento dessa espécie na região Norte Fluminense que carece de novas culturas capazes de gerar renda aos produtores locais. O objetivo deste trabalho foi avaliar a divergência genética entre seis cultivares e 19 acessos de goiabeiras, por meio de marcadores moleculares RAPD e características morfoagronômicas. Foram obtidas 117 marcas polimórficas, utilizando-se 28 iniciadores. Os resultados mostraram uma concordância parcial entre os métodos de agrupamentos estudados, com a formação de 12 grupos. O acesso Vita 3 e o acesso 6 foram os mais divergentes, apresentando distância genética de 0,663. A análise comparativa dos agrupamentos revelou que os marcadores RAPD e os descritores morfológicos foram eficientes para discriminação dos acessos e que houve variabilidade genética potencial para uso em Programa de Melhoramento Genético.The knowledge of the genetic and phenotypic variability among different accessions of guava is important for supporting improvement programs of this specie in northern Rio de Janeiro state, which needs new cultivars able to generate income for local farmers. This work aimed to evaluate the genetic divergence among six cultivars and 19 accessions of guava via RAPD molecular markers and morphologicalcharacteristics. One hundred and seventeen polymorphic markers were obtained from 28 primers. The results showed a partial agreement between the methods of studied groupings, with the formation of 12 groups. The accessions ‘Vita 3’and ‘6’ were the most divergent, showing genetic distance of 0.663. The comparative analysis of groupings showed that RAPD markers and morphological descriptors were effective in discriminating the accessions and to show potentialgenetic variability useful in genetic improvement programs.

  16. Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure

    Science.gov (United States)

    Chen, Hua; Slatkin, Montgomery

    2013-01-01

    It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144−0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

  17. Fast genomic predictions via Bayesian G-BLUP and multilocus models of threshold traits including censored Gaussian data.

    Science.gov (United States)

    Kärkkäinen, Hanni P; Sillanpää, Mikko J

    2013-09-04

    Because of the increased availability of genome-wide sets of molecular markers along with reduced cost of genotyping large samples of individuals, genomic estimated breeding values have become an essential resource in plant and animal breeding. Bayesian methods for breeding value estimation have proven to be accurate and efficient; however, the ever-increasing data sets are placing heavy demands on the parameter estimation algorithms. Although a commendable number of fast estimation algorithms are available for Bayesian models of continuous Gaussian traits, there is a shortage for corresponding models of discrete or censored phenotypes. In this work, we consider a threshold approach of binary, ordinal, and censored Gaussian observations for Bayesian multilocus association models and Bayesian genomic best linear unbiased prediction and present a high-speed generalized expectation maximization algorithm for parameter estimation under these models. We demonstrate our method with simulated and real data. Our example analyses suggest that the use of the extra information present in an ordered categorical or censored Gaussian data set, instead of dichotomizing the data into case-control observations, increases the accuracy of genomic breeding values predicted by Bayesian multilocus association models or by Bayesian genomic best linear unbiased prediction. Furthermore, the example analyses indicate that the correct threshold model is more accurate than the directly used Gaussian model with a censored Gaussian data, while with a binary or an ordinal data the superiority of the threshold model could not be confirmed.

  18. Multilocus Sequence-Based Analysis Delineates a Clonal Population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of Human Origin ▿

    Science.gov (United States)

    Aujoulat, Fabien; Jumas-Bilak, Estelle; Masnou, Agnès; Sallé, Fanny; Faure, Denis; Segonds, Christine; Marchandin, Hélène; Teyssier, Corinne

    2011-01-01

    The genus Agrobacterium includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species Agrobacterium (Rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination Agrobacterium tumefaciens. In order to study the relative distribution of Agrobacterium strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (atpD, zwf, trpE, groEL, dnaK, glnA, and rpoB) present on the circular chromosome of A. tumefaciens C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus Agrobacterium. PMID:21398532

  19. Multilocus sequence-based analysis delineates a clonal population of Agrobacterium (Rhizobium) radiobacter (Agrobacterium tumefaciens) of human origin.

    Science.gov (United States)

    Aujoulat, Fabien; Jumas-Bilak, Estelle; Masnou, Agnès; Sallé, Fanny; Faure, Denis; Segonds, Christine; Marchandin, Hélène; Teyssier, Corinne

    2011-05-01

    The genus Agrobacterium includes plant-associated bacteria and opportunistic human pathogens. Taxonomy and nomenclature within the genus remain controversial. In particular, isolates of human origin were all affiliated with the species Agrobacterium (Rhizobium) radiobacter, while phytopathogenic strains were designated under the synonym denomination Agrobacterium tumefaciens. In order to study the relative distribution of Agrobacterium strains according to their origins, we performed a multilocus sequence-based analysis (MLSA) on a large collection of 89 clinical and environmental strains from various origins. We proposed an MLSA scheme based on the partial sequence of 7 housekeeping genes (atpD, zwf, trpE, groEL, dnaK, glnA, and rpoB) present on the circular chromosome of A. tumefaciens C58. Multilocus phylogeny revealed that 88% of the clinical strains belong to genovar A7, which formed a homogeneous population with linkage disequilibrium, suggesting a low rate of recombination. Comparison of genomic fingerprints obtained by pulsed-field gel electrophoresis (PFGE) showed that the strains of genovar A7 were epidemiologically unrelated. We present genetic evidence that genovar A7 may constitute a human-associated population distinct from the environmental population. Also, phenotypic characteristics, such as culture at 42°C, agree with this statement. This human-associated population might represent a potential novel species in the genus Agrobacterium.

  20. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers.

    Science.gov (United States)

    Gupta, Mamta; Verma, Bhawna; Kumar, Naresh; Chahota, Rakesh K; Rathour, Rajeev; Sharma, Shyam K; Bhatia, Sabhyata; Sharma, Tilak R

    2012-01-01

    Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil.

  1. Efficiency of RAPD versus SSR markers for determining genetic diversity among popcorn lines.

    Science.gov (United States)

    Leal, A A; Mangolin, C A; do Amaral, A T; Gonçalves, L S A; Scapim, C A; Mott, A S; Eloi, I B O; Cordovés, V; da Silva, M F P

    2010-01-05

    Using only one type of marker to quantify genetic diversity generates results that have been questioned in terms of reliability, when compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, we quantified genetic diversity among 10 S(7) inbred popcorn lines using both RAPD and SSR markers, and we evaluated how well these two types of markers discriminated the popcorn genotypes. These popcorn genotypes: "Yellow Pearl Popcorn" (P1-1 and P1-5), "Zélia" (P1-2 and P1-4), "Curagua" (P1-3), "IAC 112" (P9-1 and P9-2), "Avati Pichinga" (P9-3 and P9-5), and "Pisankalla" (P9-4) have different soil and climate adaptations. Using RAPD marker analysis, each primer yielded bands of variable intensities that were easily detected, as well as non-specific bands, which were discarded from the analysis. The nine primers used yielded 126 bands, of which 104 were classified as polymorphic, giving an average of 11.6 polymorphisms per primer. Using SSR procedures, the number of alleles per locus ranged from two to five, giving a total of 47 alleles for the 14 SSR loci. When comparing the groups formed using SSR and RAPD markers, there were similarities in the combinations of genotypes from the same genealogy. Correlation between genetic distances obtained through RAPD and SSR markers was relatively high (0.5453), indicating that both techniques are efficient for evaluating genetic diversity in the genotypes of popcorn that we evaluated, though RAPDs yielded more polymorphisms.

  2. RAPD and SSR Polymorphisms in Mutant Lines of Transgenic Wheat Mediated by Low Energy Ion Beam

    Science.gov (United States)

    Wang, Tiegu; Huang, Qunce; Feng, Weisen

    2007-10-01

    Two types of markers-random amplified polymorphic DNA (RAPD) and simple sequence repeat DNA (SSR)-have been used to characterize the genetic diversity among nine mutant lines of transgenic wheat intermediated by low energy ion beam and their four receptor cultivars. The objectives of this study were to analyze RAPD-based and SSR-based genetic variance among transgenic wheat lines and with their receptors, and to find specific genetic markers of special traits of transgenic wheat lines. 170 RAPD primers were amplified to 733 fragments in all the experimental materials. There were 121 polymorphic fragments out of the 733 fragments with a ratio of polymorphic fragments of 16.5%. 29 SSR primer pairs were amplified to 83 fragments in all the experiment materials. There were 57 polymorphic fragments out of the 83 fragments with a ratio of polymorphic fragments of 68.7%. The dendrograms were prepared based on a genetic distance matrix using the UPGMA (Unweighted Pair-group Method with Arithmetic averaging) algorithm, which corresponded well to the results of the wheat pedigree analysis and separated the 13 genotypes into four groups. Association analysis between RAPD and SSR markers with the special traits of transgenic wheat mutant lines discovered that three RAPD markers, s1, opt-16, and f14, were significantly associated with the muticate trait, while three SSR markers, Rht8 (Xgwm261), Rht-B1b, and Rht-D1b, highly associated with the dwarf trait. These markers will be useful for marker-assistant breeding and can be used as candidate markers for further gene mapping and cloning.

  3. Evaluation of genetic diversity in Piper spp using RAPD and SRAP markers.

    Science.gov (United States)

    Jiang, Y; Liu, J-P

    2011-11-29

    Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority.

  4. RAPD-PCR – still a suitable Method for Genetically Underexplored Species?

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    Konstanze Ursula Behrmann

    2015-11-01

    Full Text Available Saithe (Pollachius virens is a commercially important fish species; the annual catch quota in the Northeast Atlantic exceeds 100.000 t. Despite that saithe is underexplored from a fish population genetically view. Because saithe is a highly migratory species, which undergoes a long larval drift, the population structure of saithe within the Northeast Atlantic is not fully understood. Models used as a basis for the management plan are based on tagging studies, which have been carried out in the 1960th. But still there are doubts regarding the numbers of stocks living in the Northeast Atlantic. Migration routes are affected by salmon farming, growing steadily from the 1990th. In the last years a hyperstability of the saithe stock in the North Sea had been detected underlining the need to have a closer look on the saithe stocks in the Northeast Atlantic. Random amplified polymorphic DNA (RAPD - PCR is a DNA fingerprinting technique often used in species identification and population genetic research for species, whose genome has not been sequenced very extensive as being the case for most of the food fishes. We applied RAPD-PCR in a study of saithe populations from the North Atlantic. The suitability of RAPD-PCR was improved by optimisations for enhanced reproducibility. The “classical” protocol for RAPD-PCR was modified by increasing the annealing temperature and shortening the time of annealing, providing a much better reproducibility. Thus, RAPD-PCR was found to be a straightforward and low-cost way, compared to other population genetic tools, to get a first insight into the population structure of less sequenced fish species within a very short time, being useful for preliminary studies or laboratories without large capacities for DNA sequencing.

  5. Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization.

    Science.gov (United States)

    Haley, S D; Afanador, L K; Miklas, P N; Stavely, J R; Kelly, J D

    1994-06-01

    The development and use of RAPD markers for applications in crop improvement has recently generated considerable interest within the plant breeding community. One potential application of RAPDs is their use for "tagging" simply-inherited (monogenic) pest-resistance genes and enabling more efficient identification and selection of genotypes carrying specific combinations of resistance genes. In this report, we propose and describe the use of heterogeneous inbred populations as sources of near-isogenic lines (NILs) for targeting RAPD markers linked to major pest resistance genes. The development of these NILs for RAPD marker analyses involved a sequence of line and mass selection during successive generations of inbreeding. DNA bulks derived from the NILs were used to identify a RAPD marker (designated OK14620, generated by 5'-CCCGCTACAC-3' decamer) that was tightly linked (2.23±1.33 centiMorgans) to an important rust [Uromyces appendiculatus (Pers.) Unger var. appendiculatus] resistance gene (Ur-3) in common bean (Phaseolus vulgaris L.). The efficiency of this approach was demonstrated by a low rate of false-positives identified, the tightness of the linkage identified, and the ability to detect polymorphism between genomic regions that are representative of the same gene pool of common bean. This method of deriving NILs should find application by researchers interested in utilizing marker-assisted selection for one or more major pest resistance genes. The identification of OK14620 should help to facilitate continued use of the Ur-3 resistance source and will now enable marker-assisted pyramiding of three different bean rust resistance sources (two previously tagged) to provide effective and stable resistance to this important pathogen.

  6. Identification of RAPD markers linked to a major rust resistance gene block in common bean.

    Science.gov (United States)

    Haley, S D; Miklas, P N; Stavely, J R; Byrum, J; Kelly, J D

    1993-05-01

    Rust in bean (Phaseolus vulgaris L.), caused byUromyces appendiculatus (Pers.) Unger var.appendiculatus [ =U. phaseoli (Reben) Wint.], is a major disease problem and production constraint in many parts of the world. The predominant form of genetic control of the pathogen is a series of major genes which necessitate the development of efficient selection strategies. Our objective was focused on the identification of RAPD (random amplified polymorphic DNA) markers linked to a major bean rust resistance gene block enabling marker-based selection and facilitating resistance gene pyramiding into susceptible bean germplasm. Using pooled DNA samples of genotyped individuals from two segregating populations, we identified two RAPD markers linked to the gene block of interest. One such RAPD, OF10970 (generated by a 5'-GGAAGCTTGG-3' decamer), was found to be closely linked (2.15±1.50 centi Morgans) in coupling with the resistance gene block. The other identified RAPD, OI19460 (generated by a 5'-AATGCGGGAG-3' decamer), was shown to be more tightly linked (also in coupling) than OF10970 as no recombinants were detected among 97 BC6F2 segregating individuals in the mapping population. Analysis of a collection of resistant and susceptible cultivars and experimental lines, of both Mesoamerican and Andean origin, revealed that: (1) recombination between OF10970 and the gene block has occurred as evidenced by the presence of the DNA fragment in several susceptible genotypes, (2) recombination between OI19460 and the gene block has also occurred indicating that the marker is not located within the gene block itself, and (3) marker-facilitated selection using these RAPD markers, and another previously identified, will enable gene pyramiding in Andean germplasm and certain Mesoamerican bean races in which the resistance gene block does not traditionally exist. Observations of variable recombination among Mesoamerican bean races suggested suppression of recombination between

  7. Multilocus sequence typing of IncN plasmids

    DEFF Research Database (Denmark)

    García-Fernández, Aurora; Villa, Laura; Moodley, Arshnee

    2011-01-01

    categorization of IncN plasmids. METHODS: Twelve fully sequenced IncN plasmids available at GenBank were analysed in silico for selecting the loci for the IncN-specific pMLST. A total of 58 plasmids originating from different reservoirs (human, pig, poultry, cattle and horses) and geographic regions (Italy......OBJECTIVES: Incompatibility group N (IncN) plasmids have been associated with the dissemination of antimicrobial resistance and are a major vehicle for the spread of blaVIM-1 in humans and blaCTX-M-1 in animals. A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid...

  8. Bayesian analysis of multilocus association in quantitative and qualitative traits.

    Science.gov (United States)

    Kilpikari, Riika; Sillanpää, Mikko J

    2003-09-01

    A Bayesian model-based method for multilocus association analysis of quantitative and qualitative (binary) traits is presented. The method selects a trait-associated subset of markers among candidates, and is equally applicable for analyzing wide chromosomal segments (genome scans) and small candidate regions. The method can be applied in situations involving missing genotype data. The number of trait loci, their marker positions, and the magnitudes of their gene effects (strengths of association) are all estimated simultaneously. The inference of parameters is based on their posterior distributions, which are obtained through Markov chain Monte Carlo simulations. The strengths of the approach are: 1) flexible use of oligogenic models with unknown number of loci, 2) performing the estimation of association jointly with model selection, and 3) avoidance of the multiple testing problem, which typically complicates the approaches based on association testing. The performance of the method was tested and compared to the multilocus conditional search procedure by analyzing two simulated data sets. We also applied the method to cystic fibrosis haplotype data (two-locus haplotypes), where gene position has already been identified. The method is implemented as a software package, which is freely available for research purposes under the name BAMA. Copyright 2003 Wiley-Liss, Inc.

  9. Comparison of Multilocus Variable-Number Tandem-Repeat Analysis and Multilocus Sequence Typing for Differentiation of Hemolytic-Uremic Syndrome-Associated Escherichia coli (HUSEC) Collection Strains▿

    Science.gov (United States)

    Jenke, Christian; Lindstedt, Björn Arne; Harmsen, Dag; Karch, Helge; Brandal, Lin Thorstensen; Mellmann, Alexander

    2011-01-01

    Multilocus variable-number tandem-repeat analysis (MLVA) was compared to multilocus sequence typing (MLST) to differentiate hemolytic uremic syndrome-associated enterohemorrhagic Escherichia coli strains. Although MLVA—like MLST—was highly discriminatory (index of diversity, 0.988 versus 0.984), a low level of concordance demonstrated the limited ability of MLVA to reflect long-term evolutionary events. PMID:21832012

  10. Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis

    Directory of Open Access Journals (Sweden)

    Susan eJoseph

    2012-11-01

    Full Text Available Cronobacter spp. (previously known as Enterobacter sakazakii is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. One recognised route of infection being the consumption of contaminated infant formula. As a recently recognised bacterial pathogen of considerable importance and regulatory control, appropriate detection and identification schemes are required. The application of multilocus sequence typing (MLST and analysis (MLSA of the seven alleles atpD, fusA, glnS, gltB, gyrB, infB and ppsA (concatenated length 3036 base pairs has led to considerable advances in our understanding of the genus. This approach is supported by both the reliability of DNA sequencing over subjective phenotyping and the establishment of a MLST database which has open access and is also curated; http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of the newly recognised genus, instrumental in the formal recognition of new Cronobacter species (C. universalis and C. condimenti and revealed the high clonality of strains and the association of clonal complex 4 with neonatal meningitis cases. Clearly the MLST approach has considerable benefits over the use of non-DNA sequence based methods of analysis for newly emergent bacterial pathogens. The application of MLST and MLSA has dramatically enabled us to better understand this opportunistic bacterium which can cause irreparable damage to a newborn baby’s brain, and has contributed to improved control measures to protect neonatal health.

  11. Antimicrobial susceptibility among clinical Nocardia species identified by multilocus sequence analysis.

    Science.gov (United States)

    McTaggart, Lisa R; Doucet, Jennifer; Witkowska, Maria; Richardson, Susan E

    2015-01-01

    Antimicrobial susceptibility patterns of 112 clinical isolates, 28 type strains, and 9 reference strains of Nocardia were determined using the Sensititre Rapmyco microdilution panel (Thermo Fisher, Inc.). Isolates were identified by highly discriminatory multilocus sequence analysis and were chosen to represent the diversity of species recovered from clinical specimens in Ontario, Canada. Susceptibility to the most commonly used drug, trimethoprim-sulfamethoxazole, was observed in 97% of isolates. Linezolid and amikacin were also highly effective; 100% and 99% of all isolates demonstrated a susceptible phenotype. For the remaining antimicrobials, resistance was species specific with isolates of Nocardia otitidiscaviarum, N. brasiliensis, N. abscessus complex, N. nova complex, N. transvalensis complex, N. farcinica, and N. cyriacigeorgica displaying the traditional characteristic drug pattern types. In addition, the antimicrobial susceptibility profiles of a variety of rarely encountered species isolated from clinical specimens are reported for the first time and were categorized into four additional drug pattern types. Finally, MICs for the control strains N. nova ATCC BAA-2227, N. asteroides ATCC 19247(T), and N. farcinica ATCC 23826 were robustly determined to demonstrate method reproducibility and suitability of the commercial Sensititre Rapmyco panel for antimicrobial susceptibility testing of Nocardia spp. isolated from clinical specimens. The reported values will facilitate quality control and standardization among laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. 'Food addiction' and its association with a dopaminergic multilocus genetic profile.

    Science.gov (United States)

    Davis, Caroline; Loxton, Natalie J; Levitan, Robert D; Kaplan, Allan S; Carter, Jacqueline C; Kennedy, James L

    2013-06-13

    Our objective was to employ a novel genetic methodology - whereby functional variants of the dopamine pathway were aggregated to reflect a polygenic liability - in the study of food addiction. We anticipated that the composite index of elevated dopamine signaling (a multilocus genetic profile score [MLGP]) would distinguish those with a designation of food addiction (according to the Yale Food Addiction Scale [YFAS] criteria), and age and weight equivalent controls. Our second aim was to assess whether this index was positively associated with eating-related sub-phenotypes of food addiction (e.g. binge eating and food cravings). Adults (n=120) recruited from the community were solicited for an overeating/overweight study. Eating-behavior questionnaires were completed and a blood sample was taken for genotyping. The YFAS identified 21 participants with food addiction. As predicted, the MLGP score was higher in those with YFAS-diagnosed food addiction, and it correlated positively with binge eating, food cravings, and emotional overeating. We then tested a multiple-mediation model proposing that reward-driven overeating facilitates the relationship between the MLGP score and food addiction. The model was statistically significant, supporting the view that the relationship between a composite genetic index of dopamine signaling and food addiction is mediated by certain aspects of reward-responsive overeating. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Inference of antibiotic resistance and virulence among diverse group A Streptococcus strains using emm sequencing and multilocus genotyping methods.

    Directory of Open Access Journals (Sweden)

    David Metzgar

    Full Text Available BACKGROUND: Group A Streptococcus pyogenes (GAS exhibits a high degree of clinically relevant phenotypic diversity. Strains vary widely in terms of antibiotic resistance (AbR, clinical severity, and transmission rate. Currently, strain identification is achieved by emm typing (direct sequencing of the genomic segment coding for the antigenic portion of the M protein or by multilocus genotyping methods. Phenotype analysis, including critical AbR typing, is generally achieved by much slower and more laborious direct culture-based methods. METHODOLOGY/PRINCIPAL FINDINGS: We compare genotype identification (by emm typing and PCR/ESI-MS with directly measured phenotypes (AbR and outbreak associations for 802 clinical isolates of GAS collected from symptomatic patients over a period of 6 years at 10 military facilities in the United States. All independent strain characterization methods are highly correlated. This shows that recombination, horizontal transfer, and other forms of reassortment are rare in GAS insofar as housekeeping genes, primary virulence and antibiotic resistance determinants, and the emm gene are concerned. Therefore, genotyping methods offer an efficient way to predict emm type and the associated AbR and virulence phenotypes. CONCLUSIONS/SIGNIFICANCE: The data presented here, combined with much historical data, suggest that emm typing assays and faster molecular methods that infer emm type from genomic signatures could be used to efficiently infer critical phenotypic characteristics based on robust genotype: phenotype correlations. This, in turn, would enable faster and better-targeted responses during identified outbreaks of constitutively resistant or particularly virulent emm types.

  14. Diversidade genética de três estoques de piapara (Leporinus elongatus, utilizando RAPD = Genetic diversity of three stocks of piapara (Leporinus elongatus, using RAPD

    Directory of Open Access Journals (Sweden)

    Patrícia Cristina Gomes

    2008-04-01

    Full Text Available Recentemente a produção aquícola brasileira tem apresentado grandeprogresso. Dentre as espécies nativas cultivadas no Brasil, a piapara (Leporinus elongatus tem sido amplamente preconizada. Com objetivo de avaliar os programas de repovoamento, foram analisadas a variabilidade e a divergência genética de três estoques de piapara com a técnica de RAPD (Random Amplified Polymorphic. O primeiro estoque pertence à Estação de Aquicultura e Hidrologia da Duke Energy International (A; o segundo, à piscicultura de Rolândia (B e o terceiro, ao Programa de Repovoamento dos Rios do Paraná (C. Os dezprimers para RAPD utilizados produziram 105 fragmentos polimórficos, conferindo um polimorfismo de 98,1% para os três estoques avaliados. A porcentagem de locos polimórficos e índice de Shannon foi superior para o estoque A. Porém, todos valores foram elevados, indicando alta diversidade intrapopulacional. Os valores de Gst indicam que houvebaixa diferenciação genética entre os estoques A x B e moderada diferenciação entre os demais. O Nm foi maior entre os estoques A x B. A distância genética e o dendrograma indicam que os estoques A x B são menos distantes geneticamente.Latelly, aquiculture production in Brazil has made great strides. Among the native species cultivated in Brazil, piapara (Leporinus elogatus has been widely praised. With the objective of evaluating restocking programs, the variability and genetic divergence ofthree piapara stocks were analyzed using the RAPD (Random Amplified Polymorphic DNA technique. The first stock belongs to the Aquiculture and Hydrology Station of Duke Energy International (A; the second one belongs to a fish farm in the city of Rolândia(B; and the third to the River Restocking Program of Paraná (C. The ten primers used for RAPD produced 105 polymorphic loci, conferring a polymorphism of 98.1% for the three evaluated stocks. Polymorphic loci percentage and Shannon index were higher for stock A

  15. Genotoxicity evaluation of ionic liquid 1-octyl-3-methylimidazolium bromide in freshwater planarian Dugesia japonica using RAPD assay.

    Science.gov (United States)

    Zhang, He-Cai; Shi, Chang-Ying; Yang, Hui-Hui; Chen, Guang-Wen; Liu, De-Zeng

    2016-12-01

    The randomly amplified polymorphic DNA (RAPD) assay has been used to detect DNA alternation and mutation recently. However, the effectiveness of this method in detecting DNA damage in planarians, a model organism for assessing the toxicity of environmental pollutants is unknown. In the present study, RAPD assay was used to detect the DNA damage in planarians treated by the ionic liquid 1-octyl-3-methylimidazolium bromide ([C8mim]Br) for the first time. Among the 20 test RAPD primers, 13 primers with 60-70% GC content produced unique polymorphic band profiles. A total of 60 bands were observed in the untreated control planarians. In comparison with the control group, the [C8mim]Br-treated groups displayed differences in RAPD patterns in the band intensity, disappearance of normal bands and appearance of new bands. The variation of RAPD profiles showed both concentration- and time-effect relationships. Meanwhile, the genomic template stability (GTS) of treated planarians decreased and exhibited negative correlation to the exposure concentration and time of [C8mim]Br. Our results suggested that [C8mim]Br had genotoxic effects on planarians, and this DNA damage analysis would lay the foundation for further elucidating the toxicity mechanisms of ionic liquids on planarians. Furthermore, RAPD analysis was proved to be a highly sensitive method for the detection of DNA damage induced by environmental pollutants like toxic chemicals on planarians. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Genetic relationships among ten endod types as revealed by a combination of morphological, RAPD and AFLP markers.

    Science.gov (United States)

    Semagn, Kassa

    2002-01-01

    The genetic relationships among ten types of endod (Phytolacca dodecandra) cultivated by the Institute of Pathobiology of the Addis Ababa University to combat the disease bilharzia in Ethiopia were studied using morphology and molecular markers. A total of 18 morphological characters, 194 amplified fragment length polymorphism (AFLP) and 42 random amplified polymorphic DNA (RAPD) markers were used to determine genetic proximity between types. Genetic distance and cluster analysis of the AFLP data revealed the lack of genetic difference between E47 and E48 but relatively wider genetic difference among the other endod types. Cluster and principal component analyses performed on the AFLP and RAPD markers demonstrated the presence of distinct separation of E56 but not that of E44 from the others. The AFLP and RAPD data, thcrefore, did not support the hypothesis that the superiority of E44 in agronomic traits and molluscicidal potency is linked to its distinct genetic difference from the other endod types. Matrices correspondence tests demonstrated the presence of greater correspondence between AFLP and RAPD data (r = 0.842) but not between the morphology and that of AFLP and RAPD. This indicates the correspondence more between the two DNA markers systems than either of them with morphological traits. The cophenetic correlation coefficients also revealed poor fit for morphology (r = 0.716), good fit for RAPD (r = 0.872) and very good fit for AFLP (r = 0.975), reflecting the hyper-variability and higher resolving power of AFLP.

  17. Molecular Identification of Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) Markers.

    Science.gov (United States)

    Al-Khalifah, Nasser S; Shanavaskhan, A E

    2017-01-01

    Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.

  18. Genotyping isolates of the entomopathogenic fungus beauveria bassiana by RAPD with fluorescent labels

    Science.gov (United States)

    Berretta; Lecuona; Zandomeni; Grau

    1998-03-01

    Random amplified polymorphic DNA (RAPD) with incorporation of fluorescent deoxynucleotides was used to examine the genetic diversity among Beauveria bassiana isolates from Argentina and Brazil. High-resolution DNA fingerprints were generated on line, during polyacrylamide gel electrophoresis of amplification products, by automated laser fluorescence analysis. Each isolate displayed a distinct genotype. Cluster analysis showed a high level of variability among these genotypes. No correlation with geographical origin or host was detected. Nevertheless, a phenetic group of 80% similarity represented mainly the isolates exhibiting high virulence against the sugar cane borer, Diatraea saccharalis. Fluorescence-based RAPD fingerprints provide a useful tool for identifying entomopathogenic fungi, and this technique is specially applicable to screening many isolates in population studies. Copyright 1998 Academic Press.

  19. Testing Taxonomic and Biogeographical Relationships in a Narrow Mediterranean Endemic Complex (Hippocrepis balearica) using RAPD Markers

    Science.gov (United States)

    ROSSELLÓ, JOSEP A.; CEBRIÁN, M. CARMEN; MAYOL, MARIA

    2002-01-01

    Analyses of RAPD profiles from 17 populations of the Hippocrepis balearica complex revealed a highly structured geographic pattern, not only among continental–insular areas but also within the eastern Balearic islands. In marked contrast to previous morphometric results, a clear separation between continental and insular samples was found, and intermediates between H. balearica and H. valentina samples were not detected. Molecular data indicated that western and eastern Balearic populations of the complex (H. grosii and H. balearica) were more closely related to each other than to continental populations (H. valentina). Multivariate analyses of the RAPD data clearly indicated that the similarities between continental and eastern Balearic samples of the H. balearica complex recovered by morphometric methods are due either to parallel evolution or to retention of plesiomorphic features. PMID:12096744

  20. Molecular Polymorphisms in Tunisian Pomegranate (Punica granatum L. as Revealed by RAPD Fingerprints

    Directory of Open Access Journals (Sweden)

    Jemni Chibani

    2010-01-01

    Full Text Available The genetic diversity among Tunisian pomegranate cultivars has been investigated. Using universal primers, the random amplified polymorphic DNA (RAPD method was used to generate banding profiles from a set of twelve cultivars. Data was then computed with appropriate programs to construct a dendrogram illustrating the relationships between the studied cultivars. Our data proved the efficiency of the designed method to examine the DNA polymorphism in this crop since the tested primers are characterized by a collective resolving power of 12.83. In addition, the cluster analysis has exhibited a parsimonious tree branching independent from the geographic origin of the cultivars. In spite of the relatively low number of primers and cultivars, RAPD constitutes an appropriate procedure to assess the genetic diversity and to survey the phylogenetic relationships in this crop.

  1. [Identification of Aloe species by random amplified polymorphic DNA (RAPD) analysis].

    Science.gov (United States)

    Shioda, Hiroko; Satoh, Kanako; Nagai, Fumiko; Okubo, Tomoko; Seto, Takako; Hamano, Tomoko; Kamimura, Hisashi; Kano, Itsu

    2003-08-01

    Juice and integument of leaves of 3 Aloe species, Aloe vera, A. ferox and A. africana, are not allowed to be used as food according to the Pharmaceutical Affairs Law in Japan. On the other hand, whole leaves of A. arborescens can be used as food. The present study was designed to distinguish Aloe species by random amplified polymorphic DNA (RAPD) analysis. DNA was isolated from fresh and dried leaves of the 4 Aloe species. Five out of 32 different 10-mer primers examined were useful for analysis. By comparison of the characteristic bands of PCR products on agarose gel, it was possible to distinguish the 4 species. Thus, the botanical species of Aloe in commercial food products can be identified by RAPD analysis.

  2. RAPD fingerprint construction and genetic similarity of Mesona chinensis (Lamiaceae) in China.

    Science.gov (United States)

    Zhang, G F; Guan, J M; Lai, X P; Lin, J; Liu, J M; Xu, H H

    2012-10-04

    Mesona chinensis is an economically important agricultural crop, primarily cultivated for making grass jelly. It was originally discovered in South China. We examined 18 cultivars, including cultivars from Guangdong, Fujian, and Guangxi, China, Taiwan, and Indonesia, and a hybrid (a cross between cultivars from Indonesia and Guangdong), based on RAPD markers. The genetic similarity coefficient was calculated by NTSYS 2.10 and the clustering analysis was made by UPGMA. PCR amplification with 10 primers produced 163 bands; 94% of the amplified loci were polymorphic. The primers S208, S206, and S253 could completely distinguish all 19 samples by constructing a DNA fingerprint. Cluster analysis divided the 19 cultivars into five groups, with an overall genetic similarity coefficient of 0.68. Correlations were found among regional distributions, parental sources, and RAPD markers, demonstrating the rich genetic diversity of these 19 cultivars of M. chinensis. This study provides useful information for the classification, identification, and breeding of M. chinensis.

  3. Genetic Diversity Analysis of Iranian Improved Rice Cultivars through RAPD Markers

    Directory of Open Access Journals (Sweden)

    Ghaffar KIANI

    2011-08-01

    Full Text Available The aim of this study was to evaluate the genetic diversity of Iranian improved rice varieties. Sixteen rice varieties of particular interest to breeding programs were evaluated by means of random amplified polymorphic DNA (RAPD technique. The number of amplification products generated by each primer varied from 4 (OPB-04 to 11 (OPD-11 with an average of 8.2 bands per primer. Out of 49 bands, 33 (67.35% were found to be polymorphic for one or more cultivars ranging from 4 to 9 fragments per primer. The size of amplified fragments ranged between 350 to 1800 bp. Pair-wise Nei and Li�s (1979 similarity estimated the range of 0.59 to 0.98 between rice cultivars. Results illustrate the potential of RAPD markers to distinguish improved cultivars at DNA level. The information will facilitate selection of genotypes to serve as parents for effective rice breeding programs in Iran.

  4. Genetic diversity of alfalfa domesticated varietal populations from Libyan genbank revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    Ahsyee Salem R.

    2013-01-01

    Full Text Available Alfalfa (Medicago sativa L. is an important forage legume in Libya. The genetic diversity of nine alfalfa domesticated varietal populations was studied using thirteen RAPD primer combinations. The number of polymorphic fragments detected per primer combination ranged from 8 to 46 bands with an average of 24 bands. The number of polymorphic bands detected was from 6 (Atalia population to 37 (Gabsia population. The lowest genetic distance was 0.058 and the highest was 0.655. The average genetic distance was (0.356. The dendrogram based on Ward’s minimum variance clustering method grouped the nine populations into the two main clusters. The first group included Fazania, Atalia, Masratia, Zawia, Denamo Ferade and Arezona. The second group was composed of Tagoria, Gabsia and Wade Alrabeh. The simplicity of RAPD assays for detection of genetic polymorphisms is confirmed in our study, and results can be utilized in breeding practice.

  5. Genetic characterization of early maturing maize hybrids (Zea mays L. obtained by protein and RAPD markers

    Directory of Open Access Journals (Sweden)

    Bauer Iva

    2005-01-01

    Full Text Available Knowledge of maize germplasm genetic diversity is important for planning breeding programmes, germplasm conservation per se etc. Genetic variability of maize hybrids grown in the fields is also very important because genetic uniformity implies risks of genetic vulnerability to stress factors and can cause great losts in yield. Early maturing maize hybrids are characterized by shorter vegetation period and they are grown in areas with shorter vegetation season. Because of different climatic conditions in these areas lines and hybrids are developed with different features in respect to drought resistance and disease resistance. The objective of our study was to characterize set of early maturing maize hybrids with protein and RAPD markers and to compare this clasification with their pedigree information. RAPD markers gave significantly higher rate of polymorphism than protein markers. Better corelation was found among pedigree information and protein markers.

  6. Genotyping of Pseudomonas aeruginosa strains isolated from burn patients by RAPD-PCR.

    Science.gov (United States)

    Nanvazadeh, Fatemeh; Khosravi, Azar Dokht; Zolfaghari, Mohammad Reza; Parhizgari, Najmeh

    2013-11-01

    Pseudomonas aeruginosa is one of the important causes of nosocomial infections that easily gains resistance to many antibiotics. This opportunistic pathogen is a major health hazard particularly in immunodeficient patients, patients in intensive care units (ICU) and burn units with life threatening outcome. The bacterium may be originated from different or common sources, and comprises a high colonization and transmission capacity. The aim of present study was to investigate the genotypic variation of Pseudomonas aeroginosa strains isolated from burn patients by using Random Amplified Polymorphic DNA (RAPD) method. Totally 70 clinical samples were collected from burn patients in Taleghani Burn Hospital of Ahvaz. Fifty out of total samples were positive for P. aeruginosa by application of conventional culture and biochemical identification tests. DNA was extracted from the isolates and the RAPD-PCR method was applied to the DNA extracts according to standard method using a short single primer of 272. The technique created repetitive electrophoresis patterns which was used for genotypic differentiation. RAPD-PCR, created 9 genotypic profiles designated as I-IX with base pair length ranging from 180 to 2700. Each genotype showed between 3 and 6 different weight DNA bands. Genotype I was the most prevalent, identified in 10 bacterial isolates (20%). Genotypes I, II and VI were mostly common in patients with more severe burn, and were mainly isolated from wound and blood samples obtained from the same patients. In present study, we found RAPD-PCR technique as a useful tool for investigation of the genetic variation among P. aeruginosa strains. This is a rapid, low cost, genotypic method with high discriminatory power. The results could assist to screen for the original of infection caused by this organism with subsequent control of colonization and transmission. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

  7. Genetic relatedness of artichoke (Cynara scolymus L.) hybrids using random amplified polymorphic DNA (RAPD) fingerprinting.

    Science.gov (United States)

    Sharaf-Eldin, M A; Al-Tamimi, A; Alam, P; Elkholy, S F; Jordan, J R

    2015-12-28

    The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level.

  8. CHARACTERIZATION OF A NEW BIOTYPE Moringa OF SAUDI ARABIA USING RAPD AND ISSR MARKERS

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    Iyan Robiansyah

    2015-11-01

    Full Text Available Moringa peregrina and M. oleifera are the only Moringa species found in Saudi Arabia. Both species are drought resistant and have very high nutritional and medicinal properties. Detection of genetic diversity is of great value for the improvement of nutritional and medicinal value of these plants. The aim of the present study was to characterize a new biotype Moringa observed in Al Bahah Region, Saudi Arabia. We used 11 RAPD and 15 ISSR primers to characterize and compare the new biotype with M. peregrina and M. oleifera. Level of polymorphism generated by each marker was calculated. We also calculate Nei and Li’s coefficient to measure the genetic distance between the studied species. Level of polymorphism generated by RAPD and ISSR was 46% and 57%, respectively. RAPD and ISSR primers revealed that the new biotype shared 55 amplicons (45.08% with both M. peregrina and M. oleifera, 28 amplicons with M. peregrina (22.95%, 21 amplicons (17.21% with M. oleifera, and displayed 18 unshared amplicons (14.75%. Based on RAPD data, genetic distance between M. oleifera and M. peregrina was 0.32, whereas genetic distance between the new biotype and M. oleifera and M. peregrina was 0.21 and 0.29, respectively. For ISSR data, genetic distance between M. oleifera and M. peregrina was 0.5, whereas genetic distance between the new biotype and M. oleifera and M. peregrina was 0.36 and 0.34, respectively. Based on these results we suggested that the new biotype is a hybrid crossbred between M. peregrina and M. oleifera.

  9. Variety discrimination of Tigridia pavonia (L.f.) DC. assesed by different length RAPD primers

    OpenAIRE

    José Luis Piña-Escutia

    2010-01-01

    Tigridia pavonia (L.f.) DC. is one of the important phytogenetic resources of México. This species is used as ornamental, food and medicinal purposes. Despite its ornamental and economic potential, there is little information about the genetic variability. In this study, randomly amplified polymorphic DNA (RAPD) primers of 10, 15 and 20 bases were used to assess the level of genetic variation among nine botanical varieties of Tigridia pavoniacollected in three localities within State of Méxic...

  10. Effect of nickel on regeneration in Jatropha curcas L. and assessment of genotoxicity using RAPD markers

    KAUST Repository

    Sarkar, Tanmoy

    2010-07-08

    The aim of the present study was to determine the effect of nickel on shoot regeneration in tissue culture as well as to identify polymorphisms induced in leaf explants exposed to nickel through random amplified polymorphic DNA (RAPD). In vitro leaf explants of Jatropha curcas were grown in nickel amended Murashige and Skoog (MS) medium at four different concentrations (0, 0.01, 0.1, 1 mM) for 3 weeks. Percent regeneration, number of shoots produced and genotoxic effects were evaluated by RAPD using leaf explants obtained from the first three treatments following 5 weeks of their subsequent subculture in metal free MS medium. Percent regeneration decreased with increase in addition of nickel to the medium up to 14 days from 42.31% in control to zero in 1.0 mM. The number of shoot buds scored after 5 weeks was higher in control as compared to all other treatments except in one of the metal free subculture medium wherein the shoot number was higher in 0.01 mM treatment (mean = 7.80) than control (mean = 7.60). RAPD analysis produced only 5 polymorphic bands (3.225%) out of a total of 155 bands from 18 selected primers. Only three primers OPK-19, OPP-2, OPN-08 produced polymorphic bands. The dendrogram showed three groups A, B, and C. Group A samples showed 100% genetic similarity within them. Samples between groups B and C were more genetically distant from each other as compared to samples between groups A and B as well as groups A and C. Cluster analysis based on RAPD data correlated with treatments. © 2010 Springer Science+Business Media, LLC.

  11. MCMC multilocus lod scores: application of a new approach.

    Science.gov (United States)

    George, Andrew W; Wijsman, Ellen M; Thompson, Elizabeth A

    2005-01-01

    On extended pedigrees with extensive missing data, the calculation of multilocus likelihoods for linkage analysis is often beyond the computational bounds of exact methods. Growing interest therefore surrounds the implementation of Monte Carlo estimation methods. In this paper, we demonstrate the speed and accuracy of a new Markov chain Monte Carlo method for the estimation of linkage likelihoods through an analysis of real data from a study of early-onset Alzheimer's disease. For those data sets where comparison with exact analysis is possible, we achieved up to a 100-fold increase in speed. Our approach is implemented in the program lm_bayes within the framework of the freely available MORGAN 2.6 package for Monte Carlo genetic analysis (http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml).

  12. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from......Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS......) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time...

  13. Genetic Diversity Analysis of Iranian Jujube Ecotypes (Ziziphus spp. Using RAPD Molecular Marker

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    S Abbasi

    2012-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. is a valuable medicinal plant which is important in Iranian traditional medicines. Although the regional plants such as jujube play an important role in our economy, but they are forgotten in research and technology. Considering the economic and medicinal importance of jujube, the first step in breeding programs is determination of the genetic diversity among the individuals. 34 ecotypes of jujube, which have been collected from eight provinces of Iran, were used in this study. The genetic relationships of Iranian jujube ecotypes were analyzed using Random Amplified Polymorphic DNA (RAPD marker. Six out of 15 random decamer primers applied for RAPD analysis, showed an informative polymorphism. According to clustering analysis using UPGMA's methods, the ecotypes were classified into two major groups at the 0.81 level of genetic similarity. The highest value of similarity coefficient (0.92 was detected between Mazandaran and Golestan ecotypes and the most genetic diversity was observed in ecotypes of Khorasan-Jonoubi. The affinity of Khorasan-Jonoubi and Esfahan ecotypes indicated a possible common origin for the variation in these areas. Results indicated that RAPD analysis could be successfully used for the estimation of genetic diversity among Ziziphus ecotypes and it can be useful for further investigations.

  14. Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn

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    G.I. BARTISH

    2008-12-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to characterize a part of a sea buckthorn gene bank collected for plant breeding purposes. Molecular markers were generated in 55 cultivars and accessions, representing five subspecies of Hippophae rhamnoides L. and intraspecific hybrids between different subspecies. Sixty-three markers were used to generate a Dice's similarity coefficient matrix of pairwise comparisons between individual RAPD profiles. Cluster (UPGMA and principal co-ordinate analyses, based on this matrix, revealed clustering of plants into groups which generally correspond to their taxonomic classification or geographic origin. The analysis of molecular variance (AMOVA was found useful for estimating components of genetic variation between and within taxonomic and geographic groups of accessions and cultivars. Whereas both alternatives for grouping the material (taxonomic or geographic origin resulted in significant between-group variation, the major part of molecular variance (approximately 75% was still attributed to variation within groups. We conclude that the RAPD analysis is useful for clarification of taxonomic and geographic origin of accessions and cultivars of sea buckthorn.

  15. Genetic Diversity in Commercial Rapeseed (Brassica napus L. Varieties from Turkey as Revealed by RAPD

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    Özlem ÖZBEK

    2013-02-01

    Full Text Available In cultivated commercial crop species, genetic diversity tends to decrease because of the extensive breeding processes. Therefore, germplasm of commercial crop species, such as Brassica napus L. should be evaluated and the genotypes, which have higher genetic diversity index, should be addressed as potential parental cross materials in breeding programs. In this study, the genetic diversity was analysed by using randomly amplified polymorphic DNA analysis (RAPD technique in nine Turkish commercial rapeseed varieties. The RAPD primers (10-mer oligonucleotides produced 51 scorable loci, 31 loci of which were polymorphic (60.78% and 20 loci (39.22% were monomorphic The RAPD bands were scored as binary matrix data and were analysed using POPGENE version 1.32. At locus level, the values of genetic diversity within population (Hs and total (HT were 0.15 and 0.19 respectively. The genetic differentiation (GST and the gene flow (Nm values between the populations were 0.20 and 2.05 respectively. The mean number of alleles (na, the mean number of effective alleles (nae, and the mean value of genetic diversity (He were 2.00, 1.26, and 0.19 respectively. According to Pearson’s correlation, multiple regression and principal component analyses, eco-geographical conditions in combination had significant effect on genetic indices of commercial B. napus L. varieties were discussed.

  16. Genetic relatedness of soybean genotypes based on agromorphological traits and RAPD markers

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    Perić Vesna

    2014-01-01

    Full Text Available Modern agriculture, breeding procedures, as well as competition among breeding institutions contribute to further reduction of already narrowed diversity of soybean commercial varieties. The objective of the study was to characterize eighteen soybean cultivars from three different breeding programs for agro-morphological traits and to reveal genetic diversity using molecular markers. Morphological description was performed with 13 qualitative and 9 quantitative traits. The genetic relationships were estimated using 21 RAPD markers. PIC was calculated for RAPD data, while the diversity of qualitative traits was described by Shannon genetic diversity index. Cluster analysis based on qualitative morphological characters showed clear separation of genotypes on the basis of their plant growth type. PC analysis performed for quantitative traits divided genotypes according to their maturity group. Grouping pattern based on molecular marker data was in agreement with pedigree of cultivars. A great similarity was found, primarily between the varieties under the same institution, and then among all examined varieties. Comparison of three methods in the assessment of diversity indicated that morphological markers might provide useful information in breeding process and allow classification by pedigree to some extent, but RAPD markers were found to be superior in assessing differences among genetically very similar genotypes. [Projekat Ministarstva nauke Republike Srbije, br. TR-31068

  17. Genetic diversity analysis of chewing sugarcane (Saccharum officinarum L. varieties by using RAPD markers

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    S. M. Sarid Ullah

    2013-01-01

    Full Text Available In the present study an efficient and easy method was followed for the isolation of DNA from meristem cylinder in five chewing sugarcane varieties, namely Amrita, Bomaby, Babulal (Co.527, Q83 and Misrimala. The quality and quantity of DNA were assured by visual estimation using agarose gel electrophoresis and UV spectrophotometry. The highest amount of DNA was retrieved from the Amrita (3250 ng/ml and the lowest amount was attained from the variety Q83 (1450 ng/ml. The amount of recovered DNA was enough for PCR amplification and marker studies such as random amplified polymorphic DNA (RAPD. Using RAPD markers, bands obtained from fingerprinting (190 bp to 1200 bp showed 73.5% polymorphism. The dendrogram, based on linkage distance using unweighted pair group method of arithmetic means (UPGMA, indicated segregation of the five chewing varieties of sugarcane into two main clusters. Amrita, Bombay and Misrimala were grouped in cluster 1 (C1 followed by sub-clusters. Babulal and Q83 were grouped in cluster 2 (C2. The results of the present investigation also revealed that the twenty RAPD primers were able to identify and classify the chewing sugarcane varieties based on their genetic relationship.

  18. Detection of toxin genes and RAPD analysis of bacillus cereus isolates from different soil types

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    Savic Dejana

    2015-01-01

    Full Text Available The aim of this study was to detect genes for enterotoxins (hbla, entFM and bceT and for emetic toxin (cer, to determine antibiotic resistance, and to estimate intraspecies diversity in B. cereus isolates by RAPD analysis. B. cereus was identified in 12 out of 117 indigenous Bacillus spp. using the classical microbiological methods and PCR. All isolates were resistant to penicillin and ampicillin, two to tetracyclin and four to trimethoprim-sulphamethoxazole. Also, all isolates produced inducible penicillinases and β-lactamase. Toxin genes were detected with PCR. EntFM and cer genes were present in all isolates, hbla in all, but two, and bceT in none. RAPD analysis was performed with four different primers, two of them designed for this study. The intraspecies diversity revealed 10 different patterns at the 90% similarity level. Two separate clusters were formed regardless of a soil type or utilization. The detection of genes encoding toxins in all B. cereus isolates indicated these bacteria as potentially pathogenic and seriously for human health. Regardless of a soil type or utilization, the RAPD analysis showed high intraspecies heterogeneity in B. cereus isolates. To the best of our knowledge, this is the first study to analyse the presence of entero- and emetic toxin genes and genetic heterogeneity in B. cereus isolates from different soil types and different soil utilization in Serbia. [Projekat Ministarstva nauke Republike Srbije, br. TR37006

  19. Phylogeography and RAPD-PCR variation in Hoplias malabaricus (Bloch, 1794 (Pisces, Teleostei in southeastern Brazil

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    Dergam Jorge A.

    2002-01-01

    Full Text Available In the Rio Doce basin of southeastern Brazil, the freshwater fish Hoplias malabaricus (trahira is a widespread predatory characin and one of the few resilient native fishes in a highly impacted lake system. In order to test for genetic differentiation in populations within this basin and for biogeographic relationships among populations of this species in other basins, a study was conducted using RAPD-PCR analysis of Rio Doce samples (N = 63 and phylogeographic analyses with mitochondrial DNA (mtDNA haplotypes, including the Rio Grande and Macacu river basins. In the Rio Doce basin, the patterns of genetic similarity of RAPD-PCR markers (individual fingerprinting and Nei?s genetic distance suggest the existence of two genetically different groups, one composed of the lacustrine populations Carioca and Dom Helvécio, and the other of riverine and the remaining lacustrine populations. The differences in the RAPD-PCR patterns may be explained by the existence of sub-basins within this lacustrine system. A maximum parsimony tree of cytochrome b fragment (383 base pairs supports the view that trahiras of the Rio Doce share a complex biogeographic history with those of neighboring basins. The phylogeographic patterns may be explained by a common history of the watersheds of the Rio Doce, Paraíba do Sul, and Rio Grande basins, corroborating the hypothesis of a Plio-Pleistocene separation of these drainage systems, forming the Mantiqueira "divortium aquarium".

  20. Comprehensive genetic discrimination of Leonurus cardiaca populations by AFLP, ISSR, RAPD and IRAP molecular markers.

    Science.gov (United States)

    Khadivi-Khub, Abdollah; Soorni, Aboozar

    2014-06-01

    Leonurus cardiaca is well known for its medicinal importance. In this investigation, genotypic characterization of this species from six eco-geographical regions of Iran was evaluated by four molecular techniques (AFLP, RAPD, ISSR and IRAP). A total of 899 polymorphic fragments were detected by used molecular markers (AFLP = 356, RAPD = 325, ISSR = 113 and IRAP = 105) with an overall average polymorphism of 81.24%. Genetic variation calculated using Shannon's Information index (I) and Nei's gene diversity index (H) showed high genetic diversity in studied germplasm. Also, analysis of molecular variance showed high genetic variation among (55%) and within populations (45%). UPGMA dendrogram constructed from combined data of molecular markers distinguished studied populations in accordance with the results obtained by each marker which all individuals were clearly differentiated into two major clusters. The correlation coefficients were statistically significant for all marker systems with the highest correlation between similarity matrixes of RAPD and ISSR markers (r = 0.82). The present results have an important implication for L. cardiaca germplasm characterization, improvement, and conservation. Furthermore, the characterized individuals exhibited a great deal of molecular variation and they seem to have a rich gene pool for breeding programs.

  1. [PCR-RAPD typing of carbapenem-resistant Pseudomonas aeruginosa strains].

    Science.gov (United States)

    Bogiel, Tomasz; Gospodarek, Eugenia

    2010-01-01

    P. aeruginosa rods are opportunistic pathogens responsible generally for nosocomial infections. Resistance to carbapenems, observed among them, is a serious threat due to ability to be transmitted between bacterial species. The aim of our study was to evaluate the usefulness of PCR-RAPD technique in typing of 16 carbapenem-resistant P. aeruginosa strains isolated in 2007 from different patients of University HospitalNo. 1 of dr A. Jurasz Collegium Medicum of L. Rydygier in Bydgoszcz Nicolaus Copernicus University in Toruń. Study shows increasing frequency of isolation that type of strains when compared to 2006. Percentage of carbapenem-resistant isolates raised from 12,4% in 2006 to 22.9% in 2007. The majority of examined strains were obtained from patients of the Intensive Care Units (25.0%) and were isolated from bronchoalveolar lavage (25.0%), urine (25.0%) and wound swabs (18.8%) samples. Examined P. aeruginosa strains demonstrated resistance to doripenem (81.3%) and piperacillin (75.0%) and susceptibility to colistin (100.0%), amikacin (81.3%), netilmicin and norfloxacin (75.0% each). Using PCR-RAPD amplification with 208 and 272 primers, 14 and 16 DNA patterns were obtained, respectively. Usefulness of PCR-RAPD in carbapenem-resistant P. aeruginosa strains typing was proved in case of strains presenting similar and/or different antimicrobials susceptibility patterns.

  2. RAPD markers linked to a block of genes conferring rust resistance to the common bean

    Directory of Open Access Journals (Sweden)

    Faleiro Fábio Gelape

    2000-01-01

    Full Text Available Rust, caused by the fungus Uromyces appendiculatus, may cause a significant loss to common bean (Phaseolus vulgaris L. yield. RAPD markers tightly linked to the resistance genes may be used in breeding programs to aid the development of rust-resistant bean cultivars. In this sense, the objective of the present work was to identify RAPD markers linked to a rust resistance gene block present in the cultivar Ouro Negro. Two hundred and fourteen F2 individuals from a cross between the resistant cultivar Ouro Negro and the susceptible cultivar US Pinto 111 were inoculated with a mixture of eight races of U. appendiculatus. The segregation ratio obtained suggested that resistance is monogenic and dominant. Bulked segregant analysis was used in conjunction with the RAPD technique to search for markers linked to rust resistance genes. Two molecular markers flanking the rust resistance gene block were identified, one at 5.8 ± 1.6 cM (OX11(630 and the other at 7.7 ± 1.7 cM (OF10(1,050 of the gene. Simulated indirect selection efficiency in the F2 population using the two markers was 100%. The molecular markers identified in this work are currently being used for the selection of disease-resistant plants in the commom bean breeding program of the Federal University of Viçosa.

  3. Molecular characterization of Giardia psittaci by multilocus sequence analysis.

    Science.gov (United States)

    Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

    2012-12-01

    Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. RAPD markers for screening shoot gall maker (Betousa stylophora Swinhoe tolerant genotypes of amla (Phyllanthus emblica L.

    Directory of Open Access Journals (Sweden)

    Sethuraman Thilaga

    2017-12-01

    Full Text Available Phyllanthus emblica Linn. is the most important medicinally useful tree crop in Asian Subcontinent and is severely infested by Betousa stylophora Swinhoe, known as shoot gall maker (SGM. This pest tunnels the shoots of seedlings and actively growing branches of trees and develops gall, leading to stunted growth, unusual branching and death of actively growing shoots. Our study revealed that trees possessing smooth bark were free from the attack of this pest than those with rough bark surface. Unfortunately, this character is not detectable either at seedling stage or during early growth of trees in the orchard. RAPD genetic fingerprinting of trees possessing smooth and rough bark revealed distinguishable and highly reproducible DNA banding pattern between the two genotypes. Of the 20 RAPD primers tested, five of them produced distinguishable RAPD bands between rough and smooth barked genotypes of P. emblica. Trees with smooth bark produced five unique RAPD bands with molecular weight ranging from 350 bp to 1500 bp and those with rough bark produced six RAPD bands (350 bp–650 bp to utilize these DNA bands as potential DNA marker for screening tolerant genotypes of this crop against SGM. The utility of this finding in genetic improvement of this tree crop against SGM is discussed.

  5. EVALUASI KERAGAMAN GENETIK IKAN KANCRA DENGAN MENGGUNAKAN MARKER Mt DNA D-loop DAN RANDOM AMPLIFIED POLYMORPHISM DNA (RAPD

    Directory of Open Access Journals (Sweden)

    Estu Nugroho

    2016-11-01

    Full Text Available Variasi genetik ikan kancra yang dikoleksi dari daerah Kuningan (Pesawahan, Gandasoli, dan Ragawacana dan Sumedang di Jawa Barat telah diteliti dengan menggunakan polimorfisme Mitokondria DNA D-loop dan Random Amplified Polymorphism DNA (RAPD. Berdasarkan analisis Mt DNA tidak terdapat perbedaan yang nyata antara ras ikan kancra dari empat lokasi tersebut. Sedangkan analisis RAPD menunjukkan perbedaan yang nyata. Panjang daerah Mt DNA D-loop ikan kancra berkisar antara 700--800 bp. Satu komposit haplotype terdeteksi dengan menggunakan 4 enzim restriksi yaitu Rsa I, Nde II, Taq I, dan Sac I pada sekuens D-loop. Dua dari 20 primer RAPD menunjukkan perbedaan yang nyata di antara keempat populasi ikan kancra. Jarak genetik berdasarkan polimorfisme dua primer tersebut adalah 0,349. The aim of this research was to evaluate genetic variability of Tor soro. The genetic variability of Tor soro collected from Kuningan (Pesawahan, Gandasoli, and Ragawacana and Sumedang, West Java were examined using polymorphism of the mitochondria DNA (MtDNA D-loop and RAPD markers. Based on MtDNA D-loop analysis, there was no significant different among collection. The length size of MtDNA D-loop region was approximately 700--800 bp. A composite haplotype was detected using four endonuclease i.e. Rsa I, Nde II, Taq I, and Sac I. Two of 20 RAPD primers showed significantly different among collections. Average genetic distance based on the polymorphism of two primers was 0.349.

  6. Characterization of European Yersinia enterocolitica 1A strains using restriction fragment length polymorphism and multilocus sequence analysis.

    Science.gov (United States)

    Murros, A; Säde, E; Johansson, P; Korkeala, H; Fredriksson-Ahomaa, M; Björkroth, J

    2016-10-01

    Yersinia enterocolitica is currently divided into two subspecies: subsp. enterocolitica including highly pathogenic strains of biotype 1B and subsp. palearctica including nonpathogenic strains of biotype 1A and moderately pathogenic strains of biotypes 2-5. In this work, we characterized 162 Y. enterocolitica strains of biotype 1A and 50 strains of biotypes 2-4 isolated from human, animal and food samples by restriction fragment length polymorphism using the HindIII restriction enzyme. Phylogenetic relatedness of 20 representative Y. enterocolitica strains including 15 biotype 1A strains was further studied by the multilocus sequence analysis of four housekeeping genes (glnA, gyrB, recA and HSP60). In all the analyses, biotype 1A strains formed a separate genomic group, which differed from Y. enterocolitica subsp. enterocolitica and from the strains of biotypes 2-4 of Y. enterocolitica subsp. palearctica. Based on these results, biotype 1A strains considered nonpathogenic should not be included in subspecies palearctica containing pathogenic strains of biotypes 2-5. Yersinia enterocolitica strains are currently divided into six biotypes and two subspecies. Strains of biotype 1A, which are phenotypically and genotypically very heterogeneous, are classified as subspecies palearctica. In this study, European Y. enterocolitica 1A strains isolated from both human and nonhuman sources were characterized using restriction fragment length polymorphism and multilocus sequence analysis. The European biotype 1A strains formed a separate group, which differed from strains belonging to subspecies enterocolitica and palearctica. This may indicate that the current division between the two subspecies is not sufficient considering the strain diversity within Y. enterocolitica. © 2016 The Society for Applied Microbiology.

  7. Mouse phenotyping.

    Science.gov (United States)

    Fuchs, Helmut; Gailus-Durner, Valérie; Adler, Thure; Aguilar-Pimentel, Juan Antonio; Becker, Lore; Calzada-Wack, Julia; Da Silva-Buttkus, Patricia; Neff, Frauke; Götz, Alexander; Hans, Wolfgang; Hölter, Sabine M; Horsch, Marion; Kastenmüller, Gabi; Kemter, Elisabeth; Lengger, Christoph; Maier, Holger; Matloka, Mikolaj; Möller, Gabriele; Naton, Beatrix; Prehn, Cornelia; Puk, Oliver; Rácz, Ildikó; Rathkolb, Birgit; Römisch-Margl, Werner; Rozman, Jan; Wang-Sattler, Rui; Schrewe, Anja; Stöger, Claudia; Tost, Monica; Adamski, Jerzy; Aigner, Bernhard; Beckers, Johannes; Behrendt, Heidrun; Busch, Dirk H; Esposito, Irene; Graw, Jochen; Illig, Thomas; Ivandic, Boris; Klingenspor, Martin; Klopstock, Thomas; Kremmer, Elisabeth; Mempel, Martin; Neschen, Susanne; Ollert, Markus; Schulz, Holger; Suhre, Karsten; Wolf, Eckhard; Wurst, Wolfgang; Zimmer, Andreas; Hrabě de Angelis, Martin

    2011-02-01

    Model organisms like the mouse are important tools to learn more about gene function in man. Within the last 20 years many mutant mouse lines have been generated by different methods such as ENU mutagenesis, constitutive and conditional knock-out approaches, knock-down, introduction of human genes, and knock-in techniques, thus creating models which mimic human conditions. Due to pleiotropic effects, one gene may have different functions in different organ systems or time points during development. Therefore mutant mouse lines have to be phenotyped comprehensively in a highly standardized manner to enable the detection of phenotypes which might otherwise remain hidden. The German Mouse Clinic (GMC) has been established at the Helmholtz Zentrum München as a phenotyping platform with open access to the scientific community (www.mousclinic.de; [1]). The GMC is a member of the EUMODIC consortium which created the European standard workflow EMPReSSslim for the systemic phenotyping of mouse models (http://www.eumodic.org/[2]). Copyright © 2010 Elsevier Inc. All rights reserved.

  8. Genetic distances in soybean based on RAPD markers Distâncias genéticas em soja com base em marcadores RAPD

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    RONAN XAVIER CORRÊA

    1999-01-01

    Full Text Available Four methods were applied to determine pairwise genetic distances among five soybean genotypes which are potential genitors for a mapping population. Additionally, individual plants from the most divergent pair of genotypes were evaluated by the RAPD technique to determine their degree of homozygosity. Genetic distances based on RAPD data were calculated by the modified Rogers' distance, and also by the following arithmetical complements of similarity: simple match, Nei and Li, and Gower. These genetic distances were similar, presenting a correlation coefficient ranging from 0.99 to 1.00. In all four methods lines UFV 91-717 and Ichigowase were the most divergent ones (4.53 to 21.43%. DNA samples from five plants from each of the two most divergent genotypes were amplified with 28 different primers. Among the amplified products, only five were polymorphic in each group (2.10%, demonstrating their high intragroup degree of homozygosity. These homozygosity were maintained when DNA samples from 12 plants from each of the two most divergent genotypes were amplified. These parameters were extremely useful for the confirmation of the chosen pair of genitors to generate a mapping population.Aplicaram-se quatro métodos para determinar as distâncias genéticas entre cinco cultivares de soja, que são genitores potenciais para uma população de mapeamento genético. Adicionalmente, o grau de homozigose do par de genótipos mais divergente foi avaliado por meio da técnica de RAPD. Calcularam-se as distâncias genéticas fundadas em dados obtidos pela técnica de RAPD pela distância modificada de Rogers e pelos seguintes complementos aritméticos de similaridade: distância simples; Nei e Li, e Gower. As distâncias genéticas foram similares, apresentando valores de coeficiente de correlação de 0,99 a 1,00. Nos quatro métodos, as linhagens UFV 91-717 e Ichigowase foram as mais divergentes (4,53 to 21,43%. Amostras de DNA de cinco plantas de cada

  9. Molecular heterogeneity of Malassezia pachydermatis through RAPD-PCR = Heterogeneidade molecular da Malassezia pachydermatis através de RAPD-PCR

    Directory of Open Access Journals (Sweden)

    Patrícia da Silva Nascente

    2010-04-01

    Full Text Available Several methodologies in molecular biology have been used in theinvestigation of Malassezia pachydermatis and its differentiation into subtypes. Recent molecular research of this species includes the use of samples isolated from canine otitis externa and dermatitis, as well as from healthy animals, having in view an epidemiologicalstudy of the yeast. The aim of this study was to identify molecular differences in M. pachydermatis samples isolated from dogs with otitis externa. The M. pachydermatis strains were analyzed by means of the Random Amplification Primer DNA - Polimerase Chain Reaction (RAPD–PCR for molecular heterogeneity research. DNA extraction was carried out with phenol-chloroform and the RAPD technique using the AGAATCCGCC primer. A variation was observed in the number and arrangement of the bands among the 49 studied isolates, grouped into nine patterns. Isolate groupings were not found to be related to animal breed, age or sex. It was concluded that M. pachydermatis has differences in its molecular profile, as shown by the molecular technique (RAPD – PCR, which allows isolates to be classified into nine subtypes.Várias metodologias em biologia molecular têm sido aplicadas para estudar a M. pachydermatis diferenciando-a em subgrupos. Recentemente utiliza-se a investigação molecular desta espécie isolada de otite externa e dermatite, e também de isolados da mesma de animais hígidos, para um estudo epidemiológico da levedura. O objetivo deste trabalho foi identificar diferenças moleculares entre isolados de M. pachydermatis obtidos de casos de otite externa canina. Para isto, amostras da levedura provenientes de cães com esta enfermidade foram estudadas através da técnica de Polimorfismo de DNA Amplificado aoAcaso - Reação da Polimerase em Cadeia (RAPD–PCR para pesquisa de heterogeneidade molecular. A extração de DNA foi realizada no processo fenol-cloroformio e a técnica de RAPD foi estudada com o primer

  10. Multilocus detection of wolf x dog hybridization in italy, and guidelines for marker selection.

    Science.gov (United States)

    Randi, Ettore; Hulva, Pavel; Fabbri, Elena; Galaverni, Marco; Galov, Ana; Kusak, Josip; Bigi, Daniele; Bolfíková, Barbora Černá; Smetanová, Milena; Caniglia, Romolo

    2014-01-01

    Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past

  11. Multilocus detection of wolf x dog hybridization in italy, and guidelines for marker selection.

    Directory of Open Access Journals (Sweden)

    Ettore Randi

    Full Text Available Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus, or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis. Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the

  12. A multilocus sequence analysis approach to the phylogeny and taxonomy of the Halobacteriales.

    Science.gov (United States)

    Papke, R Thane; White, Emma; Reddy, Prajwal; Weigel, Griffin; Kamekura, Masahiro; Minegishi, Hiroaki; Usami, Ron; Ventosa, Antonio

    2011-12-01

    Members of the order Halobacteriales are obligate extreme halophiles that belong to the domain Archaea. The classification of the Halobacteriales currently relies on a polyphasic approach, which integrates phenotypic, genotypic and chemotaxonomic characterization. However, the most utilized genetic marker for phylogeny, the 16S rRNA gene, has multiple drawbacks for use with the Halobacteriales: the species of many genera exhibit large intragenic differences between multiple ribosomal RNA operons, the gene is too conserved to discriminate reliably at the species level and it appears to be the most frequently recombined gene between closely related species. Moreover, the Halobacteriales is a rapidly expanding group due to recent successes at cultivating novel strains from a diverse set of hypersaline environments; a fast, reliable, inexpensive, portable molecular method for discriminating species is required for their investigation. Recently, multilocus sequence analysis (MLSA) has been shown to be an effective tool for strain identification and taxonomic designation, even for those taxa that experience frequent lateral gene transfer and homologous recombination. In this study, MLSA was utilized for evolutionary and taxonomic investigation of the Halobacteriales. Efficacy of the MLSA approach was tested across a hierarchical gradient using 52 halobacterial strains, representing 33 species (including names without standing in nomenclature) and 14 genera. A subset of 21 strains from the genus Haloarcula was analysed separately to test the sensitivity and relevance of the MLSA approach among closely related strains and species. The results demonstrated that MLSA differentiated individual strains, reliably grouped strains into species and species into genera and identified potential novel species and also family-like relationships. This study demonstrates that MLSA is a rapid and informative molecular method that will probably accommodate strain analysis at any taxonomic

  13. Differing lifestyles of Staphylococcus epidermidis as revealed through Bayesian clustering of multilocus sequence types.

    Science.gov (United States)

    Thomas, Jonathan C; Zhang, Liangfen; Robinson, D Ashley

    2014-03-01

    Staphylococcus epidermidis is part of the normal bacterial flora of human skin and a leading cause of infections associated with indwelling medical devices. Previous phylogenetic analyses of subgenomic data have been unable to distinguish between S. epidermidis strains with nosocomial or commensal lifestyles, despite the identification of specific phenotypes and accessory genes that may contribute to such lifestyles. To attempt to better define the population structure of this species, the international S. epidermidis multilocus sequence typing database was analyzed with the Bayesian clustering programs STRUCTURE and BAPS. A total of six genetic clusters (GCs) were identified. A local population of S. epidermidis from clinical specimens was classified according to these six GCs, and further characterized for antibiotic susceptibilities, biofilm, and various genetic markers. GC5 was abundant and significantly enriched for isolates that were resistant to four classes of antibiotics, high biofilm production, and positive for the virulence markers icaA, IS256, and sesD/bhp, indicating its potential clinical relevance. In contrast, GC2 was rare and contained the only isolates positive for the putative commensal marker, fdh. GC1 and GC6 were abundant but not significantly associated with any of the examined characteristics, except for sesF/aap and GC6. GC3 was rare and identified as a potential genetic sink that received, but did not donate, core genetic material from other GCs. In conclusion, population genetics analyses were essential for identifying clusters of strains that may differ in their adaptation to nosocomial or commensal lifestyles. These results provide a new, population genetics framework for studying S. epidermidis. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Freqüência de híbridos em cruzamento entre tangerina 'cravo' e laranja 'pêra': análise de marcadores morfológicos e RAPD Hybrid frequency between tangerine 'cravo' and orange 'pêra' crossing: analysis of morphological and RAPD markers

    Directory of Open Access Journals (Sweden)

    ROBERTO PEDROSO DE OLIVEIRA

    2000-09-01

    Full Text Available Os objetivos deste trabalho foram avaliar a freqüência de híbridos de cruzamento entre tangerina 'Cravo' (Citrus reticulata Blanco e laranja 'Pêra' (Citrus sinensis (L. Osbeck, o uso de marcadores morfológicos e moleculares (RAPD na identificação precoce de plantas zigóticas, e a variabilidade dos híbridos. A porcentagem de híbridos foi maior na população germinada em placas de Petri (19,4%. Verificou-se que quanto maior a competição entre os "seedlings" por espaço e nutrientes, menor a freqüência de plantas híbridas. A identificação dos híbridos não foi possível apenas com o uso de marcadores morfológicos. A análise morfológica dos híbridos revelou elevada variabilidade.The objectives of this work were to evaluate the hybrid frequency from the cross between tangerine 'Cravo' (Citrus reticulata Blanco and sweet orange 'Pêra' (Citrus sinensis (L. Osbeck, the use of morphological and RAPD markers for early identification of zygotic plants between parents with similar phenotype, and the morphological variability among the hybrids. Plants germinated on Petri dishes showed the higher hybrid percentage (19.4%. Hybrid plant frequency was inversely proportional to the competition level for space and nutrients among the hybrids. Accurate hybrid identification is not possible using morphological markers alone. The hybrids selected showed high morphological variability.

  15. Characterization of environmental Pseudomonas aeruginosa using multilocus sequence typing scheme.

    Science.gov (United States)

    Radó, Júlia; Kaszab, Edit; Petrovics, Tünde; Pászti, Judit; Kriszt, Balázs; Szoboszlay, Sándor

    2017-10-01

    The objectives of this study were to examine environmental (hydrocarbon degrading) Pseudomonas aeruginosa isolates with Multilocus Sequence Typing (MLST) and to determine their relevant features, such as serotype, virulence genes, biofilm forming ability and hydrocarbon degrading capacity. The diversity of environmental isolates was assessed with an MLST scheme. Investigation of virulence determinants included serotyping, hemolytic activity test and the detection of virulence genes exoS, exoY, exoT, exoU, exoA. Biofilm forming ability was examined in a modified microtiter assay, hydrocarbon degrading capacity was determined with gravimetric methods. The majority of environmental isolates shared the same MLST profiles with isolates of cystic fibrosis (CF). Virulence patterns and serotypes were slightly connected to the phylogenetic localization, but further clinically important features such as antibiotic resistance were not. At least one of the examined environmental isolates was multidrug-resistant, virulent and had biofilm forming ability such as nosocomial P. aeruginosa and retained its hydrocarbon degradation ability. The current theses that distinguish isolates originating from different sources are questionable; environmental P. aeruginosa can be a potential risk to public health and cannot be excluded as an external (non-nosocomial) source of infections, especially in patients with CF. Further studies such as pulsed-field gel electrophoresis (PFGE) and the determination of other clinically important virulence factors are needed to confirm these findings.

  16. Multilocus Sequence Typing for Interpreting Blood Isolates of Staphylococcus epidermidis

    Directory of Open Access Journals (Sweden)

    Prannda Sharma

    2014-01-01

    Full Text Available Staphylococcus epidermidis is an important cause of nosocomial infection and bacteremia. It is also a common contaminant of blood cultures and, as a result, there is frequently uncertainty as to its diagnostic significance when recovered in the clinical laboratory. One molecular strategy that might be of value in clarifying the interpretation of S. epidermidis identified in blood culture is multilocus sequence typing. Here, we examined 100 isolates of this species (50 blood isolates representing true bacteremia, 25 likely contaminant isolates, and 25 skin isolates and the ability of sequence typing to differentiate them. Three machine learning algorithms (classification regression tree, support vector machine, and nearest neighbor were employed. Genetic variability was substantial between isolates, with 44 sequence types found in 100 isolates. Sequence types 2 and 5 were most commonly identified. However, among the classification algorithms we employed, none were effective, with CART and SVM both yielding only 73% diagnostic accuracy and nearest neighbor analysis yielding only 53% accuracy. Our data mirror previous studies examining the presence or absence of pathogenic genes in that the overlap between truly significant organisms and contaminants appears to prevent the use of MLST in the clarification of blood cultures recovering S. epidermidis.

  17. Genetic analysis of dermatophilus spp. using multilocus enzyme electrophoresis.

    Science.gov (United States)

    Trott, D J; Masters, A M; Carson, J M; Ellis, T M; Hampson, D J

    1995-01-01

    Multilocus enzyme electrophoresis was used to examine a collection of 41 mainly Australian isolates of Dermatophilus congolensis that had been cultured from sheep, cattle, horses, a goat, a marsupial and Chelonids. Allelic variation was examined at 16 enzyme loci. The isolates were divided into eight distinct electrophoretic types (ETs) with a mean genetic diversity per locus of 0.41. The three isolates from Chelonids represented a distinct clone in ET 1 which was separated from the remaining cluster of isolates of D. congolensis by a genetic distance of 0.852. These findings supported a previous proposal that the isolates from Chelonids represent a new species of Dermatophilus. The other 38 D. congolensis isolates were separated into two divisions (I and II) by a genetic distance of 0.560. The divisions were both subdivided into groups that either only contained alpha-hemolytic or beta-hemolytic isolates, but all isolates in each ET had only one hemolytic pattern. Isolates originating from the same animal species, or from the same geographic location, were not all closely related genetically. The allocation of isolates into ETs correlated well with their distribution into DNA restriction endonuclease analysis patterns previously established for the collection. Although relatively few distinct strains of D. congolensis were identified amongst the collection, significant genetic diversity existed within this population.

  18. Extraordinary multilocus genetic organization in mole crickets, Gryllotalpidae.

    Science.gov (United States)

    Nevo, E; Beiles, A; Korol, A B; Robin, Y I; Pavlicek, T; Hamilton, W

    2000-04-01

    Allozymic diversity at 21 loci was analyzed in 470 individuals of three species of mole cricket superspecies, Gryllotalpa gryllotalpa (two new chromosomal species, G. tali and G. marismortui) and G. africana in Israel, which are distributed along a southward transect of increasing aridity. Two outstanding findings emerged in G. tali and G. marismortui: (1) genetic polymorphism was high but heterozygosity very low, indicating significant deviations from Hardy-Weinberg expectations; and (2) significant linkage disequilibria at an unprecedented level for outbreeders and remarkable intersite differences. The results may characterize subterranean gryllotalpids worldwide because a single sample of Neocurtilla hexadactyla from Tefé, Amazonia, shows the same features. Significant variation of heterozygote paucity among loci, combined with the biology of the species, rejects the simple explanation of inbreeding or any other single explanatory model. Likewise, direct selection against heterozygotes or specific multilocus associations can explain, but is not necessary nor likely to explain, the observed results in mole crickets. To explain these results, we developed a multiple-factor mathematical model combining niche viability selection, niche choice, and positive assortative mating. This model involves a special case of Wahlund effect and inbreeding. Simulations based on this model showed that a combination of these three mechanisms may produce the observed distribution of alleles, via selection on a few loci, to affect the entire genome organization.

  19. Multilocus sequence analysis for Leishmania braziliensis outbreak investigation.

    Directory of Open Access Journals (Sweden)

    Mariel A Marlow

    2014-02-01

    Full Text Available With the emergence of leishmaniasis in new regions around the world, molecular epidemiological methods with adequate discriminatory power, reproducibility, high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease. As multilocus sequence analysis (MLSA has been projected as the future gold standard technique for Leishmania species characterization, we propose a MLSA panel of six housekeeping gene loci (6pgd, mpi, icd, hsp70, mdhmt, mdhnc for investigating intraspecific genetic variation of L. (Viannia braziliensis strains and compare the resulting genetic clusters with several epidemiological factors relevant to outbreak investigation. The recent outbreak of cutaneous leishmaniasis caused by L. (V. braziliensis in the southern Brazilian state of Santa Catarina is used to demonstrate the applicability of this technique. Sequenced fragments from six genetic markers from 86 L. (V. braziliensis strains from twelve Brazilian states, including 33 strains from Santa Catarina, were used to determine clonal complexes, genetic structure, and phylogenic networks. Associations between genetic clusters and networks with epidemiological characteristics of patients were investigated. MLSA revealed epidemiological patterns among L. (V. braziliensis strains, even identifying strains from imported cases among the Santa Catarina strains that presented extensive homogeneity. Evidence presented here has demonstrated MLSA possesses adequate discriminatory power for outbreak investigation, as well as other potential uses in the molecular epidemiology of leishmaniasis.

  20. Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces.

    Science.gov (United States)

    Labeda, David P

    2011-10-01

    The identification and classification of species within the genus Streptomyces is difficult because there are presently 576 species with validly published names and this number increases every year. The value of multilocus sequence analysis applied to the systematics of Streptomyces species has been well demonstrated in several recently published papers. In this study the sequence fragments of four housekeeping genes, atpD, recA, rpoB and trpB, were determined for the type strains of 10 known phytopathogenic species of the genus Streptomyces, including Streptomyces scabiei, Streptomyces acidiscabies, Streptomyces europaeiscabiei, Streptomyces luridiscabiei, Streptomyces niveiscabiei, Streptomyces puniciscabiei, Streptomyces reticuliscabiei, Streptomyces stelliscabiei, Streptomyces turgidiscabies and Streptomyces ipomoeae, as well as six uncharacterized phytopathogenic Streptomyces isolates. The type strains of 52 other species, including 19 species observed to be phylogenetically closely related to these, based on 16S rRNA gene sequence analysis, were also included in the study. Phylogenetic analysis of single gene alignments and a concatenated four-gene alignment demonstrated that the phytopathogenic species are taxonomically distinct from each other in spite of high 16S rRNA gene sequence similarities and provided a tool for the identification of unknown putative phytopathogenic Streptomyces strains at the species level.

  1. Multilocus Phylogenetics Show High Intraspecific Variability within Fusarium avenaceum

    Directory of Open Access Journals (Sweden)

    Tomasz Kulik

    2011-08-01

    Full Text Available Fusarium avenaceum is a common soil saprophyte and plant pathogen of a variety of hosts worldwide. This pathogen is often involved in the crown rot and head blight of cereals that affects grain yield and quality. F. avenaceum contaminates grain with enniatins more than any species, and they are often detected at the highest prevalence among fusarial toxins in certain geographic areas. We studied intraspecific variability of F. avenaceum based on partial sequences of elongation factor-1 alpha, enniatin synthase, intergenic spacer of rDNA, arylamine N-acetyltransferase and RNA polymerase II data sets. The phylogenetic analyses incorporated a collection of 63 F. avenaceum isolates of various origin among which 41 were associated with wheat. Analyses of the multilocus sequence (MLS data indicated a high level of genetic variation within the isolates studied with no significant linkage disequilibrium. Correspondingly, maximum parsimony analyses of both MLS and individual data sets showed lack of clear phylogenetic structure within F. avenaceum in relation to host (wheat and geographic origin. Lack of host specialization indicates no host selective pressure in driving F. avenaceum evolution, while no geographic lineage structure indicates widespread distribution of genotypes that resulted in nullifying the effects of geographic isolation on the evolution of this species. Moreover, significant incongruence between all individual tree topologies and little clonality is consistent with frequent recombination within F. avenaceum.

  2. Development of a multilocus sequence typing scheme for Rhodococcus equi.

    Science.gov (United States)

    Duquesne, Fabien; Houssin, Emilie; Sévin, Corinne; Duytschaever, Lucille; Tapprest, Jackie; Fretin, David; Hébert, Laurent; Laugier, Claire; Petry, Sandrine

    2017-10-01

    Rhodococcus equi causes pulmonary and extrapulmonary infections in animals and humans, with endemic situations and significant young foal mortality in stud farms worldwide. Despite its economic impact in the horse-breeding industry, the broad geographic and host distribution, global diversity and population structure of R. equi remain poorly characterised. In this context, we developed a multilocus sequence typing (MLST) scheme using 89 clinical and environmental R. equi of various origins and eight Rhodococcus sp. Data can be accessed at http://pubmlst.org/rhodococcus/. A clonal R. equi population was observed with 16 out of 37 sequence types (STs) grouped into six clonal complexes (CC) based on single-locus variants. One of the six CCs (CC3) is not host-specific, suggesting potential exchanges between different R. equi reservoirs. Most of the virulent equine R. equi CCs/unlinked STs were plasmid-type-specific. Despite this, marked genetic variability with the circulation of multiple R. equi genotypes was generally observed even within the same animal. Focusing on outbreaks, data indicated (i) the potential contagious transmission of R. equi during the 2012-Mayotte equine outbreak because of the poor genotype diversity of clinical strains; (ii) a potential porcine outbreak among the 30 Belgian farms investigated in 2013. This first Rhodococcus equi MLST is a powerful tool for further epidemiological investigations and population biology studies of R. equi isolates. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Genotyping of Nocardia farcinica with multilocus sequence typing.

    Science.gov (United States)

    Du, P; Hou, X; Xie, Y; Xu, S; Li, L; Zhang, J; Wan, K; Lou, Y; Li, Z

    2016-05-01

    Nocardia are aerobic Gram-positive saprophytes that are widely distributed in nature, but some species cause nocardiosis, especially opportunistic infections that affect immunocompromised patients mostly. In this study, we developed a multilocus sequence typing (MLST) scheme using seven housekeeping genes (gyrB, hsp65, secA1, rpoB, rpoA, recA, and trpB) for genotyping the most common clinical species, Nocardia farcinica (37 clinical isolates from the patients with nocardiosis and seven from animals in China and 15 reference strains). The results showed that using these loci could perform accurate identification among different species, and high discriminative power within the N. farcinica species. Of the 59 N. farcinica isolates, 44 sequence types have been identified; 32 STs covering 46 isolates could be assigned to six clonal complexes that encompassed most of the collected strains. The results showed that these strains displayed a sufficiently informative population structure using this method. Our study also provided a suitable approach for epidemiological studies of N. farcinica. A large clonal complex comprising 16 strains was identified, and was notable for its wide distribution and host adaptation. This complex should be monitored closely and merits further study.

  4. A multilocus timescale for the origin of extant amphibians.

    Science.gov (United States)

    San Mauro, Diego

    2010-08-01

    One of the most hotly debated topics in vertebrate evolution is the origin of extant amphibians (Lissamphibia). The recent contribution of molecular data is shedding new light on this debate, but many important questions still remain unresolved. I have assembled a large and comprehensive multilocus dataset (the largest to date in terms of number and heterogeneity of sequence characters) combining mitogenomic and nuclear information from 23 genes for a sufficiently dense taxon sampling with the key major lineages of extant amphibians. This dataset has been used to infer a robust phylogenetic framework and molecular timescale for the origin of extant amphibians employing the most recent phylogenetic and dating methods, as well as several alternative calibration schemes. The monophyly of each extant amphibian order and the sister group relationship between frogs and salamanders (Batrachia hypothesis) are all strongly supported. Dating analyses (all methods and calibration schemes used) suggest that the origin of extant amphibians (divergence between caecilian and batrachians) occurred in the Late Carboniferous, around 315 Mya, and the divergence between frogs and salamanders occurred in the Early Permian, around 290 Mya. These age estimates are more consistent with the fossil record than previous older estimates, and more in line with the Temnospondyli or the Lepospondyli hypotheses of lissamphibian ancestry (although the polyphyly hypothesis cannot be completely ruled out). Copyright 2010 Elsevier Inc. All rights reserved.

  5. High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires

    DEFF Research Database (Denmark)

    Tulsiani, Suhella; Craig, S B; Graham, G C

    2010-01-01

    could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild...

  6. Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE using RAPD Markers

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    Luciana do Valle Rego Oliveira

    2010-04-01

    Full Text Available In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95% were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.Neste trabalho, marcadores moleculares de RAPD foram utilizados para acessar a variabilidade genética e estudar as relações interespecíficas e intraespecífica em um grupo de 37 espécies, compreendendo 56 plantas individuais. Um total de 15 primers foram selecionados para amplificação do DNA. De um total de 221 bandas analisadas, 209 (95% foram polimórficas. O nível de similaridade genética interespecífica variou de 37% entre Catasetum complanatum e Catasetum laminatums a 83% entre Catasetum triodon e Catasetum uncatum. A similaridade genética intraespecífica variou de 88% entre os indivíduos de Catasetum triodon a 93% entre os indivíduos de Catasetum atratum e Catasetum macrocarpum. Os resultados deste trabalho contribuem para o entendimento das relações interespecíficas no gênero Catasetum, para definir estratégias para o estabelecimento de um banco de germoplasma e para dar suporte a programas de melhoramento.

  7. Genetic and metabolic diversity in Stevia rebaudiana using RAPD and HPTLC analysis.

    Science.gov (United States)

    Chester, Karishma; Tamboli, Ennus Tajuddin; Parveen, Rabea; Ahmad, Sayeed

    2013-06-01

    Stevia rebaudiana Bertoni (Asteraceae) is an important medicinal plant and is much used due to its zero calories sweetening property. Stevia leaves as well as its extracts and pure compounds are currently used in the preparation of several medicines, food products and neutraceuticals. To study the genetic and metabolic variability in S. rebaudiana among accessions of different geographical regions of India using random amplified polymorphic DNA (RAPD) markers and high-performance thin layer chromatography (HPTLC) analysis. The RAPD analysis of Stevia rebaudiana (11 accessions) was carried out using 20 random operon primers. Dendrogram was constructed for cluster analysis based on the unweighted pair group method with arithmetic means (UPGMA) using Winboot. The HPTLC analysis of all samples was carried out on silica using acetone:ethyl acetate:water (5:4:1, v/v/v) for fingerprinting and quantification of stevioside and rebaudioside A at 360 nm after spraying with anisaldehyde sulphuric acid. Ten out of 20 primers screened were found most informative; amplification products of the genotypes yielded a total of 87 scorable bands (67 polymorphic), whereas genetic similarity (GS) coefficient (0.01-0.08) and polymorphism (67.24-92.40%) showed huge variability. Similarly, HPTLC analysis showed large variation among different samples with respect to their presence or absence of metabolite and their concentration. Out of the 11 Stevia accessions, Delhi and Mohali varieties showed much relatedness with each other and were concluded to be the superior genotype in context to RAPD and HPTLC analysis. The information obtained here could be valuable for devising strategies for cultivating this medicinal plant.

  8. Analysis of genetic diversity and structure in Ethiopian populations of Phytolacca dodecandra using RAPD.

    Science.gov (United States)

    Semagn, K; Stedje, B; Bjornstad, A

    2001-01-01

    The genetic diversity and structure in 17 wild populations (249 individuals) of Phytolacca dodecandra (endod) sampled along altitudinal gradients of 1600-3000 meters above sea level (m.a.s.l.) in Ethiopia was studied using random amplified polymorphic DNA (RAPD). A total of 70 polymorphic loci (P) scored from 12 RAPD primers were used to calculate different diversity indices within and between populations, habitats, geographical regions, climatic zones and altitude groups. The number of polymorphic loci and overall Shannon information measure (H) in the populations varied from 30 to 55 and from 0.228 to 0.418, respectively. In general, differences in population variability were found significantly correlated to effective population size. Both P and H were significantly higher in an undisturbed than in a disturbed habitat, and in the lowland and central-highland than in the highland altitude group. However, for both parameters the differences were not statistically significant between regions and climatic zones. Genetic distance between populations varied from 0.301 to 0.628. Cluster analysis performed using the genetic distance matrix revealed a clear separation of the highland populations (2501-3000 m.a.s.l.) from those of the lowland/central-highlands (1600-2500 m.a.s.l.) irrespective of their geographical regions and climatic zones. Analysis of molecular variance (AMOVA) indicated that differences in habitat, geographical regions and climatic zones explained 4.6%, 2.5% and 4.6%, respectively. But none of these differences were significant. Altitude explained 17.2% of the total variance and was highly significant. The data, therefore, clearly indicated the association of genetic structure in endod with altitude. The proportion of RAPD variation found among populations (21.2-35.0%) was somewhat intermediate between values reported for selfing and outcrossing species. The fixation index (FST) values (0.350 to 0.384) indicated very high genetic differentiation among

  9. Genetic variation detected by RAPD markers in natural populations of babassu palm (Attalea speciosa Mart.).

    Science.gov (United States)

    Santos, M F; Damasceno-Silva, K J; Carvalhaes, M A; Lima, P S C

    2015-06-10

    The purpose of this study was to analyze the effects of management on the genetic structure of natural populations of Attalea speciosa in the State of Piauí, Brazil, using random-amplified polymorphic DNA (RAPD) markers. Three babassu populations under different management systems were selected. Polymerase chain reactions were performed for 20 RAPD primers. A total of 146 bands were generated, 141 of which were polymorphic (96.58%), with a variation of 4 and 12 loci and an average of 7 bands per primer. A dendrogram revealed a clear separation between the three populations (0.57). Data reliability and node consistency were verified by bootstrap values and the cophenetic correlation coefficient (88.15%). Coefficients of similarity between pairs of genotypes ranged from 0.26 to 0.86, with a mean of 0.57. Nei's genetic diversity index (HE) value of the population sampled in Teresina was 0.212, of Esperantina it was 0.195, and of José de Freitas it was 0.207. After the HE was decomposed, the complete diversity was found to be 0.3213. Genetic differentiation between populations was 0.362, and the estimation of gene flow between populations was low (0.879). Analysis of molecular variance revealed that 59.52% of the variation was contained within populations, and 40.48% was between populations. RAPD markers were effective for genetic diversity analysis within and between natural babassu populations, and exhibited a high level of polymorphism. Genetic diversity was the highest within populations; variability was lower in the managed populations than in the undisturbed populations.

  10. Genome flux in tomato cell clones cultured in vitro in different physiological equilibria. II. A RAPD analysis of variability.

    Science.gov (United States)

    Bogani, P; Simoni, A; Lio', P; Scialpi, A; Buiatti, M

    1996-10-01

    An analysis of the effect of changing physiological conditions on genome evolution in tomato cell populations has been carried out on long-term in vitro cultured clones grown on different auxin-cytokinin equilibria or selected for low-high competence for active defense against Fusarium oxysporum f.sp. lycopersici. RAPD analysis, confirmed through pattern rehybridization, was used as a random tool to measure the genetic variability. Through the use of a modified ANOVA, variation was shown to depend on both the initial genotype and the physiological conditions. Pattern correlation analysis through a mutual information algorithm suggested the fixation of RAPD patterns specific to physiological equilibria. The results are discussed in view of the possible relevance for evolution at hierarchical levels higher than cell populations. Key words : tomato clones, somaclonal variation, RAPD, coadaptation.

  11. Caracterización de bacterias aisladas en larvas de p.v. mediante rapds

    OpenAIRE

    Cedeño, Ricardo

    2003-01-01

    Caracterización de bacterias aisladas en larvas de P.V. mediante RAPDs La “Vibriosis luminiscente” reportada por varios laboratorios de larvas del Ecuador es asociada principalmente a la bacteria Vibrio harveyi. Los métodos de identificación bacteriana tradicionales se basan en la observación de características morfológicas y pruebas bioquímicas, sin embargo la identificación de especies bacterianas y en especial de Vibrios ambientales ha presentado ciertas dificultades debido al tiempo qu...

  12. Identification of the Polish strains of Chalara ovoidea using RAPD molecular markers

    OpenAIRE

    Tadeusz Kowalski; Wojciech Kraj

    2011-01-01

    On the basis of morphological features and RAPD markers the strains of Chalara ovoidea found in Poland on planks and on stems of beech trees were identified. As reference strains the cultures taken from CBS Utrecht were employed; they were cultures CBS 354.76 and CBS 136.88. The amplification of genomic DNA was conducted using 10 primers (OPA01-OPA10), 7 of which (OPA01-OPA05, OPA09, OPA10) gave positive results. In total 42 fragment of DNA (bands) were obtained. In case of primers OPA03, OPA...

  13. Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.

    Science.gov (United States)

    Zargar, Sajad Majeed; Farhat, Sufia; Mahajan, Reetika; Bhakhri, Ayushi; Sharma, Arjun

    2016-01-01

    Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

  14. Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions

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    A.G.A. Khaled

    2015-12-01

    Full Text Available Genetic variability and identification of some molecular markers were studied in twenty promising lines of wheat using agronomic traits, ISSR (inter simple sequences repeats and RAPD (random amplified polymorphic DNA markers. Significant variation was evidenced in all agronomic traits. The lines proved to be superior to the check cultivar Sahel1 in yield and its component traits. Lines L2, L7 and L8 were the best in most yield component traits in both seasons. Moreover, Lines L2, L4, L5, L7 and L8 showed drought tolerance by which they displayed high performance in agronomic traits as well as a low drought susceptibility index. The percentage of polymorphism was 39.3% and 53.2% for ISSRs and RAPDs, respectively. UBC-881 belonged to penta-nucleotide repeat sequences (GGGTG that produced the highest level of polymorphism, while UBC-846 belonged to di-nucleotide repeat sequences (CA that produced the lowest level of polymorphism. Genetic similarities among wheat lines based on ISSR and RAPD markers ranged from 0.81 to 1.00 and from 0.86 to 0.98, respectively. There was a low average of PIC (polymorphism information content values which were 0.10 (ISSR and 0.15 (RAPD. The RAPD technique exhibited a higher marker index (MI = 0.69 compared to ISSR (MI = 0.43. There was insignificant correlation between ISSR and RAPD data (0.168, p > 0.05. There were two markers (UBC-881450bp and OPF-10540bp, on each of which two traits regressed significantly. The associated markers each explained a maximum regression of 18.92–34.95% of the total available variation for individual associated traits.

  15. Identification of species of leishmania isolated from patients with cutaneous leishmaniasis in Kermanshah; using RAPD-PCR technique

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    Yazdan Hamzavi

    2010-09-01

    Full Text Available Annually many numbers of pationts with Cutaneous Leishmaniasis (CL have been reported in Kermanshah province- IRAN. The study aimed to identify species of Leishmania isolated from patients with CT in Kermanshah. Seven isolates of Leishmania obtained from patients with CL, without any travelling to other provinces, were cultured in NNN medium. After mass production of leptomonads in RPMI 1640 medium DNA was purified and the species were diagnosed using RAPD-PCR technique. The study of electrophoretic fingerprints of the product of RAPD-PCR in seven isolates showed that Leshmania major was the causative agent of CL patients in Kermanshah province. More studies in this field recommended.

  16. GENETIC DIVERSITY OF WILD AND FARMED KALIBAUS (Labeo calbasu, Hamilton, 1822) BY RAPD ANALYSIS OF THE GENOMIC DNA

    OpenAIRE

    Mostafa, M. G.; Ishtiaq Ahmed, A. S.; M. G. Mustafa; M.G. Rabbane; M.G. Islam; Rafiquzzaman, S. M.

    2009-01-01

    Genetic diversity of two wild Kalibaus, Labeo calbasu populations and one hatchery stock was studied using random amplified polymorphic DNA (RAPD) method. The three 10–mer random primers (OPA01, OPB02 and OPC03) yielded a total of 26 reproducible and consistently scorable RAPD bands of which 15 (57.69%) were considered as polymorphic (P95) indicating a high level of genetic variation in all the studied populations. Among the three populations, Padma population shows low level of genetic diver...

  17. Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

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    Daniele Salvi

    Full Text Available The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML and Bayesian (BA methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA and coalescent based (BA approaches and consistently supported three main clades: (i Crassostrea, (ii Saccostrea, and (iii an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea, Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea and Ostreinae (including Ostreinae and Lophinae taxa are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

  18. Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

    Science.gov (United States)

    Salvi, Daniele; Macali, Armando; Mariottini, Paolo

    2014-01-01

    The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

  19. Global convergence properties in multilocus viability selection models: the additive model and the Hardy-Weinberg law.

    Science.gov (United States)

    Karlin, S; Liberman, U

    1990-01-01

    A natural coordinate system is introduced for the analysis of the global stability of the Hardy-Weinberg (HW) polymorphism under the general multilocus additive viability model. A global convergence criterion is developed and used to prove that the HW polymorphism is globally stable when each of the loci is diallelic, provided the loci are overdominant and the multilocus recombination is positive. As a corollary the multilocus Hardy-Weinberg law for neutral selection is derived.

  20. Phylogeny and classification of Dickeya based on multilocus sequence analysis.

    Science.gov (United States)

    Marrero, Glorimar; Schneider, Kevin L; Jenkins, Daniel M; Alvarez, Anne M

    2013-09-01

    Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.

  1. Multilocus sequence typing of Ochrobactrum spp. isolated from gastric niche.

    Science.gov (United States)

    Kulkarni, Girish; Gohil, Kushal; Misra, Vatsala; Kakrani, Arjun L; Misra, Sri P; Patole, Milind; Shouche, Yogesh; Dharne, Mahesh

    The human stomach is colonized by diverse bacterial species. The presence of non-Helicobacter pylori bacteria in urease-positive biopsies of individuals has been reported. Bacteria belonging to the Ochrobactrum genus have been documented in the human gastric niche. The co-occurrence of Ochrobactrum spp. with H. pylori was previously reported in an antral biopsy of a non-ulcer dyspeptic (NUD) subject from Northern India. There is no information on the genetic diversity of Ochrobactrum spp. isolated from the gastric niche in the stomach. We aimed to study the species distribution and diversity of Ochrobactrum spp. with and without H. pylori in urease-positive biopsies across three different geographical regions in India. Sixty-two Ochrobactrum isolates recovered from patients with an upper gastric disorder (n=218) were subjected to molecular identification and multilocus sequence typing. H. pylori DNA was found in the majority of biopsies, which had a variable degree of Ochrobactrum spp present. Interestingly, some of the urease-positive biopsies only had Ochrobactrum without any H. pylori DNA. Based on phylogenetic analysis, the Ochrobactrum isolates were distributed into the O. intermedium, O. anthropi and O. oryzae groups. This indicates there are multiple species in the gastric niche irrespective of the presence or absence of H. pylori. Antibiotyping based on colistin and polymyxin B could differentiate between O. intermedium and O. anthropi without revealing the resistance-driven diversity. Considering the prevalence of multiple Ochrobactrum spp. in the human gastric niche, it is important to evaluate the commensal and/or pathogenic nature of non-H. pylori bacteria with respect to their geographical distribution, lifestyle and nutrition needs. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

  2. Relationships between some Thai cultivars of pineapple (Ananas comosus revealed by RAPD analysis

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    Siam Popluechai

    2007-11-01

    Full Text Available RAPD analysis of nine Thai pineapple cultivars, including 'Phulae', 'Sawee', 'Tradsithong', 'Phuket', 'Pattavia', 'Intrachitdang', 'Intrachitkhow', 'Petburi No.1', and 'Nanglae', showed that, of 40 arbitrary 10- mer primers, 17 primers gave 206 DNA fragments ranging from 510 to 4,700 bp. One hundred and forty-five (70.4% of the amplified fragments were polymorphic. RAPD analysis using NTSYS-pc Version 2.01e also showed that the similarity coefficients among the cultivars were 0.643-0. 963. The dendrogram indicated that the cultivars were clustered into 3 groups, consistent with the morphological data. The first group, consisting of 'Phuket', 'Phulae', 'Tradsithong', 'Sawee', and 'Petburi No.1', had morphological characteristics of the Queen group, while those of the second ('Intrachitdang' and 'Intrachitkow' and the third ('Nanglae' and 'Pattavia' groups could be determined morphologically to be members of the Spanish and Cayenne groups, respectively. 'Intrachitdang' and 'Intrachitkow' have similarity coefficient of 0.963, while that of 'Phulae' and 'Phuket' is 0.950. These pairs of cultivars are probably the same cultivars. The morphological differences between them are probably caused by mutations, differences in environment and agricultural practices, or combinations of these factors.

  3. Essential oil diversity and molecular characterization of Ephedra species using RAPD analysis

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    M. Ehtesham-Gharaee

    2017-07-01

    Full Text Available Background and objectives: The genus Ephedra (Ephedraceae consists of about 40 species of mostly shrubs and rarely small trees around the world. In the present study, the essential oil (EO diversity and genetic relationships were investigated in six Ephedra species from Iran using Random Amplified Polymorphic DNA (RAPD markers. Methods: Theplants were collected from two different provinces; Azarbayjan (north-west and Khorasan (north-east of Iran. The EOs were obtained by hydro-distillation and analyzed by GC and GC/MS. The DNA was extracted from the aerial parts of the plants using a Qiagen Dneasy Plant Mini Kit. Amplification was performed using decamer RAPD primers. Results: A total of 187 bands were scored and used for the analysis of genetic distances. Genetic distance values ranged from 0.25 to 0.95.The analysis showed the highest genetic diversity (25% between E. foliata with other species. Ephedra foliata formed a distinct group. Ephedra strobilacea was found to be the most similar to E. sarcocarpa (male.Conclusion: High genetic and EO diversity was demonstrated in this genus which should be further studied in order to make more efficient use of the species and considering relevant conservation programs.

  4. Genetic variation and phylogenetic relationships in oil palm (Elaeis guineensis Jacq. based on RAPD analysis

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    Nualsri, C.

    2005-05-01

    Full Text Available The genetic variability and phylogenetic relationships in oil palm (Elaeis guineensis Jacq. were studied using RAPD (Random Amplified Polymorphic DNA. Leaf samples of 151 plants were collected from different areas in southern Thailand. DNA from the leaf samples was isolated using CTAB buffer and screened by decamer oligonucleotide primers. Among the total of 160 primers screened, 7 primers (OPB-08, OPR-11, OPT-06, OPT-19, OPAB-01, OPAB-09 and OPAB-14 were chosen to analyse for genetic variation in 151 individuals representing 52 dura, 60 tenera and 39 pisifera. Two hundred and nine amplified fragments were obtained from 7 primers with an average of 29.85 RAPD markers per primer. A dendrogram showing genetic similarities among oil palm was constructed based on polymorphic bands using UPGMA (Unweighted Pair-Group Method Using Arithmetic Average. Cluster analysis was performed using the SPSS program, which revealed four major clusters: 1 dura, tenera and pisifera from Paorong Oil Palm Company, Oil Palm Research Center, dura and tenera from private plantation in Krabi, and dura from Thepa Research Station;2 dura and tenera from Thai Boonthong Company, pisifera and tenera from Thepa Research Station, dura, tenera and pisifera from Klong Hoi Khong Research Station; 3 and 4 dura and tenera from Univanit Company, respectively. In general, a similarity index showed relatively high levels of 0.6 or greater.

  5. Morphological characterization and molecular fingerprinting of Nostoc strains by multiplex RAPD.

    Science.gov (United States)

    Hillol, Chakdar; Pabbi, Sunil

    2012-01-01

    Morphological parameters studied for the twenty selected Nostoc strains were mostly found to be consistent with the earlier reports. But the shape of akinetes observed in this study was a little deviation from the existing descriptions and heterocyst frequency was also found to be different in different strains in spite of growing in the same nitrogen free media. Multiplex RAPD produced reproducible and completely polymorphic amplification profiles for all the strains including some strain specific unique bands which are intended to be useful for identification of those strains. At least one to a maximum of two unique bands was produced by different dual primer combinations. For ten strains out of twenty, strain specific bands were found to be generated. Cluster analysis revealed a vast heterogeneity among these Nostoc strains and no specific clustering based on geographical origin was found except a few strains. It was also observed that morphological data may not necessarily correspond to the genetic data in most of the cases. CCC92 (Nostoc muscorum) and CCC48 (Nostoc punctiforme) showed a high degree of similarity which was well supported by high bootstrap value. The level of similarity of the strains ranged from 0.15 to 0.94. Cluster analysis based on multiplex RAPD showed a good fit revealing the discriminatory power of this technique.

  6. Photodynamic Treatment versus Antibiotic Treatment on Helicobacter pylori Using RAPD-PCR

    Science.gov (United States)

    El-Batanouny, M. H.; Amin, R. M.; Ibrahium, M. K.; El Gohary, S.; Naga, M. I.; Salama, M. S.

    2009-09-01

    Helicobacter pylori is one of the most common causes of chronic bacterial infections in humans and is important in the pathogenesis of gastrointestinal disease, such as duodenal ulcer, gastric ulcer, Gastric adenocarcinoma, and lymphoma. Gastric adenocarcinoma remains one of the leading causes of cancer death in the world. The objective of this study was to assess the effect of photodynamic treatment and medication treatment of Helicobacter pylori using RAPD-PCR. The lethal photosensitization effect was determined by mixing suspensions of H.pylori with Toluidine blue O (TBO) and plating out on blood agar before irradiation with Helium neon (He-Ne) 632.8 nm. The susceptibility of Helicobacter pylori isolates to metronidazole and azithromycin were examined by E-test. Nine random primers were used to screen genetic polymorphism in DNA of different H.pylori groups. Six of them produced RAPD products while three failed to generate any product. The resulting data showed that, although the overall genetic differences between control groups and laser treated groups was higher than that between control groups and azithromycin treated groups yet it still law genetic variability. The main cause of cell death of PDT using TBO as a photosensitizer was mainly cell wall and cytoplasmic membrane.

  7. Identification of Verbena officinalis based on ITS sequence analysis and RAPD-derived molecular markers.

    Science.gov (United States)

    Ruzicka, Joana; Lukas, Brigitte; Merza, Lina; Göhler, Irina; Abel, Gudrun; Popp, Michael; Novak, Johannes

    2009-09-01

    Verbenae herba is a widely used drug and consists of the aerial parts of Verbena officinalis (Verbenaceae). Until now, the identification has been performed based on morphological and phytochemical analyses, which are not reliable enough to distinguish Verbena officinalis from other relevant species of the genus Verbena. Hence, impurities and adulterants, negatively influencing the therapeutic effect of the drug, may remain undetected. In an attempt to generate an accurate authentication method we used two different DNA-based approaches: comparison of ITS sequences and molecular markers (RAPD). Both approaches generally enabled discrimination of V. officinalis from the rest of the genus despite the intraspecific variation existing within V. officinalis. The application of the two independent methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, however, a SCAR marker and primers for HRM were derived from the RAPD results. The SCAR marker could distinguish V. officinalis from all other verbena species except its closest relative V. hastata, while discrimination of V. officinalis even from V. hastata was unproblematic with HRM.

  8. Study of genetic variation in some Iranian saffron accessions using molecular markers of RAPD and ISSR

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    Majid Shokrpour

    2017-01-01

    Full Text Available Saffron (Crocus sativus L. is one of the most valuable medicinal and spice herbs in the world. In spite of the ancient cultivation history in Iran, there are limited breeding studies on the plant due to its vegetative reproduction. In order to evaluation genetic diversity of Iranian saffron germplasm, sixty-five different saffron accessions from the main cultivation areas in Khorasan including Torbat heidarieh, Gonabad, Mahvelat, Ghaenat and Ferdows were collected and were studied by molecular markers. The used RAPD and ISSR primers produced 43 and 122 polymorphic markers loci, respectively, and totally 165 markers with average of 7.5 markers by each primer, totally. Diversity index ranged from 0.36 to 0.7 with average of 0.23. Also, marker index with the average of 0.16 varied in the range of 0.2 to 0.7. The accessions from Ghaenat and Mahvelat had the maximum (83.03% and the minimum (52.73% polymorphism, respectively. Grouping the studied saffron accessions using cluster analysis displayed four distinct groups which had little correspondence to their collection areas, while clustering for the main cultivation areas had relatively good correspondence to their geographical distances. So, it is expected to have nearly approaching improvements of qualitative and quantitative yields via the selection of superior clones of saffron. Key words: Saffron, Molecular variation, Germplasm, RAPD, ISSR, Khorasan region, clustering .

  9. A new strategy for identification of currant (Ribes nigrum L.) cultivars using RAPD markers.

    Science.gov (United States)

    Huo, J; Yang, G; Zhang, Y; Li, F

    2013-06-21

    We developed a new approach using RAPD fingerprints to distinguish 37 currant cultivars from northeastern China based on optimization of RAPD by choosing 11 nucleotide primers and strict screening PCR annealing temperature. We found that the manual cultivar identification diagram (MCID) approach clearly developed fingerprints from 8 different primers that were useful for cultivar identification; a cultivar identification diagram (CID) was readily constructed. This CID allows efficient currant cultivar identification, providing information to separate all the currant cultivars from each other, based on the detail polymorphic bands from the corresponding primers, which were marked in the correct positions on the currant CID. According to the CID, 10 currant cultivars in 5 groups were randomly selected for the referable and workable identification of this strategy. The results proved the workability and efficiency of the MCID method, facilitating the identification of fruit cultivars with DNA markers. This MCID approach will be useful for early identification of seedlings in the nursery industry and protection of cultivar rights.

  10. Infraspecific differentiation of garlic (Allium sativum L.) by isozyme and RAPD markers.

    Science.gov (United States)

    Maaß, H I; Klaas, M

    1995-07-01

    Garlic (Allium sativum L.) is a sterile species of considerable variability with respect to morphological and physiological features. The crop presumably originated in West to Middle Asia from its progenitor A. longicuspis Regel and was transported from there to the Mediterranean and other areas of cultivation. In order to clarify older classification schemes, often based on small or biased collections, we used isozyme and RAPD markers to analyze and structure a collection of 300 accessions, many of which were gathered in Middle Asia close to the assumed center of origin. All of the accessions were first investigated with isozymes, and 48 were selected for a RAPD analysis. The resulting molecular markers were used to construct neighbor-joining dendrograms to group the accessions and to indicate the genetic distances between them. Based on the dendrograms and in conjunction with some morphological features, we propose an infraspecific classification of garlic with four major groups. In agreement with the results of other workers, A. longicuspis lies within the range of the species A. sativum. Numerous forms with varying degrees of domestication are part of our longicuspis group, from which presumably the more derived cultivar groups originated. The origin and spreading of the crop are discussed with respect to the geographical distribution and the genetic distances of the accessions.

  11. Diversidade genética entre acessos de açaizeiro baseada em marcadores RAPD Genetic diversity among accessions of assai palm based on rapd markers

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    Maria do Socorro Padilha de Oliveira

    2007-12-01

    Full Text Available Caracterizou-se a diversidade genética entre acessos de açaizeiro por meio de marcadores RAPD. Foram analisados 116 acessos conservados na coleção de germoplasma da Embrapa Amazônia Oriental, Belém, PA com base em 28 primers. A matriz binária foi utilizada para a obtenção das dissimilaridades genéticas, pelo complemento artimético do coeficiente de similaridade de Dice, e também para a análise de bootstrap. As dissimilaridades genéticas foram representadas em um dendrograma gerado pelo método UPGMA. Os primers revelaram 263 bandas polimórficas e apresentaram ampla diversidade genética entre os acessos, variando de 0,06 a 0,67, sendo dois acessos de Chaves, PA, os mais divergentes. Mas, alguns acessos da mesma procedência apresentaram baixas dissimilaridades. O dendrograma permitiu a formação de oito grupos, delimitados pela dissimilaridade genética média (dg m: 0,40: dois formados por um único acesso; dois constituídos por dois acessos e os demais por vários subgrupos com acessos de diferentes locais. O número ideal de bandas para a estimativa da diversidade genética entre os 116 acessos foi de 180. Logo, o número de bandas empregado neste estudo foi eficiente para caracterizar com precisão as relações genéticas entre os acessos de açaizeiro. Os acessos divergentes devem ser úteis na formação de coleções nucleares e em programas de melhoramento genético.One characterized the genetic diversity among accessions of assai palm using RAPD markers. One hundred and sixteen accessions conserved in the Embrapa Eastern Amazon germplasm collection, in Belém, PA, were analyzed using 28 primers. The data of the binary matrix were used to estimate the genetic dissimilarities using the arithmetical complement of Dice similarity coefficient and also for the bootstrap analysis. The genetic dissimilarities were represented in a dendrogram generated by the UPGMA method. The primers revealed 263 polymorphic RAPD loci

  12. Peruvian Maca (Lepidium peruvianum): (I) Phytochemical and Genetic Differences in Three Maca Phenotypes.

    Science.gov (United States)

    Meissner, Henry O; Mscisz, Alina; Mrozikiewicz, Mieczyslaw; Baraniak, Marek; Mielcarek, Sebastian; Kedzia, Bogdan; Piatkowska, Ewa; Jólkowska, Justyna; Pisulewski, Pawel

    2015-09-01

    Glucosinolates were previously reported as physiologically-important constituents present in Peruvian Maca (Lepidium peruvianum Chacon) and linked to various therapeutic functions of differently-colored Peruvian Maca hypocotyls. In two separate Trials, three colours of Maca hypocotyls "Black", "Red" and "Yellow" (termed "Maca phenotypes"), were selected from mixed crops of Peruvian Maca for laboratory studies as fresh and after being dried. Individual Maca phenotypes were cultivated in the highlands of the Peruvian Andes at 4,200m a.s.l. (Junin and Ninacaca). Glucosinolate levels, chromatographic HPLC profiles and DNA variability in the investigated Maca phenotypes are presented. Genotypic profiles were determined by the ISSR-PCR and RAPD techniques. Compared to the Black and Red phenotypes, the Yellow phenotype contained much lower Glucosinolate levels measured against Glucotropaeolin and m-methoxy-glucotropaeolin standards, and exhibited different RAPD and ISSR-PCR reactions. The Red Maca phenotype showed the highest concentrations of Glucosinolates as compared to the Black and Yellow Maca. It appears that the traditional system used by natives of the Peruvian Andean highlands in preparing Maca as a vegetable dish (boiling dried Maca after soaking in water), to supplement their daily meals, is as effective as laboratory methods - for extracting Glucosinolates, which are considered to be one of the key bioactive constituents responsible for therapeutic functions of Peruvian Maca phenotypes. It is reasonable to assume that the HPLC and DNA techniques combined, or separately, may assist in determining ID and "Fingerprints" identifying individual Peruvian Maca phenotypes, hence confirming the authenticity of marketable Maca products. The above assumptions warrant further laboratory testing.

  13. RAPD-PCR and real-time PCR HRM based genetic variation evaluations of Urtica dioica parts, ecotypes and evaluations of morphotypes in Turkey.

    Science.gov (United States)

    Uzonur, Irem; Akdeniz, Gamze; Katmer, Zeynep; Ersoy, Seyda Karaman

    2013-01-01

    Urtica dioica is an ethnobotanically and medicinally important Complementary and Alternative Medicine (CAM) plant worldwide and in Turkey; 90 % of herbal CAM applications depend on it in Turkey. It has a wide range of habitats in nearly all continents. It is found in all three phytogeographical regions in Turkey (Euro-Siberian, Irano-Turanian, Mediterranean) with high adaptivity to heterogeneous geographies such as climate, soil types and altitudes. This fact in relation to the assessment of chemical constituents of the plant and combining with further genetic and morphological variation data can assist and enhance the works for the utility and reliability of CAM applications in effect and activity of this plant species. In this work we have made some preliminary experiments with novel approaches to reveal the ecotypes and genetic variation of mighty ecotypes of Urtica dioica from different phytogeographical regions of Turkey (Euro-Siberian and Mediterranean). The ecotypes have heterogeneity in both its parts (leaf, stem, root) as revealed by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) using random primers and High-resolution Melt (HRM) analysis using Urtica dioica specific primers and universal chloroplast DNA (cpDNA) primers and morphological traits such as phenolic contents and antioxidant capacities of plants' leaf infusions as used in medicinal applications in Turkey. This work will contribute a lot for the development of molecular markers to detect the genetic variation and heterogeneity of Urtica dioica to further relate with expected phenotypes that are most useful and relevant in CAM applications.

  14. Phenotypic and Genotypic Characterization of Staphylococcus aureus Strains from Italian Dairy Products

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    Stefano Morandi

    2009-01-01

    Full Text Available Staphylococcus aureus is a known major cause of foodborne illnesses, and milk and dairy products are often contaminated by enterotoxigenic strains of this bacterium. In the present study, 122 S. aureus isolates collected from different dairy products were characterised by phenotypic properties, by the distribution of genes encoding staphylococcal enterotoxins (sea, sec, sed, seg, seh, sei, sej, and sel and by randomly amplified polymorphic DNA PCR (RAPD-PCR. Moreover, strain resistance to vancomycin and methicillin (oxacillin was studied. The differences in the RAPD-PCR profiles obtained with the primers M13 and AP4 revealed the presence of a great genetic heterogeneity among the different S. aureus strains. Using the primer AP4 and M13, eight groups were distinguished by RAPD-PCR cluster analysis, although, except in few cases, it was not possible to correlate the isolates of different animal species (cow or ovine with the presence of se genes. None of the isolates showed resistance to vancomycin or methicillin.

  15. Subspeciation of Bifidobacterium longum by multilocus approaches and amplified fragment length polymorphism: Description of B. longum subsp. suillum subsp. nov., isolated from the faeces of piglets.

    Science.gov (United States)

    Yanokura, Emiko; Oki, Kaihei; Makino, Hiroshi; Modesto, Monica; Pot, Bruno; Mattarelli, Paola; Biavati, Bruno; Watanabe, Koichi

    2015-07-01

    The species Bifidobacterium longum is currently divided into three subspecies, B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. This classification was based on an assessment of accumulated information on the species' phenotypic and genotypic features. The three subspecies of B. longum were investigated using genotypic identification [amplified-fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST)]. By using the AFLP and the MLSA methods, we allocated 25 strains of B. longum into three major clusters corresponding to the three subspecies; the cluster comprising the strains of B. longum subsp. suis was further divided into two subclusters differentiable by the ability to produce urease. By using the MLST method, the 25 strains of B. longum were divided into eight groups: four major groups corresponding to the results obtained by AFLP and MLSA, plus four minor disparate groups. The results of AFLP, MLSA and MLST analyses were consistent and revealed a novel subspeciation of B. longum, which comprised three known subspecies and a novel subspecies of urease-negative B. longum, for which the name B. longum subsp. suillum subsp. nov. is proposed, with type strain Su 851(T)=DSM 28597(T)=JCM 19995(T). Copyright © 2015 Elsevier GmbH. All rights reserved.

  16. Reduction of species in the wild potato Solanum section Petota series Longipedicellata : AFLP, RAPD and chloroplast SSR data

    NARCIS (Netherlands)

    Berg, van den R.G.; Bryan, G.J.; Rio, del A.; Spooner, D.M.

    2002-01-01

    Species boundaries were assessed with three molecular markers [AFLPs, RAPDs and chloroplast simple sequence repeats (cpSSRs)] for all six species of wild potatoes (Solanum section Petota) assigned to ser. Longipedicellata: Solanum fendleri, S. hjertingii, S. matehualae, S. papita, S. polytrichon and

  17. Analysis of genetic variability in soursop Annona muricata L populations from Central Java and East Java based on random amplified polymorphic DNA RAPD marker

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    Suratman Suratman

    2014-08-01

    Full Text Available The objective of this research was to determine genetic variability of the soursop (Annona muricata L. populations from Central Java and East Java based on RAPD markers. Leaves of 40 individuals were collected from 4 soursop populations in Central Java and East Java, include : Sukoharjo, Karanganyar (Central Java, and Ngawi, Pacitan (East Java. Genomic DNA was extracted from the leaves by the CTAB extraction procedure with some modifications. A total of 15 RAPD primers were purchased from commercial source and tested to find specific diagnostic markers for each individuals by RAPD-PCR. The measurement of soursop population genetic distance was based on similarity coefficient using method of Group Average Clustering and Unweight Pair Group Method Arithmetic (UPGMA of NTSYS program version 2.02i. Results showed that each soursop population collected from different localities seemed have variability in RAPD profiles by using different primers. Four RAPD polymorphic primer was selected from 15 RAPD primers, namely A18, A20, P10 and P11. A total of 58 bands produced, varying from 9 to 20 bands per primer. The selected four RAPD primers produced 57 polymorphic bands, whereas polymorphism for each primer ranged from 95 % to 100 %. Dendrogram indicated that four soursop populations tend to segregate form two separated clade. The sample collected from Sukoharjo formed a separate cluster while the sample collected from Ngawi, Pacitan and Karanganyar grouped together in other cluster and diverged from population Sukoharjo.

  18. A multilocus linkage disequilibrium measure based on mutual information theory and its applications.

    Science.gov (United States)

    Zhang, Lei; Liu, Jianfeng; Deng, Hong-Wen

    2009-12-01

    Evaluating the patterns of linkage disequilibrium (LD) is important for association mapping study as well as for studying the genomic architecture of human genome (e.g., haplotype block structures). Commonly used bi-allelic pairwise measures for assessing LD between two loci, such as r(2) and D', may not make full and efficient use of modern multilocus data. Though extended to multilocus scenarios, their performance is still questionable. Meanwhile, most existing measures for an entire multilocus region, such as normalized entropy difference, do not consider existence of LD heterogeneity across the region under investigation. Additionally, these existing multilocus measures cannot handle distant regions where long-range LD patterns may exist. In this study, we proposed a novel multilocus LD measure developed based on mutual information theory. Our proposed measure described LD pattern between two chromosome regions each of which may consist of multiple loci (including multi-allele loci). As such, the proposed measure can better characterize LD patterns between two arbitrary regions. As potential applications, we developed algorithms on the proposed measure for partitioning haplotype blocks and for selecting haplotype tagging SNPs (htSNPs), which were helpful for follow-up association tests. The results on both simulated and empirical data showed that our LD measure had distinct advantages over pairwise and other multilocus measures. First, our measure was more robust, and can capture comprehensively the LD information between neighboring as well as disjointed regions. Second, haplotype blocks were better described via our proposed measure. Furthermore, association tests with htSNPs from the proposed algorithm had improved power over tests on single markers and on haplotypes.

  19. Genetic diversity of Bemisia tabaci (Genn. Populations in Brazil revealed by RAPD markers

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    L.H.C. Lima

    2002-01-01

    Full Text Available Bemisia tabaci (Genn. was considered a secondary pest in Brazil until 1990, despite being an efficient geminivirus vector in beans and soybean. In 1991, a new biotype, known as B. tabaci B biotype (=B. argentifolii was detected attacking weed plants and causing phytotoxic problems in Cucurbitaceae. Nowadays, B. tabaci is considered one of the most damaging whitefly pests in agricultural systems worldwide that transmits more than 60 different plant viruses. Little is known about the genetic variability of these populations in Brazil. Knowledge of the genetic variation within whitefly populations is necessary for their efficient control and management. The objectives of the present study were to use RAPD markers (1 to estimate the genetic diversity of B. tabaci populations, (2 to study the genetic relationships among B. tabaci biotypes and two other whitefly species and (3 to discriminate between B. tabaci biotypes. A sample of 109 B. tabaci female individuals obtained from 12 populations in Brazil were analyzed and compared to the A biotype from Arizona (USA and B biotype from California (USA and Paraguay. Trialeurodes vaporariorum and Aleurodicus cocois samples were also included. A total of 72 markers were generated by five RAPD primers and used in the analysis. All primers produced RAPD patterns that clearly distinguished the Bemisia biotypes and the two other whitefly species. Results also showed that populations of the B biotype have considerable genetic variability. An average Jaccard similarity of 0.73 was observed among the B biotype individuals analyzed. Cluster analysis demonstrated that, in general, Brazilian biotype B individuals are scattered independently in the localities where samples were collected. Nevertheless, some clusters were evident, joining individuals according to the host plants. AMOVA showed that most of the total genetic variation is found within populations (56.70%, but a significant portion of the variation is found

  20. Survey of Bemisia tabaci (Gennadius (Hemiptera: Aleyrodidae biotypes in Brazil using RAPD markers

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    L.H.C. Lima

    2000-12-01

    Full Text Available In 1991, the poinsettia strain, silverleaf whitefly or B biotype of Bemisia tabaci was detected in Brazil. This variant is a far more serious agricultural pest than the previously prevalent non-B (BR biotype. The correct identification of B. tabaci is problematic since it is highly polymorphic with extreme plasticity in key morphological characters that vary according to the host. RAPD-PCR was used to survey the B biotype and other biotypes of B. tabaci in Brazil. Whiteflies were collected from cultivated plants and weeds from 57 different localities and on 27 distinct crops. RAPD analyses using two selected 10-mer primers reliably identified the BR biotype and the B biotype of B. tabaci and also differentiated other whitefly species. The presence of the B biotype was confirmed in 20 Brazilian states. The BR and B biotypes of B. tabaci were found to coexist in the whitefly populations of three different localities: Jaboticabal, SP; Rondonópolis and Cuiabá, MT, and Goiânia, GO.Em 1991, um novo biótipo de Bemisia tabaci denominado de raça B, mosca branca da poinsétia ou mosca da folha prateada foi detectado no Brasil. Esta praga trouxe muitos prejuízos e danos à agricultura nacional, por ser mais agressiva do que a existente anteriormente, conhecida como B. tabaci ou B. tabaci biótipo BR (não B. A relação taxonômica entre B. tabaci e B. tabaci biótipo B não é clara e não existem evidências morfológicas consistentes que possam distinguir esses dois biótipos. RAPD-PCR tem sido utilizada para identificação de biótipos presentes nas populações, utilizando-se, como padrões de referência, adultos de Bemisia tabaci das raças A e B provenientes dos Estados Unidos. As coletas de mosca branca foram feitas em 27 culturas e plantas daninhas em 57 localidades do país. As populações foram então analisadas, observando-se que a população predominante em 20 estados brasileiros é de B. tabaci biótipo B. Os biótipos BR e B foram

  1. Multilocus DNA Sequence Comparisons Rapidly Identify Pathogenic Molds

    Science.gov (United States)

    Rakeman, Jennifer L.; Bui, Uyen; LaFe, Karen; Chen, Yi-Ching; Honeycutt, Rhonda J.; Cookson, Brad T.

    2005-01-01

    The increasing incidence of opportunistic fungal infections necessitates rapid and accurate identification of the associated fungi to facilitate optimal patient treatment. Traditional phenotype-based identification methods utilized in clinical laboratories rely on the production and recognition of reproductive structures, making identification difficult or impossible when these structures are not observed. We hypothesized that DNA sequence analysis of multiple loci is useful for rapidly identifying medically important molds. Our study included the analysis of the D1/D2 hypervariable region of the 28S ribosomal gene and the internal transcribed spacer (ITS) regions 1 and 2 of the rRNA operon. Two hundred one strains, including 143 clinical isolates and 58 reference and type strains, representing 43 recognized species and one possible new species, were examined. We generated a phenotypically validated database of 118 diagnostic alleles. DNA length polymorphisms detected among ITS1 and ITS2 PCR products can differentiate 20 of 33 species of molds tested, and ITS DNA sequence analysis permits identification of all species tested. For 42 of 44 species tested, conspecific strains displayed >99% sequence identity at ITS1 and ITS2; sequevars were detected in two species. For all 44 species, identifications by genotypic and traditional phenotypic methods were 100% concordant. Because dendrograms based on ITS sequence analysis are similar in topology to 28S-based trees, we conclude that ITS sequences provide phylogenetically valid information and can be utilized to identify clinically important molds. Additionally, this phenotypically validated database of ITS sequences will be useful for identifying new species of pathogenic molds. PMID:16000456

  2. Integration of least angle regression with empirical Bayes for multi-locus genome-wide association studies

    Science.gov (United States)

    Multi-locus genome-wide association studies has become the state-of-the-art procedure to identify quantitative trait loci (QTL) associated with traits simultaneously. However, implementation of multi-locus model is still difficult. In this study, we integrated least angle regression with empirical B...

  3. Multilocus sequence analysis of Pasteurella multocida demonstrates a type species under development.

    Science.gov (United States)

    Bisgaard, Magne; Petersen, Andreas; Christensen, Henrik

    2013-03-01

    The aim of the present study was to use multilocus sequence typing (MLST) of a diverse collection of Pasteurella multocida with regard to animal source, place and date of collection, including all available serovars of Carter, Heddleston, Little & Lyon, Namioka, Cornelius and Roberts, to further investigate the evolution of this species with a focus on two lineages, A (P. multocida subsp. multocida and P. multocida subsp. gallicida) and B (P. multocida subsp. septica), previously reported. Isolates of P. multocida (n = 116) including reference strains of major serotyping systems were investigated by MLST based on partial sequences of the genes adk, est, gdh, mdh, pgi, pmi and zwf, and 67 sequence types (STs) were observed. Phylogenetic analysis of these concatenated sequences confirmed the separation of groups A (41 STs, 71 isolates) and B (22 STs, 38 isolates) out of the 67 STs. All Carter serovars, 12 Heddleston serovars, all three Little-Lyon types, six out of seven Namioka serovars, all five Roberts types and all four Cornelius serovars were allocated to the A group, while group B included the remaining four Heddleston serovars, 6, 7, 8 and 13, in addition to Namioka type 8 : A. The overrepresentation of reference strains of serotyping systems in the A group contrasts with the high number of isolates obtained from diseased birds in the B group, the effect of which should be addressed in future vaccine development. Isolates from birds (25) dominated the B group, which also included four isolates from Felidae, whereas group A included isolates from all types of hosts. The evolutionary implications of the lack of capsular type D, pig and bovine isolates in group B, as well as its association with Aves and Felidae that also applied to the whole Rural Industries Research and Development Corporation (RIRDC) MLST database, need further investigation. The combination of rpoB and 16S rRNA gene sequence comparison as well as the developed PCR test assigned

  4. Clonal dissemination of multilocus sequence type 11 Klebsiella pneumoniae carbapenemase - producing K. pneumoniae in a Chinese teaching hospital.

    Science.gov (United States)

    Sun, Kangde; Chen, Xu; Li, Chunsheng; Yu, Zhongmin; Zhou, Qi; Yan, Yuzhong

    2015-02-01

    Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae has disseminated rapidly in China. We aimed to analyze the molecular epidemiology of four KPC-producing K. pneumoniae strains isolated from a suspected clonal outbreak during a 3-month period and to track the dissemination of KPC-producing K. pneumonia retrospectively. We created antimicrobial susceptibility profiles using an automated broth microdilution system and broth microdilution methods. We screened carbapenemase and KPC phenotypes using the modified Hodge test and meropenem-boronic acid (BA) disk test, respectively. We identified β-lactamase genes with PCR and sequencing. We investigated clonal relatedness for epidemiological comparison using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). All isolates expressed multidrug resistance and yielded positive results for the modified Hodge and meropenem-BA disk tests. The isolates all carried blaKPC -2 , and coproduced CTX-M-type extended-spectrum β-lactamase. PFGE and MLST showed that the isolates were clonally related. The PFGE patterns of these isolates had ≥90% similarity. We found a single clone, sequence type (ST) 11, and its typical dissemination mode resembled clonal spread. The dissemination of KPC-producing K. pneumoniae is clonally related and there is probable local transmission of a successful ST11 clone. © 2014 APMIS. Published by John Wiley & Sons Ltd.

  5. Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers.

    Science.gov (United States)

    Cerqueira-Silva, C B M; Conceição, L D H C S; Santos, E S L; Cardoso-Silva, C B; Pereira, A S; Oliveira, A C; Corrêa, R X

    2010-12-21

    The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.

  6. Identification of zygotic and nucellar tangerine seedlings (Citrus spp. using RAPD

    Directory of Open Access Journals (Sweden)

    Bastianel Marinês

    1998-01-01

    Full Text Available The randomly amplified polymorphic DNA (RAPD technique was used to distinguish nucellar and zygotic seedlings resulting from crosses between the ?Montenegrina? (Citrus deliciosa Tenore and? King? (C. nobilis Loureiro tangerines. The aim of the present study was to develop tangerine varieties with a reduced number of seeds and organoleptic characteristics similar to the ?Montenegrina? tangerine. Embryos were isolated from seeds, cultivated in vitro, and acclimated in a greenhouse. Four random primers were used to identify 54 plants of sexual origin from a total of 202 individuals. The degree of polymorphism of each primer was reflected in the number of zygotic plants obtained per primer. Cluster analysis of parents and progeny separated the individuals into distinct groups with a maximum genetic dissimilarity of 20%.

  7. RAPD markers indicate the occurrence of structured populations in a migratory freshwater fish species

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    Hatanaka Terumi

    2003-01-01

    Full Text Available Many factors have contributed to the destruction of fish habitats. Hydroelectric dams, water pollution and other environmental changes have resulted in the eradication of natural stocks. The aim of this study was to detect the genetic variation in Prochilodus marggravii from three collection sites in the area of influence of the Três Marias dam (MG on the São Francisco river (Brazil, using the RAPD technique. The results obtained revealed that the fish in the downstream region nearest the dam have a higher similarity coefficient than those from the other sampling sites that may be related to differences in environmental characteristics in these regions. Additionaly, significant differences in the band frequencies were observed from one collection site to another. These both findings suggest the occurrence of a structured population and have important implications for the conservation of the genetic variability of distinct natural P. marggravii stocks.

  8. Genetic diversity of improved salt tolerant calli of maize (Zea mays L.) using RAPD

    Science.gov (United States)

    Saputro, Triono Bagus; Dianawati, Siti; Sholihah, Nur Fadlillatus; Ermavitalini, Dini

    2017-06-01

    Maize is one of important cultivated plants in the world, in terms of production rates, utilization rates and demands. Unfortunately, the increment of demands were not followed by the increase of production rates since the cultivation area were significantly decrease. Coastal area is the marginal land that have a good potential to extend the cultivation area. The main challenge of this area is the high content of salt. The aims of this research were try to induce a new varian of local maize through in vitro culture and observe its genetic variation using RAPD. Bluto variety from Madura island was used as an explant in callus induction. Induction of callus were conducted using MS basal medium supplemented with 3 mg/L of 2,4 D under dark condition. While the selection stage was conducted using MS basal medium supplemented with 3 mg/L of 2,4 D with the addition of various concentration of NaCl (0 mg/L; 2500 mg/L; 5000 mg/L; and 7500 mg/L). The research were arranged in a completely randomized design with three replications. The exposion of NaCl were significantly decrease the mass of maize callus. The highest addition of callus weight was 210 mgs in control treatment, while the lowest is in 7500 mg/L with 3 mgs. The RAPD technique was utilized to characterize the genotype of maize callus. Out of five primers, only three primers can produce polymorphic bands named OPA10, OPB07 and OPC02. Taken together, the surviving callus of Bluto varians can be further developed as potential somaclone that has high tolerance to salt stress.

  9. Assessment of genetic stability in micropropagules of Jatropha curcas genotypes by RAPD and AFLP analysis

    KAUST Repository

    Sharma, Sweta K.

    2011-07-01

    Jatropha curcas (Euphorbiaceae), a drought resistant non edible oil yielding plant, has acquired significant importance as an alternative renewable energy source. Low and inconsistent yields found in field plantations prompted for identification of high yielding clones and their large scale multiplication by vegetative propagation to obtain true to type plants. In the current investigation plantlets of J. curcas generated by axillary bud proliferation (micropropagation) using nodal segments obtained from selected high yielding genotypes were assessed for their genetic stability using Randomly Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) analyses. For RAPD analysis, 21 out of 52 arbitrary decamer primers screened gave clear reproducible bands. In the micropropagated plantlets obtained from the 2nd sub-culture, 4 out of a total of 177 bands scored were polymorphic, but in the 8th and 16th sub-cultures (culture cycle) no polymorphisms were detected. AFLP analysis revealed 0.63%, 0% and 0% polymorphism in the 2nd, 8th and 16th generations, respectively. When different genotypes, viz. IC 56557 16, IC 56557 34 and IC 56557 13, were assessed by AFLP, 0%, 0.31% and 0.47% polymorphisms were found, respectively, indicating a difference in genetic stability among the different genotypes. To the best of our knowledge this is the first report on assessment of genetic stability of micropropagated plantlets in J. curcas and suggests that axillary shoot proliferation can safely be used as an efficient micropropagation method for mass propagation of J. curcas. © 2011 Elsevier B.V.

  10. Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes

    Directory of Open Access Journals (Sweden)

    Slobodan Katic

    2011-08-01

    Full Text Available Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm.

  11. MARCADORES RAPD PARA MAPEAMENTO GENÉTICO E SELEÇÃO DE HÍBRIDOS DE CITROS RAPD MARKERS TO GENETIC MAPPING AND SELECTION OF CITRUS HYBRIDS

    Directory of Open Access Journals (Sweden)

    ROBERTO PEDROSO DE OLIVEIRA

    2001-12-01

    Full Text Available Os marcadores moleculares apresentam várias aplicações no melhoramento de plantas, permitindo uma série de análises genéticas. Este trabalho foi realizado com o objetivo de estabelecer marcadores RAPD para serem utilizados em estudos de mapeamento genético e na seleção de híbridos entre tangerina-'Cravo' (Citrus reticulata Blanco e laranja-'Pêra' (C. sinensis (L. Osbeck. Extraiu-se DNA de folhas dos parentais e de seis híbridos F1. As reações de amplificação foram preparadas em 13 uL de solução, constituída por tampão 1x GIBCO BRL; soluções 1,54 mM de MgCl2 e 0,2 mM de cada dNTP; 15 ng de cada 'primer'; 1,5 unidade de 'Taq DNA Polymerase' e 15 ng de DNA genômico. As reações foram realizadas em termocicladores programados para 36 ciclos de 1 min a 92ºC, 1 min a 36ºC, 2 min a 72ºC e 10 min de extensão a 72ºC. Foram testados 'primers' decâmeros arbitrários dos 'kits' A, AB, AT, AV, B, C, D, E, G, H, M, N, P, Q, R e U da Operon, sendo selecionados 113 por apresentarem polimorfismo, com número de marcadores variando de 1 a 6 por 'primer'. Esses 'primers' amplificaram 201 (23,13% bandas polimórficas, aplicáveis no mapeamento genético e seleção de híbridos. A freqüência de 'primers' com 1; 2; 3; 4; 5 e 6 bandas polimórficas foi de 49,5%, 33,6%, 9,7%, 4,4%, 1,8% e 1,0%, respectivamente.Molecular markers have many applications in plant breeding, enabling some types of genetic analyses. The aim of this work was to establish RAPD markers to be used to genetic mapping studies and selection of hybrids between 'Cravo' tangerine (Citrus reticulata Blanco and 'Pêra' orange (C. sinensis (L. Osbeck. DNA of the parents and six hybrids F1 was isolated from the leaves. The amplification reactions were performed in volumes of 13 µL, composed by GIBCO BRL 1x buffer, 1,54 mM MgCl2, 0,2 mM of each dNTP, 15 ng of each primer, 1,5 unit of Taq DNA Polymerase and 15 ng of genomic DNA. These reactions were carried out in

  12. Similaridade genética entre clones de seringueira (Hevea brasiliensis, por meio de marcadores RAPD Genetic similarity among rubber tree (Hevea brasiliensis clones using RAPD markers

    Directory of Open Access Journals (Sweden)

    Karine Cristina Bicalho

    2008-10-01

    Full Text Available A seringueira [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] é uma espécie nativa da região amazônica e compreende a maior fonte produtora de borracha natural do mundo. Na busca de condições mais favoráveis ao cultivo, além da busca pela auto-suficiência na produção de borracha natural, o cultivo da seringueira migrou para outras regiões do país. Objetivou-se, com o presente trabalho, estimar a similaridade genética de genótipos de seringueira, provenientes de regiões distintas do país, Lavras-MG (UFLA e Campinas-SP (IAC, por meio de marcadores moleculares RAPD. A análise foi efetuada em 41 indivíduos, representados por 17 genótipos diferentes, com base em 19 primers, que geraram 121 fragmentos polimórficos. Os dados foram analisados utilizando o software NTSYS-pc - 2.1, por meio do coeficiente de Dice e pelo método das médias (UPGMA. A similaridade genética entre o material analisado variou de 0,56 a 1,00. Na análise do dendrograma, foram observados 18 grupos. Os clones (RRIM600, GT1, PB235, PL PIM e FX2261, utilizados em diferentes repetições, foram idênticos, quando comparados entre si, entretanto o mesmo não foi observado para os clones identificados como RRIM 701. Os resultados obtidos sugerem que o material avaliado na UFLA é o mesmo implantado no IAC, exceto o RRIM 701, mostrando uma ampla variabilidade genética, disponível para estudos e propagação da cultura.The rubber tree [Hevea brasiliensis (Willd. ex. Adr. de Juss Muell.-Arg.] is a native species from Amazon region, and represents the biggest source of natural rubber in the world.. However, the rubber tree culture has had an expansion to other brazilian regions, in search of more favorable conditions for its cultivation and self-sufficiency in natural rubber. The aim of this work was to estimate genetic similarity among rubber tree clones, from different Brazilian regions, Lavras (UFLA and Campinas (IAC, by using RAPD molecular markers

  13. Genetic variability of Pantaneiro horse using RAPD-PCR markers Variabilidade genética do cavalo Pantaneiro utilizando marcadores RAPD-PCR

    Directory of Open Access Journals (Sweden)

    Andréa Alves do Egito

    2007-08-01

    Full Text Available Blood samples were collected from Pantaneiro Horses in five regions of Mato Grosso do Sul and Mato Grosso States. Arabian, Mangalarga Marchador and Thoroughbred were also included to estimate genetic distances and the existing variability among and within these breeds by RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction molecular markers. From 146 primers, 13 were chosen for amplification and 44 polymorphic bands were generated. The analysis of molecular variance (AMOVA indicated that the greatest portion of detected variability was due to differences between individuals within populations (75.47%. Analysis of the genetic variability between pairs of populations presented higher estimates for the five Pantaneiro populations with the Arabian breed, while lowest estimates were presented by pairs formed among the Pantaneiro populations with the Mangalarga Marchador. Highest genic diversity was shown by the Pantaneiro (0.3396, which also showed highest genetic distance with the Arabian and lowest with Mangalarga Marchador breed. UPGMA dendrogram showed distinct differences between naturalized (Pantaneiro and Mangalarga Marchador and exotic (Arabian and Thoroughbred breeds. In the dendrogram generated by UPGMA method, the similarity matrix generated by the Jaccard coefficient showed distinction between the naturalised breeds, Pantaneiro and Mangalarga Marchador, and the exotic breeds, Árab and English Thoroughbred. Results suggest that the Pantaneiro presents a higher genetic variability than the other studied breeds and has a close relationship with the Mangalarga Marchador.Amostras de sangue foram coletadas de cavalos Pantaneiros de cinco regiões dos estados de Mato Grosso do Sul e Mato Grosso. As raças Mangalarga Marchador, Árabe e Puro-Sangue Inglês (PSI usando marcadores moleculares RAPD-PCR (Random Amplified Polymorphic DNA - Polymerase Chain Reaction foram incluídas no intuito de se calcular as distâncias gen

  14. Variabilidade genética em búfalos estimada por marcadores RAPD Genetic variability of buffaloes estimated by RAPD markers

    Directory of Open Access Journals (Sweden)

    Maria do Socorro Maués Albuquerque

    2006-04-01

    Full Text Available O objetivo deste trabalho foi caracterizar, por meio de marcadores RAPD, dois grupos genéticos de búfalos, Carabao e tipo Baio, que estão sendo conservados in situ, assim como verificar as relações genéticas entre eles e os outros três grupos genéticos de búfalos existentes no Brasil, Murrah, Jafarabadi e Mediterrâneo, considerados raças comerciais. Foram estudados 48 animais de cada grupo, com exceção dos grupos Murrah e Mediterrâneo, com 47 e 42 animais, respectivamente, compreendendo um total de 233 animais. Os 21 iniciadores polimórficos geraram 98 marcadores. A variabilidade genética entre e dentro dos grupos foi estimada em 26,5 e 73,5%, respectivamente, sugerindo divergência significativa entre os cinco grupos genéticos. Na análise entre pares de grupos, foi verificado que a maior e a menor divergência estavam em torno de 40 e 18%, quando se compararam os grupos Carabao x Mediterrâneo e Murrah x Jafarabadi, respectivamente. Entre os grupos Baio e Murrah, a análise revelou divergência genética de 20,42%, indicando que esses grupos são distintos. Os cinco grupos são geneticamente distintos, o que reforça a necessidade de conservação dos grupos genéticos Carabao e Baio, ameaçados de extinção no Brasil.The objective of this work was to characterize genetically, using RAPD markers, two genetic groups of buffalos, Carabao and Baio, which are being conserved in situ, as well as to verify the genetic relationship among them and the other three genetic groups of buffalos raised in Brazil, considered as commercial breeds: Murrah, Jaffarabadi and Mediterrâneo. Forty eight animals of each group were studied, with the exception of the Murrah and Mediterrâneo, in which 47 and 42 animals, respectively, were sampled, comprising a total of 233 animals. The 21 polymorphic primers produced 98 markers. Genetic variability within and between groups was estimated in 26.5 and 73.5%, respectively, suggesting a significant

  15. Inheritance of rapeseed (Brassica napus)-specific RAPD markers and a transgene in the cross B.juncea x (B.juncea x B.napus)

    DEFF Research Database (Denmark)

    Frello, S.; Hansen, K.R.; Jensen, J.

    1995-01-01

    We have examined the inheritance of 20 rapeseed (Brassica napus)-specific RAPD (randomly amplified polymorphic DNA) markers from transgenic, herbicide-tolerant rapeseed in 54 plants of the BC1 generation from the cross B. juncea x (B. juncea x B. napus). Hybridization between B. juncea and B. napus......, with B. juncea as the female parent, was successful both in controlled crosses and spontaneously in the field. The controlled backcrossing of selected hybrids to B. juncea, again with B. juncea as the female parent, also resulted in many seeds. The BC1 plants contained from 0 to 20 of the rapeseed RAPD...... markers, and the frequency of inheritance of individual RAPD markers ranged from 19% to 93%. The transgene was found in 52% of the plants analyzed. Five synteny groups of RAPD markers were identified. In the hybrids pollen fertility was 0-28%. The hybrids with the highest pollen fertility were selected...

  16. Engineering super mycovirus donor strains of chestnut blight fungus by systematic disruption of multilocus vic genes

    OpenAIRE

    Zhang, Dong-Xiu; Nuss, Donald L.

    2016-01-01

    Allorecognition, termed “vegetative incompatibility” (vic), in filamentous fungi limits the efficacy of virulence-attenuating mycoviruses for biological control (hypovirulence). Because mycoviruses lead exclusive intracellular lifestyles, horizontal transmission relies on cytoplasmic exchange during hyphal fusion (anastomosis). Fusion between vic-incompatible strains results in localized cell death restricting mycovirus transmission. We report the systematic disruption of multilocus vic genes...

  17. Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

    OpenAIRE

    Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

    2009-01-01

    Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly.

  18. Multilocus Sequence Analysis for Typing Leptospira interrogans and Leptospira kirschneri▿ †

    Science.gov (United States)

    Leon, Albertine; Pronost, Stéphane; Fortier, Guillaume; Andre-Fontaine, Geneviève; Leclercq, Roland

    2010-01-01

    Fifty-three strains belonging to the pathogenic species Leptospira interrogans and Leptospira kirschneri were analyzed by multilocus sequence analysis. The species formed two distinct branches. In the L. interrogans branch, the phylogenetic tree clustered the strains into three subgroups. Genogroups and serogroups were superimposed but not strictly. PMID:19955271

  19. Core genome multilocus sequence typing scheme for high-resolution typing of enterococcus faecium

    NARCIS (Netherlands)

    De Been, Mark; Pinholt, Mette; Top, Janetta|info:eu-repo/dai/nl/304818984; Bletz, Stefan; Mellmann, Alexander; Van Schaik, Willem|info:eu-repo/dai/nl/279958846; Brouwer, Ellen|info:eu-repo/dai/nl/304815667; Rogers, Malbert; Kraat, Yvette; Bonten, Marc|info:eu-repo/dai/nl/123144337; Corander, Jukka; Westh, Henrik; Harmsen, Dag; Willems, Rob J L|info:eu-repo/dai/nl/106866370

    2015-01-01

    Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrugresistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due

  20. A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies

    KAUST Repository

    Zhang, Han

    2013-09-11

    As increasing evidence suggests that multiple correlated genetic variants could jointly influence the outcome, a multilocus test that aggregates association evidence across multiple genetic markers in a considered gene or a genomic region may be more powerful than a single-marker test for detecting susceptibility loci. We propose a multilocus test, AdaJoint, which adopts a variable selection procedure to identify a subset of genetic markers that jointly show the strongest association signal, and defines the test statistic based on the selected genetic markers. The P-value from the AdaJoint test is evaluated by a computationally efficient algorithm that effectively adjusts for multiple-comparison, and is hundreds of times faster than the standard permutation method. Simulation studies demonstrate that AdaJoint has the most robust performance among several commonly used multilocus tests. We perform multilocus analysis of over 26,000 genes/regions on two genome-wide association studies of pancreatic cancer. Compared with its competitors, AdaJoint identifies a much stronger association between the gene CLPTM1L and pancreatic cancer risk (6.0 × 10(-8)), with the signal optimally captured by two correlated single-nucleotide polymorphisms (SNPs). Finally, we show AdaJoint as a powerful tool for mapping cis-regulating methylation quantitative trait loci on normal breast tissues, and find many CpG sites whose methylation levels are jointly regulated by multiple SNPs nearby.

  1. Genetic Relationships among Reptilian and Mammalian Campylobacter fetus Strains Determined by Multilocus Sequence Typing

    NARCIS (Netherlands)

    Dingle, K.E.; Blaser, M.J.; Tu, Z.C.; Pruckler, J.; Fitzgerald, C.; Bergen, van M.A.P.; Lawson, A.J.; Owen, R.J.; Wagenaar, J.A.

    2010-01-01

    Reptile Campylobacter fetus isolates and closely related strains causing human disease were characterized by multilocus sequence typing. They shared similar to 90% nucleotide sequence identity with classical mammalian C. fetus, and there was evidence of recombination among members of these two

  2. Multilocus sequence typing confirms synonymy but highlights differences between Candida albicans and Candida stellatoidea.

    NARCIS (Netherlands)

    Jacobsen, M.D.; Boekhout, T.; Odds, F.C.

    2008-01-01

    We used multi-locus sequence typing (MLST) to investigate 35 yeast isolates representing the two genome-sequenced strains plus the type strain of Candida albicans, four isolates originally identified as Candida stellatoidea type I and 28 representing type strains of other species now regarded as

  3. Application of random amplified polymorphic DNA (RAPD) analysis for identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets.

    Science.gov (United States)

    Asensio, Luis; González, Isabel; Fernández, Alicia; Rodríguez, Miguel A; Lobo, Esther; Hernández, Pablo E; García, Teresa; Martín, Rosario

    2002-02-01

    A random amplified polymorphic DNA (RAPD) method was developed for the specific identification of grouper (Epinephelus guaza), wreck fish (Polyprion americanus), and Nile perch (Lates niloticus) fillets. Using two different reaction primers (S1 and L1), RAPD analysis produced clear fingerprints from which the three fish species could be easily identified. This approach is rapid and reliable and offers the potential to detect fraudulent or unintentional mislabeling of these species in routine seafood authentication analysis.

  4. Random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing in the analysis of a hospital outbreak of Salmonella enteritidis

    DEFF Research Database (Denmark)

    Skibsted, U.; Baggesen, Dorte Lau; Dessau, R.

    1998-01-01

    Isolates of Salmonella Enteritidis from 81 patients from Herlev Hospital or from Copenhagen County were analysed by random amplification of polymorphic DNA (RAPD), pulsed-field gel electrophoresis (PFGE) and phage-typing. Fourteen polymorphic markers from five decamer primers unambiguously placed...... that RAPD is useful as a tool in investigations of microbial outbreaks in its own right, or to supplement phage-typing and PFGE of Salmonella Enteritidis....

  5. Relationship among phenotypic plasticity, phenotypic fluctuations ...

    Indian Academy of Sciences (India)

    Prakash

    These results provide quantitative formulation on canalization and genetic assimilation, in terms of fluctuations of gene expression levels. [Kaneko K 2009 Relationship among phenotypic plasticity, phenotypic fluctuations, robustness, and evolvability; Waddington's legacy revisited under the spirit of Einstein; J. Biosci.

  6. Diversidade genética de Chenopodium ambrosioides da região cacaueira da Bahia com base em marcadores RAPD Genetic diversity based on RAPD markers of Chenopodium ambrosioides from the cocoa region of Bahia State, Brazil

    Directory of Open Access Journals (Sweden)

    Simone Gualberto Santos

    2006-01-01

    Full Text Available Chenopodium ambrosioides L., conhecida no Brasil por suas propriedades medicinais e usada principalmente para o controle de verminoses intestinais, é pouco estudada quanto à diversidade genética. O objetivo deste trabalho foi avaliar a diversidade genética de 16 indivíduos de C. ambrosioides, provenientes de diferentes municípios da região cacaueira da Bahia, pela técnica de RAPD (DNA polimórfico amplificado ao acaso. Apenas 6,9% das 216 bandas RAPD amplificadas foram polimórficas e a análise de agrupamento evidenciou que não há formação de grupos por área de coleta. Portanto, há pequena variabilidade entre os materiais e esta variabilidade encontra-se distribuída entre as regiões amostradas.Chenopodium ambrosioides L. is known in many parts of Brazil for its medicinal properties, mainly used to control intestinal worms. Its genetic diversity is little studied. The objective of this work was to evaluate the genetic variability of 16 accessions of C. ambrosioides from the cocoa region of Bahia State, Brazil, by the RAPD technique (Random Amplified Polymorphic DNA. Only 6.9% of the 216 amplified RAPD bands were polymorphic and the pattern of dispersion of individuals showed no clustering related to sample site. Therefore, there is low variability among accessions and it is distributed among the accessions from the entire sampled region.

  7. Polyembryony and identification of Volkamerian lemon zygotic and nucellar seedlings using RAPD Poliembrionia e identificação de seedlings zigóticos e nucelares de limão volkameriano com RAPD

    Directory of Open Access Journals (Sweden)

    María Andrade-Rodríguez

    2004-06-01

    Full Text Available The objectives of this work were to evaluate the frequency of polyembryony, and to identify zygotic and nucellar seedlings of Citrus volkameriana using RAPD. Twenty-five polyembryonic and eight monoembryonic seeds were cultivated in vitrofor six months. DNA from seedlings was extracted and used in combination with five RAPD primers to identify zygotic or nucellar origin of the seedlings. Environmental conditions of the year affected significantly (POs objetivos deste trabalho foram avaliar a freqüência da poliembrionia e indentificar os seedlings zigóticos e nucelares de Citrus volkameriana usando RAPD. Cultivaram-se in vitro 25 sementes poliembriônicas e 8 monoembriônicas, por seis meses. Extraiu-se o DNA dos seedlings e usou-se em combinação com cinco primers RAPD para identificar a origem zigótica e nucelar das plântulas. Os resultados mostraram que as condições ambientais do ano afetaram significativamente (P<0,05 as características morfológicas dos frutos e o número de embriões por semente. Os índices de sementes poliembriônicas variaram nos três anos de avaliação (30,9%, 44,8% e 54,4%. As características morfológicas não se correlacionaram com a poliembrionia. A cultura in vitro possibilita que todos os embriões de cada semente cresçam, favorecendo os seedlings identificados como zigóticos. Nas sementes poliembriônicas e monoembriônicas, 25,9% e 87,5% dos seedlings, respectivamente, originaram-se sexualmente. Nem todos os seedlings zigóticos foram produzidos por embriões localizados no micrófilo das sementes poliembriônicas.

  8. Uso do Random Amplified Polymorphic DNA (RAPD no estudo populacional do Triatoma brasiliensis Neiva, 1911 Use of Random Amplified Polymorphic DNA (RAPD in the populational study of Triatoma brasiliensis Neiva, 1911

    Directory of Open Access Journals (Sweden)

    Érika C. Borges

    2000-01-01

    Full Text Available Para o estudo de variabilidade genética em Triatoma brasiliensis, o principal vetor da doença de Chagas no Nordeste brasileiro, espécimes de três diferentes populações intradomiciliares foram analisados. Regiões do DNA genômico foram amplificadas utilizando dois iniciadores randômicos através da técnica de RAPD (Random Amplified Polymorphic DNA, visualizados em géis de poliacrilamida corados pela prata. Os perfis originados se mostraram bastante homogêneos quando comparados intrapopulacionalmente. Populações capturadas em duas regiões diferentes do Estado do Ceará também apresentaram homogeneidade entre si, mas, quando comparadas com a população proveniente do Piauí, foi possível diferenciá-las. Esses resultados, preliminares, indicam que o RAPD pode ser usado com sucesso nos estudos de variabilidade em triatomíneos, bem como sugerem a existência de variabilidade entre diferentes populações de T. brasiliensis pertencentes a uma mesma subespécie.We evaluated the genetic variability of Triatoma brasiliensis, the main vector of Chagas disease in Northeast Brazil, using specimens from three populations. Regions of genomic DNA were amplified by RAPD (Random Amplified Polimorphic DNA, using two primers. The products were visualized after polyacrylamide gel electrophoresis followed by silver staining. A dendrogram constructed through the Dice similarity coefficient allowed for separation of the tested specimens into three distinct groups. The populations captured in areas from Ceará State showed similar profiles, but different from that captured in Piauí State. Our results indicate that RAPD can be used successfully in triatomine studies and suggest the presence of genetic variability between different populations of T. brasiliensis.

  9. Use of RAPD analysis to assess the threat of interspecific hybridization to the critically endangered Polemonium kiushianum in Japan.

    Science.gov (United States)

    Matoba, Hideyuki; Inaba, Kazufumi; Nagano, Katsuya; Uchiyama, Hiroshi

    2011-01-01

    Polemonium kiushianum is a critically endangered species of which only eight populations exist in semi-natural grasslands of the Mt. Aso area of Kyushu, Japan. Habitat modification and the risk of hybridization with non-indigenous horticultural congeners, such as P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense, pose increasing threats to P. kiushianum. To develop a DNA marker that distinguishes P. kiushianum from other Polemonium species, we performed random amplified polymorphic DNA (RAPD) analysis and selected an approximately 500-bp fragment generated by the OPB06 RAPD primer. In addition, we designed a primer pair, H11F/R, based on the nucleotide sequences of the fragments derived from P. caeruleum subsp. caeruleum and P. caeruleum subsp. yezoense var. yezoense. The results with the H11F/R primers indicated that most extant P. kiushianum plants in natural populations are not genetically contaminated by hybridization with non-indigenous horticultural species.

  10. ANALYSES OF GENETIC VARIABILITY IN LENTINULA EDODES THROUGH MYCELIA RESPONSES TO DIFFERENT ABIOTIC CONDITIONS AND RAPD MOLECULAR MARKERS

    Directory of Open Access Journals (Sweden)

    Maki Cristina Sayuri

    2001-01-01

    Full Text Available The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7 and four different temperatures (16, 25, 28 and 37ºC was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivation ranged between 25 and 28ºC. The water content was lower in strains grown at 37ºC. Among 20 OPA primers (Operon Technologies, Inc. used for the RAPD analyses, seventeen presented good polymorphism (OPA01 to OPA05, OPA07 to OPA14, OPA17 to OPA20. The clustering based on similarity coefficients allowed the separation of strain in two groups with different geographic origins.

  11. Efficacy of RAPD, ISSR and DAMD markers in assessment of genetic variability and population structure of wild Musa acuminata colla.

    Science.gov (United States)

    Lamare, Animos; Rao, Satyawada Rama

    2015-07-01

    North east India is considered as one of the major biodiversity hotspots worldwide and centre of origin of several plant species including Musa. Musa acuminata Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Three single primer based DNA marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplification of minisatellites DNA (DAMD) were used for diversity diagnostics among 25 genotypes of wild M. acuminata collected from Meghalaya province of north east India. A total of 58 primers (26-RAPD, 21-ISSR, and11-DAMD) yielded 451 DNA fragments, of which 395 (87.58 %) were found to be polymorphic in nature. The polymorphic information content (PIC) values were almost identical for each marker system. The resolving power of the marker system was found to be highest in RAPD (3.96) whereas ISSR resolved highest marker index (16.39) in the study. Selected amplicon data obtained through single primer amplification reactions were utilized for determination of diversity within and among the populations of M. acuminata. Nei's genetic differentiation (Gst) value (0.451) indicated higher proportion of the genetic variation within the populations which is supported by the AMOVA analysis (88 %). The study provides insight into the efficacy of RAPD, ISSR and DAMD to analyse the genetic variation existing in the wild Musa germplasm, which can further be exploited for quality trait improvement and domestication of such important horticultural crops. The genetic diversity based population structure may shed light on the genetic basis of speciation and evolution of various species within the genus Musa.

  12. Identification of Leishmania Species Causing Cutaneous Leishmaniasis Using Random Amplified Polymorphic DNA (RAPD-PCR in Kharve, Iran

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    Fatemeh Saadabadi

    2013-05-01

    Full Text Available Background: Leishmaniasis, especially cutaneous leishmaniasis, is considered an important health problem in many parts of Iran including Kharve, Khorasan Razavi province. Cutaneous leishmaniasis is caused by various species of Leishmania, each having a different secondary host. Thus, identifying the parasites’ specie is of paramount importance for containment strategy planning. The morphological differentiation of Leishmania species is not possible, rendering the molecular methods as the sole means to this purpose. Therefore, to identify the causative agent of cutaneous leishmaniasis in Kharve, Random Amplified Polymorphic DNA-PCR (RAPD-PCR was used. Methods: The disease was first confirmed by direct smears. Samples were gathered from 22 patients with established cutaneous leishmaniasis. The samples were immediately cultured in NNN medium, followed by sub-culture in RPMI-1640. Afterwards, DNA was extracted and amplified using RAPD-PCR. Electrophoresis patterns from each isolate were compared with reference strains of Leishmania major (L. major and Leishmania tropica (L. tropica. Results: The results of this study indicated that the parasite causing cutaneous leishmaniasis in Kharve is L. tropica. Conclusion: It seems that L. tropica is the only causative agent of cutaneous leishmaniasis in Kharve, and RAPD-PCR is a suitable tool for Leishmania characterization in epidemiological studies.

  13. RAPD fingerprint to appraise the genetic fidelity of in vitro propagated Araucaria excelsa R. Br. var. glauca plantlets.

    Science.gov (United States)

    Sarmast, Mostafa Khoshhal; Salehi, Hassan; Ramezani, Amin; Abolimoghadam, Ali Asghar; Niazi, Ali; Khosh-Khui, Morteza

    2012-03-01

    Randomly amplified polymorphic DNA (RAPD) was used as a tool to assess the genetic fidelity of in vitro propagated Araucaria excelsa R. Br. var. glauca with explants taken from orthotropic stem along with their related mother plants after treatment with kinetin, 2iP, BA (0.02-0.26 mg/l) and TDZ (0.001-1 mg/l) to produce axillary shoots. TDZ and kinetin induced more shoot and higher length per explant. Results showed a total of 1,676 fragments were generated with 12 RAPD primers in micropropagated plants and their donor mother plants. The number of loci ranged from 6 in OPB 12-18 in OPY 07 with a size ranging from 250 bp in OPH 19-3500 bp in OPH 11. Cluster analysis of RAPD data using UPGMA (unweighted pair group method with arithmetic average) revealed more than 92% genetic similarities between tissue cultured plants and their corresponding mother plant measured by the Jaccard's similarity coefficient. Similarity matrix and PCoA (two dimensional principal coordinate analysis) resulted in the same affinity. Primers had shown 36% polymorphism. However, careful monitoring of tissue culture derived plants might be needed to determine that rooted shoots are adventitious in origin.

  14. Genetic Diversity Analysis of Elops machnata (Forskal Populations in South East and West Coasts of India Using RAPD Markers

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    Vellaichamy RAMANADEVI

    2014-12-01

    Full Text Available The Random Amplified Polymorphic DNA (RAPD technique was used to study the genetic diversity of four Elops machnata populations in South India. Elops machnata is considered as a least concern species (LC, categorized by the International Union for Conservation and Nature (IUCN. The population trends are currently stable in Indian Ocean, Eastern Africa, but are unknown throughout the rest of its expansive range, especially in Indian estuaries. Among the ten RAPD primers tested, eight primers got amplified and gave scorable bands. In total, 119 scorable bands were observed in all populations. The overall observed and effective number of alleles was found to be 2.000 ± 0.000 and 1.5307 ± 0.2503 respectively for the entire population. The overall polymorphic loci were 61.00% and the overall gene flow among the four populations was predicted to 0.1032. The genetic distance and geographic distance between the four populations showed a positive correlation. The highest genetic similarity (0.6824 was found between Parangipettai and Muthupettai population, which reflected the geographical relationship between them. Tow main clusters were obtained based on UPGMA dendrogram. This study proves that RAPD analysis has the ability to discriminate E. machnata populations in South Indian coastal waters.

  15. GENETIC DIVERSITY OF WILD AND FARMED KALIBAUS (Labeo calbasu, Hamilton, 1822 BY RAPD ANALYSIS OF THE GENOMIC DNA

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    M.G. Mostafa

    2009-04-01

    Full Text Available Genetic diversity of two wild Kalibaus, Labeo calbasu populations and one hatchery stock was studied using random amplified polymorphic DNA (RAPD method. The three 10–mer random primers (OPA01, OPB02 and OPC03 yielded a total of 26 reproducible and consistently scorable RAPD bands of which 15 (57.69% were considered as polymorphic (P95 indicating a high level of genetic variation in all the studied populations. Among the three populations, Padma population shows low level of genetic diversity (0.1238 compared to other two and it might be caused by habitat degradation in many ways which ultimately affects the genetic variation of Kalibaus. The UPGMA dendrogram based on Nei’s (1972 original measures of genetic distance (D indicated the segregation of two wild and hatchery populations of L. calbasu into two distinct clusters: the Hatchery and Padma populations produced one cluster whereas the Jamuna population belonged to another cluster. This indicates that hatchery brood stock is derived from Padma River. Nevertheless, the preliminary study revealed that RAPD technique could be an effective tool in the assessment of population genetic structure of Kalibaus.

  16. Genetic variation of Melia azedarach in community forests of West Java assessed by RAPD

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    YULIANTI

    2011-04-01

    Full Text Available Yulianti, Siregar IZ, Wijayanto N, Tapa Darma IGK, Syamsuwida D (2011 Genetic variation of Melia azedarach in community forests of West Java assessed by RAPD. Biodiversitas 12: 64-69. Melia azedarach L. or mindi (local name is one of the widely planted exotic species in Indonesia, mostly found in community forests in West Java. However, improving and increasing the productivity of mindi commmunity plantation in West Java requires information on patterns of existing genetic diversity. The present work was aimed at estimating the genetic variation of mindi by using RAPD markers. Outcome of the activities was to propose appropriate conservation and management strategies of genetic resources in order to support the establishment of seed sources. Six populations of mindi plantation in the community forests were chosen for this research, i.e Sukaraja (Bogor-1, Megamendung (Bogor-2, Bandung, Purwakarta, Sumedang and Kuningan. Five primers (OPA-07, OPY-13, OPY-16, OPA-09 and OPO-05 producing reproducible bands were analysed for 120 selected mother trees in total, in which 20 trees per locality were sampled. Data were analysed using Popgene ver 1.31, NTSYS 2.02 and GenAlEx 6.3. Based on the analysis, the observed number of alleles per locus ranging from 1.43 to 1.60, and percentage of polymorphic loci (PPL ranging from 43.33 to 60.00.%. The levels of genetic variation were considered as moderate for all populations (He range from 0.1603 to 0.1956 and the the mean level of genetic diversity between population (Gst was 0.3005. Cluster analysis and Principal Coordinates showed three main groups, the first group consists of 4 populations i.e Bandung, Kuningan, Purwakarta and Megamendung, the second was Sukaraja and the third was Sumedang. Based on Analysis of Molecular Variance (AMOVA, the Percentages of Molecular Variance within population (69% is higher than that of between populations (31%. The moderate level of genetic variation in the community

  17. Isozyme, ISSR and RAPD profiling of genotypes in marvel grass (Dichanthium annulatum).

    Science.gov (United States)

    Saxena, Raghvendra; Chandra, Amaresh

    2010-11-01

    Genetic analysis of 30 accessions of marvel grass (Dichanthium annulatum Forsk.), a tropical range grass collected from grasslands and open fields of drier regions, was carried out with the objectives of identifying unique materials that could be used in developing the core germplasm for such regions as well as to explore gene (s) for drought tolerance. Five inter-simple sequence repeat (ISSR) primers [(CA)4, (AGAC), (GACA) 4; 27 random amplified polymorphic DNA (RAPD) and four enzyme systems were employed in the present study. In total, ISSR yielded 61 (52 polymorphic), RAPD 269 (253 polymorphic) and enzyme 55 isozymes (44 polymorphic) bands. The average polymorphic information content (PIC) and marker index (MI) across all polymorphic bands of 3 markers systems ranged from 0.419 to 0.480 and 4.34 to 5.25 respectively Dendrogram analysis revealed three main clusters with all three markers. Four enzymes namely esterase (EST), polyphenoloxidase (PPO), peroxidase (PRX) and superoxide dismutase (SOD) revealed 55 alleles from a total of 16 enzyme-coding loci. Of these, 14 loci and 44 alleles were polymorphic. The mean number of alleles per locus was 3.43. Mean heterozygosity observed among the polymorphic loci ranged from 0.406 (SOD) to 0.836 (EST) and accession wise from 0.679 (1G3108) to 0.743 (IGKMD-10). Though there was intermixing of few accessions of one agro-climatic region to another largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 iterations also showed large numbers of nodes (11 to 17) having strong clustering (> 50 bootstrap values) in all three marker systems. The accessions of the arid and drier regions forming one cluster are assigned as distinct core collection of Dichanthium and can be targeted for isolation of gene (s) for drought tolerance. Variations in isozyme allele numbers and high PIC (0.48) and MI (4.98) as observed with ISSR markers indicated their usefulness for germplasm characterization.

  18. Assessment of genetic diversity in Trigonella foenum-graecum and Trigonella caerulea using ISSR and RAPD markers

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    Ranjekar Prabhakar K

    2004-07-01

    Full Text Available Abstract Background Various species of genus Trigonella are important from medical and culinary aspect. Among these, Trigonella foenum-graecum is commonly grown as a vegetable. This anti-diabetic herb can lower blood glucose and cholesterol levels. Another species, Trigonella caerulea is used as food in the form of young seedlings. This herb is also used in cheese making. However, little is known about the genetic variation present in these species. In this report we describe the use of ISSR and RAPD markers to study genetic diversity in both, Trigonella foenum-graecum and Trigonella caerulea. Results Seventeen accessions of Trigonella foenum-graecum and nine accessions of Trigonella caerulea representing various countries were analyzed using ISSR and RAPD markers. Genetic diversity parameters (average number of alleles per polymorphic locus, percent polymorphism, average heterozygosity and marker index were calculated for ISSR, RAPD and ISSR+RAPD approaches in both the species. Dendrograms were constructed using UPGMA algorithm based on the similarity index values for both Trigonella foenum-graecum and Trigonella caerulea. The UPGMA analysis showed that plants from different geographical regions were distributed in different groups in both the species. In Trigonella foenum-graecum accessions from Pakistan and Afghanistan were grouped together in one cluster but accessions from India and Nepal were grouped together in another cluster. However, in both the species accessions from Turkey did not group together and fell in different clusters. Conclusions Based on genetic similarity indices, higher diversity was observed in Trigonella caerulea as compared to Trigonella foenum-graecum. The genetic similarity matrices generated by ISSR and RAPD markers in both species were highly correlated (r = 0.78 at p = 0.001 for Trigonella foenum-graecum and r = 0.98 at p = 0.001 for Trigonella caerulea indicating congruence between these two systems

  19. Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers Diversidade genética em germoplasma tropical de cebola estimada via marcadores RAPD

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    Maria do Desterro M dos Santos

    2012-03-01

    Full Text Available Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7% were monomorphic and 102 (16.3% were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical', for which the genetic origin (with few exceptions can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in

  20. Genetic variability in clones of 'Prata Anã' bananas based on phenotypic and molecular markers

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    Francisco Ermelindo Rodrigues

    2012-01-01

    Full Text Available The objective of this study was to examine the molecular and phenotypic variability of 'Prata Anã' banana clones cultivated in northern Minas Gerais State. For the phenotypic and molecular characterization, the clones were collected from five properties. The morphological characterization of 20 clones was accomplished through a qualitative evaluation of 74 descriptors. For the molecular evaluations, 45 clones were collected, and 14 Random Amplified Polymorphic DNA primers were used. Among the 74 morphological descriptors evaluated in the 20 'Prata Anã' banana tree clones, 53 descriptors presented in the same homogeneous class for all clones. The presence of anthocyanin in the pseudostem (ANT and the shape (BUS and flexion (FLX of the bunch clearly differentiated the 'Prata Anã' banana clones from the commercial cultivar. A total of 176 bands were produced from the molecular analysis using the 14 RAPD primers; there were 116 monomorphic and 60 polymorphic bands, with an average polymorphism percentage of 52.2%. The amplification using the OPP 14 primer resulted in the greatest percentage of polymorphic bands at 88%. The dendrogram indicated that each of the 45 'Prata Anã' clones that were evaluated using RAPD markers clustered with the commercial 'Prata Anã' cultivar.

  1. Epidemiological markers in Neisseria meningitidis: an estimate of the performance of genotyping vs phenotyping

    DEFF Research Database (Denmark)

    Weis, N; Lind, I

    1998-01-01

    In order to estimate the performance of genotypic vs phenotypic characterization of Neisseria meningitidis, 2 methods, DNA fingerprinting and multilocus enzyme electrophoresis (MEE), were assessed as regards applicability, reproducibility and discriminating capacity. 50 serogroup B and 52 serogroup...... defined by DNA fingerprinting and MEE as compared to that defined by phenotypic characteristics (serogroup, serotype, serosubtype and sulphonamide resistance) was as follows: for serogroup B strains from patients, 11 and 12 vs 8; for serogroup C strains from patients, 10 and 15 vs 8; and for serogroup C...... carrier strains, 12 and 19 genotypes vs 10 phenotypes were defined. By use of both DNA fingerprinting and MEE the number of genotypes defined for the 3 groups of strains was 14, 17 and 19, respectively. DNA fingerprinting and MEE showed a discriminating capacity superior to that of phenotyping...

  2. Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae as revealed by RAPD fingerprinting

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    El-Bous, M.

    2011-12-01

    Full Text Available Taxonomic considerations among and within some Egyptian taxa of Capparis and related genera (Capparaceae as revealed by RAPD fingerprinting.- This investigation was carried out to assess the taxonomic relationships among eight taxa of the Egyptian members of Capparaceae based on random amplified polymorphic DNA markers, and to compare the results with those obtained from morphological studies. A total of 46 bands were scored for three RAPD primers corresponding to an average of 15.3 bands per primer. The three primers (A03, A07 and A09 revealed eight polymorphic RAPD markers among the studied taxa ranging in size from 200 bp to 1000 bp. Jaccard’s coefficient of similarity varied from 0.28 to 0.84, indicative of high level of genetic variation among the genotypes studied. UPGMA cluster analysis indicated three distinct clusters, one comprised Cleome amblyocarpa and Gynandropsis gynandra, while another included two clusters at 0.74 phenon line; one for Capparis decidua, and the other for Capparis sinaica and all varieties of Capparis spinosa. The four varieties of Capparis spinosa were segregated at 0.84 phenon line. However, one of these varieties was more closely related to Capparis sinaica than to the other three varieties of C. spinosa. The RAPD analysis reported here confirms previous studies based on morphological markers.Consideraciones taxonómicas sobre algunos taxones egipcios de Capparis y géneros relacionados (Capparaceae a partir de RAPDs.- El objetivo de este trabajo es investigar las relaciones taxonómicas entre ocho taxones pertenecientes a las Capparaceae en base a marcadores de tipo RAPD, y comparar los resultados con los obtenidos previamente en estudios morfológicos. Se han contabilizado un total de 46 bandas para tres pares de cebadores, con una media de 15,3 bandas por cebador. Los tres pares de cebadores (A03, A07 y A09 revelan ocho marcadores polimórficos entre los taxones estudiados, de entre 200 y 1000 pares de

  3. RAPD analysis of the genetic diversity of mango (Mangifera indica) germplasm in Brazil.

    Science.gov (United States)

    Souza, I G B; Valente, S E S; Britto, F B; de Souza, V A B; Lima, P S C

    2011-12-14

    We evaluated genetic variability of mango (Mangifera indica) accessions maintained in the Active Germplasm Bank of Embrapa Meio-Norte in Teresina, Piauí, Brazil, using RAPDs. Among these accessions, 35 originated from plantings in Brazil, six from the USA and one from India. Genomic DNA, extracted from leaf material using a commercial purification kit, was subjected to PCR with the primers A01, A09, G03, G10, N05, and M16. Fifty-five polymorphic loci were identified, with mean of 9.16 ± 3.31 bands per primer and 100% polymorphism. Application of unweighted pair group method using arithmetic average cluster analysis demonstrated five genotypic groups among the accessions examined. The genotypes Rosa 41, Rosa 48 and Rosa 49 were highly similar (94% similarity), whereas genotypes Sensation and Rosa 18 were the most divergent (only 7% similarity). The mango accessions were found to have considerable genetic variability, demonstrating the importance of analyzing each genotype in a collection in order to efficiently maintain the germplasm collection.

  4. Dispersal of the cotton boll weevil (Coleoptera: Curculionidae) in South America: evidence of RAPD analysis.

    Science.gov (United States)

    Scataglini, M A; Confalonieri, V A; Lanteri, A A

    2000-01-01

    RAPD technique provides useful information on the geographic origin and dispersal of the boll weevil Anthonomus grandis in South America. Nine populations from Argentina, Brazil, Paraguay, Mexico and USA were analyzed. Weevils were captured on native plants (Misiones province, Argentina) and on cotton cultures, except the sample from the United States (USDA laboratory-reared colony). A sample of the 'Peruvian square weevil', A. vestitus, from Ecuador, was included in the analysis in order to compare interspecific variation. The four primers used in the analysis revealed 41 'anonymous loci'. The neighbor-joining tree based on Nei's distances and values of Nm (migrants per generation), indicate that genetic similarity between samples from Tecomán (Mexico) and Puerto Iguazú (Argentina), is higher than among remaining South American populations. This result supports an hypothesis of natural occurrence of the boll weevil in South America, prior to extensive cotton cultivation. Population outbreaks of the species would be associated with increase of agricultural lands.

  5. Identification of the 1RS rye chromosomal segment in wheat by RAPD analysis.

    Science.gov (United States)

    Iqbal, M J; Rayburn, A L

    1995-11-01

    The introgression of rye DNA into the wheat genome was studied using random decamer and specific primers with the polymerase chain reaction (PCR). DNA from paired near-isolines in Chisholm and Arkan backgrounds differing with respect to the presence of a 1 RS.1 BL translocation was amplified with 120 arbitrary sequence primers. Two of the primers (OPR 19 and OPJ07) amplified rye-specific DNA fragments. The OPR19 primer amplified a 1.35-kb fragment that appeared to be specific to the 1 RS.1 BL translocation, based on its presence only in lines carrying the 1 RS. 1 BL translocation. A fragment of the same size was also amplified in 1 RS.1 AL translocation lines. This 1 RS. 1 BL marker locus was designated Ximc 1. The other primer, OPJ07, amplified a 1.2-kb DNA sequence, that was designated Ximc 2, specific to the wheat-rye translocation in various wheat backgrounds. The sequences of the two marker loci were found to be different from each other. The Ximc 1 locus was a low-copy sequence which was also present in Balboa rye genomic DNA. Through the use of specific primers, the presence of the rye-specific marker was confirmed in hexaploid as well as in tetraploid wheat backgrounds. The use of RAPDs for the study of smaller alien introgressions into wheat is discussed.

  6. Characterization of the Second Generation Cryopreserved Dendrobium Bobby Messina Using Histological and RAPD Analyses

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    Jessica Jeyanthi James Antony

    2015-12-01

    Full Text Available This study was conducted to detect the morphological, histological and molecular diff erences in the second generation of the PVS2 cryopreserved Dendrobium Bobby Messina [DBM] (18 months old culture plantlets. Morphological analyses indicated that similarities and diff erences in cryopreserved DBM plantlets comparing to control stock culture based on selected morphological criteria. Morphological criteria, such as root length, number of shoot per explant and shoot length displayed diff erences, while the other three criteria, leaf diameter, leaf length and PLBs size were similar in cryopreserved compared to the control stock culture plant. Higher amount of homogenous cell population and denser cytoplasm were observed in cryopreserved PLBs compared to control stock culture PLBs based on histological analysis. This suggests the existance of somatic embryogenesis development mechanism taking place during the recovery and regeneration of the cryopreserved PLBs. However, RAPD analyses based on 10 primers indicated that cryopreserved DBM regenerated from vitrifi cation method generated a total of 20 to 39.9% polymorphic bands as compared to stock culture indicating potential somaclonal variation. Hence, an increase percentage of polymorphics bands in cryopreserved plantlets 18 months post cryopreservation as compared to previous report of 10% polymorphic bands in cryopreserved DBM 3 months post cryopreservation.

  7. Genetic Analysis of Pinus sylvestris L. and Pinus sylvestris forma turfosa L. Using RAPD Markers

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    Beáta ÁBRAHÁM

    2010-03-01

    Full Text Available The purpose of the present study was to determine the level of genetic diversity within and among Ciuc basin, Romania (populations from Mohos and Luci raised bogs in Harghita Mountain and Sumuleu in Ciuc Mountain Pinus sylvestris populations using molecular markers. Two of populations (Mohos and Luci seems to be the descendants that survived the continental glaciation. Genetic diversity was analyzed by RAPD (Random Amplified Polymorphic DNA. Nine primers were selected for analysis, which generated reproducible bands. On base of presence or absence of homologues bands Nei’s gene diversity, the percentage of polymorphic loci and Nei’s unbiased genetic distance were calculated. The level of genetic variation among populations was found to be low. For both populations the variation values among populations were higher than within populations. The fossil records and geological historical data explain the extremely low genetic diversity of this species. Pinus sylvestris experienced strong bottlenecks during its evolutionary history, which caused the loss of genetic variation. Genetic drift and breeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity and genetic differentiation of populations. Human activities may have accelerated the loss of genetic diversity in Pinus sylvestris.

  8. Genetic polymorphism, molecular characterization and relatedness of Macrobrachium species (Palaemonidae) based on RAPD-PCR.

    Science.gov (United States)

    Guerra, A L; Lima, A V B; Taddei, F G; Castiglioni, L

    2010-11-30

    The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species.

  9. Identification of hybrids of intra and interspecific crosses in Annonaceae by RAPD markers

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    Danuza Araújo de Souza

    2010-01-01

    Full Text Available The purpose of this work was to identify hybrids in intraspecific crosses between sugar apple accessions and interspecific crosses between sugar apple and atemoya accessions by using RAPD markers. Four sugar apple accessions were selected: Seedless P1, P2, P3 and P4 and the atemoya cultivar Gefner (G1. In the pre-female phase the flowers were adequately protected and reciprocal crosses were performed. In crosses where the sugar apple accession Seedless P1 was used as the male parent, the fruits contained seeds, indicating that the pollen grains of Seedless P1 are viable. The fruits of reciprocal crosses where Seedless P1 was used as a female parent contained no seeds. The percentage of true hybrids in the crosses P4 x Seedless P1, P3 x Seedless P1, P2 x Seedless P1, and G1 x Seedless P1 were, respectively, 100%, 95.55%, 82.86%, and 44.44%. Primer OPF10 was efficient in obtaining polymorphic bands in all Annonaceae hybrid populations.

  10. Assessment of genetic diversity among moderately drought tolerant landraces of rice using RAPD markers

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    Md. Shariful Islam

    2013-01-01

    Full Text Available Genetic diversity and relationships among six rice genotypes were investigated using five random amplified polymorphic DNA (RAPD markers. A total of 69 alleles were amplified, of which 66 were polymorphic. The size of the amplified alleles was between 0.25 and 2.35 kbp. The number of polymorphic alleles detected with each primer ranged from 7 to 24 with an average of 13.2 per primer and the polymorphism information content (PIC values varied from 0.8672 to 0.9471. Pair-wise similarity estimated the range of 0.308 to 0.718 among all the genotypes and the highest genetic similarity was found between Maloti and BRRI dhan53. Cluster analysis using UPGMA (unweighted pair group method with arithmetic averages revealed three clusters at genetic similarity of 46%. A moderately drought tolerant landrace, Boalia, formed a single cluster and the remaining genotypes grouped into distinct clusters based on their relatedness. The results showed a high level of genetic diversity among studied genotypes and this information will assist in conservation as well as selection of parents during breeding programs for the development of drought tolerant rice varieties in near future.

  11. Characterization of Listeria monocytogenes and Listeria innocua from a vegetable processing plant by RAPD and REA.

    Science.gov (United States)

    Aguado, V; Vitas, A I; García-Jalón, I

    2004-02-01

    The incidence of Listeria monocytogenes in a vegetable processing plant was investigated over a 23-month period. Frozen ready-to-eat vegetable samples, well as the plant environment, were sampled. The molecular subtyping techniques, Random Amplified Polymorphic DNA (RAPD) and Restriction Endonuclease Analyses (REA), were performed to help investigate the origin and routes of Listeria dissemination. The low and sporadic incidence of L. monocytogenes made it impossible to establish an epidemiological sequence in the processing plant, though a case of cross-contamination between tomato and ratatouille was detected. Listeria innocua subtyping, however, allowed us to determine the prevalence of several strains in vegetables, and their presence on machinery samples suggested the possibility of cross-contamination during processing. The low incidence of L. monocytogenes indicated that the risk of listeriosis transmission by vegetable consumption is low. On the other hand, the isolation of the same strain of L. innocua in several surveys pointed out the risk of colonisation on surfaces and machinery. The persistence of Listeria spp. is a cause for concern as can lead to future contamination of vegetables processed in the plant and to a possible increased risk for health. Therefore, periodic controls for the presence of Listeria spp. and a further review of the cleaning and disinfection procedures used in frozen vegetable plants are recommended.

  12. RAPD-PCR reveals genetic polymorphism among Leishmania major strains from Tunisian patients.

    Science.gov (United States)

    Yazidi, Rihab; Bettaieb, Jihene; Ghawar, Wissem; Jaouadi, Kaouther; Châabane, Sana; Zaatour, Amor; Ben Salah, Afif

    2015-07-14

    Zoonotic cutaneous leishmaniasis caused by Leishmania (L.) major is endemoepidemic in the Center and South of Tunisia. The clinical course of the disease varies widely among different patients and geographic regions. Although genetic diversity in L. major parasites has been suggested as a potential factor influencing their pathogenic variability, little information on genetic polymorphism among L. major strains is available in the literature. This work aimed to estimate the genetic variability within different isolates of L. major. Our sample comprised 39 isolates (confirmed as L. major by restriction fragment length polymorphism typing) from patients experiencing the same clinical manifestations but living in different regions of Tunisia where L. major is endemic. Random amplified polymorphic DNA (RAPD) PCR marker polymorphism was estimated by calculating Nei and Li's genetic distances and by an analysis of molecular variance (AMOVA). Analysis of the genetic diversity among the isolates revealed a high level of polymorphism (43 %) among them. AMOVA indicated that the highest variability (99 %) existed within the study regions. Our results revealed a heterogeneous genetic profile for L. major with similar clinical manifestations occurring within the different geographical regions. Additional L. major isolates from patients, insect vectors, and reservoir hosts from different endemic foci should be collected for further analysis.

  13. Characterisation of the genetic diversity of Brucella by multilocus sequencing

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    MacMillan Alastair P

    2007-04-01

    Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

  14. Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.

    Science.gov (United States)

    Kingry, Luke C; Rowe, Lori A; Respicio-Kingry, Laurel B; Beard, Charles B; Schriefer, Martin E; Petersen, Jeannine M

    2016-04-01

    Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST) is a recently developed methodology that simplifies genomic analyses by transforming millions of base pairs of sequence into character data for each gene. We sequenced 13 US Y. pestis isolates with known epidemiologic relationships. Sequences were assembled de novo, and multilocus sequence typing alleles were assigned by comparison against 3979 open reading frames from the reference strain CO92. Allele-based cluster analysis accurately grouped the 13 isolates, as well as 9 publicly available Y. pestis isolates, by their epidemiologic relationships. Our findings indicate wgMLST is a simplified, sensitive, and scalable tool for epidemiologic analysis of Y. pestis strains. Published by Elsevier Inc.

  15. Genetic relationships between clinical and non-clinical strains of Yersinia enterocolitica biovar 1A as revealed by multilocus enzyme electrophoresis and multilocus restriction typing

    Science.gov (United States)

    2010-01-01

    Background Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE) and multilocus restriction typing (MLRT) using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation. Results All loci were polymorphic and generated 62 electrophoretic types (ETs) and 12 restriction types (RTs). The mean genetic diversity (H) of the strains by MLEE and MLRT was 0.566 and 0.441 respectively. MLEE (DI = 0.98) was more discriminatory and clustered Y. enterocolitica biovar 1A strains into four groups, while MLRT (DI = 0.77) identified two distinct groups. BURST (Based Upon Related Sequence Types) analysis of the MLRT data suggested aquatic serotype O:6,30-6,31 isolates to be the ancestral strains from which, clinical O:6,30-6,31 strains might have originated by host adaptation and genetic change. Conclusion MLEE revealed greater genetic diversity among strains of Y. enterocolitica biovar 1A and clustered strains in four groups, while MLRT grouped the strains into two groups. BURST analysis of MLRT data nevertheless provided newer insights into the probable evolution of clinical strains from aquatic strains. PMID:20509911

  16. Genetic relationships between clinical and non-clinical strains of Yersinia enterocolitica biovar 1A as revealed by multilocus enzyme electrophoresis and multilocus restriction typing

    Directory of Open Access Journals (Sweden)

    Virdi Jugsharan S

    2010-05-01

    Full Text Available Abstract Background Genetic relationships among 81 strains of Y. enterocolitica biovar 1A isolated from clinical and non-clinical sources were discerned by multilocus enzyme electrophoresis (MLEE and multilocus restriction typing (MLRT using six loci each. Such studies may reveal associations between the genotypes of the strains and their sources of isolation. Results All loci were polymorphic and generated 62 electrophoretic types (ETs and 12 restriction types (RTs. The mean genetic diversity (H of the strains by MLEE and MLRT was 0.566 and 0.441 respectively. MLEE (DI = 0.98 was more discriminatory and clustered Y. enterocolitica biovar 1A strains into four groups, while MLRT (DI = 0.77 identified two distinct groups. BURST (Based Upon Related Sequence Types analysis of the MLRT data suggested aquatic serotype O:6,30-6,31 isolates to be the ancestral strains from which, clinical O:6,30-6,31 strains might have originated by host adaptation and genetic change. Conclusion MLEE revealed greater genetic diversity among strains of Y. enterocolitica biovar 1A and clustered strains in four groups, while MLRT grouped the strains into two groups. BURST analysis of MLRT data nevertheless provided newer insights into the probable evolution of clinical strains from aquatic strains.

  17. Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni

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    Nash John HE

    2008-08-01

    Full Text Available Abstract Background Multi-Locus Sequence Typing (MLST has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci. Results Our results indicate that, in general, there is significant concordance between strain relationships established by MLST and those based on shared gene content as established by CGH. While MLST has significant predictive power with respect to overall genome similarity of isolates, we also found evidence for significant differences in genomic content among strains that would otherwise appear to be highly related based on their MLST profiles. Conclusion The extensive genomic mosaicism between closely related strains has important implications in the context of establishing strain to strain relationships because it suggests that the exact gene content of strains, and by extension their phenotype, is less likely to be "predicted" based on a small number of typing loci. This in turn suggests that a greater emphasis should be placed on analyzing genes of clinical interest as we forge ahead with the next generation of molecular typing methods.

  18. Multilocus enzyme electrophoresis typing of Candida albicans populations isolated from healthy children according to socioeconomic background

    OpenAIRE

    Marcelo Fabiano Gomes Boriollo; Edvaldo Antônio Ribeiro Rosa; Wagner Luis de Carvalho Bernardo; Denise Madalena Palomari Spolidorio; Reginaldo Bruno Gonçalves; José Francisco Höfling

    2005-01-01

    The aim of this research was to evaluate the genetic diversity within and between C. albicans populations isolated from the oral cavity of healthy Brazilian children classified into five socioeconomic categories (A to E). Multilocus Enzyme Electrophoresis (MLEE) analysis was the method used to assess genetic diversity. High genetic diversity was observed in all populations that showed predominance of some C. albicans subtypes (Electrophoretic Types - ETs). However, no correlation was observed...

  19. A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes▿ †

    Science.gov (United States)

    Margos, Gabriele; Vollmer, Stephanie A.; Cornet, Muriel; Garnier, Martine; Fingerle, Volker; Wilske, Bettina; Bormane, Antra; Vitorino, Liliana; Collares-Pereira, Margarida; Drancourt, Michel; Kurtenbach, Klaus

    2009-01-01

    Analysis of Lyme borreliosis (LB) spirochetes, using a novel multilocus sequence analysis scheme, revealed that OspA serotype 4 strains (a rodent-associated ecotype) of Borrelia garinii were sufficiently genetically distinct from bird-associated B. garinii strains to deserve species status. We suggest that OspA serotype 4 strains be raised to species status and named Borrelia bavariensis sp. nov. The rooted phylogenetic trees provide novel insights into the evolutionary history of LB spirochetes. PMID:19542332

  20. Identification of Bacterial Plant Pathogens Using Multilocus Polymerase Chain Reaction/Electrospray Ionization-Mass Spectrometry

    Science.gov (United States)

    2008-01-01

    allows for a multilocus identification with significantly less time and effort. This paper describes the first application of this technology to plant...Garden hyacinth ; The Netherlands 1 Xanthomonas oryzae pv. oryzae VPI-33; ATCC 35933 Rice; India 4 Xanthomonas oryzae pv. oryzicola FB-1312 Rice; unknown...Paul, MN. 14. McCoy, W. F., and Olson, B. H. 1985. Fluorometric determination of the DNA concentration in municipal drinking water . Appl. Environ

  1. Allelic diversity and population structure of Bacillus sphaericus as revealed by multilocus sequence typing.

    Science.gov (United States)

    Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming

    2011-08-01

    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains.

  2. Allelic Diversity and Population Structure of Bacillus sphaericus as Revealed by Multilocus Sequence Typing ▿ †

    Science.gov (United States)

    Ge, Yong; Hu, Xiaomin; Zheng, Dasheng; Wu, Yiming; Yuan, Zhiming

    2011-01-01

    The genetic diversity of 35 Bacillus sphaericus strains was analyzed by a newly developed multilocus sequence typing (MLST) scheme, toxin gene pool survey, and mosquito bioassay. The results demonstrated that strains assigned to the same sequence type (ST) had the same occurrence of toxin genes. Further sequence analysis revealed that toxic strains presented a nearly clonal population structure, whereas nontoxic strains had a high level of heterogeneity and were significantly distinct from toxic strains. PMID:21685170

  3. Análise da recuperação do genitor recorrente em maracujazeiro-azedo por meio de marcadores RAPD Recovery analysis of recurrent genitor in sour passion fruit through RAPD markers

    Directory of Open Access Journals (Sweden)

    Kenia Gracielle da Fonseca

    2009-03-01

    Full Text Available O Brasil é o maior produtor mundial de maracujá, entretanto tem-se observado redução na produtividade do maracujazeiro nos últimos anos, devido, principalmente, a fatores fitossanitários. Na Embrapa Cerrados, a transferência de genes de resistência de espécies silvestres para as comerciais de maracujazeiro tem sido feita por meio de hibridações interespecíficas seguidas de um programa de retrocruzamentos auxiliados por marcadores moleculares. Este trabalho teve por objetivo verificar a recuperação do genoma recorrente nas plantas RC4 e RC5 [(Passiflora edulis x Passiflora setacea x Passiflora edulis ] com base em marcadores RAPD. O estudo foi desenvolvido no Laboratório de Genética e Biologia Molecular da Embrapa Cerrados. Amostras de DNA de cada material genético (17 plantas RC4, 16 plantas RC5, Passiflora edulis e Passiflora setacea foram amplificadas para obtenção de marcadores RAPD. Foram utilizados 12 primers decâmeros para as plantas RC4 e 14 primers decâmeros para as plantas RC5. Os marcadores RAPD gerados foram convertidos em matriz de dados binários. Verificou-se alta porcentagem de marcadores polimórficos em consequência do cruzamento-base interespecífico. A menor similaridade genética foi observada entre as espécies P. edulis e P. setacea, evidenciando a grande distância genética dessas espécies.Brazil is the largest world producer of passion fruit, however, it has been observed a reduction in the productivity in recent years due, mainly, to phytosanitary factors. At Embrapa Cerrados, the transfer of resistance genes from wild to commercial species of passion fruit has been made through interspecific hybridations, followed by a backcrossing molecular marker-assisted program. The objective this work was to verify the recovery of recurrent genome at the plants RC4 and RC5 [(Passiflora edulis x Passiflora setacea x Passiflora edulis] based on RAPD markers. The study was developed at Embrapa Cerrados

  4. Caracterização de três genótipos de umezeiro (Prunus mume Sieb. et Zucc. por marcadores RAPD Characterization of three mume genotypes (Prunus mume Sieb. et Zucc. by RAPD markers

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    Newton Alex Mayer

    2008-12-01

    Full Text Available Um projeto de pesquisa visando à utilização de clones de umezeiro (Prunus mume Sieb. et Zucc. como porta-enxertos para pessegueiro [Prunus persica (L. Batsch] está sendo conduzido na FCAV/UNESP, Câmpus de Jaboticabal-SP, com promissoras perspectivas de sucesso. Três genótipos de umezeiro foram selecionados de acordo com características agronômicas desejáveis para esta finalidade. A distinção dos três genótipos entre si, baseada exclusivamente em características morfológicas, apresenta limitações. Dessa forma, o objetivo do presente trabalho foi identificar marcadores RAPD capazes de diferenciar e caracterizar os Clones 05, 15 e a cv. Rigitano (Clone 10 de umezeiro, utilizando-se das cultivares Aurora-1 e Okinawa de pessegueiro como outgroup. Dos 220 primers testados, foram selecionados 42, que amplificaram todos os cinco genótipos. Verificou-se que os marcadores RAPD permitiram a distinção entre o Clone 05, o Clone 15 e a cv. Rigitano de umezeiro, demonstrando a existência de variabilidade genética entre os mesmos. Dentre os três genótipos de umezeiro estudados, constatou-se que a similaridade genética é maior entre o Clone 05 e o Clone 15.A research project with the objective do develop mume clones (Prunus mume Sieb. et Zucc., to be used as rootstocks for peach tree [Prunus persica (L. Batsch] is been carried out at the Faculdade de Ciências Agrárias e Veterinárias (FCAV/UNESP, Jaboticabal Campus, São Paulo State, Brazil. These project showed promising perspectives of success, with three clones that were selected according to their characteristics for peach rootstock. But the distinction of the three clones among them, based only in morphologic characteristics, has presented limitations. The objective of the present research was to identify RAPD markers able to characterize and differentiate the 05 and 15 Clones and Rigitano mume cultivar, using Aurora-1 and Okinawa peach tree as outgroup. Among the 220 tested

  5. Genetic variations among passion fruit species using rapd markers Variação genética entre espécies de maracujá utilizando marcadores rapd

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    Ana Paula de Andrade Aukar

    2002-12-01

    Full Text Available It has been evaluated the genetic variability through the use of RAPD molecular markers on the following passionflower species: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims and its botanical variety P. edulis Sims f. flavicarpa Deg. In this research work, the analyses of the random amplified polymorphic DNA products (RAPD were employed to estimate the genetic diversity and the taxonomic linkage within the species above. The total of 21 primers were used in this study which generated 270 different polymorphic products. It was possible to detect that the Passiflora species had shown a similarity of 17,3%, and between Passiflora edulis Sims and Passiflora edulis Sims f. flavicarpa a similarity of 34,35% has been found. The rate of similarity within edulis specie is low, making it clear that a large variability between the yellow and the purple forms exists.Foram avaliadas as variações genéticas através de marcadores moleculares RAPD, as seguintes espécies de maracujá: Passiflora amethystina, P. caerulea, P. cincinnata, P. coccinea, P. serrato digitata, P. foetida, P. maliformis, P. alata, P. giberti, P. laurifolia, P. macrocarpa, P. nitida, P. setacea, P. suberosa, P. ligularis, P. capsularis, P. edulis Sims e sua variedade botânica P. edulis Sims f. flavicarpa Deg. Neste estudo, a análise dos produtos da amplificação ao acaso do DNA polimórfico (RAPD foi usada para estimar a diversidade genética e as relações taxonômicas entre as espécies. Foram utilizados 21 "primers", que produziram um total de 270 bandas polimórficas. Verificou-se que as espécies de Passiflora apresentaram uma média de similaridade de 17,3%, e entre Passiflora edulis Sims e Passiflora edulis Sims f. flavicarpa, de 34,35%. Pode-se perceber que o valor de

  6. RAPDs na caracterização genético-molecular e no estudo da variabilidade genética de cultivares de ameixeira RAPDs on genetic-molecular characterization and genetic variabiliti study of plums

    Directory of Open Access Journals (Sweden)

    Valmor João Bianchi

    2003-08-01

    Full Text Available Marcadores moleculares têm sido amplamente utilizados nas mais variadas espécies frutíferas para análise de "fingerprinting", para o processo de certificação de material vegetal e como ferramenta auxiliar em programas de melhoramento genético, para acessar a variabilidade genética entre genótipos. Dado a importância da cultura da ameixeira para a região Sul do Brasil, o presente trabalho teve por finalidade contribuir para a caracterização genético-molecular de 17 cultivares. As cultivares foram analisadas com 12 marcadores RAPD, que produziram 187 polimorfismos. O marcador OP A20 foi o mais polimórfico, produzindo 26 perfis diferentes. A análise de agrupamento, realizada com o método UPGMA, produziu um dendrograma que permitiu uma clara separação das cultivares em três grupos, correspondentes às suas respectivas espécies, Prunus salicina, Prunus domestica e Prunus cerasifera. O alto grau de polimorfismo detectado pelos marcadores RAPD confirma o potencial da técnica na análise de "fingerprinting" e sua utilidade na estimativa da variabilidade genética entre cultivares de ameixeira.Molecular markers have been used thoroughly in many fruit crops species for fingerprinting analysis during the vegetal material certification process, and as an auxiliary tool in breeding programs to access genetic variability among genotypes. The plum is an important crop in Southern Brazil. The present paper aims to contribute for the genetic-molecular characterization of 17 plum cultivars, which were analyzed with 12 RAPD markers that produced 187 polymorphisms. The OP A20 marker was the most polymorphic, producing 26 different profiles. The cluster analysis was represented by a dendrogram using the UPGMA method, and showed a clear cultivar separation in to three groups corresponding to the species, Prunus salicina, Prunus domestica and Prunus cerasifera, respectively. A high degree of polymorphism was detected by the RAPD markers in the

  7. Pseudomonas aeruginosa in Dairy Goats: Genotypic and Phenotypic Comparison of Intramammary and Environmental Isolates

    Science.gov (United States)

    Scaccabarozzi, Licia; Leoni, Livia; Ballarini, Annalisa; Barberio, Antonio; Locatelli, Clara; Casula, Antonio; Bronzo, Valerio; Pisoni, Giuliano; Jousson, Olivier; Morandi, Stefano; Rapetti, Luca; García-Fernández, Aurora; Moroni, Paolo

    2015-01-01

    Following the identification of a case of severe clinical mastitis in a Saanen dairy goat (goat A), an average of 26 lactating goats in the herd was monitored over a period of 11 months. Milk microbiological analysis revealed the presence of Pseudomonas aeruginosa in 7 of the goats. Among these 7 does, only goat A showed clinical signs of mastitis. The 7 P. aeruginosa isolates from the goat milk and 26 P. aeruginosa isolates from environmental samples were clustered by RAPD-PCR and PFGE analyses in 3 genotypes (G1, G2, G3) and 4 clusters (A, B, C, D), respectively. PFGE clusters A and B correlated with the G1 genotype and included the 7 milk isolates. Although it was not possible to identify the infection source, these results strongly suggest a spreading of the infection from goat A. Clusters C and D overlapped with genotypes G2 and G3, respectively, and included only environmental isolates. The outcome of the antimicrobial susceptibility test performed on the isolates revealed 2 main patterns of multiple resistance to beta-lactam antibiotics and macrolides. Virulence related phenotypes were analyzed, such as swarming and swimming motility, production of biofilm and production of secreted virulence factors. The isolates had distinct phenotypic profiles, corresponding to genotypes G1, G2 and G3. Overall, correlation analysis showed a strong correlation between sampling source, RAPD genotype, PFGE clusters, and phenotypic clusters. The comparison of the levels of virulence related phenotypes did not indicate a higher pathogenic potential in the milk isolates as compared to the environmental isolates. PMID:26606430

  8. Pseudomonas aeruginosa in Dairy Goats: Genotypic and Phenotypic Comparison of Intramammary and Environmental Isolates.

    Science.gov (United States)

    Scaccabarozzi, Licia; Leoni, Livia; Ballarini, Annalisa; Barberio, Antonio; Locatelli, Clara; Casula, Antonio; Bronzo, Valerio; Pisoni, Giuliano; Jousson, Olivier; Morandi, Stefano; Rapetti, Luca; García-Fernández, Aurora; Moroni, Paolo

    2015-01-01

    Following the identification of a case of severe clinical mastitis in a Saanen dairy goat (goat A), an average of 26 lactating goats in the herd was monitored over a period of 11 months. Milk microbiological analysis revealed the presence of Pseudomonas aeruginosa in 7 of the goats. Among these 7 does, only goat A showed clinical signs of mastitis. The 7 P. aeruginosa isolates from the goat milk and 26 P. aeruginosa isolates from environmental samples were clustered by RAPD-PCR and PFGE analyses in 3 genotypes (G1, G2, G3) and 4 clusters (A, B, C, D), respectively. PFGE clusters A and B correlated with the G1 genotype and included the 7 milk isolates. Although it was not possible to identify the infection source, these results strongly suggest a spreading of the infection from goat A. Clusters C and D overlapped with genotypes G2 and G3, respectively, and included only environmental isolates. The outcome of the antimicrobial susceptibility test performed on the isolates revealed 2 main patterns of multiple resistance to beta-lactam antibiotics and macrolides. Virulence related phenotypes were analyzed, such as swarming and swimming motility, production of biofilm and production of secreted virulence factors. The isolates had distinct phenotypic profiles, corresponding to genotypes G1, G2 and G3. Overall, correlation analysis showed a strong correlation between sampling source, RAPD genotype, PFGE clusters, and phenotypic clusters. The comparison of the levels of virulence related phenotypes did not indicate a higher pathogenic potential in the milk isolates as compared to the environmental isolates.

  9. Pseudomonas aeruginosa in Dairy Goats: Genotypic and Phenotypic Comparison of Intramammary and Environmental Isolates.

    Directory of Open Access Journals (Sweden)

    Licia Scaccabarozzi

    Full Text Available Following the identification of a case of severe clinical mastitis in a Saanen dairy goat (goat A, an average of 26 lactating goats in the herd was monitored over a period of 11 months. Milk microbiological analysis revealed the presence of Pseudomonas aeruginosa in 7 of the goats. Among these 7 does, only goat A showed clinical signs of mastitis. The 7 P. aeruginosa isolates from the goat milk and 26 P. aeruginosa isolates from environmental samples were clustered by RAPD-PCR and PFGE analyses in 3 genotypes (G1, G2, G3 and 4 clusters (A, B, C, D, respectively. PFGE clusters A and B correlated with the G1 genotype and included the 7 milk isolates. Although it was not possible to identify the infection source, these results strongly suggest a spreading of the infection from goat A. Clusters C and D overlapped with genotypes G2 and G3, respectively, and included only environmental isolates. The outcome of the antimicrobial susceptibility test performed on the isolates revealed 2 main patterns of multiple resistance to beta-lactam antibiotics and macrolides. Virulence related phenotypes were analyzed, such as swarming and swimming motility, production of biofilm and production of secreted virulence factors. The isolates had distinct phenotypic profiles, corresponding to genotypes G1, G2 and G3. Overall, correlation analysis showed a strong correlation between sampling source, RAPD genotype, PFGE clusters, and phenotypic clusters. The comparison of the levels of virulence related phenotypes did not indicate a higher pathogenic potential in the milk isolates as compared to the environmental isolates.

  10. RAPD-based genotyping of Malassezia pachydermatis from Domestic and wild animals

    Directory of Open Access Journals (Sweden)

    Franciele Cristina Kagueyama

    2016-10-01

    Full Text Available Malassezia pachydermatis (M. pachydermatis is a fungus of importance in human and veterinary medicine. Although a part of the normal microbiota, it can sometimes be present in its pathogenic form, particularly causing otitis and dermatitis in animals. Among human beings, it mainly affects immune compromised patients and newborns, causing simple pustulosis, seborrheic dermatitis, tinea versicolor or fungemia. This study aimed to analyze the genomic polymorphism in M. pachydermatis samples isolated from Canis familiaris (domestic dog, Felis catus (domestic cat, and Myrmecophaga tridactyla (giant anteater. Two hundred and fourteen samples were collected and cultured in Sabouraud agar with chloranphenicol (100mg L-1 and incubated at 37 °C for a period of 7 to 10 days. One hundred and sixty six samples that appeared morphologically comparable to yeast cultures were processed for DNA extraction and PCR was performed for a specific region in the Internal Transcribed Spacer (ITS of M. pachydermatis. Among these, seven (4.21% were negative and 159 (95.79% were positive. Of the 159 positive samples, 102 (64.15% were from animals with clinical signs and 57 (35.85% without clinical signs. Fifty-seven samples were selected at random for RAPD-PCR based genotyping and distributed into four genetic groups. Types I and II were more frequent in animals with clinical signs while type III was frequent in healthy animals. Type IV occurred evenly across animals with or without clinical signs. These results indicate differences in pathogenicity of the fungus based on the genotype.

  11. RAPD analysis of Sclerotium rolfsii isolates causing collar rot of eggplant and tomato

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    N. Parvin

    2016-08-01

    Full Text Available Eight isolates of Sclerotium rolfsii from four strategically geographical sites of Bangladesh were characterized and their cultural properties like average linear mycelial growth, colony colour, colony consistency, growth pattern and sclerotia formation were studied. Isolates varied in mycelial growth and other growth characteristics and were grouped into three. The highest linear growth was displayed by S8. DNA concentration of eight isolates varied from 1150-7200 ng/μl. DNA fingerprinting by RAPD prompted the grouping of isolates. Selected 3 primers generated 20 bands with size ranging from 100-1500 bp. Out of the 20 bands, 9 bands (45% were polymorphic and 11 bands (55% were monomorphic among the eight isolates of Sclerotium rolfsii. The co-efficient of gene differentiation (Gst was 1.000 reflecting the existence of high level of genetic variations among the 8 isolates. The lowest genetic distance and highest inter isolate similarity was found in S1 and S2 which would be homogeneous. The highest genetic distance and lowest inter isolate similarity found in S3, S7 and S3, S8 pair which would be most divergent isolates. The cluster analysis also revealed that S3, S7 and S8 belong to different clusters. All five varieties of eggplant and tomatoes were graded as susceptible when inoculated with eight isolates. Plant mortality 93.33% was recorded in S4, S6 and in S8. Considering the isolate factor the most virulent isolate would be S8 whereas the less virulent isolate would be S2 and S7. Host plant of S8 was tomato collected from Thakurgaon. S2 and S7 were collected from BAU farm and Dinajpur and host plants were lentil and tomato respectively. It is evident that Sclerotium rolfsii from Thakurgaon on host tomato is more virulent.

  12. Identification of the Polish strains of Chalara ovoidea using RAPD molecular markers

    Directory of Open Access Journals (Sweden)

    Tadeusz Kowalski

    2011-01-01

    Full Text Available On the basis of morphological features and RAPD markers the strains of Chalara ovoidea found in Poland on planks and on stems of beech trees were identified. As reference strains the cultures taken from CBS Utrecht were employed; they were cultures CBS 354.76 and CBS 136.88. The amplification of genomic DNA was conducted using 10 primers (OPA01-OPA10, 7 of which (OPA01-OPA05, OPA09, OPA10 gave positive results. In total 42 fragment of DNA (bands were obtained. In case of primers OPA03, OPA04, OPA05, and OPA09 all obtained fragments for analyzed strains were fully monomorphic. This means, that no genetic variability was found using the above mentioned primers. Low genetic variability was ascertained in the analysis of frequency of occurrence of DNA fragments using other primers, namely OPA01, OPA02, and OPA10. The matrix and dendrogram of genetic affinities among different strains of Chalara, calculated using the Jaccard’s similarity coefficient suggested, that the most similar strains are the ones coming from Poland (HMIPC 16136 and HMIPC16664 as well as the strain CBS 136.88, while somewhat different from them is the strain CBS 354.76. To determine, how exactly did the dendrogram reflect genetic affinity among analyzed strains, the Mantel’s test was employed. The correlation coefficient amounted to 0.78, suggesting that the strains under study had been grouped properly. The results showed, that the fungal strains found in southern Poland represent the species Chalara ovoidea.

  13. A Penalized Mixture Model Approach in Genotype/Phenotype Association Analysis for Quantitative Phenotypes

    Science.gov (United States)

    Li, Lang; Borges, Silvana; Jason, Robarge D.; Shen, Changyu; Desta, Zeruesenay; Flockhart, David

    2010-01-01

    A mixture normal model has been developed to partition genotypes in predicting quantitative phenotypes. Its estimation and inference are performed through an EM algorithm. This approach can conduct simultaneous genotype clustering and hypothesis testing. It is a valuable method for predicting the distribution of quantitative phenotypes among multi-locus genotypes across genes or within a gene. This mixture model’s performance is evaluated in data analyses for two pharmacogenetics studies. In one example, thirty five CYP2D6 genotypes were partitioned into three groups to predict pharmacokinetics of a breast cancer drug, Tamoxifen, a CYP2D6 substrate (p-value = 0.04). In a second example, seventeen CYP2B6 genotypes were categorized into three clusters to predict CYP2B6 protein expression (p-value = 0.002). The biological validities of both partitions are examined using established function of CYP2D6 and CYP2B6 alleles. In both examples, we observed genotypes clustered in the same group to have high functional similarities. The power and recovery rate of the true partition for the mixture model approach are investigated in statistical simulation studies, where it outperforms another published method. PMID:20467479

  14. A Penalized Mixture Model Approach in Genotype/Phenotype Association Analysis for Quantitative Phenotypes

    Directory of Open Access Journals (Sweden)

    Lang Li

    2010-04-01

    Full Text Available A mixture normal model has been developed to partition genotypes in predicting quantitative phenotypes. Its estimation and inference are performed through an EM algorithm. This approach can conduct simultaneous genotype clustering and hypothesis testing. It is a valuable method for predicting the distribution of quantitative phenotypes among multi-locus genotypes across genes or within a gene. This mixture model’s performance is evaluated in data analyses for two pharmacogenetics studies. In one example, thirty five CYP2D6 genotypes were partitioned into three groups to predict pharmacokinetics of a breast cancer drug, Tamoxifen, a CYP2D6 substrate (p-value = 0.04. In a second example, seventeen CYP2B6 genotypes were categorized into three clusters to predict CYP2B6 protein expression (p-value = 0.002. The biological validities of both partitions are examined using established function of CYP2D6 and CYP2B6 alleles. In both examples, we observed genotypes clustered in the same group to have high functional similarities. The power and recovery rate of the true partition for the mixture model approach are investigated in statistical simulation studies, where it outperforms another published method.

  15. Analysis of genetic diversity of Sclerotinia sclerotiorum from eggplant by mycelial compatibility, random amplification of polymorphic DNA (RAPD and simple sequence repeat (SSR analyses

    Directory of Open Access Journals (Sweden)

    Fatih Mehmet Tok

    2016-09-01

    Full Text Available The genetic diversity and pathogenicity/virulence among 60 eggplant Sclerotinia sclerotiorum isolates collected from six different geographic regions of Turkey were analysed using mycelial compatibility groupings (MCGs, random amplified polymorphic DNA (RAPD and simple sequence repeat (SSR polymorphism. By MCG tests, the isolates were classified into 22 groups. Out of 22 MCGs, 36% were represented each by a single isolate. The isolates showed great variability for virulence regardless of MCG and geographic origin. Based on the results of RAPD and SSR analyses, 60 S. sclerotiorum isolates representing 22 MCGs were grouped in 2 and 3 distinct clusters, respectively. Analyses using RAPD and SSR markers illustrated that cluster groupings or genetic distance of S. sclerotiorum populations from eggplant were not distinctly relative to the MCG, geographical origin and virulence diversity. The patterns obtained revealed a high heterogeneity of genetic composition and suggested the occurrence of clonal and sexual reproduction of S. sclerotiorum on eggplant in the areas surveyed.

  16. ANALYSES OF GENETIC VARIABILITY IN LENTINULA EDODES THROUGH MYCELIA RESPONSES TO DIFFERENT ABIOTIC CONDITIONS AND RAPD MOLECULAR MARKERS

    OpenAIRE

    Cristina Sayuri Maki; Flavia França Teixeira; Edilson Paiva; Luzia Doretto Paccola-Meirelles

    2001-01-01

    The growth of thirty-four Lentinula edodes strains submitted to different mycelial cultivation conditions (pH and temperature) was evaluated and strain variability was assessed by RAPD molecular markers. The growth at three pH values (5, 6 and 7) and four different temperatures (16, 25, 28 and 37ºC) was measured using the in vitro mycelial development rate and water retention as parameters. Mycelial cultivation was successful at all pH tested, while the ideal temperature for mycelial cultivat...

  17. Comparison of the yeast microbiota of different varieties of cool-climate grapes by PCR-RAPD

    Directory of Open Access Journals (Sweden)

    Iwona Drożdż

    2015-08-01

    Full Text Available The yeast microbiota occurring on different varieties of grapes grown in cool-climate is not completely researched. Therefore, its identification is important to research. On the other hand, yeasts occurring in these fruits can be potentially used as starter cultures to obtain particularly demanded features in the production of wine. In addition, rapid methods for yeast identification allow to eliminate the contamination with pathogenic yeasts, which could cause the loss of wine production. The aim of the study was to isolate and identify the yeasts occurring on the surface of the different varieties of white and red grapes, grown in cool-climate of Poland. Also, the aim was to compare the qualitative and quantitative composition of yeasts on the tested grapes. The 84 cultures of yeasts were isolated, that were initially macroscopic and microscopic analyzed and the purity of cultures was rated on the WL medium. Identification of yeasts by PCR-RAPD was carried using the M13 primer. In the PCR-RFLP method ITS1 and ITS4 primers, as well as restriction enzymes HhaI, HinfI, HaeIII, were used. Preliminary identification of yeasts by standard methods produced results very different from the results obtained by molecular methods. Among the isolated microorganisms yeasts were dominating, but bacteria and molds were also present. Using the PCR-RAPD method most strains of yeasts were identified. Yeast microflora of different varieties of white and red grapes was very similar as the same species of yeasts were identified. Yeasts of the genus Saccharomyces were present in all varieties of grapes. The Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Metschnikowia pulcherrima, Rhodotorula minuta, Pichia kluyveri, Hanseniaspora uvarum and Rhodotorula mucilaginosa were identified by PCR-RAPD. 4 of the 33 tested strains of yeasts were identified by PCR-RFLP. By PCR-RAPD only Hanseniaspora uvarum was identified. The quantity and quality of microorganisms living

  18. Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water.

    LENUS (Irish Health Repository)

    Ryan, Michael P

    2011-08-30

    Abstract Background Ralstonia pickettii is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of Ralstonia collected from a variety of sources. Results Ralstonia isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16S-23S rRNA Interspatial region (ISR) iii) the fliC gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated R. pickettii isolates as actually being the closely related species R. insidiosa. PCR-ribotyping of the 16S-23S rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly. Conclusions R. pickettii species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. R. insidiosa can at present only be distinguished from R. pickettii using species specific PCR. R. pickettii and R. insidiosa isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.

  19. Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques Variabilidade genética de isolados Brasileiros de Alternaria alternata por meio de marcadores moleculares de AFLP e RAPD

    Directory of Open Access Journals (Sweden)

    Francisco Dini-Andreote

    2009-09-01

    Full Text Available The Alternaria brown spot (ABS is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens. The application of two molecular markers Random Amplified Polymorphic DNA (RAPD and Amplified Fragment Length Polymorphism (AFLP had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA. Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control.A mancha marrom ou mancha de Alternaria é uma doença causada pelo fungo Alternaria alternata f. sp. citri, encontrada no Brasil desde 2001 em plantas de tangerina e seus híbridos. Por se tratar de uma doença recente no Brasil, a epidemiologia e variabilidade genética deste patógeno compõem importantes pontos a serem estudados. Este trabalho teve como objetivo avaliar a variabilidade genética deste pat

  20. Low Divergence of Clonorchis sinensis in China Based on Multilocus Analysis.

    Directory of Open Access Journals (Sweden)

    Jiufeng Sun

    Full Text Available Clonorchis sinensis, an ancient parasite that infects a number of piscivorous mammals, attracts significant public health interest due to zoonotic exposure risks in Asia. The available studies are insufficient to reflect the prevalence, geographic distribution, and intraspecific genetic diversity of C. sinensis in endemic areas. Here, a multilocus analysis based on eight genes (ITS1, act, tub, ef-1a, cox1, cox3, nad4 and nad5 [4.986 kb] was employed to explore the intra-species genetic construction of C. sinensis in China. Two hundred and fifty-six C. sinensis isolates were obtained from environmental reservoirs from 17 provinces of China. A total of 254 recognized Multilocus Types (MSTs showed high diversity among these isolates using multilocus analysis. The comparison analysis of nuclear and mitochondrial phylogeny supports separate clusters in a nuclear dendrogram. Genetic differentiation analysis of three clusters (A, B, and C showed low divergence within populations. Most isolates from clusters B and C are geographically limited to central China, while cluster A is extraordinarily genetically diverse. Further genetic analyses between different geographic distributions, water bodies and hosts support the low population divergence. The latter haplotype analyses were consistent with the phylogenetic and genetic differentiation results. A recombination network based on concatenated sequences showed a concentrated linkage recombination population in cox1, cox3, nad4 and nad5, with spatial structuring in ITS1. Coupled with the history record and archaeological evidence of C. sinensis infection in mummified desiccated feces, these data point to an ancient origin of C. sinensis in China. In conclusion, we present a likely phylogenetic structure of the C. sinensis population in mainland China, highlighting its possible tendency for biogeographic expansion. Meanwhile, ITS1 was found to be an effective marker for tracking C. sinensis infection

  1. Multilocus Sequence Typing Identifies Epidemic Clones of Flavobacterium psychrophilum in Nordic Countries

    DEFF Research Database (Denmark)

    Nilsen, Hanne; Sundell, Krister; Duchaud, Eric

    2014-01-01

    , Norway, and Sweden. Multilocus sequence typing of 560 geographically and temporally disparate F. psychrophilum isolates collected from various sources between 1983 and 2012 revealed 81 different sequence types (STs) belonging to 12 clonal complexes (CCs) and 30 singleton STs. The largest CC, CC-ST10...... of genetically distinct CCs in the Nordic countries and points out specific F. psychrophilum STs posing a threat to the salmonid production. The study provides a significant contribution toward mapping the genetic diversity of F. psychrophilum globally and support for the existence of an epidemic population...

  2. RAPD markers and black pine (Pinus nigra Arnold intraspecies taxonomy - Evidence from the study of nine populations

    Directory of Open Access Journals (Sweden)

    Zlatko Liber

    2011-01-01

    Full Text Available Although intraspecies researches within the black pine (Pinus nigra Arnold have a long tradition, the intraspecies taxonomy, classification and chorology are still unclear. Among the numerous reasons that have caused this situation the most important are: the absence of a study that would completely cover the whole range of this species, the impossibility of connection of results of the existing detailed studies of certain areas, and the high variability of traits which have been used so far. Since the characteristics of the molecular systematic techniques could make possible the research free of the mentioned shortages, the intention of this study was to determine the relationships among nine populations of black pine using the random amplified polymorphic DNA (RAPD. The obtained results were compared to the recent results of the morphological and anatomical analysis of the leaves of the same populations. The RAPD results clearly divided the Croatian populations from populations of Austria (subsp. nigra and Turkey (subsp. pallasiana, while among Croatian populations, as in previous study, the existence of several groups (subsp. illyrica, subsp. dalmatica and transitional population between them was noticed. It is assumed that the optimisations conducted in this study will finally make possible estimating the relationships on the level of the whole range of the black pine and the classification based on molecular traits that are probably less dependent on environmental influences than it has been the case with the characteristics mostly used so far.

  3. Genetic differentiation of cercariae infrapopulations of the avian schistosome Trichobilharzia szidati based on RAPD markers and mitochondrial cox1 gene.

    Science.gov (United States)

    Korsunenko, Anna; Chrisanfova, Galina; Lopatkin, Anton; Beer, Sergey A; Voronin, Mikhail; Ryskov, Alexey P; Semyenova, Seraphima K

    2012-02-01

    Avian schistosome Trichobilharzia szidati is a member of the largest genus within the family Schistosomatidae (Trematoda). Population genetic structure of Trichobilharzia spp. schistosomes, causative agents of cercarial dermatitis in humans, has not been studied yet. The knowledge of the genetic structure of trichobilharzian populations is essential for understanding the host-parasite coevolutionary dynamics and epidemiology strategies. Here we examined genetic diversity in three geographically isolated local populations of T. szidati cercariae inhabiting Russia based on nuclear (randomly amplified polymorphic DNA, RAPD) and mt (cox1) markers. We analyzed T. szidati cercariae shed from seven naturally infected snails of Lymnaea stagnalis. Using three random primers, we demonstrated genetic variation among populations, thus posing genetic structure across geographic sites. Moreover, T. szidati cercariae have been genetically structured among hosts (infrapopulations). Molecular variance analysis was performed to test the significance of genetic differentiation within and between local populations. Of total parasitic diversity, 18.8% was partitioned between populations, whereas the higher contribution (48.9%) corresponds to the differences among individual cercariae within infrapopulations. In contrast to RAPD markers, a 1,125-bp fragment of cox1 mt gene failed to provide any significant within-species structure. The lack of geographic structuring was detected using unique haplotypes which were determined in the current work for Moscow and Western Siberian local populations as well as obtained previously for European isolates (Czech Republic and Germany). All T. szidati/Trichobilharzia ocellata haplotypes were found to be mixed across their geographical origin.

  4. Authentication of Cordyceps sinensis by DNA Analyses: Comparison of ITS Sequence Analysis and RAPD-Derived Molecular Markers

    Directory of Open Access Journals (Sweden)

    Kelly Y. C. Lam

    2015-12-01

    Full Text Available Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM. In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS sequences and the random amplified polymorphic DNA (RAPD-sequence characterized amplified region (SCAR were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps.

  5. Identifikasi simplisia yang dijual sebagai Strychnos ligustrina BI. di pasar tradisional Surabaya dengan metode random amplified polymorphic DNA (RAPD

    Directory of Open Access Journals (Sweden)

    Oeke Yunita

    2012-02-01

    Full Text Available Authentication of Strychnos ligustrina Bl. had been performed at molecular level (DNA with Random Amplified Polymorphic DNA (RAPD method, based on the amplification of random DNA fragments by Polymerase Chain Reaction (PCR with a single arbitrar primer. The aim of this research was obtaining similar banding patterns between DNA of plant Strychnos ligustrina Bl. and DNA of it lignum on local market. Strychnos ligustrina Bl. was determined by UPT Balai Konservasi Tumbuhan Kebun Raya Purwodadi and plants sold as Strychnos ligustrina Bl. were collected as lignum from traditional market at Wonokromo, Rungkut, Genteng, Benowo dan Pabean. DNA from these plants were extracted by modified Cetyltrimethylammonium bromide (CTAB method and amplified by RAPD method. Amplification had been performed by primer OPO-4 had shown banding patterns on the gel electrophoresis which banding patterns were shown by Strychnos ligustrina Bl. and plants sold as Strychnos ligustrina Bl. on Benowo. Based on this early result, we assume that plants sold as Strychnos ligustrina Bl. on Benowo has closely genetic relationship with Strychnos ligustrina Bl.

  6. Application of DNA (RAPD and ultrastructure to detect the effect of cadmium stress in Egyptian clover and Sudan grass plantlets

    Directory of Open Access Journals (Sweden)

    Amina A. Aly

    2012-04-01

    Full Text Available BackgroundIn recent years, several plant species have been used as bioindicators to evaluate the toxicity of environmental contaminants on vegetal organisms. In this study, Egyptian clover and Sudan grass seedlings were grown in four cadmium (Cd concentration levels (0.0, 25, 50 and 100 µM in MS media to analyze growth responses, Cd accumulation in the shoots and roots of plantlets, proline contents, chlorophylls content and MDA levels of both plantlets. As well as RAPD analysis and leaves ultrastructure were detected.ResultsThe results showed that there was a significant decrease in root and shoot lengths, Chl a, Chl b, total Chl and carotenoids contents for both Egyptian clover and Sudan grass. However, there was a significant increase in Cd accumulation, proline and malondialdehyde (MDA levels. The genetic variation between Egyptian clover and Sudan grass were evaluated using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR markers to establish specific DNA markers associated with Cd stress. The results of transimssion electron microscopy (TEM showed a clear disorder in the Cd treated Egyptian clover and Sudan grass seedlings.ConclusionIn conclusion, biochemical, molecular and ultrastructure changes in Egyptian clover and Sudan grass could be used as a useful biomarker assay for the detection of genotoxic effects of Cd stress on plants. However, it is necessary to be further confirmed and optimized in the future research.

  7. Application of RAPD-PCR for Determining the Clonality of Methicillin Resistant Staphylococcus aureus Isolated from Different Hospitals

    Directory of Open Access Journals (Sweden)

    Neslihan Idil

    2014-08-01

    Full Text Available Randomly amplified polymorphic DNA (RAPD-PCR was applied with ten random 10-mer primers to examine the molecular diversity among methicillin resistant Staphylococcus aureus (MRSA strains in the hospitals and to investigate the epidemiological spread of these strains between different hospitals. The main objective of the study was to identify appropriate primers, which successfully established the clonality of MRSA. Three of the primers yielded particularly discriminatory patterns and they were used to perform the RAPD analysis which revealed different bands ranging from 200 to 1500 bp. Dendogram was created by the un-weighted pair group method using arithmetic (UPGMA average clustering and it was constructed based on the combination results of the new primers (S224, S232 and S395 which represented a novel approach for rapid screening of the strains and also provided the opportunity for monitoring the emergence and determining clonal dissemination of MRSA strains between the hospitals. Dendogram generated two main groups (Group I and II with three clusters (A, B and C and indicated that the strains isolated from the same hospital were closely related and they placed together in the same group. This technique could be of attractive use in controlling the sources and routes of transmission, tracking the spread of strains within hospital and between the hospitals, and especially preventing the nosocomial infections caused by the MRSA.

  8. Diversidade genética de porta-enxertos cítricos baseada em marcadores moleculares RAPD

    Directory of Open Access Journals (Sweden)

    Schäfer Gilmar

    2004-01-01

    Full Text Available Este trabalho teve como objetivo caracterizar a diversidade genética, através do marcador molecular RAPD, dos porta-enxertos da Coleção de Citros da Estação Experimental Agronômica da Universidade Federal do Rio Grande do Sul (EEA/UFRGS e acessos de porta-enxertos cítricos coletados em viveiristas da Região do Vale do Rio Caí do estado do Rio Grande do Sul. Para tanto, coletaram-se folhas de nove porta-enxertos cítricos da EEA/UFRGS e de dez acessos de trifoliata (Poncirus trifoliata de viveiristas. Com o uso de nove seqüências inicializadoras, foi possível separar os porta-enxertos cítricos em dois grupos principais, um formado pelo limoeiro ?Cravo? e outro pelo trifoliata e seus híbridos, apresentando alta dissimilaridade genética entre os grupos. Marcadores moleculares RAPD foram eficientes para caracterizar variedades de porta-enxertos de citros e para separar o porta-enxerto P. trifoliata de seus híbridos podendo serem utilizados para caracterização de plantas matrizes, análise de variabilidade genética entre genitores em programas de melhoramento genético de porta-enxertos e para identificar a origem sexual ou nucelar de mudas de trifoliata em viveiros comerciais.

  9. Diversity of the genus Ocimum (Lamiaceae through morpho-molecular (RAPD and chemical (GC–MS analysis

    Directory of Open Access Journals (Sweden)

    Tanmay Chowdhury

    2017-06-01

    Full Text Available In this present study, we have described the diversity of nine Ocimum genotypes naturally grown in the Dakshin Dinajpur district of West Bengal, India. Their diversity was determined on the basis of morphological, chemical and randomly amplified polymorphic DNA (RAPD to determine the level of variation present in the genus Ocimum. Among nine Ocimum genotypes six (O. americanum, O. × africanum, O. basilicum, O. gratissimum, O. kilimandscharicum and O. tenuiflorum are found to be different Ocimum species and the rest are as varieties. A total of 18 qualitative and 17 quantitative morphological traits and chemical compositions were evaluated. Significant variations were observed in the morphological traits except O. × africanum and O. basilicum species. Cluster generated from the morphological data showed two different groups viz. basilicum group and sanctum group. Chemical analysis did not show much variation between morphologically similar species viz. O. × africanum and O. basilicum. However, RAPD analyses clearly showed that O. × africanum and O. basilicum are different species. Thus the combined analyses of morphological traits, chemical and molecular markers represent the best possible approach to confirm taxonomic delineation. Moreover, we are reporting O. × africanum for the first time from this region as well as from West Bengal, India.

  10. A RAPD-PCR-based genetic diversity analysis of Helicoverpa armigera and H. zea populations in Brazil.

    Science.gov (United States)

    Lopes, H M; Bastos, C S; Boiteux, L S; Foresti, J; Suinaga, F A

    2017-09-21

    Helicoverpa armigera is the most significant pest of agriculture in Asia, Europe, Africa, and Australasia, causing damage to crops greater than US$2 billion annually and until 2013 it was not detected in Brazil. Helicoverpa zea is restricted to the American continent and is important to corn and a secondary pest of cotton and tomatoes. The wide range of crops exploited by H. armigera (mainly cotton, soybeans, chickpea, and corn), the possible mating between these species can promote population shifts, that could be assessed by RAPD-PCR technique. Therefore, the aim of this study was to determine the genetic diversity of H. armigera and H. zea populations by RAPD-PCR analysis. The most important result was the clustering of one H. armigera population in a group predominantly formed by H. zea. It could indicate a possible occurrence of an interspecific cross between these species. This is a concern to Brazilian agriculture due to the possibility of selection of hybrids well adapted to the American environment, which would be inherited from H. zea. The other noxious fact is the possible development of new biotypes resistant to insectides or Bt toxins expressed in transgenic crops, came from H. armigera gene pool.

  11. Usefulness of phenotypic and genotypic methods for metallo-beta-lactamases detection in carbapenem-resistant Acinetobacter baumannii strains.

    Science.gov (United States)

    Szejbach, Aleksandra; Mikucka, Agnieszka; Bogiel, Tomasz; Gospodarek, Eugenia

    2013-01-21

    Acinetobacter baumannii is an opportunistic microorganism with an increasing role in nosocomial outbreaks. For the last 2 decades, a growing number of carbapenem-resistant A. baumannii strains have been identified, including the metallo-beta-lactamases (MBLs) producers. The study aimed to investigate the genetic relatedness of, and MBLs production among, a collection of A. baumannii isolates from Poland. This study involved 78 clinical isolates of carbapenem-resistant A. baumannii. Strain typing of the isolates was performed using PCR-RAPD. The presence of MBLs was phenotypically determined using different double disc synergy tests (DDST), the imipenem/EDTA combination disk test (CDT) and Etest MBL. blaIMP and blaVIM genes were detected using a duplex PCR assay. The isolates were divided into 18 PCR-RAPD patterns. Among 18 examined isolates, 94.4% were MBL-positive by the phenotypic method relying on comparing the bacteria growth inhibition zones diameters between imipenem/EDTA and imipenem discs, 88.9% using Etest MBL, 66.7% using the double disc synergy test with ceftazidime, imipenem, meropenem and EDTA, and 88.9% using a corresponding method with 2-MPA. The existence of blaIMP was identified in 8 (10.3%) strains. MBLs production was an important mechanism of carbapenem resistance among A. baumannii isolates in Poland. Laboratories should routinely screen for MBLs among A. baumannii isolates.

  12. PENENTUAN VARIASI GENETIK IKAN BATAK (Tor soro DARI SUMATERA UTARA DAN JAWA BARAT DENGAN METODE ANALISIS RANDOM AMPLIFIED POLYMORPHISM DNA (RAPD

    Directory of Open Access Journals (Sweden)

    Sidi Asih

    2016-12-01

    Full Text Available Variasi genetik ikan batak yang dikoleksi dari daerah Asahan, Aek Sarul (Tarutung, Aek Sirambe, Bahorok (Sumatera Utara, dan Sumedang (Jawa Barat telah diteliti menggunakan metode Random Amplified Polymorphism DNA (RAPD. Primer yang digunakan untuk analisis adalah OPC-01 dan OPC-02. Dari 2 primer yang digunakan hanya OPC-01 yang menunjukkan hasil PCR yang memberikan Polimorfisme. Berdasarkan nilai rata-rata heterozigositas (0,08—0,1250 dan persentase lokus polimorfik (22%—33% secara umum menunjukkan bahwa keragaman genetik ikan batak yang dianalisis tergolong rendah. Hasil analisis RAPD juga menunjukkan bahwa secara genetik tidak ada perbedaan yang nyata di antara kelima populasi ikan batak. The genetic variabilities of Tor soro collected from Asahan, Aek Sarula (Tarutung, Aek Sirambe, Bahorok (North Sumatra, and Sumedang (West Java were examined by RAPD. Primers used for analysis were OPC-01 and OPC-02. From both of the primers, only OPC-01 showed polymorphism. Based on the heterozigosity (0.08—0.1250 and percentage of polimorphyc locus value (22%—33%, indicated that genetic variation of Tor soro of North Sumatra was low. The RAPD analisis showed that no significantly difference among five population.

  13. Conversion of chromosome-specific RAPDs into SCAR-based anchor markers for onion linkage maps and its application to genetic analyses inother Allium species

    NARCIS (Netherlands)

    Masuzaki, S.; Miyazaki, T.; McCallum, J.; Heusden, van A.W.; Kik, C.; Yamashita, K.; Tashiro, Y.

    2008-01-01

    Integration of previously developed Allium cepa linkage maps requires the availability of anchor markers for each of the eight chromosomes of shallot (A. cepa L. common group Aggregatum). To this end, eight RAPD markers originating from our previous research were converted into SCAR markers via

  14. Usefulness of McRAPD for typing and importance of biofilm production in a case of nosocomial ventriculoperitoneal shunt infection caused by Candida lusitaniae.

    Science.gov (United States)

    Hamal, Petr; Hanzen, Juraj; Horn, Frantisek; Trtkova, Jitka; Ruskova, Lenka; Vecerova, Renata; Ruzicka, Filip; Vollekova, Anna; Raclavsky, Vladislav

    2011-09-01

    A case report of ventriculoperitoneal shunt infection caused by Candida lusitaniae in a 6-year-old patient with cerebral astrocytoma and obstructive hydrocephalus is presented briefly with emphasis on the course of antifungal treatment. Seven isolates recovered subsequently from the cerebrospinal fluid were studied retrospectively. To confirm identity, isolates were typed using pulsed-field gel electrophoresis and melting curve of random amplified polymorphic DNA (McRAPD). Further, the ability to form biofilm and its susceptibility to systemic antifungals were evaluated. Using McRAPD, identity of C. lusitaniae isolates showing slight microevolutionary changes in karyotypes was undoubtedly confirmed; successful application of numerical interpretation of McRAPD for typing is demonstrated here for the first time. The strain was also recognized as a strong biofilm producer. Moreover, minimum biofilm inhibitory concentrations were very high, in contrast to low antifungal minimum inhibitory concentrations of isolates. It can be concluded that McRAPD seems to be a simple and reliable method not only for identification but also for typing of yeasts. A ventriculoperitoneal shunt colonized by C. lusitaniae was revealed as the source of this nosocomial infection, and the ability of the strain to form biofilm on its surface likely caused treatment failure.

  15. Assessment of DNA Damage by RAPD in Paracentrotus lividus Embryos Exposed to Amniotic Fluid from Residents Living Close to Waste Landfill Sites

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    Maurizio Guida

    2010-01-01

    Full Text Available The aim of this study was to assess the genotoxic effects of environmental chemicals on residents living near landfills. The study was based on samples of amniotic fluid from women living in the intensely polluted areas around the Campania region of Italy compared to a nonexposed control group. We evaluated the genetic effects that this amniotic fluids collected in contaminated sites had on Paracentrotus lividus embryos. DNA damage was detected through changes in RAPD (Random Amplified Polymorphism DNA profiles. The absence of the amplified DNA fragments indicated deletions in Paracentrotus lividus DNA exposed to the contaminated amniotic fluids when compared to equal exposure to uncontaminated fluids. These results show the ability of RAPD-PCR to detect and isolate DNA sequences representing genetic alterations induced in P. lividus embryos. Using this method, we identified two candidate target regions for DNA alterations in the genome of P. lividus. Our research indicates that RAPD-PCR in P. lividus embryo DNA can provide a molecular approach for studying DNA damage from pollutants that can impact human health. To our knowledge, this is the first time that assessment of DNA damage in P. lividus embryos has been tested using the RAPD strategy after exposure to amniotic fluid from residents near waste landfill sites.

  16. Multilocus heterozygosity and inbreeding depression in an insular house sparrow metapopulation.

    Science.gov (United States)

    Jensen, Henrik; Bremset, Erlend Myre; Ringsby, Thor Harald; Saether, Bernt-Erik

    2007-10-01

    Inbreeding causes reduction of genetic variability that may have severe fitness consequences. In spite of its potentially huge impact on viability and evolutionary processes especially in small populations, quantitative demonstrations of genetic and demographic effects of inbreeding in natural populations are few. Here, we examine the relationship between individual inbreeding coefficients (F) and individual standardized multilocus heterozygosity (H) in an insular metapopulation of house sparrows (Passer domesticus) in northern Norway in order to evaluate whether H is a good predictor for F. We then relate variation in fitness (i.e. the probability of surviving from fledging to recruitment) to F and H, which enables us to examine whether inbreeding depression is associated with a reduction in genetic variability. The average level of inbreeding in the house sparrow metapopulation was high, and there was large inter-individual variation in F. As expected, standardized multilocus heterozygosity decreased with the level of inbreeding. The probability of recruitment was significantly negatively related to F, and, accordingly, increased with H. However, H explained no significant additional variation in recruitment rate than was explained by F. This suggests that H is a good predictor for F in this metapopulation, and that an increase in F is likely to be associated with a general increase in the level of homozygosity on loci across the genome, which has severe fitness consequences.

  17. Characterization Through Multilocus Sequence Analysis of Borrelia turdi Isolates from Portugal.

    Science.gov (United States)

    Norte, Ana Cláudia; Araújo, Pedro Miguel; da Silva, Luís Pascoal; Tenreiro, Paulo Quadros; Ramos, Jaime A; Núncio, Maria Sofia; Zé-Zé, Líbia; de Carvalho, Isabel Lopes

    2016-11-01

    Borrelia turdi is a spirochete from the Borrelia burgdorferi complex, first reported in Japan, that has been increasingly detected in Europe. This genospecies is mostly associated with avian hosts and their ornithophilic ticks such as Ixodes frontalis. In this study, we isolated B. turdi from five I. frontalis feeding on Turdus merula, Turdus philomelos, Parus major and Troglodytes troglodytes, and one Ixodes ricinus feeding on a T. merula in Portugal. These isolates were genetically characterised according to their 5S-23S rRNA intergenic spacer, 16S rRNA and through typing of seven housekeeping genes (multilocus sequence typing). Multilocus sequence analyses revealed that the strains isolated in our study, although belonging to B. turdi genospecies, are not identical to the B. turdi reference strain Ya501. Instead, our strains are separated into a clear defined group, suggesting that the European samples diverged genetically from the strain originally detected in Japan. Population analysis of 5S-23S rRNA sequences can further resolve subpopulations within B. turdi, but more samples from a large geographical scale and host range would be needed to assess potential phylogeographical patterns within this genospecies.

  18. Evolution in Australasian mangrove forests: multilocus phylogenetic analysis of the Gerygone warblers (Aves: Acanthizidae.

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    Árpád S Nyári

    Full Text Available The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae. The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci. Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster.

  19. Visualization of pairwise and multilocus linkage disequilibrium structure using latent forests.

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    Raphaël Mourad

    Full Text Available Linkage disequilibrium study represents a major issue in statistical genetics as it plays a fundamental role in gene mapping and helps us to learn more about human history. The linkage disequilibrium complex structure makes its exploratory data analysis essential yet challenging. Visualization methods, such as the triangular heat map implemented in Haploview, provide simple and useful tools to help understand complex genetic patterns, but remain insufficient to fully describe them. Probabilistic graphical models have been widely recognized as a powerful formalism allowing a concise and accurate modeling of dependences between variables. In this paper, we propose a method for short-range, long-range and chromosome-wide linkage disequilibrium visualization using forests of hierarchical latent class models. Thanks to its hierarchical nature, our method is shown to provide a compact view of both pairwise and multilocus linkage disequilibrium spatial structures for the geneticist. Besides, a multilocus linkage disequilibrium measure has been designed to evaluate linkage disequilibrium in hierarchy clusters. To learn the proposed model, a new scalable algorithm is presented. It constrains the dependence scope, relying on physical positions, and is able to deal with more than one hundred thousand single nucleotide polymorphisms. The proposed algorithm is fast and does not require phase genotypic data.

  20. Development of a multilocus-based approach for sponge (phylum Porifera) identification: refinement and limitations

    Science.gov (United States)

    Yang, Qi; Franco, Christopher M. M.; Sorokin, Shirley J.; Zhang, Wei

    2017-01-01

    For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3–D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity. The reliability of SIP was validated by phylogenetic analysis. The 28S rRNA gene and COI mtDNA performed better than the ITS region in classifying sponges at various taxonomic levels. A major limitation is that the databases are not well populated and possess low diversity, making it difficult to conduct the molecular identification protocol. The identification is also impacted by the accuracy of the morphological classification of the sponges whose sequences have been submitted to the database. Re-examination of the morphological identification further demonstrated and improved the reliability of sponge identification by SIP. Integrated with morphological identification, the multilocus-based SIP offers an improved protocol for more reliable and effective sponge identification, by coupling the accuracy of different DNA markers. PMID:28150727

  1. Clonal diversity and population genetic structure of arbuscular mycorrhizal fungi (Glomus spp.) studied by multilocus genotyping of single spores

    DEFF Research Database (Denmark)

    Holtgrewe-Stukenbrock, Eva; Rosendahl, Søren

    2005-01-01

    A nested multiplex PCR (polymerase chain reaction) approach was used for multilocus genotyping of arbuscular mycorrhizal fungal populations. This method allowed us to amplify multiple loci from Glomus single spores in a single PCR amplification. Variable introns in the two protein coding genes Gm......FOX2 and GmTOR2 were applied as codominant genetic markers together with the LSU rDNA.   Genetic structure of Glomus spp. populations from an organically and a conventionally cultured field were compared by hierarchical sampling of spores from four plots in each field. Multilocus genotypes were...

  2. Genotype to phenotype

    National Research Council Canada - National Science Library

    Malcolm, Sue; Goodship, Timothy H. J

    2001-01-01

    ... Disorders Molecular Genetics of Hypertension Human Gene EvolutionAnalysis of Multifactorial Disease Transcription Factors Molecular Genetics of Cancer, Second edition Genotype to Phenotype, second e...

  3. Evaluation of 41 candidate gene variants for obesity in the EPIC-Potsdam cohort by multi-locus stepwise regression.

    Science.gov (United States)

    Knüppel, Sven; Rohde, Klaus; Meidtner, Karina; Drogan, Dagmar; Holzhütter, Hermann-Georg; Boeing, Heiner; Fisher, Eva

    2013-01-01

    Obesity has become a leading preventable cause of morbidity and mortality in many parts of the world. It is thought to originate from multiple genetic and environmental determinants. The aim of the current study was to introduce haplotype-based multi-locus stepwise regression (MSR) as a method to investigate combinations of unlinked single nucleotide polymorphisms (SNPs) for obesity phenotypes. In 2,122 healthy randomly selected men and women of the EPIC-Potsdam cohort, the association between 41 SNPs from 18 obesity-candidate genes and either body mass index (BMI, mean=25.9 kg/m(2), SD=4.1) or waist circumference (WC, mean=85.2 cm, SD=12.6) was assessed. Single SNP analyses were done by using linear regression adjusted for age, sex, and other covariates. Subsequently, MSR was applied to search for the 'best' SNP combinations. Combinations were selected according to specific AICc and p-value criteria. Model uncertainty was accounted for by a permutation test. The strongest single SNP effects on BMI were found for TBC1D1 rs637797 (β = -0.33, SE=0.13), FTO rs9939609 (β=0.28, SE=0.13), MC4R rs17700144 (β=0.41, SE=0.15), and MC4R rs10871777 (β=0.34, SE=0.14). All these SNPs showed similar effects on waist circumference. The two 'best' six-SNP combinations for BMI (global p-value= 3.45⋅10(-6) and 6.82⋅10(-6)) showed effects ranging from -1.70 (SE=0.34) to 0.74 kg/m(2) (SE=0.21) per allele combination. We selected two six-SNP combinations on waist circumference (global p-value = 7.80⋅10(-6) and 9.76⋅10(-6)) with an allele combination effect of -2.96 cm (SE=0.76) at maximum. Additional adjustment for BMI revealed 15 three-SNP combinations (global p-values ranged from 3.09⋅10(-4) to 1.02⋅10(-2)). However, after carrying out the permutation test all SNP combinations lost significance indicating that the statistical associations might have occurred by chance. MSR provides a tool to search for risk-related SNP combinations of common traits or

  4. Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.).

    Science.gov (United States)

    Dolman, Gaynor; Joseph, Leo

    2016-10-22

    During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. Our results contribute to awareness of increased population sizes, following significant contractions, as having been important

  5. Optimisation et application de la RAPD (random amplified polymorphic DNA dans un programme de sélection récurrente chez le cotonnier (Gossypium spp.

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    Jean-Pierre Baudoin

    1997-01-01

    Full Text Available Optimization and application of RAPD (random amplified polymorphic DNA in a recurrent selection programme of cotton (Gossypium spp..Using DNA extracted from différent wild and cultivated species of cotton, we analyzed and optimized the parameters for the random amplification of polymorphic DNA (RAPD. All the parameters have an effect on the final result but the concentrations of template DNA, magnésium chloride, deoxynucleoside triphosphates, and the température of dénaturation seem to be the most important factors. The optimization was performed by successive adjustements of the standard RAPD conditions and by taking into accourir the manufacturera' recommendations for each reagent. The optimized conditions were then used to assist an interspecific hybridization programme involving two allotetraploid trispecific hybrids [(Gossypium thurberi Tod. x G. sturtianum Will. doubled x G. hirsutum L., designated by G405] and [(G. hirsutum x G. raimondii Ulbr. doubled x G. sturtianum, designated by G376]. Both trispecific hybrids were backcrossed with three varieties (LPB5, NC8 and C2 of the cultivated upland cotton G. hirsutum. In RAPD analysis, thirty random decamer primera generated 375 RAPD markers. Analysis of genetic similarity from the RAPD data with UPGMA and Jaccard's distance revealed 78.3-78.7% similarity between the three varieties of G. hirsutum and 31.3-39.2% similarity between G. hirsutum and the wild diploid species (G. thurberi, G. raimondii and G. sturtianum. The genetic similarity within backcross 1 progenies showed values ranging between 63.2-78.0% for the cross G405 x LPB5, 75.0-80.4% for G405 x NC8, 63.9-82.2% for G405 x C2, 76.3-83% for G376 x C2 and 64.9-79.8% for the cross G376 x LPB5. This study allowed to choose within the first backcross progenies having the searched trait, those sharing the highest genetic similarity with the cultivated parent G. hirsutum. Résulta indicate that RAPD analysis can be used to accelerate the

  6. Evaluation of Leishmania (Leishmania chagasi strains isolated from dogs originating from two visceral leishmaniasis-endemic areas in Brazil using multilocus enzyme electrophoresis

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    Carlos Eduardo Ribeiro Coutinho

    2011-10-01

    Full Text Available INTRODUCTION: Domestic dogs are the most important reservoir in the peridomestic transmission cycle of Leishmania (Leishmania chagasi. The genetic variability of subpopulations of this parasite circulating in dogs has not been thoroughly analyzed in Brazil, even though this knowledge has important implications in the clinical-epidemiological context. METHODS: The objective of this study was to evaluate and compare the phenotypic variability of 153 L. chagasi strains isolated from dogs originating from the municipalities of Rio de Janeiro (n = 57 and Belo Horizonte (n = 96, where the disease is endemic. Strains isolated only from intact skin were selected and analyzed by multilocus enzyme electrophoresis using nine enzyme systems (6PG, GPI, NH1 and NH2, G6P, PGM, MDH, ME, and IDHNADP. RESULTS: The electrophoretic profile was identical for all isolates analyzed and was the same as that of the L. chagasi reference strain (MHOM/BR/74/PP75. Phenetic analysis showed a similarity index of one for all strains, with the isolates sharing 100% of the characteristics analyzed. CONCLUSIONS: The results demonstrate that the L. chagasi populations circulating in dogs from Rio de Janeiro and Belo Horizonte belong to a single zymodeme.

  7. Multilocus sequence typing and CTX-M characterization of ESBL-producing E. coli: a prospective single-centre study in Lower Saxony, Germany.

    Science.gov (United States)

    Gerhold, G; Schulze, M H; Gross, U; Bohne, W

    2016-11-01

    The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria is a serious threat for current healthcare settings. In this study we investigated the molecular epidemiology of ESBL-producing E. coli at the University Medical Center Göttingen in Lower Saxony, Germany. All E. coli isolates with an ESBL phenotype were collected during a 6-month period in 2014. Multilocus sequence typing and CTX-M characterization were performed on 160 isolates. Of the ESBL-producing isolates 95·6% were CTX-M positive. Compared to recent Germany-wide studies, we found CTX-M-1 to occur in higher frequency than CTX-M-15 (44·4% vs. 34·4%). CTX-M-14 and CTX-M-27 were detected at 9·4% and 5·0%, respectively. The globally dominant sequence type (ST) 131, which is often associated with CTX-M-15, occurred at a relatively low rate of 24%. Major non-ST131 sequence types were ST101 (5%), ST58 (5%), ST10 (4·4%), ST38 (4·4%), ST410 (3·8%) and ST453 (3·1%). Several of these major sequence types were previously shown to be associated with livestock farming. Together, our study indicates that E. coli lineage distribution in individual healthcare settings can significantly differ from average numbers obtained in nationwide studies.

  8. RAPD analysis of genetic variability in a multiprovenance base population of Eucalyptus grandis hill ex maiden Variabilidade genética através da técnica RAPD de uma população-base multiprocedências de Eucalyptus grandis hill ex maiden

    Directory of Open Access Journals (Sweden)

    Susi Meire Maximino Leite

    2008-12-01

    Full Text Available This study aimed to evaluate the genetic variability among individuals of a base population of Eucalyptus grandis and to build a molecular marker database for the analyzed populations. The Eucalyptus grandis base population comprised 327 individuals from Coff's Harbour, Atherton and Rio Claro. A few plants came from other sites (Belthorpe MT. Pandanus, Kenilworth, Yabbra, etc.. Since this base population had a heterogeneous composition, the groups were divided according to geographic localization (latitude and longitude, and genetic breeding level. Thus, the influence of those two factors (geographic localization and genetic breeding level on the genetic variability detected was discussed. The RAPD technique allowed the evaluation of 70 loci. The binary matrix was used to estimate the genetic similarity among individuals using Jaccard's Coefficient. Parametric statistical tests were used to compare within-group similarity of the means. The obtained results showed that the base population had wide genetic variability and a mean genetic similarity of 0.328. Sub-group 3 (wild materials from the Atherton region showed mean genetic similarity of 0.318. S.P.A. (from Coff's Harbour region had a mean genetic similarity of 0.322 and was found to be very important for maintenance of variation in the base population. This can be explained since the individuals from those groups accounted for most of the base population (48.3% for it. The base population plants with genetic similarity higher than 0.60 should be phenotypically analyzed again in order to clarify the tendency of genetic variability during breeding programs.Este estudo visou avaliar a variabilidade e distância genética dentro de uma população-base de melhoramento genético de Eucalyptus grandis. A avaliação da variabilidade genética tem como objetivos principais analisar a base genética da população-base e montar um banco de dados marcadores moleculares da população em an

  9. RAPD and ISSR marker assessment of genetic diversity in Citrullus colocynthis (L.) Schrad: a unique source of germplasm highly adapted to drought and high-temperature stress.

    Science.gov (United States)

    Verma, Kumar Sambhav; Ul Haq, Shamshad; Kachhwaha, Sumita; Kothari, S L

    2017-10-01

    Citrullus colocynthis (L.) Schrad. (Cucurbitaceae) shows high levels of variation in fruit color, fruit stripe pattern, seed coat color, and size. Thirty-eight accessions of C. colocynthis plants from different parts of semi-arid Rajasthan were collected and genetic diversity was assessed using random-amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Out of 65 RAPD decamer primers, 50 primers produced 549 scorable bands of which 318 were polymorphic. Polymorphic banding patterns with the number of amplified fragments varied from 5 (OPA-08 and OPF-9) to 19 (OPT-20) in the molecular size range of 150-6000 bp. Percent polymorphism ranged from 22.2% (OPA-09) to 83.3% (OPE-12) with 55.14% polymorphism. Out of the 20 ISSR primers screened, 13 primers produced 166 amplification products, of which 99 were polymorphic. The number of bands amplified per primer varied between 9 (UBC-807, 802) and 16 (UBC-803, 812) with average band size between 250 and 4000 bp. Percent polymorphism ranged from 45.4% (UBC-815) to 73.3% (UBC-814) with 65.05% polymorphism. Dendrogram constructed on the basis of RAPD + ISSR polymorphism separated the accessions into four distinct clusters at 72% variation with Jaccard's similarity coefficient ranging from minimum 0.64 to 0.95. The matrices for RAPD and ISSR were also compared using Mantel's test and obtained correlation value (r = 0.7947). Discriminating power of RAPD and ISSR markers was assessed by calculating polymorphic information content, multiplex ratio, marker index, and resolving power. Approx. 50% RAPD and ISSR markers showed PIC value and heterozygosity (H) ≥ 0.50, indicating marker as informative. The primers that showed higher polymorphism had higher RP, MR, and MI values.

  10. Identification of RAPD markers linked to digestive amylase genes using near isogenic lines of the silkworm, Bombyx mori.

    Science.gov (United States)

    Ashwath, S K; Sreekumar, S; Toms, J T; Dandin, S B; Kamble, C K

    2010-01-01

    Digestive amylase has been identified as a useful marker for breeding in the silkwrom, Bombyx mori L (Lepidoptera: Bombycidae), due to its wide genetic divergence, its role in better digestibility and robustness. The low yielding indigenous B. mori breeds of tropics like India are characterized by high activity amylase genes controlled by Amy d(iv) or d(v) alleles, while the high yielding breeds of temperate origin are endowed with 'null' type (Amy d(n)) with low activity. For improving the digestibility and survival of temperate breeds of Japanese origin, Near Isogenic Lines (NILs) were developed introgressing the Amy d(iv) and d(v) alleles from the Donor Parents (DPs) into the genetic background of the Recurrent Parents (RPs) with 'null' type of amylase, which showed significant improvement in viability of the NILs. With the objective to know whether the amylase gene itself may confer higher survival by improving digestibility or some other closely linked genes flanking the amylase locus is responsible for better viability of the NILs, RAPD profiles among six B. mori breeds comprising of the DPs, RPs, and NILs developed through introgression of Amy d(iv) or d(v) alleles were analysed using 27 sets of RAPD primers. Out of the 27 primers, six (OPA01, OPA06, OPA09, OPA15, OPAH03, and OPAH05) showed RAPD products linked to the amylase genes of the DPs introgressed in the NILs, which were absent in their respective RPs. Three amplicons of 1584 bp, 1904 bp, and 1232 bp were specific to Amy d(iv) allele and one amplified product of 1776 bp was found to be linked with the Amy d(v) allele. Interestingly, two PCR products of 2628 and 1375 bp were associated with both Amy d(iv) and d(v) alleles. The results are discussed in light of further characterization of these amplified products leading to identification of DNA sequences that may be responsible for better digestibility and higher survival in B. mori.

  11. Caracterização de genótipos de Citrus spp. através de marcadores RAPD Characterization of citrus genotypes (Citrus spp using RAPDs markers

    Directory of Open Access Journals (Sweden)

    Marinês Bastianel

    2001-10-01

    Full Text Available Em programas de melhoramento de citros, a caracterização adequada dos recursos genéticos disponíveis é de grande importância, principalmente devido às características biológicas da cultura, como a heterozigosidade, a embrionia nucelar e o longo ciclo reprodutivo. A facilidade com que ocorrem hibridações (interespecíficas e intergenéricas e a embrionia nucelar favoreceram a formação e a preservação de novas combinações, classificadas como espécies. Neste estudo, marcadores RAPDs foram utilizados para analisar 15 acessos de Citrus spp., sendo quatro variedades de laranjeiras doce (C. sinensis Osbeck, quatro tangerineiras (C. reticulata Blanco, C. nobilis Loureiro, C. sunki Loureiro e C. deliciosa Tenore, uma laranjeira azeda (C. aurantium L., um pomeleiro (C. paradisi Macf., uma torangeira (C. grandis Osbeck, uma cidreira (C. medica L., uma limeira ácida (C. latifolia e dois híbridos (Citrus clementina T. x (C. tangerina T. x C. paradisi Macf.. Doze sequências iniciadoras aleatórias foram utilizadas para estudar os 15 genótipos, encontrando-se um grau de similaridade mínimio de 0,81 ("Simple Matching" entre as tangerineiras. Os menores graus de similaridade foram encontrados entre as espécies de Citrus menos aparentadas (C. medica, C. grandis e C. latifolia. As quatro cultivares de laranjeiras doces não puderam ser diferenciadas pelos marcadores RAPD utilizados, apresentando similaridade máxima.In citrus improvement programs the characterization of the available genetic resources is of great importance, mainly concerning biological characteristics of the culture, as the heterozigosity, nucellar the embriony and long reproductive cycle. Favored by nucellar embriony interespecific and intergeneric hybridizations and genotypes preservation happen easily. RAPDs markers were used to analyze 15 Citrus spp., four sweet orange (C. sinensis Osbeck, (C. medica, C. grandis e C. latifolia, four mandarins (C. reticulata Blanco, C

  12. Variabilidade genética de acessos silvestres e comerciais de Passiflora edulis Sims. com base em marcadores RAPD Genetic variability of wild and commercial passion fruit (Passiflora edulis Sims. accessions using RAPD markers

    Directory of Open Access Journals (Sweden)

    Graciele Bellon

    2007-04-01

    Full Text Available No Cerrado brasileiro, há uma grande diversidade de cores, tamanhos e aromas de frutos em acessos silvestres de P. edulis. Estes acessos também são importantes fontes de resistência a doenças, podendo ser incorporados em programas de melhoramento genético do maracujazeiro azedo. Neste trabalho, objetivou-se estimar a variabilidade genética existente em acessos silvestres e comerciais de P. edulis utilizando-se de marcadores RAPD. O DNA genômico de cada acesso foi extraído e amplificado com treze iniciadores decâmeros (OPD-04, OPD-07, OPD-08, OPD-16, OPE-18, OPE-20, OPF-01, OPF-14, OPG-05, OPG-08, OPH-04, OPH-12 e OPH-16 para a obtenção dos marcadores RAPD. Os marcadores obtidos foram convertidos em uma matriz de dados binários, a partir da qual foram estimadas as distâncias genéticas entre os acessos e realizadas análises de agrupamento e de dispersão gráfica. Um total de 187 marcadores foi gerado, sendo que apenas 28 (14,97% deles foram monomórficos. As distâncias genéticas entre os 15 acessos de maracujazeiro variaram de 0,091 a 0,496. Os marcadores moleculares demonstraram a alta variabilidade genética dos acessos de P. edulis, sendo que os acessos de frutos amarelos apresentaram maior distanciamento em relação aos de frutos roxos. Menores distâncias genéticas foram verificadas entre os acessos de mesma origem geográfica.There are a great diversity of colors, sizes and aromas of fruits in wild accessions of P. edulis in Brazilian Savannah. These accessions are also important resistance sources against illness which can be incorpored in passionfruit breeding programs. In this work, the objetive was to evaluate the genetic variability in wild and commercial P. edulis accessions using RAPD markers. The genomic DNA of each accession was extracted and amplified using thirteen decamer primers (OPD-04, OPD-07, OPD-08, OPD-16, OPE-18, OPE-20, OPF-01, OPF-14, OPG-05, OPG-08, OPH-04, OPH-12 and OPH-16 to obtain RAPD markers

  13. Similaridade genética de populações naturais de pimenta-de-macaco por análise RAPD Genetic similarity of natural populations of pimenta-de-macaco (Piper aduncum L. obtained throug RAPD analysis

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    José Maria D. Gaia

    2004-12-01

    Full Text Available A espécie conhecida como pimenta-de-macaco (Piper aduncum L. possui grande potencial para exploração econômica em função da comprovada utilidade do seu óleo essencial na agricultura e saúde humana. O objetivo deste trabalho foi caracterizar a diversidade genética de populações naturais dessa planta. Um total de dezoito acessos da planta, provenientes de quatro procedências da Amazônia Brasileira, foi examinado por meio de locos de DNA, gerados por análise RAPD (polimorfismo de DNA amplificado ao acaso. O estudo evidenciou a existência de real diversidade entre as populações examinadas, sendo provável que dentro das localidades investigadas, os padrões da diversidade genética acompanhem os padrões de distribuição geográfica.The species known as pimenta-de-macaco (Piper aduncum L. has great economic explotation potential based on the proved usefulness of the essential oil in agriculture and human health. The genetic diversity of their natural populations was characterized. A total of eighteen accessions of the plant, obtained from four different origins in the Brazilian Amazon, was examined by means of DNA loci, generated by RAPD analysis. Real genetic diversity was observed between the analyzed populations and it appear that the patterns of the genetic diversity follow the patterns of the geographical distribution.

  14. Clinical phenotypes of asthma

    NARCIS (Netherlands)

    Bel, Elisabeth H.

    2004-01-01

    PURPOSE OF REVIEW: Asthma is a phenotypically heterogeneous disorder and, over the years, many different clinical subtypes of asthma have been described. A precise definition of asthma phenotypes is now becoming more and more important, not only for a better understanding of pathophysiologic

  15. Zinc Resistance within Swine-Associated Methicillin-Resistant Staphylococcus aureus Isolates in the United States Is Associated with Multilocus Sequence Type Lineage.

    Science.gov (United States)

    Hau, Samantha J; Frana, Timothy; Sun, Jisun; Davies, Peter R; Nicholson, Tracy L

    2017-08-01

    Zinc resistance in livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence type 398 (ST398) is primarily mediated by the czrC gene colocated with the mecA gene, encoding methicillin resistance, within the type V staphylococcal cassette chromosome mec (SCC mec ) element. Because czrC and mecA are located within the same mobile genetic element, it has been suggested that the use of zinc in feed as an antidiarrheal agent has the potential to contribute to the emergence and spread of methicillin-resistant S. aureus (MRSA) in swine, through increased selection pressure to maintain the SCC mec element in isolates obtained from pigs. In this study, we report the prevalence of the czrC gene and phenotypic zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates, MRSA ST5 isolates from humans with no swine contact, and U.S. swine-associated LA-MRSA ST398 isolates. We demonstrated that the prevalence of zinc resistance in U.S. swine-associated LA-MRSA ST5 isolates was significantly lower than the prevalence of zinc resistance in MRSA ST5 isolates from humans with no swine contact and swine-associated LA-MRSA ST398 isolates, as well as prevalences from previous reports describing zinc resistance in other LA-MRSA ST398 isolates. Collectively, our data suggest that selection pressure associated with zinc supplementation in feed is unlikely to have played a significant role in the emergence of LA-MRSA ST5 in the U.S. swine population. Additionally, our data indicate that zinc resistance is associated with the multilocus sequence type lineage, suggesting a potential link between the genetic lineage and the carriage of resistance determinants. IMPORTANCE Our data suggest that coselection thought to be associated with the use of zinc in feed as an antimicrobial agent is not playing a role in the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) ST5 in the U.S. swine population. Additionally, our data indicate

  16. Molecular Analysis of Date Palm Genetic Diversity Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSRs).

    Science.gov (United States)

    El Sharabasy, Sherif F; Soliman, Khaled A

    2017-01-01

    The date palm is an ancient domesticated plant with great diversity and has been cultivated in the Middle East and North Africa for at last 5000 years. Date palm cultivars are classified based on the fruit moisture content, as dry, semidry, and soft dates. There are a number of biochemical and molecular techniques available for characterization of the date palm variation. This chapter focuses on the DNA-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) techniques, in addition to biochemical markers based on isozyme analysis. These techniques coupled with appropriate statistical tools proved useful for determining phylogenetic relationships among date palm cultivars and provide information resources for date palm gene banks.

  17. Analysis of evolutionary relationship between Astasia longa and Euglena gracilis by using RAPD Technique and cladistic analysis

    Science.gov (United States)

    Wang, Jiang-Xin; Shi, Zhi-Xin; Gan, Xiao-Ni; Xie, Shu-Lian

    2001-03-01

    Although both Astasia longa and Euglena gracilis belong to different genera, they share many morphological characters except that A. longa has no chloroplast. In the 1940's, on the basis of the finding that in darkness or upon addition of some chemicals, E. gracilis would fade reversibly or irreversibly, some scholars hypothesised that A. longa evolved from E. gracilis by losing chloroplast. The author's use of RAPD and cladistic analyses in a study on the evolutionary relationship between A. longa and E. gracilis showed that the A. longa's relationship with E. gracilis was closer than that with other green euglenoids. This proves the hypothesis that A. longa evolved from E. gracilis is reasonable. The results of this study suggest that saprophytic colorless euglenoids were transformed from green euglenoids by losing their choroplasts.

  18. Distribution of Penicillium commune isolates in cheese dairies mapped using secondary metabolite profiles, morphotypes, RAPD and AFLP fingerprinting

    DEFF Research Database (Denmark)

    Lund, Flemming; Nielsen, A.B.; Skouboe, P.

    2003-01-01

    In an 8-year study of the diversity and distribution of Penicillium commune contaminants in two different cheese dairies, swab and air samples were taken from the production plants, the processing environment and contaminated cheeses. A total of 321 Penicillium commune isolates were characterized...... using morphotypes (colony morphology and colours) and secondary metabolite profiles. Based on production of secondary metabolites the P. commune isolates were classified into 6 groups. The genetic diversity of the P. commune isolates was assessed using randomly amplified polymorphic DNA (RAPD...... morphotyping, P. commune isolates with identical profiles using all four typing techniques were interpreted as closely related isolates with a common origin and the distribution of these isolates in the processing environment indicated possible contamination points in the cheese dairies. The coating process...

  19. MOLECULAR CHARACTERIZATION BY USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD ANALYSIS OF SALMONELLA ENTERITIDIS ISOLATES RECOVERED FROM AVIAN AND HUMAN SOURCES

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    E. YAQOOB, I. HUSSAIN AND S. U. RAHMAN

    2007-04-01

    Full Text Available Random amplified polymorphic DNA (RAPD analysis was applied for molecular characterization of five Salmonella enteritidis strains from different avian sources and human cases of infection. A total of 16 primers were used and only five primers showed good discriminatory power for all five isolates. Dendrogram showed a common lineage among all five isolates. There was a close genetic relationship among isolates of eggs and human sources, while there was less pronounced homology among isolates of broiler meat and human sources. On the basis of results we have found that an endemic strain of S. enteritidis is prevalent between the poultry derived food and humans which gives us an insight to genetic diversity of S. enteritidis from these sources.

  20. Comparison between Oligoryzomys nigripes and O. flavescens by RAPD and genetic diversity in O. nigripes (Rodentia, Cricetidae

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    AJ Mossi

    Full Text Available The genus of Oligoryzomys includes species of small size, morphologically similar, which may impede taxonomic identification, mainly between O. flavescens (Waterhouse, 1837 and O. nigripes (Olfers, 1818. The main objective of this work was to investigate whether the RAPD markers are capable of genetically differentiating the specimens O. nigripes and O. flavescens, coming from Rio Grande do Sul (RS and Santa Catarina (SC states, and also to estimate the genetic variability among populations of O. nigripes, with the Uruguay River as a geographical barrier. For this purpose, samples were collected in fragments of forests situated in the North of RS, at FLONA (Floresta Nacional de Passo Fundo and in fragments from SC, close to the Uruguay River. The karyotyping of two samples for each species was carried out and compared using the RAPD technique together with non- karyotyped individuals. Samples of O. nigripes presented 2n = 62; NA = 82, with submetacentric arms on the largest chromosomes, while samples of O. flavescens showed 2n = 64; NA = 66, with the largest chromosomes presenting acrocentric morphology, making such a result the main difference between the species. The analysis was able to detect two distinct groups, being the first one with karyotyped O. flavescens and the second with karyotyped O. nigripes. Identification afforded 211 loci, among them 181 (85.78% polymorphic. The Jaccard similarity coefficient was in the range of 0.45 to 0.87. The UPGMA and Main Coordinate Analysis techniques demonstrated the existence of heterogeneous genetics among populations, but did not separate them completely in terms of geographical standards, and they are not influenced by the Uruguay River, which did not act as an efficient barrier.

  1. Genética poblacional de cobayas de Colombia, Cavia spp. (Rodentia: Caviidae con marcadores moleculares RAPD

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    Héctor Aníbal Campos

    2008-09-01

    Full Text Available En el presente estudio, mostramos los primeros resultados moleculares de formas colombianas de Cavia. Claramente, la población silvestre de C. anolaimae fue genéticamente diferenciada de la forma doméstica, C. porcellus, tal como ha sido demostrado por otros autores utilizando resultados morfométricos, osteológicos y cariotípicos. Ambas especies mostraron un considerable nivel de diversidad genética, aunque el segundo taxon mostró niveles mayores de esta diversidad. Los niveles de heterogeneidad genética también fueron mayores entre las poblaciones de C. porcellus (F ST = 0.254 que entre las poblaciones de C. anolaimae (F ST = 0.118. Esos niveles significativos de heterogeneidad genética, y los consiguientes bajos niveles de flujo génico, fueron discutidos comparativamente con los resultados por otros autores analizando otros marcadores moleculares (citocromo-b mitocondrial. Los resultados aquí mostrados son coherentes con un complejo proceso de domesticación en Cavia porcellus.Population genetics of Colombian Guinea Pigs, Cavia spp. (Rodentia: Caviidae with RAPD molecular markers. The genus Cavia occurs in South America, mainly in grasslands.. We collected blood samples from 97 individuals in six field populations and analyzed them with RAPD molecular markers. One wild type (C. anolaimae was differentiated from the domestic form (C. porcellus, in agreement with other authors who used morphological, osteological and karyotipic results. Genetic diversity was considerable in both species, but higher in C. porcellus. The levels of genetic heterogeneity were also higher among the populations of C. porcellus (F ST = 0.254 than among the populations of C. anolaimae (F ST = 0.118. These significant levels of genetic heterogeneity, and the low levels of gene flow, were consistent with a complex domestication process for Cavia porcellus. Rev. Biol. Trop. 56 (3: 1481-1501. Epub 2008 September 30.

  2. In vitro propagation and assessment of genetic stability of acclimated plantlets of Cornus alba L. using RAPD and ISSR markers.

    Science.gov (United States)

    Ilczuk, Agnieszka; Jacygrad, Ewelina

    2016-01-01

    Cornus alba L. (white dogwood) is an important ornamental shrub having a wide range of applications such as reforestation programs and soil retention systems. The vegetative propagation of dogwood by cuttings may be slow, difficult, and cultivar dependent; therefore, an improved micropropagation method was developed. Nodal stem segments of C. alba cultivars 'Aurea' and 'Elegantissima' were cultured on media enriched with six different sources of macronutrients. Media were supplemented with either N6-benzyladenine (BA) or thidiazuron (TDZ) in combination with 1-naphthaleneacetic acid (NAA). Regardless of the cultivar, the best shoot proliferation was observed on Lloyd and McCown medium (woody plant medium (WPM)) at pH 6.2, containing 1.0 mg L-1 BA, 0.1 mg L-1 NAA, and 20-30 g L-1 sucrose. Rooting of regenerated shoots was achieved by an in vitro method when different concentrations of NAA or indole-3-butyric acid (IBA) were tested. Microcuttings were rooted for 8 wk on medium enriched with 0.25 mg L-1 NAA and potted into P9 containers in the greenhouse. The final survival rate of the plants after 20 wk was 80% for 'Aurea' and 90% for 'Elegantissima'. Genetic stability of the micropropagated plants was confirmed by using two DNA-based molecular marker techniques. A total of 30 random amplified polymorphic DNA (RAPD) and 20 inter-simple sequence repeat (ISSR) primers resulted in 197-199 and 184-187 distinct and reproducible band classes, respectively, in 'Aurea' and 'Elegantissima' plantlets. All of the RAPD and ISSR profiles were monomorphic and comparable with the mother plant.

  3. Identification of a novel Getah virus by Virus-Discovery-cDNA random amplified polymorphic DNA (RAPD

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    Hu Tingsong

    2012-12-01

    Full Text Available Abstract Background The identification of new virus strains is important for the study of infectious disease, but current (or existing molecular biology methods are limited since the target sequence must be known to design genome-specific PCR primers. Thus, we developed a new method for the discovery of unknown viruses based on the cDNA - random amplified polymorphic DNA (cDNA-RAPD technique. Getah virus, belonging to the family Togaviridae in the genus Alphavirus, is a mosquito-borne enveloped RNA virus that was identified using the Virus-Discovery-cDNA RAPD (VIDISCR method. Results A novel Getah virus was identified by VIDISCR from suckling mice exposed to mosquitoes (Aedes albopictus collected in Yunnan Province, China. The non-structural protein gene, nsP3, the structural protein gene, the capsid protein gene, and the 3'-untranslated region (UTR of the novel Getah virus isolate were cloned and sequenced. Nucleotide sequence identities of each gene were determined to be 97.1–99.3%, 94.9–99.4%, and 93.6–99.9%, respectively, when compared with the genomes of 10 other representative strains of Getah virus. Conclusions The VIDISCR method was able to identify known virus isolates and a novel isolate of Getah virus from infected mice. Phylogenetic analysis indicated that the YN08 isolate was more closely related to the Hebei HB0234 strain than the YN0540 strain, and more genetically distinct from the MM2021 Malaysia primitive strain.

  4. The Comparison of Streptococcus agalactiae Isolated from Fish and Bovine using Multilocus Sequence Typing

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    ANGELA MARIANA LUSIASTUTI

    2013-12-01

    Full Text Available Multilocus sequence typing (MLST has greater utility for determining the recent ancestral lineage and the relatedness of individual strains. Group B streptococci (GBS is one of the major causes of subclinical mastitis of dairy cattle in several countries. GBS also sporadically causes epizootic infections in fish. The aim of this study was to compare the evolutionary lineage of fish and bovine isolates in relation to the S. agalactiae global population as a whole by comparing the MLST profiles. Twenty S. agalactiae isolates were obtained from dairy cattle and fish. PCR products were amplified with seven different oligonucleotide primer pairs designed from the NEM316 GBS genome sequence. Clone complexes demonstrated that bovine and fish isolates were separate populations. These findings lead us to conclude that fish S. agalactiae is not a zoonotic agent for bovine. MLST could help clarify the emergence of pathogenic clones and to decide whether the host acts as a reservoir for another pathogenic lineage.

  5. Multilocus DNA sequencing of the whiskey fungus reveals a continental-scale speciation pattern.

    Science.gov (United States)

    Scott, J A; Ewaze, J O; Summerbell, R C; Arocha-Rosete, Y; Maharaj, A; Guardiola, Y; Saleh, M; Wong, B; Bogale, M; O'Hara, M J; Untereiner, W A

    2016-12-01

    Baudoinia was described to accommodate a single species, B. compniacensis . Known as the 'whiskey fungus', this species is the predominant member of a ubiquitous microbial community known colloquially as 'warehouse staining' that develops on outdoor surfaces subject to periodic exposure to ethanolic vapours near distilleries and bakeries. Here we examine 19 strains recovered from environmental samples near industrial settings in North America, South America, the Caribbean, Europe and the Far East. Molecular phylogenetic analysis of a portion of the nucLSU rRNA gene confirms that Baudoinia is a monophyletic lineage within the Teratosphaeriaceae ( Capnodiales ). Multilocus phylogenetic analysis of nucITS rRNA (ITS1-5.8S-ITS2) and partial nucLSU rRNA, beta-tubulin (TUB) and elongation factor 1-alpha (TEF1) gene sequences further indicates that Baudoinia consists of five strongly supported, geographically patterned lineages representing four new species (viz. Baudoinia antilliensis , B. caledoniensis , B. orientalis and B. panamericana ).

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

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    Jaehyuk Choi

    2013-12-01

    Full Text Available Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980’s. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

  7. Addictive behaviors and addiction-prone personality traits: associations with a dopamine multilocus genetic profile.

    Science.gov (United States)

    Davis, Caroline; Loxton, Natalie J

    2013-07-01

    The purpose of this study was to examine reward-related genetic risk for addictive behaviors in a healthy community sample (n=217) of men and women. We tested a mediation model predicting that a quantitative multilocus genetic profile score - reflecting the additive effects of alleles known to confer relatively increased dopamine signaling in the ventral striatum - would relate positively to a composite measure of addictive behaviors, and that this association would be mediated by personality traits consistently associated with addiction disorders. Our model was strongly supported by the data, and accounted for 24% of the variance in addictive behaviors. These data suggest that brain reward processes tend to exert their influence on addiction risk by their role in the development of relatively stable personality traits associated with addictive behaviors. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone.

    Science.gov (United States)

    Morehouse, Erica A; James, Timothy Y; Ganley, Austen R D; Vilgalys, Rytas; Berger, Lee; Murphy, Peter J; Longcore, Joyce E

    2003-02-01

    Chytridiomycosis is a recently identified fungal disease associated with global population declines of frogs. Although the fungus, Batrachochytrium dendrobatidis, is considered an emerging pathogen, little is known about its population genetics, including the origin of the current epidemic and how this relates to the dispersal ability of the fungus. In this study, we use multilocus sequence typing to examine genetic diversity and relationships among 35 fungal strains from North America, Africa and Australia. Only five variable nucleotide positions were detected among 10 loci (5918 bp). This low level of genetic variation is consistent with the description of B. dendrobatidis as a recently emerged disease agent. Fixed (i.e. 100%) or nearly fixed frequencies of heterozygous genotypes at two loci suggested that B. dendrobatidis is diploid and primarily reproduces clonally. In contrast to the lack of nucleotide polymorphism, electrophoretic karyotyping of multiple strains demonstrated a number of chromosome length polymorphisms.

  9. Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae.

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    Om P Rajora

    Full Text Available Natural plant populations are often adapted to their local climate and environmental conditions, and populations of forest trees offer some of the best examples of this pattern. However, little empirical work has focused on the relative contribution of single-locus versus multilocus effects to the genetic architecture of local adaptation in plants/forest trees. Here, we employ eastern white pine (Pinus strobus to test the hypothesis that it is the inter-genic effects that primarily drive climate-induced local adaptation. The genetic structure of 29 range-wide natural populations of eastern white pine was determined in relation to local climatic factors using both a reference set of SSR markers, and SNPs located in candidate genes putatively involved in adaptive response to climate. Comparisons were made between marker sets using standard single-locus outlier analysis, single-locus and multilocus environment association analyses and a novel implementation of Population Graphs. Magnitudes of population structure were similar between the two marker sets. Outlier loci consistent with diversifying selection were rare for both SNPs and SSRs. However, genetic distances based on the multilocus among population covariances (cGD were significantly more correlated to climate, even after correcting for spatial effects, for SNPs as compared to SSRs. Coalescent simulations confirmed that the differences in mutation rates between SSRs and SNPs did not affect the topologies of the Population Graphs, and hence values of cGD and their correlations with associated climate variables. We conclude that the multilocus covariances among populations primarily reflect adaptation to local climate and environment in eastern white pine. This result highlights the complexity of the genetic architecture of adaptive traits, as well as the need to consider multilocus effects in studies of local adaptation.

  10. Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data

    Science.gov (United States)

    2013-01-01

    Background Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. Results To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. Conclusions Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera. PMID:23586586

  11. Multi-locus estimates of population structure and migration in a fence lizard hybrid zone.

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    Adam D Leaché

    Full Text Available A hybrid zone between two species of lizards in the genus Sceloporus (S. cowlesi and S. tristichus on the Mogollon Rim in Arizona provides a unique opportunity to study the processes of lineage divergence and merging. This hybrid zone involves complex interactions between 2 morphologically and ecologically divergent subspecies, 3 chromosomal groups, and 4 mitochondrial DNA (mtDNA clades. The spatial patterns of divergence between morphology, chromosomes and mtDNA are discordant, and determining which of these character types (if any reflects the underlying population-level lineages that are of interest has remained impeded by character conflict. The focus of this study is to estimate the number of populations interacting in the hybrid zone using multi-locus nuclear data, and to then estimate the migration rates and divergence time between the inferred populations. Multi-locus estimates of population structure and gene flow were obtained from 12 anonymous nuclear loci sequenced for 93 specimens of Sceloporus. Population structure estimates support two populations, and this result is robust to changes to the prior probability distribution used in the Bayesian analysis and the use of spatially-explicit or non-spatial models. A coalescent analysis of population divergence suggests that gene flow is high between the two populations, and that the timing of divergence is restricted to the Pleistocene. The hybrid zone is more accurately described as involving two populations belonging to S. tristichus, and the presence of S. cowlesi mtDNA haplotypes in the hybrid zone is an anomaly resulting from mitochondrial introgression.

  12. Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis.

    Science.gov (United States)

    Labeda, David P; Dunlap, Christopher A; Rong, Xiaoying; Huang, Ying; Doroghazi, James R; Ju, Kou-San; Metcalf, William W

    2017-04-01

    The family Streptomycetaceae, notably species in the genus Streptomyces, have long been the subject of investigation due to their well-known ability to produce secondary metabolites. The emergence of drug resistant pathogens and the relative ease of producing genome sequences has renewed the importance of Streptomyces as producers of new natural products and resulted in revived efforts in isolating and describing strains from novel environments. A previous large study of the phylogeny in the Streptomycetaceae based on 16S rRNA gene sequences provided a useful framework for the relationships among species, but did not always have sufficient resolution to provide definitive identification. Multi-locus sequence analysis of 5 house-keeping genes has been shown to provide improved taxonomic resolution of Streptomyces species in a number of previous reports so a comprehensive study was undertaken to evaluate evolutionary relationships among species within the family Streptomycetaceae where type strains are available in the ARS Culture Collection or genome sequences are available in GenBank. The results of the analysis supported the distinctiveness of Kitasatospora and Streptacidiphilus as validly named genera since they cluster outside of the phylogenetic radiation of the genus Streptomyces. There is also support for the transfer of a number of Streptomyces species to the genus Kitasatospora as well for reducing at least 31 species clusters to a single taxon. The multi-locus sequence database resulting from the study is a useful tool for identification of new isolates and the phylogenetic analysis presented also provides a road map for planning future genome sequencing efforts in the Streptomycetaceae.

  13. Underestimated effect sizes in GWAS: fundamental limitations of single SNP analysis for dichotomous phenotypes.

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    Sven Stringer

    Full Text Available Complex diseases are often highly heritable. However, for many complex traits only a small proportion of the heritability can be explained by observed genetic variants in traditional genome-wide association (GWA studies. Moreover, for some of those traits few significant SNPs have been identified. Single SNP association methods test for association at a single SNP, ignoring the effect of other SNPs. We show using a simple multi-locus odds model of complex disease that moderate to large effect sizes of causal variants may be estimated as relatively small effect sizes in single SNP association testing. This underestimation effect is most severe for diseases influenced by numerous risk variants. We relate the underestimation effect to the concept of non-collapsibility found in the statistics literature. As described, continuous phenotypes generated with linear genetic models are not affected by this underestimation effect. Since many GWA studies apply single SNP analysis to dichotomous phenotypes, previously reported results potentially underestimate true effect sizes, thereby impeding identification of true effect SNPs. Therefore, when a multi-locus model of disease risk is assumed, a multi SNP analysis may be more appropriate.

  14. Accounting for genetic interactions improves modeling of individual quantitative trait phenotypes in yeast.

    Science.gov (United States)

    Forsberg, Simon K G; Bloom, Joshua S; Sadhu, Meru J; Kruglyak, Leonid; Carlborg, Örjan

    2017-04-01

    Experiments in model organisms report abundant genetic interactions underlying biologically important traits, whereas quantitative genetics theory predicts, and data support, the notion that most genetic variance in populations is additive. Here we describe networks of capacitating genetic interactions that contribute to quantitative trait variation in a large yeast intercross population. The additive variance explained by individual loci in a network is highly dependent on the allele frequencies of the interacting loci. Modeling of phenotypes for multilocus genotype classes in the epistatic networks is often improved by accounting for the interactions. We discuss the implications of these results for attempts to dissect genetic architectures and to predict individual phenotypes and long-term responses to selection.

  15. Genetic structure of annual ryegrass (Lolium multiflorum populations estimated by RAPD Estrutura genética de populações de azevém anual (Lolium multiflorum estimada por RAPD

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    Eduardo Alano Vieira

    2004-01-01

    Full Text Available Annual ryegrass is a temperate climate annual foraging grass, grown mostly in the South of Brazil, especially in the state of Rio Grande do Sul. Despite its importance, little is known about its genetic diversity, both within and among the populations cultivated. This knowledge is of fundamental importance for developing breeding and conservation strategies. The aim of this study was to characterize the genetic diversity and structure of four populations of annual ryegrass. Three of the populations were located in Rio Grande do Sul and the fourth in Uruguay. RAPD markers were used to study the genetic diversity and structure of these populations. Analysis of 375 individuals sampled from the populations, using six RAPD primers, generated a total of 82 amplified bands. They included 73 polymorphic bands (89,02%. The value of the total genetic diversity index obtained, (0,71 was high, indicating the presence of wide genetic diversity in the four populations. Genetic structure analysis revealed that 98% of total diversity is intrapopulational, whereas interpopulational genetic diversity was only 2%. These results suggest that before these populations separated, they had gone through a period of gene exchange and, even after the separation event, gene frequency stayed at levels similar to the original levels, with no differential selection for these genes in the different cultivation areas.O azevém anual é a gramínea anual forrageira de clima temperado de maior utilização no sul do Brasil, particularmente no Estado do Rio Grande do Sul. Apesar de toda a importância que a espécie apresenta, pouco se conhece a respeito da diversidade genética presente entre e dentro das populações cultivadas. Este conhecimento é de fundamental importância para o estabelecimento das estratégias de melhoramento genético e de conservação destes materiais. O objetivo deste estudo foi caracterizar a diversidade genética e a estrutura genética de quatro

  16. Divergência genética em tomate estimada por marcadores RAPD em comparação com descritores multicategóricos Genetic divergence among tomato accessions using RAPD markers and its comparison with multicategoric descriptors

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    Leandro SA Gonçalves

    2008-09-01

    Full Text Available A estimativa da variabilidade genética existente em um banco de germoplasma é importante não só para a conservação dos recursos genéticos, mas também para aplicações no melhoramento de plantas. O presente trabalho teve como objetivo estudar a divergência genética entre 78 acessos de uma coleção de germoplasma de tomateiro, com base em 74 marcadores RAPD e correlacionar esses resultados àqueles da caracterização morfoagronômica realizada para 27 descritores. Foi utilizado o agrupamento hierárquico UPGMA para analisar os dados, observando-se a formação de 13 grupos. Esses grupos foram correlacionados a cinco descritores (hábito de crescimento, tipo de folha, cor do fruto, número de lóculos e formato do fruto. Alguns grupos apresentaram peculiaridades, a exemplo do grupo IV, que reuniu acessos com frutos no formato de pêra; o grupo VII com acessos resistentes a murcha-bacteriana e o grupo IX, que englobou acessos com folhas do tipo batata. As análises por bootstrap revelaram poucos agrupamentos consistentes. Houve correlação positiva e altamente significativa entre as matrizes geradas pelos 27 descritores qualitativos e pelos marcadores RAPD (t = 14,02. A correlação de Mantel (r = 0,39 foi altamente significativa, porém de baixa magnitude. O baixo valor verificado para esta correlação sugere que ambas as etapas de caracterização (morfoagronômica e molecular são importantes para um conhecimento mais amplo e melhor discriminação entre os acessos de tomate.The estimation of genetic variability in a germplasm bank is important not only for the conservation of the genetic resources, but also for applications in plant breeding. The genetic divergence among 78 tomato accessions was studied, based on 74 RAPD markers. Also, a correlation between the molecular profile and 27 morphological and agronomic data was performed. Cluster analysis (UPGMA, used to study the data, resulted in 13 groups that were correlated with

  17. Analysis of the genetic diversity in Metopolophium dirhodum (Walker (Hemiptera, Aphididae by RAPD markers Análise da diversidade genética de Metopolophium dirhodum (Walker (Hemiptera, Aphididae por meio de marcadores RAPD

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    Marcelo Lopes-da-Silva

    2007-03-01

    Full Text Available The emergence of host-races within aphids may constitute an obstacle to pest management by means of plant resistance. There are examples of host-races within cereals aphids, but their occurrence in Rose Grain Aphid, Metopolophium dirhodum (Walker, 1849, has not been reported yet. In this work, RAPD markers were used to assess effects of the hosts and geographic distance on the genetic diversity of M. dirhodum lineages. Twenty-three clones were collected on oats and wheat in twelve localitites of southern Brazil. From twenty-seven primers tested, only four primers showed polymorphisms. Fourteen different genotypes were revealed by cluster analysis. Five genotypes were collected only on wheat; seven only on oats and two were collected in both hosts. Genetic and geographical distances among all clonal lineages were not correlated. Analysis of molecular variance showed that some molecular markers are not randomly distributed among clonal lineages collected on oats and on wheat. These results suggest the existence of host-races within M. dirhodum, which should be further investigated using a combination of ecological and genetic data.A emergência de raças hospedeiro-especialistas em afídeos pode constituir um obstáculo ao manejo de pragas por meio de plantas resistentes. Existem exemplos de raças hospedeiro-especialistas em afídeos de cereais, embora a ocorrência de raça hospedeiro-especialista no pulgão-verde-pálido-do-trigo Metopolophium dirhodum (Walker, 1849 (Hemiptera, Aphididae não tenha sido relatada ainda. Marcadores RAPD foram utilizados para avaliar os efeitos da distância geográfica e do hospedeiro sobre a diversidade genética de linhas clonais de M. dirhodum. Vinte e três clones foram coletados em aveia e trigo em doze localidades do sul do Brasil. De vinte e sete iniciadores usados para a análise, apenas quatro iniciadores mostraram polimorfismos. A análise de agrupamento por similaridade genética revelou haver quatorze

  18. Determining Phylogenetic Relationships Among Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Haider, Nadia

    2017-01-01

    Investigation of genetic variation and phylogenetic relationships among date palm (Phoenix dactylifera L.) cultivars is useful for their conservation and genetic improvement. Various molecular markers such as restriction fragment length polymorphisms (RFLPs), simple sequence repeat (SSR), representational difference analysis (RDA), and amplified fragment length polymorphism (AFLP) have been developed to molecularly characterize date palm cultivars. PCR-based markers random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) are powerful tools to determine the relatedness of date palm cultivars that are difficult to distinguish morphologically. In this chapter, the principles, materials, and methods of RAPD and ISSR techniques are presented. Analysis of data generated from these two techniques and the use of these data to reveal phylogenetic relationships among date palm cultivars are also discussed.

  19. Identification and characterization of Fusarium sp. using ITS and RAPD causing fusarium wilt of tomato isolated from Assam, North East India

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    Irom Manoj Singha

    2016-06-01

    Full Text Available Fusarium oxysporum which causes wilt is a serious pathogen. Fusarium isolates were isolated from Assam located in North East region of India. Morphological identification of Fusarium isolates was done using conidial and hyphal structures. Molecular identification of Fusarium isolates was done by amplifying the internal transcribed spacer (ITS region of the conserved ribosomal DNA using primers ITS1 and ITS4. All the ITS sequences were compared for gaps and similarity. Further, characterization of random amplified polymorphic DNA (RAPD was carried out using 40 primers. 15 primers that gave reproducible results were selected. RAPD was used to observe the relatedness among these isolates. Thus, it was concluded that molecular profiling using ITS is an indispensable method for identification studies.

  20. Low Genetic Diversity Among Garlic (Allium sativum L. Accessions Detected Using Random Amplified Polymorphic DNA (RAPD Escasa Diversidad Genética entre Accesiones de Ajo (Allium sativum L. Detectada Mediante ADN Polimórfico Amplificado al Azar (RAPD

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    Mario Paredes C

    2008-03-01

    Full Text Available Garlic (Allium sativum L. is a species of vegetative propagation, showing high morphological diversity. Besides, its clones have specific adaptations to different agroclimatic regions. The objective of this study was to determine the genetic diversity of 65 garlic clones collected in Chile and introduced from different countries, by using RAPD (Random Amplified Polymorphic DNA. Fourty random primers of 10 mers generated a total of 398 bands with an 87% of polymorphism. Each primer amplified between two and 20 bands. The size of the fragments obtained fluctuated between 3200 and 369 bp. The results showed that the clones analyzed had a genetic similarity rate of 94%. In addition, 70% of them were clustered in one major group. However, in spite of that situation several clones have different agronomic characteristicsEl ajo (Allium sativum L. es una especie de propagación vegetativa, que presenta una amplia variabilidad morfológica. Los clones de esta especie tienen una adaptación específica a diferentes regiones agroclimáticas. El objetivo de este estudio fue determinar la diversidad genética existente en 65 clones de ajos colectados en Chile e introducidos desde diferentes países, utilizando RAPD (ADN Polimórfico Amplificado al Azar. Para esta evaluación se utilizaron 40 partidores de 10-mers. Los partidores generaron entre dos y 20 bandas, observándose un alto número de patrones con bandas múltiples. Los fragmentos generados difieren en su tamaño entre 3.200 y 369 pb. Los partidores generaron 398 bandas, de las cuales un 87% fueron polimórficas. El análisis estadístico realizado detectó una similitud genética alta, de un 94% entre las accesiones evaluadas, donde aproximadamente un 70% de los clones formaron un grupo homogéneo. Sin embargo, este grupo incluye clones que presentan diferentes características agronómicas

  1. Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers.

    Science.gov (United States)

    Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A

    2014-01-01

    DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes.

  2. Molecular phylogenetic relationships among four species of the mangrove tree genus Bruguiera (Rhizophoraceae, as revealed by chromosome and RAPD markers

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    Pragnya Sahoo

    2007-06-01

    Full Text Available Analysis of karyotype, nuclear DNA content and RAPD markers were performed in four species of Bruguiera (Rhizophoraceae of Bhitarkanika mangrove forests, Orissa, India. Detailed karyotype analysis revealing 2n=34 in B. cylindrica and 2n=36 in B. gymnorrhiza was reported for the first time and 2n=34 in B. parviflora and B. sexangula was confirmed. On the basis of the common types of chromosomes present among Bruguiera, two distinct groups were found; one consists of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula. The symmetrical karyotype with same chromosome types grouped B. cylindrica and B. parviflora together and presence of Type E chromosomes placed B. gymnorrhiza and B. sexangula in a separate group, suggesting their closer affinity in their respective group. Analysis of chromosome length, volume, INV and 4C DNA content confirmed this division. Nuclear DNA content was two-fold higher (~17.0 pg in the second group than in the first (~8.0 pg. The amplification products generated through RAPD revealed 1-9 amplicons with size variations from 600 bp to 2 500 bp with 49.31% genetic similarity between B. gymnorrhiza and B. sexangula and 47.10% in between B. cylindrica and B. parviflora. The high copy number marker band (~ 1 100 bp yielded in OPN-15 primer in B. parviflora the characteristic DNA marker, which was cloned and used as probes for assessment of genetic diversity, and demonstrated its close genetic affinity to B. cylindrica. B. gymnorrhiza and B. sexangula also produced similar marker bands of ~600 bp and ~2 200 bp in the same primer. All of the cytological, 4C DNA content and RAPD data confirmed the existence of two taxonomically distinct groups of Bruguiera: one consisting of B. cylindrica and B. parviflora and the other of B. gymnorrhiza and B. sexangula as placed earlier (1862 in the tribe Rhizophoreae by Bentham and Hooker, on the basis of the flowering habits of Bruguiera. Genetically, the B

  3. RAPD-PCR typing of Yersinia enterocolitica (Enterobacteriaceae O:3 serotype strains isolated from pigs and humans

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    Tereza Cristina A. Leal

    1999-09-01

    Full Text Available Sixteen strains of Yersinia enterocolitica serotype O:3, isolated from apparently healthy pigs collected in Rio de Janeiro, and four human strains of serotypes O:4, O:5, O:6 and O:13 were analyzed by RAPD-PCR. The strains were grouped into five genotypic profiles according to the amplification patterns obtained with three random primers. Fifteen of the 16 pig strains had identical amplification patterns, which was named genotypic profile 1. The one different profile was named genotypic profile 2. Genotypic profile 1 was also exhibited by the O:6 human serotype strain. The O:4 and O:13 human serotype strains showed similar amplification profiles with two primers. However, the third primer induced a distinct profile in each strain. Therefore, these two strains were placed into genotypic profile 3 and 4, respectively. Each primer produced a completely different amplification profile in the O:5 human serotype strain; therefore, it was named genotypic profile 5. The presence or absence of plasmids in the strains studied did not affect the amplification results. These results show that genetic variations can exist within a serotype, and strains of different serotypes can exhibit the same amplification profile when compared using other primers.Foram utilizados três "primers" aleatórios para caracterizar pela técnica RAPD-PCR 16 cepas de Yersinia enterocolitica do sorotipo O:3, isoladas de suínos sadios do Rio de Janeiro. Pelos resultados dos padrões de amplificação, as 16 cepas dos suínos e as 4 cepas humanas usadas como referência (sorotipos O:4, O:5, O:6 e O:13 foram agrupadas em 5 perfis genotípicos. Quinze cepas de suínos apresentaram um padrão de amplificação idêntico (perfil genotípico 1 e somente uma apresentou um perfil de amplificação diferente (perfil genotípico 2. O mesmo padrão de amplificação do perfil genotípico 1 foi também observado em uma cepa humana do sorotipo O:6. As cepas humanas dos sorotipos O:4 e O:13

  4. Phenotypic and molecular variation in the green and black poison-dart frog Dendrobates auratus (Anura: Dendrobatidae from Costa Rica

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    Lisa D Patrick

    2009-11-01

    Full Text Available The green and black poison-dart frog Dendrobates auratus exhibits high intraspecific variation in hue color and pattern throughout its range, making it a very popular species in the pet trade. We analyzed the correspondence between color variation and molecular variation of D. auratus from Costa Rica using RAPD analysis. Twenty-six random primers were analyzed for variation in 99 individuals from seven populations. Color pattern was scored from digital images of the dorsal and ventral views. In general, frogs from the Caribbean coast had significantly more light coloration than black color but cannot be grouped by population based only on hue pattern. Only 3 RAPD primers were found to be polymorphic, representing a total of 16 loci. Most of the molecular variation encountered here occurs within populations, thus making unclear the degree of population structure and differentiation. Further examination of COI mtDNA sequences from our samples also supports these results. Partial Mantel correlations suggested that the pattern of molecular variation is not congruent with the variation in color pattern in this species, an outcome that is discussed in terms of phenotypic evolution. Rev. Biol. Trop. 57 (Suppl. 1: 313-321. Epub 2009 November 30.

  5. Caracterização de isolados de Diplodia pinea da região Sul do Brasil por meio da compatibilidade micelial e de marcadores RAPD

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    Paula Rachel Rabelo Corrêa Corrêa

    2016-03-01

    Full Text Available RESUMO O objetivo do trabalho foi caracterizar quatro isolados de Diplodiapinea da região Sul do Brasil e estimar sua variabilidade genética, baseados na compatibilidade vegetativa e marcadores RAPD. Na compatibilidade vegetativa, os isolados foram pareados em placas de Petri com meio BDA e formaram linhas escuras quando incompatíveis e linhas claras cotonosas quando incompatíveis. Para a caracterização molecular dos isolados, a extração de DNA foi realizada em amostras obtidas de micélio cultivado em meio BDA dos isolados originais e os monospóricos derivados. O DNA das amostras foi avaliado em reação de polimerase em cadeia (PCR, utilizando onze sequências diferentes de primers RAPD inespecíficos. O agrupamento dos morfotipos foi realizado pelo método UPGMA e coeficiente de similaridade de Jaccard. Somente um marcador RAPD mostrou polimorfismo, indicando que os isolados apresentam pequena divergência genética, porém suficiente para indicar mais de morfotipo presente.

  6. Comparison of multilocus sequence analysis and virulence genotyping of Escherichia coli from live birds, retail poultry meat, and human extraintestinal infection.

    Science.gov (United States)

    Danzeisen, Jessica L; Wannemuehler, Yvonne; Nolan, Lisa K; Johnson, Timothy J

    2013-03-01

    To examine the correlations between virulence genotyping and multilocus sequence analysis of Escherichia coli from poultry and humans, 88 isolates were examined. The isolates were selected from a population of over 1000 based on their assignment to nine different virulence genotyping clusters. Clustering based on multilocus sequence analysis mostly correlated with virulence genotyping, although multilocus sequence analysis demonstrated higher discriminatory ability and greater reliability related to inferred phylogenetic relationships. No distinct patterns in host source were observed using inferred phylogeny through multilocus sequence analysis, indicating that human, avian, and retail meat isolates are diverse, and some belong to multiple shared clonal complexes. Clonal complexes with host source overlap included ST95 and ST23 and additional novel groups, underscoring the diversity of avian pathogenic E. coli and the potential importance of these novel groups as avian and zoonotic pathogens.

  7. Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST

    Science.gov (United States)

    We constructed several multilocus Deoxyribonucleic acid (DNA) sequence datasets to assess the phylogenetic diversity of insecticolous fusaria, especially focusing on those housed in the Agricultural Research Service Collection of Entomopathogenic Fungi (ARSEF), and to facilitate molecular identifica...

  8. Inconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires reevaluation of current diagnostics.

    Science.gov (United States)

    van der Graaf-van Bloois, Linda; Miller, William G; Yee, Emma; Rijnsburger, Martine; Wagenaar, Jaap A; Duim, Birgitta

    2014-12-01

    Classifications of the Campylobacter fetus subspecies fetus and venerealis were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the C. fetus subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of C. fetus, which are based on the closed genomes of five C. fetus strains. Phylogenetic analysis of the core genomes of 23 C. fetus strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing, sap typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined C. fetus subsp. fetus strains to C. fetus subsp. venerealis strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of C. fetus subspecies identification by phenotypic assays. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. An efficient and rapid DNA minipreparation procedure suitable for PCR/SSR and RAPD analyses in tropical forest tree species

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    Ana Lilia Alzate-Marin

    2009-10-01

    Full Text Available An efficient and rapid DNA minipreparation modified method for frozen samples was developed for five tropical tree species: Copaifera langsdorffii, Hymenaea courbaril, Eugenia uniflora, Tabebuia roseo alba and Cariniana estrellensis. This procedure that dispenses the use of liquid nitrogen, phenol and the addition of proteinase K, is an adaptation of the CTAB-based DNA extraction method. The modifications included the use of PVP to eliminate the polyphenols, only one chloroform-isoamyl alcohol step and the addition of RNase immediately after extraction with chloroform. The yields of the DNA samples ranged from 25.7 to 42.1 µg from 100 mg leaf tissue. The DNA samples extracted by this method were successfully used for PCR (SSR and RAPD analyses in these five and other twelve tropical tree species.Este trabalho teve como objetivo otimizar um protocolo econômico, rápido e eficaz de minipreparação de DNA genômico, para as espécies florestais Copaifera langsdorffii (Óleo de Copaíba, Hymenaea courbaril (Jatobá, Eugenia uniflora (Pitanga, Tabebuia roseo alba (Ipê Branco e Cariniana estrellensis (Jequitibá Branco. Este método é uma adaptação da técnica de extração CTAB de Doyle e Doyle (1990, o qual consiste principalmente na adição de PVP para eliminar polifenoles, somente uma etapa de extração com clorofórmio-álcool isoamílico e a adição da RNase A imediatamente após a extração com clorofórmio. O método também dispensa o uso de nitrogênio líquido, o uso do fenol e a adição de proteinase K. Os DNAs das espécies florestais extraídos apresentaram alto rendimento e boa qualidade, com rendimento de 25.7 a 42.1 µg de DNA a partir de 100 mg de tecido foliar congelado. Com este protocolo, em apenas 1 dia de trabalho, uma pessoa pode completar o isolamento do DNA de aproximadamente 50 amostras de folhas (dependendo da capacidade da centrífuga. O DNA obtido pode ser usado para métodos de análise baseados em PCR (SSR e

  10. Relation of the multilocus genetic composite reflecting high dopamine signaling capacity to future increases in BMI.

    Science.gov (United States)

    Yokum, Sonja; Marti, C Nathan; Smolen, Andrew; Stice, Eric

    2015-04-01

    Because food intake exerts its rewarding effect by increasing dopamine (DA) signaling in reward circuitry, it theoretically follows that individuals with a greater number of genotypes putatively associated with high DA signaling capacity are at increased risk for overeating and subsequent weight gain. We tested the association between the multilocus genetic composite risk score, defined by the total number of genotypes putatively associated with greater DA signaling capacity (i.e. TaqIA A2 allele, DRD2-141C Ins/Del and Del/Del genotypes, DRD4-S allele, DAT1-S allele, and COMT Val/Val genotype), and future increases in Body Mass Index (BMI) in three prospective studies. Participants in Study 1 (N = 30; M age = 15.2; M baseline BMI = 26.9), Study 2 (N = 34; M age = 20.9; M baseline BMI = 28.2), and Study 3 (N = 162; M age = 15.3, M baseline BMI = 20.8) provided saliva samples from which epithelial cells were collected, permitting DNA extraction. The multilocus genetic composite risk score was associated with future increases in BMI in all three studies (Study 1, r = 0.37; Study 2, r = 0.22; Study 3, r = 0.14) and the overall sample (r = 0.19). DRD4-S was associated with increases in BMI in Study 1 (r = 0.42), Study 2 (r = 0.27), and in the overall sample (r = 0.17). DAT1-S was associated with increases in BMI in Study 3 (r = 0.17) and in the overall sample (r = 0.12). There were no associations between the other genotypes (TaqIA, COMT, and DRD2-141C) and change in BMI over 2-year follow-up. Data suggest that individuals with a genetic propensity for greater DA signaling capacity are at risk for future weight gain and that combining alleles that theoretically have a similar function may provide a more reliable method of modeling genetic risk associated with future weight gain than individual genotypes. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Relation of the multilocus genetic composite reflecting high dopamine signaling capacity to future increases in BMI☆

    Science.gov (United States)

    Yokum, Sonja; Marti, C. Nathan; Smolen, Andrew; Stice, Eric

    2014-01-01

    Because food intake exerts its rewarding effect by increasing dopamine (DA) signaling in reward circuitry, it theoretically follows that individuals with a greater number of genotypes putatively associated with high DA signaling capacity are at increased risk for overeating and subsequent weight gain. We tested the association between the multilocus genetic composite risk score, defined by the total number of genotypes putatively associated with greater DA signaling capacity (i.e. TaqIA A2 allele, DRD2-141C Ins/Del and Del/Del genotypes, DRD4-S allele, DAT1-S allele, and COMT Val/Val genotype), and future increases in Body Mass Index (BMI) in three prospective studies. Participants in Study 1 (N = 30; M age = 15.2; M baseline BMI = 26.9), Study 2 (N = 34; M age = 20.9; M baseline BMI = 28.2), and Study 3 (N = 162; M age = 15.3, M baseline BMI = 20.8) provided saliva samples from which epithelial cells were collected, permitting DNA extraction. The multilocus genetic composite risk score was associated with future increases in BMI in all three studies (Study 1, r = 0.37; Study 2, r = 0.22; Study 3, r = 0.14) and the overall sample (r = 0.19). DRD4-S was associated with increases in BMI in Study 1 (r = 0.42), Study 2 (r = 0.27), and in the overall sample (r = 0.17). DAT1-S was associated with increases in BMI in Study 3 (r = 0.17) and in the overall sample (r = 0.12). There were no associations between the other genotypes (TaqIA, COMT, and DRD2-141C) and change in BMI over 2-year follow-up. Data suggest that individuals with a genetic propensity for greater DA signaling capacity are at risk for future weight gain and that combining alleles that theoretically have a similar function may provide a more reliable method of modeling genetic risk associated with future weight gain than individual genotypes. PMID:25523644

  12. Molecular Epidemiologic Analysis of Enterococcus faecalis Isolates in Cuba by Multilocus Sequence Typing

    Science.gov (United States)

    Kobayashi, Nobumichi; Nagashima, Shigeo

    2009-01-01

    We carried out the first study of Enterococcus faecalis clinical isolates in Cuba by multilocus sequence typing linking the molecular typing data with the presence of virulence determinants and the antibiotic resistance genes. A total of 23 E. faecalis isolates recovered from several clinic sources and geographic areas of Cuba during a period between 2000 and 2005 were typed by multilocus sequence typing. Thirteen sequence types (STs) including five novel STs were identified, and the ST 64 (clonal complex [CC] 8), ST 6 (CC2), ST 21(CC21), and ST 16 (CC58) were found in more than one strain. Sixty-seven percent of STs corresponded to STs reported previously in Spain, Poland, and The Netherlands, and other STs (ST115, ST64, ST6, and ST40) were genetically close to those detected in the United States. Prevalence of both antimicrobial resistance genes [aac(6′)-aph(2″), aph(3′), ant(6), ant(3″)(9), aph(2″)-Id, aph(2″)-Ic, erm(B), erm(A), erm(C), mef(A), tet(M), and tet(L)] and virulence genes (agg, gelE, cylA, esp, ccf, and efaAfs) were examined by polymerase chain reaction. Aminoglycoside resistance genes aac(6′)-Ie-aph(2″)-Ia, aph(3′), ant(6), ant(3″)(9) were more frequently detected in ST6, ST16, ST23, ST64, and ST115. The multidrug resistance was distributed to all STs detected, except for ST117 and singleton ST225. The presence of cyl gene was specifically linked to the ST64 and ST16. Presence of the esp, gel, and agg genes was not specific to any particular ST. This research provided the first insight into the population structure of E. faecalis in Cuba, that is, most Cuban strains were related to European strains, whereas others to U.S. strains. The CC2, CC21, and CC8, three of the biggest CCs in the world, were evidently circulating in Cuba, associated with multidrug resistance and virulence traits. PMID:19857135

  13. Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach

    Directory of Open Access Journals (Sweden)

    Ramirez Mário

    2009-05-01

    Full Text Available Abstract Background Multilocus Sequence Typing (MLST is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence of housekeeping genes that result in each strain having a distinct numerical allelic profile, which is abbreviated to a unique identifier: the sequence type (ST. The relatedness between two strains can then be inferred by the differences between allelic profiles. For a more comprehensive analysis of the possible patterns of evolutionary descent, a set of rules were proposed and implemented in the eBURST algorithm. These rules allow the division of a data set into several clusters of related strains, dubbed clonal complexes, by implementing a simple model of clonal expansion and diversification. Within each clonal complex, the rules identify which links between STs correspond to the most probable pattern of descent. However, the eBURST algorithm is not globally optimized, which can result in links, within the clonal complexes, that violate the rules proposed. Results Here, we present a globally optimized implementation of the eBURST algorithm – goeBURST. The search for a global optimal solution led to the formalization of the problem as a graphic matroid, for which greedy algorithms that provide an optimal solution exist. Several public data sets of MLST data were tested and differences between the two implementations were found and are discussed for five bacterial species: Enterococcus faecium, Streptococcus pneumoniae, Burkholderia pseudomallei, Campylobacter jejuni and Neisseria spp.. A novel feature implemented in goeBURST is the representation of the level of tiebreak rule reached before deciding if a link should be drawn, which can used to visually evaluate the reliability of the represented hypothetical pattern of descent. Conclusion goeBURST is a globally optimized implementation of the eBURST algorithm, that

  14. Characterization of sulphonamide-resistant Escherichia coli using comparison of sul2 gene sequences and multilocus sequence typing

    DEFF Research Database (Denmark)

    Trobos, Margarita; Christensen, Henrik; Sunde, Marianne

    2009-01-01

    The sul2 gene encodes sulphonamide resistance (Sul(R)) and is commonly found in Escherichia coli from different hosts. We typed E coli isolates by multilocus sequence typing (MLST) and compared the results to sequence variation of sul2, in order to investigate the relation to host origin of patho...... horizontal transfer of sul2.......The sul2 gene encodes sulphonamide resistance (Sul(R)) and is commonly found in Escherichia coli from different hosts. We typed E coli isolates by multilocus sequence typing (MLST) and compared the results to sequence variation of sul2, in order to investigate the relation to host origin...... of pathogenic and commensal E coli strains and to investigate whether transfer of sul2 into different genomic lineages has happened multiple times. Sixty-eight E coli isolated in Denmark and Norway from different hosts and years were MLST typed and sul2 PCR products were sequenced and compared. PFGE...

  15. Statistical analysis of binary data generated from multilocus dominant DNA markers.

    Science.gov (United States)

    Khang, T F; Yap, V B

    2010-11-01

    The use of methodologies such as RAPD and AFLP for studying genetic variation in natural populations is widespread in the ecology community. Because data generated using these methods exhibit dominance, their statistical treatment is less straightforward. Several estimators have been proposed for estimating population genetic parameters, assuming simple random sampling and the Hardy-Weinberg (HW) law. The merits of these estimators remain unclear because no comparative studies of their theoretical properties have been carried out. Furthermore, ascertainment bias has not been explicitly modelled. Here, we present a comparison of a set of candidate estimators of null allele frequency (q), locus-specific heterozygosity (h) and average heterozygosity () in terms of their bias, standard error, and root mean square error (RMSE). For estimating q and h, we show that none of the estimators considered has the least RMSE over the parameter space. Our proposed zero-correction procedure, however, generally leads to estimators with improved RMSE. Assuming a beta model for the distribution of null homozygote proportions, we show how correction for ascertainment bias can be carried out using a linear transform of the sample average of h and the truncated beta-binomial likelihood. Simulation results indicate that the maximum likelihood and empirical Bayes estimator of have negligible bias and similar RMSE. Ascertainment bias in estimators of is most pronounced when the beta distribution is J-shaped and negligible when the latter is inverse J-shaped. The validity of the current findings depends importantly on the HW assumption-a point that we illustrate using data from two published studies. © 2010 Blackwell Publishing Ltd.

  16. Accurate Identification of Common Pathogenic Nocardia Species: Evaluation of a Multilocus Sequence Analysis Platform and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

    Science.gov (United States)

    Chen, Sharon C-A.; Fan, Xin; Zhang, Li; Li, Hai-Xia; Hou, Xin; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Species identification of Nocardia is not straightforward due to rapidly evolving taxonomy, insufficient discriminatory power of conventional phenotypic methods and also of single gene locus analysis including 16S rRNA gene sequencing. Here we evaluated the ability of a 5-locus (16S rRNA, gyrB, secA1, hsp65 and rpoB) multilocus sequence analysis (MLSA) approach as well as that of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in comparison with sequencing of the 5’-end 606 bp partial 16S rRNA gene to provide identification of 25 clinical isolates of Nocardia. The 5’-end 606 bp 16S rRNA gene sequencing successfully assigned 24 of 25 (96%) clinical isolates to species level, namely Nocardia cyriacigeorgica (n = 12, 48%), N. farcinica (n = 9, 36%), N. abscessus (n = 2, 8%) and N. otitidiscaviarum (n = 1, 4%). MLSA showed concordance with 16S rRNA gene sequencing results for the same 24 isolates. However, MLSA was able to identify the remaining isolate as N. wallacei, and clustered N. cyriacigeorgica into three subgroups. None of the clinical isolates were correctly identified to the species level by MALDI-TOF MS analysis using the manufacturer-provided database. A small “in-house” spectral database was established incorporating spectra of five clinical isolates representing the five species identified in this study. After complementation with the “in-house” database, of the remaining 20 isolates, 19 (95%) were correctly identified to species level (score ≥ 2.00) and one (an N. abscessus strain) to genus level (score ≥ 1.70 and Nocardia. MALDI-TOF MS can provide rapid and accurate identification but is reliant on a robust mass spectra database. PMID:26808813

  17. Accurate Identification of Common Pathogenic Nocardia Species: Evaluation of a Multilocus Sequence Analysis Platform and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

    Science.gov (United States)

    Xiao, Meng; Pang, Lu; Chen, Sharon C-A; Fan, Xin; Zhang, Li; Li, Hai-Xia; Hou, Xin; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Species identification of Nocardia is not straightforward due to rapidly evolving taxonomy, insufficient discriminatory power of conventional phenotypic methods and also of single gene locus analysis including 16S rRNA gene sequencing. Here we evaluated the ability of a 5-locus (16S rRNA, gyrB, secA1, hsp65 and rpoB) multilocus sequence analysis (MLSA) approach as well as that of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in comparison with sequencing of the 5'-end 606 bp partial 16S rRNA gene to provide identification of 25 clinical isolates of Nocardia. The 5'-end 606 bp 16S rRNA gene sequencing successfully assigned 24 of 25 (96%) clinical isolates to species level, namely Nocardia cyriacigeorgica (n = 12, 48%), N. farcinica (n = 9, 36%), N. abscessus (n = 2, 8%) and N. otitidiscaviarum (n = 1, 4%). MLSA showed concordance with 16S rRNA gene sequencing results for the same 24 isolates. However, MLSA was able to identify the remaining isolate as N. wallacei, and clustered N. cyriacigeorgica into three subgroups. None of the clinical isolates were correctly identified to the species level by MALDI-TOF MS analysis using the manufacturer-provided database. A small "in-house" spectral database was established incorporating spectra of five clinical isolates representing the five species identified in this study. After complementation with the "in-house" database, of the remaining 20 isolates, 19 (95%) were correctly identified to species level (score ≥ 2.00) and one (an N. abscessus strain) to genus level (score ≥ 1.70 and Nocardia. MALDI-TOF MS can provide rapid and accurate identification but is reliant on a robust mass spectra database.

  18. Comparison by multilocus variable-number tandem repeat analysis and antimicrobial resistance among atypical enteropathogenic Escherichia coli strains isolated from food samples and human and animal faecal specimens.

    Science.gov (United States)

    Wang, L; Nakamura, H; Kage-Nakadai, E; Hara-Kudo, Y; Nishikawa, Y

    2017-01-01

    This study assessed whether multilocus variable-number tandem repeat analysis (MLVA) and antimicrobial susceptibility testing discriminated diarrhoeagenic atypical enteropathogenic Escherichia coli (aEPEC) from aEPEC indigenous to domestic animals or healthy people. MLVA genotyping of 142 aEPEC strains isolated from foods and faecal samples of domestic animals and humans revealed 126 distinct MLVA profiles that distributed to four clusters, yielding a Simpson's index of diversity (D) of 99·8%. Cluster 2 included 87% of cattle isolates and 67% of patient isolates. The plurality (15/34, 44%) of strains from healthy humans mapped to Cluster 1, while half (18/41, 44%) of the swine strains belonged to Cluster 4. Testing for antimicrobial susceptibility revealed that 52 strains (37%) of aEPEC were resistant to one or more agents; only 10 strains (7%) exhibited resistance to more than three agents. Strains isolated from swine or food exhibited a wider variety of resistance phenotypes than bovine or human strains. MLVA assigned the aEPEC isolates from cattle and patients to Cluster 2, distinct from aEPEC from other sources. Hog yards may be a larger source of drug-resistant strains than are cattle ranches. MLVA suggests that human diarrhoeagenic aEPEC are derived from cattle and are distinct from strains carried by healthy people and other animals. Cattle appear to be reservoirs of human diarrhoeagenic aEPEC. © 2016 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

  19. Internalin profiling and multilocus sequence typing suggest four Listeria innocua subgroups with different evolutionary distances from Listeria monocytogenes

    OpenAIRE

    Chen, Jianshun; Chen, Qiaomiao; Jiang, Lingli; Cheng, Changyong; Bai, Fan; Wang, Jun; Mo, Fan; Fang, Weihuan

    2010-01-01

    Abstract Background Ecological, biochemical and genetic resemblance as well as clear differences of virulence between L. monocytogenes and L. innocua make this bacterial clade attractive as a model to examine evolution of pathogenicity. This study was attempted to examine the population structure of L. innocua and the microevolution in the L. innocua-L. monocytogenes clade via profiling of 37 internalin genes and multilocus sequence typing based on the sequences of 9 unlinked genes gyrB, sigB...

  20. Multilocus genotyping of Giardia duodenalis in captive non-human primates in Sichuan and Guizhou provinces, Southwestern China.

    Directory of Open Access Journals (Sweden)

    Zhijun Zhong

    Full Text Available Giardia duodenalis is a common human and animal pathogen. It has been increasingly reported in wild and captive non-human primates (NHPs in recent years. However, multilocus genotyping information for G. duodenalis infecting NHPs in southwestern China is limited. In the present study, the prevalence and multilocus genotypes (MLGs of G. duodenalis in captive NHPs in southwestern China were determined. We examined 207 fecal samples from NHPs in Sichuan and Guizhou provinces, and 16 specimens were positive for G. duodenalis. The overall infection rate was 7.7%, and only assemblage B was identified. G. duodenalis was detect positive in northern white-cheeked gibbon (14/36, 38.9%, crab-eating macaque (1/60, 1.7% and rhesus macaques (1/101, 0.9%. Multilocus sequence typing based on beta-giardin (bg, triose phosphate isomerase (tpi and glutamate dehydrogenase (gdh revealed nine different assemblage B MLGs (five known genotypes and four novel genotypes. Based on a phylogenetic analysis, one potentially zoonotic genotype of MLG SW7 was identified in a northern white-cheeked gibbon. A high degree of genetic diversity within assemblage B was observed in captive northern white-cheeked gibbons in Southwestern China, including a potentially zoonotic genotype, MLG SW7. To the best of our knowledge, this is the first report using a MLGs approach to identify G. duodenalis in captive NHPs in Southwestern China.

  1. Phenotypic variation in sexually and asexually recruited individuals of the Baltic Sea endemic macroalga Fucus radicans: in the field and after growth in a common-garden

    Directory of Open Access Journals (Sweden)

    Johannesson Kerstin

    2012-02-01

    Full Text Available Abstract Background Most species of brown macroalgae recruit exclusively sexually. However, Fucus radicans, a dominant species in the northern Baltic Sea, recruits new attached thalli both sexually and asexually. The level of asexual recruitment varies among populations from complete sexual recruitment to almost (> 90% monoclonal populations. If phenotypic traits have substantial inherited variation, low levels of sexual activity will decrease population variation in these traits, which may affect function and resilience of the species. We assessed the level of inherited variation in nine phenotypic traits by comparing variation within and among three monoclonal groups and one group of unique multilocus genotypes (MLGs sampled in the wild. Results Of the nine phenotypic traits, recovery after freezing, recovery after desiccation, and phlorotannin content showed substantial inherited variation, that is, phenotypic variation in these traits were to a large extend genetically determined. In contrast, variation in six other phenotypic traits (growth rate, palatability to isopod grazers, thallus width, distance between dichotomies, water content after desiccation and photochemical yield under ambient conditions did not show significant signals of genetic variation at the power of analyses used in the study. Averaged over all nine traits, phenotypic variation within monoclonal groups was only 68% of the variation within the group of different MLGs showing that genotype diversity does affect the overall level of phenotypic variation in this species. Conclusions Our result indicates that, in general, phenotypic diversity in populations of Fucus radicans increases with increased multilocus genotype (MLG diversity, but effects are specific for individual traits. In the light of Fucus radicans being a foundation species of the northern Baltic Sea, we propose that increased MLG diversity (leading to increased trait variation will promote ecosystem function

  2. Phenotypic variation in sexually and asexually recruited individuals of the Baltic Sea endemic macroalga Fucus radicans: in the field and after growth in a common-garden.

    Science.gov (United States)

    Johannesson, Kerstin; Forslund, Helena; Capetillo, Nastassja Astrand; Kautsky, Lena; Johansson, Daniel; Pereyra, Ricardo T; Råberg, Sonja

    2012-02-22

    Most species of brown macroalgae recruit exclusively sexually. However, Fucus radicans, a dominant species in the northern Baltic Sea, recruits new attached thalli both sexually and asexually. The level of asexual recruitment varies among populations from complete sexual recruitment to almost (> 90%) monoclonal populations. If phenotypic traits have substantial inherited variation, low levels of sexual activity will decrease population variation in these traits, which may affect function and resilience of the species. We assessed the level of inherited variation in nine phenotypic traits by comparing variation within and among three monoclonal groups and one group of unique multilocus genotypes (MLGs) sampled in the wild. Of the nine phenotypic traits, recovery after freezing, recovery after desiccation, and phlorotannin content showed substantial inherited variation, that is, phenotypic variation in these traits were to a large extend genetically determined. In contrast, variation in six other phenotypic traits (growth rate, palatability to isopod grazers, thallus width, distance between dichotomies, water content after desiccation and photochemical yield under ambient conditions) did not show significant signals of genetic variation at the power of analyses used in the study. Averaged over all nine traits, phenotypic variation within monoclonal groups was only 68% of the variation within the group of different MLGs showing that genotype diversity does affect the overall level of phenotypic variation in this species. Our result indicates that, in general, phenotypic diversity in populations of Fucus radicans increases with increased multilocus genotype (MLG) diversity, but effects are specific for individual traits. In the light of Fucus radicans being a foundation species of the northern Baltic Sea, we propose that increased MLG diversity (leading to increased trait variation) will promote ecosystem function and resilience in areas where F. radicans is common

  3. Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae: Insights from RAPD and ISSR Variation

    Directory of Open Access Journals (Sweden)

    Pei-Luen Lu

    2016-08-01

    Full Text Available The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis, endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD and inter simple sequence repeats (ISSR to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon’s index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested.

  4. Genetic diversity and population differentiation of chestnut blight fungus, Cryphonectria parasitica, in China as revealed by RAPD.

    Science.gov (United States)

    Yan, Boqian; Li, Zuozhou; Huang, Hongwen; Qin, Ling

    2007-06-01

    Seventeen Cryphonectria parasitica populations sampled from six regions in China were investigated using RAPD. Across all 169 isolates from the 17 populations evaluated, 52 of the 71 markers (73%) were polymorphic, total genetic diversity (h) was 0.1463, and Shannon's index was 0.2312. Diversity within populations accounted for 74% of total genetic diversity, and genetic differentiation among populations was 0.26 (G (ST) = 0.26). Gene flow was 1.4 among the populations; higher gene flow was found among populations within regions and among regions [N (m) (G (SR)) = 2.8 and N (m) (G (RT)) = 3.5]. The unweighted pair group mean analysis (UPGMA) dendrogram revealed two distinct clusters: the northern China group and the southern China group. The spatial autocorrelation analysis revealed that the variation at most loci was randomly distributed and lacked spatial structure, but several loci and closer distances were spatially structured. Human activity and habitat could also be important factors affecting genetic structure among C. parasitica populations in China. Genetic diversity was highest in Southwest China, descending in an orderly fashion to Northeast China. This pattern indicated that Southwest China might be the center of origin of C. parasitica in China. The present study provides useful information for understanding the origin and spread of chestnut blight fungus in China and valuable data for formulating relevant strategies for controlling the disease in China.

  5. IDENTIFICAÇÃO DE MARCADOR RAPD E SCAR RELACIONADOS AO CARACTERE FLORESCIMENTO PRECOCE EM Eucalyptus grandis

    Directory of Open Access Journals (Sweden)

    Douglas Silva Domingues

    2006-08-01

    Full Text Available No melhoramento genético de eucalipto, existem ainda poucos instrumentos disponíveis para acelerar a seleção de genótipos superiores, e uma das principais estratégias sugeridas para se acelerar este processo é a identificação de marcadores moleculares ligados a caracteres de interesse. Foram avaliados 81 marcadores RAPD em uma progênie F1 de Eucalyptus grandis W. Hill ex Maiden segregante para o caractere florescimento precoce utilizando-se a técnica de Bulked Segregant Analysis (BSA. Dentre esses marcadores, um se mostrou relacionado ao caractere, sendo então convertido em Sequence Characterized Amplified Region (SCAR, avaliado em cada indivíduo da progênie e validado em outras progênies que apresentam o caractere. O SCAR mostrou-se informativo na progênie que apresenta um dos parentais como doador do fragmento polimórfico, com eficiência de 60%. Esses resultados descrevem o primeiro marcador SCAR desenvolvido para eucalipto e confirmam a utilidade da técnica de BSA como ferramenta molecular no melhoramento genético florestal e que poderia ser empregada para localização de marcadores ligados a diferentes caracteres silviculturais.

  6. Micropropagation of annatto (Bixa orellana L.) from mature tree and assessment of genetic fidelity of micropropagated plants with RAPD markers.

    Science.gov (United States)

    Siril, E A; Joseph, Nisha

    2013-01-01

    An in vitro propagation technique based on axillary bud proliferation was developed for the first time to mature annatto (Bixa orellana L.) tree. Nodal segments cultured on Murashige and Skoog (MS) medium supplemented with 1.0 μM benzyl adenine (BA) and tender coconut water (10 %) showed significantly high (P < 0.05) explant response (67.0 %), development of elongated shoots (3.36), shoot buds (8.9) and shoot elongation (3.53 cm). Cytokinins like zeatin, isopentenyl adenine (2-iP), kinetin, or thidiazuron (TDZ) were inferior to BA to induce multiple shoots. Seasonal variations significantly affected the in vitro response of nodal explants. In vitro rooting experiments have showed 55.6 % rooting on MS medium containing 15 μM indole-3-butyric acid (IBA). Alternatively, in vitro raised shoots were rooted (61.1 %) ex vitro, by 10 mM indole-3-butyric acid (IBA) for 30 s. The results of the RAPD marker system revealed the genetic stability among the micropropagated plants. The present protocol in brief, can be used for the clonal propagation of the superior genotype and preservation of germplasm.

  7. [RAPD analysis of the intraspecific and interspecific variation and phylogenetic relationships of Aegilops L. species with the U genome].

    Science.gov (United States)

    Goriunova, S V; Chikida, N N; Kochieva, E Z

    2010-07-01

    RAPD analysis was used to study the genetic variation and phylogenetic relationships of polyploid Aegilops species with the U genome. In total, 115 DNA samples of eight polyploid species containing the U genome and the diploid species Ae. umbellulata (U) were examined. Substantial interspecific polymorphism was observed for the majority of the polyploid species with the U genome (interspecific differences, 0.01-0,2; proportion of polymorphic loci, 56.6-88.2%). Aegilops triuncialis was identified as the only alloploid species with low interspecific polymorphism (interspecific differences, 0-0.01, P = 50%) in the U-genome group. The U-genome Aegilops species proved to be separated from other species of the genus. The phylogenetic relationships were established for the U-genome species. The greatest separation within the U-genome group was observed for the US-genome species Ae. kotschyi and Ae. variabilis. The tetraploid species Ae. triaristata and Ae. columnaris, which had the UX genome, and the hexaploid species Ae. recta (UXN) were found to be related to each other and separate from the UM-genome species. A similarity was observed between the U M-genome species Ae. ovata and Ae. biuncialis, which had the UM genome, and the ancestral diploid U-genome species Ae. umbellulata. The UC-genome species Ae. triuncialis was rather separate and slightly similar to the UX-genome species.

  8. How does Trypanosoma equiperdum fit into the Trypanozoon group? A cluster analysis by RAPD and multiplex-endonuclease genotyping approach.

    Science.gov (United States)

    Claes, F; Agbo, E C; Radwanska, M; Te Pas, M F W; Baltz, T; De Waal, D T; Goddeeris, B M; Claassen, E; Büscher, P

    2003-05-01

    The pathogenic trypanosomes Trypanosoma equiperdum, T. evansi as well as T. brucei are morphologically identical. In horses, these parasites are considered to cause respectively dourine, surra and nagana. Previous molecular attempts to differentiate these species were not successful for T. evansi and T. equiperdum; only T. b. brucei could be differentiated to a certain extent. In this study we analysed 10 T. equiperdum, 8 T. evansi and 4 T. b. brucei using Random Amplified Polymorphic DNA (RAPD) and multiplex-endonuclease fingerprinting, a modified AFLP technique. The results obtained confirm the homogeneity of the T. evansi group tested. The T. b. brucei clustered out in a heterogenous group. For T. equiperdum the situation is more complex: 8 out of 10 T. equiperdum clustered together with the T. evansi group, while 2 T. equiperdum strains were more related to T. b. brucei. Hence, 2 hypotheses can be formulated: (1) only 2 T. equiperdum strains are genuine T. equiperdum causing dourine; all other T. equiperdum strains actually are T. evansi causing surra or (2) T. equiperdum does not exist at all. In that case, the different clinical outcome of horse infections with T. evansi or T. b. brucei is primarily related to the host immune response.

  9. ASSESSMENTS OF GENETIC DIVERSITY IN COUNTRY BEAN (Lablab purpureus L. USING RAPD MARKER AGAINST PHOTO-INSENSITIVITY

    Directory of Open Access Journals (Sweden)

    BISWAS MD. SANAULLAH

    2012-12-01

    Full Text Available RAPD marker was used to evaluate genetic relationships among 11 genotypes of country bean, including first three genotypes were photo-insensitive and the rests were sensitive. The genotypes were grouped into two major clusters where photo-insensitive genotypes remain in cluster I and sensitive genotypes remain in cluster II. A total of 26 bands were detected, of which 57.69% were polymorphic and the remaining were monomorphic across all genotypes. A highest level of genetic distance was observed between CB04 and CB06 while the lowest level of genetic distance showed between CB01 and CB03. The highest similarity index between the genotypes CB01 and CB03 indicated less divergence between them. Low similarity indices were observed between CB04 and CB06, which indicated more divergence. Crossing between the genotypes with low similarity coefficient will manifest high heterosis. The identified genetically distinct cultivars could be potentially important source of germplasm for further improvement of country bean.

  10. Differentiation of Xylella fastidiosa strains via multilocus sequence analysis of environmentally mediated genes (MLSA-E).

    Science.gov (United States)

    Parker, Jennifer K; Havird, Justin C; De La Fuente, Leonardo

    2012-03-01

    Isolates of the plant pathogen Xylella fastidiosa are genetically very similar, but studies on their biological traits have indicated differences in virulence and infection symptomatology. Taxonomic analyses have identified several subspecies, and phylogenetic analyses of housekeeping genes have shown broad host-based genetic differences; however, results are still inconclusive for genetic differentiation of isolates within subspecies. This study employs multilocus sequence analysis of environmentally mediated genes (MLSA-E; genes influenced by environmental factors) to investigate X. fastidiosa relationships and differentiate isolates with low genetic variability. Potential environmentally mediated genes, including host colonization and survival genes related to infection establishment, were identified a priori. The ratio of the rate of nonsynonymous substitutions to the rate of synonymous substitutions (dN/dS) was calculated to select genes that may be under increased positive selection compared to previously studied housekeeping genes. Nine genes were sequenced from 54 X. fastidiosa isolates infecting different host plants across the United States. Results of maximum likelihood (ML) and Bayesian phylogenetic (BP) analyses are in agreement with known X. fastidiosa subspecies clades but show novel within-subspecies differentiation, including geographic differentiation, and provide additional information regarding host-based isolate variation and specificity. dN/dS ratios of environmentally mediated genes, though fastidiosa isolates. Discovering the genetic relationships between X. fastidiosa isolates will provide new insights into the epidemiology of populations of X. fastidiosa, allowing improved disease management in economically important crops.

  11. Multilocus adaptation associated with heat resistance in reef-building corals.

    Science.gov (United States)

    Bay, Rachael A; Palumbi, Stephen R

    2014-12-15

    The evolution of tolerance to future climate change depends on the standing stock of genetic variation for resistance to climate-related impacts, but genes contributing to climate tolerance in wild populations are poorly described in number and effect. Physiology and gene expression patterns have shown that corals living in naturally high-temperature microclimates are more resistant to bleaching because of both acclimation and fixed effects, including adaptation. To search for potential genetic correlates of these fixed effects, we genotyped 15,399 single nucleotide polymorphisms (SNPs) in 23 individual tabletop corals, Acropora hyacinthus, within a natural temperature mosaic in backreef lagoons on Ofu Island, American Samoa. Despite overall lack of population substructure, we identified 114 highly divergent SNPs as candidates for environmental selection, via multiple stringent outlier tests, and correlations with temperature. Corals from the warmest reef location had higher minor allele frequencies across these candidate SNPs, a pattern not seen for noncandidate loci. Furthermore, within backreef pools, colonies in the warmest microclimates had a higher number and frequency of alternative alleles at candidate loci. These data suggest mild selection for alternate alleles at many loci in these corals during high heat episodes and possible maintenance of extensive polymorphism through multilocus balancing selection in a heterogeneous environment. In this case, a natural population harbors a reservoir of alleles preadapted to high temperatures, suggesting potential for future evolutionary response to climate change. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. [Multilocus sequence typing analysis of 47 Campylobacter jejuni strains isolated from poultry in Hubei province].

    Science.gov (United States)

    Dong, Jun; Han, Mei; Zhou, Kang; Luo, Qingping; Shao, Huabin; Zhang, Tengfei

    2016-01-04

    To study the epidemiological and molecular characteristics of Campylobacter jejuni in poultry in Hubei province, we used multilocus sequence typing method to classify 47 local C. jejuni strains. Genomic DNA of each isolated strain was extract, seven housekeeping genes including aspA, g1nA, g1tA, glyA, pgm, tkt and uncA were amplified by PCR and sequenced, and then the sequences of genes were analyzed using MLST database. There were a total of 38 sequence types and 10 clonal complexes, and ST353 and ST464 complexes were the largest amount of the population of C. jejuni analyzed, of which 2 new allelic profile and 25 new sequence types were found. Phylogenetic tree shows that sequence types from different types of poultry and different regions were different. Forty-seven C. jejuni strains isolated from poultry in Hubei were analyzed using MLST and showed abundant genetic diversity, it will provide scientific data to the epidemiological investigation of C. jejuni in Hubei, China.

  13. Multilocus sequence typing and antimicrobial resistance of Campylobacter jejuni isolated from dairy calves in Austria

    Directory of Open Access Journals (Sweden)

    Daniela eKlein-Jöbstl

    2016-02-01

    Full Text Available Human campylobacteriosis is primarily associated with poultry but also cattle. In this study, 55 Campylobacter jejuni strains isolated from 382 dairy calves’ feces were differentiated by multilocus sequence typing and tested for antimicrobial resistance. The most prevalent sequence type (ST was ST883 (20.0%, followed by ST48 (14.5%, and ST50 (9.1%. In contrast to ST48 and ST50, ST883 has rarely been described in cattle previously. Furthermore, risk factor analysis was performed for the presence of the most prevalent STs in these calves. Multiple regression analysis revealed that the type of farm (organic versus conventional and calf housing (place, and individual versus group were identified as significantly (p<0.05 associated with the presence of ST883 in calves, and ST50 was associated with calf diarrhea. Antimicrobial resistance was detected in 58.2% of the isolates. Most of the resistant isolates (81.3% were resistant to more than one antimicrobial. Most frequently, resistance to ciprofloxacin (49.1%, followed by nalidixic acid with (42.8%, and tetracycline (14.5% was observed. The results of the present study support the hypothesis that dairy calves may serve as a potential reservoir for Campylobacter jejuni and pose a risk for transmission, including antimicrobial resistant isolates to the environment and to humans.

  14. Multilocus Sequence Typing of Strains of Bacterial Spot of Lettuce Collected in the United States.

    Science.gov (United States)

    Fayette, Joubert; Raid, Richard; Roberts, Pamela D; Jones, Jeffrey B; Pernezny, Ken; Bull, Carolee T; Goss, Erica M

    2016-11-01

    Studies on genetic diversity and recombination in bacterial pathogens are providing a better understanding of the mechanisms shaping bacterial diversity, which can affect disease control. Xanthomonas campestris pv. vitians, causal agent of bacterial leaf spot of lettuce, is a threat to the worldwide lettuce industry. We examined the genetic variation within a sample of 83 strains from California, Florida, and Ohio using multilocus sequence typing of six housekeeping genes, totaling 2.7 kb. Additionally, polymorphism in two virulence-related genes, hrpB2 and a putative glycosyl hydrolase, were examined. Based on housekeeping genes, we found three genetic groups of strains that were all able to induce the disease. These included strains collected from weeds and irrigation water that had haplotypes identical to strains from diseased lettuce. High linkage disequilibrium across the sequenced loci indicates that the pathogen is predominantly clonal but recombination has contributed to the observed sequence variation. Although there was significant genetic variation in X. campestris pv. vitians within and among sampled states, identical haplotypes were observed across all three states. This finding suggests that seedborne inoculum may contribute to the diversity of X. campestris pv. vitians in the United States. Knowledge of the genetic structure of the pathogen may be used for developing resistant lettuce varieties.

  15. Variation in Campylobacter Multilocus Sequence Typing Subtypes from Chickens as Detected on Three Plating Media.

    Science.gov (United States)

    Berrang, M E; Ladely, S R; Meinersmann, R J; Line, J E; Oakley, B B; Cox, N A

    2016-11-01

    The objective of this study was to compare subtypes of Campylobacter jejuni and Campylobacter coli detected on three selective Campylobacter plating media to determine whether each medium selected for different subtypes. Fifty ceca and 50 carcasses (representing 50 flocks) were collected from the evisceration line in a commercial broiler processing plant. Campylobacter was cultured and isolated from cecal contents and carcass rinses on Campy-Cefex, Campy Line, and RF Campylobacter jejuni/coli agars. When a positive result was obtained with all three media, one colony of the most prevalent morphology on each medium was selected for further analysis by full genome sequencing and multilocus sequence typing. Sequence types were assigned according to PubMLST. A total of 49 samples were positive for Campylobacter on all three media. Forty samples contained only C. jejuni , three had only C. coli , and both species were detected in six samples. From 71% of samples, Campylobacter isolates of the same sequence type were recovered on all three media. From 81.6% of samples, isolates were all from the same clonal complex. From significantly fewer samples (26%, P Campylobacter jejuni/coli . From one sample, three sequence types were detected. In most cases, all three plating media allowed detection of the same type of Campylobacter from complex naturally contaminated chicken samples.

  16. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture.

    Science.gov (United States)

    Wang, Wei-Kuang; Ho, Chuan-Wen; Hung, Kuo-Hsiang; Wang, Kuo-Hsiung; Huang, Chi-Chun; Araki, Hitoshi; Hwang, Chi-Chuan; Hsu, Tsai-Wen; Osada, Naoki; Chiang, Tzen-Yuh

    2010-10-01

    • Outcrossing Arabidopsis species that diverged from their inbreeding relative Arabidopsis thaliana 5 million yr ago and display a biogeographical pattern of interspecific sympatry vs intraspecific allopatry provides an ideal model for studying impacts of gene introgression and polyploidization on species diversification. • Flow cytometry analyses detected ploidy polymorphisms of 2× and 4× in Arabidopsis lyrata ssp. kamchatica of Taiwan. Genomic divergence between species/subspecies was estimated based on 98 randomly chosen nuclear genes. Multilocus analyses revealed a mosaic genome in diploid A. l. kamchatica composed of Arabidopsis halleri-like and A. lyrata-like alleles. • Coalescent analyses suggest that the segregation of ancestral polymorphisms alone cannot explain the high inconsistency between gene trees across loci, and that gene introgression via diploid A. l. kamchatica likely distorts the molecular phylogenies of Arabidopsis species. However, not all genes migrated across species freely. Gene ontology analyses suggested that some nonmigrating genes were constrained by natural selection. • High levels of estimated ancestral polymorphisms between A. halleri and A. lyrata suggest that gene flow between these species has not completely ceased since their initial isolation. Polymorphism data of extant populations also imply recent gene flow between the species. Our study reveals that interspecific gene flow affects the genome evolution in Arabidopsis. © The Authors (2010). Journal compilation © New Phytologist Trust (2010).

  17. Mathematical limits of multilocus models: the genetic transmission of bipolar disorder.

    Science.gov (United States)

    Craddock, N; Khodel, V; Van Eerdewegh, P; Reich, T

    1995-09-01

    We describe a simple, graphical method for determining plausible modes of inheritance for complex traits and apply this to bipolar disorder. The constraints that allele frequencies and penetrances lie in the interval 0-1 impose limits on recurrence risks, KR, in relatives of an affected proband for a given population prevalence, KP. We have investigated these limits for KR in three classes of relatives (MZ co-twin, sibling, and parent/offspring) for the general single-locus model and for two types of multilocus models: heterogeneity and multiplicative. In our models we have assumed Hardy-Weinberg equilibrium, an all-or-none trait, absence of nongenetic resemblance between relatives, and negligible mutation at the disease loci. Although the true values of KP and the KR's are only approximately known, observed population and family data for bipolar disorder are inconsistent with a single-locus model or with any heterogeneity model. In contrast, multiplicative models involving three or more loci are consistent with observed data and, thus, represent plausible models for the inheritance of bipolar disorders. Studies to determine the genetic basis of most bipolar disorder should use methods capable of detecting interacting oligogenes.

  18. Multilocus phylogeny and MALDI-TOF analysis of the plant pathogenic species Alternaria dauci and relatives

    DEFF Research Database (Denmark)

    Brun, Sophie; Madrid, Hugo; Gerrits Van Den Ende, Bert

    2013-01-01

    The genus Alternaria includes numerous phytopathogenic species, many of which are economically relevant. Traditionally, identification has been based on morphology, but is often hampered by the tendency of some strains to become sterile in culture and by the existence of species-complexes of morp......The genus Alternaria includes numerous phytopathogenic species, many of which are economically relevant. Traditionally, identification has been based on morphology, but is often hampered by the tendency of some strains to become sterile in culture and by the existence of species......-complexes of morphologically similar taxa. This study aimed to assess if strains of four closely-related plant pathogens, i.e., accurately Alternaria dauci (ten strains), Alternaria porri (six), Alternaria solani (ten), and Alternaria tomatophila (ten) could be identified using multilocus phylogenetic analysis and Matrix......-Assisted Laser Desorption Ionisation Time of Flight (MALDI-TOF) profiling of proteins. Phylogenetic analyses were performed on three loci, i.e., the internal transcribed spacer (ITS) region of rRNA, and the glyceraldehyde-3-phosphate dehydrogenase (gpd) and Alternaria major antigen (Alt a 1) genes. Phylogenetic...

  19. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples.

    Science.gov (United States)

    Zolfo, Moreno; Tett, Adrian; Jousson, Olivier; Donati, Claudio; Segata, Nicola

    2017-01-25

    Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Diversification of the silverspot butterflies (Nymphalidae) in the Neotropics inferred from multi-locus DNA sequences.

    Science.gov (United States)

    Massardo, Darli; Fornel, Rodrigo; Kronforst, Marcus; Gonçalves, Gislene Lopes; Moreira, Gilson Rudinei Pires

    2015-01-01

    The tribe Heliconiini (Lepidoptera: Nymphalidae) is a diverse group of butterflies distributed throughout the Neotropics, which has been studied extensively, in particular the genus Heliconius. However, most of the other lineages, such as Dione, which are less diverse and considered basal within the group, have received little attention. Basic information, such as species limits and geographical distributions remain uncertain for this genus. Here we used multilocus DNA sequence data and the geographical distribution analysis across the entire range of Dione in the Neotropical region in order to make inferences on the evolutionary history of this poorly explored lineage. Bayesian time-tree reconstruction allows inferring two major diversification events in this tribe around 25mya. Lineages thought to be ancient, such as Dione and Agraulis, are as recent as Heliconius. Dione formed a monophyletic clade, sister to the genus Agraulis. Dione juno, D. glycera and D. moneta were reciprocally monophyletic and formed genetic clusters, with the first two more close related than each other in relation to the third. Divergence time estimates support the hypothesis that speciation in Dione coincided with both the rise of Passifloraceae (the host plants) and the uplift of the Andes. Since the sister species D. glycera and D. moneta are specialized feeders on passion-vine lineages that are endemic to areas located either within or adjacent to the Andes, we inferred that they co-speciated with their host plants during this vicariant event. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Multilocus Sequence Typing of the Clinical Isolates of Salmonella Enterica Serovar Typhimurium in Tehran Hospitals

    Directory of Open Access Journals (Sweden)

    Reza Ranjbar

    2017-09-01

    Full Text Available Background: Salmonella enterica serovar Typhimurium is one of the most important serovars of Salmonella enterica and is associated with human salmonellosis worldwide. Many epidemiological studies have focused on the characteristics of Salmonella Typhimurium in many countries as well as in Asia. This study was conducted to investigate the genetic characteristics of Salmonella Typhimurium using multilocus sequence typing (MLST. Methods: Clinical samples (urine, blood, and stool were collected from patients, who were admitted to 2 hospitals in Tehran between April and September, 2015. Salmonella Typhimurium strains were identified by conventional standard biochemical and serological testing. The antibiotic susceptibility patterns of the Salmonella Typhimurium isolates against 16 antibiotics was determined using the disk diffusion assay. The clonal relationship between the strains of Salmonella Typhimurium was analyzed using MLST. Results: Among the 68 Salmonella isolates, 31% (n=21 were Salmonella Typhimurium. Of the total 21 Salmonella Typhimurium isolates, 76% (n=16 were multidrug-resistant and showed resistance to 3 or more antibiotic families. The Salmonella Typhimurium isolates were assigned to 2 sequence types: ST19 and ST328. ST19 was more common (86%. Both sequence types were further assigned to 1 eBURST group. Conclusion: This is the first study of its kind in Iran to determine the sequence types of the clinical isolates of Salmonella Typhimurium in Tehran hospitals using MLST. ST19 was detected as the major sequence type of Salmonella Typhimurium.

  2. A multilocus candidate approach identifies ACE and HIF1A as susceptibility genes for cellulite.

    Science.gov (United States)

    Emanuele, E; Bertona, M; Geroldi, D

    2010-08-01

    Cellulite is a common complex cosmetic problem for many post-adolescent women characterised by relief alterations of the skin surface, which give the skin an orange-peel appearance. Although genetic factors have been suggested to play a role in the development of cellulite, the genetic background of this condition remains unclear. We therefore conducted a multi-locus genetic study examining the potential associations of candidate gene variants in oestrogen receptors, endothelial function/adipose tissue hypoxia, lipid metabolism, extracellular matrix homeostasis, inflammation and adipose tissue biology, with the risk of cellulite. Using a case-control study of 200 lean women with cellulite and 200 age- and BMI-matched controls (grade 0 according to Nurnberger-Muller scale), we examined the association of cellulite with 25 polymorphisms in 15 candidate genes. Two of the 25 polymorphisms were significantly associated with cellulite at the P cellulite were 1.19 (95% CI: 1.10-1.51; P cellulite, may provide novel information on the pathophysiology of this common cosmetic problem, and offer a topic for research for novel beautification interventions.

  3. Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae, a Dominant Alpine Species in Taiwan.

    Directory of Open Access Journals (Sweden)

    Chi-Chun Huang

    Full Text Available Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

  4. Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan.

    Science.gov (United States)

    Huang, Chi-Chun; Hsu, Tsai-Wen; Wang, Hao-Ven; Liu, Zin-Huang; Chen, Yi-Yen; Chiu, Chi-Te; Huang, Chao-Li; Hung, Kuo-Hsiang; Chiang, Tzen-Yuh

    2016-01-01

    Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.

  5. mlstdbNet – distributed multi-locus sequence typing (MLST databases

    Directory of Open Access Journals (Sweden)

    Maiden Martin CJ

    2004-07-01

    Full Text Available Abstract Background Multi-locus sequence typing (MLST is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet. Results The software enables multiple isolate databases to query a single profiles database that contains allelic profile and sequence definitions. This separation enables isolate databases to be established by individual laboratories, each customised to the needs of the particular project and with appropriate access restrictions, while maintaining the benefits of a single definitive source of profile and sequence information. Databases are described by an XML file that is parsed by a Perl CGI script. The software offers a large number of ways to query the databases and to further break down and export the results generated. Additional features can be enabled by installing third-party (freely available tools. Conclusion Development of a distributed structure for MLST databases offers scalability and flexibility, allowing participating centres to maintain ownership of their own data, without introducing duplication and data integrity issues.

  6. Multilocus Sequence Typing of Borrelia burgdorferi Suggests Existence of Lineages with Differential Pathogenic Properties in Humans

    Science.gov (United States)

    Hanincova, Klara; Mukherjee, Priyanka; Ogden, Nicholas H.; Margos, Gabriele; Wormser, Gary P.; Reed, Kurt D.; Meece, Jennifer K.; Vandermause, Mary F.; Schwartz, Ira

    2013-01-01

    The clinical manifestations of Lyme disease, caused by Borrelia burgdorferi, vary considerably in different patients, possibly due to infection by strains with varying pathogenicity. Both rRNA intergenic spacer and ospC typing methods have proven to be useful tools for categorizing B. burgdorferi strains that vary in their tendency to disseminate in humans. Neither method, however, is suitable for inferring intraspecific relationships among strains that are important for understanding the evolution of pathogenicity and the geographic spread of disease. In this study, multilocus sequence typing (MLST) was employed to investigate the population structure of B. burgdorferi recovered from human Lyme disease patients. A total of 146 clinical isolates from patients in New York and Wisconsin were divided into 53 sequence types (STs). A goeBURST analysis, that also included previously published STs from the northeastern and upper Midwestern US and adjoining areas of Canada, identified 11 major and 3 minor clonal complexes, as well as 14 singletons. The data revealed that patients from New York and Wisconsin were infected with two distinct, but genetically and phylogenetically closely related, populations of B. burgdorferi. Importantly, the data suggest the existence of B. burgdorferi lineages with differential capabilities for dissemination in humans. Interestingly, the data also indicate that MLST is better able to predict the outcome of localized or disseminated infection than is ospC typing. PMID:24069170

  7. Multilocus coalescent species delimitation to evaluate traditionally defined morphotypes in Hydrangea sect. Asperae (Hydrangeaceae).

    Science.gov (United States)

    De Smet, Yannick; De Clerck, Olivier; Uemachi, Tatsuya; Granados Mendoza, Carolina; Wanke, Stefan; Goetghebeur, Paul; Samain, Marie-Stéphanie

    2017-09-01

    The number of species recognized in section Asperae of the flowering plant genus Hydrangea differs widely between subsequent revisions. This variation is largely centered around the H. aspera species complex, with numbers of recognized species varying from one to nearly a dozen. Despite indications of molecular variation in this complex, no sequence-based species delimitation methods have been employed to evaluate the primarily morphology-based species boundaries. In the present study, a multi-locus coalescent-based approach to species delimitation is employed in order to identify separate evolutionary lines within H. sect. Asperae, using four chloroplast and four nuclear molecular markers. Eight lineages were recovered within the focal group, of which five correspond with named morphotypes. The other three lineages illustrate types of conflict between molecular species delimitation and traditional morphology-based taxonomy. One molecular lineage comprises two named morphotypes, which possibly diverged recently enough to not have developed sufficient molecular divergence. A second conflict is found in H. strigosa. This morphotype is recovered as a separate lineage when occurring in geographic isolation, but when occurring in sympatry with two other morphotypes (H. aspera and H. robusta), the coalescent species delimitation lumps these taxa into a single putative species. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Cephalothrix gen. nov. (Cyanobacteria): towards an intraspecific phylogenetic evaluation by multilocus analyses.

    Science.gov (United States)

    da Silva Malone, Camila Francieli; Rigonato, Janaína; Laughinghouse, Haywood Dail; Schmidt, Éder Carlos; Bouzon, Zenilda Laurita; Wilmotte, Annick; Fiore, Marli Fátima; Sant'Anna, Célia Leite

    2015-09-01

    For more than a decade, the taxonomy of the Phormidiaceae has been problematic, since morphologically similar organisms represent phylogenetically distinct entities. Based on 16S rRNA gene sequence analyses, the polyphyletic genus Phormidium and other gas-vacuolated oscillatorioids appear scattered throughout the cyanobacterial tree of life. Recently, several studies have focused on understanding the oscillatorioid taxa at the generic level. At the specific level, few studies have characterized cyanobacterial strains using combined datasets (morphology, ultrastructure and molecular multilocus analyses). Using a multifaceted approach, we propose a new, well-defined genus, Cephalothrix gen. nov., by analysing seven filamentous strains that are morphologically 'intermediate' between gas-vacuolated taxa and Phormidium. Furthermore, we characterize two novel species: Cephalothrix komarekiana sp. nov. (strains CCIBt 3277, CCIBt 3279, CCIBt 3523, CCALA 155, SAG 75.79 and UTEX 1580) and Cephalothrix lacustris sp. nov. (strain CCIBt 3261). The generic name and specific epithets are proposed under the provisions of the International Code of Nomenclature for Algae, Fungi, and Plants.

  9. Multi-locus sequence typing confirms the clonality of Trichomonas gallinae isolates circulating in European finches.

    Science.gov (United States)

    Ganas, Petra; Jaskulska, Barbara; Lawson, Becki; Zadravec, Marko; Hess, Michael; Bilic, Ivana

    2014-04-01

    In recent years, Trichomonas gallinae emerged as the causative agent of an infectious disease of passerine birds in Europe leading to epidemic mortality of especially greenfinches Chloris chloris and chaffinches Fringilla coelebs. After the appearance of finch trichomonosis in the UK and Fennoscandia, the disease spread to Central Europe. Finch trichomonosis first reached Austria and Slovenia in 2012. In the present study the genetic heterogeneity of T. gallinae isolates from incidents in Austria and Slovenia were investigated and compared with British isolates. For this purpose comparative sequence analyses of the four genomic loci ITS1-5.8S-ITS2, 18S rRNA, rpb1 and Fe-hydrogenase were performed. The results corroborate that one clonal T. gallinae strain caused the emerging infectious disease within passerine birds and that the disease is continuing to spread in Europe. The same clonal strain was also found in a columbid bird from Austria. Additionally, the present study demonstrates clearly the importance of multi-locus sequence typing for discrimination of circulating T. gallinae strains.

  10. Identification of Coxiella burnetii genotypes in Croatia using multi-locus VNTR analysis.

    Science.gov (United States)

    Račić, Ivana; Spičić, Silvio; Galov, Ana; Duvnjak, Sanja; Zdelar-Tuk, Maja; Vujnović, Anja; Habrun, Boris; Cvetnić, Zeljko

    2014-10-10

    Although Q fever affects humans and animals in Croatia, we are unaware of genotyping studies of Croatian strains of the causative pathogen Coxiella burnetii, which would greatly assist monitoring and control efforts. Here 3261 human and animal samples were screened for C. burnetii DNA by conventional PCR, and 335 (10.3%) were positive. Of these positive samples, 82 were genotyped at 17 loci using the relatively new method of multi-locus variable number tandem repeat analysis (MLVA). We identified 13 C. burnetii genotypes not previously reported anywhere in the world. Two of these 13 genotypes are typical of the continental part of Croatia and share more similarity with genotypes outside Croatia than with genotypes within the country. The remaining 11 novel genotypes are typical of the coastal part of Croatia and show more similarity to one another than to genotypes outside the country. Our findings shed new light on the phylogeny of C. burnetii strains and may help establish MLVA as a standard technique for Coxiella genotyping. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Molecular Epidemiology of Pasteurella multocida Circulating in India by Multilocus Sequence Typing.

    Science.gov (United States)

    Sarangi, L N; Thomas, P; Gupta, S K; Kumar, S; Viswas, K N; Singh, V P

    2016-04-01

    Multilocus sequence typing (MLST), a sequence-based typing method for bacterial pathogens, is currently the best method for long-term epidemiological study and to understand the population structure of the bacteria. This investigation was carried out to study the diversity of Pasteurella multocida isolates circulating in India. Ten different sequence types (ST) identified in this study are ST 122 from cattle, goat, mithun and pig; ST 50 from pig; ST 9 from cattle and sheep; ST 229 from cattle and goat; ST 71 and ST 277 from cattle; and ST 129, ST 280, ST 281 and ST 282 from avian species. Of these, ST 277, ST 280, ST 281 and ST 282 were identified for the first time. The analysis of results provides novel epidemiological information on the circulation of multiple STs across India. The majority of STs or their variants identified in this study have already been reported from different parts of the globe. This suggests that probably transboundary spread of strains across countries and continents has occurred across evolutionary time and is still happening. The isolation of ST 122 from small ruminants and pigs suggests that these species may be included in the preventive vaccination policy for effective control of haemorrhagic septicaemia in India. © 2014 Blackwell Verlag GmbH.

  12. [Multilocus sequence-typing for characterization of Moscow strains of Haemophilus influenzae type b].

    Science.gov (United States)

    Platonov, A E; Mironov, K O; Iatsyshina, S B; Koroleva, I S; Platonova, O V; Gushchin, A E; Shipulin, G A

    2003-01-01

    Haemophilius influenzae, type b (Hib) bacteria, were genotyped by multilocus sequence typing (MLST) using 5 loci (adk, fucK, mdh, pgi, recA). 42 Moscow Hib strains (including 38 isolates form cerebrospinal fluid of children, who had purulent meningitis in 1999-2001, and 4 strains isolated from healthy carriers of Hib), as well as 2 strains from Yekaterinburg were studied. In MLST a strain is characterized, by alleles and their combinations (an allele profile) referred to also as sequence-type (ST). 9 Sts were identified within the Russian Hib bacteria: ST-1 was found in 25 strains (57%), ST-12 was found in 8 strains (18%), ST-11 was found in 4 strains (9%) and ST-15 was found in 2 strains (4.5%); all other STs strains (13, 14, 16, 17, 51) were found in isolated cases (2.3%). A comparison of allelic profiles and of nucleotide sequences showed that 93% of Russian isolates, i.e. strain with ST-1, 11, 12, 13, 15 and 17, belong to one and the same clonal complex. 2 isolates from Norway and Sweden from among 7 foreign Hib strains studied up to now can be described as belonging to the same clonal complex; 5 Hib strains were different from the Russian ones.

  13. Intraspecific differentiation of Colletotrichum gloeosporioides sensu lato based on in silico multilocus PCR-RFLP fingerprinting.

    Science.gov (United States)

    Ramdeen, Stephen; Rampersad, Sephra N

    2013-02-01

    Colletotrichum gloeosporioides sensu lato is one of the most common and widely distributed plant pathogens in the world. Understanding fungal biodiversity is hinged on accurate identification and delimitation at the inter- and intraspecific levels. Sequences of the ITS1-5.8S-ITS2 region (ITS), β-tubulin (TUB), actin (ACT), and glyceraldehyde-3-phosphate dehydrogenase (GPDH) genes of 30 C. gloeosporioides sensu lato isolates, collected from anthracnose infected papaya fruits grown in the main production areas in Trinidad, were analyzed by in silico PCR-RFLP analysis with the aim of identifying which gene region(s) had the highest level of intraspecific polymorphism. Restriction site polymorphisms generated from 13 restriction enzymes enabled the identification of specific enzymes that were successful at intraspecific discrimination of the C. gloeosporioides isolates. Genetic distance values were reflective of the level of polymorphisms obtained for the four different gene regions. In both cases (calculated genetic distance and percentage of polymorphic loci from RFLP profiles), ACT and ITS gene regions had the highest level of restriction site polymorphisms and genetic diversity, GPDH and TUB had the lowest. Cluster analysis based on PCR-RFLP genetic distance data revealed sub-specific placement of the isolates which appeared to be gene-dependent. The implications of these findings are discussed relative to biodiversity monitoring and the need for multilocus, polyphasic investigations which must take into account the possibility of exaggerated estimates of genetic diversity.

  14. Mathematical limits of multilocus models: The genetic transmission of bipolar disorder

    Energy Technology Data Exchange (ETDEWEB)

    Craddock, N.; Khodel, V.; Van Eerdewegh, P.; Reich, T. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1995-09-01

    We describe a simple, graphical method for determining plausible modes of inheritance for complex traits and apply this to bipolar disorder. The constraints that allele frequencies and penetrances lie in the interval 0-1 impose limits on recurrence risks, K{sub R}, in relatives of an affected proband for a given population prevalence, K{sub p}. We have investigated these limits for K{sub R} in three classes of relatives (MZ co-twin, sibling, and parent/offspring) for the general single-locus model and for two types of multilocus models: heterogeneity and multiplicative. In our models we have assumed Hardy-Weinberg equilibrium, an all-or-none trait, absence of nongenetic resemblance between relatives, and negligible mutation at the disease loci. Although the true values of K{sub p} and the K{sub R}`s are only approximately known, observed population and family data for bipolar disorder are inconsistent with a single-locus model or with any heterogeneity model. In contrast, multiplicative models involving three or more loci are consistent with observed data and, thus, represent plausible models for the inheritance of bipolar disorder. Studies to determine the genetic basis of most bipolar disorder should use methods capable of detecting interacting oligogenes. 32 refs., 5 figs.

  15. Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

    Directory of Open Access Journals (Sweden)

    Lam Connie

    2012-05-01

    Full Text Available Abstract Background Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs analysis (MLVA to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. Results MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. Conclusions MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing.

  16. Multilocus sequence type profiles of Bacillus cereus isolates from infant formula in China.

    Science.gov (United States)

    Yang, Yong; Yu, Xiaofeng; Zhan, Li; Chen, Jiancai; Zhang, Yunyi; Zhang, Junyan; Chen, Honghu; Zhang, Zheng; Zhang, Yanjun; Lu, Yiyu; Mei, Lingling

    2017-04-01

    Bacillus cereus sensu stricto is an opportunistic foodborne pathogen. The multilocus sequence type (MLST) of 74 B. cereus isolated from 513 non-random infant formula in China was analyzed. Of 64 sequence types (STs) detected, 50 STs and 6 alleles were newly found in PubMLST database. All isolates except for one singleton (ST-1049), were classified into 7 clonal complexes (CC) by BURST (n-4), in which CC1 with core ancestral clone ST-26 was the largest group including 86% isolates, and CC2, 3, 9, 10 and 13 were first reported in China. MLST profiles of the isolates from 8 infant formula brands were compared. It was found the brands might be potentially tracked by the variety of STs, such as ST-1049 of singleton and ST-1062 of isolate from goat milk source, though they could not be easily tracked just by clonal complex types of the isolates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Antimicrobial susceptibility and multilocus sequence typing of Mycoplasma capricolum subsp. capricolum.

    Science.gov (United States)

    Tatay-Dualde, Juan; Prats-van der Ham, Miranda; de la Fe, Christian; Paterna, Ana; Sánchez, Antonio; Corrales, Juan Carlos; Contreras, Antonio; Tola, Sebastiana; Gómez-Martin, Ángel

    2017-01-01

    Mycoplasma capricolum subsp. capricolum is one of the causative agents of contagious agalactia (CA). Nevertheless, there is still a lack of information about its antimicrobial susceptibility and genetic characteristics. Therefore, the aim of this work was to study the antimicrobial and genetic variability of different Mycoplasma capricolum subsp. capricolum field isolates. For this purpose, the growth inhibition effect of 18 antimicrobials and a multilocus sequence typing (MLST) scheme based on five housekeeping genes (fusA, glpQ, gyrB, lepA and rpoB) were performed on 32 selected field isolates from Italy and Spain.The results showed a wide range of growth inhibitory effects for almost all the antimicrobials studied. Macrolides presented lower efficacy inhibiting Mcc growth than in previous works performed on other CA-causative mycoplasmas. Erythromycin was not able to inhibit the growth of any of the studied strains, contrary to doxycycline, which inhibited the growth of all of them from low concentrations. On the other hand, the study of the concatenated genes revealed a high genetic variability among the different Mcc isolates. Hence, these genetic variations were greater than the ones reported in prior works on other mycoplasma species.

  18. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    Directory of Open Access Journals (Sweden)

    Sergio Alvarez-Pérez

    Full Text Available The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA of four core housekeeping genes (rrs, gyrB, rpoB and rpoD. A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1; P. fluorescens, P. lutea and P. syringae (NG 2; and P. rhizosphaerae (NG 3. Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  19. Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny.

    Science.gov (United States)

    Zhou, Li-Wei; Cao, Yun; Wu, Sheng-Hua; Vlasák, Josef; Li, De-Wei; Li, Meng-Jie; Dai, Yu-Cheng

    2015-06-01

    Species of the Ganoderma lucidum complex are used in many types of health products. However, the taxonomy of this complex has long been chaotic, thus limiting its uses. In the present study, 32 collections of the complex from Asia, Europe and North America were analyzed from both morphological and molecular phylogenetic perspectives. The combined dataset, including an outgroup, comprised 33 ITS, 24 tef1α, 24 rpb1 and 21 rpb2 sequences, of which 19 ITS, 20 tef1α, 20 rpb1 and 17 rpb2 sequences were newly generated. A total of 13 species of the complex were recovered in the multilocus phylogeny. These 13 species were not strongly supported as a single monophyletic lineage, and were further grouped into three lineages that cannot be defined by their geographic distributions. Clade A comprised Ganoderma curtisii, Ganoderma flexipes, Ganoderma lingzhi, Ganoderma multipileum, Ganoderma resinaceum, Ganoderma sessile, Ganoderma sichuanense and Ganoderma tropicum, Clade B comprised G. lucidum, Ganoderma oregonense and Ganoderma tsugae, and Clade C comprised Ganoderma boninense and Ganoderma zonatum. A dichotomous key to the 13 species is provided, and their key morphological characters from context, pores, cuticle cells and basidiospores are presented in a table. The taxonomic positions of these species are briefly discussed. Noteworthy, the epitypification of G. sichuanense is rejected. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Individual multi-locus heterozygosity is associated with lower morning plasma cortisol concentrations.

    Science.gov (United States)

    Zgaga, Lina; Vitart, Veronique; Hayward, Caroline; Kastelan, Darko; Polasek, Ozren; Jakovljevic, Miro; Kolcic, Ivana; Biloglav, Zrinka; Wright, Alan F; Campbell, Harry; Walker, Brian R; Rudan, Igor

    2013-07-01

    Stress is implicated as a risk factor for numerous illnesses in humans, putatively in part mediated by biological responses to stress, such as elevated cortisol concentrations. The theory of genetic homoeostasis suggests that individual heterozygosity facilitates compensation for environmental stresses. We hypothesized that heterozygosity ameliorates the biological response to a given level of perceived stress, reflected in lower plasma cortisol concentrations. We examined the role of heterozygosity in the association between perceived psychological stress and morning cortisol concentrations in 854 individuals from the isolated island of Vis, Croatia. Cortisol concentrations were measured in morning plasma samples. A total of 1184 autosomal microsatellite markers were genotyped and individual multi-locus heterozygosity (MLH) was calculated as the proportion of heterozygous markers. The General Health Questionnaire with 30 items (GHQ-30) was used to assess the degree of psychological distress. MEAN MLH WAS 34.850.45% (RANGE: 31.97-36.22%). Psychological distress (GHQ Likert score >31) was more prevalent in women (37 vs 18% in men, Pclasses (β=-3.59, Pmorning plasma cortisol concentrations (P=0.005). More heterozygous individuals, as measured by microsatellite markers, had lower morning plasma cortisol concentrations for a given level of perceived psychological stress. This may be important, as higher cortisol concentrations may increase the allostatic load and be associated with a higher risk of stress-related illness.

  1. Genetic relationships among Enterococcus faecalis isolates from different sources as revealed by multilocus sequence typing.

    Science.gov (United States)

    Chen, X; Song, Y Q; Xu, H Y; Menghe, B L G; Zhang, H P; Sun, Z H

    2015-08-01

    Enterococcus faecalis is part of the natural gut flora of humans and other mammals; some isolates are also used in food production. So, it is important to evaluate the genetic diversity and phylogenetic relationships among E. faecalis isolates from different sources. Multilocus sequence typing protocol was used to compare 39 E. faecalis isolates from Chinese traditional food products (including dairy products, acidic gruel) and 4 published E. faecalis isolates from other sources including human-derived isolates employing 5 housekeeping genes (groEL, clpX, recA, rpoB, and pepC). A total of 23 unique sequence types were identified, which were grouped into 5 clonal complexes and 10 singletons. The value of standardized index of association of the alleles (IA(S)=0.1465) and network structure indicated a high frequency of intraspecies recombination across these isolates. Enterococcus faecalis lineages also exhibited clearly source-clustered distributions. The isolates from dairy source were clustered together. However, the relationship between isolates from acidic gruel and one isolate from a human source was close. The MLST scheme presented in this study provides a sharable and continuously growing sequence database enabling global comparison of strains from different sources, and will further advance our understanding of the microbial ecology of this important species. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  2. Down Syndrome: Cognitive Phenotype

    Science.gov (United States)

    Silverman, Wayne

    2007-01-01

    Down syndrome is the most prevalent cause of intellectual impairment associated with a genetic anomaly, in this case, trisomy of chromosome 21. It affects both physical and cognitive development and produces a characteristic phenotype, although affected individuals vary considerably with respect to severity of specific impairments. Studies…

  3. The DFNA10 phenotype.

    NARCIS (Netherlands)

    Leenheer, E. de; Huygen, P.L.M.; Wayne, S.; Smith, R.J.H.; Cremers, C.W.R.J.

    2001-01-01

    We present a detailed analysis of the DFNA10 phenotype based on data from 25 hearing-impaired persons coming from a large American pedigree segregating for deafness at the DFNA10 locus (chromosome 6q22.3-23.2). Cross-sectional analysis of air conduction threshold-on-age data from all available

  4. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  5. Phenotypic integration: studying the ecology and evolution of complex phenotypes

    National Research Council Canada - National Science Library

    Pigliucci, Massimo; Preston, Katherine

    2004-01-01

    .... Studying the Plasticity of Phenotypic Integration in a Model Organism, 155 Massimo Pigliucci 8. Integrating Phenotypic Plasticity When Death Is on the Line: Insights from Predator-Prey Systems...

  6. Diversidade genética de Enterolobium contortisiliquum (Vell. Morong. no Baixo Rio São Francisco, por meio de marcadores RAPD Genetic diversity of Enterolobium contortisiliquum (Vell. Morong. in the low San Francisco river by RAPD markers

    Directory of Open Access Journals (Sweden)

    Georgea da Cruz Santana

    2008-06-01

    Full Text Available Enterolobium contortisiliquum Vell. Morong (Leguminosae-Mimosoideae é uma espécie muito utilizada em programas de recuperação de matas ciliares no Baixo Rio São Francisco, devido ao seu rápido crescimento inicial. Assim, o objetivo deste trabalho foi avaliar, por meio de marcadores moleculares RAPD, a diversidade genética de oito indivíduos de uma população remanescente dessa espécie, visando contribuir para a definição de estratégias de coleta de sementes. Os indivíduos estão situados em uma área de 100 ha de mata ciliar do Baixo Rio São Francisco. Para a extração do DNA, pelo método CTAB 2%, foram utilizadas folhas tenras dos indivíduos. Testaram-se 20 oligonucleotídios de 10 bases de seqüência arbitrária, cujos produtos foram separados em gel de agarose 0,8%, submetidos à eletroforese horizontal, corados com brometo-de-etídio e visualizados em luz ultravioleta. A similaridade genética entre os indivíduos foi calculada pelo Coeficiente de Similaridade de Jaccard e a construção do dendrograma, realizada utilizando-se o método UPGMA. O valor médio de diversidade genética entre as matrizes foi de 49%, variando de 33 a 85%. Os indivíduos 6 e 7 apresentaram relativa proximidade genética (67%, não sendo indicado o plantio de suas mudas ou semeadura direta para recuperação de área ciliar em locais muito próximos. A partir dos resultados observados, podem-se desenvolver estratégias para a coleta de sementes e produção de mudas, auxiliando, assim, programas de restauração ambiental.Enterolobium contortisiliquum Vell. Morong (Leguminosae-Mimosoideae is very much used in riparian forest restoration programs in the Low San Francisco River because of its fast initial growth. The objective of this work was to evaluate by RAPD molecular markers the genetic diversity of eight individuals of a remaining population of this species, in order to contribute for the definition of strategies for seed production. The

  7. Genetic divergence among elephantgrass cultivars assessed by RAPD markers in composit samples Divergência genética entre cultivares de capim-elefante avaliada por marcadores RAPD em amostras compostas

    Directory of Open Access Journals (Sweden)

    Rogério Figueiredo Daher

    2002-12-01

    Full Text Available Elephantgrass (Pennisetum purpureum Schum. is native to regions of tropical Africa and was introduced in Brazil around 1920 through plantings imported from Cuba. It is currently one of the most widespread forage plants throughout the country. At first, there were two cultivars, Napier and Mercker, with well defined characteristics. New genotypes arose and it is believed that the large number of cultivars existing today in germplasm bank is due to duplicates. DNA markers for cultivar characterization are a very valuable tool, especially in situations where morphological and isoenzymatic markers have already been used as in the case of elephantgrass. Thus RAPD markers were used to estimate the genetic divergence among the Napier group elephantgrass cultivars from the elephantgrass Active Germplasm Bank at EMBRAPA Dairy Cattle. The polymerase chain reaction with 37 arbitrary primers from the OPERON Technologies series supplied 94 polymorphic and 73 monomorphic bands. From the matrix of complement of the Nei index, cluster analysis by the Tocher optimization method formed three clusters. Pearson correlation among genetic distance estimates obtained from the DNA markers and the isoenzymatic markers showed the consistency of both the methods in assessing genetic divergence among elephantgrass cultivars. No duplicates were found in the treatments assessed.O capim-elefante (Pennisetum purpureum Schum. é nativo de regiões da África Tropical e foi introduzido no Brasil por volta de 1920, por meio de mudas provenientes de Cuba, e é, atualmente, uma das forrageiras mais difundidas em todo o país. No início de sua utilização, existiam praticamente dois cultivares com características bem definidas, Napier e Mercker. Com o decorrer do tempo, surgiram novos genótipos e acredita-se que o grande número de cultivares existentes atualmente no Banco de Germoplasma da espécie se deva à ocorrência de duplicatas. O uso de marcadores de DNA na caracteriza

  8. From metabolome to phenotype

    DEFF Research Database (Denmark)

    Khakimov, Bekzod; Rasmussen, Morten Arendt; Kannangara, Rubini Maya

    2017-01-01

    The development of crop varieties tolerant to growth temperature fluctuations and improved nutritional value is crucial due to climate change and global population growth. This study investigated the metabolite patterns of developing barley seed as a function of genotype and growth temperature fo...... their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production....

  9. Genetic and phenotypic evidence of the Salmonella enterica serotype Enteritidis human-animal interface in Chile

    Directory of Open Access Journals (Sweden)

    Patricio eRetamal

    2015-05-01

    Full Text Available Salmonella enterica serotype Enteritidis is a worldwide zoonotic agent that has been recognized as a very important food-borne bacterial pathogen, mainly associated with consumption of poultry products. The aim of this work was to determine genotypic and phenotypic evidence of S. Enteritidis transmission among seabirds, poultry and humans in Chile. Genotyping was performed using PCR-based virulotyping, pulse-field gel electrophoresis (PFGE and multi-locus sequence typing (MLST. Pathogenicity-associated phenotypes were determined with survival to free radicals, acidic pH, starvation, antimicrobial resistance, and survival within human dendritic cells. As result of PCR and PFGE assays, some isolates from the three hosts showed identical genotypic patterns, and through MLST it was determined that all of them belong to sequence type 11. Results of phenotypic assays showed diversity of survival capabilities among isolates. When results were analyzed according to bacterial host, statistical differences were identified in starvation and dendritic cells survival assays. In addition, isolates from seabirds showed the highest rates of resistance to gentamycin, tetracycline and ampicillin. Overall, the very close genetic and phenotypic traits shown by isolates from humans, poultry and seabirds suggest the inter-species transmission of S. Enteritidis bacteria between hosts, likely through anthropogenic environmental contamination that determines infection of seabirds with bacteria that are potentially pathogenic for other susceptible organism, including humans.

  10. Multilocus sequence typing of Lactobacillus casei isolates from naturally fermented foods in China and Mongolia.

    Science.gov (United States)

    Bao, Qiuhua; Song, Yuqin; Xu, Haiyan; Yu, Jie; Zhang, Wenyi; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

    2016-07-01

    Lactobacillus casei is a lactic acid bacterium used in manufacturing of many fermented food products. To investigate the genetic diversity and population biology of this food-related bacterium, 224 Lb. casei isolates and 5 reference isolates were examined by multilocus sequence typing (MLST). Among them, 224 Lb. casei isolates were isolated from homemade fermented foods, including naturally fermented dairy products, acidic gruel, and Sichuan pickles from 38 different regions in China and Mongolia. The MLST scheme was developed based on the analysis of 10 selected housekeeping genes (carB, clpX, dnaA, groEL, murE, pyrG, pheS, recA, rpoC, and uvrC). All 229 isolates could be allocated to 171 unique sequence types, including 25 clonal complexes and 71 singletons. The high index of association value (1.3524) and standardized index of association value (0.1503) indicate the formation of an underlying clonal population by all the isolates. However, split-decomposition, relative frequency of occurrence of recombination and mutation, and relative effect of recombination and mutation in the diversification values confirm that recombination may have occurred, and were more frequent than mutation during the evolution of Lb. casei. Results from Structure analyses (version 2.3; http://pritch.bsd.uchicago.edu/structure.html) demonstrated that there were 5 lineages in the Lb. casei isolates, and the overall relatedness built by minimum spanning tree showed no clear relationship between the clonal complexes with either the isolation sources or sampling locations of the isolates. Our newly developed MLST scheme of Lb. casei was an easy and valuable tool that, together with the construction of an MLST database, will contribute to further detailed studies on the evolution and population genetics of Lb. casei from various niches. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  11. Multilocus Sequence Typing Scheme versus Pulsed-Field Gel Electrophoresis for Typing Mycobacterium abscessus Isolates

    Science.gov (United States)

    Machado, Gabriel Esquitini; Matsumoto, Cristianne Kayoko; Chimara, Erica; Duarte, Rafael da Silva; de Freitas, Denise; Palaci, Moises; Hadad, David Jamil; Lima, Karla Valéria Batista; Lopes, Maria Luiza; Ramos, Jesus Pais; Campos, Carlos Eduardo; Caldas, Paulo César; Heym, Beate

    2014-01-01

    Outbreaks of infections by rapidly growing mycobacteria following invasive procedures, such as ophthalmological, laparoscopic, arthroscopic, plastic, and cardiac surgeries, mesotherapy, and vaccination, have been detected in Brazil since 1998. Members of the Mycobacterium chelonae-Mycobacterium abscessus group have caused most of these outbreaks. As part of an epidemiological investigation, the isolates were typed by pulsed-field gel electrophoresis (PFGE). In this project, we performed a large-scale comparison of PFGE profiles with the results of a recently developed multilocus sequence typing (MLST) scheme for M. abscessus. Ninety-three isolates were analyzed, with 40 M. abscessus subsp. abscessus isolates, 47 M. abscessus subsp. bolletii isolates, and six isolates with no assigned subspecies. Forty-five isolates were obtained during five outbreaks, and 48 were sporadic isolates that were not associated with outbreaks. For MLST, seven housekeeping genes (argH, cya, glpK, gnd, murC, pta, and purH) were sequenced, and each isolate was assigned a sequence type (ST) from the combination of obtained alleles. The PFGE patterns of DraI-digested DNA were compared with the MLST results. All isolates were analyzable by both methods. Isolates from monoclonal outbreaks showed unique STs and indistinguishable or very similar PFGE patterns. Thirty-three STs and 49 unique PFGE patterns were identified among the 93 isolates. The Simpson's index of diversity values for MLST and PFGE were 0.69 and 0.93, respectively, for M. abscessus subsp. abscessus and 0.96 and 0.97, respectively, for M. abscessus subsp. bolletii. In conclusion, the MLST scheme showed 100% typeability and grouped monoclonal outbreak isolates in agreement with PFGE, but it was less discriminative than PFGE for M. abscessus. PMID:24899019

  12. Multilocus species tree analyses resolve the radiation of the widespread Bufo bufo species group (Anura, Bufonidae).

    Science.gov (United States)

    Recuero, E; Canestrelli, D; Vörös, J; Szabó, K; Poyarkov, N A; Arntzen, J W; Crnobrnja-Isailovic, J; Kidov, A A; Cogălniceanu, D; Caputo, F P; Nascetti, G; Martínez-Solano, I

    2012-01-01

    New analytical methods are improving our ability to reconstruct robust species trees from multilocus datasets, despite difficulties in phylogenetic reconstruction associated with recent, rapid divergence, incomplete lineage sorting and/or introgression. In this study, we applied these methods to resolve the radiation of toads in the Bufo bufo (Anura, Bufonidae) species group, ranging from the Iberian Peninsula and North Africa to Siberia, based on sequences from two mitochondrial and four nuclear DNA regions (3490 base pairs). We obtained a fully-resolved topology, with the recently described Bufo eichwaldi from the Talysh Mountains in south Azerbaijan and Iran as the sister taxon to a clade including: (1) north African, Iberian, and most French populations, referred herein to Bufo spinosus based on the implied inclusion of populations from its type locality and (2) a second clade, sister to B. spinosus, including two sister subclades: one with all samples of Bufo verrucosissimus from the Caucasus and another one with samples of B. bufo from northern France to Russia, including the Apennine and Balkan peninsulas and most of Anatolia. Coalescent-based estimations of time to most recent common ancestors for each species and selected subclades allowed historical reconstruction of the diversification of the species group in the context of Mediterranean paleogeography and indicated a long evolutionary history in this region. Finally, we used our data to delimit the ranges of the four species, particularly the more widespread and historically confused B. spinosus and B. bufo, and identify potential contact zones, some of which show striking parallels with other co-distributed species. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Multilocus association testing of quantitative traits based on partial least-squares analysis.

    Directory of Open Access Journals (Sweden)

    Feng Zhang

    Full Text Available Because of combining the genetic information of multiple loci, multilocus association studies (MLAS are expected to be more powerful than single locus association studies (SLAS in disease genes mapping. However, some researchers found that MLAS had similar or reduced power relative to SLAS, which was partly attributed to the increased degrees of freedom (dfs in MLAS. Based on partial least-squares (PLS analysis, we develop a MLAS approach, while avoiding large dfs in MLAS. In this approach, genotypes are first decomposed into the PLS components that not only capture majority of the genetic information of multiple loci, but also are relevant for target traits. The extracted PLS components are then regressed on target traits to detect association under multilinear regression. Simulation study based on real data from the HapMap project were used to assess the performance of our PLS-based MLAS as well as other popular multilinear regression-based MLAS approaches under various scenarios, considering genetic effects and linkage disequilibrium structure of candidate genetic regions. Using PLS-based MLAS approach, we conducted a genome-wide MLAS of lean body mass, and compared it with our previous genome-wide SLAS of lean body mass. Simulations and real data analyses results support the improved power of our PLS-based MLAS in disease genes mapping relative to other three MLAS approaches investigated in this study. We aim to provide an effective and powerful MLAS approach, which may help to overcome the limitations of SLAS in disease genes mapping.

  14. Genotyping of Indian antigenic, vaccine, and field Brucella spp. using multilocus sequence typing.

    Science.gov (United States)

    Shome, Rajeswari; Krithiga, Natesan; Shankaranarayana, Padmashree B; Jegadesan, Sankarasubramanian; Udayakumar S, Vishnu; Shome, Bibek Ranjan; Saikia, Girin Kumar; Sharma, Narendra Kumar; Chauhan, Harshad; Chandel, Bharat Singh; Jeyaprakash, Rajendhran; Rahman, Habibur

    2016-03-31

    Brucellosis is one of the most important zoonotic diseases that affects multiple livestock species and causes great economic losses. The highly conserved genomes of Brucella, with > 90% homology among species, makes it important to study the genetic diversity circulating in the country. A total of 26 Brucella spp. (4 reference strains and 22 field isolates) and 1 B. melitensis draft genome sequence from India (B. melitensis Bm IND1) were included for sequence typing. The field isolates were identified by biochemical tests and confirmed by both conventional and quantitative polymerase chain reaction (qPCR) targeting bcsp 31Brucella genus-specific marker. Brucella speciation and biotyping was done by Bruce ladder, probe qPCR, and AMOS PCRs, respectively, and genotyping was done by multilocus sequence typing (MLST). The MLST typing of 27 Brucella spp. revealed five distinct sequence types (STs); the B. abortus S99 reference strain and 21 B. abortus field isolates belonged to ST1. On the other hand, the vaccine strain B. abortus S19 was genotyped as ST5. Similarly, B. melitensis 16M reference strain and one B. melitensis field isolate were grouped into ST7. Another B. melitensis field isolate belonged to ST8 (draft genome sequence from India), and only B. suis 1330 reference strain was found to be ST14. The sequences revealed genetic similarity of the Indian strains to the global reference and field strains. The study highlights the usefulness of MLST for typing of field isolates and validation of reference strains used for diagnosis and vaccination against brucellosis.

  15. Multilocus sequence typing indicates diverse origins of invasive Candida tropicalis isolates in China.

    Science.gov (United States)

    Fan, Xin; Xiao, Meng; Wang, He; Zhang, Li; Kong, Fanrong; Lu, Juan; Hu, Zhidong; Kang, Mei; Xu, Yingchun

    2014-01-01

    According to data from the China Hospital Invasive Fungal Surveillance Net (CHIF-NET) 2010, Candida tropicalis (C. tropicalis) is the third most common pathogen causing invasive candidiasis. Moreover, the majority of fluconazole-resistant C. tropicalis isolates were from a single hospital. Therefore, a molecular epidemiological survey is necessary to investigate the genetic relatedness of C. tropicalis isolates in China. In this study, 48 C. tropicalis isolates causing invasive fungal infections from four tertiary hospitals in China were studied. All the isolates were identified by sequencing the internal transcribed spacer region. Antifungal susceptibility to triazoles, amphotericin B, and caspofungin was determined by the Clinical and Laboratory Standards Institute standard broth microdilution method. Multilocus sequence typing (MLST) was performed, and phylogenetic analysis was further performed by the eBURST and maximum parsimony (MP) methods to characterize the genetic relatedness of isolates. MLST discriminated 40 diploid sequence types (DSTs) among 48 isolates, including 36 novel DSTs, and the XYR1 gene showed the highest discriminatory power. The DSTs obtained from this study were compared with those of previously reported C. tropicalis isolates, and there was poor type alignment with regional strains. Nine groups and 11 singletons were identified by eBURST, whereas two groups and 10 subgroups were clustered by MP analysis. Generally, there were no obvious correlations between clonal clusters generated and the specimen source or hospital origin. Seven fluconazole-resistant isolates were confirmed and assigned to three distinguishable branches. The results suggested diverse origins of invasive C. tropicalis isolates in China. Although most invasive C. tropicalis strains in the mainland of China were clustered with previously characterized Asian isolates, major C. tropicalis clusters identified in this study were genetically distinct from those of other

  16. An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

    Directory of Open Access Journals (Sweden)

    Sabrina Weiss

    2016-09-01

    Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

  17. Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

    Directory of Open Access Journals (Sweden)

    Pruckler James M

    2008-11-01

    Full Text Available Abstract Background Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI illness were clonal or formed clonal complexes. Results A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27, gastrointestinal (GI illness (n = 18, and associated isolates from food (n = 10 were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates. Conclusion STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and

  18. Optimization of multilocus sequence analysis for identification of species in the genus Vibrio.

    Science.gov (United States)

    Gabriel, Michael W; Matsui, George Y; Friedman, Robert; Lovell, Charles R

    2014-09-01

    Multilocus sequence analysis (MLSA) is an important method for identification of taxa that are not well differentiated by 16S rRNA gene sequences alone. In this procedure, concatenated sequences of selected genes are constructed and then analyzed. The effects that the number and the order of genes used in MLSA have on reconstruction of phylogenetic relationships were examined. The recA, rpoA, gapA, 16S rRNA gene, gyrB, and ftsZ sequences from 56 species of the genus Vibrio were used to construct molecular phylogenies, and these were evaluated individually and using various gene combinations. Phylogenies from two-gene sequences employing recA and rpoA in both possible gene orders were different. The addition of the gapA gene sequence, producing all six possible concatenated sequences, reduced the differences in phylogenies to degrees of statistical (bootstrap) support for some nodes. The overall statistical support for the phylogenetic tree, assayed on the basis of a reliability score (calculated from the number of nodes having bootstrap values of ≥ 80 divided by the total number of nodes) increased with increasing numbers of genes used, up to a maximum of four. No further improvement was observed from addition of the fifth gene sequence (ftsZ), and addition of the sixth gene (gyrB) resulted in lower proportions of strongly supported nodes. Reductions in the numbers of strongly supported nodes were also observed when maximum parsimony was employed for tree construction. Use of a small number of gene sequences in MLSA resulted in accurate identification of Vibrio species. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  19. Multilocus phylogeny and MALDI-TOF analysis of the plant pathogenic species Alternaria dauci and relatives.

    Science.gov (United States)

    Brun, Sophie; Madrid, Hugo; Gerrits Van Den Ende, Bert; Andersen, Birgitte; Marinach-Patrice, Carine; Mazier, Dominique; De Hoog, G Sybren

    2013-01-01

    The genus Alternaria includes numerous phytopathogenic species, many of which are economically relevant. Traditionally, identification has been based on morphology, but is often hampered by the tendency of some strains to become sterile in culture and by the existence of species-complexes of morphologically similar taxa. This study aimed to assess if strains of four closely-related plant pathogens, i.e., accurately Alternaria dauci (ten strains), Alternaria porri (six), Alternaria solani (ten), and Alternaria tomatophila (ten) could be identified using multilocus phylogenetic analysis and Matrix-Assisted Laser Desorption Ionisation Time of Flight (MALDI-TOF) profiling of proteins. Phylogenetic analyses were performed on three loci, i.e., the internal transcribed spacer (ITS) region of rRNA, and the glyceraldehyde-3-phosphate dehydrogenase (gpd) and Alternaria major antigen (Alt a 1) genes. Phylogenetic trees based on ITS sequences did not differentiate strains of A. solani, A. tomatophila, and A. porri, but these three species formed a clade separate from strains of A. dauci. The resolution improved in trees based on gpd and Alt a 1, which distinguished strains of the four species as separate clades. However, none provided significant bootstrap support for all four species, which could only be achieved when results for the three loci were combined. MALDI-TOF-based dendrograms showed three major clusters. The first comprised all A. dauci strains, the second included five strains of A. porri and one of A. solani, and the third included all strains of A. tomatophila, as well as all but one strain of A. solani, and one strain of A. porri. Thus, this study shows the usefulness of MALDI-TOF mass spectrometry as a promising tool for identification of these four species of Alternaria which are closely-related plant pathogens. Copyright © 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  20. A multilocus molecular phylogeny of the endemic North American camel spider family Eremobatidae (Arachnida: Solifugae).

    Science.gov (United States)

    Cushing, Paula E; Graham, Matthew R; Prendini, Lorenzo; Brookhart, Jack O

    2015-11-01

    Camel spiders (Solifugae) are a diverse but poorly studied order of arachnids. No robust phylogenetic analysis has ever been carried out for the order or for any family within the Solifugae. We present a molecular phylogenetic analysis of the endemic North American family Eremobatidae Kraepelin, 1899, the first such analysis of a family of Solifugae. We use a multi-locus exemplar approach using DNA sequences from partial nuclear (28S rDNA and Histone H3) and mitochondrial (16S rRNA and Cytochrome c Oxidase I) gene loci for 81 ingroup exemplars representing all genera of Eremobatidae and most species groups within the genera Eremobates Banks, 1900, Eremochelis Roewer, 1934, and Hemerotrecha Banks, 1903. Maximum Likelihood and two Bayesian analyses consistently recovered the monophyly of Eremobatidae, Eremorhax Roewer, 1934 and Eremothera Muma, 1951 along with a group comprising all subfamily Eremobatinae Kraepelin, 1901 exemplars except Horribates bantai Muma, 1989 and a group comprising all Eremocosta Roewer, 1934 exemplars except Eremocosta acuitalpanensis (Vasquez and Gavin, 2000). The subfamily Therobatinae Muma, 1951 and the genera Chanbria Muma, 1951, Hemerotrecha, Eremochelis, and Eremobates were polyphyletic or paraphyletic. Only the banksi group of Hemerotrecha was monophyletic; the other species groups recognized within Eremobates, Eremochelis, and Hemerotrecha were paraphyletic or polyphyletic. We found no support for the monophyly of the subfamily Therobatinae. A time-calibrated phylogeny dated the most recent common ancestor of extant eremobatids to the late Eocene to early Miocene, with a mean estimate in the late Oligocene (32.2 Ma). Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Population structure of clinical Vibrio parahaemolyticus from 17 coastal countries, determined through multilocus sequence analysis.

    Science.gov (United States)

    Han, Dongsheng; Tang, Hui; Lu, Jun; Wang, Guangzhou; Zhou, Lin; Min, Lingfeng; Han, Chongxu

    2014-01-01

    Vibrio parahaemolyticus is a leading cause of food-borne gastroenteritis worldwide. Although this bacterium has been the subject of much research, the population structure of clinical strains from worldwide collections remains largely undescribed, and the recorded outbreaks of V. parahaemolyticus gastroenteritis highlight the need for the subtyping of this species. We present a broad phylogenetic analysis of 490 clinical V. parahaemolyticus isolates from 17 coastal countries through multilocus sequence analysis (MLST). The 490 tested isolates fell into 161 sequence types (STs). The eBURST algorithm revealed that the 161 clinically relevant STs belonged to 8 clonal complexes, 11 doublets, and 94 singletons, showing a high level of genetic diversity. CC3 was found to be a global epidemic clone of V. parahaemolyticus, and ST-3 was the only ST with an international distribution. recA was observed to be evolving more rapidly, exhibiting the highest degree of nucleotide diversity (0.028) and the largest number of polymorphic nucleotide sites (177). We also found that the high variability of recA was an important cause of differences between the results of the eBURST and ME tree analyses, suggesting that recA has a much greater influence on the apparent evolutionary classification of V. parahaemolyticus based on the current MLST scheme. In conclusion, it is evident that a high degree of genetic diversity within the V. parahaemolyticus population and multiple sequence types are contributing to the burden of disease around the world. MLST, with a fully extractable database, is a powerful system for analysis of the clonal relationships of strains at a global scale. With the addition of more strains, the pubMLST database will provide more detailed and accurate information, which will be conducive to our future research on the population structure of V. parahaemolyticus.

  2. Multilocus sequence typing of Trichomonas vaginalis clinical samples from Amsterdam, the Netherlands.

    Science.gov (United States)

    van der Veer, C; Himschoot, M; Bruisten, S M

    2016-10-13

    In this cross-sectional epidemiological study we aimed to identify molecular profiles for Trichomonas vaginalis and to determine how these molecular profiles were related to patient demographic and clinical characteristics. Molecular typing methods previously identified two genetically distinct subpopulations for T. vaginalis; however, few molecular epidemiological studies have been performed. We now increased the sensitivity of a previously described multilocus sequence typing (MLST) tool for T. vaginalis by using nested PCR. This enabled the typing of direct patient samples. From January to December 2014, we collected all T. vaginalis positive samples as detected by routine laboratory testing. Samples from patients either came from general practitioners offices or from the sexually transmitted infections (STI) clinic in Amsterdam. Epidemiological data for the STI clinic patients were retrieved from electronic patient files. The primary outcome was the success rate of genotyping direct T. vaginalis positive samples. The secondary outcome was the relation between T. vaginalis genotypes and risk factors for STI. All 7 MLST loci were successfully typed for 71/87 clinical samples. The 71 typed samples came from 69 patients, the majority of whom were women (n=62; 90%) and half (n=34; 49%) were STI clinic patients. Samples segregated into a two population structure for T. vaginalis representing genotypes I and II. Genotype I was most common (n=40; 59.7%). STI clinic patients infected with genotype II reported more sexual partners in the preceding 6 months than patients infected with genotype I (p=0.028). No other associations for gender, age, ethnicity, urogenital discharge or co-occurring STIs with T. vaginalis genotype were found. MLST with nested PCR is a sensitive typing method that allows typing of direct (uncultured) patient material. Genotype II is possibly more prevalent in high-risk sexual networks. Published by the BMJ Publishing Group Limited. For

  3. Development of a single multi-locus sequence typing scheme for Taylorella equigenitalis and Taylorella asinigenitalis.

    Science.gov (United States)

    Duquesne, Fabien; Hébert, Laurent; Breuil, Marie-France; Matsuda, Motoo; Laugier, Claire; Petry, Sandrine

    2013-12-27

    We describe here the development of a multilocus sequence typing (MLST) scheme for Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), and Taylorella asinigenitalis, a nonpathogenic bacterium. MLST was performed on a set of 163 strains collected in several countries over 35 years (1977-2012). The MLST data were analyzed using START2, MEGA 5.05 and eBURST, and can be accessed at http://pubmlst.org/taylorella/. Our results revealed a clonal population with 39 sequence types (ST) and no common ST between the two Taylorella species. The eBURST analysis grouped the 27 T. equigenitalis STs into four clonal complexes (CC1-4) and five unlinked STs. The 12 T. asinigenitalis STs were grouped into three clonal complexes (CC5-7) and five unlinked STs, among which CC1 (68.1% of the 113 T. equigenitalis) and CC5 (58.0% of the 50 T. asinigenitalis) were dominants. The CC1, still in circulation in France, contains isolates from the first CEM outbreaks that simultaneously emerged in several countries in the late 1970s. The emergence in different countries (e.g. France, Japan, and United Arab Emirates) of STs without any genetic relationship to CC1 suggests the existence of a natural worldwide reservoir that remains to be identified. T. asinigenitalis appears to behave same way since the American, Swedish and French isolates have unrelated STs. This first Taylorella sp. MLST is a powerful tool for further epidemiological investigations and population biology studies of the Taylorella genus. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica.

    Directory of Open Access Journals (Sweden)

    Mark Achtman

    Full Text Available Salmonella enterica subspecies enterica is traditionally subdivided into serovars by serological and nutritional characteristics. We used Multilocus Sequence Typing (MLST to assign 4,257 isolates from 554 serovars to 1092 sequence types (STs. The majority of the isolates and many STs were grouped into 138 genetically closely related clusters called eBurstGroups (eBGs. Many eBGs correspond to a serovar, for example most Typhimurium are in eBG1 and most Enteritidis are in eBG4, but many eBGs contained more than one serovar. Furthermore, most serovars were polyphyletic and are distributed across multiple unrelated eBGs. Thus, serovar designations confounded genetically unrelated isolates and failed to recognize natural evolutionary groupings. An inability of serotyping to correctly group isolates was most apparent for Paratyphi B and its variant Java. Most Paratyphi B were included within a sub-cluster of STs belonging to eBG5, which also encompasses a separate sub-cluster of Java STs. However, diphasic Java variants were also found in two other eBGs and monophasic Java variants were in four other eBGs or STs, one of which is in subspecies salamae and a second of which includes isolates assigned to Enteritidis, Dublin and monophasic Paratyphi B. Similarly, Choleraesuis was found in eBG6 and is closely related to Paratyphi C, which is in eBG20. However, Choleraesuis var. Decatur consists of isolates from seven other, unrelated eBGs or STs. The serological assignment of these Decatur isolates to Choleraesuis likely reflects lateral gene transfer of flagellar genes between unrelated bacteria plus purifying selection. By confounding multiple evolutionary groups, serotyping can be misleading about the disease potential of S. enterica. Unlike serotyping, MLST recognizes evolutionary groupings and we recommend that Salmonella classification by serotyping should be replaced by MLST or its equivalents.

  5. A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis.

    Science.gov (United States)

    Azevedo, Helton; Lopes, Fabricio; Silla, Paulo; Hungria, Mariangela

    2015-01-01

    Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria. Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species. A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in

  6. Distribution of Campylobacter jejuni multilocus sequence types isolated from chickens in Poland.

    Science.gov (United States)

    Wieczorek, K; Denis, E; Lachtara, B; Osek, J

    2017-03-01

    Poultry is recognized as the most important source of food-related transmission of Campylobacter jejuni to humans and campylobacteriosis is the most commonly reported zoonotic bacterial disease in the European Union. It has been documented that C. jejuni is genetically diverse and analyses of bacterial isolates usually show a large strain variety. Therefore, molecular typing of strains represents an important tool to study the genetic diversity of isolates and to trace individual strains that cause human infections. The aim of the study was characterization of genetic population structure and antimicrobial resistance (AMR) of C. jejuni isolated from Polish chickens. C. jejuni from chicken ceca and the corresponding carcasses (72 and 61 strains, respectively), originating from 128 flocks in Poland during February 2011 and May 2013, were used in the study. The isolates were tested for their population structure and genetic diversity using a multilocus sequence typing (MLST) scheme with connection to their antimicrobial resistance. The molecular analysis of 133 C. jejuni generated 39 different sequence types (ST); 3 of them were defined for the first time. Additionally, 16 STs were represented by single isolates. The most common STs observed were 6411 (16.5% isolates) and 257 (15.0% strains). The first mentioned ST was resistant to 3 different classes of antibiotics, i.e., quinolones, tetracyclines, and aminoglycosides. Overall, 125 (94.4%) of C. jejuni isolates demonstrated antimicrobial resistance and the most frequent AMR profile observed was ciprofloxacin, nalidixic acid, tetracycline (47.4% strains). Likewise, the clonal complexes CC 257 and CC 353 were defined as the predominant molecular groups covering altogether 37 C. jejuni strains. No associations between CCs and the origin of the samples as well as the place of isolation were found. This study highlights that the C. jejuni population from chickens in Poland was diverse and showed a weak clonal structure.

  7. Multi-locus assortment (MLA for transgene dispersal and elimination in mosquito populations.

    Directory of Open Access Journals (Sweden)

    Jason L Rasgon

    Full Text Available BACKGROUND: Replacement of wild-type mosquito populations with genetically modified versions is being explored as a potential strategy to control vector-borne diseases. Due to lower expected relative fitness of transgenic individuals, transgenes must be driven into populations for these scenarios to be successful. Several gene drive mechanisms exist in a theoretical sense but none are currently workable in mosquitoes. Even if strategies were workable, it would be very difficult to recall released transgenes in the event of unforeseen consequences. What is needed is a way to test transgenes in the field for feasibility, efficacy and safety prior to releasing an active drive mechanism. METHODOLOGY/PRINCIPAL FINDINGS: We outline a method, termed Multi-locus assortment (MLA, to spread transgenes into vector populations by the release of genetically-modified mosquitoes carrying multiple stable transgene inserts. Simulations indicate that [1] insects do not have to carry transgenes at more than 4 loci, [2] transgenes can be maintained at high levels by sequential small releases, the frequency of which depends on the construct fitness cost, and [3] in the case of unforeseen negative non-target effects, transgenes can be eliminated from the population by halting transgenic releases and/or mass releases of wild-type insects. We also discuss potential methods to create MLA mosquito strains in the laboratory. CONCLUSIONS/SIGNIFICANCE: While not as efficient as active drive mechanisms, MLA has other advantages: [1] MLA strains can be constructed for some mosquito species with currently-available technology, [2] MLA will allow the ecological components of transgenic mosquito releases to be tested before actual gene drive mechanisms are ready to be deployed, [3] since MLA is not self-propagating, the risk of an accidental premature release into nature is minimized, and [4] in the case that active gene drive mechanisms prove impossible to develop, the MLA

  8. Multi-locus assortment (MLA) for transgene dispersal and elimination in mosquito populations.

    Science.gov (United States)

    Rasgon, Jason L

    2009-06-08

    Replacement of wild-type mosquito populations with genetically modified versions is being explored as a potential strategy to control vector-borne diseases. Due to lower expected relative fitness of transgenic individuals, transgenes must be driven into populations for these scenarios to be successful. Several gene drive mechanisms exist in a theoretical sense but none are currently workable in mosquitoes. Even if strategies were workable, it would be very difficult to recall released transgenes in the event of unforeseen consequences. What is needed is a way to test transgenes in the field for feasibility, efficacy and safety prior to releasing an active drive mechanism. We outline a method, termed Multi-locus assortment (MLA), to spread transgenes into vector populations by the release of genetically-modified mosquitoes carrying multiple stable transgene inserts. Simulations indicate that [1] insects do not have to carry transgenes at more than 4 loci, [2] transgenes can be maintained at high levels by sequential small releases, the frequency of which depends on the construct fitness cost, and [3] in the case of unforeseen negative non-target effects, transgenes can be eliminated from the population by halting transgenic releases and/or mass releases of wild-type insects. We also discuss potential methods to create MLA mosquito strains in the laboratory. While not as efficient as active drive mechanisms, MLA has other advantages: [1] MLA strains can be constructed for some mosquito species with currently-available technology, [2] MLA will allow the ecological components of transgenic mosquito releases to be tested before actual gene drive mechanisms are ready to be deployed, [3] since MLA is not self-propagating, the risk of an accidental premature release into nature is minimized, and [4] in the case that active gene drive mechanisms prove impossible to develop, the MLA approach can be used as a back-up transgene dispersal mechanism for disease control efforts

  9. Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases.

    Science.gov (United States)

    Muñoz, Marina; Ríos-Chaparro, Dora Inés; Patarroyo, Manuel Alfonso; Ramírez, Juan David

    2017-03-14

    Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes' contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity.

  10. A single multilocus sequence typing (MLST scheme for seven pathogenic Leptospira species.

    Directory of Open Access Journals (Sweden)

    Siriphan Boonsilp

    Full Text Available The available Leptospira multilocus sequence typing (MLST scheme supported by a MLST website is limited to L. interrogans and L. kirschneri. Our aim was to broaden the utility of this scheme to incorporate a total of seven pathogenic species.We modified the existing scheme by replacing one of the seven MLST loci (fadD was changed to caiB, as the former gene did not appear to be present in some pathogenic species. Comparison of the original and modified schemes using data for L. interrogans and L. kirschneri demonstrated that the discriminatory power of the two schemes was not significantly different. The modified scheme was used to further characterize 325 isolates (L. alexanderi [n = 5], L. borgpetersenii [n = 34], L. interrogans [n = 222], L. kirschneri [n = 29], L. noguchii [n = 9], L. santarosai [n = 10], and L. weilii [n = 16]. Phylogenetic analysis using concatenated sequences of the 7 loci demonstrated that each species corresponded to a discrete clade, and that no strains were misclassified at the species level. Comparison between genotype and serovar was possible for 254 isolates. Of the 31 sequence types (STs represented by at least two isolates, 18 STs included isolates assigned to two or three different serovars. Conversely, 14 serovars were identified that contained between 2 to 10 different STs. New observations were made on the global phylogeography of Leptospira spp., and the utility of MLST in making associations between human disease and specific maintenance hosts was demonstrated.The new MLST scheme, supported by an updated MLST website, allows the characterization and species assignment of isolates of the seven major pathogenic species associated with leptospirosis.

  11. Assessment of two multilocus sequence typing (MLST) schemes available for Streptococcus mutans.

    Science.gov (United States)

    Momeni, Stephanie S; Whiddon, Jennifer; Cheon, Kyounga; Moser, Stephen A; Childers, Noel K

    2015-12-01

    Two multilocus sequencing typing (MLST) schemes are currently available for Streptococcus mutans. The first, introduced by Nakano et al. in 2007, consists of 8 conserved housekeeping genes. The second, introduced in 2010 by Do et al., includes 6 housekeeping genes and 2 putative virulence genes. The purpose of the current study was to compare the two MLST schemes for use in validating repetitive extragenic palindromic polymerase chain reaction (rep-PCR) genotypes. Thirty-three S. mutans isolates, representing the 11 most commonly occurring rep-PCR genotype groups, were selected for MLST. MLST was performed with SYBR Green™ PCR with published primers for both MLST schemes. Amplicons were purified, sequenced, and data checked against the www.PubMLST.org database for allelic and sequence type (ST) assignment. Discriminatory power, congruence, and convenience criteria were evaluated. Concatenated sequences for each scheme were analyzed using MEGA to generate phylogenetic trees using minimum evolution with bootstrap. No significant difference in discriminatory power was observed between the two MLST schemes for S. mutans. Clonal clusters were consistent for both schemes. Overall, MLST demonstrated marginally greater discriminatory power than rep-PCR; however all methods were found to be congruent. New alleles and ST are reported for each scheme and added to the PubMLST database. Clonality, supported by both methods and rep-PCR, indicates S. mutans genotypes are shared between unrelated subjects. Both Nakano and Do schemes demonstrates similar genotype discrimination for S. mutans isolates suggesting each are well designed and may be used to verify rep-PCR genotypes. Copyright © 2015. Published by Elsevier Ltd.

  12. Multilocus Genetic Characterization of Lactobacillus fermentum Isolated from Ready-to-Eat Canned Food.

    Science.gov (United States)

    Sulaiman, Irshad M; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

    2017-06-01

    The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.

  13. Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing

    Science.gov (United States)

    Hoffmaster, Alex R; Novak, Ryan T; Marston, Chung K; Gee, Jay E; Helsel, Leta; Pruckler, James M; Wilkins, Patricia P

    2008-01-01

    Background Bacillus cereus is most commonly associated with foodborne illness (diarrheal and emetic) but is also an opportunistic pathogen that can cause severe and fatal infections. Several multilocus sequence typing (MLST) schemes have recently been developed to genotype B. cereus and analysis has suggested a clonal or weakly clonal population structure for B. cereus and its close relatives B. anthracis and B. thuringiensis. In this study we used MLST to determine if B. cereus isolates associated with illnesses of varying severity (e.g., severe, systemic vs. gastrointestinal (GI) illness) were clonal or formed clonal complexes. Results A retrospective analysis of 55 clinical B. cereus isolates submitted to the Centers for Disease Control and Prevention between 1954 and 2004 was conducted. Clinical isolates from severe infections (n = 27), gastrointestinal (GI) illness (n = 18), and associated isolates from food (n = 10) were selected for analysis using MLST. The 55 isolates were diverse and comprised 38 sequence types (ST) in two distinct clades. Of the 27 isolates associated with serious illness, 13 clustered in clade 1 while 14 were in clade 2. Isolates associated with GI illness were also found throughout clades 1 and 2, while no isolates in this study belonged to clade 3. All the isolates from this study belonging to the clade 1/cereus III lineage were associated with severe disease while isolates belonging to clade1/cereus II contained isolates primarily associated with severe disease and emetic illness. Only three STs were observed more than once for epidemiologically distinct isolates. Conclusion STs of clinical B. cereus isolates were phylogenetically diverse and distributed among two of three previously described clades. Greater numbers of strains will need to be analyzed to confirm if specific lineages or clonal complexes are more likely to contain clinical isolates or be associated with specific illness, similar to B. anthracis and emetic B. cereus

  14. Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

    Science.gov (United States)

    de Been, Mark; Pinholt, Mette; Top, Janetta; Bletz, Stefan; Mellmann, Alexander; van Schaik, Willem; Brouwer, Ellen; Rogers, Malbert; Kraat, Yvette; Bonten, Marc; Corander, Jukka; Westh, Henrik; Harmsen, Dag; Willems, Rob J L

    2015-12-01

    Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism(SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

  15. Death or survival from invasive pneumococcal disease in Scotland: associations with serogroups and multilocus sequence types

    Science.gov (United States)

    Lamb, Karen; Diggle, Mathew; Robertson, Chris; Greenhalgh, David; Mitchell, Tim J.; Smith, Andrew; Jefferies, Johanna M. C.; Clarke, Stuart C.; McMenamin, Jim; Edwards, Giles F. S.

    2011-01-01

    We describe associations between death from invasive pneumococcal disease (IPD) and particular serogroups and sequence types (STs) determined by multilocus sequence typing (MLST) using data from Scotland. All IPD episodes where blood or cerebrospinal fluid (CSF) culture isolates were referred to the Scottish Haemophilus, Legionella, Meningococcal and Pneumococcal Reference Laboratory (SHLMPRL) from January 1992 to February 2007 were matched to death certification records by the General Register Office for Scotland. This represented 5959 patients. The median number of IPD cases in Scotland each year was 292. Deaths, from any cause, within 30 days of pneumococcal culture from blood or CSF were considered to have IPD as a contributing factor. Eight hundred and thirty-three patients died within 30 days of culture of Streptococcus pneumoniae from blood or CSF [13.95 %; 95 % confidence interval (13.10, 14.80)]. The highest death rates were in patients over the age of 75. Serotyping data exist for all years but MLST data were only available from 2001 onward. The risk ratio of dying from infection due to particular serogroups or STs compared to dying from IPD due to all other serogroups or STs was calculated. Fisher’s exact test with Bonferroni adjustment for multiple testing was used. Age adjustment was accomplished using the Cochran–Mantel–Haenszel test and 95 % confidence intervals were reported. Serogroups 3, 11 and 16 have increased probability of causing fatal IPD in Scotland while serogroup 1 IPD has a reduced probability of causing death. None of the 20 most common STs were significantly associated with death within 30 days of pneumococcal culture, after age adjustment. We conclude that there is a stronger association between a fatal outcome and pneumococcal capsular serogroup than there is between a fatal outcome and ST. PMID:21393453

  16. A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae)

    Science.gov (United States)

    2014-01-01

    Background Bushbabies (Galagidae) are among the most morphologically cryptic of all primates and their diversity and relationships are some of the most longstanding problems in primatology. Our knowledge of galagid evolutionary history has been limited by a lack of appropriate molecular data and a paucity of fossils. Most phylogenetic studies have produced conflicting results for many clades, and even the relationships among genera remain uncertain. To clarify galagid evolutionary history, we assembled the largest molecular dataset for galagos to date by sequencing 27 independent loci. We inferred phylogenetic relationships using concatenated maximum-likelihood and Bayesian analyses, and also coalescent-based species tree methods to account for gene tree heterogeneity due to incomplete lineage sorting. Results The genus Euoticus was identified as sister taxon to the rest of the galagids and the genus Galagoides was not recovered as monophyletic, suggesting that a new generic name for the Zanzibar complex is required. Despite the amount of genetic data collected in this study, the monophyly of the family Lorisidae remained poorly supported, probably due to the short internode between the Lorisidae/Galagidae split and the origin of the African and Asian lorisid clades. One major result was the relatively old origin for the most recent common ancestor of all living galagids soon after the Eocene-Oligocene boundary. Conclusions Using a multilocus approach, our results suggest an early origin for the crown Galagidae, soon after the Eocene-Oligocene boundary, making Euoticus one of the oldest lineages within extant Primates. This result also implies that one – or possibly more – stem radiations diverged in the Late Eocene and persisted for several million years alongside members of the crown group. PMID:24694188

  17. Development and evaluation of a multi-locus sequence typing scheme for Mycoplasma synoviae.

    Science.gov (United States)

    Dijkman, R; Feberwee, A; Landman, W J M

    2016-08-01

    Reproducible molecular Mycoplasma synoviae typing techniques with sufficient discriminatory power may help to expand knowledge on its epidemiology and contribute to the improvement of control and eradication programmes of this mycoplasma species. The present study describes the development and validation of a novel multi-locus sequence typing (MLST) scheme for M. synoviae. Thirteen M. synoviae isolates originating from different poultry categories, farms and lesions, were subjected to whole genome sequencing. Their sequences were compared to that of M. synoviae reference strain MS53. A high number of single nucleotide polymorphisms (SNPs) indicating considerable genetic diversity were identified. SNPs were present in over 40 putative target genes for MLST of which five target genes were selected (nanA, uvrA, lepA, ruvB and ugpA) for the MLST scheme. This scheme was evaluated analysing 209 M. synoviae samples from different countries, categories of poultry, farms and lesions. Eleven clonal clusters and 76 different sequence types (STs) were obtained. Clustering occurred following geographical origin, supporting the hypothesis of regional population evolution. M. synoviae samples obtained from epidemiologically linked outbreaks often harboured the same ST. In contrast, multiple M. synoviae lineages were found in samples originating from swollen joints or oviducts from hens that produce eggs with eggshell apex abnormalities indicating that further research is needed to identify the genetic factors of M. synoviae that may explain its variations in tissue tropism and disease inducing potential. Furthermore, MLST proved to have a higher discriminatory power compared to variable lipoprotein and haemagglutinin A typing, which generated 50 different genotypes on the same database.

  18. Genetic distance estimated by RAPD markers and its relationship with hybrid performance in maize Distância genética estimada por marcadores RAPD e sua relação com o desempenho de híbridos em milho

    Directory of Open Access Journals (Sweden)

    Daniela Cristina Bruel

    2006-10-01

    Full Text Available The objective of this work was to evaluate the genetic diversity of 16 maize inbred lines, and to determine the correlation between genetic distance and hybrid performance, using random amplified polymorphic DNA (RAPD molecular markers. Twenty-two different random primers were used, which resulted in the amplification of 265 fragments, 237 (84.44% of them being polymorphic. A genetic similarity matrix was created from the RAPD data, using Jaccard coefficient, and a dendrogram was constructed. Hybrid analyses were carried out using random block design and Griffing method VI for diallel crossings. The genetic associations showed five distinct heterotic groups. Correlations between genetic divergences detected by RAPD, as well as the means observed in the diallel crossings were positive and significant for plant height, ear height, prolificacy, and grain weight. The correlation of genetic divergences, detected by RAPD, and the specific combining ability between heterotic group associations, showed significance in all characteristics under study, except prolificacy. A direct relationship between genetic divergence and productivity was found in 79.2% of the 120 hybrids confirming the hypothesis that genetic divergence is directly related to the performance of hybrids and is efficient in predicting it.Este trabalho teve por objetivo utilizar marcadores moleculares de DNA (RAPD, para analisar a diversidade genética entre 16 linhagens elite de milho e estimar a correlação entre a distância e o desempenho de híbridos. Vinte e dois primers aleatórios resultaram na amplificação de 265 fragmentos, dos quais 237 (84,44% foram polimórficos. A partir dos marcadores RAPD, uma matriz de similaridade genética foi gerada, tendo-se usado o coeficiente de Jaccard, e um dendrograma foi construído. Para a avaliação dos híbridos resultantes dos dialelos, utilizaram-se blocos ao acaso e o método IV de Griffing. As associações genéticas obtidas

  19. Clonal expansion of the Pseudogymnoascus destructans genotype in North America is accompanied by significant variation in phenotypic expression.

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    Jordan Khankhet

    Full Text Available Pseudogymnoascus destructans is the causative agent of an emerging infectious disease that threatens populations of several North American bat species. The fungal disease was first observed in 2006 and has since caused the death of nearly six million bats. The disease, commonly known as white-nose syndrome, is characterized by a cutaneous infection with P. destructans causing erosions and ulcers in the skin of nose, ears and/or wings of bats. Previous studies based on sequences from eight loci have found that isolates of P. destructans from bats in the US all belong to one multilocus genotype. Using the same multilocus sequence typing method, we found that isolates from eastern and central Canada also had the same genotype as those from the US, consistent with the clonal expansion of P. destructans into Canada. However, our PCR fingerprinting revealed that among the 112 North American isolates we analyzed, three, all from Canada, showed minor genetic variation. Furthermore, we found significant variations among isolates in mycelial growth rate; the production of mycelial exudates; and pigment production and diffusion into agar media. These phenotypic differences were influenced by culture medium and incubation temperature, indicating significant variation in environmental condition--dependent phenotypic expression among isolates of the clonal P. destructans genotype in North America.

  20. Analysis of population genetic structure and variability using RAPD markers in the endemic and endangered Limonium dufourii (Plumbaginaceae).

    Science.gov (United States)

    Palacios, C; González-Candelas, F

    1997-12-01

    Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii. The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii, which is a requisite in order to establish efficient conservation measures for this species.