Sample records for molecular markers rapd

  1. Assessing Cheatgrass (Bromus tectorum) genetic diversity and population structure using RAPD and microsatellite molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two molecular marker systems, random amplified polymorphic DNA (RAPD) and microsatellites, were used to evaluate population diversity and differentiation in four northern Nevada Bromus tectorum populations. We found 16 RAPD primers that yielded 165 strong repeatable bands. Of those bands, 60 (35.8%...

  2. Identification of RAPD markers and their use for molecular mapping in pea (Pisum sativum L.).

    PubMed

    Cheghamirza, Kianoosh; Koveza, Oksana; Konovalov, Fedor; Gostimsky, Sergei

    2002-01-01

    The RAPD method (Random Amplified Polymorphic DNA) was used for identifying and mapping new molecular markers in pea. RAPD analysis of various cultivars and lines of pea was carried out using 10-mer random primers. The presence of multiple polymorphism between cultivars and lines was revealed; at least one fragment for any given primer was present in the DNA of one form of pea and absent in the DNA of another line or cultivar. To detect molecular markers linked to the genes of chi-15, xa-18 and also to the 12 morphological markers of the L-1238 line, the F2 populations (Chi-15 ? L-1238), (Vio ? L-1238), (Xa-18 ? L-1238), (L-111 ? Chi-15) and (L-84 ? Xa-18) were studied via bulked segregant analysis. DNA molecular analysis of F1 hybrids revealed the presence of parental polymorphic fragments in all of the populations. The study of the F2 plants showed that the obtained fragments are inherited as Mendelian factors. 13 RAPD-markers linked to genes of A/a (flower color), I/i (seed color), Gp/gp (pod color), R/r (seed form), S/s (seeds linkage), and also to genes of Chi-15/chi-15 (leaf color) and Xa-18/xa-18 (leaf color) were discovered. The study of individual plant DNA from the F2 populations allowed us to determine the genetic distances between genes and the RAPD markers linked to them. PMID:12378223

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

    PubMed

    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. PMID:24562682

  4. Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs

    Microsoft Academic Search

    M. Ragot; D. A. Hoisington

    1993-01-01

    Three molecular marker protocols, chemiluminescent restriction fragment length polymorphisms (c-RFLPs), radioactivity-based restriction fragment length polymorphisms (r-RFLPs), and randomly amplified DNA polymorphisms (RAPDs) were compared in terms of cost and time efficiency. Estimates of cost of supplies and time requirements were obtained from simulations of maize (Zea mays L.) genotyping experiments utilizing protocols currently in use. The increase in total cost

  5. Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee

    Microsoft Academic Search

    Greg J. Hunt; Robert E. Page

    1992-01-01

    The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random

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

    PubMed

    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. PMID:19350481

  7. [RAPD and SCAR molecular markers linked to the sexuality of cycads (Cycas tanqingii D. Y. Wang)].

    PubMed

    Jing, Jian-Zhou; Jin, Hong; Li, Dong-Liang; Chen, Xiao-Ke; Zhang, Yong

    2007-11-01

    The random amplified polymorphic DNA (RAPD) technique was used to amplify DNA fragment, aiming at finding markers linked to the sex trait in Cycas tanqingii D. Y. Wang. A total number of 160 random primers were screened in the RAPD-PCR and more than 2500 RAPD fragments were generated from the male or the female plants. One fragment of about 500 bp was amplified steadily and repeatedly by the S0465 (CCCCGGTAAC) primer only from female plants but not male plants. The RAPD marker was then converted into female-linked dominant SCAR (Sequence Characterized Amplified Regions) marker named STQC-S465-483. The development of this sex-linked SCAR marker provides a possibility of identifying the sex of Cycas tanqingii before sexual maturation, which is very important to in situ or ex situ conservation. PMID:18257243

  8. Molecular identification of five Indian sciaenids (pisces: perciformes, sciaenidae) using RAPD markers

    Microsoft Academic Search

    Wazir S. Lakra; M. Goswami; V. Mohindra; K. K. Lal; P. Punia

    2007-01-01

    The randomly amplified polymorphic DNA (RAPD) markers were used to detect interspecific genetic variability and genetic relatedness\\u000a among five Indian sciaenids namely Otolithes cuvieri, Johnieops sina, Johnieops macrorhynus, Johnieops vogleri and Protonibea diacanthus for the first time. Eight RAPD primers (OPA01, OPA06, OPA07, OPA18, OPP12, OPP14, OPP16 and OPP11) generated 40 species specific\\u000a diagnostic bands. The highest genetic divergence was

  9. Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker

    PubMed Central

    Khatun, M. Mahfuza; Hossain, Khondoker Moazzem; Mahbubur Rahman, S. M.

    2012-01-01

    In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle’s were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources. PMID:25049622

  10. Molecular Characterization of Selected Local and Exotic Cattle Using RAPD Marker.

    PubMed

    Khatun, M Mahfuza; Hossain, Khondoker Moazzem; Mahbubur Rahman, S M

    2012-06-01

    In order to develop specific genetic markers and determine the genetic diversity of Bangladeshi native cattle (Pabna, Red Chittagong) and exotic breeds (Sahiwal), randomly amplified polymorphic DNA (RAPD) analysis was performed using 12 primers. Genomic DNA was extracted from 20 cattle (local and exotic) blood samples and extracted DNA was observed by gel electrophoresis. Among the random primers three were matched and found to be polymorphic. Genetic relations between cattle's were determined by RAPD polymorphisms from a total of 66.67%. Statistical analysis of the data, estimating the genetic distances between cattle and sketching the cluster trees were estimated by using MEGA 5.05 software. Comparatively highest genetic distance (0.834) was found between RCC-82 and SL-623. The lowest genetic distance (0.031) was observed between M-1222 and M-5730. The genetic diversity of Red Chittagong and Sahiwal cattle was relatively higher for a prescribed breed. Adequate diversity in performance and adaptability can be exploited from the study results for actual improvement accruing to conservation and development of indigenous cattle resources. PMID:25049622

  11. FROM RAPDS TO SNPS: THE DEVELOPMENT OF MORE EFFECTIVE AND EFFICIENT MOLECULAR MARKERS IN CUCUMBER (CUCUMIS SATIVUS L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic base of cucumber is narrow (3-8%), and thus, the recovery of new markers from screening experiments is typically low. The majority of markers on current genetic linkage maps are RAPDs, which are inefficient for genotyping numerous individuals during marker-assisted selection (MAS). The...

  12. Identification of apple cultivars using RAPD markers

    Microsoft Academic Search

    B. Koller; A. Lehmann; J. M. McDermott; C. Gessler

    1993-01-01

    Eleven apple cultivars were differentiated using randomly amplified polymorphic DNA (RAPD) markers obtained by the polymerase chain reaction (PCR). The variability of the technique and of the origin of the DNA extract was analyzed. A set of bands consistent in their presence or absence was chosen to create a differentiating band pattern. A key is proposed by which one can

  13. Molecular variation of Sporisorium scitamineum in mainland China revealed by RAPD and SRAP markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sugarcane smut caused by the fungus Sporisorium scitamineum is found worldwide in sugarcane producing countries and can cause serious loss in stalk yield and sugar quality. In order to reveal the molecular evolution of S. scitamineum, twenty-three S. scitamineum isolates collected from the six prima...

  14. Molecular Profiling for Genetic Variability in Capsicum Species Based on ISSR and RAPD Markers

    Microsoft Academic Search

    Sanjog T. Thul; Mahendra P. Darokar; Ajit K. Shasany; Suman P. S. Khanuja

    The taxonomic identity of Capsicum species is found to be difficult as it displays variations at morpho-chemical characters. Twenty-two accessions of six Capsicum species, namely, C. annuum, C. baccatum, C. chinense, C. eximium, C. frutescens, and C. luteum were investigated for phenotypic diversity based on flower color and for genetic differences by molecular makers. The genetic\\u000a cluster analyses of 27

  15. Screening and Characterization of RAPD Markers in Viscerotropic Leishmania Parasites

    PubMed Central

    Mkada–Driss, Imen; Talbi, Chiraz; Guerbouj, Souheila; Driss, Mehdi; Elamine, Elwaleed M.; Cupolillo, Elisa; Mukhtar, Moawia M.; Guizani, Ikram

    2014-01-01

    Visceral leishmaniasis (VL) is mainly due to the Leishmania donovani complex. VL is endemic in many countries worldwide including East Africa and the Mediterranean region where the epidemiology is complex. Taxonomy of these pathogens is under controversy but there is a correlation between their genetic diversity and geographical origin. With steady increase in genome knowledge, RAPD is still a useful approach to identify and characterize novel DNA markers. Our aim was to identify and characterize polymorphic DNA markers in VL Leishmania parasites in diverse geographic regions using RAPD in order to constitute a pool of PCR targets having the potential to differentiate among the VL parasites. 100 different oligonucleotide decamers having arbitrary DNA sequences were screened for reproducible amplification and a selection of 28 was used to amplify DNA from 12 L. donovani, L. archibaldi and L. infantum strains having diverse origins. A total of 155 bands were amplified of which 60.65% appeared polymorphic. 7 out of 28 primers provided monomorphic patterns. Phenetic analysis allowed clustering the parasites according to their geographical origin. Differentially amplified bands were selected, among them 22 RAPD products were successfully cloned and sequenced. Bioinformatic analysis allowed mapping of the markers and sequences and priming sites analysis. This study was complemented with Southern-blot to confirm assignment of markers to the kDNA. The bioinformatic analysis identified 16 nuclear and 3 minicircle markers. Analysis of these markers highlighted polymorphisms at RAPD priming sites with mainly 5? end transversions, and presence of inter– and intra– taxonomic complex sequence and microsatellites variations; a bias in transitions over transversions and indels between the different sequences compared is observed, which is however less marked between L. infantum and L. donovani. The study delivers a pool of well-documented polymorphic DNA markers, to develop molecular diagnostics assays to characterize and differentiate VL causing agents. PMID:25313833

  16. A review of random amplified polymorphic DNA (RAPD) markers in fish research

    Microsoft Academic Search

    Bahy A. Ali; Tian-Hua Huang; Da-Nian Qin; Xiao-Mei Wang

    2004-01-01

    During the last 15 years, molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The ease and simplicity of RAPD (randomly amplified polymorphic DNA) techniques make it ideal for genetic mapping, plant and animal breeding programs, and DNA fingerprinting, with particular utility in the field of population genetics. This review summarizes the use of RAPD

  17. Elucidating Genetic Diversity among Sour Orange Rootstocks: a Comparative Study of the Efficiency of RAPD and SSR Markers.

    PubMed

    Lamine, Myriam; Mliki, Ahmed

    2015-03-01

    In order to compare the effectiveness of two molecular marker systems, a set of six RAPD and nine SSR markers were used to study the genetic diversity in a population of 46 sour orange accessions, a common rootstock used in almost all citrus orchards in Tunisia. Genetic diversity parameters [average and effective number of alleles, percentage of polymorphism, polymorphic information content (PIC), effective marker index (EMI), and marker index (MI) parameters] for RAPD, SSR, and RAPD?+?SSR were determined in order to assess the efficiency of the two marker systems. The results revealed that these parameters were significantly higher when using RAPD markers. Similarly, cluster analysis using the results of RAPD was practically the same as that obtained when combining data from the two marker systems (RAPD?+?SSR) demonstrating the efficiency of RAPD in discriminating between sour orange accessions. Therefore, the use of SSR markers, known to be more efficient and discriminatory, does not bring significant supplementary information in this work. Indeed, results would have been obtained using only the RAPD markers. Accordingly, this work highlights the efficiency and advantages of RAPD, as an easy and efficient technique, in studying citrus rootstock's genetic diversity, and establishing genetic relationships among citrus accessions. PMID:25586488

  18. A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers.

    PubMed

    Yu, Xiaoxia; Li, Xiaolei; Ma, Yanhong; Yu, Zhuo; Li, Zaozhe

    2012-03-30

    Using a population of 105 interspecific F(2) hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. 'Fairway' as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future. PMID:22462407

  19. Use of AFLP and RAPD molecular genetic markers and cytogenetic analysis to explore relationships among taxa of the Patagonian Bromus setifolius complex

    PubMed Central

    2009-01-01

    Bromus setifolius var. pictus (Hook) Skottsb., B. setifolius var. setifolius Presl. and B.setifolius var. brevifolius Ness are three native Patagonian taxa in the section Pnigma Dumort of the genus Bromus L. AFLP and RAPD analysis, in conjunction with genetic distance measurements and statistical techniques, revealed variation within this group and indicated that B. setifolius var. brevifolius was closely related to B. setifolius var. pictus, with both taxa being more distantly related to B. setifolius var. setifolius. Cytogenetic analysis confirmed the chromosomal number of B. setifolius var. pictus (2n = 70) and B. setifolius var. setifolius (2n = 28) and showed for the first time that B. setifolius var. brevifolius had 2n = 70. The combination of molecular genetic and cytogenetic evidence supported a species status for two of the three taxa and suggested hypotheses for the evolutionary origin of these complex taxa. Species status was also indicated for B. setifolius var. setifolius. Based on these findings, we suggest that B. setifolius var. pictus be referred to as B. pictus Hook var. pictus, and B. setifolius var brevifolius as B. pictus Hook var brevifolius. The correlation between AFLP diversity and variation in ecological parameters suggested that this marker system could be used to assess breeding progress and to monitor the domestication of Patagonian Bromus species for agronomic use. PMID:21637686

  20. A method to measure genetic distance between allogamous populations of alfalfa (Medicago sativa) using RAPD molecular markers.

    PubMed

    Ghérardi, M; Mangin, B; Goffinet, B; Bonnet, D; Huguet, T

    1998-03-01

    Alfalfa (Medicago sativa L.) is a forage legume of world-wide importance whose both allogamous and autotetraploid nature maximizes the genetic diversity within natural and cultivated populations. This genetic diversity makes difficult the discrimination between two related populations. We analyzed this genetic diversity by screening DNA from individual plants of eight cultivated and natural populations of M. sativa and M. ?falcata using the RAPD method. A high level of genetic variation was found within and between populations. Using five primers, 64 intense bands were scored as present or absent across all populations. Most of the loci were revealed to be highly polymorphic whereas very few population-specific polymorphisms were identified. From these observations, we adopted a method based on the Roger's genetic distance between populations using the observed frequency of bands to discriminate populations pairwise. Except for one case, the between-population distances were all significantly different from zero. We have also determined the minimal number of bands and individuals required to test for the significance of between-population distances. PMID:24710879

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

    Microsoft Academic Search

    J. B. dos Santos; J. Nienhuis; P. Skroch; J. Tivang; M. K. Slocum

    1994-01-01

    Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars.

  2. Miscanthus: genetic diversity and genotype identification using ISSR and RAPD markers.

    PubMed

    Cichorz, Sandra; Go?ka, Maria; Litwiniec, Anna

    2014-10-01

    Due to the limited number of molecular studies focused on European gene pool investigation, it is necessary to perform plant material recognition. Eighteen accessions of three Miscanthus species, namely, M. × giganteus, M. sinensis, M. sacchariflorus were evaluated with the use of molecular marker systems such as: inter simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPD), and by estimation of ploidy level based on flow cytometry. As a result, only one ISSR primer (ISSR1) and three RAPD primers (RAPD1, RAPD2, RAPD4) were required to identify all genotypes. Moreover, the use of the above mentioned molecular markers enable the proper species recognition of the interspecific hybrid M. × giganteus "Floridulus," which has been previously mislabeled as M. floridulus. The highest genetic similarity coefficient (0.94) was observed between M. × giganteus clones, which indicates that the genetic diversity within this species was very low. Whereas M. sinensis genotypes represented a relatively wide diversity with similarity coefficient of 0.58. Cluster analysis using UPGMA grouped the 18 accessions in three clusters according to species affiliation including relabeled M. × giganteus "Floridulus," which proved to be closely related to M.  × giganteus. Similar groupings were evident in the PCoA analysis. PMID:24880640

  3. Assessment of genetic relatedness of the genera Ananas and Pseudananas confirmed by RAPD markers

    Microsoft Academic Search

    Claudete de Fátima Ruas; Paulo Maurício Ruas; José Renato S. Cabral

    2001-01-01

    Genetic relationships among 18 accessions, including 16 of Ananas and two of Pseudananas, were investigated using RAPD molecular markers. The procedure for DNA extraction was adapted from the method of Dellaporta\\u000a et al. (1983) where an incubation in proteinase K and a purification step were included. From the total of 148 markers scored,132\\u000a (89.2%) were polymorphic. The similarity matrix was

  4. Evaluation of RFLP and RAPD markers in a comparison of Brassica napus breeding lines

    Microsoft Academic Search

    C. Halldén; N.-O. Nilsson; I. M. Rading; T. Säll

    1994-01-01

    RFLP and RAPD markers were evaluated and compared for their ability to determine genetic relationships in a set of three B. napus breeding lines. Using a total of 50 RFLP and 92 RAPD markers, the relatedness between the lines was determined. In total, the RFLP and the RAPD analysis revealed more than 500 and 400 bands, respectively. The relative frequencies

  5. Genetic relationship of Mediterranean mandarins (Citrus deliciosa Tenore) using RAPD markers

    Microsoft Academic Search

    M. A. Machado; H. D. Coletta Filho; M. L. P. N. Targon; J. Pompeu

    1995-01-01

    Random amplified polymorphic DNA (RAPD) analysis was carried out to evaluate polymorphism and genetic similarity between 39 Mediterranean mandarin genotypes. One hundred eleven amplification products were identified using 21 random primers. An average of 2.2 RAPD markers was obtained for each primer, corresponding to 42% of the amplification products. Genotype-specific RAPD markers were also found, mainly in known hybrids. UPGMA

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

    PubMed Central

    2010-01-01

    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. PMID:21637428

  7. The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var.

    E-print Network

    Macdonald, Ellen

    The development of RAPD and microsatellite markers in lodgepole pine (Pinus contorta var. latifolia pine (Pinus contorta var. latifolia) have been developed. We detected 52 decameric oligonucleotides polymorphism, RAPD, microsatellite, SSR, Pinus contorta var. latifolia. Résumé : Deux types de marqueurs

  8. RAPD markers in diversity detection and variety identification of Tibetan hulless barley

    Microsoft Academic Search

    Zeng Yu; Lan Li-Qiong; Luo Huan; Bai Jie; Yang Man-Ye; Miao Chen; Cai Ying-Fan; Qiang Xiao-Lin; Chen Fang

    2002-01-01

    RAPD markers were generated from 6 groups of Tibetan hulless barley (23 varieties): Lasagoumang, QB, Zangqing, Guoluo, Dongqing,\\u000a and Hymalayia. Of the 48 fragments generated by 5 selected primers (among 68 primers), 44 appeared to be polymorphic (92%).\\u000a Cluster analysis was performed (RAPDistance 1.04). The 23 varieties were divided into 2 groups, and the molecular foundation\\u000a of genetic diversity was

  9. Molecular analysis of silver crucian carp ( Carassius auratus gibelio Bloch) clones by SCAR markers

    Microsoft Academic Search

    Li Zhou; Yang Wang; Jian-Fang Gui

    2001-01-01

    Random amplified polymorphic DNA (RAPD) molecular markers specific for one, two or three clones have been identified from five gynogenetic clones of silver crucian carp (Carassius auratus gibelio Bloch) using RAPD markers developed earlier. In this study, three RAPD markers (RA1-PA, RA2-EF and RA4-D) produced by Opj-1, and two RAPD DNA fragments (RA3-PAD and RA5-D) produced by Opj-7, were selected

  10. A comparative analysis of the genetic diversity between inbred lines of Zinnia elegans using morphological traits and RAPD and ISSR markers

    Microsoft Academic Search

    Y. M. Ye; J. W. Zhang; G. G. Ning; M. Z. Bao

    2008-01-01

    Genetic diversity within Zinnia elegans is key to the genetic improvement of this important ornamental species. Here, morphological traits and RAPD and ISSR molecular markers were used to assess levels of polymorphism across 20 inbred lines. Thirty-four morphological traits were scored and also 147 RAPD marker-fragments, as amplified by 12 arbitrary primers, and 128 ISSR marker-fragments as generated by 9

  11. Use of RAPD and AFLP markers to identify inter- and intraspecific hybrids of Mentha.

    PubMed

    Shasany, A K; Darokar, M P; Dhawan, S; Gupta, A K; Gupta, S; Shukla, A K; Patra, N K; Khanuja, S P S

    2005-01-01

    Three controlled crosses were carried out involving Mentha arvensis and Mentha spicata [M. spicata CIMAP/C30 x M. spicata CIMAP/C33 (cv. Neera); M. arvensis CIMAP/C18 x CIMAP/C17 (cv. Kalka); and M. arvensis CIMAP/C17 x M. spicata CIMAP/C33]. The parents were subjected to random amplified polymorphic DNA (RAPD) analysis with 80 primers, and polymorphic primers were tested for detecting coinherited RAPD profiles among the progeny of these crosses. Of 50 seedlings tested from each intraspecific cross, all demonstrated dominant profiles with the selected RAPD primers except the detected hybrid from respective crosses. Coinherited markers could be detected with the primers OPJ 01, MAP 06, OPT 08, and OPO 20 for M. arvensis; OPJ 05, OPJ 14, OPO 19, and OPT 09 for M. spicata; and OPJ 07, OPJ 10, OPJ 11, OPJ 14, and OPO 02 for the cross M. arvensis x M. spicata. In our amplified fragment length polymorphism (AFLP) analysis, 40 coinherited marker fragments were identified for the cross involving M. arvensis, 32 for the cross involving M. spicata, and 41 for the interspecific cross between M. arvensis and M. spicata. In all crosses, similarity values between the parents were less than those between the parents and the hybrids. Although RAPD markers are generally considered dominant, it is possible to identify a few codominant markers that behave like restriction fragment length polymorphism (RFLP) markers. This molecular marker system may be helpful in rapidly screening out hybrids in crops where cross-pollination is a problem. PMID:16135712

  12. Template mixing: a method of enhancing detection and interpretation of codominant RAPD markers

    Microsoft Academic Search

    T. M. Davis; H. Yu; K. M. Haigis; P. J. McGowan

    1995-01-01

    Ten codominant RAPD markers, ranging in size from about 300 to about 1350 bp, were identified in mapping populations of chickpea (Cicer arietinum L.) and diploid strawberry (Fragaria vesca L.). A distinguishing feature of all ten markers, and perhaps of codominant RAPD markers in general, was the presence in heterozygous individuals of a non-parental, heteroduplex band migrating more slowly than

  13. Analysis of annual Medicago species using RAPD markers.

    PubMed

    Brummer, E C; Bouton, J H; Kochert, G

    1995-04-01

    Annual species of the genus Medicago have attracted interest as green manure and temporary forage crops. This study was conducted to determine if randomly amplified polymorphic DNA (RAPD) markers could be used to assess the variability within and among species. Several accessions of each six species (M. scutellata Mill., M. disciformis DC., M. murex Willd., M. truncatula Gaertn., M. polymorpha L., and M. rugosa Desr.) were studied. A phylogeny reconstructed with the computer program Phylogenetic Analysis Using Parsimony (PAUP) showed the same relationships as traditional taxonomy. Variation was present among accessions of all species. Several accessions were considerably different from others within the species (one of each M. scutellata and M. polymorpha) and four accessions of M. murex were differentiated by both morphology and RAPD banding patterns from the other accessions. These accessions may be useful to include in a core collection. Variation within accessions was present. Although the species are autogamous, the original seed collections may have been made from a number of plants in the same area. Also, some outcrossing or seed mixing may have occurred. Finally, at least 10 RAPD primers appear to be necessary in order to develop reliable estimates of relatedness among annual Medicago accessions. PMID:7774803

  14. Identification of random amplified polymorphic DNA (RAPD) marker for differentiating male from female and sporophytic thalli of Gracilaria changii (Rhodophyta)

    Microsoft Academic Search

    M. C. Sim; P. E. Lim; S. Y. Gan; S. M. Phang

    2007-01-01

    There have been limited reports on molecular sex markers for macroalgae. We report the use of random amplified polymorphic\\u000a DNA analysis (RAPD) to identify molecular sex markers for Gracilaria changii (Xia et Abbott) Abbott, Zhang et Xia. Two DNA extraction methods were used: a modified CTAB and phenol-chloroform combination\\u000a method and the DNeasy Plant Mini Kit. The CTAB and phenol-chloroform

  15. Analysis of the genetic diversity among mandarins (Citrus spp.) using RAPD markers

    Microsoft Academic Search

    H. D. Coletta Filho; M. A. Machado; M. L. P. N. Targon; M. C. P. Q. D. G. Moreira; J. Pompeu

    1998-01-01

    RAPD markers were used to evaluate genetic similarity among 35 mandarin accessions, including 10 species and 7 hybrids. One\\u000a octamer and twenty-two decamer primers produced 109 RAPDs, 45 of which were polymorphic. Jaccard coefficient was used to calculate\\u000a genetic similarity, and UPGMA to generate the phenogram. The RAPDs obtained were sufficient to generate some accession-specific\\u000a markers, and to separate these

  16. Genetic relationships between Lolium (Poaceae) species revealed by RAPD markers.

    PubMed

    Ma, X; Gu, X-Y; Chen, T-T; Chen, S-Y; Huang, L-K; Zhang, X-Q

    2013-01-01

    The genus Lolium is one of the most important groupings of temperate forage grasses, including about eight recognized species that are native to some temperate and subtropical regions of the northern hemisphere. We examined genetic relationships among 18 accessions representing all Lolium species using RAPD markers. Among 50 random primers that we screened, 13 gave reproducible amplification banding patterns. Each of these 13 primers generated 19-43 scorable fragments. A total of 367 RAPD fragments were detected, of which 95.9% were polymorphic across all the Lolium accessions. Dice's coefficient of dissimilarity ranged from 0.016 to 0.622, which is indicative of substantial genetic variations in these Lolium accessions. A neighbor-joining cluster analysis, with bootstrap permutation, produced an unrooted dendrogram, which grouped 18 accessions into two main clades, supporting high bootstrap values (98 and 96%). The first clade included the self-pollinated species, L. persicum, L. temulentum, L. remotum, and L. subulatum. The cross-pollinated species, i.e., L. multiflorum, L. perenne, L. rigidum, and L. canariense, composed the second clade, in which L. canariense formed a distinct subclade, indicating its higher genetic separation from other allogamous species. The value of r = 0.97 in the Mantel test for cophenetic correlation applied to the cluster analysis indicated the high degree of fit of the accessions to a group. A principal coordinate analysis, whose first three coordinates explained 72.6% of the variation, showed similar groupings as in the cluster analysis. The genetic relationships estimated by the polymorphism of RAPD markers are basically in agreement with those previously inferred with other genetic markers. PMID:23546973

  17. Linkage map of the honey bee, Apis mellifera, based on RAPD markers

    Microsoft Academic Search

    Greg J. Hunt; Robert E. Page

    1995-01-01

    A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an

  18. Genetic diversity among maize (Zea mays L.) landraces assessed by RAPD markers

    Microsoft Academic Search

    Valdemar P. Carvalho; Claudete F. Ruas; Josué M. Ferreira; Rosângela M. P. Moreira; Paulo M. Ruas

    2004-01-01

    The genetic relationships among 81 maize accessions consisting 79 landraces and two improved varieties, maintained by farmers in southern Brazil were investigated using Random Amplified Polymorphic DNA (RAPD). Thirty-two highly informative primers amplified 255 markers of which 184 (72.2%) were polymorphics. Based on the RAPD markers, a dendrogram was constructed using the UPGMA method. The range of genetic similarity was

  19. Genomic mapping in Pinus pinaster (maritime pine) using RAPD and protein markers

    Microsoft Academic Search

    C Plomion; N Bahrman; C-E Durel; D M O'Malley

    1995-01-01

    A detailed genomic map was constructed for one F1 individual of maritime pine, using randomly amplified polymorphic DNA (RAPD) and protein markers scored on megagametophytes of germinated seeds. Proteins allowed the localization of exclusively coding DNA in the large genome of this Pinus species, mapped with RAPD markers that essentially fall within repetitive (i.e. mostly noncoding) DNA. Dot blots experiments

  20. Identification of a RAPD marker linked to a brown planthopper resistance gene in rice

    Microsoft Academic Search

    Yong-Hee Jeon; Sang-Nag Ahn; Hae-Chune Choi; Tae-Ryong Hahn; Huhn-Pal Moon

    1999-01-01

    Summary We report the tagging of a brown planthopper (BPH) resistance gene (Bph-1) in rice using RAPD and RFLP markers. The Korean rice variety 'Gayabyeo' has dominant duplicate genes including Bph-1 conferring resistance to biotype 1 of BPH. Bulked segregant RAPD analysis was employed for rapid identification of DNA markers linked to resistance genes. For tagging these two genes, an

  1. A GENETIC LINKAGE MAP FOR HAZELNUT (CORYLUS AVELLANA L.) BASED ON RAPD AND SSR MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. RAPD markers in testcross configuration segregating 1:1, were used to construct maps for each paren...

  2. Evidence for RAPD heteroduplex formation in cranberry: implications for pedigree and genetic-relatedness studies and a source of co-dominant RAPD markers

    Microsoft Academic Search

    R. G. Novy; N. Vorsa

    1996-01-01

    Silver-stained random amplified polymorphic DNA (ssRAPD) markers have been identified that are always jointly present or absent in the ssRAPD profiles of cranberry varieties. On the basis of segregation data and the ability to re-create these “associated ssRAPDs” through the intermixing of amplified DNA from individuals lacking them, five of the six pairs of associated ssRAPDs analyzed were shown to

  3. [The polymorphism of proteins, RAPD-PCR and ISSR-PCR markers in European and American bison and cattle].

    PubMed

    Glazko, V I; Dyman', T N; Tarasiuk, S I; Dubin, A V

    1999-01-01

    The comparative analysis of genetic differentiations between three species of Bovinae--Bos taurus, Bison bonasus, Bison bison with the use of different types of molecular-genetic markers--genetical-biochemical (35 loci) and DNA markers (RAPD-PCR, ISSR-PCR) was carried out. It was shown, that the evaluation of interspecies genetic interrelations was connected more with the determined molecular-genetic markers (loci), included in analysis, than with the marker's belonging to certain type (protein polymorphism, variability of DNA repeat distributions). PMID:10707408

  4. Characterization of four B-chromosome-specific RAPDs and the development of SCAR markers on the maize B-chromosome.

    PubMed

    Kao, Kuo-Wei; Lin, Chien-Yu; Peng, Shu-Fen; Cheng, Ya-Ming

    2015-04-01

    Understanding the molecular organization of the maize B-chromosome is hindered by its high homology with A-chromosomes. Recently, various approaches have been employed to overcome this hindrance, and several B-chromosome-specific sequences have been identified. Here, we cloned and characterized four previously published B-chromosome-specific RAPD fragments in detail. The results of sequence analysis, Southern hybridization and fluorescence in situ hybridization revealed that the four RAPD fragments are repetitive and present on both the B- and A-chromosomes, which supports an A-chromosome origin of the B-chromosome. We further developed four sequence-characterized amplified region (SCAR) markers derived from the four B-chromosome-specific RAPDs. These markers amplified PCR products exclusively in plants with B-chromosomes and were further mapped to definite distal heterochromatic regions of the B-chromosome by 15 B-A translocations. Furthermore, reverse transcriptase-PCR revealed that two of the four B-chromosome-specific RAPD fragments are transcriptionally active. These results demonstrate the feasibility of using B-chromosome-specific RAPD sequences to generate SCAR markers specific to the B-chromosome and might apply to other sequences of the maize B-chromosome. PMID:25258187

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

    PubMed

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

    2012-01-01

    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. PMID:23143935

  6. Analysis of genetic heterogeneity among five gynogenetic clones of silver crucian carp, Carassius auratus gibelio Bloch, based on detection of RAPD molecular markers

    Microsoft Academic Search

    L. Zhou; Y. Wang; J. F. Gui

    2000-01-01

    The gynogenetic silver crucian carp, Carassius auratus gibelio, is a unique model system for studying evolutionary genetics and selective breeding, owing to its specific genetic background and reproductive modes. Five gynogenetic clones were analyzed by the random amplified polymorphic DNA (RAPD) technique, using 30 10-nucleotide-long primers. Twenty-six primers produced well-amplified DNA fragments with reproducible banding patterns, and 24 primers were

  7. Comparison of ISSR and RAPD markers to characterize three Chilean Nothofagus species

    Microsoft Academic Search

    C. Mattioni; M. Casasoli; M. Gonzalez; R. Ipinza; F. Villani

    2002-01-01

    The present study is the first report of fingerprinting on three Chilean Nothofagus species using ISSR and RAPD markers; 61 Nothofagus nervosa, 32 Nothofagus obliqua and 32 Nothafagus dombeyi individual trees, sampled from collection and natural sites, were analyzed. Among 45 primers tested, the 6 ISSR and 6 RAPD primers selected for the analysis generated a total of 63 ISSR

  8. A comparative analysis of genetic diversity in blackgram genotypes using RAPD and ISSR markers

    Microsoft Academic Search

    J. Souframanien; T. Gopalakrishna

    2004-01-01

    Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were used to study the DNA polymorphism in elite blackgram genotypes. A total of 25 random and 16 ISSR primers were used. Amplification of genomic DNA of the 18 genotypes, using RAPD analysis, yielded 104 fragments that could be scored, of which 44 were polymorphic, with an average of

  9. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers

    Microsoft Academic Search

    C. Orozco-Castillo; K. J. Chalmers; R. Waugh; W. Powell

    1994-01-01

    RAPD (randomly amplified polymorphic DNA) markers generated by arbitary decamers have been successfully employed to detect genetic polymorphisms between coffee species and between Coffea arabica genotypes. The RAPD profiles were used to construct dendrograms and these were consistent with the known history and evolution of Coffea arabica. Material originating from Ethiopia and the arabica sub-groups — C. arabica var. typica

  10. Evaluation of RAPD markers for taxonomic relationships in some aquatic species of Utricularia L. (Lentibulariaceae)

    Microsoft Academic Search

    Mohammad Oliur Rahman

    2006-01-01

    Random amplified polymorphic DNA (RAPD) markers were used to assess relationship across nine aquatic species of Utricularia. The highest numbers of RAPD bands were detected in Utricularia bremii and U. intermedia. The highest genetic similarity was observed between U. australis and U. dimorphantha; between U. australis and U. vulgaris; and between U. dimorphantha and U. macrorhiza indicating that these species

  11. Identification of Anoectochilus formosanus and Anoectochilus koshunensis species with RAPD markers.

    PubMed

    Cheng, K T; Fu, L C; Wang, C S; Hsu, F L; Tsay, H S

    1998-02-01

    RAPD (random amplified polymorphic DNA) markers were developed to distinguish Anoectochilus formosanus from Anoectochilus koshunensis and their putative hybrids. Morphological differentiation of these two species beyond the flowering period is difficult. RAPD markers provide a rapid and easy tool for identification of the two Anoectochilus species. In the study, forty arbitrary decamer primers were screened, and nineteen species-specific RAPD markers generated from polymerase chain reactions (PCR) with eight random primers were obtained. Nine were specific to A. formosanus and ten to A. koshunensis. Two primers, OPC-08 and OPL-07, produced two markers, one specific to A. formosanus and the other specific to A. koshunensis, which simultaneously appeared in the hybrids pattern. The RAPD markers can be applied both to identification of A. formosanus and A. koshunensis species and to assessment of the extent fo hybridization in hybrids between them. This information facilitates the breeding program process. PMID:17253217

  12. Genetic diversity in Lima bean (Phaseolus lunatus L.) as revealed by RAPD markers

    Microsoft Academic Search

    B. Fofana; X. Vekemans; P. du Jardin; J. P. Baudoin

    1997-01-01

    The genetic variability of 46 accessions of the Lima bean (P. lunatus L.) including 16 wild forms and 30 landraces belonging\\u000a to the three cultigroups Big lima, Sieva, Potato, and their intermediates, was evaluated using RAPD (Random amplified polymorphic\\u000a DNA) markers. Twelve oligonucleotide primers produced 172 RAPD markers which allowed the differentiation of two main groups:\\u000a the mesoamerican and the

  13. Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers.

    PubMed

    Kumar, Mahadeo; Kumar, Sharad

    2014-11-01

    Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88% polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0%) amount of genetic homogeneity was observed in mice samples and the least (79.3%) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments. PMID:25074272

  14. The Diversity of Karyotypes and Genomes within Section Syllinum of the Genus Linum (Linaceae) Revealed by Molecular Cytogenetic Markers and RAPD Analysis

    PubMed Central

    Nosova, Inna V.; Amosova, Alexandra V.; Samatadze, Tatiana E.; Yurkevich, Olga Yu.; Melnikova, Nataliya V.; Zelenina, Daria A.; Volkov, Alexander A.; Muravenko, Olga V.

    2015-01-01

    The wide variation in chromosome number found in species of the genus Linum (2n = 16, 18, 20, 26, 28, 30, 32, 36, 42, 72, 84) indicates that chromosomal mutations have played an important role in the speciation of this taxon. To contribute to a better understanding of the genetic diversity and species relationships in this genus, comparative studies of karyotypes and genomes of species within section Syllinum Griseb. (2n = 26, 28) were carried out. Elongated with 9-aminoacridine chromosomes of 10 species of section Syllinum were investigated by C- and DAPI/?-banding, CMA and Ag-NOR-staining, FISH with probes of rDNA and of telomere repeats. RAPD analysis was also performed. All the chromosome pairs in karyotypes of the studied species were identified. Chromosome DAPI/C-banding patterns of 28-chromosomal species were highly similar. Two of the species differed from the others in chromosomal location of rDNA sites. B chromosomes were revealed in all the 28-chromosomal species. Chromosomes of Linum nodiflorum L. (2n = 26) and the 28-chromosomal species were similar in DAPI/C-banding pattern and localization of several rDNA sites, but they differed in chromosomal size and number. The karyotype of L. nodiflorum was characterized by an intercalary site of telomere repeat, one additional 26S rDNA site and also by the absence of B chromosomes. Structural similarities between different chromosome pairs in karyotypes of the studied species were found indicating their tetraploid origin. RAPD analysis did not distinguish the species except L. nodiflorum. The species of section Syllinum probably originated from a common tetraploid ancestor. The 28-chromosomal species were closely related, but L. nodiflorum diverged significantly from the rest of the species probably due to chromosomal rearrangements occurring during evolution. PMID:25835524

  15. Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata , Using RAPD and ISSR Markers

    Microsoft Academic Search

    Zhi-Yong Zhang; Yong-Yan Chen; De-Zhu Li

    2005-01-01

    With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low\\u000a genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the

  16. Identification of RAPD and SCAR markers associated with yield traits in the Indian tropical tasar silkworm Antheraea mylitta drury

    PubMed Central

    Dutta, Suhrid R.; Kar, Prasanta K.; Srivastava, Ashok K.; Sinha, Manoj K.; Shankar, Jai; Ghosh, Ananta K.

    2012-01-01

    The tropical tasar silkworm, Antheraea mylitta, is a semi-domesticated vanya silk-producing insect of high economic importance. To date, no molecular marker associated with cocoon and shell weights has been identified in this species. In this report, we identified a randomly amplified polymorphic DNA (RAPD) marker and examined its inheritance, and also developed a stable diagnostic sequence-characterized amplified region (SCAR) marker. Silkworms were divided into groups with high (HCSW) and low (LCSW) cocoon and shell weights, and the F2 progeny of a cross between these two groups were obtained. DNA from these silkworms was screened by PCR using 34 random primers and the resulting RAPD fragments were used for cluster analysis and discriminant function analysis (DFA). The clustering pattern in a UPGMA-based dendogram and DFA clearly distinguished the HCSW and LCSW groups. Multiple regression analysis identified five markers associated with cocoon and shell weights. The marker OPW16905 bp showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F2 progeny. Cloning and sequencing of this 905 bp fragment showed 88% identity between its 134 nucleotides and the Bmc-1/Yamato-like retroposon of A. mylitta. This marker was further converted into a diagnostic SCAR marker (SCOPW 16826 bp). The SCAR marker developed here may be useful in identifying the right parental stock of tasar silk-worms for high cocoon and shell weights in breeding programs designed to enhance the productivity of tasar silk. PMID:23271934

  17. Characterization of the USDA Poa pratensis collection usingRAPD markers and agronomic descriptors

    Microsoft Academic Search

    R. C. Johnson; W. J. Johnston; C. T. Golob; M. C. Nelson; R. J. Soreng

    2002-01-01

    Characterization of germplasm collections is critical to assesscollection diversity and enhance utilization. A Poapratensis L. germplasm collection of 228 accessionsrepresenting 26 countries, along with 17 commercial check cultivars,was characterized using 86 random amplified polymorphic DNA(RAPD) markers and 17 agronomic descriptors. The Dicesimilarity coefficient used for RAPD data ranged from 0.56 to 0.95and average Euclidean distance used for agronomic data ranged

  18. Detection of DNA Polymorphisms in Sugarbeet Bulks by SRAP and RAPD Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The random amplified polymorphic DNA (RAPD) marker system has been used in many different applications involving the detection of DNA sequence polymorphism, but most often in construction of linkage maps and in bulk segregant analysis (BSA) for identification of markers linked to genes of interest....

  19. Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content.

    PubMed

    Kumar, Anil; Sharma, Netrapal; Panwar, Preety; Gupta, Arun K

    2012-04-01

    Fifty-two genotypes of Eleusine coracana collected from Uttarakhand hills were subjected to simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD)-PCR and protein profiling analysis to investigate the variation in protein content. The main objective of the present study was to detect variability among E. coracana and also assess the discriminating ability of these three molecular methods. A total of 21 RAPD and 24 SSR primers were assayed for their specificity in detecting genetic variability in E. coracana, of which 20 RAPD and 21 SSR primers were highly reproducible and were found suitable for use in PCR analysis. Assessing genetic diversity among E. coracana genotypes by RAPD-PCR using 20 polymorphic primers yielded 56 different RAPD markers which clustered the genotypes into different groups on the basis of protein content. Similarly, SSR-PCR with 21 polymorphic primers clustered the genotypes into different groups. On the other hand, biochemical typing of E. coracana using whole seed proteins generated profiles that showed no major difference indicating the technique to be not useful in typing genotypes of this crop. However, a few of the genotypes showed the presence of a unique band of 32 kDa that needs to be further investigated to understand the role of the protein from nutritional point of view, if any. In the present study, significant negative correlation (r = -0.69*) was found between the protein and calcium content of finger millet genotypes. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis based seed storage proteins generated profiles showed no major differences in banding pattern among 52 finger millet genotypes while quantitative estimation of seed storage protein fractions using Lowry method revealed that glutelin was highest followed by prolamin, globulin and albumin. PMID:22167326

  20. Utility of RAPD Markers in Evaluating the Status of the Hawaiian Tree Fern Cibotium Dheleniae1

    E-print Network

    Carpenter, Kent E.

    Utility of RAPD Markers in Evaluating the Status of the Hawaiian Tree Fern Cibotium Dheleniae1 occurring populations. Investigations of the Hawaiian pteri- dophytes over the past decade have revealed. Endemic island species, such as Hawaiian Cibotium, frequently exhibit large amounts of morphological

  1. The use of RAPD markers for identification of cultivated grapevine ( Vitis vinifera L.)

    Microsoft Academic Search

    S. Moreno; Y. Gogorcena; J. M. Ortiz

    1995-01-01

    Polymorphism among 31 grapevine accessions was studied utilizing random amplified polymorphic DNA (RAPD) markers. Fourteen decamer oligonucleotide primers were tested. All experiments were repeated three times. Primers could be grouped according to the polymorphism obtained as well as the constancy of results. Choosing the right primers, all varieties and some of the clones could be discriminated using reliable bands. Synonymies

  2. Genetic analysis among selected vernonia lines through seed oil content, fatty acids and RAPD DNA markers

    Microsoft Academic Search

    S. P. Ramalema; H. Shimelis; I. Ncube; K. K. Kunert; P. W. Mashela

    2010-01-01

    Vernonia (Vernonia galamensis) is a new potential industrial oilseed crop. The seeds of this crop contain unusual naturally epoxidised fatty acids which are used in the production of various industrial products. The objective of this study was to evaluate and select vernonia lines in Limpopo province through seed oil content, fatty acid content and RAPD DNA markers. Significant differences were

  3. Random amplified polymorphic DNA (RAPD) markers for genetic analysis in micropropagated plants of Populus deltoides Marsh

    Microsoft Academic Search

    Vijay Rani; Ajay Parida; S. N. Raina

    1995-01-01

    RAPD markers were used to assess genetic fidelity of 23 micropropagated plants of a single clone (L34) of Populus deltoides. Eleven arbitrary 10-base primers were successfully used to amplify DNA from in vivo and in vitro material. Of these, 5 distinguished a total of 13 polymorphisms common across 6 micropropagated plants. Apart from these 6 plants, the amplification products were

  4. Genetic linkage mapping in peach using morphological, RFLP and RAPD markers

    Microsoft Academic Search

    S. Rajapakse; L. E. Belthoff; G. He; A. E. Estager; R. Scorza; I. Verde; R. E. Ballard; W. V. Baird; A. Callahan; R. Monet; A. G. Abbott

    1995-01-01

    We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F2 individuals derived from the self-fertilization of four F1 individuals of a cross between ‘New Jersey Pillar’ and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh

  5. Genetic diversity in sacaca (Croton cajucara Benth.) accessed by RAPD markers

    Microsoft Academic Search

    P. C. S. Angelo

    Genetic diversity in sacaca (Croton cajucara Benth.) accessed by RAPD markers. In 1971, sacaca (Croton cajucara Benth.) was identified as a source of linalool which can be extracted from leaves and tiny branches, without the need to harvest the whole plant. Linalool is priced at US$ 13 - 15.00, per flask with 100 ml of a 97% solution. In purer

  6. Identification of RAPD marker associated with brown rust resistance in sugarcane

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Susceptibility to brown rust caused by Puccinia melanocephala is a major reason for the withdrawal of sugarcane cultivars from production. An efficient way to control the disease is to breed cultivars with durable resistance. Our aim was to identify random amplified polymorphic DNA (RAPD) markers ...

  7. Fingerprinting of alfalfa meiotic mutants using RAPD markers

    Microsoft Academic Search

    G. Barcaccia; S. Tavoletti; M. Pezzotti; M. Falcinelli; F. Veronesi

    1994-01-01

    Polymerase chain reaction (PCR), with single ten-base-long nucleotide primers, was used to amplify random regions of genomic DNA from eleven diploid meiotic mutants (2n egg, 2n pollen and jumbo pollen producers) of the Medicago sativa-coerulea-falcata complex. Electrophoretic patterns of the resulting random amplified polymorphic DNA (RAPD) fragments were evaluated to develop a graphical representation of amplification products from which conserved

  8. A male and hermaphrodite specific RAPD marker for papaya ( Carica papaya L.)

    Microsoft Academic Search

    N. Urasaki; M. Tokumoto; K. Tarora; Y. Ban; T. Kayano; H. Tanaka; H. Oku; I. Chinen; R. Terauchi

    2002-01-01

    The random amplified polymorphic DNA (RAPD) technique was used to determine the sex of a dioecious species, Carica papaya L., with three sex types, male, female and hermaphrodite. A 450 bp marker fragment, named PSDM(Papaya Sex Determination Marker),\\u000a exists in all male and hermaphrodite plants but not in the female plants so far analyzed. The DNA sequence of PSDM exhibited

  9. Assessment of diversity in Harpagophytum with RAPD and ISSR markers provides evidence of introgression.

    PubMed

    Muzila, Mbaki; Werlemark, Gun; Ortiz, Rodomiro; Sehic, Jasna; Fatih, Moneim; Setshogo, Moffat; Mpoloka, Wata; Nybom, Hilde

    2014-10-01

    The genus Harpagophytum has two species: H. procumbens which is an important medicinal plant in southern Africa, and H. zeyheri. Genetic diversity in 96 samples, obtained by germinating seeds collected from Botswana, was assessed using six inter-simple sequence repeat (ISSR) and 10 random amplified polymorphic DNA (RAPD) primers. These DNA markers yielded a total of 138 polymorphic bands. Polymorphism information content (PIC) ranged from 0.06 to 0.39 for ISSR primers, and from 0.09 to 0.43 for RAPD primers. Jaccard's similarity coefficients were highest when seedlings derived from the same fruit capsule were compared, while seedlings from different fruits on the same plant had intermediate values. The lowest values were recorded among seedlings from different plants. These results were consistent with an outcrossing breeding system in Harpagophytum. Analysis of molecular variance revealed significant differentiation (P<0.01) between taxonomic units within Harpagophytum. About 39% of the variability occurred between the two species, H. procumbens and H. zeyheri. Plants with an intermediate morphology, i.e. putative hybrids (PH), showed 21% differentiation when compared with H. procumbens ssp. procumbens (PP), and 19% when compared with H. procumbens ssp. transvaalense (PT) or with H. zeyheri (ZZ). In addition, a deviating variant of PT was identified, here termed 'procumbens new variety' (PN). PN showed only 9% differentiation when compared with PT, 22% when compared with PP or with PH, and 41% when compared with ZZ. Considerable differentiation between the two Harpagophytum species was revealed also by a cluster analysis. Introgression was, however, suggested by the intermediate position of the putative hybrid plants in a principal component analysis while inter-specific gene flow was shown by a Bayesian genetic structure analysis. PMID:25363276

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

    PubMed Central

    Nagl, Nevena; Taski-Ajdukovic, Ksenija; Barac, Goran; Baburski, Aleksandar; Seccareccia, Ivana; Milic, Dragan; Katic, Slobodan

    2011-01-01

    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. PMID:21954370

  11. Genetic diversity in Kenyan populations of Acacia senegal (L.) willd revealed by combined RAPD and ISSR markers

    Microsoft Academic Search

    Chiveu Chemulanga Josiah; Dangasuk Otto George; Omunyin Michael Eleazar; Wachira Francis Nyamu

    2008-01-01

    Acacia senegal belongs to the subgenus, Aculeiferum. It is an African arid and semi arid zone multipurpose tree species, highly valued for gum arabic production, agroforestry and desertification control besides other multiple uses. Genetic variation and resulting variable groupings were assessed using combined RAPD+ISSR markers within and among four Kenyan populations of A. senegal. Using 10 RAPD and 5 ISSR

  12. Targeted mapping and linkage analysis of morphological isozyme, and RAPD markers in peach.

    PubMed

    Chaparro, J X; Werner, D J; O'Malley, D; Sederoff, R R

    1994-02-01

    Nine different F2 families of peach [Prunus persica (L.) Batsch] were analyzed for linkage relationships between 14 morphological and two isozyme loci. Linkage was detected between weeping (We) and white flower (W), 33 cM; double flower (Dl) and pillar (Br), 10 cM; and flesh color (Y) and malate dehydrogenase (Mdh1), 26 cM. A leaf variant phenotypically distinct from the previously reported wavy-leaf (Wa) mutant in peach was found in progeny of 'Davie II'. The new willow-leaf character (designated Wa2) was closely linked (0.4 cM) to a new dwarf phenotype (designated Dw3). Two families derived from the pollen-fertile cultivar 'White Glory' segregated for pollen sterility, but segregation did not follow a 3?1 ratio. Evidence is presented suggesting that 'White Glory' possesses a pollen-sterility gene (designated Ps2) that is non-allelic to the previously reported pollen-sterility gene (Ps) in peach. Ps2 was linked to both weeping (We-Ps2, 15.5 cM) and white flower (Ps2-W, 25.3 cM). A genomic map of peach containing 83 RAPD, one isozyme, and four morphological markers was generated using an F2 family obtained by selfing an NC174RL x 'Pillar' F1. A total of 83 RAPD markers were assigned to 15 linkage groups. Various RAPD markers were linked to morphological traits. Bulked segregant analysis was used to identify RAPD markers flanking the red-leaf (Gr) and Mdh1 loci in the NC174RL x 'Pillar' and 'Marsun' x 'White Glory' F2 families, respectively. Three markers flanking Mdh1 and ten markers flanking Gr were identified. The combination of RAPD markers and bulked segregant analysis provides an efficient method of identifying markers flanking traits of interest. Markers linked to traits that can only be scored late in development are potentially useful for marker-aided selection in trees. Alternatives for obtaining additional map order information for repulsion-phase markers in large F2 populations are proposed. PMID:24190466

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Molecular characterization and genetic diversity analysis of Jatropha curcas L. in India using RAPD and AFLP analysis.

    PubMed

    Pamidimarri, D V N Sudheer; Mastan, Shaik G; Rahman, Hifzur; Reddy, Muppala P

    2010-06-01

    Jatropha curcas L. belongs to family Euphorbiaceae, native to South America and widely distributed in South and Central America, attained significant importance for its seed oil which can be converted to biodiesel, a renewable energy source alternative to conventional petro-diesel. Very few attempts were made to understand the extent of genetic diversity that exists in J. curcas. Therefore, the present investigation was undertaken to asses the genetic diversity among 28 diverse germplasm collected from distinct geographical areas in India. The overall percentage of polymorphism (PP) was found to be 50.70 and 60.95 by RAPD and AFLP, respectively. The mean PP was found to be 9.72 and 20.57 by RAPD and AFLP, respectively. The mean genetic similarity was observed to be 0.89 by RAPD and 0.88 by AFLP. Among the germplasm JCI20 found to be the most diverged one. The dendrogram analysis of RAPD and AFLP data showed good congruence, but better resolution and more polymorphism was observed with AFLP. When the dendrogram of RAPD was compared with AFLP dendrogram, the major clustering pattern was found to be similar; however, changes in minor grouping were observed. In both RAPD and AFLP analysis clustering of germplasm did not show any correlation with the geographical area of collection. Low genetic diversity observed in J. curcas and the clustering pattern indicates that the distribution of species might have happened through anthropogenic activity and warrants the need for widening the genetic base. The present study will provide pavement for further intra-population studies on narrow geographical areas, to understand the population genetic structure, phylogeography, molecular ecological studies. The marker information and the characterized germplasm help in further improvement of the species through marker assisted breeding programs. PMID:19688277

  15. Haploid Origin of Cork Oak Anther Embryos Detected by Enzyme and RAPD Gene Markers.

    PubMed

    Bueno; Agundez; Gomez; Carrascosa; Manzanera

    2000-05-01

    In vitro-induced cork oak (Quercus suber L.) embryos from anther cultures proved to be of haploid origin both by enzyme and RAPD gene marker analysis. The problem considered was to ascertain if embryo cultures originated either from a single haploid cell, from a microspore, or from multiple haploid cells. Therefore, a heterozygotic gene was searched for in the parent tree. The gene coding for shikimate dehydrogenase (SKDH1) proved to be heterozygous in the parental tree, and subsequently, these allozymes were screened for the embryos induced in anther cultures from the same tree. Only haploid embryos were found, confirming the microspore origin. Different genotypes were not identified inside each anther by isozyme analysis, probably because of selective pressure for one embryo early in development, but both parental SKDH1 alleles were found in the embryos of different anthers. The banding patterns detected by RAPD markers permitted the identification of multiple microspore origins inside each anther. PMID:10817971

  16. Genotyping with RAPD and microsatellite markers resolves pathotype diversity in the ascochyta blight pathogen of chickpea

    Microsoft Academic Search

    S. M. Udupa; F. Weigand; M. C. Saxena; G. Kahl

    1998-01-01

    The poor definition of variation in the ascochyta blight fungus (Ascochyta rabiei) has historically hindered breeding for resistance to the chickpea (Cicer arietinum L.) blight disease in West Asia and North Africa. We have employed 14 RAPD markers and an oligonucleotide probe complementary\\u000a to the microsatellite sequence (GATA)4 to construct a genotype-specific DNA fragment profile from periodically sampled Syrian field

  17. RAPD markers linked to a clubroot-resistance locus in Brassica rapa L

    Microsoft Academic Search

    Yasuhisa Kuginuki; Hidetoshi Ajisaka; Mamiko Yui; Hiroaki Yoshikawa; Ken-ichi Hida; Masashi Hirai

    1997-01-01

    Linkage of random amplified polymorphic DNA (RAPD) markers with resistance genes to clubroot (Plasmodiophora brassicae Wor.)\\u000a in Brassica rapa L. was studied in a doubled haploid (DH population obtained by microspore culture. Thirty-six DH lines were\\u000a obtained from F1 plants from a cross between susceptible ‘Homei P09’ and resistant ‘Siloga S2’ plants. ‘Homei P09’ was a DH line obtained\\u000a by

  18. Genetic analysis of Turkish rice varieties ( Oryza sativa L.) using seed storage proteins and RAPD markers

    Microsoft Academic Search

    Emel Banu Buyukunal Bal; Sultan Bay

    2010-01-01

    Due to an increasing demand for rice in Turkey, assessing and maintaining genetic variability in rice cultivars is essential\\u000a for the success of rice breeding programs. Genetic polymorphisms in seed storage proteins (SSP) and RAPD markers were evaluated\\u000a among different Turkish cultivars of Oryza sativa L. Twenty-one rice cultivars of Turkish origin and 11 rice cultivars from Bulgaria, France, Italy

  19. Identification of Tuber magnatum Pico DNA markers by RAPD analysis

    Microsoft Academic Search

    Lucia Potenza; Antonella Amicucci; Ismaela Rossi; Francesco Palma; Roberta Bellis; Paola Cardoni; Vilberto Stocchi

    1994-01-01

    Different species of truffle were studied in order to identify species-specific markers. The isolation of two Tuber magnatum Pico markers is reported. One of these could be used as a probe in dot blot hybridization, allowing the development of a rapid test able to identify Tuber magnatum species.

  20. Genetic relationships and discrimination of ten influential Upland cotton varieties using RAPD markers.

    PubMed

    Lu, J.; Myers, O.

    2002-08-01

    Influential Upland cotton ( Gossypium hirsutum L.) varieties are those that have the higher genetic contributions to modern Upland cultivars than other germplasms. Our previous research has shown significant differences in general combining ability (GCA) effects for yield, yield components, and fiber properties among ten influential cotton varieties. In this study, we used random amplified polymorphic DNA (RAPD) data to evaluate DNA variation of these ten varieties. Of 86 random decamer primers screened for their capability of amplifying DNA via the polymerase chain reaction (PCR), 63 generated a total of 312 DNA fragments. Forty two bands were polymorphic, which showed a low percentage (13.5%) of DNA variation among these influential varieties. Genetic similarities among the ten varieties based on RAPD data were from 92.7% to 97.6%. All of the varieties were individually identified by variety specific markers in genetic fingerprinting. One primer, UBC-149, amplified a 1,430-bp DNA fragment that was absent in five varieties and present in the other five varieties. This RAPD marker had significant negative relationships with GCA-effect estimates for seed cotton yield, lint yield, number of bolls per plant and micronaire, and significant positive relationships with GCA effects for boll size and seed index. This finding, for the first time, identifies a DNA fragment in cotton that is a potential DNA marker linked to a yield gene(s) or a yield-related gene(s). PMID:12582535

  1. Species recognition of congeneric acanthocephalans in slider turtles by random-amplified polymorphic DNA (RAPD) markers.

    PubMed

    Dezfuli, B S; Tinti, F

    1998-08-01

    Species recognition of acanthocephalans of the genus Neoechinorhynchus (Hamann, 1892) found in the freshwater turtle Trachemys scripta (Wied, 1838) has previously been based primarily on female body and egg morphology. Observed morphological plasticity within and among species may lead to the misclassification of female specimens and leaves males of different species completely indistinguishable. Here, random-amplified polymorphic DNA (RAPD) analysis was used to genetically characterize samples of Neoechinorhynchus pseudemydis (Cable and Hopp, 1954), Neoechinorhynchus emydis (Leidy, 1851), and Neoechinorhynchus emyditoides (Fisher, 1960). Amplifications performed with 3 decamer oligonucleotides showed banding patterns with a few diagnostic fragments that allowed the recognition of N. pseudemydis specimens from those of the N. emydis-N. emyditoides group. No primer gave a species-specific locus that allowed the differentiation of N. emydis from N. emyditoides specimens, suggesting that they could belong to a sole taxon. The species assignment of females of uncertain classification and of males is fully reliable using RAPD markers. Thus, identification of acanthocephalan species by RAPD in the helminth infracommunities could potentially be very useful to determine community structure. RAPD and other polymerase chain reaction-based methods have some practical advantages over multilocus discriminant analysis, such as the ability to use ethanol-stored specimens and small tissue samples of parasites. PMID:9714226

  2. Linkage map of Japanese black pine based on AFLP and RAPD markers including markers linked to resistance against the pine needle gall midge

    Microsoft Academic Search

    E. Hayashi; T. Kondo; K. Terada; N. Kuramoto; Y. Goto; M. Okamura; H. Kawasaki

    2001-01-01

    Macrogametophytes derived from the seeds of a tree resistant to pine needle gall midge (PGM) were analyzed using amplified\\u000a fragment length polymorphism (AFLP). A total of 244 segregating loci were detected among 71 macrogametophytes. Combining the\\u000a AFLP results with previously reported segregation data for 127 random amplified polymorphic DNA (RAPD) markers, 157 AFLP and\\u000a 50 RAPD markers with confirmed map

  3. Phylogenetic relationships among Saccharum clones in Pakistan revealed by RAPD markers.

    PubMed

    Nawaz, S; Khan, F A; Tabasum, S; Zakria, M; Saeed, A; Iqbal, M Z

    2010-01-01

    Forty sugarcane genotypes (clones), including elite lines, commercial cultivars of Saccharum officinarum and S. barberi clones, were fingerprinted with 30 RAPD markers, using a PCR-based marker assay. The genetic distance for RAPD data was determined according to Nei, and relationships between accessions were graphed in a dendrogram. Genetic distance values ranging from 16.2 to 86.3% were observed among the 40 sugarcane accessions. The lowest genetic distance was found between genotypes US-406 and US-186. These two genotypes differed from each other in only 25 bands with 15 different primers. Genotypes Col-54 and CP-72-2086 were the second most similar group, with a genetic distance of 19.46%. The most dissimilar of all the accessions were CP-77-400 and US-133, with a genetic distance of 86.3%. RAPD fingerprints help sugarcane breeders clarify the genetic pedigree of commercial sugarcane varieties and can be used to evaluate the efficiency of conventional breeding methods. PMID:20799164

  4. A first linkage map of pecan cultivars based on RAPD and AFLP markers.

    PubMed

    Beedanagari, Sudheer R; Dove, Sue K; Wood, Bruce W; Conner, Patrick J

    2005-04-01

    We report here the first genetic linkage maps of pecan [Carya illinoinensis (Wangenh.) K. Koch], using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers. Independent maps were constructed for the cultivars 'Pawnee' and 'Elliot' using the double pseudo-testcross mapping strategy and 120 F1 seedlings from a full-sib family. A total of 477 markers, including 217 RAPD, 258 AFLP, and two morphological markers were used in linkage analysis. The 'Pawnee' linkage map has 218 markers, comprising 176 testcross and 42 intercross markers placed in 16 major and 13 minor (doublets and triplets) linkage groups. The 'Pawnee' linkage map covered 2,227 cM with an average map distance of 12.7 cM between adjacent markers. The 'Elliot' linkage map has 174 markers comprising 150 testcross and 22 intercross markers placed in 17 major and nine minor linkage groups. The 'Elliot' map covered 1,698 cM with an average map distance of 11.2 cM between adjacent markers. Segregation ratios for dichogamy type and stigma color were not significantly different from 1:1, suggesting that both traits are controlled by single loci with protogyny and green stigmas dominant to protandry and red stigmas. These loci were tightly linked (1.9 cM) and were placed in 'Elliot' linkage group 16. These linkage maps are an important first step towards the detection of genes controlling horticulturally important traits such as nut size, nut maturity date, kernel quality, and disease resistance. PMID:15782296

  5. Assessment of genetic fidelity of micropropagated plants of Simmondsia chinensis (Link) Schneider using RAPD and ISSR markers

    Microsoft Academic Search

    Sunil Kumar; Manisha Mangal; A. K. Dhawan; Narender Singh

    RAPD (random amplified polymorphic DNA) and ISSR (inter simple sequence repeat) markers were screened to test the genetic\\u000a integrity of jojoba (Simmondsia chinensis) plants multiplied through axillary bud multiplication from nodal segments. The in vitro raised plantlets were maintained\\u000a for up to 12 in vitro subcultures. During the study a total of 48 (32 RAPD and 16 ISSR) primers were

  6. Linkage map of the honey bee, Apis mellifera, based on RAPD markers

    SciTech Connect

    Hunt, G.J.; Page, R.E. Jr. [Univ. of California, Davis, CA (United States)

    1995-03-01

    A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be {approximately}3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. 71 refs., 6 figs., 1 tab.

  7. Linkage Map of the Honey Bee, Apis Mellifera, Based on Rapd Markers

    PubMed Central

    Hunt, G. J.; Page-Jr, R. E.

    1995-01-01

    A linkage map was constructed for the honey bee based on the segregation of 365 random amplified polymorphic DNA (RAPD) markers in haploid male progeny of a single female bee. The X locus for sex determination and genes for black body color and malate dehydrogenase were mapped to separate linkage groups. RAPD markers were very efficient for mapping, with an average of about 2.8 loci mapped for each 10-nucleotide primer that was used in polymerase chain reactions. The mean interval size between markers on the map was 9.1 cM. The map covered 3110 cM of linked markers on 26 linkage groups. We estimate the total genome size to be ~3450 cM. The size of the map indicated a very high recombination rate for the honey bee. The relationship of physical to genetic distance was estimated at 52 kb/cM, suggesting that map-based cloning of genes will be feasible for this species. PMID:7768445

  8. Relating Morphologic and RAPD Marker Varlation to Collection Site Environment in wild Populations of Red Clover (Trifolium Pratense L.)

    Microsoft Academic Search

    S. L. Greene; M. Gritsenko; G. Vandemark

    2004-01-01

    Although genotypic and phenotypic markers are used to describe genetic diversity, describing patterns of variationattributable to geographic differentiation is complex.We examined concordance between morphologic and RAPDmarker classification of 33 wild red clover populations collected from the Caucasus Mountains, Russia andcompared how morphologic and RAPD markers differed in their correspondence to collection site attributes.Wealso examined if wild red clover populations collected

  9. RAPD and ISSR-assisted identification and development of three new SCAR markers specific for the Thinopyrum elongatum E (Poaceae) genome.

    PubMed

    Xu, G H; Su, W Y; Shu, Y J; Cong, W W; Wu, L; Guo, C H

    2012-01-01

    Diploid Thinopyrum elongatum, a wild relative of wheat, contains many agronomically desirable traits and has potential for increasing genetic variability and introducing desirable characters in this crop. Few molecular markers are available for rapid screening of T. elongatum genome segments in the wheat genetic background. We used 36 RAPD primers and 33 ISSR primers to screen for polymorphisms in the common wheat variety Chinese Spring and in T. elongatum. Two RAPD markers and one ISSR marker, designated OPF03(1407), LW10(1487) and UBC841(701), were identified and were specific for the T. elongatum E genome. Three pairs of primers flanking these specific sequences were designed to produce SCAR markers. All three SCAR markers were T. elongatum E genome-specific. Two of these SCAR markers, SCAR(807) and SCAR(577), were present in all seven T. elongatum chromosomes, while SCAR(839) was specific for T. elongatum chromosomes 2E and 3E. These newly developed SCAR markers should be useful for detecting alien genome chromatin or chromosome segments in the genetic background of common wheat. PMID:22843051

  10. Genetic diversity assessment of summer squash landraces using molecular markers.

    PubMed

    Mady, Emad A; Helaly, Alaa Al-Din; Abu El-Hamd, Abdel Naem; Abdou, Arafa; Shanan, Shamel A; Craker, Lyle E

    2013-07-01

    Plant identification, classification, and genotyping within a germplasm collection are essential elements for establishing a breeding program that enhances the probability of plants with desirable characteristics in the market place. In this study, random amplified polymorphic DNA (RAPD) was used as a molecular tool to assess the diversity and relationship among 20 summer squash (Curcubita pepo L.) landraces traditionally used to treat hypertension and prostate hyperplasia. A total of 10 RAPD primers produced 65 reproducible bands of which 46 (70.77 %) were polymorphic, indicating a large number of genotypes within the summer squash lines. Cluster analysis divided the summer squash germplasm into two groups, one including one landrace and a second containing 19 landraces that could be divided into five sub-groups. Results of this study indicate the potential of RAPD markers for the identification and assessment of genetic variations among squash landraces and provide a number of choices for developing a successful breeding program to improve summer squash. PMID:23666102

  11. MOLECULAR MARKERS IN WILD TURKEY

    E-print Network

    Latch, Emily K.

    and conservation of wildlife species. In the wild turkey (Meleagris gallopavo), these markers have been used, hybridization, Meleagris gallopavo, micro- satellite, mitochondrial, molecular marker, population, subspecies

  12. Genetic Linkage Maps of Eucalyptus Grandis and Eucalyptus Urophylla Using a Pseudo-Testcross: Mapping Strategy and Rapd Markers

    PubMed Central

    Grattapaglia, D.; Sederoff, R.

    1994-01-01

    We have used a ``two-way pseudo-testcross'' mapping strategy in combination with the random amplified polymorhic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F(1) progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, ? = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support >/=1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organism. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the paradigm of a species index map to the heterodox proposal of constructing several maps for individual trees of a population, therefore mitigating the problem of linkage equilibrium between marker and trait loci for the application of marker assisted strategies in tree breeding. PMID:7982566

  13. RAPD markers linked to a gene for resistance to pine needle gall midge in Japanese black pine (Pinus thunbergii)

    Microsoft Academic Search

    T. Kondo; K. Terada; E. Hayashi; N. Kuramoto; M. Okamura; H. Kawasaki

    2000-01-01

    Linkage of RAPD markers to a single dominant gene for resistance to pine needle gall midge was investigated in Japanese black\\u000a pine (Pinus thunbergii). Three primers that generated linked markers were found after 1160 primers were screened by bulked segregant analysis. The\\u000a distances between the resistance gene, R, and the marker genes OPC06580, OPD01700, and OPAX192100 were 5.1 cM, 6.7

  14. Genetic linkage mapping in peach using morphological, RFLP and RAPD markers.

    PubMed

    Rajapakse, S; Belthoff, L E; He, G; Estager, A E; Scorza, R; Verde, I; Ballard, R E; Baird, W V; Callahan, A; Monet, R; Abbott, A G

    1995-03-01

    We have constructed a genetic linkage map of peach [Prunus persica (L.) Batsch] consisting of RFLP, RAPD and morphological markers, based on 71 F2 individuals derived from the self-fertilization of four F1 individuals of a cross between 'New Jersey Pillar' and KV 77119. This progeny, designated as the West Virginia (WV) family, segregates for genes controlling canopy shape, fruit flesh color, and flower petal color, size and number. The segregation of 65 markers, comprising 46 RFLP loci, 12 RAPD loci and seven morphological loci, was analyzed. Low-copy genomic and cDNA probes were used in the RFLP analysis. The current genetic map for the WV family contains 47 markers assigned to eight linkage groups covering 332 centi Morgans (cM) of the peach nuclear genome. The average distance between two adjacent markers is 8 cM. Linkage was detected between Pillar (Pi) and double flowers (Dl) RFLP markers linked to Pi and flesh color (?) loci were also found. Eighteen markers remain unassigned. The individuals analyzed for linkage were not a random sample of all F2 trees, as an excess of pillar trees were chosen for analysis. Because of this, Pi and eight other markers that deviated significantly from the expected Mendelian ratios (e.g., 1?2?1 or 3?1) were not eliminated from the linkage analysis. Genomic clones that detect RFLPs in the WV family also detect significant levels of polymorphism among the 34 peach cultivars examined. Unique fingerprint patterns were created for all the cultivars using only six clones detecting nine RFLP fragments. This suggests that RFLP markers from the WV family have a high probability of being polymorphic in crosses generated with other peach cultivars, making them ideal for anchor loci. This possibility was examined by testing RFLP markers developed with the WV family in three other unrelated peach families. In each of these three peach families respectively 43%, 54% and 36% of RFLP loci detected in the WV family were also polymorphic. This finding supports the possibility that these RFLP markers may serve as anchor loci in many other peach crosses. PMID:24173944

  15. Identification of RAPD markers linked to a black leaf spot resistance gene in Chinese elm.

    PubMed

    Benet, H; Guries, R P; Boury, S; Smalley, E B

    1995-06-01

    Black leaf spot (Stegophora ulmea) is a common foliage disease on Chinese (Ulmus parvifolia) and Siberian elms (U. pumila), two species which have been widely used as sources of Dutch-elm disease-resistance genes for interspecific elm hybrids. A dominant gene controlling resistance to black leaf spot was identified in a population derived from self-pollination of a single U. parvifolia tree. Using RAPD markers, in combination with bulked segregant analysis, we have identified three markers linked to this resistance gene. A survey of Chinese-elm hybrids revealed that the same gene is likely to confer a high level of resistance to black leaf spot in interspecific elm hybrids, although other genetic factors may also be involved in the determination of a disease phenotype. PMID:24173064

  16. Efficient identification of ornamental peach cultivars using RAPD markers with a manual cultivar identification diagram strategy.

    PubMed

    Han, J; Wang, W Y; Leng, X P; Guo, L; Yu, M L; Jiang, W B; Ma, R J

    2014-01-01

    One of the most important uses of DNA markers is cultivar identification. However, no DNA fingerprint analysis strategy is available for making DNA markers helpful in practical plant cultivar identification, especially for the identification of a large number of cultivars. We developed a manual cultivar identification diagram strategy for efficient identification of plant cultivars, from which a cultivar identification diagram (CID) of genotyped plant individuals can be constructed manually. This CID could be used as a reference for quick identification of plant cultivars of interest. We used 11-mer RAPD primers to amplify DNA samples of 32 ornamental peach genotypes; all the cultivars were well distinguished by fingerprints from 6 primers. The utility of this CID was verified by identification of three randomly chosen groups of cultivars among the 32 ones that we selected. This CID generated will be useful for the identification of commercially important ornamental peach cultivars. PMID:24446285

  17. Genetic variation among cultivars of red clover (Trifolium pratense L.) detected by RAPD markers amplified from bulk genomic DNA

    Microsoft Academic Search

    Prasert Kongkiatngam; Bruce E. Coulman; Marc G. Fortin

    1996-01-01

    The use of random amplified polymorphic DNA (RAPD) markers obtained from bulked samples was investigated for cultivar identification in red clover. Pooled samples were examined in order to minimize variation within cultivars. To determine the appropriate number of individuals to include in the bulked samples representing each cultivar, DNA samples from two, three, four, five, ten and twenty individuals were

  18. Genetic variation within and between two cultivars of red clover ( Trifolium pratense L.): Comparisons of morphological, isozyme, and RAPD markers

    Microsoft Academic Search

    P. Kongkiatngam; M. G. Fortin; B. E. Coulman

    1995-01-01

    Summary Morphological, isozyme and random amplified polymorphic DNA (RAPD) markers were used to estimate genetic variation within and between cultivars of red clover (Trifolium pratense L.), an important temperate forage legume. Two cultivars of red clover, Essi from Europe and Ottawa from Canada, were evaluated. Six monogenic morphological characters were observed for 80 plants from each of these two cultivars.

  19. Megagametophyte-derived linkage maps of white spruce ( Picea glauca ) based on RAPD, SCAR and ESTP markers

    Microsoft Academic Search

    I. Gosselin; Y. Zhou; J. Bousquet; N. Isabel

    2002-01-01

    We have constructed linkage maps for two parents of white spruce [Picea glauca (Moench) Voss]. Haploid megagametophytes from 92 and 96 seeds of parents M2 and 80132, respectively, were analysed with RAPD, SCAR and ESTP markers. Fragments segregating in a 1:1 Mendelian ratio were classified and mapped using MAPMAKER, GMENDEL and JOINMAP. For M2, the analysis with JOINMAP resulted in

  20. A RAPD-derived STS marker is linked to a bacterial wilt ( Burkholderia caryophylli ) resistance gene in carnation

    Microsoft Academic Search

    Takashi Onozaki; Natsu Tanikawa; Mitsuyasu Taneya; Kiyofumi Kudo; Takuya Funayama; Hiroshi Ikeda; Michio Shibata

    2004-01-01

    Bacterial wilt caused by Burkholderia caryophylli is one of the most important and damaging diseases of carnations (Dianthus caryophyllus) in Japan. We aimed to identify random amplified polymorphic DNA (RAPD) markers associated with the genes controlling bacterial wilt resistance in a resistance-segregating population of 134 progeny plants derived from a cross between ‘Carnation Nou No. 1’ (a carnation breeding line

  1. IDENTIFICATION AND CONFIRMATION OF RAPD MARKERS AND ANDROMONOECIOUS ASSOCIATED WITH QUANTITATIVE TRAIT LOCI FOR SUGARS IN MELON

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our objectives were to identify randomly amplified polymorphic DNA (RAPD) markers associated with quantitative trait loci (QTL) for sucrose, total soluble solids (TSS), and sucrose percentage of total sugars (SPTS) using bulked segregant analysis in an F2 population from the melon (Cucumis melo L.) ...

  2. Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers

    Microsoft Academic Search

    Aymé Fernandez Calienes; Jorge Fraga; Jean-Pierre Pointier; Mary Yong; Jorge Sanchez; Christine Coustau; Alfredo Gutiérrez; André Théron

    2004-01-01

    Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del R??o) exhibited the amplification patterns of

  3. Genetic insight into Mediterranean chukar (Alectoris chukar, Galliformes) populations inferred from mitochondrial DNA and RAPD markers.

    PubMed

    Barbanera, Filippo; Guerrini, Monica; Hadjigerou, Pantelis; Panayides, Panicos; Sokos, Christos; Wilkinson, Peter; Khan, Aleem A; Khan, Bakht Y; Cappelli, Fabio; Dini, Fernando

    2007-11-01

    The chukar (Alectoris chukar, Galliformes) is one of the most important game birds as it is widely distributed and hunted over the whole of its range. The aim of this work was to assess the genetic differentiation as well as the possible presence of hybrid specimens in A. chukar populations from Italy, Greece and Cyprus. To provide phylogenetic context, conspecific, allopatric specimens from Israel, Georgia, Armenia, Kazakhstan, Afghanistan, Pakistan, Mongolia, China and USA were compared. Sequencing of the mitochondrial DNA (mtDNA) Control Region supplied information on the ancestry of A. chukar populations, whereas Random Amplified Polymorphic DNA (RAPD) fingerprinting was used to assess whether hybridization had occurred. The Italian population was found to be an inter-specific mixture of A. chukar and A. rufa (i.e., the red-legged partridge) mtDNA lineages, whereas the representatives from Greece and Cyprus showed only the A. chukar maternal line. RAPD markers revealed introgression with A. rufa genes in the Italian population, whereas no A. chukar x A. rufa hybrid specimens were detected in the eastern Mediterranean populations. The genetic data obtained from the Italian A. chukar population as well as from a few Greek specimens pointed against their Mediterranean kinship, suggesting relationships with A. chukar subspecies from the easternmost part of the Asian continent. PMID:17286187

  4. Genetic stability of micropropagated almond plantlets, as assessed by RAPD and ISSR markers

    Microsoft Academic Search

    M. Martins; D. Sarmento; M. M. Oliveira

    2004-01-01

    Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD

  5. Detection and genetic distance of resistant populations of Pseudosuccinea columella (Mollusca: Lymnaeidae) to Fasciola hepatica (Trematoda: Digenea) using RAPD markers.

    PubMed

    Calienes, Aymé Fernandez; Fraga, Jorge; Pointier, Jean-Pierre; Yong, Mary; Sanchez, Jorge; Coustau, Christine; Gutiérrez, Alfredo; Théron, André

    2004-09-01

    Twelve natural populations of Pseudosuccinea columella snails, sampled in the western and central regions of Cuba, were analyzed using the RAPD-PCR technique to screen for resistance to Fasciola hepatica. Ten OPA primers previously shown to produce marker bands for resistance and susceptibility were tested. A new population of P. columella (El Azufre, Pinar del Río) exhibited the amplification patterns of resistant snails, and its resistant status was confirmed after experimental exposure to miracidia. No genetic variability was detected across or within the susceptible isolates. Similarly, the novel resistant isolate displayed an RAPD profile identical to the profile of two other isolates previously identified as resistant to F. hepatica. However, clear differences in RAPD banding patterns and genetic distance were observed between resistant and susceptible isolates. PMID:15301979

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

    PubMed Central

    Dangi, Rakhee S; Lagu, Meena D; Choudhary, Lal B; Ranjekar, Prabhakar K; Gupta, Vidya S

    2004-01-01

    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. Implications of these observations in the analysis of genetic diversity and in supporting the possible Center of Origin and/or Diversity for Trigonella are discussed. PMID:15285785

  7. [Tagging and mapping of QTLs controlling lint yield and yield components in upland cotton (Gossypium hirsutum L.) using SSR and RAPD markers].

    PubMed

    Yin, Jian-Mei; Wu, Yao-Ting; Zhang, Jun; Zhang, Tian-Zhen; Guo, Wang-Zhen; Zhu, Xie-Fei

    2002-01-01

    Using interval mapping and marker simple regression methods, the QTLs of yield and its components in (Simian 3 x TM-1) F2 and F2:3, were tagged and Mapped with 39 SSR and 10 RAPD markers having polymorphism between parents screened from 301 pair SSR primers and 1040 RAPD primers. Simian 3 is being grown extensively in Yangtze River cotton-growing valley characterized as high productivity with more bolls and higher lint percent, whereas TM-1, Genetic standard in Upland cotton with more heavy boll weight. In the present report, two QTLs controlling boll size with 18.2% and 21.0% phenotype variance explained in F2:3 generation, one QTL controlling lint percent with 24.9% phenotype variance explained in F2 generation and 5.9% in F2:3 generation and one QTL controlling 100-seed weight with 15.6% phenotype variance explained in F2:3 generation were mapped in Chromosome 9. Additionally, another QTL responsible for 100-seed weight was identified and mapped at the same position in Chromosome 9 in F2:3 generation. It is worth for further to be studied whether it is one QTL for pleiotrophism or two closely linked QTLs. The molecular markers mapped and tagged closely with main QTLs of yield traits in this paper can be used for MAS in cotton high-yield breeding program. PMID:12148276

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

    PubMed

    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. PMID:24941038

  9. RAPD Markers to Evaluate Callus Tissue of Cereus peruvianus Mill. (Cactaceae) Maintained in Different Growth Regulator Combinations

    Microsoft Academic Search

    Claudete A. Mangolin; Laura M. M. Ottoboni; Maria de Fátima P. S. Machado

    2002-01-01

    RAPD markers were used to detect DNA polymorphisms in callus tissues maintained at different auxin and cytokinin combinations. There is a higher level of genetic variablity in callus tissue maintained with the highest kinetin versus2, 4-D concentration. Callus tissues subcultured in a 4.0 mg\\/L 2,4-D and 4.0 mg\\/L kinetin combination showed high similarity and can be recommended as more suitable

  10. Determination of genetic stability in long-term micropropagated shoots of Pinus thunbergii Parl. using RAPD markers

    Microsoft Academic Search

    S. Goto; R. C. Thakur; K. Ishii

    1998-01-01

    Random amplified polymorphic DNA (RAPD) markers were used to determine the genetic stability of long-term (more than 10 years)\\u000a micropropagated shoots of Japanese black pine (Pinus thunbergii Parl.). Thirty-six shoots consisting of three morphotypes (short, medium, and long needles) were randomly chosen from about\\u000a 4,000 micropropagated shoots regenerated from the explants of a single nematode-resistant mother plant. Out of 126

  11. Marker Assisted Selection (MAS) for chickpea Fusarium oxysporum wilt resistant genotypes using PCR based molecular markers.

    PubMed

    Ahmad, Zakia; Mumtaz, Abdul Samad; Ghafoor, Abdul; Ali, Amjad; Nisar, Mohammad

    2014-10-01

    The exploration of genetically superior accessions is the key source of germplasm conservation and potential breeding material for the future. To meet the demand of better yielding chickpea cultivars in Pakistan the present study was organized to select more stable and resistant lines from indigenous as well as exotic chickpea germplasm obtained from Plant Genetic Resource Institute (PGRI), National Agricultural Research Centre, Islamabad, Pakistan. For the identification and evaluation of chickpea wilt resistant lines against Fusarium oxysporum f. sp. ciceris (Schlechtends), the germplasm was tested in the field for the selection of wilt resistant lines and the PCR based molecular markers were investigated to use Marker Assisted Selection (MAS) for selection of the desirable cultivars. In field trial, 70 % accessions were resistant to wilt disease, while the remaining 30 % have shown susceptibility to the disease. A total of 5 RAPD and 15 SSR markers were screened for molecular based characterization of wilt response. The data of molecular markers were scored by the presence (1) and absence (0) of allele and subjected to statistical analysis. The analysis was based on coefficient of molecular similarity using UPGMA and sorted the germplasm into two groups based on disease response. Among the total used RAPD/SSR primers, only TA194 SSR marker showed linkage to wilt resistant locus at 85 % probability. The linkage of a marker was reconfirmed by receiver operating characteristic curve. The use of the sorted wilt resistant genotypes through SSR marker TA194 can make available ample prospect in MAS breeding for yield improvement of the crop in Pakistan. PMID:25017202

  12. Emerging molecular markers of cancer

    Microsoft Academic Search

    David Sidransky

    2002-01-01

    Alterations in gene sequences, expression levels and protein structure or function have been associated with every type of cancer. These 'molecular markers' can be useful in detecting cancer, determining prognosis and monitoring disease progression or therapeutic response. But what is the best way to identify molecular markers and can they be easily incorporated into the clinical setting?

  13. Use of random amplified polymorphic DNA (RAPD) markers in the discrimination and verification of genotypes in Eucalyptus.

    PubMed

    Keil, M; Griffin, A R

    1994-10-01

    We carried out four separate studies using random amplified polymorphic DNA (RAPD) markers to analyse samples of Eucalyptus supplied by several different organisations. The objective was to examine the reproducibility of the RAPD technique and its ability to discriminate between individual genotypes for verification of clonal identities. We found that RAPD profiles that are unique to a genotype can be generated reliably and simply and that even closely related genotypes can be distinguished. In addition, in each of the four studies, we detected cases where the plant material studied had been mis-sampled or mis-labelled (i.e. the RAPD profiles were not consistent with the identification numbers): (1) ramets of a Eucalyptus grandis clone were found to be derived from 2 different clones; (2) ramets labelled as 2 different Eucalyptus hybrid clones were found to be the same clone, owing to a mis-planted clonal hedge; (3) samples supplied as a single progeny of a controlled E. nitens cross were derived from two crosses involving different pairs of parents; (4) mis-labelling was detected for ramets of 4 of a set of 10 clones of E. grandis and E. camaldulensis. For three of the four studies, the detection of genotype mis-identifications was unexpected, suggesting that labelling or sampling errors during the handling of plant material are a frequent occurrence, with potentially serious economic consequences. PMID:24177893

  14. Genetic diversity in potato field populations of Thanatephorus cucumeris AG-3, revealed by ITS polymorphism and RAPD markers.

    PubMed

    Justesen, Annemarie Fejer; Yohalem, David; Bay, Anne; Nicolaisen, Mogens

    2003-11-01

    DNA sequence analysis of the internal transcribed spacer region 1 (ITS1) and random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability in relation to agronomic and regional factors among 60 isolates of Thanatephorus cucumeris (anamorph Rhizoctonia solani) collected from lesions on potato stems or sclerotia of potato tubers. Based on comparative sequence analysis it was shown that all isolates belonged to anastomosis group 3 subgroup Potato Type (AG-3 PT). ITS1 sequence polymorphisms were found within 45 of the 60 isolates showing that different types of the ITS-region are present in individual isolates. Cloning and sequence analysis of the ITS1 region from three selected isolates with sequence polymorphism showed that two different ITS1-types were present in each isolate. RAPD analysis identified 51 RAPD-phenotypes among the 60 investigated isolates indicating a high level of diversity within the subgroup AG-3 PT. Putative clonal isolates with identical RAPD- and ITS1-types were identified within fields, and in one case the same phenotype was found in two different fields separated by several hundred kilometers. Population subdivision analysis based on phenotypic as well as genotypic diversities showed differentiation among populations from different fields when isolates were sampled from tubers, indicating restricted gene flow among soil populations. Low differentiation was seen among field populations sampled from stems, indicating that gene flow is taking place. The population structure was not influenced by the previous crop in the rotation nor by the two cultivars 'Sava' and 'Bintje'. PMID:15000234

  15. Population genetics with RAPD-PCR markers: the breeding structure of Aedes aegypti in Puerto Rico

    Microsoft Academic Search

    Barbara L Apostol; William C Black; Paul Reiter; Barry R Miller; William C Black IV

    1996-01-01

    RAPD-PCR polymorphisms at 57 presumptive loci were used to examine the breeding structure of the mosquito Aedes aegypti in Puerto Rico. Mosquitoes were sampled from 16 locations in six cities and samples were located in a nested spatial design to examine local patterns of gene flow. Allele frequencies were estimated assuming (1) that genomic regions amplified by RAPD-PCR segregate as

  16. Microevolutionary Patterns and Molecular Markers: The Genetics of Geographic Variation in Ascaris suum

    PubMed Central

    Nadler, S. A.

    1996-01-01

    Molecular markers have been used only rarely to characterize the population genetic structure of nematodes. Published studies have suggested that different taxa may show distinct genetic architectures. Isoenzyme and RAPD markers have been used to investigate geographic variation of Ascaris suum at the level of infrapopulations (nematodes within individual hosts), within localities, and among geographic regions. Independent estimates of genetic differentiation among population samples based on isoenzyme and RAPD data showed similar patterns and substantial correlation. Heterozygote deficiencies within infrapopulations and large values for inbreeding coefficients among infrapopulations suggested that the composition of these populations was not consistent with a model of random recruitment from a large panmictic pool of life-cycle stages. Both isoenzyme and RAPD markers revealed moderate levels of genetic differentiation among samples representing infrapopulations and localities. Of total gene diversity, 9.4% (isoenzyme) and 9.2% (RAPD) was partitioned among infrapopulations. Geographic localities accounted for 7.8% (isoenzyme) and 6.2% (RAPD) of total diversity. Only infrapopulations from the same farm had low levels of differentiation. PMID:19277145

  17. Utility of RAPD marker for genetic diversity analysis in gamma rays and ethyl methane sulphonate (EMS)-treated Jatropha curcas plants.

    PubMed

    Dhakshanamoorthy, Dharman; Selvaraj, Radhakrishnan; Chidambaram, Alagappan

    2015-02-01

    The presence of important chemical and physical properties in Jatropha curcas makes it a valuable raw material for numerous industrial applications, including the production of biofuel. Hence, the researcher's interest is diversified to develop more and better varieties with outstanding agronomic characteristics using conventional breeding. Among these, mutation breeding is one of the best approaches to bring genetic changes in plant species. The aim of this study is to evaluate the diversity and genetic relationship among J. curcas mutants, which were obtained from different doses of gamma rays (control, 5 Kr, 10 Kr, 15 Kr, 20 Kr and 25 Kr) and EMS (1%, 2%, 3% and 4%), using RAPD marker. Among the 21 random primers, 20 produced polymorphic bands. The primers, OPM-14 and OPAW-13, produced a minimum number of bands (3) each across the ten mutants, while the primer OPF-13 produced the maximum number of bands (10), followed by the primers OPU-13, OPAM-06, OPAW-09 and OPD-05, which produced 9 bands each. The number of amplicons varied from 3 to 10, with an average of 7 bands, out of which 4.57 were polymorphic. The percentage of polymorphism ranged from 0.00 to 100 with an average of 57%. In the present study, RAPD markers were found most polymorphic, with an average polymorphism information content (PIC) value of 0.347, effective multiplex ratio (EMR) of 35.14, marker index (MI) of 14.19, resolution power (Rp) of 11.19, effective marker index (EMI) of 8.21 and genotype index (GI) of 0.36, indicating that random primers are useful in studies of genetic characterization in J. curcas mutant plants. In a dendrogram constructed based on Jaccard's similarity coefficients, the mutants were grouped into three main clusters viz., (a) control, 10 Kr, 15 Kr, 20 Kr, 2% EMS, and 3% EMS, (b) 5 Kr and 1% EMS, and (c) 25 Kr and 4% EMS mutants. Based on the attributes of the random primers and polymorphism studied, it is concluded that RAPD analysis offers a useful molecular marker for the identification of the mutants in gamma rays and EMS treated plants. PMID:25557365

  18. Isolation and characterization of RAPD-based markers linked to the beet cyst nematode resistance locus (Hs1 (pat-1)) on chromosome 1 of B. patellaris.

    PubMed

    Salentijn, E M; Arens-De Reuver, M J; Lange, W; De Bock, T S; Stiekema, W J; Klein-Lankhorst, R M

    1995-05-01

    A beet cyst nematode (BCN)-resistant telosomic addition of B. patellaris chromosome 1 in B. vulgaris was used to isolate 6 RAPD markers linked to the BCN resistance locus Hs1 (pat-1). Southern analysis showed that the analyzed RAPD products contain either low-, middle or high-repetitive DNA. The relative positions of the random amplified polymorphic DNA (RAPD) markers and of the restriction fragment length polymorphism (RFLP) loci corresponding to the low-repetitive RAPD products were determined by deletion mapping using a panel of seven nematode-resistant B. patellaris chromosome-1 fragment additions. One RAPD marker, OPB11800, was found to be present in two copies on the long arm telosome of B. patellaris chromosome 1. These copies are closely linked to the BCN resistance gene and flank the gene on both sides. On the basis of the nucleotide sequence of OPB11800, sequence-tagged site (STS) primers were developed that amplify specific fragments derived from the two OPB11800 loci. These STS markers can be used in the map-based cloning of the BCN gene, as they define start and finishing points of a chromosomal walk towards the Hs1 (pat-1) locus. Two copies of the middle-repetitive OPX21100 marker were mapped in the same interval of the deletion mapping panel as the resistance gene locus and thereby belong to the nearest markers as yet found for the BCN gene in B. patellaris. PMID:24172934

  19. Identification of specific molecular markers linked to the rust resistance gene M4 in flax

    Microsoft Academic Search

    T. Y. Bo; J. J. Ma; J. X. Chen; T. Y. Miao; W. X. Zhai

    2008-01-01

    To identify molecular markers linked to the flax rust-resistance gene M4, RAPD analysis of NM4 (a near-isogenic line containing the M4 gene) and the recurrent parent Bison was performed using 540 decamer primers. The primer OPA18 amplified a specific fragment,\\u000a OPA18432, in the NM4 line. The OPA18432 marker was found to be closely linked to the M4 gene, with a

  20. Comparative analysis of genetic relationship and diagnostic markers of several taxa of Guizotia Cass. (Asteraceae) as revealed by AFLPs and RAPDs

    Microsoft Academic Search

    M. Geleta; T. Bryngelsson; E. Bekele; K. Dagne

    2007-01-01

    Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) were employed to examine the genetic\\u000a relationship between Guizotia taxa, to suggest the taxonomic status of some of these taxa, and to identify their diagnostic markers. Results from AFLPs\\u000a and RAPDs share some features in common, both revealing G. scabra ssp. schimperi as the most closely related taxon to

  1. The use of RAPD markers to distinguish among juniper and cedar cultivars

    Microsoft Academic Search

    Tom Hsiang; Junbin Huang

    2000-01-01

    Abstract: Two species of Chamaecyparis,and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were,subjected to random,amplified polymorphic,DNA (RAPD) analysis using seven primers. Un- weighted,pair group method,with averages (UPGMA) and principal component,analyses of genetic distances between cultivars showed,that 42 polymorphic,RAPD bands could distinguish among,all cultivars and properly group them,by species and genera. Where the origin of a

  2. Conservation genetics of endangered Brasenia schreberi based on RAPD and AFLP markers

    Microsoft Academic Search

    Changkyun Kim; Hye Ryun Na; Hong-Keun Choi

    2008-01-01

    Brasenia schreberi J.F. Gmelin is a declared endangered species found in the lakes and ponds of South Korea. For planning its conservation strategy,\\u000a we examined the genetic diversity within and among six populations, using randomly amplified polymorphic DNA (RAPD) and amplified\\u000a fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per loci with AFLP (69.3%) than RAPD (36.8%).\\u000a High genetic

  3. Genetic diversity of spineless Cereus jamacaru accessions using morphological and molecular markers.

    PubMed

    Oliveira, F I C; Bordallo, P N; Castro, A C R; Correia, D

    2013-01-01

    This is the first study to examine the genetic diversity of mandacaru cactus (Cereus jamacaru P. DC.). Plants of spineless mandacaru are commonly found in gardens and parks of urban areas in northeastern Brazil. In addition to exploring their ornamental potential, morphological, and genetic characterization may contribute to the development of plant materials that can be used as a source of macromolecules of potential economic interest. The goal of this study was to estimate the genetic variability of spineless mandacaru accessions using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers, and to characterize their morphology. Ten samples of newly emitted shoots with differentiated areolas and ribs were collected from each accession from the Cactaceous Germplasm Collection of Embrapa Agroindústria Tropical, in Fortaleza, CE. Shoot shape and aspects of spine primordia (presence, location, grouping, and size of spines) were evaluated. The morphological analysis showed that the spineless mandacaru presented spine primordia. Twenty-six RAPD and 15 ISSR primers were polymorphic. A total of 262 markers were obtained, 129 of which were polymorphic. The average polymorphism of ISSR markers was higher than that of RAPD markers. The dendrograms for both analyses showed differentiation between accessions. Nevertheless, the molecular markers detected higher levels of diversity and a different pattern of diversity than those found using morphological markers. The molecular results revealed significant genetic variability both within and between groups. PMID:24222234

  4. Development and use of molecular markers: past and present.

    PubMed

    Grover, Atul; Sharma, P C

    2014-11-28

    Abstract Molecular markers, due to their stability, cost-effectiveness and ease of use provide an immensely popular tool for a variety of applications including genome mapping, gene tagging, genetic diversity diversity, phylogenetic analysis and forensic investigations. In the last three decades, a number of molecular marker techniques have been developed and exploited worldwide in different systems. However, only a handful of these techniques, namely RFLPs, RAPDs, AFLPs, ISSRs, SSRs and SNPs have received global acceptance. A recent revolution in DNA sequencing techniques has taken the discovery and application of molecular markers to high-throughput and ultrahigh-throughput levels. Although, the choice of marker will obviously depend on the targeted use, microsatellites, SNPs and genotyping by sequencing (GBS) largely fulfill most of the user requirements. Further, modern transcriptomic and functional markers will lead the ventures onto high-density genetic map construction, identification of QTLs, breeding and conservation strategies in times to come in combination with other high throughput techniques. This review presents an overview of different marker technologies and their variants with a comparative account of their characteristic features and applications. PMID:25430893

  5. Phylogenetic analysis in the genus Cicer and cultivated chickpea using RAPD and ISSR markers

    Microsoft Academic Search

    M. Iruela; J. Rubio; J. I. Cubero; J. Gil; T. Millán

    2002-01-01

    Seventy five accessions belonging to 14 species of the genus Cicer were analysed with PCR-based molecular markers to determine their phylogenetic relationships. Eight of the species were annuals\\u000a and included the Section Monocicer which contains cultivated chickpea (Cicer arietinum L.). The remaining six species were perennials (five from Section Polycicer and one from Section Acanthocicer). More than\\u000a one accession per

  6. Genetic diversity in three populations of Avicennia marina along the eastcoast of India by RAPD markers.

    PubMed

    Hazarika, Dimendra; Thangaraj, M; Sahu, Sunil Kumar; Kathiresan, K

    2013-05-01

    Genetic diversity was analysed in three populations of the mangrove species, Avicennia marina by using random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR). Ten random decamer primers were used to score the diversity from three locations of eastcoast of India: Parangipettai (Tamil Nadu), Kakkinada (Andhra Pradesh) and Sundarbans (West Bengal). These primers produced 388 scorable DNA fragments, of which 252 (64.98%) were polymorphic, 182 (46.90%) were monomorphic, and 14 (3.61%) were unique. RAPD banding patterns displayed variations between and within the populations, while, there was no morphological variation. PMID:24617156

  7. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers.

    PubMed

    Medhi, K; Sarmah, D K; Deka, M; Bhau, B S

    2014-12-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  8. High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers

    PubMed Central

    Medhi, K.; Sarmah, D.K.; Deka, M.; Bhau, B.S.

    2014-01-01

    The genetic diversity in Zanthoxylum species viz.  Zanthoxylum nitidum, Zanthoxylum oxyphyllum and Zanthoxylum rhesta collected from the Upper Brahmaputra Valley Zone of Assam (NE India) was amplified using 13 random amplified polymorphic DNA (RAPD) markers and 9 inter-simple sequence repeat (ISSR) markers. RAPD markers were able to detect 81.82% polymorphism whereas ISSR detected 98.02% polymorphism. The genetic similarities were analyzed from the dendrogram constructed by RAPD and ISSR fingerprinting methods which divided the 3 species of Zanthoxylum into 3 clear different clusters. The principle component analysis (PCA) was carried out to confirm the clustering pattern of RAPD and ISSR analysis. Analysis of molecular variance (AMOVA) revealed the presence of significant variability between different Zanthoxylum species and within the species by both RAPD and ISSR markers. Z. nitidum was found to be sharing a high degree of variation with the other two Zanthoxylum species under study. The Nei's gene diversity (h), Shannon's information index (I), observed number of alleles (na) and effective number of alleles (ne) were also found to be higher in ISSR markers (0.3526, 0.5230, 1.9802 and 1.6145) than in RAPD markers (0.3144, 0.4610, 1.8182 and 1.5571). The values for total genotype diversity for among population (HT), within population diversity (Hs) and gene flow (Nm) were more in ISSR (0.3491, 0.2644 and 1.5610) than RAPD (0.3128, 0.2264 and 1.3087) but the mean coefficient of gene differentiation (GST) was more in RAPD (0.2764) than ISSR (0.2426). A comparison of this two finger printing methods was done by calculating MR, EMI and MI. The correlation coefficient between data matrices of RAPD and ISSR based on Mantel test was found to be significant (r = 0.65612). PMID:25606454

  9. Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

    PubMed Central

    Achar, Devaraja; Awati, Mallikarjuana G.; Udayakumar, M.; Prasad, T. G.

    2015-01-01

    Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection.

  10. The use of RAPD markers to distinguish among juniper and cedar cultivars

    E-print Network

    Hsiang, Tom

    Huang Abstract: Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis, phylogénétique. [Traduit par la Rédaction] Hsiang and Huang 659 Introduction The genera Juniperus

  11. Efficiency of RAPD, SSR and cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions.

    PubMed

    Panwar, Preety; Saini, R K; Sharma, Netrapal; Yadav, Dinesh; Kumar, Anil

    2010-12-01

    Finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. Three DNA marker techniques, random amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P(450) gene based markers were used for the detection of genetic polymorphism in 83 accessions of finger millet collected from various geographical regions of India and Africa. A total of 18 RAPD, 10 SSR and 10 pairs of cytochrome P(450) gene based markers were generated 56.17, 70.19 and 54.29% polymorphism, respectively. Mean polymorphism information content (PIC) for each of these marker systems (0.280 for RAPD, 0.89 for SSR and 0.327 for cytochrome P(450) gene based markers) suggested that SSR marker were highly effective in determining polymorphism. The phenograms based on the three markers data indicate that genotypes from different geographical regions are clearly distinguishable as separate clusters. Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.90 for all the three marker systems. The dendrograms and PCA plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Based on the results of present study, SSR and cytochrome P(450) gene based markers appear to be particularly useful for the estimation of genetic diversity. This study reveals the potential of RAPD, SSR and gene based markers for characterizing germplasm of Eleusine coracana and narrow down the vast germplasm into distinct core groups. PMID:20333550

  12. Genetic Diversity Among Wheat Cultivars Using Molecular Markers

    Microsoft Academic Search

    Babak Abdollahi Mandoulakani; Ali-Akbar Shahnejat-Bushehri; Badredin Ebrahim Sayed Tabatabaei; Sepideh Torabi; Alireza Mohammadi Hajiabad

    2010-01-01

    The objective of this study was to compare amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and DNA amplification fingerprinting (DAF) marker systems for estimating genetic diversity among 13 Iranian wheat (Triticum aestivum L.) cultivars through average expected heterozygosity (Hav), sum of effective number of alleles (SENA), and marker index (MI). The AFLP markers had the highest values

  13. MOLECULAR MARKERS IN RICE BREEDING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Researchers in the USDA/TAES/TAMU Molecular Genetics Laboratory are continuing to develop and analyze markers for several economically important traits in rice. We are presently active in a multi-institute Coordinated Agricultural Project (RiceCAP) funded by the USDA National Research Initiative to ...

  14. Inheritance of plant regeneration from maize ( Zea mays L.) shoot meristem cultures derived from germinated seeds and the identification of associated RAPD and SSR markers

    Microsoft Academic Search

    W. Li; G. Sun; J. Liu; P. Masilamany; J. H. Taylor; W. Yan; K. J. Kasha; K. P. Pauls

    2004-01-01

    The inheritance of shoot regeneration through shoot-tip meristem culture derived from maize seedling was evaluated, and the markers (RAPD and SSR) associated with this regeneration character were identified both in a group of North American maize inbreds and a crossing population. A discrete distribution of percent regeneration and no. of shoots per explant was observed in the inbred group and

  15. Extension of the linkage map in Citrus using random amplified polymorphic DNA (RAPD) markers and RFLP mapping of cold-acclimation-responsive loci

    Microsoft Academic Search

    Q. Cai; C. L. Guy; G. A. Moore

    1994-01-01

    Genetic mapping with RAPD markers has been initiated in Citrus. Reproducible polymorphism of amplified DNA fragments was obtained with approximately half of the 140 random primers tested, revealing 266 segregating loci. These were tested for linkage using 60 BC1 progeny from an intergeneric cross of Citrus grandis (L.) Osb. x [Citrus grandis (L.) Osb. x Poncirus trifoliata (L.) Raf.]. A

  16. Molecular markers for yellow stem borer Scirpophaga incertulas (Walker) resistance in rice

    Microsoft Academic Search

    A. Selvi; P. Shanmugasundaram; S. Mohan Kumar; J. A. J. Raja

    2002-01-01

    Breeding for yellow stem borer resistance in rice is difficult owing to the complex genetics of the trait and inherent difficulties\\u000a in screening. Identification of molecular markers linked to the trait would enhance phenotypic evaluation for the trait. An\\u000a F2 population was developed using parents contrasting in their reaction to yellow stem borer resistance. Random Amplified Polymorphic\\u000a DNA (RAPD) analysis,in

  17. Phylogenetic analysis in the Festuca-Lolium complex using molecular markers and ITS rDNA

    Microsoft Academic Search

    G. Charmet; C. Ravel; F. Balfourier

    1997-01-01

    Molecular markers were used to investigate phylogenetic relationships among the eight species of ryegrass (Lolium) and 11 species of fescue (Festuca). RAPD and RFLP analyses were carried out on total bulked DNA from each population. Factorial analysis of a phenetic distance\\u000a matrix yielded three major groups: (1) fine-leaved fescues, (2) broad-leaved fescues and (3) ryegrasses. Six non-coding regions\\u000a of chloroplastic

  18. Comparative evaluation of genetic diversity using RAPD, SSR and cytochrome P450 gene based markers with respect to calcium content in finger millet (Eleusine coracana L. Gaertn.).

    PubMed

    Panwar, Preety; Nath, Manoj; Yadav, Vijay Kumar; Kumar, Anil

    2010-08-01

    Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. 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 P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300-450 mg/100 g), medium calcium (200-300 mg/100 g) and low calcium (100-200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops. PMID:20861563

  19. Micropropagation and validation of genetic and biochemical fidelity amongst regenerants of Cassia angustifolia Vahl employing RAPD marker and HPLC.

    PubMed

    Chetri, Siva K; Sardar, Pratima Rani; Agrawal, Veena

    2014-10-01

    In vitro protocol has been established for clonal propagation of Cassia angustifolia Vahl which is an important source of anticancerous bioactive compounds, sennoside A and B. Nodal explants excised from field raised elite plant (showing optimum level of sennoside A and B) of C. angustifolia when reared on Murashige and Skoog's medium augmented with different cytokinins, viz. N(6)-benzyladenine (BA), N(6)-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn) differentiated multiple shoots in their axils. Of the three cytokinins, BA at 5 ?M proved optimum for differentiating multiple shoots in 95 % cultures with an average of 9.14 shoots per explant within 8 weeks of culture. Nearly, 95 % of the excised in vitro shoots rooted on half strength MS medium supplemented with 10 ?M indole-3-butyric acid (IBA). The phenotypically similar micropropagated plants were evaluated for their genetic fidelity employing random amplified polymorphic DNA (RAPD) markers. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 36 scorable bands, ranging in size from 100 to 1,000 bp were generated amongst them by the RAPD primers. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant proving their true to the type nature. Besides, high performance liquid chromatography evaluation of the sennoside A and B content amongst leaves of the mature regenerants and the elite mother plant too revealed consistency in their content. PMID:25320475

  20. RAPD-based SCAR marker SCA 12 linked to recessive gene conferring resistance to anthracnose in sorghum [Sorghum bicolor (L.) Moench].

    PubMed

    Singh, Monika; Chaudhary, K; Boora, K S

    2006-12-01

    Anthracnose, caused by Colletotrichum graminicola, infects all aerial parts of sorghum, Sorghum bicolor (L.) Moench, plants and causes loss of as much as 70%. F(1) and F(2) plants inoculated with local isolates of C. graminicola indicated that resistance to anthracnose in sorghum accession G 73 segregated as a recessive trait in a cross with susceptible cultivar HC 136. To facilitate the use of marker-assisted selection in sorghum breeding programs, a PCR-based specific sequence characterized amplified region (SCAR) marker was developed. A total of 29 resistant and 20 susceptible recombinant inbred lines (RILs) derived from a HC 136 x G 73 cross was used for bulked segregant analysis to identify a RAPD marker closely linked to a gene for resistance to anthracnose. The polymorphism between the parents HC 136 and G 73 was evaluated using 84 random sequence decamer primers. Among these, only 24 primers generated polymorphism. On bulked segregant analysis, primer OPA 12 amplified a unique band of 383 bp only in the resistant parent G 73 and resistant bulk. Segregation analysis of individual RILs showed the marker OPA 12(383) was 6.03 cM from the locus governing resistance to anthracnose. The marker OPA 12(383) was cloned and sequenced. Based on the sequence of cloned RAPD product, a pair of SCAR markers SCA 12-1 and SCA 12-2 was designed using the MacVector program, which specifically amplified this RAPD fragment in resistant parent G 73, resistant bulk and respective RILs. Therefore, it was confirmed that SCAR marker SCA 12 is at the same locus as RAPD marker OPA 12(383) and hence, is linked to the gene for resistance to anthracnose. PMID:17063339

  1. Comparison of RAPD and AFLP Marker Analysis as a Means to Study the Genetic Structure of Botrytis cinerea Populations

    Microsoft Academic Search

    C. Moyano; C. Alfonso; J. Gallego; R. Raposo; P. Melgarejo

    2003-01-01

    To assess the genetic relationships of Botrytis cinerea populations in Almería (Spain), 44 isolates of B. cinerea, collected from six commercial greenhouses (subpopulations), were analysed by Random Amplified Polymorphic DNA (RAPD) and amplified-fragment length polymorphism (AFLP). Polymorphisms were more frequently detected per primer with AFLP than with RAPD (16 compared to 4). However, RAPD detected polymorphisms more frequently per loci

  2. Molecular marker-based characterization in candidate plus trees of Pongamia pinnata, a potential biodiesel legume

    PubMed Central

    Kesari, Vigya; Madurai Sathyanarayana, Vinod; Parida, Ajay; Rangan, Latha

    2010-01-01

    Background and aims Pongamia pinnata, a legume tree, has many traditional uses and is a potential biodiesel plant. Despite its importance and the availability of appropriate molecular genetic tools, the full potential of Pongamia is yet to be realized. The objective of this study was to assess genetic diversity among 10 systematically characterized candidate plus trees (CPTs) of P. pinnata from North Guwahati. Methodology The application and informativeness of polymerase chain reaction-based molecular markers [random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and amplified fragment length polymorphism (AFLP)] to assess the genetic variability and relatedness among 10 CPTs of P. pinnata were investigated. Principal results Polymorphism rates of 10.48, 10.08 and 100 % were achieved using 18 RAPD, 12 ISSR and 4 AFLP primer combinations, respectively. Polymorphic information content (PIC) varied in the range 0.33–0.49, 0.18–0.49 and 0.26–0.34 for RAPD, ISSR and AFLP markers, respectively, whereas the corresponding average marker index (MI) values for the above markers were 7.48, 6.69 and 30.75. Based on Nei's gene diversity and Shannon's information index, inter-population diversity (hsp) was highest when compared with intra-population diversity (hpop) and the gene flow (Nm) ranged from a moderate value of 0.607 to a high value of 6.287 for the three DNA markers. Clustering of individuals was not similar when RAPD- and ISSR-derived dendrogram analyses were compared with that of AFLP. The Mantel test cophenetic correlation coefficient was higher for AFLP (r = 0.98) than for ISSR (r = 0.73) and RAPD (r = 0.84). Molecular markers discriminated the individuals efficiently and generated a high similarity in dendrogram topologies derived using unweighted pair-group arithmetic average, although some differences were observed. The three-dimensional scaling by principal coordinate analysis supported the result of clustering. Conclusions Comparing the results obtained with the three DNA markers, AFLP indicated higher efficiency for estimating the levels of genetic diversity and proved to be reliable for fingerprinting, mapping and diversity studies in Pongamia in view of their suitability for energy production purposes. PMID:22476075

  3. Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust (Uromyces viciae-fabae) in Vicia faba L.

    PubMed

    Avila, C M; Sillero, J C; Rubiales, D; Moreno, M T; Torres, A M

    2003-07-01

    Bulk segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a gene determining hypersensitive resistance in Vicia faba line 2N52 against race 1 of the rust fungus Uromyces viciae-fabae. The monogenic nature of the resistance was determined by analyzing the F(2) population from a cross between resistant line 2N52 and susceptible line VF-176, and further confirmed in the F(2:3)-derived families. Linkage of the RAPD markers was confirmed by screening 55 F(2) plants segregating for resistance. Three RAPD markers (OPD13(736), OPL18(1032) and OPI20(900)) were mapped in coupling phase to the resistance gene for race 1 ( Uvf-1). No recombinants between OPI20(900) and Uvf-1 were detected. Two additional markers (OPP02(1172) and OPR07(930)) were linked to the gene in repulsion phase at a distance of 9.9 and 11.5 cM, respectively. The application of marker-assisted selection to develop new faba bean varieties with rust resistance genes is discussed. PMID:12698251

  4. Late-onset neonatal group B streptococcal disease associated with breast milk transmission: molecular typing using RAPD-PCR.

    PubMed

    Brandolini, Micaela; Corbella, Marta; Cambieri, Patrizia; Barbarini, Daniela; Sassera, Davide; Stronati, Mauro; Marone, Piero

    2014-03-01

    Group B Streptococcus (GBS) is considered to be the major cause of neonatal sepsis and meningitis of bacterial origin. Late-onset GBS infection is infrequent and occurs between 1 week and 3 months of age. The transmission of GBS through the ingestion of breast milk is reported in the literature, but only a few of these cases have been confirmed by molecular techniques. In this article we report five cases of late-onset GBS disease: transmission through maternal milk was confirmed in four cases, using the random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) typing assay. In addition, the RAPD-PCR assay showed that each of the isolated clones belonged to a different RAPD genotype, thus revealing that the late-onset GBS infections were not epidemiologically related. PMID:24709469

  5. Inter- and intra-specific genetic diversity of Iranian yarrow species Achillea santolina and Achillea tenuifolia based on ISSR and RAPD markers.

    PubMed

    Ebrahimi, M; Farajpour, M; Rahimmalek, M

    2012-01-01

    Cultivation and preservation of yarrow has recently attracted wide attention due to its beneficial properties; however, genetic variation of Achillea species is still relatively unknown. We used RAPD and ISSR markers to assess genetic diversity in 16 accessions of yarrow belonging to two species native to Iran. Seven ISSR and nine RAPD primers generated 187 amplified fragments, of which 159 were polymorphic. The similarity coefficient among Achillea tenuifolia accessions ranged from 61 to 86%, and from 40 to 84% among A. santolina accessions. A low similarity was observed between these two species (mean similarity = 0.36%). This low similarity is consistent with their geographical distribution. According to the results of cluster and PCA analyses, the two species completely separated from each other. These markers will aid in the identification of elite genotypes for domestication and breeding programs. PMID:23007980

  6. Molecular Marker Discovery and Genetic Map Visualisation

    Microsoft Academic Search

    Chris Duran; David Edwards; Jacqueline Batley

    \\u000a The bulk of variation at the nucleotide level is often not visible at the phenotypic level. However, this variation can be\\u000a exploited using molecular genetic marker systems. Molecular genetic markers represent one of the most powerful tools for genome\\u000a analysis and permit the association of heritable traits with underlying genomic variation. Molecular marker technology has\\u000a developed rapidly over the last

  7. Identification of RAPD markers linked to the Uvf-1 gene conferring hypersensitive resistance against rust ( Uromyces viciae-fabae ) in Vicia faba L

    Microsoft Academic Search

    C. M. Avila; J. C. Sillero; D. Rubiales; M. T. Moreno; A. M. Torres

    2003-01-01

    Bulk segregant analysis was used to identify random amplified polymorphic DNA (RAPD) markers linked to a gene determining hypersensitive resistance in Vicia faba line 2N52 against race 1 of the rust fungus Uromyces viciae-fabae. The monogenic nature of the resistance was determined by analyzing the F 2 population from a cross between resistant line 2N52 and susceptible line VF-176, and

  8. Species-diagnostic markers in Larix spp. based on RAPDs and nuclear, cpDNA, and mtDNA gene sequences, and their phylogenetic implications

    Microsoft Academic Search

    Marie-Claude Gros-Louis; Jean Bousquet; Luc E. Pâques; Nathalie Isabel

    2005-01-01

    Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among\\u000a four larch species [Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had\\u000a good diagnostic value, and 3 out of 12 nuclear

  9. Genetic variability and relationships among thirty genotypes of finger millet (Eleusine coracana L. Gaertn.) using RAPD markers.

    PubMed

    Das, Swanalata; Mishra, Rama Chandra; Rout, Gyana Ranjan; Aparajita, Subhashree

    2007-01-01

    Ragi or finger millet (Eleusine coracana L.) is an important crop used for food, forage, and industrial products. It is distributed in tropical and temperate regions of the world. The germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or varieties identification has relied on morphological characters like growth habit, leaf architecture or floral morphology. Investigation through RAPD (random amplified polymorphic DNA) markers was undertaken for identification and determination of the genetic variation among thirty genotypes of ragi of the family Poaceae. Thirteen selected decamer primers were used for genetic analysis. A total of 124 distinct DNA fragments ranging from 300-3000 bp was amplified by using selected random RAPD marker. The genetic similarity was evaluated on the basis of the presence or absence of bands. Cluster analysis was made by the similarity coefficient. It indicated that the 30 genotypes of ragi form two major clusters, first, a major cluster having only one genotype, i. e. Dibyasinha and a second major cluster having twenty-nine genotypes. The second major cluster again subdivides into two minor clusters. A first minor cluster has only three varieties, i. e. Neelachal, OEB-56 and Chilika. The genotypes Neelachal and OEB-56 exhibit a 86% similarity with each other and 80% similarity with Chilika. A second minor cluster has 26 genotypes and is divided into two sub-minor clusters. The first sub-minor cluster has only one genotype (VL-322). The second sub-minor cluster again subdivides into two groups. One group has one genotype and the second group again is divided into two sub-groups, one with 13 genotypes and the other with 11 genotypes. The highest similarity coefficient was detected in a genotype collected from southern India and the least from northern India. The genotypes of finger millet collected from diverse agroclimatic regions of India constitute a wide genetic base. This is helpful in breeding programs and a major input into conservation biology of cereal crop. PMID:17425116

  10. The concordance of terpenoid, ISSR and RAPD markers, and ITS sequence data sets among genotypes: an example from Juniperus

    Microsoft Academic Search

    Robert P. Adams; Andrea E. Schwarzbach; R. Naresh Pandey

    2003-01-01

    Twelve individual genotypes selected from Juniperus populations, varieties and species were analyzed using ITS sequences, RAPDs, ISSRs, and leaf volatile terpenoids. These four data sets, all analyzed in the same manner, illustrated that these data sets can be used at different organizational levels: specific, inter-specific and intraspecific. Similarity matrices for the ITS, RAPD, and ISSR data sets were highly correlated

  11. Development of molecular markers linked to the ‘Fiesta’ linkage group 7 major QTL for fire blight resistance and their application for marker-assisted selection

    Microsoft Academic Search

    Muhammad A. Khan; Charles-Eric Durel; Brion Duffy; Damien Drouet; Markus Kellerhals; Cesare Gessler; Andrea Patocchi

    2007-01-01

    A fire blight resistance QTL explaining 34.3%-46.6% of the phenotypic variation was recently identified on linkage group 7 of apple cultivar 'Fiesta' (F7). However, markers flanking this QTL were AFLP and RAPD markers un- suitable for marker-assisted selection (MAS). Two RAPD markers bracketing the QTL have been transformed into SCAR (sequence-characterized amplified region) markers, and an SSR marker specific for

  12. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn.

    PubMed

    Cha, Thye San; Anne-Marie, Kaben; Chuah, Tse Seng

    2014-02-01

    Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species. PMID:24374894

  13. A genetic linkage map of quinoa ( Chenopodium quinoa) based on AFLP, RAPD, and SSR markers.

    PubMed

    Maughan, P J; Bonifacio, A; Jellen, E N; Stevens, M R; Coleman, C E; Ricks, M; Mason, S L; Jarvis, D E; Gardunia, B W; Fairbanks, D J

    2004-10-01

    Quinoa ( Chenopodium quinoa Willd.) is an important seed crop for human consumption in the Andean region of South America. It is the primary staple in areas too arid or saline for the major cereal crops. The objective of this project was to build the first genetic linkage map of quinoa. Selection of the mapping population was based on a preliminary genetic similarity analysis of four potential mapping parents. Breeding lines 'Ku-2' and '0654', a Chilean lowland type and a Peruvian Altiplano type, respectively, showed a low similarity coefficient of 0.31 and were selected to form an F(2) mapping population. The genetic map is based on 80 F(2) individuals from this population and consists of 230 amplified length polymorphism (AFLP), 19 simple-sequence repeat (SSR), and six randomly amplified polymorphic DNA markers. The map spans 1,020 cM and contains 35 linkage groups with an average marker density of 4.0 cM per marker. Clustering of AFLP markers was not observed. Additionally, we report the primer sequences and map locations for 19 SSR markers that will be valuable tools for future quinoa genome analysis. This map provides a key starting point for genetic dissection of agronomically important characteristics of quinoa, including seed saponin content, grain yield, maturity, and resistance to disease, frost, and drought. Current efforts are geared towards the generation of more than 200 mapped SSR markers and the development of several recombinant-inbred mapping populations. PMID:15309300

  14. Micropropagation of annatto (Bixa orellana L.) from mature tree and assessment of genetic fidelity of micropropagated plants with RAPD markers.

    PubMed

    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 ?M benzyl adenine (BA) and tender coconut water (10 %) showed significantly high (P?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. PMID:24381446

  15. In vitro clonal propagation and genetic fidelity of the regenerants of Spilanthes calva DC. using RAPD and ISSR marker.

    PubMed

    Razaq, Mohd; Heikrujam, Monika; Chetri, Siva K; Agrawal, Veena

    2013-04-01

    An efficient in vitro protocol has been established for clonal propagation of elite plant of Spilanthes calva DC., an important source of spilanthol, an antimalarial larvicidal compound. Nodal explants excised from field grown plant of S. calva DC. when reared on Murashige and Skoog's medium augmented with different cytokinins, viz. N(6)-Benzyladenine (BA), N(6)-(2-isopentenyl) adenine (2iP) and 6-furfuryl aminopurine (Kn), differentiated multiple shoots from the axils. BA at 10 ?M proved optimum for elicitation of multiple shoots in 91.6 % cultures with an average of 7.12 shoots per explant within 6 weeks. The excised shoots rooted on half strength Murashige and Skoog's medium supplemented with 0.1 ?M IBA. Micropropagated plants were hardened and transferred to field for acclimatization, where 95 % plants survived and were phenotypically similar to the donor plant. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to evaluate the genetic fidelity amongst the regenerants. Eleven individuals, randomly chosen amongst a population of 120 regenerants were compared with the donor plant. A total of 71 scorable bands, ranging in size from 100 bp to 1,100 bp were generated by a combination of the two markers in the aforesaid plants. All banding profiles from micropropagated plants were monomorphic and similar to those of mother plant. The similarity values amongst the aforesaid plants varied from 0.967 to 1.000. The dendrogram generated through UPGMA (Unweighted Pair Group Method with arithmetic mean) analysis revealed 98 % similarity amongst them, thus confirming the genetic fidelity of the in vitro clones. PMID:24431493

  16. Biparental inheritance of RAPD markers in males of the pseudo-arrhenotokous mite Typhlodromus pyri.

    PubMed

    Perrot-Minnot, M J; Navajas, M

    1995-10-01

    In pseudo-arrhenotokous mites, haploid males develop from fertilized eggs that undergo paternal genome loss (PGL) during early embryogenesis. We present evidence that some of the paternal genome may be retained in males of the predatory mite Typhlodromus pyri Scheuten (Acari: Phytoseiidae). Two reproductively compatible populations were differentiated by two random amplified polymorphic DNA markers and the inheritance pattern in the offspring was analysed. Maternal transmission rates are variable and independent of the sex of the offspring and of the marker. These data suggest a nuclear origin and independent segregation of the markers. One marker (330 base pairs (bp)) was paternally transmitted to male as well as female offspring, the other (990 bp) was paternally transmitted to all females and some of the male offspring. We propose that the paternal set of inactivated chromosomes may be partially retained in some tissues of the haploid males or, alternatively, that a B chromosome does not follow the process of PGL in male embryos, thereby segregating with the maternal set. The possible mechanisms controlling the condensation and the segregation of the chromosome(s) retained are discussed on the basis of current hypotheses on chromosome inactivation in insects. PMID:18470210

  17. Identification of co-dominant RAPD markers tightly linked to fruit skin color in apple

    Microsoft Academic Search

    F. S. Cheng; N. F. Weeden; S. K. Brown

    1996-01-01

    A simple genetic basis for the red\\/yellow skincolor polymorphism in apple was verified using DNA markers. Bulked segregant analysis identified one 10-base oligomer that generated different fragments in each of the bulks. After testing the primer in four populations, two fragments were found to be associated with red skin color and another two fragments associated with yellow skin color. Three

  18. Genetic linkage map of ISSR and RAPD markers in Einkorn wheat in relation to that of RFLP markers

    Microsoft Academic Search

    T. Kojima; T. Nagaoka; K. Noda; Y. Ogihara

    1998-01-01

    The potential of PCR-based markers for construction of a genetic linkage map in Einkorn wheat was investigated. From a comparison\\u000a of polymorphisms between two Einkorn wheats, Triticum monococcum (Mn) and T. boeoticum (Bt), we obtained 49 polymorphic bands produced by 33 primers for inter-simple sequence repeat (ISSR) and 36 polymorphic\\u000a bands shown by 25 combinations of random amplified polymorphic DNA

  19. Varijabilnost germplazme lucerne (Medicago spp.) procijenjena RAPD markerima

    Microsoft Academic Search

    Marijana TUCAK

    The aim of the study was to analyse the level of genetic variability and germplasm diversity of 17 alfalfa (Medicago spp.) cultivars\\/populations with different geographic origin by RAPD markers. 93 polymorphic markers were found across 340 individual plants by six primers. Genetic distance within germplasm varied from 0.28 to 0.42. Variability within cultivars and populations estimated by analysis of molecular

  20. High frequency plantlet regeneration from rhizomatous buds in Mantisia spathulata Schult. and Mantisia wengeri Fischer and analysis of genetic uniformity using RAPD markers.

    PubMed

    Bhowmik, Sudipta Shekhar D; Kumaria, Suman; Rao, S R; Tandon, Pramod

    2009-02-01

    A protocol has been devised for enhanced in vitro regeneration of critically endangered Mantisia spathulata Schult. and Mantisia wengeri Fischer. Highest Bud Forming Capacity (BFC) of 6.10 +/- 0.55 with an average of 19.93 +/- 3.19 roots was obtained for M. spathulata within 5-6 weeks in Murashige and Skoogs (MS) medium supplemented with a combination of 10.0 microM of N6-benzyladenine (BA) and 2.5 microM of alpha-naphtalene acetic acid (NAA). For M. wengeri, BFC of 7.82 +/- 0.73 and 20.86 +/- 1.65 roots was achieved in MS media supplemented with a combination of 5.0 microM BA and 2.5 microM of NAA RAPD markers were used to evaluate the genetic stability of in vitro raised hardened plantlets. Similarity coefficient among the regenerated plants ranged between 0.85-0.98 for M. spathulata and 0.83-0.98 for M. wengeri. Maximum of 88 and 90% genetic similarity were obtained between in vitro raised hardened plantlets and mother stock of M. spathulata and M. wengeri, respectively through RAPD analysis. The hardened plantlets after RAPD analysis on being transferred to soil of experimental garden showed no marked phenotypic variations in vegetative or floral characteristics. PMID:19374170

  1. Identification of co-dominant RAPD markers tightly linked to fruit skin color in apple.

    PubMed

    Cheng, F S; Weeden, N F; Brown, S K

    1996-07-01

    A simple genetic basis for the red/yellow skincolor polymorphism in apple was verified using DNA markers. Bulked segregant analysis identified one 10-base oligomer that generated different fragments in each of the bulks. After testing the primer in four populations, two fragments were found to be associated with red skin color and another two fragments associated with yellow skin color. Three of the fragments (1160, 1180, and 1230 bp) were partly sequenced and found to share high sequence homology, suggesting these were generated from the same locus. A pair of universal primers were designed to amplify the fragments. In the 'Rome Beauty' x 'White Angel' population, two fragments were associated with red skin color; one fragment designated as A(1) (1160 bp) was from 'Rome Beauty' and another fragment (A(2), 1180 bp) was from 'White Angel'. Progeny possessing both fragments, or either one, had red fruit. Both parents displayed an alternate fragment, a(1) (1230 bp), associated with yellowskinned fruit. In three other crosses tested, only fragment A(1) co-segregated with red skin color; two fragments, a(1) and a(2) (1230 bp and 1320 bp), were associated with yellow skin color. Our results are consistent with the hypothesis that the red/yellow dimorphism is controlled by a monogenic system with the presence of the red anthocyanin pigmentation being dominant. There was no indication that other modifier genes could reverse the effect of the locus (R f ) linked to the markers. Examination of amplification products in 56 apple cultivars and advanced breeding selections demonstrated that the universal primers could be used to correctly predict fruit skin color in most cases. PMID:24162221

  2. CHARACTERIZING SAFFLOWER GERMPLASM WITH AFLP MOLECULAR MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers are useful to improve germplasm collection management and for identifying genes for future enhancement and breeding. Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. After DNA e...

  3. (ISEA) MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  4. MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

    Source apportionment based on organic molecular markers provides a promising approach for meeting the Detroit Exposure and Aerosol Research Study (DEARS) objective of comparing source contributions between community air monitoring stations and various neighborhoods. Source appor...

  5. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Characterization of safflower (Carthamus tinctorius L.) germplasm with molecular markers is needed to enhance germplasm management and utilization. Amplified Fragment Length Polymorphism (AFLP) analysis was completed in safflower using two selective primer pairs resulting in 102 unambiguous polymor...

  6. Mycelial Propagation and Molecular Phylogenetic Relationships of Commercially Cultivated Agrocybe cylindracea based on ITS Sequences and RAPD

    PubMed Central

    Alam, Nuhu; Kim, Jeong Hwa; Shim, Mi Ja; Lee, U Youn

    2010-01-01

    This study evaluated the optimal vegetative growth conditions and molecular phylogenetic relationships of eleven strains of Agrocybe cylindracea collected from different ecological regions of Korea, China and Taiwan. The optimal temperature and pH for mycelial growth were observed at 25? and 6. Potato dextrose agar and Hennerberg were the favorable media for vegetative growth, whereas glucose tryptone was unfavorable. Dextrin, maltose, and fructose were the most effective carbon sources. The most suitable nitrogen sources were arginine and glycine, whereas methionine, alanine, histidine, and urea were least effective for the mycelial propagation of A. cylindracea. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The sequence of ITS2 was more variable than that of ITS1, while the 5.8S sequences were identical. The reciprocal homologies of the ITS sequences ranged from 98 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) using 20 arbitrary primers. Fifteen primers efficiently amplified the genomic DNA. The average number of polymorphic bands observed per primer was 3.8. The numbers of amplified bands varied based on the primers and strains, with polymorphic fragments ranging from 0.1 to 2.9 kb. The results of RAPD analysis were similar to the ITS region sequences. The results revealed that RAPD and ITS techniques were well suited for detecting the genetic diversity of all A. cylindracea strains tested. PMID:23956633

  7. GENETIC VARIATION AT ALLOZYME AND RAPD MARKERS IN PINUS LONGAEVA (PINACEAE) OF THE WHITE MOUNTAINS ,C ALIFORNIA1

    Microsoft Academic Search

    SEOK-WOO LEE; F. T HOMAS LEDIG; DAVID R. JOHNSON

    We compared genetic diversity estimated from allozymes and from random amplified polymorphic DNA (RAPDs) in a sample of 210 Great Basin bristlecone pines (Pinus longaeva Bailey) from three groves in the White Mountains, California, USA. The White Mountains are the most westerly extension of bristlecone pine and home to the oldest known living trees. We assayed two forks of each

  8. DISPERSAL PATTERN OF BLACK-BILLED MAGPIES (PICA HUDSONIA) MEASURED BY MOLECULAR GENETIC (RAPD) ANALYSIS

    Microsoft Academic Search

    XIAO-HONG WANGAND; Charles H. Trost

    2001-01-01

    Black-billed Magpies (Pica hudsonia) are a relatively sedentary corvid, with greater dispersal of females than males. To genetically confirm that dispersal pattern, 29 reproductively active adults were captured over two years and were scored for primer-spe- cific random amplified polymorphic DNA (RAPD) bands (53 polymorphic bands in 1996 and 104 in 1997). In both years, we captured more previously banded

  9. Genetic relationships and diversity among Tibetan wheat, common wheat and European spelt wheat revealed by RAPD markers

    Microsoft Academic Search

    Qixin Sun; Zhongfu Ni; Zhiyong Liu; Jianwei Gao; Tiecheng Huang

    1998-01-01

    An endemic hexaploid wheat found in Tibet, China was taxonomically classified as a subspecies in common wheat, i.e. Triticum\\u000a aestivum ssp. tibetanum. Seven accessions of the Tibetan wheat, 22 cultivars of common wheat and 17 lines of spelt wheat were\\u000a used for RAPD analysis to study the genetic relationships of the Tibetan wheat with common wheat and spelt wheat, and

  10. Glioma biology and molecular markers.

    PubMed

    Cohen, Adam L; Colman, Howard

    2015-01-01

    The tumors classified as gliomas include a wide variety of histologies including the more common (astrocytoma, glioblastoma), as well as the less common histologies (oligodendroglioma, mixed oligoastrocytoma, pilocytic astrocytoma). Recent efforts at comprehensive genetic characterization of various primary brain tumor types have identified a number of common alterations and pathways common to multiple tumor types. Common pathways in glioma biology include growth factor receptor tyrosine kinases and their downstream signaling via the MAP kinase cascade or PI3K signaling, loss of apoptosis through p53, cell cycle regulation, angiogenesis via VEGF signaling, and invasion. However, in addition to these common general pathway alterations, a number of specific alterations have been identified in particular tumor types, and a number of these have direct therapeutic implications. These include mutations or fusions in the BRAF gene seen in pilocytic astrocytomas (and gangliogliomas). In oligodendrogliomas, mutations in IDH1 and codeletion of chromosomes 1p and 19q are associated with improved survival with upfront use of combined chemotherapy and radiation, and these tumors also have unique mutations of CIC and FUBP1 genes. Low grade gliomas are increasingly seen to be divided into two groups based on IDH mutation status, with astrocytomas developing through IDH mutation followed by p53 mutation, while poor prognosis low grade gliomas and primary glioblastomas (GBMs) are characterized by EGFR amplification, loss of PTEN, and loss of cyclin-dependent kinase inhibitors. GBMs can be further characterized based on gene expression and gene methylation patterns into three or four distinct subgroups. Prognostic markers in diffuse gliomas include IDH mutation, 1p/19q codeletion, and MGMT methylation, and MGMT is also a predictive marker in elderly patients with glioblastoma treated with temozolomide monotherapy. PMID:25468223

  11. Citrus phylogeny and genetic origin of important species as investigated by molecular markers

    Microsoft Academic Search

    E. Nicolosi; Z. N. Deng; A. Gentile; S. La Malfa; G. Continella; E. Tribulato

    2000-01-01

    Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes analyzed included 36 accessions belonging\\u000a to Citrus together with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus

  12. Harnessing the annotated EST information in molecular marker development for crop improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Marker-assisted selection has become an integral component of many crop breeding programs in both the private and public sectors throughout the world. Various markers, such as RFLP, RAPD, AFLP and SSR are being used by the crop breeding community. The advent of high throughput sequencing technology ...

  13. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.).

    PubMed

    Robarts, Daniel W H; Wolfe, Andrea D

    2014-07-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  14. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    PubMed Central

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  15. Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

    Microsoft Academic Search

    Chris Duran; Nikki Appleby; David Edwards; Jacqueline Batley

    2009-01-01

    Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and enable the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade and two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) now predominate applications in

  16. Assessment of genetic diversity in cultivars and wild accessions of Luohanguo ( Siraitia grosvenorii [Swingle] A. M. Lu et Z. Y. Zhang), a species with edible and medicinal sweet fruits endemic to southern China, using RAPD and AFLP markers

    Microsoft Academic Search

    Shao-Qing Tang; Xiao-Yun Bin; Yun-Tao Peng; Jun-Ya Zhou; Li Wang; Yang Zhong

    2007-01-01

    Genetic variation of wild populations and cultivars of Luohanguo (Siraitia grosvenorii), a plant species endemic to southern China, was assessed using random amplified polymorphic DNA (RAPD) and amplified fragment\\u000a length polymorphism (AFLP) markers. Based on the results for 130 individuals from seven populations, a high level of genetic\\u000a diversity of Luohanguo was observed at the species level. The percentage of

  17. The analysis of paternity and maternity in the marine hydrozoan Hydractinia symbiolongicarpus using randomly amplified polymorphic DNA (RAPD) markers

    Microsoft Academic Search

    D. R. LEVITAN; R. K. GROSBERG

    1993-01-01

    For organisms in which direct observation of mating and subsequent dispersal of offspring and relatives is impossible, patterns of reproductive success and genealogical relationship can only be established using genetic markers. The ideal genetic assay would (1) employ highly polymorphic genetic markers for distinguishing among indi- viduals; (2) use little tissue f or analysing early lif e-history stages; and (3)

  18. Micropropagtion of Terminalia bellerica from nodal explants of mature tree and assessment of genetic fidelity using ISSR and RAPD markers.

    PubMed

    Dangi, Bhawna; Khurana-Kaul, Varsha; Kothari, S L; Kachhwaha, Sumita

    2014-10-01

    The present study reports an efficient in vitro micropropagation protocol for a medicinally important tree, Terminalia bellerica Roxb. from nodal segments of a 30 years old tree. Nodal segments taken from the mature tree in March-April and cultured on half strength MS medium gave the best shoot bud proliferation response. Combinations of serial transfer technique (ST) and incorporation of antioxidants (AO) [polyvinylpyrrolidone, PVP (50 mg l(-1))?+?ascorbic acid (100 mg l(-1))?+?citric acid (10 mg l(-1))] in the culture medium aided to minimize browning and improve explant survival during shoot bud induction. Highest multiplication of shoots was achieved on medium supplemented with 6-benzyladenine (BA, 8.8 ?M) and ?-naphthalene acetic acid (NAA, 2.6 ?M) in addition to antioxidants. Shoot elongation was obtained on MS medium containing BA (4.4 ?M)?+?phloroglucinol (PG, 3.9 ?M). Elongated shoots were transferred to half strength MS medium containing indole-3-butyric acid (IBA, 2.5 ?M) for root development. The acclimatization of plantlets was carried out under greenhouse conditions. The genetic fidelity of the regenerated plants was checked using inter simple sequence repeats (ISSR) and randomly amplified polymorphic DNA (RAPD) analysis. Comparison of the bands among the regenerants and mother plant confirmed true-to-type clonal plants. PMID:25320474

  19. Genetic diversity of Macrophomina phaseolina isolates from certain agro-climatic regions of India by using RAPD markers.

    PubMed

    Babu, Bandamaravuri Kishore; Reddy, S S; Yadav, Mukesh K; Sukumar, M; Mishra, Vijendra; Saxena, A K; Arora, Dilip K

    2010-06-01

    Genetic diversity analysis of Macrophomina phaseolina isolates obtained from different host range and diverse geographical locations in India was carried out using RAPD fingerprinting. Of the thirteen 10-mer random primers used, primer OPB-08 gave the maximum polymorphism and the UPGMA clustering could separate 50 isolates in to ten groups at more than 65% similarity level. The ten clusters correlated well with the geographical locations with exceptions for isolates obtained from Eastern and Western Ghats. There was a segregation of isolates from these two geographical locations in to two clusters thus, distributing 10 genotypes in to eight geographical locations. All the isolates M. phaseolina irrespective of their host and geographical origin, exhibited two representative monomorphic bands at 250 bp and 1 kb, presence of these bands suggests that isolates might have evolved from a common ancestor but due to geographical isolation fallowed by natural selection and genetic drift might have segregated in to subpopulations. Genetic similarity in the pathogenic population reflects the dispersal of single lineage in all locations in India. PMID:23100828

  20. [Genetic diversity evaluation of cultivars (G. hirsumtum L.) from the Changjiang river valley and Tellow river valley by RAPD markers].

    PubMed

    Xu, Q H; Zhang, X L; Nie, Y C

    2001-01-01

    Forty-one polymorphic decamer primers with clear and repeated band pattern, which were screened out from 300 randomly selected primers, were applied to assess genetic diversity of cultivars (G. hirsumtum L.) from the Changjiang river valley and the Yellow river valley by RAPD analysis. Eighty-four polymorphic loci were obtained from 84 cultivars from the Changjiang river valley and 96 polymorphic loci were obtained from 68 cultivars from the Yellow river valley. Jaccard's genetic similarity coefficients were calculated using the software of NTSYS-pc version 1.80, and two dendrograms were constructed by the unweighted pair group method of arithmetic average (UPGMA). Mean similarity coefficient among cultivars from the Changjiang river valley was up to 0.631. And cultivars from the Yellow river valley had an average similarity coefficient of 0.632. Compared similarity coefficient matrices and frequency distribution of pairwise similarity coefficients, a conclusion was drawn that cultivars from the two areas had nearly the same level of genetic diversity. Same base germplasm, breeding objectives, breeding methods and strategy could be attributed to similar genetic diversity between the two areas. PMID:11480182

  1. Comparison of RAPD and morpho?nut markers for revealing genetic relationships between chestnut species (Castanea spp.) and New Zealand chestnut selections

    Microsoft Academic Search

    N. C. Oraguzie; D. L. Mcneil; A. M. Paterson; H. Chapman

    1998-01-01

    This study explored different character data sets (random amplified polymorphic DNA (RAPD) and morpho?nut characters), techniques, and systematic methodologies in an attempt to reconstruct the phylogenetic relationships and origins of New Zealand chestnut (Castanea spp.) selections. The study was prompted by confusion regarding the relationships of New Zealand chestnut selections and the introduced chestnut species in New Zealand. RAPDs demonstrated

  2. The role of molecular markers and marker assisted selection in breeding for organic agriculture

    Microsoft Academic Search

    E. T. Lammerts van Bueren; G. Backes; H. de Vriend; H. Østergård

    2010-01-01

    Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make\\u000a selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for\\u000a the organic sector the appropriateness of molecular markers is not self-evident and is often debated. Organic and low-input\\u000a farming conditions require breeding for robust

  3. Low Genetic Differentiation of and Close Evolutionary Relationships between Anas platyrhynchos and Anas poecilorhyncha : RAPD–PCR Evidence

    Microsoft Academic Search

    I. V. Kulikova; G. N. Chelomina; Yu. N. Zhuravlev

    2003-01-01

    Using RAPD–PCR, we examined genetic diversity and phylogenetic relationships in two groups of river ducks: Anas platyrhynchos, A. poecilorhyncha, A. streperaand A. crecca, A. formosa, A. querquedula. Molecular taxon-specific markers were found for teals (A. crecca, A. formosa, A. querquedula) and gadwall (A. strepera). Each of the species examined was shown to exhibit high genetic diversity. The mean levels of

  4. Genetic relationship among 19 accessions of six species of Chenopodium L., by Random Amplified Polymorphic DNA fragments (RAPD)

    Microsoft Academic Search

    Paulo M. Ruas; Alejandro Bonifacio; Claudete F. Ruas; Daniel J. Fairbanks; William R. Andersen

    1999-01-01

    The RAPD technique was used to identify genetic relationships in 19 accessions, including six species of the genus Chenopodium. A dendrogram was constructed using UPGMA from 399 DNA markers. The molecular data clustered species and accessions into five different groups. Group 1 with three cultivated varieties of C. nuttalliae, Group 2 included eight cultivars and two wild varieties of C.

  5. REDUCTION OF SPECIES IN THE WILD POTATO SOLANUM SECTION PETOTA SERIES LONGIPEDICELLATA: AFLP, RAPD AND CHLOROPLAST SSR DATA.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Species boundaries were assessed with three molecular markers (AFLPs, RAPDs, chloroplast microsatellites, also known as chloroplast single sequence repeats [cpSSRs]) for all six species of wild potatoes (Solanum L. section Petota Dumort.) assigned to ser. Longipedicellata: S. fendleri, S. hjertingii...

  6. Development of a sex-specific molecular marker for Japanese hop Humulus Japonicus Siebold & Zucc

    Microsoft Academic Search

    O. S. Aleksandrov; M. G. Divashuk; G. I. Karlov

    2011-01-01

    Japanese hop (Humulus japonicus Siebold & Zucc.) is a dioecious plant and a suitable model for studying the XX\\/XY1Y2 system of sex chromosomes. To develop a sex-specific marker, 12 RAPD and 36 ISSR markers were analyzed on the basis of pools\\u000a of male and female plants identified after flowering. We were the first to identify ISSR marker K-16, which manifested

  7. Genetic diversity of Pleurotus pulmonarius revealed by RAPD, ISSR, and SRAP fingerprinting.

    PubMed

    Yin, Yonggang; Liu, Yu; Li, Huamin; Zhao, Shuang; Wang, Shouxian; Liu, Ying; Wu, Di; Xu, Feng

    2014-03-01

    Pleurotus pulmonarius is one of the most widely cultivated and popular edible fungi in the genus Pleurotus. Three molecular markers were used to analyze the genetic diversity of 15 Chinese P. pulmonarius cultivars. In total, 21 random amplified polymorphic DNA (RAPD), 20 inter-simple sequence repeat (ISSR), and 20 sequence-related amplified polymorphism (SRAP) primers or primer pairs were selected for generating data based on their clear banding profiles produced. With the use of these RAPD, ISSR, and SRAP primers or primer pairs, a total of 361 RAPD, 283 ISSR, and 131 SRAP fragments were detected, of which 287 (79.5 %) RAPD, 211 (74.6 %) ISSR, and 98 (74.8 %) SRAP fragments were polymorphic. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of these three methods were structured similarly, grouping the 15 tested strains into four clades. Subsequently, visual DNA fingerprinting and cluster analysis were performed to evaluate the resolving power of the combined RAPD, ISSR, and SRAP markers in the differentiation among these strains. The results of this study demonstrated that each method above could efficiently differentiate P. pulmonarius cultivars and could thus be considered an efficient tool for surveying genetic diversity of P. pulmonarius. PMID:24241329

  8. Molecular Marker Systems for Oenothera Genetics

    PubMed Central

    Rauwolf, Uwe; Golczyk, Hieronim; Meurer, Jörg; Herrmann, Reinhold G.; Greiner, Stephan

    2008-01-01

    The genus Oenothera has an outstanding scientific tradition. It has been a model for studying aspects of chromosome evolution and speciation, including the impact of plastid nuclear co-evolution. A large collection of strains analyzed during a century of experimental work and unique genetic possibilities allow the exchange of genetically definable plastids, individual or multiple chromosomes, and/or entire haploid genomes (Renner complexes) between species. However, molecular genetic approaches for the genus are largely lacking. In this study, we describe the development of efficient PCR-based marker systems for both the nuclear genome and the plastome. They allow distinguishing individual chromosomes, Renner complexes, plastomes, and subplastomes. We demonstrate their application by monitoring interspecific exchanges of genomes, chromosome pairs, and/or plastids during crossing programs, e.g., to produce plastome–genome incompatible hybrids. Using an appropriate partial permanent translocation heterozygous hybrid, linkage group 7 of the molecular map could be assigned to chromosome 9·8 of the classical Oenothera map. Finally, we provide the first direct molecular evidence that homologous recombination and free segregation of chromosomes in permanent translocation heterozygous strains is suppressed. PMID:18791241

  9. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.; D'Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

    1991-12-15

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

  10. SELECTION OF INTERSPECIFIC SUGARCANE HYBRIDS USING MICROSATELLITE DNA MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three types of species-specific DNA markers, namely, PCR, RAPD, and microsatellites, have been recently developed at the USDA-ARS, SRRC, Sugarcane Research Unit, Houma, Louisiana. Of these, the microsatellite markers are the most polymorphic and can produce distinctive fingerprints (or molecular al...

  11. Molecular variation and population structure in Elymus trachycaulus and comparison with its morphologically similar E. alaskanus

    Microsoft Academic Search

    M. Gaudett; B. Salomon; G. Sun

    2005-01-01

    Random amplified polymorphic DNA (RAPD) markers were used to determine the levels and pattern of molecular variation in four populations of Elymus trachycaulus, and to estimate genetic similarity among different populations of E. trachycaulus from British Columbia and the Northwest Territories and one population of Elymus alaskanus from the Northwest Territories. Based on 124 RAPD bands (loci), mean percent polymorphic

  12. The evolution of molecular markers — just a matter of fashion?

    Microsoft Academic Search

    Christian Schlötterer

    2004-01-01

    In less than half a century, molecular markers have totally changed our view of nature, and in the process they have evolved themselves. However, all of the molecular methods developed over the years to detect variation do so in one of only three conceptually different classes of marker: protein variants (allozymes), DNA sequence polymorphism and DNA repeat variation. The latest

  13. Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers

    PubMed Central

    Abbasi, Pervaiz A.; Miller, Sally A.; Meulia, Tea; Hoitink, Harry A. J.; Kim, Jin-Man

    1999-01-01

    Randomly amplified polymorphic DNA (RAPD) analysis and the PCR assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of Trichoderma hamatum 382, a biocontrol agent utilized in compost-amended mixes. Distinct and reproducible fingerprints were obtained upon amplification of purified genomic DNA of T. hamatum 382 with the random primers OPE-16, OPH-19, and OPH-20. Three amplified DNA fragments of 0.35 (OPE-160.35), 0.6 (OPH-190.6), and 0.65 (OPH-200.65) kb were diagnostic for T. hamatum 382, clearly distinguishing it from 53 isolates of four other Trichoderma spp. tested. Some isolates of T. hamatum shared these low-molecular-weight fragments with T. hamatum 382. However, RAPD analysis of isolates of T. hamatum with all three random primers used in consecutive PCR tests distinguished T. hamatum 382 from other isolates of T. hamatum. These three RAPD amplicons were cloned and sequenced, and pairs of oligonucleotide primers for each cloned fragment were designed. Use of the primers in the PCR assay resulted in the amplification of DNA fragments of the same size as the cloned RAPD fragments from genomic DNA of T. hamatum 382. A combination of dilution plating on a semiselective medium for Trichoderma spp. and PCR, with the RAPD primers OPH-19, OPE-16, and OPH-20 or the three sequence-characterized primers, was used successfully to verify the presence of T. hamatum 382 propagules in nine different soil, compost, and potting mix samples. All 23 Trichoderma isolates recovered on semiselective medium from commercial potting mixes fortified with T. hamatum 382 were identified as T. hamatum 382, whereas 274 Trichoderma isolates recovered from the other nine samples were negative in the PCR assay. Thus, this highly specific combination of techniques allowed detection and enumeration of propagules of T. hamatum 382 in fortified compost-amended potting mixes. Sequence-characterized amplified region markers also facilitated the development of a very simple procedure to amplify DNA of T. hamatum 382 directly from fortified compost-amended potting mixes. PMID:10583998

  14. Genetic approaches for studying myiasis-causing flies: molecular markers and mitochondrial genomics.

    PubMed

    de Azeredo-Espin, Ana Maria Lima; Lessinger, Ana Cláudia

    2006-01-01

    "Myiasis-causing flies" is a generic term that includes species from numerous dipteran families, mainly Calliphoridae and Oestridae, of which blowflies, screwworm flies and botflies are among the most important. This group of flies is characterized by the ability of their larvae to develop in animal flesh. When the host is a live vertebrate, such parasitism by dipterous larvae is known as primary myiasis. Myiasis-causing flies can be classified as saprophagous (free-living species), facultative or obligate parasites. Many of these flies are of great medical and veterinary importance in Brazil because of their role as key livestock insect-pests and vectors of pathogens, in addition to being considered important legal evidence in forensic entomology. The characterization of myiasis-causing flies using molecular markers to study mtDNA (by RFLP) and nuclear DNA (by RAPD and microsatellite) has been used to identify the evolutionary mechanisms responsible for specific patterns of genetic variability. These approaches have been successfully used to analyze the population structures of the New World screwworm fly Cochliomyia hominivorax and the botfly Dermatobia hominis. In this review, various aspects of the organization, evolution and potential applications of the mitochondrial genome of myiasis-causing flies in Brazil, and the analysis of nuclear markers in genetic studies of populations, are discussed. PMID:16502089

  15. The use of random amplified polymorphic DNA (RAPD) analysis for studies of genetic variation in populations of Coccinella septempunctata in Belgium.

    PubMed

    Haubruge, Eric; Vanlerberghe-Masutti, Flavie; Collignon, Pierre; Francis, Frédéric

    2002-01-01

    The movement and dispersion of Coccinella septempunctata and its efficacy as aphid control agent over large areas is not really understood because of the difficulty in identifying the origins of predators. To quantify the genetic diversity within the species and monitor the spatial foraging, populations were sampled from Belgium and analysed for RAPD DNA variation. Twenty decamer primers generated more than hundred polymorphic RAPD bands and pairwise distances were calculated between populations according to Nei and Li, then used to construct a radial neighbour-joining dendrogram and examine intra- and inter-population variance coefficients, by analysis of molecular variation (AMOVA). This study shows that while a number of factors can complicate the use and interpretation of RAPD fragments as genetic markers, RAPD analysis can be a valuable technique for studies of intra-specific genetic variation in C. septempunctata. PMID:12696422

  16. Characterization of DNA polymorphisms in Caryocar brasiliense in populations with and without thorn at the endocarp by RAPD markers.

    PubMed

    Londe, Luciana N; Ueira-Vieira, Carlos; Kerr, Warwick E; Bonetti, Ana Maria

    2010-09-01

    Caryocar brasiliense (pequi), is one of the main species at the biome of the Brazilian savannah due to its use in culinary, popular medicine, industry in general, and iron and steel industry. At São José do Xingu (MT), a tree of C. brasiliense without thorn at the endocarp was found, which enables the improvement of C. brasiliense not only for consumption but also to the high appreciation it already has. To detect the existing differences between the pequi with and without the thorn at the endocarp, RADP markers were used. The generated polymorphisms were cloned and sequenced in order to identify the sequences that are responsible for the fenotypical alteration. It was observed that the pequi without thorn is genetically isolated from the other populations of pequi with thorn at the endocarp, proving that this characteristic is related to the genetic divergence of the species. Analysis in BLASTn evidenced the similarity of the Dof1 genes of Zea mays to its gene of phosphinotricin acetyl transferase. In the analysis of BLASTx, the similarity was verified to the proteins responsible for the deficiency in ferric reductase 4, and catalase. PMID:21562705

  17. In vitro plant propagation of Catharanthus roseus and assessment of genetic fidelity of micropropagated plants by RAPD marker assay.

    PubMed

    Kumar, Ajay; Prakash, Krishna; Sinha, Rajesh Kumar; Kumar, Nitish

    2013-02-01

    An investigation was carried out to develop an efficient micropropagation protocol for Catharanthus roseus. Experiments were conducted to optimize suitable media for in vitro shoot multiplication and root induction. Out of the different media compared for in vitro shoot multiplication, Murashige and Skoog (MS) medium supplemented with 1 mg/l of 6-benzylaminopurine and 0.2 mg/l ?-naphthaleneacetic acid showed better response in terms of the emergence of shoots from axillary buds as well as proliferation and multiplication of shoots. The shoots when placed on half strength of MS medium having 1 mg/l indole 3-butyric acid and 0.25 % charcoal showed cent percent root induction with maximum number of roots per shoot (4.2) as well as maximum root length (1.72 cm). Further, clonal fidelity of the in vitro-raised plants was carried out using randomly amplified polymorphic DNA marker and results indicated that all the tissue culture-derived plants are true-to-type and there were no somaclonal variations among these plants. PMID:23292901

  18. Authentication of the medicinal plant Sennaangustifolia by RAPD profiling

    PubMed Central

    Khan, Salim; Mirza, Khanda Jabeen; Al-Qurainy, Fahad; Abdin, Malik Zainul

    2011-01-01

    In this study “RAPDmolecular marker was employed for the identification of Sennaangustifolia, Sennaacutifolia, Sennatora and Sennasophera. Total 32 decamer primers were screened in amplification with genomic DNA extracted from all species, of which 6 primers yielded species-specific reproducible bands. Out of 42 loci detected, the polymorphic, monomorphic and unique loci were 24, 2 and 16, respectively. Based on dendrogram and similarity matrix, 4 species were differentiated from each other and showed more divergence. Thus, this technique may prove and to contribute the identification of these species of Senna having similar morphology sold in the local markets. PMID:23961137

  19. Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers

    Microsoft Academic Search

    T. Nagaoka; Y. Ogihara

    1997-01-01

    Inter-simple sequence repeat polymorphic DNA (ISSR) was evaluated for its applicability as a genetic marker system in wheat.\\u000a PCR was carried out with primers that annealed to simple sequence repeats. The resultant products were subjected to agarose-gel\\u000a electrophoresis, and the banding patterns were compared among six wheat accessions containing diploid, tetraploid, and hexaploid\\u000a members. Out of 100 examined, 33 primers

  20. Biochemical and molecular markers for investigating the mode of reproduction in the facultative apomict Poa pratensis L

    Microsoft Academic Search

    A. Mazzucato; G. Barcaccia; M. Pezzotti; M. Falcinelli

    1995-01-01

    Isozymes and random amplified polymorphic DNA (RAPD) markers were used for precocious identification of non-maternal plants in progenies of the facultative apomict Poa pratensis. Four progenies obtained from controlled crosses that showed different degrees of apomixis on isozyme analysis of phospho-gluco-isomerases, esterases and peroxidases were chosen for RAPD analysis to generate genomic fingerprints using species-specific primers. At an advanced vegetative

  1. RAPD analysis reveals a low rate of outcrossing in burr medic (Medicago polymorpha L.)

    Microsoft Academic Search

    Maria Vitale; Fulvio Pupilli; Paola Labombarda; Sergio Arcioni

    1998-01-01

    Although burr medic (Medicago polymorpha L.) is commonly considered a self-pollinating species, intrapopulational variation for morphological, biochemical and molecular markers is relatively high. To investigate whether part of this variation is the result of outcrossing, we designed RAPD analysis experiments to reveal both inter- and intra-accession crossing. No cases of inter-accession hybrids were documented, but an intra-accessional crossing rate of

  2. c-GAMMA:Comparative Genome Analysis of Molecular Markers

    NASA Astrophysics Data System (ADS)

    Peterlongo, Pierre; Nicolas, Jacques; Lavenier, Dominique; Vorc'h, Raoul; Querellou, Joël

    Discovery of molecular markers for efficient identification of living organisms remains a challenge of high interest. The diversity of species can now be observed in details with low cost genomic sequences produced by new generation of sequencers. A method, called c-GAMMA, is proposed. It formalizes the design of new markers for such data. It is based on a series of filters on forbidden pairs of words, followed by an optimization step on the discriminative power of candidate markers.

  3. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Safflower (Carthamus tinctorius L.) accessions from the U.S. germplasm collection were characterized using AFLP (Amplified Length Polymorphisms) markers. Separation and scoring of 392 markers was completed using the Beckman CEQ8000 capillary electrophoresis system. Twelve plants from each of eight...

  4. Molecular markers in Tokyo Bay sediments: Sources and distribution

    Microsoft Academic Search

    N. Chalaux; H. Takada; J. M. Bayona

    1995-01-01

    The spatial distribution of different classes of molecular markers in Tokyo Bay sediments, a semi-enclosed system surrounded by one of the most urbanized areas in the world, has been investigated. In order to study the environmental stability of different chemical classes of sewage markers, their isomeric composition was determined in river particulate matter, waste-water influent and surficial sediments. Among the

  5. Patterns of Genetic Variation in in and ex situ Populations of the Threatened Chilean Vine Berberidopsis corallina , Detected Using RAPD Markers

    Microsoft Academic Search

    M. Etisham-Ul-Haq; T. R. Allnutt; C. Smith-Ram??rez; M. F. Gardner; J. J. Armesto; A. C. Newton

    2001-01-01

    Berberidopsis corallina Hook. f. (Berberidopsidaceae) is a threatened vine, endemic to the temperate rainforests of southern Chile. A RAPD analysis was carried out to assess the extent of genetic variation in remaining wild populations and in British cultivated plants, to assess the value of the latter for ex situ conservation. A total of 90 individuals (54 wild, 35 cultivated) were

  6. Identification and cloning of molecular markers for UV-B tolerant gene in wild sugarcane (Saccharum spontaneum L.).

    PubMed

    Li, Yuan; He, Yongmei; Zu, Yanqun; Zhan, Fangdong

    2011-11-01

    Previously we have selected wild sugarcane (Saccharum spontaneum L.) sterile lines that are tolerant or susceptible to UV-B radiation based on response index (RI) in a field screening test. The RI was established according to plant height, tiller number, leaf index, total biomass and brix under enhanced ultraviolet-B (UV-B, 280-310 nm) radiation. In this experiment, molecular markers linked to the UV-B tolerant and susceptible genes were identified and cloned. RAPD (Randomly amplified polymorphic DNAs) assay using 100 arbitrary primers followed by clustering analysis separated the tolerant and susceptible lines into two groups at the genetic distance of 0.380. The UV-B tolerant and susceptible gene pools were constructed and compared using the Bulked Segregate Analysis (BSA) approach. Of the 100 arbitrary RAPD primers, primer OPR16 produced polymorphic DNA banding patterns from both gene pools. The OPR16-1200 bp DNA fragment was only amplified from the tolerant lines and the OPR16-800 bp from the susceptible ones. These two PCR fragments were cloned onto T-vector. DNA sequence alignment analysis determined that 42% homology existed between the reverse and forward sequences of the OPR16-1200 bp clone, and 36% homology between the forward sequences of the OPR16-800 bp and OPR16-1200 bp clones. The two DNA clones were determined to be linked to the UV-B tolerant and susceptible genes, and they can be used to develop molecular markers for the associated traits. PMID:21925894

  7. Patterns of rapd markers and heavy metal concentrations in Perna viridis (L.), collected from metal-contaminated and uncontaminated coastal waters: are they correlated with each other?

    PubMed

    Yap, C K; Chua, B H; Teh, C H; Tan, S G; Ismail, A

    2007-05-01

    Genetic variation due to heavy metal contamination has always been an interesting topic of study. Because of the numerous contaminants being found in coastal and intertidal waters, there is always much discussion and argument as to which contaminant(s) caused the variations in the genetic structures of biomonitors. This study used a Single Primer Amplification Reaction (SPAR) technique namely Random Amplified Polymorphic DNA (RAPD) to determine the genetic diversity of the populations of the green-lipped mussel Perna viridis collected from a metal-contaminated site at Kg. Pasir Puteh and those from four relatively' uncontaminated sites (reference sites). Heavy metal levels (Cd, Cu, Pb and Zn) were also measured in the soft tissues and byssus of the mussels from all the sites. Cluster analyses employing UPGMA done based on the RAPD makers grouped the populations into two major clusters; the Bagan Tiang, Pantai Lido, Pontian and Kg. Pasir Puteh populations were in one cluster, while the Sg. Belungkor population clustered by itself. This indicated that the genetic diversity based on bands resulting from the use of all four RAPD primers on P. viridis did not indicate its potential use as a biomarker of heavy metal pollution in coastal waters. However, based on a correlation analysis between a particular metal and a band resulting from a specific RAPD primer revealed some significant (P < 0.01) correlations between the primers and the heavy metal concentrations in the byssus and soft tissues. Thus, the correlation between a particular metal and the bands resulting from the use of a specific RAPD primer on P. viridis could be used as biomonitoring tool of heavy metal pollution. PMID:17633561

  8. Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

    PubMed

    Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

    2014-01-01

    The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). PMID:24270069

  9. Genetic diversity of F1 and F2 interspecific hybrids between dwarf birch (Betula nana L.) and Himalayan birch (B. utilis var. jacquemontii (Spach) Winkl. 'Doorenbos') using RAPD-PCR markers and ploidy analysis.

    PubMed

    Czernicka, Ma?gorzata; P?awiak, Jaros?aw; Muras, Piotr

    2014-01-01

    Crosses between Betula nana and B. utilis 'Doorenbos' were undertaken in order to obtain interspecific hybrids which could be characterized by wide spreading stems, strong branching habit, decorative clear white bark and an interesting shape of purple leaves. The research purpose was to examine genetic diversity of the 16 F1 and F2 putative progenies by using the RAPD-PCR method and the ploidy analysis. A total of 242 RAPD markers were scored with 24 primers and 220 (90.9%) polymorphic bands were found. In the NJ dendrogram, cluster I consisted of the female parent--B. nana and 12 hybrids and cluster II grouped the male parent--B. utilis 'Doorenbos' with 4 hybrids (F2/2, F1/8, F1/7 and F2/1). The 2-D scaling by PCoA was in agreement with the similarity index, i.e. two hybrids (F1/8, F2/2) grouped with the male parent while others with female parent. Classification of the hybrid plants by chromosome counting demonstrated that 13 hybrids were confirmed with accurate chromosome counts as being diploid (2n=2x=28) and 3 plants (F1/7, F1/8, F2/2) as triploid with 42 chromosomes. PMID:24904928

  10. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    PubMed Central

    2012-01-01

    Background In the last 30?years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. PMID:22805587

  11. Drosophila hematopoiesis: Markers and methods for molecular genetic analysis.

    PubMed

    Evans, Cory J; Liu, Ting; Banerjee, Utpal

    2014-06-15

    Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ. PMID:24613936

  12. GENETIC MARKERS AND THEIR APPLICATION IN POULTRY BREEDING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The current chicken genetic map contains at least 1,965 loci within 50 linkage groups and it covers about 4,000 cM. About 235 of these loci have homology with known human or mammalian genes. The remaining loci are anonymous molecular DNA markers, including microsatellites, AFLP, RAPD, CR1 and othe...

  13. EST-PCR markers developed for Highbush Blueberry are also useful for genetic fingerprinting and relationship studies in Rabbiteye Blueberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Up until now, randomly amplified polymorphic DNA (RAPD) has been the only type of molecular marker used extensively in rabbiteye blueberry (Vaccinium virgatum). Here we have tested whether a type of sequence-tagged site (STS) marker which utilizes specific ~20-mer primers from Expressed Sequence Tag...

  14. DEVELOPMENT OF SIMPLE SEQUENCE REPEAT MARKERS FOR PUCCINIA GRAMINIS AND P. TRITICINA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rusts are obligate plant parasitic fungi with a complex life cycle that often includes five different spore stages. As a result, molecular studies are often performed with the asexual, dikaryotic uredinial stage (urediniospores) using dominant markers (RAPDs, AFLPs). Currently, molecular genetic and...

  15. A consensus linkage map for molecular markers and Quantitative Trait Loci associated with economically important traits in melon (Cucumis melo L.)

    PubMed Central

    2011-01-01

    Background A number of molecular marker linkage maps have been developed for melon (Cucumis melo L.) over the last two decades. However, these maps were constructed using different marker sets, thus, making comparative analysis among maps difficult. In order to solve this problem, a consensus genetic map in melon was constructed using primarily highly transferable anchor markers that have broad potential use for mapping, synteny, and comparative quantitative trait loci (QTL) analysis, increasing breeding effectiveness and efficiency via marker-assisted selection (MAS). Results Under the framework of the International Cucurbit Genomics Initiative (ICuGI, http://www.icugi.org), an integrated genetic map has been constructed by merging data from eight independent mapping experiments using a genetically diverse array of parental lines. The consensus map spans 1150 cM across the 12 melon linkage groups and is composed of 1592 markers (640 SSRs, 330 SNPs, 252 AFLPs, 239 RFLPs, 89 RAPDs, 15 IMAs, 16 indels and 11 morphological traits) with a mean marker density of 0.72 cM/marker. One hundred and ninety-six of these markers (157 SSRs, 32 SNPs, 6 indels and 1 RAPD) were newly developed, mapped or provided by industry representatives as released markers, including 27 SNPs and 5 indels from genes involved in the organic acid metabolism and transport, and 58 EST-SSRs. Additionally, 85 of 822 SSR markers contributed by Syngenta Seeds were included in the integrated map. In addition, 370 QTL controlling 62 traits from 18 previously reported mapping experiments using genetically diverse parental genotypes were also integrated into the consensus map. Some QTL associated with economically important traits detected in separate studies mapped to similar genomic positions. For example, independently identified QTL controlling fruit shape were mapped on similar genomic positions, suggesting that such QTL are possibly responsible for the phenotypic variability observed for this trait in a broad array of melon germplasm. Conclusions Even though relatively unsaturated genetic maps in a diverse set of melon market types have been published, the integrated saturated map presented herein should be considered the initial reference map for melon. Most of the mapped markers contained in the reference map are polymorphic in diverse collection of germplasm, and thus are potentially transferrable to a broad array of genetic experimentation (e.g., integration of physical and genetic maps, colinearity analysis, map-based gene cloning, epistasis dissection, and marker-assisted selection). PMID:21797998

  16. Genomic analysis in maritime pine ( Pinus pinaster ). Comparison of two RAPD maps using selfed and open-pollinated seeds of the same individual

    Microsoft Academic Search

    C. Plomion; D. M. O'Malley; C. E. Durel

    1995-01-01

    Two genomic maps were constructed for one individual tree of maritime pine, Pinus pinaster Ait., using a common set of 263 RAPD markers (random amplified polymorphic DNA). The RAPD markers were chosen from a larger number of polymorphic RAPD fragments on the basis of repeatability and inheritance in a three-generation pedigree. The maps were constructed from two independent mapping samples

  17. [Genetic polymorphism of bluegrass cultivars detected by RAPDs].

    PubMed

    Ning, Ting-Ting; Zhang, Zai-Jun; Jin, Cheng-Zan; Zhu, Ying-Guo

    2005-07-01

    Kentucky bluegrass (Poa pratensis L.) is a hardy, persistent forage and turf grass adapted to a wide range of soils and climates. Its ever-increasing adoption in highly cared-for sports fields has attracted the attention of many seed companies. However in the past, the breeding of elite varieties was often hampered by the extreme complexity of the genome. The polymorphism is important for broading the genetic basis and may be exploited for application of heterosis. The genetic relationship of 16 bluegrass cultivars, including 15 accessions Kentucky bluegrass cultivars and 1 entries Canada bluegrass (Poa compressa L.) cultivar from different breeding company were analyzed using 25 RAPD markers. 25 RAPD primers generated 218 bands, of which 196 bands (89.91%) were polymorphism. It showed that the Canada Bluegrass was separated from other Kentucky Bluegrass and genetic polymorphism in the Kentucky Bluegrass cultivars was low, the genetic similarity among the cultivars fell between 66%-98%. Dendrogram obtained using these molecular markers were partly in agreement with their separated morphologic character. Cultivars from the same company were not clustered in one group. PMID:16120587

  18. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    McCarthy, J.F.

    1990-04-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka, as a predictor of potential genotoxicity following exposure to carcinogens. This will be accomplished by quantitatively investigating the early molecular events associated with genotoxicity of various tissues of Medaka subsequent to exposure of the organism to several known carcinogens, such as diethylnitrosamine (DEN) and benzo(a)pyrene (BaP). 11 refs., 1 fig., 1 tab.

  19. Genetic diversity of different Tunisian fig ( Ficus carica L.) collections revealed by RAPD fingerprints

    Microsoft Academic Search

    AMEL SALHI-HANNACHI; KHALED CHATTI; OLFA SADDOUD; MESSAOUD MARS; ABDELMAJID RHOUMA; MOHAMED MARRAKCHI; MOKHTAR TRIFI

    2006-01-01

    The genetic diversity in Tunisian fig (Ficus carica L.) was studied using RAPD markers. Thirtyfive fig cultivars originating from diverse geographical areas and belonging to three collections were analysed. Random decamer primers were screened to assess their ability to detect polymorphisms in this crop. Fortyfour RAPD markers were revealed and used to survey the genetic diversity and to detect cases

  20. RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers

    E-print Network

    Beissinger, Steven R.

    RESEARCH ARTICLE Uncloaking a cryptic, threatened rail with molecular markers: origins Black Rail lives under dense marsh vegetation, is rarely observed, flies weakly and has a highly disjunct distribution. The largest population of rails is found in 8­10 large wetlands in San Francisco Bay

  1. Phylogenetic study of some Aporrectodea species based on molecular markers

    E-print Network

    Paris-Sud XI, Université de

    in "Advances in Earthworm Taxonomy V (Annelida: Oligochaeta), T. Pavlicek, P. Cardet, C. Csuzdi, R.C. Le Bayon earthworms play as key organisms in terrestrial ecosystems functioning, the lack of knowledge in phylogenetic earthworm taxonomy has only recently started. Molecular markers, mitochondrial and nucle- ar, are thus

  2. RAPD identification of microsatellites in Daphnia.

    PubMed

    Ender, A; Schwenk, K; Städler, T; Streit, B; Schierwater, B

    1996-06-01

    Simple sequence repeats (SSRs, or microsatellites) have been constantly gaining importance as single-locus DNA markers in population genetics and behavioural ecology. We tested a PCR-based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and screening, and the need for larger amounts of DNA. In the first step, parts of a genome are randomly amplified with arbitrary 10mer primers using RAPD fingerprinting. Labelled SSR-oligonucleotides serve as probes to detect complementary sequences in RAPD products by means of Southern analyses. Subsequently, positive RAPD fragments of suitable size are cloned and sequenced. Using GA and GT probes, we applied this approach to waterfleas (Daphnia) and revealed 37 hybridization signals in 20 RAPD profiles. Thirteen positive RAPD fragments from three Daphnia species and two hybrid 'species' were cloned and sequenced. In all cases simple sequence repeats were detected. We characterized seven perfect repeat loci, which were found to be polymorphic within and between species. PMID:8688961

  3. Reviewing and Updating the Major Molecular Markers for Stem Cells

    PubMed Central

    Calloni, Raquel; Cordero, Elvira Alicia Aparicio; Henriques, João Antonio Pêgas

    2013-01-01

    Stem cells (SC) are able to self-renew and to differentiate into many types of committed cells, making SCs interesting for cellular therapy. However, the pool of SCs in vivo and in vitro consists of a mix of cells at several stages of differentiation, making it difficult to obtain a homogeneous population of SCs for research. Therefore, it is important to isolate and characterize unambiguous molecular markers that can be applied to SCs. Here, we review classical and new candidate molecular markers that have been established to show a molecular profile for human embryonic stem cells (hESCs), mesenchymal stem cells (MSCs), and hematopoietic stem cells (HSCs). The commonly cited markers for embryonic ESCs are Nanog, Oct-4, Sox-2, Rex-1, Dnmt3b, Lin-28, Tdgf1, FoxD3, Tert, Utf-1, Gal, Cx43, Gdf3, Gtcm1, Terf1, Terf2, Lefty A, and Lefty B. MSCs are primarily identified by the expression of CD13, CD29, CD44, CD49e, CD54, CD71, CD73, CD90, CD105, CD106, CD166, and HLA-ABC and lack CD14, CD31, CD34, CD45, CD62E, CD62L, CD62P, and HLA-DR expression. HSCs are mainly isolated based on the expression of CD34, but the combination of this marker with CD133 and CD90, together with a lack of CD38 and other lineage markers, provides the most homogeneous pool of SCs. Here, we present new and alternative markers for SCs, along with microRNA profiles, for these cells. PMID:23336433

  4. [Molecular markers associated to prognosis of melanoma].

    PubMed

    Heenen, M; Laporte, M

    2003-11-01

    Melanoma prognosis is based on histological criteria such as tumor thickness (measured by Breslow index), level of invasion (Clarck's level), presence of ulceration and number of mitoses per mm2. However, these parameters do not provide a precise prognosis in all cases: thin melanomas may develop metastases and thick melanomas may remain focalized for many years. For these reasons, the search for other prognostic factors is still ongoing. Many molecules play a part in the invasiveness and metastatic dissemination of melanoma have now been identified. Expression of these molecules has been studied in primary melanoma and correlated with prognosis. An increase in the number of cells positive for Ki67 (detected by Mib1), cycline A, cycline D, p35, MMp-2, beta1 and beta3 integrins, osteonectin, the presence of an intense inflammatory infiltrate and capillary invasion are considered as factors of poor prognosis as well as the decrease in p16, p27, Melan A and nm23. The significance of CD44 modifications is still controversial. Only a small number of these different proteins has a prognostic value independent of tumor thickness. These results need to be confirmed on larger series of patients. Additional hope is given to new techniques such as the analysis of the genes implied in tumor progression by microarray technique in such a way as to provide a molecular map of each tumor. PMID:14724537

  5. DEVELOPMENT OF CO-DOMINANT MARKERS LINKED TO THE MJ-L LOCUS IN CARROT (DAUCUS CAROTA L. SSP. SATIVUS)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The majority of PCR-based markers mapped in carrot (Daucus carota) have been either random amplified polymorphic DNA (RAPD) markers or amplified fragment length polymorphism (AFLP) markers. RAPD markers suffer from poor reproducibility and both RAPD and AFLP primarily produce dominant markers. A rec...

  6. Molecular Markers for Breast Cancer: Prediction on Tumor Behavior

    PubMed Central

    Banin Hirata, Bruna Karina; Oda, Julie Massayo Maeda; Losi Guembarovski, Roberta; Ariza, Carolina Batista; de Oliveira, Carlos Eduardo Coral; Watanabe, Maria Angelica Ehara

    2014-01-01

    Breast cancer is one of the most common cancers with greater than 1,300,000 cases and 450,000 deaths each year worldwide. The development of breast cancer involves a progression through intermediate stages until the invasive carcinoma and finally into metastatic disease. Given the variability in clinical progression, the identification of markers that could predict the tumor behavior is particularly important in breast cancer. The determination of tumor markers is a useful tool for clinical management in cancer patients, assisting in diagnostic, staging, evaluation of therapeutic response, detection of recurrence and metastasis, and development of new treatment modalities. In this context, this review aims to discuss the main tumor markers in breast carcinogenesis. The most well-established breast molecular markers with prognostic and/or therapeutic value like hormone receptors, HER-2 oncogene, Ki-67, and p53 proteins, and the genes for hereditary breast cancer will be presented. Furthermore, this review shows the new molecular targets in breast cancer: CXCR4, caveolin, miRNA, and FOXP3, as promising candidates for future development of effective and targeted therapies, also with lower toxicity. PMID:24591761

  7. Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts.

    PubMed

    Gutiérrez, Alfredo; Pointier, Jean-Pierre; Fraga, Jorge; Jobet, Edouard; Modat, Sylvain; Pérez, R T; Yong, Mary; Sanchez, J; Loker, Eric S; Théron, André

    2003-01-01

    Protein electrophoresis, RAPD-PCR and nuclear rDNA ITS sequencing were performed to search for genetic differences between Pseudosuccinea columella snails susceptible and resistant to Fasciola hepatica infection. Of the 21 enzymatic loci analyzed in both populations, none of them exhibited neither within- or between-group variation. Such an absence of enzyme polymorphism support the hypothesis of selfing as the "prevalent" mating system for this hermaphroditic species. Conversely, the RAPD profiles displayed clear differences between susceptible and resistant isolates for 17 of the 26 primers tested while no within-group variation was detected. rDNA ITS sequence analysis from snails of each isolates showed only two bases that differed between groups accounting for a 0.17% of variation confirming that susceptible and resistant snails belong to the same species. This is the first time that a genetic variation using RAPD markers is demonstrated between susceptible and resistant lymnaeid snails vis-a-vis of F. hepatica infection in absence of experimental selection. PMID:14990314

  8. Molecular markers for wheat leaf rust resistance gene Lr41

    Microsoft Academic Search

    Xiaochun Sun; Guihua Bai; Brett F. Carver

    2009-01-01

    Leaf rust, caused by Puccinia triticina Eriks., is an important foliar disease of common wheat (Triticum aestivum L.) worldwide. Pyramiding several major rust-resistance genes into one adapted cultivar is one strategy for obtaining more\\u000a durable resistance. Molecular markers linked to these genes are essential tools for gene pyramiding. The rust-resistance gene\\u000a Lr41 from T.\\u000a tauschii has been introgressed into chromosome

  9. Molecular markers of pancreatic cancer: development and clinical relevance

    Microsoft Academic Search

    Lucia C. Fry; Klaus Mönkemüller; Peter Malfertheiner

    2008-01-01

    Background  The prognosis of pancreatic cancer remains poor, mainly because of its aggressive biological behaviour and late clinical diagnosis,\\u000a which precludes the application of appropriate curative therapies. Therefore, one of the major goals in clinical pancreatology\\u000a is to find molecular markers, specific and sensitive enough to make an early and correct diagnosis of pancreatic cancer, before\\u000a it has disseminated and become

  10. Molecular Markers, Natural History, and Conservation of Marine Animals

    NSDL National Science Digital Library

    Ronald Burton (Scripps Institution of Oceanography, University of California, San Diego; Marine Biology Research Division)

    2009-11-01

    Molecular genetic techniques have found broad utility in modern marine ecology, and applications continue to grow. Databases of DNA sequences now permit nonexperts to identify eggs and larval stages of many marine animals that were previously mysteries. Molecular identifications of field-collected organisms and tissues are used to help assess population connectivity, investigate marine food webs, and identify marketed commodities. Advances in technology already include prototype development of in situ robotic instrumentation for sampling and molecular identification of animal larvae. Studies of population connectivity, once limited to a few gene loci, are slowly giving way to new genomic arrays of markers and high-throughput methodologies for scoring genotypes. Population genetic theory is providing new computational techniques to assess patterns of population structure, estimate effective population sizes, and infer aspects of demographic history. In this article I review a subset of recent work in this growing area of molecular marine ecology.

  11. De Novo Transcriptome Assembly of Pummelo and Molecular Marker Development

    PubMed Central

    Liang, Mei; Yang, Xiaoming; Li, Hang; Su, Shiying; Yi, Hualin; Chai, Lijun; Deng, Xiuxin

    2015-01-01

    Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo. PMID:25799271

  12. Characterization of alien chromosomes in backcross derivatives of Triticum aestivum x Elymus rectisetus hybrids using molecular markers and sequential multi-color FISH/GISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Based on DNA sequences of genome-specific RAPD markers, sequence tagged site (STS) markers specific for W and Y genomes have been obtained. Coupling with the use of genomic in situ hybridization (GISH), these STS mar...

  13. The Promise of Novel Molecular Markers in Bladder Cancer

    PubMed Central

    Miremami, Jahan; Kyprianou, Natasha

    2014-01-01

    Bladder cancer is the fourth most common malignancy in the US and is associated with the highest cost per patient. A high likelihood of recurrence, mandating stringent surveillance protocols, has made the development of urinary markers a focus of intense pursuit with the hope of decreasing the burden this disease places on patients and the healthcare system. To date, routine use of markers is not recommended for screening or diagnosis. Interests include the development of a single urinary marker that can be used in place of or as an adjunct to current screening and surveillance techniques, as well identifying a molecular signature for an individual’s disease that can help predict progression, prognosis, and potential therapeutic response. Markers have shown potential value in improving diagnostic accuracy when used as an adjunct to current modalities, risk-stratification of patients that could aid the clinician in determining aggressiveness of surveillance, and allowing for a decrease in invasive surveillance procedures. This review discusses the current understanding of emerging biomarkers, including miRNAs, gene signatures and detection of circulating tumor cells in the blood, and their potential clinical value in bladder cancer diagnosis, as prognostic indicators, and surveillance tools, as well as limitations to their incorporation into medical practice. PMID:25535079

  14. A population genetics study of Anopheles darlingi (Diptera: Culicidae) from Colombia based on random amplified polymorphic DNA-polymerase chain reaction and amplified fragment lenght polymorphism markers.

    PubMed

    González, Ranulfo; Wilkerson, Richard; Suárez, Marco Fidel; García, Felipe; Gallego, Gerardo; Cárdenas, Heiber; Posso, Carmen Elisa; Duque, Myriam Cristina

    2007-06-01

    The genetic variation and population structure of three populations of Anopheles darlingi from Colombia were studied using random amplified polymorphic markers (RAPDs) and amplified fragment length polymorphism markers (AFLPs). Six RAPD primers produced 46 polymorphic fragments, while two AFLP primer combinations produced 197 polymorphic fragments from 71 DNA samples. Both of the evaluated genetic markers showed the presence of gene flow, suggesting that Colombian An. darlingi populations are in panmixia. Average genetic diversity, estimated from observed heterozygosity, was 0.374 (RAPD) and 0.309 (AFLP). RAPD and AFLP markers showed little evidence of geographic separation between eastern and western populations; however, the F ST values showed high gene flow between the two western populations (RAPD: F ST = 0.029; Nm: 8.5; AFLP: F ST = 0.051; Nm: 4.7). According to molecular variance analysis (AMOVA), the genetic distance between populations was significant (RAPD:phiST = 0.084; AFLP:phiST = 0.229, P < 0.001). The F ST distances and AMOVAs using AFLP loci support the differentiation of the Guyana biogeographic province population from those of the Chocó-Magdalena. In this last region, Chocó and Córdoba populations showed the highest genetic flow. PMID:17568929

  15. Review Molecular Methods: Blessing or Curse?

    Microsoft Academic Search

    Aline Finger; Charlotte Klank

    \\u000a Conservation genetic studies make use of molecular methods to obtain valuable information which help optimizing management\\u000a strategies especially for threatened species. This chapter presents an overview of different molecular markers (microsatellites,\\u000a AFLPs, RFLPs, RAPDs, mtDNA, allozymes) and their applications in conservation and genetic studies. Microsatellites have shown\\u000a to be, though expensive, currently the most popular genetic marker as the high

  16. Pyrogenic molecular markers: linking PAH with BPCA analysis.

    PubMed

    Wiedemeier, Daniel B; Brodowski, Sonja; Wiesenberg, Guido L B

    2015-01-01

    Molecular characterization of pyrogenic organic matter (PyOM) is of great interest to understand the formation and behavior of these increasingly abundant materials in the environment. Two molecular marker methods have often been used to characterize and trace PyOM: polycyclic aromatic hydrocarbon (PAH) and benzenepolycarboxylic acid (BPCA) analysis. Since both methods target pyrogenic polycyclic compounds, we investigated the linkages between the two approaches using chars that were produced under controlled conditions. Rye and maize straws and their analogues charred at 300, 400 and 500 °C, respectively, were thus analyzed with both methods. Moreover, we also measured BPCAs directly on the lipid extracts, on which PAHs were analyzed, and on the respective extraction residues, too. Both methods revealed important features of the chars, in particular the increasing degree of aromatic condensation with increasing highest heating temperature (HTT). The overlap between the two methods was identified in the lipid fraction, where the proportion of benzenetricarboxylic acids (B3CAs) correlated with PAH abundance. The results confirmed the validity and complementarity of the two molecular marker methods, which will likely continue to play a crucial role in PyOM research due to the recent developments of compound-specific PAH and BPCA stable carbon (?(13)C) and radiocarbon ((14)C) isotope methods. PMID:25084061

  17. Molecular marker from pancreatic 'juices' helps identify pancreatic cancer

    Cancer.gov

    Researchers at Mayo Clinic have developed a promising method to distinguish between pancreatic cancer and chronic pancreatitis — two disorders that are difficult to tell apart. A molecular marker obtained from pancreatic "juices" can identify almost all cases of pancreatic cancer, their study shows. The findings were being presented at Digestive Disease Week 2013 in Orlando, Fla. Pancreatic cancer and chronic pancreatitis both produce the same signs of disease in the pancreas, such as inflammation, but cancer in the organ is a life-threatening disorder that must be treated immediately and aggressively.

  18. An analysis of 14 molecular markers for monitoring osteoarthritis: segregation of the markers into clusters and distinguishing osteoarthritis at baseline

    Microsoft Academic Search

    I. G Otterness; A. C Swindell; R. O Zimmerer; A. R Poole; M Ionescu; E Weiner

    2000-01-01

    Objective To investigate the relationships between serum and urinary molecular markers (MM) used to monitor osteoarthritis.Design Forty osteoarthritis patients had blood and urine collected at baseline and 1, 3, 6 and 12 months later. Specimens from 20 controls were obtained twice at a one month interval. The concentration of 14 different markers was determined at each time point and the

  19. Genetic analysis of litchi (Litchi chinensis Sonn.) in southern China by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR).

    PubMed

    Long, Yan; Cheng, Jingliang; Mei, Zhiqiang; Zhao, Ling; Wei, Chunli; Fu, Shelly; Khan, Md Asaduzzaman; Fu, Junjiang

    2015-01-01

    Litchi (Litchi chinensis Sonn., L. chinensis), a type of tree growing in most areas of southern China, produces an edible fruit that is also a source of traditional medicine. Genetic identification of litchi species or cultivars using molecular markers is very important. In this study, a total of six litchi samples from Fujian, Hainan, Guangdong, Guangxi and Sichuan province, as well as one wild Dimocarpus confinis (D. confinis) sample from Guangxi province were collected for genetic analysis. The cluster dendrograms were constructed for genetic analysis on the basis of DNA amplification results by RAPD and ISSR. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 176 bands were found, indicating a 72.7 % polymorphism in L. chinensis DNA samples. Significant genetic distances were found among the different species or cultivars, with an index of similarity coefficient ranging from 0.59 to 0.87. Similar to RAPD results, ISSR analysis of the L. chinensis DNA samples showed a range of 0.70-0.93 similarity coefficients. The genetic distance between Hainan sample and Sichuan samples was the farthest, which is consistent with their geographic distance. Furthermore, the index of similarity coefficient between D. confinis and L. chinensis was 0.35-0.41 by RAPD and 0.38-0.48 by ISSR, indicating that these two species have significant genetic difference. This study reveals the high level of genetic differences between different litchi species or cultivars, and confirms the significance of the improved RAPD method in genetic characterization of organisms. Taken together, the improved RAPD combined with ISSR analysis can be used frequently for the genetic diversity, germplasm resources preservation, molecular-assisted breeding, and genetic characterization of various organisms. PMID:25249227

  20. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

    NASA Astrophysics Data System (ADS)

    Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

    2014-01-01

    Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

  1. Genetic variation and phylogenetic relationships among worldwide collections of the Russian wheat aphid, Diuraphis noxia (Mordvilko), inferred from allozyme and RAPD-PCR markers

    Microsoft Academic Search

    G J Puterka; W C Black; W M Steiner; R L Burton

    1993-01-01

    Genetic analyses were conducted on Diuraphis noxia (Mordvilko) populations collected from wheat, barley and other grasses from various countries throughout the world. These collections had been found to contain clones that differed in virulence from various cultivars, cuticular hydrocarbon profiles and life cycle characters. Discrete genetic markers analysed in this study included allozymes and arbitrary regions of the genome amplified

  2. Molecular tools for marker-assisted breeding of buffelgrass

    E-print Network

    Jessup, Russell William

    2005-11-01

    , 2) develop polymerase chain reaction (PCR)-based markers from selected, informative restriction fragment length polymorphism (RFLP) markers on the buffelgrass genome map, and 3) increase marker resolution near the locus conferring apomixis (PApo1...

  3. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

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

    PubMed Central

    Mahmodi, Farshid; Kadir, J. B.; Puteh, A.; Pourdad, S. S.; Nasehi, A.; Soleimani, N.

    2014-01-01

    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. PMID:25288981

  5. A novel and efficient strategy for practical identification of tomato (Solanum lycopersicon) varieties using modified RAPD fingerprints.

    PubMed

    Korir, N K; Li, X Y; Leng, X P; Wu, Z; Wang, C; Fang, J G

    2013-01-01

    Tomato breeding and variety development have led to the generation of a large number of varieties in many countries worldwide. This has created a growing and urgent need for an improved strategy for genotyping and identification since the traditional methods based on phenotype are growing unreliable. DNA markers could provide distinct benefits in tomato variety identification; however, DNA fingerprint analyses have not made DNA marker data readily usable for identification of varieties in tomato and other crops. A manual cultivar and/or variety identification diagram (MCID) strategy has been developed and has been found to make DNA markers more usable for the identification of genotyped plant individuals. We adopted this strategy, using modified RAPD markers to identify 42 tomato varieties from different geographical origins and seed merchants. All of the varieties were clearly separated and individually identified by reproducible fingerprints of only 6 RAPD primers. The tomato MCID that is generated is usable for the identification of any two or more tomato varieties. In addition, fewer primers can be used to make a distinction between varieties using this approach, since the selected fingerprints from each primer are used after they have been generated. The information in this first version of the tomato MCID can be enriched through identification and incorporation of more varieties and adaptation to other molecular markers in order to provide a more comprehensive tomato variety identification service for the horticultural industry. PMID:23913374

  6. New models and molecular markers in evaluation of developmental toxicity

    SciTech Connect

    Huuskonen, Hannele [National Product Control Agency for Welfare and Health, Chemicals Department, STTV c/o National Public Health Institute, P.O. Box 95, FIN-70701 Kuopio (Finland)]. E-mail: hannele.huuskonen@sttv.fi

    2005-09-01

    Mammalian and non-mammalian embryos and embryonic stem cells may be used as models in mechanistic studies and in testing embryotoxicity of compounds. In addition to conventional culture methods, genetic modifications and use of molecular markers offer significant advantages in mechanistic studies as well as in developing new test methods for embryotoxicity. Zebrafish model has been used for a long time and at present several applications are available. It is an easy vertebral non-mammalian model, whose genome is largely known and several genetic modifications are easily constructed to study gene expression or knocked down genes. Fluorescent marker proteins can be used also in zebrafish to indicate gene activation in transgenic models. Chemical genetics approach has been developed using zebrafish model. This is a new approach to screen small molecules that regulate signaling pathways. Embryonic stem cells have been used in mechanistic studies and mouse embryonic stem cell test has been validated to study embryotoxicity in vitro. This method has been improved using quantitative measurements of molecular endpoints by real-time RT-PCR or fluorescent activated cell sorting methods (FACS). Methods facilitating differentiation to several different cell types are available. We have studied preimplantation mouse embryos as a possible model for in vitro testing. In this method, superovulated and in vivo fertilized preimplantation embryos were collected at morula stage and cultured up to blastocysts. The mouse preimplantation culture test was improved by quantitative gene expression measurement using two-step real-time RT-PCR methods. New endpoints improve the tests of in vitro embryotoxicity because subjective assessments are replaced by objective measurements. In addition, automation is possible and less time is needed for analysis. Thus, high throughput screening will come possible to test large numbers of compounds.

  7. STRATEGIES FOR THE DEVELOPMENT AND IMPLEMENTATION OF MOLECULAR MARKERS IN PLANT BREEDING PROGRAMS.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have been slow to meet expectations, but markers are currently providing real benefits in a number of breeding programs. Improved technologies provide opportunities to increase the usefulness of markers to breeding programs by reducing their costs and labor requirements and by inc...

  8. Molecular markers for identifying municipal, domestic and agricultural sources of organic matter in natural waters.

    PubMed

    Harwood, John J

    2014-01-01

    Molecular markers can be used to determine the sources of organic pollution in water. This review summarizes progress made during the last two decades in identifying reliable molecular markers to distinguish pollution from sewage, animal production, and other sources. Two artificial sweeteners, sucralose and acesulfame-K, are sufficiently stable to be molecular markers and easily associated with domestic wastewater. Waste from different animal species may be distinguished by profiling fecal sterols and bile acids. Other markers which have been evaluated, including caffeine, detergent components, and compounds commonly leached from landfills are discussed. PMID:24200048

  9. Genetic Mapping of Quantitative Trait Loci Controlling Growth and Wood Quality Traits in Eucalyptus Grandis Using a Maternal Half-Sib Family and Rapd Markers

    PubMed Central

    Grattapaglia, D.; Bertolucci, FLG.; Penchel, R.; Sederoff, R. R.

    1996-01-01

    Quantitative trait loci (QTL) mapping of forest productivity traits was performed using an open pollinated half-sib family of Eucalyptus grandis. For volume growth, a sequential QTL mapping approach was applied using bulk segregant analysis (BSA), selective genotyping (SG) and cosegregation analysis (CSA). Despite the low heritability of this trait and the heterogeneous genetic background employed for mapping. BSA detected one putative QTL and SG two out of the three later found by CSA. The three putative QTL for volume growth were found to control 13.7% of the phenotypic variation, corresponding to an estimated 43.7% of the genetic variation. For wood specific gravity five QTL were identified controlling 24.7% of the phenotypic variation corresponding to 49% of the genetic variation. Overlapping QTL for CBH, WSG and percentage dry weight of bark were observed. A significant case of digenic epistasis was found, involving unlinked QTL for volume. Our results demonstrate the applicability of the within half-sib design for QTL mapping in forest trees and indicate the existence of major genes involved in the expression of economically important traits related to forest productivity in Eucalyptus grandis. These findings have important implications for marker-assisted tree breeding. PMID:8913761

  10. Characterization of Thinopyrum bessarabicum chromosome segments in wheat using random amplified polymorphic DNAs (RAPDs) and genomic in situ hybridization

    Microsoft Academic Search

    I. P. King; K. A. Purdie; H. N. Rezanoor; R. M. D. Koebner; T. E. Miller; S. M. Reader; P. Nicholson

    1993-01-01

    Ten random amplified polymorphic DNA (RAPD) markers specific to chromosome 5Eb of Thinopyrum bessarabicum were detected. Genomic in situ hybridization and standard cytological observations revealed that six of the markers are located on the 5Eb short arm and four are located on the 5Eb long arm. These RAPD markers have been used to confirm the identity of putative 5Eb (5A)

  11. Increased informativeness of RAPD analysis by detection of microsatellite motifs.

    PubMed

    Ramser, J; Weising, K; Chikaleke, V; Kahl, G

    1997-08-01

    The recently developed random-amplified microsatellite polymorphism (RAMPO) technique detects second-level amplification products that are useful as molecular markers. In the first step of the procedure, genomic DNA is amplified with a single arbitrary or microsatellite-complementary primer. PCR products are then electrophoretically separated, photographed, blotted and hybridized to a 32P-labeled microsatellite probe. Autoradiography reveals highly reproducible, polymorphic, probe-dependent fingerprints, which are different from the ethidium bromide staining patterns. In this paper, we report the successful application of various mono-, tri- and tetranucleotide repeat motifs as RAMPO probes. We also compare the efficiency of arbitrary vs. microsatellite primers for the generation of RAMPO patterns. Repeated rehybridization to different probes has expanded the information contained in a single random-amplified polymorphic DNA (RAPD) gel at least fivefold. Pattern complexity varies with the length and sequence of the probe. Application of the technique to a genetic relatedness study in the genus Dioscorea (yam) yielded highly informative markers, mainly at an interspecific level. PMID:9266084

  12. Identification of molecular markers associated with fruit traits in olive and assessment of olive core collection with AFLP markers and fruit traits.

    PubMed

    Ipek, M; Seker, M; Ipek, A; Gul, M K

    2015-01-01

    The purpose of this study was to characterize olive core collection with amplified fragment length polymorphism (AFLP) markers and fruit traits and to determine AFLP markers significantly associated with these fruit characters in olive. A total of 168 polymorphic AFLP markers generated by five primer combinations and nine fruit traits were used to characterize relationships between 18 olive cultivars. Although all olive cultivars were discriminated from each other by either AFLP markers (<0.75 similarity level) or fruit traits, clustering based on the AFLP markers and fruit traits was not significantly correlated (r = 0.13). Partial clustering of olive cultivars by AFLP markers according to their geographical origin was observed. Associations of AFLP markers with fruits were determined using a multiple-regression analysis with stepwise addition of AFLP markers. Significant associations between eight AFLP markers and fruit traits were identified. While five AFLP markers demonstrated significant negative correlation with fruit and stone weight, width and length and total polyphenols (P < 0.05), three AFLP markers displayed significant positive correlation with ?-tocopherol and ?-tocopherol (P < 0.01). This is the first report on the association of molecular markers with fruit traits in olive. Molecular markers associated with morphological and agronomic traits could be utilized for the breeding of olive cultivars. However, the association power of these markers needs to be confirmed in larger populations, and highly correlated markers should then be converted to PCR-based DNA markers such as sequence-characterized amplified region markers for better utilization. PMID:25867425

  13. Identifying commercially relevant Echinacea species by AFLP molecular markers.

    PubMed

    Russi, Luigi; Moretti, Chiaraluce; Raggi, Lorenzo; Albertini, Emidio; Falistocco, Egizia

    2009-11-01

    The rising interest in medicinal plants has brought several species of the genus Echinacea to the attention of many scientists. Echinacea angustifolia, E. pallida, and E. purpurea are the most important for their immunological properties, well known and widely used by the native Americans. The three species are easily distinguishable on the basis of their morphological characteristics, but it would be difficult, if not impossible, to distinguish them in commercial preparations of ground, dry plant parts of E. purpurea (the most valuable species for chemotherapeutic properties) mixed with the other two species. Species-specific molecular markers could be useful to address this issue. In the present work, using fresh material collected from cultivated Echinacea spp., AFLP analysis was used to discriminate the three species and to detect species-specific DNA fragments. By using 14 primer combinations it was possible to detect a total of 994 fragments, of which 565 were polymorphic. Overall, 89 fragments were unique to E. purpurea, 32 to E. angustifolia, and 26 to E. pallida. E+CAC/M+AAT or E+CAC/M+AGC alone provided 13, 9, and 4 or 7, 5, and 5 specific fragments for E. purpurea, E. angustifolia, and E. pallida, respectively. A validation trial to confirm the results was carried out on bulked samples of 23 accessions covering most of the genetic diversity of the three species. The results are discussed in terms of practical applications in the field of popular medicine, detecting frauds, and implications for the genus Echinacea. PMID:19935915

  14. Random amplified polymorphic DNA markers for discriminating Cochliomyia hominivorax from C. macellaria (Diptera: Calliphoridae).

    PubMed

    Skoda, S R; Skoda, S R; Pornkulwat, S; Foster, J E

    2002-02-01

    The screwworm, Cochliomyia hominivorax (Coquerel), is one of the most important pests of livestock in the Western Hemisphere. During early immature stages it is morphologically very similar (first instars are virtually indistinguishable) to the secondary screwworm, C. macellaria (Fabricius). Here, the utility of the random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) was explored as a technique for developing molecular genetic markers for these two species. Of the 120 arbitrary primers screened, 21 primers produced markers that were further investigated. Seven of the 21 primers produced clear and reproducible markers that were tested with DNA of five individuals from four populations of each species; five of these primers showed 12 RAPD markers that differentiated the species in all populations. Analyses of data from these seven primers also suggested that intraspecific polymorphisms exist that could be useful in distinguishing populations of screwworms. Some population genetic tools, such as genetic distance, cluster analysis and bootstrapping, were used to statistically explore these polymorphisms. The resulting statistics showed 100% support for the ability of RAPD-PCR to discriminate between the two species. Bootstrapping with data from one of the genetic distance calculations produced a tree with all individual screwworms in the correct populations, indicating that RAPD-PCR has promise for displaying intraspecific genetic variation that could be used in establishing the general geographic origin of screwworm samples. PMID:12020366

  15. A MOLECULAR MARKER MAP IN KANOTA X OGLE HEXAPLOID OAT (AVENA SP.) ENHANCED BY ADDITIONAL MARKERS AND A ROBUST FRAMEWORK

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. 'Kanota' X A. sativa L. cv. 'Ogle.' In the current work, 607 new markers were scored, many on a larger set of RI lin...

  16. Differential survival of mosquitofish exposed to radionuclides is dependent on RAPD genotype

    SciTech Connect

    Theodorakis, C.W. [Oak Ridge Associated Universities, TN (United States); Shugart, L.R. [Oak Ridge National Lab., TN (United States)

    1995-12-31

    In previous studies, it was found that certain RAPD (Randomly Amplified Polymorphic DNA) markers were present at higher frequencies in radionuclide-contaminated mosquitofish (Gambusia affinis) populations than in reference populations. These markers will be referred to as contaminant specific markers. In the present study, fish with and without these markers were collected from non-contaminated populations and exposed in situ to radionuclides by caging them in one of the contaminated sites. Forty fish were exposed for 1--6 weeks, after which the survivors were collected and DNA was extracted for genotypic analysis. In one experiment, the frequencies of contaminant specific markers in the survivors were compared to the frequencies of these markers in the native contaminated and uncontaminated (the source of the caged fish) populations. It was found that the genotypic distributions were more similar to the native contaminated population. In another experiment, samples of caudal fin tissue were collected for DNA extraction before and after placing fish in the cages, in order to compare survival rates of different genotypes. It was found that fish with the contaminant indicative bands had higher percent survival than the other fish. Experiments are underway or are being planned in order to determine the molecular identity of these bands and the ecological significance of altered band frequencies in hopes of developing population-level biomarkers of contaminant exposure and ecological affects.

  17. Variability of red rot-resistant somaclones of sugarcane genotype S97US297 assessed by RAPD and SSR.

    PubMed

    Shahid, M T H; Khan, F A; Saeed, A; Fareed, I

    2011-01-01

    Sugarcane breeding under climatic conditions of Pakistan is very difficult due to unavailability of viable fuzz (seed). Somaclonal variation can provide an alternative for improvement of existing genotypes. Six hundred and twenty-seven somaclones were developed from sugarcane genotype S97US297, and protocols for callogenesis and organogenesis were developed using Murashige and Skoog medium. Two types of explants, leaf and pith, and two auxins, 2,4-dichlorophenoxy acetic acid and indole-3-acetic acid, were tested to optimize callogenesis for root establishment. Leaves as explants with 3.0 mg/L 2,4-dichlorophenoxy acetic acid gave the best results, both for callus induction and proliferation. Half-strength Murashige and Skoog medium with 1.5 mg/L indole-3-butyric acid proved to be the best for rooting. Red rot-resistant somaclones of the R(2) generation along with the parent were assessed for genetic variability at the molecular level using RAPD and SSR markers. Polymorphism based on RAPD and SSR was 32 and 67%, respectively. Polymorphic information content ranged from 0.06-0.45 for RAPD and 0.06-0.47 for SSR. We conclude that somaclonal variation of sugarcane varieties is sufficient to allow selection. PMID:21948747

  18. Molecular Markers of Lung Cancer in MAYAK Workers

    SciTech Connect

    Steven A. Belinsky, PhD

    2007-02-15

    The molecular mechanisms that result in the elevated risk for lung cancer associated with exposure to radiation have not been well characterized. Workers from the MAYAK nuclear enterprise are an ideal cohort in which to study the molecular epidemiology of cancer associated with radiation exposure and to identify the genes targeted for inactivation that in turn affect individual risk for radiation-induced lung cancer. Epidemiology studies of the MAYAK cohort indicate a significantly higher frequency for adenocarcinoma and squamous cell carcinoma (SCC) in workers than in a control population and a strong correlation between these tumor types and plutonium exposure. Two hypotheses will be evaluated through the proposed studies. First, radiation exposure targets specific genes for inactivation by promoter methylation. This hypothesis is supported by our recent studies with the MAYAK population that demonstrated the targeting of the p16 gene for inactivation by promoter methylation in adenocarcinomas from workers (1). Second, genes inactivated in tumors can serve as biomarkers for lung cancer risk in a cancer-free population of workers exposed to plutonium. Support for this hypothesis is based on exciting preliminary results of our nested, case-control study of persons from the Colorado cohort. In that study, a panel of methylation markers for predicting lung cancer risk is being evaluated in sputum samples from incident lung cancer cases and controls. The first hypothesis will be tested by determining the prevalence for promoter hypermethylation of a panel of genes shown to play a critical role in the development of either adenocarcinoma and/or SCC associated with tobacco. Our initial studies on adenocarcinoma in MAYAK workers will be extended to evaluate methylation of the PAX5 {alpha}, PAX5 {beta}, H-cadherin, GATA5, and bone morphogenesis 3B (BMP3B) genes in the original sample set described under Preliminary studies. In addition, studies will be initiated in SCC from workers and controls to identify genes targeted for inactivation by plutonium in this other common histologic form of lung cancer. We will examine methylation of the p16, O{sup 6}-methylguanine-DNA methyl-transferase (MGMT), and death associated protein kinase genes ([DAP-K], evaluated previously in adenocarcinomas) as well as the new genes being assessed in the adenocarcinomas. The second hypothesis will be tested in a cross-sectional study of cancer-free workers exposed to plutonium and an unexposed population. A cohort of 700 cancer-free workers and 700 unexposed persons is being assembled, exposures are being defined, and induced sputum collected at initial entry into the study and approximately 1-year later. Exposed and unexposed persons will be matched by 5-year age intervals and smoking status (current and former). The frequency for methylation of four genes that show the greatest difference in prevalence in tumors from workers and controls will be determined in exfoliated cells within sputum. These studies will extend those in primary tumors to determine whether difference in prevalence for individual or multiple genes are detected in sputum samples from high-risk subjects exposed to plutonium. Follow-up of this cohort offers the opportunity to validate these endpoints and future biomarkers as true markers for lung cancer risk.

  19. Genetic diversity in Indonesian shallot ( Allium cepa var. ascalonicum ) and Allium × wakegi revealed by RAPD markers and origin of A. × wakegi identified by RFLP analyses of amplified chloroplast genes

    Microsoft Academic Search

    Noor Sugiharto Arifin; Yukio Ozaki; Hiroshi Okubo

    2000-01-01

    RAPD and PCR-RFLP analyses were conducted to establish the phylogenetic relationships among collected accessions of shallot and Allium × wakegi, and to assess the origin of A. × wakegi. Twenty out of 100 primers were amplified with 112 scorable bands for cluster analysis. Two main cluster groups consisting of one group for shallot and another group for A. × wakegi

  20. The molecular marker of kdr against fenpropathrin in Tetranychus cinnabarinus.

    PubMed

    Xu, Zhifeng; Shi, Li; Feng, Yaning; He, Lin

    2013-12-01

    The carmine spider mite, Tetranychus cinnabarinus (Boisduval), is one of the most important pests in agricultural industry. Pyrethroid insecticide has been used to control insects and mites worldwide. However, the intensive use of pyrethroid insecticide resulted in the development of resistance, which has mainly been induced by a variety of point mutations responsible for voltage-gated sodium channel (VGSC) insensitivity and has become the biggest obstacle to sustain the use of pyrethroid insecticide. In this study, we cloned cDNA full length of the para-homologous sodium channel gene from T. cinnabarinus named TC-vgsc. The complete open reading frame of TC-vgsc contains 6,579 nucleotides, encoding 2,193 amino acids. A point mutation, F1538I, was identified from both the DNA and RNA sequences of VGSC in fenpropathrin-resistant strain, which developed approximately 100-folds resistance against fenpropathrin. The result indicated the F1538I kdr mutation underwent DNA mutation events rather than RNA editing. Single nucleotide polymorphisms detection of F1538I mutation from indoor susceptible strain, fenpropathrin-resistant strain, and seven field populations found that this mutation appeared in all the strains (populations), but the frequency of mutation was closely related to the resistance level, with a r2 value of 0.665 (P < 0.05), that is, the higher the resistance level, the larger the mutation frequency. These results demonstrated that the F1538I mutation in the kdr gene can be used as a molecular marker for fenpropathrin-resistance monitoring in field T. cinnabarinus populations. PMID:24498748

  1. Molecular Markers of Radiation-related Normal Tissue Toxicity

    PubMed Central

    Okunieff, Paul; Chen, Yuhchyau; Maguire, David J.; Huser, Amy K.

    2009-01-01

    Over the past five decades, those interested in markers of radiation effect have focused primarily on tumor response. More recently, however, the view has broadened to include irradiated normal tissues—markers that predict unusual risk of side-effects, prognosticate during the prodromal and therapeutic phases, diagnose a particular toxicity as radiation-related, and, in the case of bioterror, allow for tissue-specific biodosimetry. Currently, there are few clinically useful radiation-related biomarkers. Notably, levels of some hormones such as thyroid-stimulating hormone (TSH) have been used successfully as markers of dysfunction, indicative of the need for replacement therapy, and for prevention of cancers. The most promising macromolecular markers are cytokines: TGF?, IL-1, IL-6, and TNF? being lead molecules in this class as both markers and targets for therapy. Genomics and proteomics are still in nascent stages and are actively being studied and developed. PMID:18506399

  2. A review on SNP and other types of molecular markers and their use in animal genetics

    Microsoft Academic Search

    Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen

    2002-01-01

    During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high

  3. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

    PubMed Central

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-01-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  4. Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants.

    PubMed

    Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

    2014-09-01

    In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops. PMID:25320561

  5. Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic

    E-print Network

    Standiford, Richard B.

    485 Molecular Markers Show How Pollen and Seed Dispersal Affect Population Genetic Structure of fragmentation and decreased population sizes is reduced genetic diversity as populations become increasingly. Earlier studies indicated biochemical differentiation of central coast populations from those of Northern

  6. Molecular markers and conservation of plant species in Latin America: the case of Phaedranassa viridflora (Amaryllidaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellites are molecular markers with great potential for investigating genetic structure of populations. This information is valuable for generating effective conservation plans. We studied the endemic and endangered Phaedranassa viridiflora (Amaryllidaceae) to show the utility of microsatelli...

  7. Molecular markers for population genetic analyses in the family Psittacidae (Psittaciformes, Aves)

    Microsoft Academic Search

    Patrícia J. Faria; Cristina Y. Miyaki

    2006-01-01

    The selection of molecular markers for population studies is an important tool for biodiversity conservation. The fam- ily Psittacidae contains many endangered and vulnerable species and we tested three kinds of molecular markers for their potential use in population studies of five psitacid species: 43 hyacinth macaws (Anodorhynchus hyacinthinus), 42 blue-and-yellow macaws (Ara ararauna), 23 red-and-green macaws (Ara chloroptera), 19

  8. Molecular Markers Reveal Exclusively Clonal Reproduction in Trichophyton rubrum

    PubMed Central

    Gräser, Y.; Kühnisch, J.; Presber, W.

    1999-01-01

    Genotypic variability among 96 Trichophyton rubrum strains which displayed different colony morphologies and were collected from four continents was investigated. Twelve markers representing 57 loci were analyzed by PCR fingerprinting, amplified fragment length polymorphism, and random amplified monomorphic DNA markers. Interestingly, none of the methods used revealed any DNA polymorphism, indicating a strictly clonal mode of reproduction and a strong adaptation to human skin. PMID:10523582

  9. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  10. RAPD typing in microbiology—a technical review

    Microsoft Academic Search

    E. G. M. Power

    1996-01-01

    Many biochemical and molecular techniques can be used for distinguishing isolates of a given bacterial species. Traditional typing techniques based on phenotypic characteristics such as serotyping are being increasingly challenged by the use of DNA-based methods. The introduction of the polymerase chain reaction (PCR) has led to typing techniques based on DNA amplification. Randomly amplified polymorphic DNA (RAPD) typing (also

  11. Analysis of plant diversity with retrotransposon-based molecular markers

    PubMed Central

    Kalendar, R; Flavell, A J; Ellis, T H N; Sjakste, T; Moisy, C; Schulman, A H

    2011-01-01

    Retrotransposons are both major generators of genetic diversity and tools for detecting the genomic changes associated with their activity because they create large and stable insertions in the genome. After the demonstration that retrotransposons are ubiquitous, active and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. These have found applications ranging from the mapping of genes responsible for particular traits and the management of backcrossing programs to analysis of population structure and diversity of wild species. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of population diversity in plants. PMID:20683483

  12. The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.

    EPA Science Inventory

    Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...

  13. Fluorescence-based AFLPs occur as the most suitable marker system for oilseed rape cultivar identification.

    PubMed

    Sobotka, Roman; Dolanská, Lenka; Curn, Vladislav; Ovesná, Jaroslava

    2004-01-01

    Three different types of molecular markers, RAPD, SSR and fluorescence-based AFLP, were evaluated and compared for their ability to identify oilseed rape cultivars. The direct comparison of RAPD, SSR and AFLP approaches in cultivar identification showed that the AFLP methodology detected polymorphisms more efficiently than either RAPD or SSR methods. For the characterisation of six oilseed rape cultivars, 60 RAPD primers were tested and only eight of them (14%) detected sufficient levels of polymorphism. Five microsatellites out of fifteen tested were polymorphic, but in all loci, except one, only two different alleles were detected. This result indicated the limited degree of polymorphism found in Brassica napus. Each of the six tested AFLP combinations detected polymorphisms, the best combination (M-CAA/E-ACT) had 26% polymorphic peaks from a total of 90 peaks and could distinguish the analysed cultivars and 4 out of 5 core lines of cultivars. The results presented show that florescence-based AFLP is, for the purposes of oilseed rape cultivar fingerprinting, a more suitable approach than either RAPD or SSR. PMID:15131347

  14. Use of molecular diversity of Mycoplasma gallisepticum by gene-targeted sequencing (GTS) and random amplified polymorphic DNA (RAPD) analysis for epidemiological studies.

    PubMed

    Ferguson, Naola M; Hepp, Diego; Sun, Shulei; Ikuta, Nilo; Levisohn, Sharon; Kleven, Stanley H; García, Maricarmen

    2005-06-01

    A total of 67 Mycoplasma gallisepticum field isolates from the USA, Israel and Australia, and 10 reference strains, were characterized by gene-targeted sequencing (GTS) analysis of portions of the putative cytadhesin pvpA gene, the cytadhesin gapA gene, the cytadhesin mgc2 gene, and an uncharacterized hypothetical surface lipoprotein-encoding gene designated genome coding DNA sequence (CDS) MGA_0319. The regions of the surface-protein-encoding genes targeted in this analysis were found to be stable within a strain, after sequencing different in vitro passages of M. gallisepticum reference strains. Gene sequences were first analysed on the basis of gene size polymorphism. The pvpA and mgc2 genes are characterized by the presence of different nucleotide insertions/deletions. However, differentiation of isolates based solely on pvpA/mgc2 PCR size polymorphism was not found to be a reliable method to differentiate among M. gallisepticum isolates. On the other hand, GTS analysis based on the nucleotide sequence identities of individual and multiple genes correlated with epidemiologically linked isolates and with random amplified polymorphic DNA (RAPD) analysis. GTS analysis of individual genes, gapA, MGA_0319, mgc2 and pvpA, identified 17, 16, 20 and 22 sequence types, respectively. GTS analysis using multiple gene sequences mgc2/pvpa and gapA/MGA_0319/mgc2/pvpA identified 38 and 40 sequence types, respectively. GTS of multiple surface-protein-encoding genes showed better discriminatory power than RAPD analysis, which identified 36 pattern types from the same panel of M. gallisepticum strains. These results are believed to provide the first evidence that typing of M. gallisepticum isolates by GTS analysis of surface-protein genes is a sensitive and reproducible typing method and will allow rapid global comparisons between laboratories. PMID:15941996

  15. A Comparison of Three Molecular Markers for the Identification of Populations of Globodera pallida.

    PubMed

    Hoolahan, Angelique H; Blok, Vivian C; Gibson, Tracey; Dowton, Mark

    2012-03-01

    Potato cyst nematodes cost the potato industry substantial financial losses annually. Through the use of molecular markers, the distribution and infestation routes of these nematodes can be better elucidated, permitting the development of more effective preventative methods. Here we assess the ability of three molecular markers to resolve multiple representatives of five Globodera pallida populations as monophyletic groups. Molecular markers included a region of the rbp-1 gene (an effector), a non-coding nuclear DNA region (the ITS region), and a novel marker for G. pallida, a ?3.4 kb non-coding mitochondrial DNA (mtDNA) region. Multiple phylogenetic analysis methods were performed on the three DNA regions separately, and on a data set of these three regions combined. The analyses of the combined data set were similar to that of the sole mtDNA marker; resolving more populations as monophyletic groups, relative to that of the ITS region and rbp-1 gene region. This suggests that individual markers may be inadequate for distinguishing populations of G. pallida. The use of this new non-coding mtDNA marker may provide further insights into the historical distribution of G. pallida, as well as enable the development of more sensitive diagnostic methods. PMID:23482966

  16. Identifying molecular markers associated with stigma characteristics in rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stigma characteristics play essential roles in hybrid seed production of rice and marker-assisted breeding plays essential role because they are quantitatively inherited with single-flowered perfect spikelet. Ninety four accessions originated from 47 countries were selected from the USDA rice core c...

  17. MOLECULAR MARKER ASSISTED BREEDING FOR DISEASE RESISTANCE IN COMMON BEAN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There have been 40 sequence characterized amplified region (SCAR) markers (http://www.usda.prosser.wsu.edu/miklas/Scartable3.pdf) generated across laboratories that are available for indirect selection of 27 qualitatively and 8 quantitatively expressed genes conditioning resistance to bacterial, fun...

  18. Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology

    PubMed Central

    Kirk, Heather; Freeland, Joanna R.

    2011-01-01

    The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. PMID:21747718

  19. Molecular markers to study competition and diversity of Rhizobium

    Microsoft Academic Search

    A. Sessitsch

    1997-01-01

    The research described in this thesis was directed to the development of molecular identification and detection techniques for studying the ecology of Rhizobium, a nitrogen- fixing bacterium of agricultural importance. Competition of inoculant strains with indigenous microbes is a serious problem in agricultural practice and was therefore addressed in this work using the developed tools. Furthermore, various molecular techniques have

  20. EVALUATION OF GENETIC DIVERSITY IN SORGHUM GERMPLASM USING MOLECULAR MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In molecular breeding, there is an increasing demand for the establishment of molecular profiles for each of germplasm accession, so that specific germplasm accession can be selected for various crop breeding purposes. Presently sorghum represents one of the largest germplasm collections, comprisin...

  1. A new set of molecular markers for the genotyping of Babesia bovis isolates.

    PubMed

    Wilkowsky, S E; Moretta, R; Mosqueda, J; Gil, G; Echaide, I; Lía, V; Falcón, A; Florin Christensen, M; Farber, M

    2009-04-01

    Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the genotyping and population genetic analysis. In this work we report a set of five molecular markers containing minisatellites that showed a variable degree of polymorphism in several American strains. We have used a bioinformatics approach to search for marker sequences contained in open reading frames. Five genes were chosen and primers were designed in conserved regions flanking the repeat region. Two of the genes were the previously described Bv80/Bb-1 and TRAP. The other three genes were named p200, Antigen 3 and Desmoyokin. Amplification by PCR, sequencing and comparative analysis of 11 strains from Argentina, Brazil, Uruguay, Mexico and USA determined that the tandem repeats varied in number and sequence among the isolates. Genome analysis of the five markers revealed that they were single copy and distributed across the four B. bovis chromosomes. When the new markers were analyzed in an experimental infection, absolute sequence conservation was found, indicating the stability of these markers during the course of infection. These markers were also stable during three syringe passages through calves. The application of this panel of molecular markers could provide new molecular tools for the genotyping of B. bovis isolates and analysis of changes in parasite populations following vaccination. PMID:19251367

  2. Characterization of Italian lentil ( Lens culinaris Medik.) germplasm by agronomic traits, biochemical and molecular markers

    Microsoft Academic Search

    Massimo Zaccardelli; Francesco Lupo; Angela Rosa Piergiovanni; Gaetano Laghetti; Gabriella Sonnante; Maria Gloria Daminati; Francesca Sparvoli; Lucia Lioi

    Genetic relationships, agronomic, nutritional and technological traits of ten Italian landraces, two improved lines and two\\u000a cultivars of lentil (Lens culinaris Medik.) were investigated using a multi-disciplinary approach. Seed storage proteins, used as biochemical markers, were able\\u000a to detect polymorphisms with variability mainly related to the polypeptide abundance. Microsatellite (SSR) molecular markers\\u000a provided very useful information on genetic variation and

  3. A review on SNP and other types of molecular markers and their use in animal genetics

    PubMed Central

    Vignal, Alain; Milan, Denis; SanCristobal, Magali; Eggen, André

    2002-01-01

    During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high degree of information provided by its large number of alleles per locus. Despite this, a new marker type, named SNP, for Single Nucleotide Polymorphism, is now on the scene and has gained high popularity, even though it is only a bi-allelic type of marker. In this review, we will discuss the reasons for this apparent step backwards, and the pertinence of the use of SNPs in animal genetics, in comparison with other marker types. PMID:12081799

  4. Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities* #

    PubMed Central

    Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita

    2014-01-01

    Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20–23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789

  5. Designing a SCAR molecular marker for monitoring Trichoderma cf. harzianum in experimental communities.

    PubMed

    Pérez, Gabriel; Verdejo, Valentina; Gondim-Porto, Clarissa; Orlando, Julieta; Carú, Margarita

    2014-11-01

    Several species of the fungal genus Trichoderma establish biological interactions with various micro- and macro-organisms. Some of these interactions are relevant in ecological terms and in biotechnological applications, such as biocontrol, where Trichoderma could be considered as an invasive species that colonizes a recipient community. The success of this invasion depends on multiple factors, which can be assayed using experimental communities as study models. Therefore, the aim of this work is to develop a species-specific sequence-characterized amplified region (SCAR) marker to monitor the colonization and growth of T. cf. harzianum when it invades experimental communities. For this study, 16 randomly amplified polymorphic DNA (RAPD) primers of 10-mer were used to generate polymorphic patterns, one of which generated a band present only in strains of T. cf. harzianum. This band was cloned, sequenced, and five primers of 20-23 mer were designed. Primer pairs 2F2/2R2 and 2F2/2R3 successfully and specifically amplified fragments of 278 and 448 bp from the T. cf. harzianum BpT10a strain DNA, respectively. Both primer pairs were also tested against the DNA from 14 strains of T. cf. harzianum and several strains of different fungal genera as specificity controls. Only the DNA from the strains of T. cf. harzianum was successfully amplified. Moreover, primer pair 2F2/2R2 was assessed by quantitative real-time polymerase chain reaction (PCR) using fungal DNA mixtures and DNA extracted from fungal experimental communities as templates. T. cf. harzianum was detectable even when as few as 100 copies of the SCAR marker were available or even when its population represented only 0.1% of the whole community. PMID:25367789

  6. Trypanosoma evansi: Genetic variability detected using amplified restriction fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analysis of Kenyan isolates

    Microsoft Academic Search

    Daniel K. Masiga; Kariuki Ndung’u; Alison Tweedie; Andrew Tait; C. Michael R. Turner

    2006-01-01

    We compared two methods to generate polymorphic markers to investigate the population genetics of Trypanosoma evansi; random amplified polymorphic DNA (RAPD) and amplified restriction fragment length polymorphism (AFLP) analyses. AFLP accessed many more polymorphisms than RAPD. Cluster analysis of the AFLP data showed that 12 T.evansi isolates were very similar (‘type A’) whereas 2 isolates differed substantially (‘type B’). Type

  7. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum  ×  Gossypium barbadense

    Microsoft Academic Search

    Dao-Hua He; Zhong-Xu Lin; Xian-Long Zhang; Yi-Chun Nie; Xiao-Ping Guo; Yan-Xin Zhang; Wu Li

    2007-01-01

    A high-density molecular marker linkage map of cotton based entirely on polymerase chain reaction-based markers is useful\\u000a for a marker-assisted breeding program. Four kinds of markers—simple sequence repeats (SSRs), sequence-related amplified polymorphism\\u000a (SRAP), random amplified polymorphic DNA (RAPD), and retrotransposon-microsatellite amplified polymorphism (REMAP)—were used\\u000a to assay an F2 population from a cross between “Handan208” (Gossypium hirsutum) and “Pima90” (Gossypium barbadense).

  8. Phylogeny of African cichlid fishes as revealed by molecular markers.

    PubMed

    Mayer, W E; Tichy, H; Klein, J

    1998-06-01

    The species flocks of cichlid fish in the three great East African Lakes, Victoria, Malawi, and Tanganyika, have arisen in each lake by explosive adaptive radiation. Various questions concerning their phylogeny have not yet been answered. In particular, the identity of the ancestral founder species and the monophyletic origin of the haplochromine cichlids from the East African lakes have not been established conclusively. In the present study, we used the anonymous nuclear DNA marker DXTU1 as a step towards answering these questions. A 280 bp-fragment of the DXTU1 locus was amplified by the polymerase chain reaction from East African lacustrine species, the East African riverine cichlid species Haplochromis bloyeti, H. burtoni and H. sparsidens, and other African cichlids. Sequencing revealed several indels and substitutions that were used as cladistically informative markers to support a phylogenetic tree constructed by the neighbor-joining method. The topology, although not supported by high bootstrap values, corresponds well to the geographical distribution and previous classification of the cichlids. Markers could be defined that: (i) differentiate East African from West African cichlids; (ii) distinguish the riverine and Lake Victoria/Malawi haplochromines from Lake Tanganyika cichlids; and (iii) indicate the existence of a monophyletic Lake Victoria cichlid superflock which includes haplochromines from satellite lakes and East African rivers. In order to resolve further the relationship of East African riverine and lacustrine species, mtDNA cytochrome b and control region segments were sequenced. The mtDNA-based trees support the notion of the monophyly of the Lake Victoria superflock but are ambiguous with respect to the phylogenetic position of the Lake Malawi flock. PMID:9675872

  9. Molecular and cellular markers of toxicity in the Japanese Medaka @

    SciTech Connect

    Shugart, L.R.; McCarthy, J.F.; D'Surney, S.J.; Greeley, M.S. Jr.; Hull, C.G.

    1990-01-01

    The Japanese Medaka (Oryzias latipes) has been recommended for use as a model organism to detect carcinogenic, teratogenic, cytotoxic, and genotoxic compounds in aquatic systems. Because a long latent period often occurs between initial contact with deleterious chemicals and subsequent expression of the pathology, we are investigating early biologically-relevant responses that can be used as genotoxicity markers of exposure and effect. This project focuses on the development of genotoxic bioassays and experimental protocols for exposing Japanese Medaka to genotoxic compounds. 21 refs., 8 figs, 2 tabs.

  10. Construction of a genetic linkage map in tetraploid species using molecular markers.

    PubMed Central

    Luo, Z W; Hackett, C A; Bradshaw, J E; McNicol, J W; Milbourne, D

    2001-01-01

    This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato. PMID:11238421

  11. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

    PubMed Central

    Buyyarapu, Ramesh; Kantety, Ramesh V.; Yu, John Z.; Saha, Sukumar; Sharma, Govind C.

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum??EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  12. Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species.

    PubMed

    Buyyarapu, Ramesh; Kantety, Ramesh V; Yu, John Z; Saha, Sukumar; Sharma, Govind C

    2011-01-01

    New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum??EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps. PMID:22315588

  13. Mapping the evolutionary twilight zone: molecular markers, populations and

    E-print Network

    Solé-Cava, Antonio M.

    Departamento de Biologia Geral, ICB, Universidade Federal de Goia´s. Cx.P. 131, 74.001-970 Goia^nia, 2 Laborato, Caixa Postal 15053, 91501-970 Porto Alegre, RS, 5 Departamento de Biologia Geral, ICB, UFMG, Belo Horizonte, MG, 6 Laborato´rio de Biodiversidade Molecular, Departamento de Gene´tica, Instituto de Biologia

  14. Molecular markers for breast cancer diagnosis, prognosis and targeted therapy.

    PubMed

    Lang, Julie E; Wecsler, Julie S; Press, Michael F; Tripathy, Debasish

    2015-01-01

    Precision medicine involves understanding the molecular drivers unique to an individual patient's cancer so that specific factors may be targeted with the goal of improved patient outcomes. The purpose of this article is to review standard of care and research grade (non-standard of care) biomarkers in breast cancer that may be useful for diagnosis, prognosis and targeted therapy. PMID:25091830

  15. Genetic diversity of Phytophthora sojae isolates in Heilongjiang Province in China assessed by RAPD and EST-SSR

    NASA Astrophysics Data System (ADS)

    Wu, J. J.; Xu, P. F.; Liu, L. J.; Wang, J. S.; Lin, W. G.; Zhang, S. Z.; Wei, L.

    Random-amplified polymorphic DNA (RAPD) and EST-SSR markers were used to estimate the genetic relationship among thirty-nine P.sojae isolates from three locations in Heilongjiang Province, and nine isolates from Ohio in America were made as reference strains. 10 of 50 RAPD primers and 5 of 33 EST-SSR were polymorphic across 48 P.sojae isolates. Similarity values among P.sojae isolates were from 49% to 82% based on the RAPD data. The similarities based on EST-SSR markers ranged from 47% to 85%. The genetic diversity revealed by EST-SSR marker analysis was higher than that obtained from RAPD. The similarity matrices for the SSR data and the RAPD data were moderately correlated (r = 0.47). Genetic similarity coefficients were also relatively lower, which demonstrated complicated genetic background within each location. The high similarity values range revealed the ability of RAPD/EST-SSR markers to distinguish even among morphological similar phytophthora.

  16. Volatility of organic molecular markers used for source apportionment analysis: measurements and implications for atmospheric lifetime.

    PubMed

    May, Andrew A; Saleh, Rawad; Hennigan, Christopher J; Donahue, Neil M; Robinson, Allen L

    2012-11-20

    Molecular markers are organic species used to define fingerprints for source apportionment of ambient fine particulate matter. Traditionally, these markers have been assumed to be stable in the atmosphere. This work investigates the gas-particle partitioning of eight organic species used as molecular markers in receptor models for biomass burning (levoglucosan), motor vehicles (5?-cholestane, n-hexacosane, n-triacontane, 1,2-benz[a]anthracene, coronene), and meat cooking (cholesterol, oleic acid). Experiments were conducted using a thermodenuder to measure the evaporation of single component particles. The data were analyzed using the integrated volume method to determine saturation concentrations and enthalpies of vaporization for each compound. The results indicate that appreciable quantities (>10%) of most of these markers exist in the gas phase under typical atmospheric conditions. Therefore, these species should be considered semivolatile. Predictions from a chemical kinetics model indicate that gas-particle partitioning has important effects on the atmospheric lifetime of these species. The atmospheric decay of semivolatile compounds proceeds much more rapidly than nonvolatile compounds because gas-phase oxidation induces evaporation of particle-phase material. Therefore, both gas-particle partitioning and chemical reactions need to be accounted for when semivolatile molecular markers are used for source apportionment studies. PMID:23013599

  17. Molecular marker based taxonomy and phylogeny of Guinea yam (Dioscorea rotundata - D. cayenensis).

    PubMed

    Ramser, J; Weising, K; Terauchi, R; Kahl, G; Lopez-Peralta, C; Terhalle, W

    1997-12-01

    Four different molecular techniques were used to assess relationships among 21 accessions of Guinea yam (Dioscorea rotundata and Dioscorea cayenensis) and 21 accessions belonging to seven putative progenitor species. Random amplified polymorphic DNA (RAPD) and microsatellite-primed PCR (MP-PCR) analysis yielded 246 informative characters that were transformed into a matrix of pairwise distances and analyzed by neighbor joining or split decomposition. Both methods gave congruent results. Well-separated groups were formed that corresponded to their species designation. Dioscorea rotundata and D. cayenensis accessions were clearly separated from each other, supporting the concept that both are distinct species. Two morphological intermediates grouped together with D. rotundata. All investigated species fell into two main clusters, one comprising D. rotundata, D. cayenensis, Dioscorea abyssinica, Dioscorea liebrechtsiana, and Dioscorea praehensilis, the other comprising Dioscorea smilacifolia, Dioscorea minutiflora, Dioscorea burkilliana, and Dioscorea togoensis. The same grouping was also obtained by comparative sequence analysis of chloroplast DNA, which supports earlier studies of nuclear rDNA variation and chloroplast restriction fragment length polymorphisms. We also analyzed the same set of Dioscorea samples with the recently developed random amplified microsatellite polymorphism (RAMPO) technique. A series of diagnostic RAMPO bands was identified that clearly distinguished between D. rotundata and D. cayenensis. Some of these bands could also be traced back to the putative progenitors of both species. The evolutionary origin of Guinea yam is discussed in light of the present results. PMID:18464876

  18. Molecular markers of anthropogenic activity in sediments of the Havel and Spree Rivers (Germany).

    PubMed

    Ricking, M; Schwarzbauer, J; Franke, S

    2003-06-01

    Detailed gas chromatographic/mass spectrometric analyses have been applied to sediment samples of the Havel and Spree River, tributaries to the Elbe River, in order to identify specific molecular markers of anthropogenic activities. Despite a wide variety of lipophilic organic compounds from diffuse anthropogenic contamination, a local emission of an industrial point source was reflected by specific markers including halogenated compounds and nitrogen containing substances (4-ethylnitrobenzene, formyl piperidine, acetyl piperidine). In addition to well-known anthropogenic markers various new molecular tracers were detected and are discussed, namely plasticizers (alkylsulfonic acid aryl esters, tributyl and tricresyl phosphates), synthetic fragrances (galaxolide, tonalide, 4-oxoisophorone), additives of personal care products (4-methoxycinnamic acid 2-ethylhexyl ester, benzyl benzoate, dibenzyl ether, benzophenone), occurring due to sewage treatment plant input. PMID:12753838

  19. Evaluation of “sequence-tagged-site” PCR products as molecular markers in wheat

    Microsoft Academic Search

    L. E. Talbert; N. K. Blake; P. W. Chee; T. K. Blake; G. M. Magyar

    1994-01-01

    The polymerase chain reaction (PCR) is an attractive technique for many genome mapping and characterization projects. One PCR approach which has been evaluated involves the use of randomly amplified polymorphic DNA (RAPD). An alternative to RAPDs is the sequence-tagged-site (STS) approach, whereby PCR primers are designed from mapped low-copy-number sequences. In this study, we sequenced and designed primers from 22

  20. Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

    PubMed Central

    Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

    2014-01-01

    Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

  1. A new set of molecular markers for the genotyping of Babesia bovis isolates

    Microsoft Academic Search

    S. E. Wilkowsky; R. Moretta; J. Mosqueda; G. Gil; I. Echaide; V. Lía; A. Falcón; M. Florin Christensen; M. Farber

    2009-01-01

    Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the

  2. Proceedings of the second international symposium on molecular markers in horticulture Acta Horticulturae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The second International Symposium on Molecular Markers in Horticulture was held at the CH2M Hill Alumni Center at Oregon State University (OSU), Corvallis (Oregon, US), from July 29 to August 1st, 2009. This symposium was convened by a scientist at the National Clonal Germplasm Repository (NCGR) of...

  3. Land ahead: using genome scans to identify molecular markers of adaptive relevance

    Microsoft Academic Search

    Rolf Holderegger; Doris Herrmann; Bénédicte Poncet; Felix Gugerli; Wilfried Thuiller; Pierre Taberlet; Ludovic Gielly; Delphine Rioux; Sabine Brodbeck; Serge Aubert; Stéphanie Manel

    2008-01-01

    Adaptation is back on the research schedules of evolutionists and ecologists. This renewed interest is driven by global change, to which species, in particular arctic and alpine ones, either react by migration or adaptation. In this overview, we give a brief introduction to the use of genome scans along with environmental data to identify molecular markers of adaptive relevance. This

  4. Progression of Hair Cell Ejection and Molecular Markers of Apoptosis in the

    E-print Network

    Progression of Hair Cell Ejection and Molecular Markers of Apoptosis in the Avian Cochlea following-dependent apoptotic death in inner ear sensory hair cells. The timing of apoptotic signaling in sensory hair cells- nocytochemical techniques to document the following responses in affected hair cells: T-cell restricted

  5. Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass

    Microsoft Academic Search

    A. P. Ramakrishnan; SUSAN E. MEYER; JENNIFER WATERS; MIKEL R. STEVENS; CRAIG E. COLEMAN; DANIEL J. FAIRBANKS

    2004-01-01

    Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass ( Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and

  6. Correlation between molecular markers and adaptively significant genetic variation in Bromus tectorum (Poaceae), an inbreedingannual grass.

    PubMed

    Ramakrishnan, Alisa P; Meyer, Susan E; Waters, Jennifer; Stevens, Mikel R; Coleman, Craig E; Fairbanks, Daniel J

    2004-06-01

    Single sequence repeat (SSR) and amplified fragment length polymorphic (AFLP) molecular marker genotypes in cheatgrass (Bromus tectorum) were compared to published data on phenotypic variation in seed dormancy, vernalization requirement, and resistance to the pathogen Ustilago bullata. Several features of cheatgrass facilitated this study: it is a recent invader in the western United States, has considerable phenotypic polymorphism, and is an obligate self-pollinator. Forty self-pollinating lines from four populations common to the three phenotypic data sets were analyzed for molecular genetic variation using seven SSR loci and 31 AFLP loci. We examined correlations between distance matrices using the Mantel test for each pair of studies. The two molecular data sets were significantly correlated (r = 0.636). The AFLP markers often distinguished among several lines with identical SSR genotypes. The AFLP data were also significantly correlated with the phenotypic data (r values from 0.4640 to 0.5658), but the SSR data were much more highly correlated (r values from 0.677 to 0.844). The difference between molecular marker systems was especially notable when an outlier population from Potosi Pass, Nevada, was excluded from the analysis. These results suggest that SSR markers may be good surrogates for phenotypic traits in population genetic studies of strongly inbreeding species such as cheatgrass. PMID:21653434

  7. An Educational Software for Simulating the Sample Size of Molecular Marker Experiments

    ERIC Educational Resources Information Center

    Helms, T. C.; Doetkott, C.

    2007-01-01

    We developed educational software to show graduate students how to plan molecular marker experiments. These computer simulations give the students feedback on the precision of their experiments. The objective of the software was to show students using a hands-on approach how: (1) environmental variation influences the range of the estimates of the…

  8. Molecular genetic variation in cultivated peanut cultivars and breeding lines revealed by highly informative SSR markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Groundnut or peanut (Arachis hypogaea L.) is an economically important crop worldwide as a source of protein and cooking oil, particularly in developing countries. Because of its narrow genetic background and shortage of polymorphic genetic markers, molecular characterization of cultivated peanuts e...

  9. Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP

    Microsoft Academic Search

    Shu-Jing Sun; Wei Gao; Shu-Qian Lin; Jian Zhu; Bao-Gui Xie; Zhi-Bin Lin

    2006-01-01

    Genetic marker technology designed to detect naturally occurring polymorphisms at the DNA level had become an invaluable and revolutionizing tool for both applied and basic studies of fungi. To eliminate the confusion on the taxonomy of Ganoderma strains, in this study, a collection of 31 accessions representative of morphotypes and some unclassified types was used for analyzing molecular diversity using

  10. Molecular markers in the Portuguese Bísaro pig: screening for breed specific microsatellites

    Microsoft Academic Search

    M. C. Guerreiro-Pereira; J. Matos; A. M. Ramos; F. Simões; A. Clemente; T. Rangel-Figueiredo

    SUMMARY - A large number of autochthonous breeds of domestic animals are endangered. The Portuguese indigenous pig breed Bísaro is reduced to a small number of animals mostly restricted to the Trás-os-Montes province. In order to prevent its extinction and preserve genetic variability fast measures are needed. Among molecular markers to assess the genetic variability microsatellites are the most widely

  11. DEVELOPMENT OF MOLECULAR MARKERS OF RESPONSE TO ASSESS THE SENSITIVITY OF CHILDREN TO ENVIRONMENTAL CHEMICALS

    EPA Science Inventory

    Development of Molecular Markers of Response to Assess the Sensitivity of Children to Environmental Chemicals J.Allen, C. Blackman, M. Blaze, D. Delker, D. DeMarini, C. Doerr, R. Grindstaff, S. Hester, C. Jones, A. Kligerman, G. Knapp, M. Kohan, C. Nelson, R. Owen, J. P...

  12. MOLECULAR DNA MARKERS UTILIZED TO DISCERN ALFALFA FALL DORMANCY CHECK CULTIVARS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alfalfa cultivars are difficult to distinguish based upon morphological traits. Only a few morphological traits have been used to describe alfalfa. Molecular markers especially simple sequence repeats (SSR) have not been utilized in alfalfa to characterize alfalfa cultivars. This study was conduct...

  13. Molecular markers highlight variation within and among Kentucky bluegrass varieties and accessions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Assessing relationships among germplasm and cultivars of Kentucky bluegrass (Poa pratensis L.) is limited to field evaluations or a small set of molecular markers. To improve the efficiency of characterizing Kentucky bluegrass cultivars and germplasm, this study was designed to develop a larger set...

  14. Supplementary Material Paper: Organic molecular markers and signature from wood combustion

    E-print Network

    Meskhidze, Nicholas

    1 Supplementary Material Paper: Organic molecular markers and signature from wood combustion of the particle, and the vaporisation of the non- refractory compounds. One of the most problematic parts mass versus the PM2.5 mass concentration from the TEOM subtracted by the BC mass colored by the nitrate

  15. Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In...

  16. Development of Public Immortal Mapping Populations, Molecular Markers, and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Past research efforts on genetic mapping in Brassica oleracea and Brassica rapa have been disconnected, utilizing separate mapping populations and different sets of molecular markers. Here we present public immortal mapping populations, molecular markers and linkage maps for rapid cycling B. rapa a...

  17. Development of molecular genetic markers from a cDNA subtraction library of Frosty Pod inoculated cacao

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have been employing a candidate gene approach to identify molecular markers associated with disease resistance in Theobroma cacao. Candidate genes can be turned into molecular markers using single strand conformation polymorphism (SSCP) analysis. As a novel approach to identifying genes associa...

  18. PCR markers distinguish Plantago major subspecies

    Microsoft Academic Search

    K. Wolff; M. Morgan-Richards

    1998-01-01

    Plantago major plants from several Scottish and Dutch locations were surveyed for their genetic variation using PCR markers, namely RAPD\\u000a analysis, anchored inter-SSR PCR, and chloroplast PCR followed by RFLP analysis. The RAPD and inter-SSR markers showed a differentiation\\u000a between the two subspecies of P. major. These results are discussed in relation to earlier results using allozyme electrophoresis, DNA fingerprinting,

  19. Biomedical wellness monitoring system based upon molecular markers

    NASA Astrophysics Data System (ADS)

    Ingram, Whitney

    2012-06-01

    We wish to assist caretakers with a sensor monitoring systems for tracking the physiological changes of homealone patients. One goal is seeking biomarkers and modern imaging sensors like stochastic optical reconstruction microscopy (STORM), which has achieved visible imaging at the nano-scale range. Imaging techniques like STORM can be combined with a fluorescent functional marker in a system to capture the early transformation signs from wellness to illness. By exploiting both microscopic knowledge of genetic pre-disposition and the macroscopic influence of epigenetic factors we hope to target these changes remotely. We adopt dual spectral infrared imaging for blind source separation (BSS) to detect angiogenesis changes and use laser speckle imaging for hypertension blood flow monitoring. Our design hypothesis for the monitoring system is guided by the user-friendly, veteran-preferred "4-Non" principles (noninvasive, non-contact, non-tethered, non-stop-to-measure) and by the NIH's "4Ps" initiatives (predictive, personalized, preemptive, and participatory). We augment the potential storage system with the recent know-how of video Compressive Sampling (CSp) from surveillance cameras. In CSp only major changes are saved, which reduces the manpower cost of caretakers and medical analysts. This CSp algorithm is based on smart associative memory (AM) matrix storage: change features and detailed scenes are written by the outer-product and read by the inner product without the usual Harsh index for image searching. From this approach, we attempt to design an effective household monitoring approach to save healthcare costs and maintain the quality of life of seniors.

  20. Genetic diversity in cultivated carioca common beans based on molecular marker analysis

    PubMed Central

    Küpper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sérgio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

    2011-01-01

    A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm. PMID:21637550

  1. Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background.

    PubMed

    Gong, Wenping; Li, Guangrong; Zhou, Jianping; Li, Genying; Liu, Cheng; Huang, Chengyan; Zhao, Zhendong; Yang, Zujun

    2014-09-01

    Aegilops uniaristata has many agronomically useful traits that can be used for wheat breeding. So far, a Triticum turgidum - Ae. uniaristata amphiploid and one set of Chinese Spring (CS) - Ae. uniaristata addition lines have been produced. To guide Ae. uniaristata chromatin transformation from these lines into cultivated wheat through chromosome engineering, reliable cytogenetic and molecular markers specific for Ae. uniaristata chromosomes need to be developed. Standard C-banding shows that C-bands mainly exist in the centromeric regions of Ae. uniaristata but rarely at the distal ends. Fluorescence in situ hybridization (FISH) using (GAA)8 as a probe showed that the hybridization signal of chromosomes 1N-7N are different, thus (GAA)8 can be used to identify all Ae. uniaristata chromosomes in wheat background simultaneously. Moreover, a total of 42 molecular markers specific for Ae. uniaristata chromosomes were developed by screening expressed sequence tag - sequence tagged site (EST-STS), expressed sequence tag - simple sequence repeat (EST-SSR), and PCR-based landmark unique gene (PLUG) primers. The markers were subsequently localized using the CS - Ae. uniaristata addition lines and different wheat cultivars as controls. The cytogenetic and molecular markers developed herein will be helpful for screening and identifying wheat - Ae. uniaristata progeny. PMID:25486537

  2. Anthropogenic Molecular Markers: Tools to Identify the Sources and Transport Pathways of Pollutants

    USGS Publications Warehouse

    Takada, H.; Satoh, F.; Bothner, Michael H.; Tripp, B.W.; Johnson, C.G.; Farrington, J.W.

    1997-01-01

    The activities of modern civilization have released to the oceans a wide variety of both mobilized natural compounds and synthetic compounds not found prior to modern times. Many of these compounds provide a means of identifying sources of inputs and pathways of movement of chemicals through oceanic ecosystems and serve as molecular markers of human activities. A coastal ocean (Tokyo Bay) and a deep ocean (Deep Water Dump Site 106 in the Western North Atlantic Ocean) example are presented. In the deep ocean study, the correlation between potential sewage marker, i.e. linear alkylbenzenes (LABs), and polychlorinated biphenyls (PCBs) concentrations indicates a contribution of sewage sludge PCBs to the dump site sediments.

  3. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

    PubMed

    Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

    2012-09-01

    Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. PMID:22564443

  4. DNA marker technologies and their applications in aquaculture genetics

    Microsoft Academic Search

    Z. J. Liu; J. F. Cordes

    2004-01-01

    The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

  5. Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers.

    PubMed

    Pavan-Kumar, A; Gireesh-Babu, P; Babu, P P Suresh; Jaiswar, A K; Hari Krishna, V; Prasasd, K Pani; Chaudhari, Aparna; Raje, S G; Chakraborty, S K; Krishna, Gopal; Lakra, W S

    2014-01-01

    The elasmobranchs (sharks, rays and skates) being the extant survivors of one of the earliest offshoots of the vertebrate evolutionary tree are good model organisms to study the primitive vertebrate conditions. They play a significant role in maintaining the ecological balance and have high economic value. Due to over-exploitation and illegal fishing worldwide, the elasmobranch stocks are being decimated at an alarming rate. Appropriate management measures are necessary for restoring depleted elasmobranch stocks. One approach for restoring stocks is implementation of conservation measures and these measures can be formulated effectively by knowing the evolutionary relationship among the elasmobranchs. In this study, a total of 30 species were chosen for molecular phylogeny studies using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA gene and nuclear Internal Transcribed Spacer 2. Among different genes, the combined dataset of COI and 12S rRNA resulted in a well resolved tree topology with significant bootstrap/posterior probabilities values. The results supported the reciprocal monophyly of sharks and batoids. Within Galeomorphii, Heterodontiformes (bullhead sharks) formed as a sister group to Lamniformes (mackerel sharks): Orectolobiformes (carpet sharks) and to Carcharhiniformes (ground sharks). Within batoids, the Myliobatiformes formed a monophyly group while Pristiformes (sawfishes) and Rhinobatiformes (guitar fishes) formed a sister group to all other batoids. PMID:24293104

  6. Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

    PubMed

    Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

    2015-03-15

    Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. PMID:25618519

  7. Discovery of Molecular Markers to Discriminate Corneal Endothelial Cells in the Human Body

    PubMed Central

    Yoshihara, Masahito; Ohmiya, Hiroko; Hara, Susumu; Kawasaki, Satoshi; Hayashizaki, Yoshihide; Itoh, Masayoshi; Kawaji, Hideya; Tsujikawa, Motokazu; Nishida, Kohji

    2015-01-01

    The corneal endothelium is a monolayer of hexagonal corneal endothelial cells (CECs) on the inner surface of the cornea. CECs are critical in maintaining corneal transparency through their barrier and pump functions. CECs in vivo have a limited capacity in proliferation, and loss of a significant number of CECs results in corneal edema called bullous keratopathy which can lead to severe visual loss. Corneal transplantation is the most effective method to treat corneal endothelial dysfunction, where it suffers from donor shortage. Therefore, regeneration of CECs from other cell types attracts increasing interests, and specific markers of CECs are crucial to identify actual CECs. However, the currently used markers are far from satisfactory because of their non-specific expression in other cell types. Here, we explored molecular markers to discriminate CECs from other cell types in the human body by integrating the published RNA-seq data of CECs and the FANTOM5 atlas representing diverse range of cell types based on expression patterns. We identified five genes, CLRN1, MRGPRX3, HTR1D, GRIP1 and ZP4 as novel markers of CECs, and the specificities of these genes were successfully confirmed by independent experiments at both the RNA and protein levels. Notably none of them have been documented in the context of CEC function. These markers could be useful for the purification of actual CECs, and also available for the evaluation of the products derived from other cell types. Our results demonstrate an effective approach to identify molecular markers for CECs and open the door for the regeneration of CECs in vitro. PMID:25807145

  8. Tumor Endothelial Marker Imaging in Melanomas Using Dual-Tracer Fluorescence Molecular Imaging

    PubMed Central

    Tichauer, Kenneth M.; Deharvengt, Sophie J.; Samkoe, Kimberley S.; Gunn, Jason R.; Bosenberg, Marcus W.; Turk, Mary-Jo; Hasan, Tayyaba; Stan, Radu V.; Pogue, Brian W.

    2014-01-01

    Purpose Cancer-specific endothelial markers available for intravascular binding are promising targets for new molecular therapies. In this study, a molecular imaging approach of quantifying endothelial marker concentrations (EMCI) is developed and tested in highly light-absorbing melanomas. The approach involves injection of targeted imaging tracer in conjunction with an untargeted tracer, which is used to account for nonspecific uptake and tissue optical property effects on measured targeted tracer concentrations. Procedures Theoretical simulations and a mouse melanoma model experiment were used to test out the EMCI approach. The tracers used in the melanoma experiments were fluorescently labeled anti-Plvap/PV1 antibody (plasmalemma vesicle associated protein Plvap/PV1 is a transmembrane protein marker exposed on the luminal surface of endothelial cells in tumor vasculature) and a fluorescent isotype control antibody, the uptakes of which were measured on a planar fluorescence imaging system. Results The EMCI model was found to be robust to experimental noise under reversible and irreversible binding conditions and was capable of predicting expected overexpression of PV1 in melanomas compared to healthy skin despite a 5-time higher measured fluorescence in healthy skin compared to melanoma: attributable to substantial light attenuation from melanin in the tumors. Conclusions This study demonstrates the potential of EMCI to quantify endothelial marker concentrations in vivo, an accomplishment that is currently unavailable through any other methods, either in vivo or ex vivo. PMID:24217944

  9. Transferability of molecular markers from major legumes to Lathyrus spp. for their application in mapping and diversity studies.

    PubMed

    Almeida, Nuno Felipe; Trindade Leitão, Susana; Caminero, Constantino; Torres, Ana Maria; Rubiales, Diego; Vaz Patto, Maria Carlota

    2014-01-01

    Lathyrus cicera L. (chickling pea) and L. sativus L. (grass pea) have great potential among grain legumes due to their adaptability to inauspicious environments, high protein content and resistance to serious diseases. Nevertheless, due to its past underused, further activities are required to exploit this potential and to capitalise on the advances in molecular biology that enable improved Lathyrus spp. breeding programmes. In this study we evaluated the transferability of molecular markers developed for closely related legume species to Lathyrus spp. (Medicago truncatula, pea, lentil, faba bean and lupin) and tested the application of those new molecular tools on Lathyrus mapping and diversity studies. Genomic and expressed sequence tag microsatellite, intron-targeted amplified polymorphic, resistance gene analogue and defence-related gene markers were tested. In total 128 (27.7 %) and 132 (28.6 %) molecular markers were successfully cross-amplified, respectively in L. cicera and L. sativus. In total, the efficiency of transferability from genomic microsatellites was 5 %, and from gene-based markers, 55 %. For L. cicera, three cleaved amplified polymorphic sequence markers and one derived cleaved amplified polymorphic sequence marker based on the cross-amplified markers were also developed. Nine of those molecular markers were suitable for mapping in a L. cicera recombinant inbred line population. From the 17 molecular markers tested for diversity analysis, six (35 %) in L. cicera and seven (41 %) in L. sativus were polymorphic and discriminate well all the L. sativus accessions. Additionally, L. cicera accessions were clearly distinguished from L. sativus accessions. This work revealed a high number of transferable molecular markers to be used in current genomic studies in Lathyrus spp. Although their usefulness was higher on diversity studies, they represent the first steps for future comparative mapping involving these species. PMID:24203465

  10. Development of molecular markers and linkage maps for the Carthamus species C. tinctorius and C. oxyacanthus.

    PubMed

    Mayerhofer, Reinhold; Archibald, Catherine; Bowles, Victoria; Good, Allen G

    2010-04-01

    A set of SSR and RFLP markers for safflower (Carthamus tinctorius) and jeweled distaff thistle (C. oxyacanthus) was generated from cDNA and genomic libraries and by mining public and proprietary sequence databases. In total, 1412 PCR-based markers and 75 RFLP markers were screened and polymorphic loci were mapped in an intraspecific F2 population of C. tinctorius and an interspecific BC1 population of C. tinctorius x C. oxyacanthus. The two populations shared one common parent and the resulting linkage maps could be compared for synteny. The level of polymorphism was low in both populations and only 8.2% and 13.7% of the analyzed markers could be mapped in the intraspecific and interspecific maps, respectively. The two maps showed significant colinearity of markers in several regions and an apparent translocation or inversion event on one linkage group. Noticeable segregation distortion was found on one linkage group of the C. tinctorius map and dense clustering of loci occurred on several linkage groups of the C. oxyacanthus map. The two maps represent the first major linkage analysis of Carthamus species. The molecular tools will be useful for a variety of genetic and genomic applications in safflower and its related species and have been used in our laboratory to map a flower color gene in C. tinctorius. PMID:20616858

  11. Multilocus microsatellite signature and identification of specific molecular markers for Leishmania aethiopica

    PubMed Central

    2013-01-01

    Background Leishmaniasis is a clinically and epidemiologically diverse zoonotic disease caused by obligatory, intracellular protozoan parasites of the genus Leishmania. Cutaneous leishmaniasis is the most widely distributed form of the disease characterized by skin lesions. Leishmania aethiopica is considered the predominant etiological agent in Ethiopia. The current study was aimed at developing multilocus microsatellite markers for L. aethiopica isolated from human cutaneous leishmaniasis patients in Ethiopia. Results L. aethiopica parasites for the study were obtained from Ethiopia and laboratory analysis was conducted at The Ohio State University. DNA was extracted from cultured parasites and an internal transcribed spacer located at the ribosomal region of L. aethiopica genomic DNA was PCR amplified for species identification. Microsatellite markers were identified using multilocus microsatellite typing. We generated an enriched genomic library, and using Primer3 software, designed PCR primers to amplify sequences flanking the detected microsatellites. Subsequent screening of the amplified markers for length variations was performed by gel electrophoresis. Using a variety of molecular methods, 22 different microsatellite markers were identified and tested for typing L. aethiopica strains using a number of clinical isolates. Of the 22 markers tested, 5 were polymorphic and showed distinctive multilocus genotypes, classifying them into four clusters. One marker was found to be specific for L. aethiopica, discriminating it from other species of Leishmania. Conclusion Multilocus microsatellite typing using the markers developed in this study could be useful for epidemiological and population genetic studies of strains of L. aethiopica in order to investigate the structure and dynamics of the corresponding natural foci. It could also help to answer specific clinical questions, such as the occurrence of local and diffuse lesions, strain correlates of parasite persistence after subclinical infection and lesion comparisons from patients suffering from L. aethiopica infections. PMID:23734874

  12. Forensic soil DNA analysis using high-throughput sequencing: a comparison of four molecular markers.

    PubMed

    Young, Jennifer M; Weyrich, Laura S; Cooper, Alan

    2014-11-01

    Soil analysis, such as mineralogy, geophysics, texture and colour, are commonly used in forensic casework to link a suspect to a crime scene. However, DNA analysis can also be applied to characterise the vast diversity of organisms present in soils. DNA metabarcoding and high-throughput sequencing (HTS) now offer a means to improve discrimination between forensic soil samples by identifying individual taxa and exploring non-culturable microbial species. Here, we compare the small-scale reproducibility and resolution of four molecular markers targeting different taxa (bacterial 16S rRNA, eukaryotic18S rRNA, plant trnL intron and fungal internal transcribed spacer I (ITS1) rDNA) to distinguish two sample sites. We also assess the background DNA level associated with each marker and examine the effects of filtering Operational Taxonomic Units (OTUs) detected in extraction blank controls. From this study, we show that non-bacterial taxa in soil, particularly fungi, can provide the greatest resolution between the sites, whereas plant markers may be problematic for forensic discrimination. ITS and 18S markers exhibit reliable amplification, and both show high discriminatory power with low background DNA levels. The 16S rRNA marker showed comparable discriminatory power post filtering; however, presented the highest level of background DNA. The discriminatory power of all markers was increased by applying OTU filtering steps, with the greatest improvement observed by the removal of any sequences detected in extraction blanks. This study demonstrates the potential use of multiple DNA markers for forensic soil analysis using HTS, and identifies some of the standardisation and evaluation steps necessary before this technique can be applied in casework. PMID:25151602

  13. Characterization of Italian grasspea ( Lathyrus sativus L.) germplasm using agronomic traits, biochemical and molecular markers

    Microsoft Academic Search

    Lucia Lioi; Francesca Sparvoli; Gabriella Sonnante; Gaetano Laghetti; Francesco Lupo; Massimo Zaccardelli

    2011-01-01

    Genetic relationships among 13 grasspea (Lathyrus sativus L.) landraces mainly collected in Southern Italy were assessed using agronomic traits, biochemical and molecular markers.\\u000a Field trials were carried out in two locations and revealed a high influence of field locations on yield, but a low genotype × environment\\u000a interaction. Despite this, the agronomic data obtained provided useful information for the choice of the

  14. Genetic analysis of apomixis in Citrus and Poncirus by molecular markers

    Microsoft Academic Search

    R. García; M. J. Asíns; J. Forner; E. A. Carbonell

    1999-01-01

    Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis\\u000a one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in\\u000a a 50-tree progeny derived from the cross C. volkameriana?P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings

  15. Genetic analysis of adaptation differences between highland and lowland tropical maize using molecular markers

    Microsoft Academic Search

    C. Jiang; G. O. Edmeades; I. Armstead; H. R. Lafitte; M. D. Hayward; D. Hoisington

    1999-01-01

    Molecular-marker loci were used to investigate the adaptation differences between highland and lowland tropical maize. An\\u000a F2 population from the cross of two inbred lines independently derived from highland and lowland maize germplasm was developed,\\u000a and extracted F3:4 lines were phenotype in replicated field trials at four thermally diverse tropical testing sites, ranging from lowland to\\u000a extreme highland (mean growing

  16. Molecular marker assisted selection and pyramiding of two QTLs for fiber strength in upland cotton.

    PubMed

    Guo, Wang-Zhen; Zhang, Tian-Zhen; Ding, Ye-Zhang; Zhu, Yi-Chao; Shen, Xin-Lian; Zhu, Xie-Fei

    2005-12-01

    Based on two major QTLs that control high fiber strength which originated from an elite fiber germ-plasm line 7235 (Gossypium hiusutum L.), the efficiency of molecular marker-assisted selection (MAS) was investigated using two populations from pedigree selection and modified backcrossing pyramiding developed for the breeding purpose. Simian 3 (SM3), a widely planted variety in the Yangtze River Valley, and 7235 were used as parents to develop the two populations. In the two major QTLs for fiber strength from 7235, QTLfs-1 could explain more than 30% of the phenotypic variation (PV) in the (7235 x TM-1) F2 population. QTLfs-2 was at first identified in another super quality fiber line HS427-10 from (HS427-10 x TM-1) F2 population with 12.5% of PV explanation,which was further also identified in 7235 line but was non-allelic with QTLfs-1. The result of molecular marker-assisted selection for fiber strength showed that the genetic effect of the QTLfs-1 was stable under different environmental conditions, and its molecular marker-assisted selection showed significant selective efficiency among breeding populations with different genetic backgrounds. QTLfs-2 also showed high selective efficiency in advanced generation populations though its effect was a little lower than the former. When QTLfs-1 was selected simultaneously with 2 molecular markers with known genetic distance, the selection efficiency for the fiber strength was greatly increased. The pyramiding for two QTLs that control high fiber strength by MAS greatly improved the selection efficiency for cotton fiber strength. This report provides a successful example of MAS pyramiding for QTL for favorable traits in breeding programs. PMID:16459656

  17. Comparison of molecular markers to detect fresh sewage in environmental waters.

    PubMed

    Ahmed, W; Goonetilleke, A; Powell, D; Chauhan, K; Gardner, T

    2009-11-01

    Human-specific Bacteroides HF183 (HS-HF183), human-specific Enterococci faecium esp (HS-esp), human-specific adenoviruses (HS-AVs) and human-specific polyomaviruses (HS-PVs) assays were evaluated in freshwater, seawater and distilled water to detect fresh sewage. The sewage spiked water samples were also tested for the concentrations of traditional fecal indicators (i.e., Escherichia coli, enterococci and Clostridium perfringens) and enteric viruses such as enteroviruses (EVs), sapoviruses (SVs), and torquetenoviruses (TVs). The overall host-specificity of the HS-HF183 marker to differentiate between humans and other animals was 98%. However, the HS-esp, HS-AVs and HS-PVs showed 100% host-specificity. All the human-specific markers showed >97% sensitivity to detect human fecal pollution. E. coli, enterococci and, C. perfringens were detected up to dilutions of sewage 10(-5), 10(-4) and 10(-3) respectively. HS-esp, HS-AVs, HS-PVs, SVs and TVs were detected up to dilution of sewage 10(-4) whilst EVs were detected up to dilution 10(-5). The ability of the HS-HF183 marker to detect fresh sewage was 3-4 orders of magnitude higher than that of the HS-esp and viral markers. The ability to detect fresh sewage in freshwater, seawater and distilled water matrices was similar for human-specific bacterial and viral marker. Based on our data, it appears that human-specific molecular markers are sensitive measures of fresh sewage pollution, and the HS-HF183 marker appears to be the most sensitive among these markers in terms of detecting fresh sewage. However, the presence of the HS-HF183 marker in environmental waters may not necessarily indicate the presence of enteric viruses due to their high abundance in sewage compared to enteric viruses. More research is required on the persistency of these markers in environmental water samples in relation to traditional fecal indicators and enteric pathogens. PMID:19818987

  18. Variability analysis of 'Persian' acid lime tree selections using agronomic and molecular markers.

    PubMed

    Santos, M G; Passos, O S; Soares Filho, W S; Girardi, E A; Gesteira, A S; Ferreira, C F

    2013-01-01

    'Persian' acid lime (PAL) is the most important triploid commercial citrus crop planted in the world. Little is known about the genetic variability of the selections used in Brazil. Therefore, 25 genotypes originating from the PAL, and three control species, Citrus sunki, C. limon, and C. aurantiifolia, were assessed using inter-simple sequence repeat (ISSR) and inter-retrotransposon amplified polymorphism (IRAP) molecular markers and agronomic traits of the fruit. The dendrograms were designed using the mean Euclidean distance for the physicochemical attributes of the fruit (weight, length, diameter, peel color, peel thickness, number of seeds, juice yield, titratable acidity, soluble solids, and ratio) and the Jaccard distances using the data from the ISSR and IRAP molecular markers. In the physicochemical analysis, the genotypes were grouped according to species. The trait that contributed most to the diversity among accessions was the number of seeds. The 17 ISSR primers produced 69 polymorphic bands in the molecular analysis, and the seven IRAP primers generated 30 polymorphic bands. The markers detected polymorphisms within and among the PALs; two groups were formed within the PALs. PMID:24222236

  19. Analysis of molecular marker expression reveals neuronal homology in distantly related arthropods.

    PubMed

    Duman-Scheel, M; Patel, N H

    1999-06-01

    Morphological studies suggest that insects and crustaceans of the Class Malacostraca (such as crayfish) share a set of homologous neurons. However, expression of molecular markers in these neurons has not been investigated, and the homology of insect and malacostracan neuroblasts, the neural stem cells that produce these neurons, has been questioned. Furthermore, it is not known whether crustaceans of the Class Branchiopoda (such as brine shrimp) or arthropods of the Order Collembola (springtails) possess neurons that are homologous to those of other arthropods. Assaying expression of molecular markers in the developing nervous systems of various arthropods could resolve some of these issues. Here, we examine expression of Even-skipped and Engrailed, two transcription factors that serve as insect embryonic CNS markers, across a number of arthropod species. This molecular analysis allows us to verify the homology of previously identified malacostracan neurons and to identify additional homologous neurons in malacostracans, collembolans and branchiopods. Engrailed expression in the neural stem cells of a number of crustaceans was also found to be conserved. We conclude that despite their distant phylogenetic relationships and divergent mechanisms of neurogenesis, insects, malacostracans, branchiopods and collembolans share many common CNS components. PMID:10225992

  20. Biological pathways, candidate genes and molecular markers associated with quality-of-life domains: an update

    PubMed Central

    Sprangers, Mirjam A.G.; Thong, Melissa S.Y.; Bartels, Meike; Barsevick, Andrea; Ordoñana, Juan; Shi, Qiuling; Wang, Xin Shelley; Klepstad, Pål; Wierenga, Eddy A.; Singh, Jasvinder A.; Sloan, Jeff A.

    2014-01-01

    Background There is compelling evidence of a genetic foundation of patient-reported QOL. Given the rapid development of substantial scientific advances in this area of research, the current paper updates and extends reviews published in 2010. Objectives The objective is to provide an updated overview of the biological pathways, candidate genes and molecular markers involved in fatigue, pain, negative (depressed mood) and positive (well-being/happiness) emotional functioning, social functioning, and overall QOL. Methods We followed a purposeful search algorithm of existing literature to capture empirical papers investigating the relationship between biological pathways and molecular markers and the identified QOL domains. Results Multiple major pathways are involved in each QOL domain. The inflammatory pathway has the strongest evidence as a controlling mechanism underlying fatigue. Inflammation and neurotransmission are key processes involved in pain perception and the COMT gene is associated with multiple sorts of pain. The neurotransmitter and neuroplasticity theories have the strongest evidence for their relationship with depression. Oxytocin-related genes and genes involved in the serotonergic and dopaminergic pathways play a role in social functioning. Inflammatory pathways, via cytokines, also play an important role in overall QOL. Conclusions Whereas the current findings need future experiments and replication efforts, they will provide researchers supportive background information when embarking on studies relating candidate genes and/or molecular markers to QOL domains. The ultimate goal of this area of research is to enhance patients’ QOL. PMID:24604075

  1. RAPD analysis with the primer L15996 of Brazilian clinical and environmental Cryptococcus neoformans isolates.

    PubMed

    Andrade-Silva, Leonardo; Ferreira-Paim, Kennio; Mora, Delio Jose; da Silva, Paulo Roberto; Andrade, Anderson Assunção; Lages-Silva, Eliane; Pedrosa, André Luiz; Silva-Vergara, Mario León

    2012-07-01

    Different methods have been used to perform the molecular characterization of Cryptococcus neoformans. Among them, RAPD analysis is able to separate isolates of the same species and genotypes. This study aimed to evaluate clinical and environmental C. neoformans isolates from Minas Gerais, Brazil by RAPD and correlate the genetic profiles with the ones obtained by URA5-RFLP, virulence factors and antifungal susceptibility patterns. Forty-five environmental (31 from areas surrounding hospital and 14 from captive bird droppings from pet-shops) and 29 clinical C. neoformans isolates were evaluated. Antifungal susceptibility tests (Clinical and Laboratory Standards Institute), URA5-RFLP analysis and the assessment of virulence factors were performed according to their original descriptions. RAPD profiles were obtained using the L15996 primer (5'-CTCCACCATTAGCACCCAAAGC-3'). RAPD analysis generated two to 20 bands for all studied isolates. The isolates presented similarities ranging from 10.8 to 100.0%. Considering a minimum identity score of 50%, four clusters were formed. Cluster I contained 10 pet-shops bird dropping isolates, cluster II contained 22 clinical isolates most of them recovered from cerebrospinal fluid, cluster III contained 14 isolates from hospital surroundings and cluster IV contained 12 environmental isolates most from hospital surroundings. Fourteen isolates were not grouped. The RAPD profiles were clustered according to their source and URA5-RFLP pattern. No correlation between virulence factors or antifungal susceptibility profile with the obtained RAPD profiles was observed. PMID:22249603

  2. Development of sequence characterized DNA markers linked to a dominant verticillium wilt resistance gene in tomato.

    PubMed

    Kawchuk, L M; Hachey, J; Lynch, D R

    1998-02-01

    Sequences were determined for codominant RAPD markers closely linked to the Ve locus, a dominant verticillium wilt resistance gene in tomato. Analysis of the sequences linked to Ve and ve revealed a perfectly homologous sequence with a central polymorphic region comprising 79 nucleotide substitutions, insertions, and deletions. Codominant and allele-specific SCARs were developed using conserved and polymorphic sequences linked to the Ve locus. High resolution linkage analysis using F2 progeny segregating for resistance and marker-assisted selection indicated that linkage between the genetic markers and the Ve locus is less than 0.67 +/- 0.49 cM. Sequences were useful in determining the molecular structure of a polymorphic genomic region closely linked to the Ve locus and in developing genetic markers that facilitated marker-assisted selection of the resistant, susceptible, heterozygous, and homozygous genotypes. PMID:9549062

  3. Molecular markers linked to the blast resistance gene pi-z in oryza sativa for use in marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have identified DNA markers that cosegregate with the blast resistance gene Pi-z using microsatellite markers found in public databases and degenerate primer pairs based on the P-loop, nucleotide binding site and kinase domain motifs of previously cloned resistance genes. These markers are ploym...

  4. An improved micropropagation of Arnebia hispidissima (Lehm.) DC. and assessment of genetic fidelity of micropropagated plants using DNA-based molecular markers.

    PubMed

    Phulwaria, Mahendra; Rai, Manoj K; Shekhawat, N S

    2013-07-01

    An efficient and improved in vitro propagation method has been developed for Arnebia hispidissima, a medicinally and pharmaceutically important plant species of arid and semiarid regions. Nodal segments (3-4 cm) with two to three nodes obtained from field grown plants were used as explants for shoot proliferation. Murashige and Skoog's (MS) medium supplemented with cytokinins with or without indole-3-acetic acid (IAA) or naphthalene acetic acid was used for shoot multiplication. Out of different PGRs combinations, MS medium containing 0.5 mg l(-1) 6-benzylaminopurine and 0.1 mg l(-1) IAA was optimal for shoot multiplication. On this medium, explants produced the highest number of shoots (47.50?±?0.38). About 90 % of shoots rooted ex vitro on sterile soilrite under the greenhouse condition when the base (2-4 mm) of shoots was treated with 300 mg l(-1) of indole-3-butyric acid for 5 min. The plantlets were hardened successfully in the greenhouse with 85-90 % survival rate. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers were employed to assess the genetic stability of in vitro-regenerated plants of A. hispidissima. Out of 40 (25 RAPD and 15 ISSR) primers screened, 15 RAPD and 7 ISSR primers produced a total number of 111 (77 RAPD and 34 ISSR) reproducible amplicons. The amplified products were monomorphic across all the micropropagated plants and were similar to the mother plant. To the best of our knowledge, it is the first report on the assessment of the genetic fidelity in micropropagated plants of A. hispidissima. PMID:23645417

  5. Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.)

    Microsoft Academic Search

    K. Yu; S. J. Park; V. Poysa; P. Gepts

    2000-01-01

    Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymor- phism with BAT93

  6. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce

    Microsoft Academic Search

    I. Paran; R. W. Michelmore

    1993-01-01

    Sequence characterized amplified regions (SCARs) were derived from eight random amplified polymorphic DNA (RAPD) markers linked to disease resistance genes in lettuce. SCARs are PCR-based markers that represent single, genetically defined loci that are identified by PCR amplification of genomic DNA with pairs of specific oligonucleotide primers; they may contain high-copy, dispersed genomic sequences within the amplified region. Amplified RAPD

  7. Molecular markers, genetic maps, and QTLs for peanut molecular breeding in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Integration of plant breeding, genetics and genomics promises to foster genetic enhancement leading to increased productivity, oil quality and resistance/tolerance to biotic and abiotic stresses. Recent advances have resulted in the development of genomic resources such as SSR markers, and genetic m...

  8. TRACKING FECAL CONTAMINATION WITH BACTEROIDALES MOLECULAR MARKERS: AN ANALYSIS OF THE DYNAMICS OF FECAL CONTAMINATION IN THE TILLAMOOK BASIN, OREGON

    EPA Science Inventory

    Although amplification of source-specific molecular markers from Bacteroidales fecal bacteria can identify several different kinds of fecal contamination in water, it remains unclear how this technique relates to fecal indicator measurements in natural waters. The objectives of t...

  9. Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)

    PubMed Central

    Douaihy, Bouchra; Sobierajska, Karolina; Jasi?ska, Anna Katarzyna; Boraty?ska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boraty?ski, Adam

    2012-01-01

    Background and aims Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. Methodology We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, 11 of which have previously been investigated using molecular markers. Three hundred and ninety-four individuals of J. excelsa were examined using nine biometric features characterizing cones, seeds and shoots, and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra- and inter-population morphological variability. Principal results The level of intra-population variability observed did not show any geographical trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation of the sampled populations into three main clusters. These results confirmed, in part, the geographical differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographical pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover, a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Conclusions Morphological variation together with genetic and biogeographic studies make an effective tool for detecting relict plant populations and also populations subjected to more intensive selection. PMID:22822421

  10. Trend of different molecular markers in the last decades for studying human migrations.

    PubMed

    Kundu, Sharbadeb; Ghosh, Sankar Kumar

    2015-02-10

    Anatomically modern humans are known to have widely migrated throughout history. Different scientific evidences suggest that the entire human population descended from just several thousand African migrants. About 85,000 years ago, the first wave of human migration was out of Africa, that followed the coasts through the Middle East, into Southern Asia via Sri Lanka, and in due course around Indonesia and into Australia. Another wave of migration between 40,000 and 12,000 years ago brought humans northward into Europe. However, the frozen north limited human expansion in Europe, and created a land bridge, "Bering land bridge", connecting Asia with North America about 25,000 years ago. Although fossil data give the most direct information about our past, it has certain anomalies. So, molecular archeologists are now using different molecular markers to trace the "most recent common ancestor" and also the migration pattern of modern humans. In this study, we have studied the trend of molecular markers and also the methodologies implemented in the last decades (2003-2014). From our observation, we can say that D-loop region of mtDNA and Y chromosome based markers are predominant. Nevertheless, mtDNA, especially the D-loop region, has some unique features, which makes it a more effective marker for tracing prehistoric footprints of modern human populations. Although, natural selection should also be taken into account in studying mtDNA based human migration. As per technology is concerned, Sanger sequencing is the major technique that is being used in almost all studies. But, the emergence of different cost-effective-and-easy-to-handle NGS platforms has increased its popularity over Sanger sequencing in studying human migration. PMID:25510397

  11. Predictive Gene Signatures: Molecular Markers Distinguishing Colon Adenomatous Polyp and Carcinoma

    PubMed Central

    Drew, Janice E.; Farquharson, Andrew J.; Mayer, Claus Dieter; Vase, Hollie F.; Coates, Philip J.; Steele, Robert J.; Carey, Francis A.

    2014-01-01

    Cancers exhibit abnormal molecular signatures associated with disease initiation and progression. Molecular signatures could improve cancer screening, detection, drug development and selection of appropriate drug therapies for individual patients. Typically only very small amounts of tissue are available from patients for analysis and biopsy samples exhibit broad heterogeneity that cannot be captured using a single marker. This report details application of an in-house custom designed GenomeLab System multiplex gene expression assay, the hCellMarkerPlex, to assess predictive gene signatures of normal, adenomatous polyp and carcinoma colon tissue using archived tissue bank material. The hCellMarkerPlex incorporates twenty-one gene markers: epithelial (EZR, KRT18, NOX1, SLC9A2), proliferation (PCNA, CCND1, MS4A12), differentiation (B4GANLT2, CDX1, CDX2), apoptotic (CASP3, NOX1, NTN1), fibroblast (FSP1, COL1A1), structural (ACTG2, CNN1, DES), gene transcription (HDAC1), stem cell (LGR5), endothelial (VWF) and mucin production (MUC2). Gene signatures distinguished normal, adenomatous polyp and carcinoma. Individual gene targets significantly contributing to molecular tissue types, classifier genes, were further characterised using real-time PCR, in-situ hybridisation and immunohistochemistry revealing aberrant epithelial expression of MS4A12, LGR5 CDX2, NOX1 and SLC9A2 prior to development of carcinoma. Identified gene signatures identify aberrant epithelial expression of genes prior to cancer development using in-house custom designed gene expression multiplex assays. This approach may be used to assist in objective classification of disease initiation, staging, progression and therapeutic responses using biopsy material. PMID:25423035

  12. RAPD analysis of herbicide-resistant Brasilian rice lines produced via mutagenesis.

    PubMed

    Sandhu, S S; Bastos, Cândido R; Azini, Luiz Ernesto; Tulmann Neto, Augusto; Colombo, Carlos

    2002-01-01

    Over the last two decades, mutational techniques have become one of the most important tools available to progressive rice- breeding programs. In a mutation-breeding program initiated in 1999 at the Instituto Agronômico of Campinas, SP, Brazil, a rice line, IAC103, was selected for mutational studies with gamma radiation and ethyl methyl sulfonate mutagenesis, with the aim of developing a herbicide-resistant crop. After mutagenesis, surviving plants were exposed to glufosinate to check for herbicide resistance, which was examined up to the second generation. A detailed RAPD analysis was made of the resistant plants. Eighty Operon technology primers were tested and 10 were selected for a detailed study of RAPD markers that could tag herbicide resistance genes. Resistant and susceptible lines produced variation in the RAPD patterns and certain bands were found only in certain lines. These results suggest genetic ligation that will be confirmed through a genetic segregation study. PMID:14963826

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

    PubMed

    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. PMID:21874670

  14. Molecular markers reveal little genetic differentiation among Aconitum noveboracense and A. columbianum (Ranunculaceae) populations.

    PubMed

    Cole, C T; Kuchenreuther, M A

    2001-02-01

    Aconitum noveboracense, a rare, herbaceous perennial, is restricted to recently unglaciated areas in Iowa, Wisconsin, Ohio, and New York, and federally classified as a threatened species. These populations may be disjuncts of the common congener, A. columbianum Nutt., which occurs in the mountains of the western United States. Morphological characters do not reliably separate these taxa. The identity of Black Hills populations, located between the ranges of the rare and common species, is also uncertain. We characterized genetic variation within and among the Aconitum populations in question using isozymes and randomly amplified polymorphic DNA (RAPDs). Isozymes indicate a high degree of similarity among all populations and a high level of genetic diversity in Black Hills populations. Of 97 scorable RAPD loci, 89.7% are polymorphic and clearly resolve most populations. Like isozymes, RAPDs indicate high levels of genetic diversity in the Black Hills and very strong similarity of these populations to A. columbianum from the Bighorn Mountains. Aconitum noveboracense populations show >80% similarity to A. columbianum populations. A population of A. uncinatum from Ohio shows the greatest differentiation from other populations. Therefore, both isozyme and RAPD data concur with the recent treatment of A. noveboracense and A. columbianum as a single species. PMID:11222254

  15. Identification of novel molecular markers through transcriptomic analysis in human fetal and adult corneal endothelial cells

    PubMed Central

    Chen, Yinyin; Huang, Kevin; Nakatsu, Martin N.; Xue, Zhigang; Deng, Sophie X.; Fan, Guoping

    2013-01-01

    The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. To better characterize CECs in different developmental stages, we profiled mRNA transcriptomes in human fetal and adult corneal endothelium with the goal to identify novel molecular markers in these cells. By comparing CECs with 12 other tissue types, we identified 245 and 284 signature genes that are highly expressed in fetal and adult CECs, respectively. Functionally, these genes are enriched in pathways characteristic of CECs, including inorganic anion transmembrane transporter, extracellular matrix structural constituent and cyclin-dependent protein kinase inhibitor activity. Importantly, several of these genes are disease target genes in hereditary corneal dystrophies, consistent with their functional significance in CEC physiology. We also identified stage-specific markers associated with CEC development, such as specific members in the transforming growth factor beta and Wnt signaling pathways only expressed in fetal, but not in adult CECs. Lastly, by the immunohistochemistry of ocular tissues, we demonstrated the unique protein localization for Wnt5a, S100A4, S100A6 and IER3, the four novel markers for fetal and adult CECs. The identification of a new panel of stage-specific markers for CECs would be very useful for characterizing CECs derived from stem cells or ex vivo expansion for cell replacement therapy. GEO accession number: GSE41616. PMID:23257286

  16. Prospective molecular markers for the identification of illegally traded angelsharks (Squatina) and dolphin (Sotalia guianensis).

    PubMed

    Falcão, L H O; Furtado-Neto, M A A; Maggioni, R; Faria, V V

    2014-01-01

    Endangered angelsharks and a protected dolphin species are illegally traded in Brazil. In this study, we determined prospective molecular markers for detecting these species in the trade of angelshark carcasses and 'dolphin' eyeball amulets. We compiled publicly available as well as new and unpublished cytochrome b (cyt b) DNA sequences for species involved in these trades. These sequences were digested in silico using restriction enzymes. We then described prospective polymerase chain reaction (PCR)-restriction fragment length polymorphism markers for distinguishing between protected species and the species whose trade was legally allowed in these two trade groups. The prospective marker for identifying angelshark carcasses consists of cyt b PCR and digestion by BstXI, BsgI, BspMI, BsrDI, and HaeII restriction enzymes. The prospective marker for identifying eyeball amulets consists of cyt b PCR and digestion by ApoI, BtsI, HindII, BsaAI, BplI, and SspI restriction enzymes. This is the first study to deposit in GenBank cyt b sequences for the angelshark species Squatina argentina, Squatina guggenheim, and Squatina occulta. Moreover, the S. argentina haplotype is the first DNA sequence for this species deposited in GenBank. PMID:25501182

  17. Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis.

    PubMed Central

    Burt, A; Carter, D A; Koenig, G L; White, T J; Taylor, J W

    1996-01-01

    Coccidioides immitis, cause of a recent epidemic of "Valley fever" in California, is typical of many eukaryotic microbes in that mating and meiosis have yet to be reported, but it is not clear whether sex is truly absent or just cryptic. To find out, we have undertaken a population genetic study using PCR amplification, screening for single-strand conformation polymorphisms, and direct DNA sequencing to find molecular markers with nucleotide-level resolution. Both population genetic and phylogenetic analyses indicate that C. immitis is almost completely recombining. To our knowledge, this study is the first to find molecular evidence for recombination in a fungus for which no sexual stage has yet been described. These results motivate a directed search for mating and meiosis and illustrate the utility of single-strand conformation polymorphism and sequencing with arbitrary primer pairs in molecular population genetics. Images Fig. 1 PMID:8570632

  18. Identification and authentication of Rosa species through development of species-specific SCAR marker(s).

    PubMed

    Bashir, K M I; Awan, F S; Khan, I A; Khan, A I; Usman, M

    2014-01-01

    Roses (Rosa indica) belong to one of the most crucial groups of plants in the floriculture industry. Rosa species have special fragrances of interest to the perfume and pharmaceutical industries. The genetic diversity of plants based on morphological characteristics is difficult to measure under natural conditions due to the influence of environmental factors, which is why a reliable fingerprinting method was developed to overcome this problem. The development of molecular markers will enable the identification of Rosa species. In the present study, randomly amplified polymorphic DNA (RAPD) analysis was done on four Rosa species, Rosa gruss-an-teplitz (Surkha), Rosa bourboniana, Rosa centifolia, and Rosa damascena. A polymorphic RAPD fragment of 391 bp was detected in R. bourboniana, which was cloned, purified, sequenced, and used to design a pair of species-specific sequence-characterized amplified region (SCAR) primers (forward and reverse). These SCAR primers were used to amplify the specific regions of the rose genome. These PCR amplifications with specific primers are less sensitive to reaction conditions, and due to their high reproducibility, these species-specific SCAR primers can be used for marker-assisted selection and identification of Rosa species. PMID:24938705

  19. Using Molecular Markers to Characterize Productivity in Chinese Hamster Ovary Cell Lines

    PubMed Central

    Edros, Raihana Z.; McDonnell, Susan; Al-Rubeai, Mohamed

    2013-01-01

    Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction. PMID:24146795

  20. Determination of specific molecular markers of biomass burning in lake sediments

    NASA Astrophysics Data System (ADS)

    Kirchgeorg, Torben; Schüpbach, Simon; Kehrwald, Natalie; McWethy, David; Barbante, Carlo

    2014-05-01

    Fire influences regional to global atmospheric chemistry and climate. Molecular markers of biomass burning archived in lake sediments are becoming increasingly important in paleoenvironmental reconstruction and may help determine interactions between climate and fire activity. One group of these molecular markers is the monosaccharide anhydrides levoglucosan, mannosan and galactosan. Several aerosol studies and recent ice core research use these compounds as a marker for biomass burning, but studies from lake sediment cores are rare. Previous sediment methods used gas chromatography - mass spectrometry and required derivatization of samples. Here, we present a high performance anion exchange chromatography-mass spectrometry method to allow separation and detection of the three monosaccharide anhydrides in lake sediments with implications for reconstructing past biomass burning events. We validated the method by quantifying levoglucosan, mannosan and galactosan in selected sediment core samples from Lake Kirkpatrick, New Zealand. The freeze-dried, milled and homogenized sediment samples were first extracted with methanol by pressurized solvent extraction, pre-concentrated and finally separated and analyzed by high performance anion exchange chromatography-mass spectrometry. We compared these isomers with macroscopic charcoal concentrations, as charcoal is a well-known proxy for biomass burning. In addition, we applied the method to a sediment core from Lake Petén Itzá, Guatemala to prove the suitability of these markers for reconstructing biomass burning history over the entire Holocene. In the Lake Kirkpatrick samples, levoglucosan, mannosan and galactosan concentrations significantly correlate with macroscopic charcoal concentrations. The three isomers are present in samples without any macroscopic charcoal, and may reflect the presence of microscopic charcoal. Levoglucosan/mannosan and levoglucosan/(mannosan+galactosan) ratios differ between samples with high macroscopic charcoal concentrations and samples without any charcoal. These ratios may help determine not only when fires occurred, but also past changes in the primary burned vegetation. However, the possibility that these isomer ratios help differentiate changes in burned vegetation needs further evaluation. The preliminary results of the Lake Petén Itzá samples demonstrate the occurrence of all three molecular markers in the entire core, covering the past approximately 10,000 years. The three monosaccharide anhydrides levoglucosan, mannosan and galactosan may be an additional tool for reconstructing past fire events over decadal to millennial time scales in sediment cores.

  1. Regulation of ubiquitin proteasome pathway molecular markers in response to endurance and resistance exercise and training.

    PubMed

    Stefanetti, Renae J; Lamon, Séverine; Wallace, Marita; Vendelbo, Mikkel H; Russell, Aaron P; Vissing, Kristian

    2014-08-01

    Knowledge on the effects of divergent exercise on ostensibly protein degradation pathways may be valuable for counteracting muscle wasting and for understanding muscle remodelling. This study examined mRNA and/or protein levels of molecular markers of the ubiquitin proteasome pathway (UPP), including FBXO32 (atrogin-1), MURF-1, FBXO40, FOXO1 and FOXO3. Protein substrates of atrogin-1-including EIF3F, MYOG and MYOD1-and of MURF-1-including PKM and MHC-were also measured. Subjects completed 10 weeks of endurance training (ET) or resistance training (RT) followed by a single-bout of endurance exercise (EE) or resistance exercise (RE). Following training, atrogin-1, FBXO40, FOXO1 and FOXO3 mRNA increased independently of exercise mode, whereas MURF-1 mRNA and FOXO3 protein increased following ET only. No change in other target proteins occurred post-training. In the trained state, single-bout EE, but not RE, increased atrogin-1, MURF-1, FBXO40, FOXO1, FOXO3 mRNA and FOXO3 protein. In contrast to EE, FBXO40 mRNA and protein decreased following single-bout RE. MURF-1 and FOXO1 protein levels as well as the protein substrates of atrogin-1 and MURF-1 were unchanged following training and single-bout exercise. This study demonstrates that the intracellular signals elicited by ET and RT result in an upregulation of UPP molecular markers, with a greater increase following ET. However, in the trained state, the expression levels of UPP molecular markers are increased following single-bout EE, but are less responsive to single-bout RE. This suggests that adaptations following endurance exercise training are more reliant on protein UPP degradation processes than adaptations following resistance exercise training. PMID:25104573

  2. Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone.

    PubMed

    Hardig, T M; Brunsfeld, S J; Fritz, R S; Morgan, M; Orians, C M

    2000-01-01

    Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization-related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows (Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD-based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter- and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered. PMID:10652072

  3. Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

    Microsoft Academic Search

    Nicolas Steenkeste; Sandra Incardona; Sophy Chy; Linda Duval; Marie-Thérèse Ekala; Pharath Lim; Sean Hewitt; Tho Sochantha; Doung Socheat; Christophe Rogier; Odile Mercereau-Puijalon; Thierry Fandeur; Frédéric Ariey

    2009-01-01

    BACKGROUND: Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach

  4. Transcriptome analysis of Capsicum annuum varieties Mandarin and Blackcluster: assembly, annotation and molecular marker discovery.

    PubMed

    Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Cho, Young-Il; Lee, Hye-Eun; Kim, Do-Sun; Woo, Jong-Gyu; Cho, Myeong-Cheoul

    2014-01-10

    Next generation sequencing technologies have proven to be a rapid and cost-effective means to assemble and characterize gene content and identify molecular markers in various organisms. Pepper (Capsicum annuum L., Solanaceae) is a major staple vegetable crop, which is economically important and has worldwide distribution. High-throughput transcriptome profiling of two pepper cultivars, Mandarin and Blackcluster, using 454 GS-FLX pyrosequencing yielded 279,221 and 316,357 sequenced reads with a total 120.44 and 142.54Mb of sequence data (average read length of 431 and 450 nucleotides). These reads resulted from 17,525 and 16,341 'isogroups' and were assembled into 19,388 and 18,057 isotigs, and 22,217 and 13,153 singletons for both the cultivars, respectively. Assembled sequences were annotated functionally based on homology to genes in multiple public databases. Detailed sequence variant analysis identified a total of 9701 and 12,741 potential SNPs which eventually resulted in 1025 and 1059 genotype specific SNPs, for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies. PMID:24125952

  5. Delimitation of Russula Subgenus Amoenula in Korea Using Three Molecular Markers

    PubMed Central

    Park, Myung Soo; Fong, Jonathan J.; Lee, Hyun; Oh, Seung-Yoon; Jung, Paul Eunil; Min, Young Ju; Seok, Soon Ja

    2013-01-01

    Distinguishing individual Russula species has been difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. Due to highly similar macroscopic features, such as the presence of a red-cap, species identification within the Russula subgenus Amoenula is particularly difficult. Three species of the subgenus Amoneula have been reported in Korea. We used a combination of morphology and three molecular markers, the internal transcribed spacer (ITS), 28S nuclear ribosomal large subunit (LSU), and RNA polymerase II gene (RPB2), for identification and study of the genetic diversity of Russula subgenus Amoenula in Korea. We identified only two species in Korea (R. mariae and R. violeipes); these two species were indistinguishable according to morphology and LSU, but were found to be reciprocally monophyletic species using ITS and RPB2. The markers, ITS, LSU, and RPB2, have been tested in the past for use as DNA barcoding markers, and findings of our study suggest that ITS and RPB2 had the best performance for the Russula subgenus Amoneula. PMID:24493939

  6. A linkage map of sweet cherry based on RAPD analysis of a microspore-derived callus culture population.

    PubMed

    Stockinger, E J; Mulinix, C A; Long, C M; Brettin, T S; Iezzoni, A F

    1996-01-01

    A partial linkage map was constructed for the sweet cherry (Prunus avium L.) cultivar Emperor Francis from a population of 56 microspore-derived callus culture individuals. The callus cultures were genotyped for two allozymes and 90 random amplified polymorphic DNA (RAPD) markers using 79 random decanucleotide DNA primers and the polymerase chain reaction (PCR). Eighty-nine markers mapped to 10 linkage groups totaling 503.3 cM. DNA blot and hybridization analysis using five cloned RAPDs as probes demonstrated that one of the decanucleotide primers amplified a region of the Emperor Francis genome containing a unique sequence, whereas the other four decanucleotide primers amplified regions of the Emperor Francis genome containing repeated sequences. The five cloned RAPD probes also recognized putative homologous regions in ground cherry, P.fruticosa Pall., and sour cherry, P. cerasus L., a naturally occurring allopolyploid between P.fruticosa and P.avium. PMID:8683097

  7. Analysis of Genetic Diversity of Chukar Partridge ( Alectoris chukar ) Populations in Khorasan-e-Razavi Province of Iran by RAPD-PCR

    Microsoft Academic Search

    Hassan Abbasi; Mojtaba Tahmoorespour; Mohammad R. Nassiri; Shahrokh Ghovvati

    2010-01-01

    RAPD markers were used to investigate population genetic parameters of an endangered partridge, Alectoris chukar, in four areas of Iran, as a part of a genetic conservation program. The aim of this study was to analyze the genetic similarity\\u000a among these populations. Blood samples from 75 birds were used for DNA extraction and RAPD-PCR analysis of 67 loci, with 28

  8. Development of Specific Sequence-Characterized Amplified Region Markers for Detecting Histoplasma capsulatum in Clinical and Environmental Samples

    PubMed Central

    Frías De León, María Guadalupe; Arenas López, Gabina; Taylor, Maria Lucia; Acosta Altamirano, Gustavo

    2012-01-01

    Sequence-characterized amplified region (SCAR) markers, generated by randomly amplified polymorphic DNA (RAPD)-PCR, were developed to detect Histoplasma capsulatum selectively in clinical and environmental samples. A 1,200-bp RAPD-PCR-specific band produced with the 1281-1283 primers was cloned, sequenced, and used to design two SCAR markers, 1281-1283220 and 1281-1283230. The specificity of these markers was confirmed by Southern hybridization. To evaluate the relevance of the SCAR markers for the diagnosis of histoplasmosis, another molecular marker (M antigen probe) was used for comparison. To validate 1281-1283220 and 1281-1283230 as new tools for the identification of H. capsulatum, the specificity and sensitivity of these markers were assessed for the detection of the pathogen in 36 clinical (17 humans, as well as 9 experimentally and 10 naturally infected nonhuman mammals) and 20 environmental (10 contaminated soil and 10 guano) samples. Although the two SCAR markers and the M antigen probe identified H. capsulatum isolates from different geographic origins in America, the 1281-1283220 SCAR marker was the most specific and detected the pathogen in all samples tested. In contrast, the 1281-1283230 SCAR marker and the M antigen probe also amplified DNA from Aspergillus niger and Cryptococcus neoformans, respectively. Both SCAR markers detected as little as 0.001 ng of H. capsulatum DNA, while the M antigen probe detected 0.5 ng of fungal DNA. The SCAR markers revealed the fungal presence better than the M antigen probe in contaminated soil and guano samples. Based on our results, the 1281-1283220 marker can be used to detect and identify H. capsulatum in samples from different sources. PMID:22189121

  9. Linkage relationships among molecular markers and storage root traits of carrot (Daucus carota L. ssp. sativus)

    Microsoft Academic Search

    B. S. Vivek; P. W. Simon

    1999-01-01

    A 109-point linkage map consisting of three phenotypic loci (P\\u000a 1,?Y\\u000a 2, and Rs), six restriction fragment length polymorphisms (RFLPs), two random amplified polymorphic DNAs (RAPDs), 96 amplified fragment\\u000a length polymorphisms (AFLPs), and two selective amplification of microsatellite polymorphic loci (SAMPL) was constructed for\\u000a carrot (Daucus carota L. ssp. sativus; 2n=2x=18). The incidence of polymorphism was 36% for RFLP probes,

  10. Utilization of molecular markers for the conservation of blood cockles, Anadara granosa (Arcidae).

    PubMed

    Chee, S Y; Azizah, M N S; Devakie, M N

    2011-01-01

    We examined genetic variation in blood cockles in an effort to obtain information useful for the sustainability, management, and the stability of this species as a major commodity in the fisheries sector. Ten populations of cockles were sampled from the north to the south of the west coast of peninsular Malaysia. The cockles were collected in collaboration with the Fisheries Research Institute, Penang. The population genetic analysis of the cockles were studied via RAPD-PCR and mtDNA sequencing. Three hundred individuals were analyzed with RAPD-PCR experiments. High gene diversity over all loci was observed (Shannon index = 0.549 ± 0.056 and Nei's gene diversity = 0.4852 ± 0.0430 among 35 loci). The second method, mtDNA sequencing, was employed to complement the information obtained from RAPD-PCR. The gene selected for mtDNA sequencing was cytochrome c oxidase I (COI). One hundred and fifty individuals were sequenced, yielding a partial gene of 585 bp. Statistical analysis showed homogeneity in general but did reveal some degree of variability between the populations in Johor and the rest of the populations. The Mantel test showed a positive but nonsignificant correlation between geographic and genetic distances (r = 0.2710, P = 0.622), as in the RAPD analysis. We propose that the homogeneity between distant populations is caused by two factors: 1) the translocation of the spats; 2) larvae are carried by current movement from the north of the peninsula to the south. The different genetic composition found in Johor could be due to pollution, mutagenic substances or physical factors such as the depth of the water column. This population genetic study is the first for this species in peninsular Malaysia. The data from this study have important implications for fishery management, conservation of blood cockles and translocation policies for aquaculture and stock enhancement programs. PMID:21732289

  11. Fasciola hepatica: identification of molecular markers for resistant and susceptible Pseudosuccinea columella snail hosts

    Microsoft Academic Search

    Alfredo Gutiérrez; Jean-Pierre Pointier; Jorge Fraga; Edouard Jobet; Sylvain Modat; R. T Pérez; Mary Yong; J Sanchez; Eric S Loker; André Théron

    2003-01-01

    Protein electrophoresis, RAPD-PCR and nuclear rDNA ITS sequencing were performed to search for genetic differences between Pseudosuccinea columella snails susceptible and resistant to Fasciola hepatica infection. Of the 21 enzymatic loci analyzed in both populations, none of them exhibited neither within- or between-group variation. Such an absence of enzyme polymorphism support the hypothesis of selfing as the “prevalent” mating system

  12. Expression of Neuroendocrine Markers in Different Molecular Subtypes of Breast Carcinoma

    PubMed Central

    Wachter, David L.; Hartmann, Arndt; Beckmann, Matthias W.; Fasching, Peter A.; Hein, Alexander; Bayer, Christian M.; Agaimy, Abbas

    2014-01-01

    Background. Carcinomas of the breast with neuroendocrine features are incorporated in the World Health Organization classification since 2003 and include well-differentiated neuroendocrine tumors, poorly differentiated neuroendocrine carcinomas/small cell carcinomas, and invasive breast carcinomas with neuroendocrine differentiation. Neuroendocrine differentiation is known to be more common in certain low-grade histologic special types and has been shown to mainly cluster to the molecular (intrinsic) luminal A subtype. Methods. We analyzed the frequency of neuroendocrine differentiation in different molecular subtypes of breast carcinomas of no histologic special type using immunohistochemical stains with specific neuroendocrine markers (chromogranin A and synaptophysin). Results. We found neuroendocrine differentiation in 20% of luminal B-like carcinomas using current WHO criteria (at least 50% of tumor cells positive for synaptophysin or chromogranin A). In contrast, no neuroendocrine differentiation was seen in luminal A-like, HER2 amplified and triple-negative carcinomas. Breast carcinomas with neuroendocrine differentiation presented with advanced stage disease and showed aggressive behavior. Conclusions. We conclude that neuroendocrine differentiation is more common than assumed in poorly differentiated luminal B-like carcinomas. Use of specific neuroendocrine markers is thus encouraged in this subtype to enhance detection of neuroendocrine differentiation and hence characterize the biological and therapeutic relevance of this finding in future studies. PMID:24701575

  13. Identification of Leaf Rust Resistance Genes in Selected Egyptian Wheat Cultivars by Molecular Markers

    PubMed Central

    Imbaby, I. A.; Mahmoud, M. A.; Hassan, M. E. M.; Abd-El-Aziz, A. R. M.

    2014-01-01

    Leaf rust, caused by Puccinia triticina Eriks., is a common and widespread disease of wheat (Triticum aestivum L.) in Egypt. Host resistance is the most economical, effective, and ecologically sustainable method of controlling the disease. Molecular markers help to determine leaf rust resistance genes (Lr genes). The objective of this study was to identify Lr genes in fifteen wheat cultivars from Egypt. Ten genes, Lr13, Lr19, Lr24, Lr26, Lr34, Lr35 Lr36, Lr37, Lr39, and Lr46, were detected in fifteen wheat cultivars using various molecular markers. The most frequently occurring genes in fifteen Egyptian wheat cultivars were Lr13, Lr24, Lr34, and Lr36 identified in all the cultivars used, followed by Lr26 and Lr35 (93%), Lr39 (66%), Lr37 (53%), and Lr46 (26.6%) of the cultivars, and finally Lr19 was present in 33.3% of cultivars. It is concluded that there was a good variation in Lr genes carried by wheat cultivars commercially grown in Egypt. Therefore, strategies for deploying resistance genes to prolong effective disease resistance are suggested to control wheat leaf rust disease. PMID:24511291

  14. Bladder Carcinoma Data with Clinical Risk Factors and Molecular Markers: A Cluster Analysis

    PubMed Central

    Redondo-Gonzalez, Enrique; de Castro, Leandro Nunes; Moreno-Sierra, Jesús; Maestro de las Casas, María Luisa; Vera-Gonzalez, Vicente; Ferrari, Daniel Gomes; Corchado, Juan Manuel

    2015-01-01

    Bladder cancer occurs in the epithelial lining of the urinary bladder and is amongst the most common types of cancer in humans, killing thousands of people a year. This paper is based on the hypothesis that the use of clinical and histopathological data together with information about the concentration of various molecular markers in patients is useful for the prediction of outcomes and the design of treatments of nonmuscle invasive bladder carcinoma (NMIBC). A population of 45 patients with a new diagnosis of NMIBC was selected. Patients with benign prostatic hyperplasia (BPH), muscle invasive bladder carcinoma (MIBC), carcinoma in situ (CIS), and NMIBC recurrent tumors were not included due to their different clinical behavior. Clinical history was obtained by means of anamnesis and physical examination, and preoperative imaging and urine cytology were carried out for all patients. Then, patients underwent conventional transurethral resection (TURBT) and some proteomic analyses quantified the biomarkers (p53, neu, and EGFR). A postoperative follow-up was performed to detect relapse and progression. Clusterings were performed to find groups with clinical, molecular markers, histopathological prognostic factors, and statistics about recurrence, progression, and overall survival of patients with NMIBC. Four groups were found according to tumor sizes, risk of relapse or progression, and biological behavior. Outlier patients were also detected and categorized according to their clinical characters and biological behavior. PMID:25866762

  15. Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers?

    PubMed Central

    Turner, Barbara; Munzinger, Jérôme; Duangjai, Sutee; Temsch, Eva M.; Stockenhuber, Reinhold; Barfuss, Michael H.J.; Chase, Mark W.; Samuel, Rosabelle

    2013-01-01

    To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK–matK and trnS–trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9 million years ago. The oldest species are around 7 million years old and the youngest ones probably much less than 1 million years. PMID:23850609

  16. Noninvasive Detection and Imaging of Molecular Markers in Live Cardiomyocytes Derived from Human Embryonic Stem Cells

    PubMed Central

    Pascut, Flavius C.; Goh, Huey T.; Welch, Nathan; Buttery, Lee D.; Denning, Chris; Notingher, Ioan

    2011-01-01

    Raman microspectroscopy (RMS) was used to detect and image molecular markers specific to cardiomyocytes (CMs) derived from human embryonic stem cells (hESCs). This technique is noninvasive and thus can be used to discriminate individual live CMs within highly heterogeneous cell populations. Principal component analysis (PCA) of the Raman spectra was used to build a classification model for identification of individual CMs. Retrospective immunostaining imaging was used as the gold standard for phenotypic identification of each cell. We were able to discriminate CMs from other phenotypes with >97% specificity and >96% sensitivity, as calculated with the use of cross-validation algorithms (target 100% specificity). A comparison between Raman spectral images corresponding to selected Raman bands identified by the PCA model and immunostaining of the same cells allowed assignment of the Raman spectral markers. We conclude that glycogen is responsible for the discrimination of CMs, whereas myofibril proteins have a lesser contribution. This study demonstrates the potential of RMS for allowing the noninvasive phenotypic identification of hESC progeny. With further development, such label-free optical techniques may enable the separation of high-purity cell populations with mature phenotypes, and provide repeated measurements to monitor time-dependent molecular changes in live hESCs during differentiation in vitro. PMID:21190678

  17. Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori.

    PubMed

    Pradeep, Appukuttannair R; Jingade, Anuradha H; Urs, Raje S

    2007-01-01

    Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.8(1050bp) was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.5(1950bp) and 825.9(710bp) showed significant association with floss content and TLD. These markers were segregated in F(2) generation and Chi-square test confirmed (chi(2) = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 +/- 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly (P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight. PMID:19662204

  18. Transcriptome survey of Patagonian southern beech Nothofagus nervosa (= N. Alpina): assembly, annotation and molecular marker discovery

    PubMed Central

    2012-01-01

    Background Nothofagus nervosa is one of the most emblematic native tree species of Patagonian temperate forests. Here, the shotgun RNA-sequencing (RNA-Seq) of the transcriptome of N. nervosa, including de novo assembly, functional annotation, and in silico discovery of potential molecular markers to support population and associations genetic studies, are described. Results Pyrosequencing of a young leaf cDNA library generated a total of 111,814 high quality reads, with an average length of 447 bp. De novo assembly using Newbler resulted into 3,005 tentative isotigs (including alternative transcripts). The non-assembled sequences (singletons) were clustered with CD-HIT-454 to identify natural and artificial duplicates from pyrosequencing reads, leading to 21,881 unique singletons. 15,497 out of 24,886 non-redundant sequences or unigenes, were successfully annotated against a plant protein database. A substantial number of simple sequence repeat markers (SSRs) were discovered in the assembled and annotated sequences. More than 40% of the SSR sequences were inside ORF sequences. To confirm the validity of these predicted markers, a subset of 73 SSRs selected through functional annotation evidences were successfully amplified from six seedlings DNA samples, being 14 polymorphic. Conclusions This paper is the first report that shows a highly precise representation of the mRNAs diversity present in young leaves of a native South American tree, N. nervosa, as well as its in silico deduced putative functionality. The reported Nothofagus transcriptome sequences represent a unique resource for genetic studies and provide a tool to discover genes of interest and genetic markers that will greatly aid questions involving evolution, ecology, and conservation using genetic and genomic approaches in the genus. PMID:22747958

  19. At3g08030 transcript: a molecular marker of seed ageing

    PubMed Central

    Garza-Caligaris, Luz Elena; Avendaño-Vázquez, Aida Odette; Alvarado-López, Sandra; Zúñiga-Sánchez, Esther; Orozco-Segovia, Alma; Pérez-Ruíz, Rigoberto V.; Gamboa-deBuen, Alicia

    2012-01-01

    Background and Aims Prolonged storage generally reduces seed viability and vigour, although the rate of deterioration varies among species and environmental conditions. Here, we suggest a possible ageing molecular marker: At3g08030 mRNA. At3g08030 is a member of the DUF642 highly conserved family of cell-wall-associated proteins that is specific for spermatophytes. Methods At3g08030 expression was performed by RT-PCR and qRT-PCR analysis in seed samples differing in their rate of germination and final germination following a matrix priming and/or controlled deterioration (rapid ageing) treatment. Key Results The At3g08030 gene transcript was present during the entire Arabidopsis thaliana plant life cycle and in seeds, during maturation, the ripening period and after germination. Matrix priming treatment increased the rate of germination of control seeds and seeds aged by controlled deterioration. Priming treatments also increased At3g08030 expression. To determine whether the orthologues of this gene are also age markers in other plant species, At3g08030 was cloned in two wild species, Ceiba aesculifolia and Wigandia urens. As in A. thaliana, the At3g08030 transcript was not present in aged seeds of the tested species but was present in recently shed seeds. A reduction in germination performance of the aged seeds under salt stress was determined by germination assays. Conclusions At3g08030 mRNA detection in a dry seed lot has potential for use as a molecular marker for germination performance in a variety of plant species. PMID:22975286

  20. Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

    PubMed Central

    Steenkeste, Nicolas; Incardona, Sandra; Chy, Sophy; Duval, Linda; Ekala, Marie-Thérèse; Lim, Pharath; Hewitt, Sean; Sochantha, Tho; Socheat, Doung; Rogier, Christophe; Mercereau-Puijalon, Odile; Fandeur, Thierry; Ariey, Frédéric

    2009-01-01

    Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the molecular methods. Dot18S and CYTB, the new methods reported herein are highly sensitive, allow parasite DNA extraction as well as genus- and species-specific diagnosis of several hundreds of samples, and are amenable to high-throughput scaling up for larger sample sizes. Such methods provide novel information on malaria prevalence and epidemiology and are suited for active malaria detection. The usefulness of such sensitive malaria diagnosis tools, especially in low endemic areas where eradication plans are now on-going, is discussed in this paper. PMID:19402894

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

    Microsoft Academic Search

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

    2009-01-01

    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

  2. ESTUDIOS DE DIVERSIDAD GENÉTICA EN CAÑA DE AZÚCAR USANDO MARCADORES RAPDs

    Microsoft Academic Search

    Karen E. Cedeño Castro; Raúl O. Castillo Torres

    Summary A molecular characterization of 249 varieties corresponding to the second half of the Germoplasm bank of CINCAE was carried out using AP-RAPDs technique. The technique combines the use of arbitrary primers with the enzimatic synthesis of multiplex copies of DNA. Twenty nine decamer primers from OPERON Technologies generated a total of 154 polymorphic bands ranging from 500-3900 bp. The

  3. A novel combined 15q11.2 duplication and a bisatellited supernumerary marker derived from chromosome 22: molecular characterization of the marker.

    PubMed

    Dutta, Usha R; Vempally, Subhash; Ranganath, Prajnya; Dalal, Ashwin

    2014-04-10

    Supernumerary marker chromosomes (SMC) are heterogeneous group of chromosomes which are reported in variable phenotypes. Approximately 70% originate from acrocentric chromosomes. Here we report a couple with recurrent miscarriages and a SMC originating from an acrocentric chromosome. The cytogenetic analysis of the husband revealed a karyotype of 47,XY+marker whereas the wife had a normal karyotype. Analysis of SMC with C-banding showed the presence of a big centromere in the center and silver staining showed prominent satellites on both sides of the marker. Apparently, microarray analysis revealed a 2.1 Mb duplication of 15q11.2 region but molecular cytogenetic analysis by fluorescence in situ hybridization (FISH) with whole chromosome paint (WCP) 15 showed that the SMC is not of chromosome 15 origin. Subsequently, FISH with centromere 22 identified the SMC to originate from chromosome 22 which was also confirmed by WCP 22. Additional dual FISH with centromere 22 and Acro-p-arm probes confirmed the centromere 22 and satellites on the SMC. Further fine mapping of the marker with Bacterial Artificial Chromosome (BAC) clones; two on chromosome 22 and four on chromosome 15 determined the marker to possess only centromere 22 sequences and that the duplication 15 exists directly on chromosome 15. In our study, we had identified and characterized a SMC showing inversion duplication 22(p11.1) combined with a direct tandem duplication of 15q11.2. The possible genotype-phenotype in relation with the two rearrangements is discussed. PMID:24508374

  4. Molecular characterization of aflatoxigenic and non-aflatoxigenic Aspergillus flavus isolates collected from corn grains.

    PubMed

    Mahmoud, M A; Ali, H M; El-Aziz, A R M; Al-Othman, M R; Al-Wadai, A S

    2014-01-01

    Twelve species from six fungal genera were found to be associated with corn (Zea mays L.) grain samples collected from three main regions of Saudi Arabia. The average frequencies of the most common genera were Aspergillus (11.4%), Fusarium (9.5%), Penicillium (5.1%), and Alternaria (5.8%). Fifteen isolates of Aspergillus flavus were screened by HPLC for their ability to produce aflatoxins (AF). The percentage of aflatoxigenic A. flavus isolates was 53%. Eight isolates produced AF, at concentrations ranging 0.7-2.9 ppb. Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers were used to genetically characterize isolates of A. flavus and to discriminate between the aflatoxigenic and non-aflatoxigenic isolates. RAPD and ISSR analysis revealed a high level of genetic diversity in the A. flavus population, which was useful for genetic characterization. The clustering in the RAPD and ISSR dendrograms obtained was unrelated to geographic origin. The RAPD and ISSR markers could not discriminate between aflatoxigenic and non-aflatoxigenic isolates, but the ISSR primers were somewhat better. PMID:25501147

  5. Cryopreservation of Dioscorea rotundata poir.: a comparative study with two cryogenic procedures and assessment of true-to-type of regenerants by RAPD analysis.

    PubMed

    Mandal, B B; Ahuja-Ghosh, Sangeeta; Srivastava, P S

    2008-01-01

    The aim of this study was to develop a cryopreservation protocol for Dioscorea rotundata with maintenance of genetic stability of regenerated plants after cryopreservation. In vitro shoot tips were cryopreserved using vitrification and encapsulation-dehydration to compare the efficacy of the two methods. Both methods produced high levels of plant regeneration from cryopreserved shoot tips. The regeneration level obtained using vitrification (71%) was not significantly different from that obtained using encapsulation-dehydration (67%). Genetic stability of plants derived from cryopreserved shoot tips was evaluated using RAPD markers. Analysis of 50 cryopreserved-derived and 20 in vitro- maintained (control) plantlets showed that 10 primers produced 77 clear, reproducible bands, with the amplification products being monomorphic for all the plantlets tested. A total of 5,390 bands obtained from this study exhibited no aberration in RAPD banding. Thus, the present study showed that both vitrification and encapsulation-dehydration methods are equally applicable to D. rotundata for cryopreservation. The in vitro plantlets derived from cryopreservation were genetically stable at the molecular level tested. PMID:18946554

  6. Five molecular markers reveal extensive morphological homoplasy and reticulate evolution in the Malva alliance (Malvaceae).

    PubMed

    Escobar García, Pedro; Schönswetter, Peter; Fuertes Aguilar, Javier; Nieto Feliner, Gonzalo; Schneeweiss, Gerald M

    2009-02-01

    The Malva alliance is a well-defined group with extensive morphological homoplasy. As a result, the relationships among the taxa as well as the evolution of morphological traits have remained elusive and the traditional classifications are highly artificial. Using five molecular markers (nuclear ITS, plastid matK plus trnK, ndhF, trnL-trnF, psbA-trnH), we arrived at a phylogenetic hypothesis of this group, the genera Alcea, Althaea and Malvalthaea being studied here for the first time with molecular data. Althaea and, in particular, Lavatera and Malva are highly polyphyletic as currently circumscribed, because their diagnostic characters, the number and degree of fusion of the epicalyx bracts, evolve in a highly homoplasious manner. In contrast, fruit morphology largely agrees with the molecularly delimited groups. Hybrid origins confirmed for the genus Malvalthaea and for Lavatera mauritanica and hybridization in the group of ruderal small-flowered mallows underline the importance of reticulate evolution in shaping the history of this group and complicating the interpretation of morphological evolution. PMID:19026753

  7. Improving the reliability of molecular sexing of birds using a W-specific marker.

    PubMed

    Shizuka, Daizaburo; Lyon, Bruce E

    2008-11-01

    Molecular techniques for identifying sex of birds utilize length differences between CHD-Z and CHD-W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W-specific primer can be used in conjunction with a pre-existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American coots (Fulica americana), a species with CHD-Z polymorphism that could not be accurately sexed using traditional methods. We developed a reverse primer GWR2 designed to sit within the intron of the W chromosome and amplify a distinctively small DNA fragment that serves as a W-specific marker. Analysis of known-sex individuals indicates that this W-specific primer provides an efficient and reliable protocol to identify the sex of F. americana. The development of such sex-specific primers will likely increase the reliability of molecular sexing methods in other birds as well. Comparisons between CHD-Z alleles of coots and common moorhens (Gallinula chloropus) revealed that CHD-Z polymorphism evolved separately in these two closely related species. We discuss the implications of repeated evolution of CHD-Z polymorphisms among birds. PMID:21586012

  8. IL-32 is a molecular marker of a host defense network in human tuberculosis

    PubMed Central

    Montoya, Dennis; Inkeles, Megan S.; Liu, Phillip T.; Realegeno, Susan; Teles, Rosane M. B.; Vaidya, Poorva; Munoz, Marcos A.; Schenk, Mirjam; Swindell, William R.; Chun, Rene; Zavala, Kathryn; Hewison, Martin; Adams, John S.; Horvath, Steve; Pellegrini, Matteo; Bloom, Barry R.; Modlin, Robert L.

    2014-01-01

    Tuberculosis is a leading cause of infectious disease–related death worldwide; however, only 10% of people infected with Mycobacterium tuberculosis develop disease. Factors that contribute to protection could prove to be promising targets for M. tuberculosis therapies. Analysis of peripheral blood gene expression profiles of active tuberculosis patients has identified correlates of risk for disease or pathogenesis. We sought to identify potential human candidate markers of host defense by studying gene expression profiles of macrophages, cells that, upon infection by M. tuberculosis, can mount an antimicrobial response. Weighted gene coexpression network analysis revealed an association between the cytokine interleukin-32 (IL-32) and the vitamin D antimicrobial pathway in a network of interferon-?– and IL-15–induced “defense response” genes. IL-32 induced the vitamin D–dependent antimicrobial peptides cathelicidin and DEFB4 and to generate antimicrobial activity in vitro, dependent on the presence of adequate 25-hydroxyvitamin D. In addition, the IL-15–induced defense response macrophage gene network was integrated with ranked pairwise comparisons of gene expression from five different clinical data sets of latent compared with active tuberculosis or healthy controls and a coexpression network derived from gene expression in patients with tuberculosis undergoing chemotherapy. Together, these analyses identified eight common genes, including IL-32, as molecular markers of latent tuberculosis and the IL-15–induced gene network. As maintaining M. tuberculosis in a latent state and preventing transition to active disease may represent a form of host resistance, these results identify IL-32 as one functional marker and potential correlate of protection against active tuberculosis. PMID:25143364

  9. gammaH2AX: a sensitive molecular marker of DNA damage and repair.

    PubMed

    Mah, L-J; El-Osta, A; Karagiannis, T C

    2010-04-01

    Phosphorylation of the Ser-139 residue of the histone variant H2AX, forming gammaH2AX, is an early cellular response to the induction of DNA double-strand breaks. Detection of this phosphorylation event has emerged as a highly specific and sensitive molecular marker for monitoring DNA damage initiation and resolution. Further, analysis of gammaH2AX foci has numerous other applications including, but not limited to, cancer and aging research. Quantitation of gammaH2AX foci has also been applied as a useful tool for the evaluation of the efficacy of various developmental drugs, particularly, radiation modifying compounds. This review focuses on the current status of gammaH2AX as a marker of DNA damage and repair in the context of ionizing radiation. Although the emphasis is on gamma-radiation-induced gammaH2AX foci, the effects of other genotoxic insults including exposure to ultraviolet rays, oxidative stress and chemical agents are also discussed. PMID:20130602

  10. Molecular marker analysis as a guide to the sources of fine organic aerosols

    SciTech Connect

    Rogge, W.F.; Cass, G.R. (California Inst. of Tech., Pasadena, CA (United States)); Hildemann, L.M. (Stanford Univ., CA (United States). Dept. of Civil Engineering); Mazurek, M.A. (Brookhaven National Lab., Upton, NY (United States)); Simoneit, B.R.T. (College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group)

    1992-07-01

    The molecular composition of fine particulate (D[sub p] [ge] 2 [mu]m) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available.

  11. Molecular marker analysis as a guide to the sources of fine organic aerosols

    SciTech Connect

    Rogge, W.F.; Cass, G.R. [California Inst. of Tech., Pasadena, CA (United States); Hildemann, L.M. [Stanford Univ., CA (United States). Dept. of Civil Engineering; Mazurek, M.A. [Brookhaven National Lab., Upton, NY (United States); Simoneit, B.R.T. [College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group

    1992-07-01

    The molecular composition of fine particulate (D{sub p} {ge} 2 {mu}m) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available.

  12. GammaH2AX as a molecular marker of aging and disease.

    PubMed

    Mah, Li-Jeen; El-Osta, Assam; Karagiannis, Tom C

    2010-02-16

    Double-strand breaks are one of the most critical DNA lesions with respect to cell-death and preservation of genomic integrity. Rapid phosphorylation of the histone variant H2AX at Ser-139 to form gammaH2AX is an early cellular response to DNA double-strand breaks. Visualization of discrete gammaH2AX foci using immunofluorescence-based assays has provided a sensitive and effective method for detecting DSBs which may be implicated in various pathologies including cancer, age-related diseases, chronic inflammatory diseases and ischemia-reperfusion injury. In this review, the potential utility and significance of gammaH2AX as a molecular marker of aging and disease is analysed. PMID:20150765

  13. Biological (molecular and cellular) markers of toxicity. Final report, September 15, 1988--September 14, 1991

    SciTech Connect

    Shugart, L.R.; D`Surney, S.J.; Gettys-Hull, C.; Greeley, M.S. Jr.

    1991-12-15

    Several molecular and cellular markers of genotoxicity were adapted for measurement in the Medaka (Oryzias latipes), and were used to describe the effects of treatment of the organism with diethylnitrosamine (DEN). NO{sup 6}-ethyl guanine adducts were detected, and a slight statistically significant, increase in DNA strand breaks was observed. These results are consistent with the hypothesis that prolonged exposure to high levels of DEN induced alkyltransferase activity which enzymatically removes any O{sup 6}-ethyl guanine adducts but does not result in strand breaks or hypomethylation of the DNA such as might be expected from excision repair of chemically modified DNA. Following a five week continuous DEN exposure with 100 percent renewal of DEN-water every third day, the F values (DNA double strandedness) increased considerably and to similar extent in fish exposed to 25, 50, and 100 ppM DEN. This has been observed also in medaka exposed to BaP.

  14. 2007 EORTC-NCI-ASCO Annual Meeting: Molecular Markers in Cancer

    PubMed Central

    Lukan, C

    2008-01-01

    The recent EORTC-NCI-ASCO Annual Meeting on ‘Molecular Markers in Cancer’ was held on 15–17 November 2007 in Brussels, Belgium. It was the largest meeting to date and marked the first year in which the American Association of Clinical Oncology (ASCO) joined in the efforts of the European Organisation for Research and Treatment of Cancer (EORTC) and the National Cancer Institute (NCI) in organizing this annual event. More than 300 clinicians, pathologists, laboratory scientists and representatives from regulatory agencies and the pharmaceutical industry came together for three days of intense discussion, debate and reflection on the latest biomarker therapeutic discoveries, strategies and clinical applications. The poster discussion sessions featured 79 research abstracts. The three most outstanding abstracts, all authored by young female researchers, were selected for presentation during the main meeting sessions. Highlights of each scientific session are presented. PMID:22275966

  15. Detecting Molecular Signatures of Life on Mars: the Life Marker Chip (lmc) Instrument

    NASA Astrophysics Data System (ADS)

    Derveni, Mariliza

    In recent years, the rise of interest in planetary exploration and the emergence of Astrobiology as a promising field of research have lead to a number of programmes aiming to develop sensitive instruments for the detection of the molecular signatures of life in extreme environments. An antibody assay-based life detection instrument, the Life Marker Chip (LMC), is currently under development by a UK-lead international consortium for the European Space Agency's (ESA) ExoMars rover. This forms part of the joint ESA/NASA Mars exploration programme with the ExoMars Rover currently scheduled for launch in 2018. The organic molecules targeted for Life detection by the LMC are based on an assumption of "Earth-like" Life on Mars -extinct and/or extant. The molecular targets for the LMC have been chosen to represent markers of extinct Life, extant Life, abiotic chemistry (e.g. of meteoritic origin) and mission-borne Earth contamination. The LMC incorporates integrated liquid sample extraction and processing for dry Martian samples, which will be collected from up to 2m below the surface of Mars, where organic molecules, if present, are expected to be better preserved. The core technology of the LMC is a combination of optical evanescent waveguides, micro-fluidics, immuno-microarrays with fluorescent labels and CCD detector readout. Phage display recombinant antibody technology has been employed in order to acquire antibodies against a number of the LMC target molecules. The LMC hardware is currently in a breadboard phase of development. The recombinant antibody development for LMC targets is an on-going project, and testing of Earth-analogue Martian samples has been initiated

  16. Clinicopathologic factors and molecular markers related to lymph node metastasis in early gastric cancer

    PubMed Central

    Jin, Eun Hyo; Lee, Dong Ho; Jung, Sung-Ae; Shim, Ki-Nam; Seo, Ji Yeon; Kim, Nayoung; Shin, Cheol Min; Yoon, Hyuk; Jung, Hyun Chae

    2015-01-01

    AIM: To analyze predictive factors for lymph node metastasis in early gastric cancer. METHODS: We analyzed 1104 patients with early gastric cancer (EGC) who underwent a gastrectomy with lymph-node dissection from May 2003 through July 2011. The clinicopathologic factors and molecular markers were assessed as predictors for lymph node metastasis. Molecular markers such as microsatellite instability, human mutL homolog 1, p53, epidermal growth factor receptor (EGFR) and human epidermal growth factor receptor 2 (HER2) were included. The ?2 test and logistic regression analysis were used to determine clinicopathologic parameters. RESULTS: Lymph node metastasis was observed in 104 (9.4%) of 1104 patients. Among 104 cases of lymph node positive patients, 24 patients (3.8%) were mucosal cancers and 80 patients (16.7%) were submucosal. According to histologic evaluation, the number of lymph node metastasis found was 4 (1.7%) for well differentiated tubular adenocarcinoma, 45 (11.3%) for moderately differentiated tubular adenocarcinoma, 36 (14.8%) for poorly differentiated tubular adenocarcinoma, and 19 (8.4%) for signet ring cell carcinoma. Of 690 EGC cases, 77 cases (11.2%) showed EGFR overexpression. HER2 overexpression was present in 110 cases (27.1%) of 406 EGC patients. With multivariate analysis, female gender (OR = 2.281, P = 0.009), presence of lymphovascular invasion (OR = 10.950, P < 0.0001), diameter (? 20 mm, OR = 3.173, P = 0.01), and EGFR overexpression (OR = 2.185, P = 0.044) were independent risk factors for lymph node involvement. CONCLUSION: Female gender, tumor size, lymphovascular invasion and EGFR overexpression were predictive risk factors for lymph node metastasis in EGC. PMID:25593477

  17. Genetic diversity in the fungus Fusarium solani f.sp. cucurbitae race 1, the casual agent of root and crown rot of cucurbits in Iran, using molecular markers.

    PubMed

    Alymanesh, M R; Falahatirastegar, M; Jafarpour, B; Mahdikhanimoghadam, E

    2009-06-01

    Fusarium solani f.sp. cucurbitae race 1 is a pathogen on cucurbit plants. In this study genetic diversity among 26 isolates of Fusarium solani f.sp. cucurbitae race 1 was studied using Restriction Fragment Length Polymorphism (RFLP) of ITS (Interal Transcribed Spacer) regions and Random Amplified Polymorphic DNAs (RAPD) markers. Outcome of digestion with six restriction enzymes including EcoR I, Rsa I, Bme 181, Msp I, Hae III and Hind III, together with the patterns of restriction fragment length polymorphism of ITS regions divided the isolates into two groups. Deoxy Ribonuckin Acid DNA pattern was obtained for the isolates using 12 random primers and genetic distance between them was calculated and relationships (by cluster analysis) determined. Among the primers used, seven primers showed polymorphism. Genetic distance between isolate pairs ranged from 0.03 to 0.48. Genetic diversity was high (e.g., the isolates were distributed into 10 genetic groups at a similarity percentage of 75). The lowest distance was observed between isolates 50 and 73 and the highest distance observed between isolates 50 and 73 with isolate 102. Restriction fragment length polymorphism results show diversity in ITS regions, without any correlation to geographic origin and RAPD. However, this genomic regions usually have high constancy in species, but in this study diversity was shown in ITS regions even for race 1. The data suggest that taxonomical situation of Foc race 1 probably needs revision. PMID:19803117

  18. Application of molecular markers for genetic discrimination of Fusarium wilt pathogen races affecting chickpea and pigeonpea in major regions of India.

    PubMed

    Datta, J; Lal, N

    2012-01-01

    (foc) and Fusarium udum (Fud) collected from major pulse growing regions of India. Out of 247 bands produced by 24 Randomly Amplified Polymorphic DNA (RAPD) primers in Foc isolates, 210 (85%) were polymorphic. A maximum of 14 amplicons were generated by primer OPF 05 whereas minimum 7 amplicons were generated by primer K7. A total of 24 alleles were produced by twelve Simple Sequence Repeats (SSR) primers with an average of two alleles per marker in foc isolates. The maximum number of 4 alleles was obtained with primer SSR 12. SSR amplicon size ranged from 100 to 400 bp. The Unweighted Pair Group Method with Arithmetic average (UPGMA) cluster analysis based on RAPD and SSR profiles grouped the fourteen foc isolates into four major clusters. The universal Inter Transcribed Spacer (ITS) primer pair amplified 630 bp bands in all fourteen foc isolates while significant length polymorphism was obtained only when analysed by restriction digestion with EcoRI and MspI enzymes. The cluster analysis of ITS—RFLP grouped all 14 Foc isolates into three major clusters. Twenty four RAPD primers generated a total of 226 bands (ranging 0.3 to 3.0 kb) in Fusarium udum with an average of 9.4 bands per primer and a total of 27 alleles were produced by twelve SSR primers with an average of 2.25 alleles per marker. All isolates amplified a single band ranging from 100 to 450 bp. The universal ITS primer pair amplified 650 bp bands in all fourteen fud isolates while significant length polymorphism was obtained only when analysed by restriction digestion with EcoRI and Hind III enzymes. The cluster analysis of ITS—RFLP grouped all 14 Fud isolates into three major clusters. The cluster analysis using various markers show the grouping of Fusarium isolates strictly according to their cultural characteristics and degree of pathogenicity and not the geographical origin. This information will be helpful for pathologists and plant breeders to design effective resistance breeding programs in chickpea and pigeonpea taking into account the diversity in wilt pathogen. PMID:23273192

  19. Highly variable microsatellite markers for the fungal and algal symbionts of the lichen Lobaria pulmonaria and challenges in developing biont-specific molecular markers for fungal associations.

    PubMed

    Widmer, Ivo; Dal Grande, Francesco; Cornejo, Carolina; Scheidegger, Christoph

    2010-07-01

    The availability of highly variable markers for the partners of a fungal symbiosis enables the integrated investigation of ecological and evolutionary processes at the symbiotic level. In this article we analyze the specificity of the first and to date only microsatellite markers that had been developed for an epiphytic lichen (Lobaria pulmonaria). We used DNA extracts from cultures of the fungal and of the green algal symbionts of L. pulmonaria as well as total DNA extracts from related Lobaria species associated with the same algal partner, and got evidence that five of the previously described microsatellite markers, proposed to be fungus-specific, are indeed alga-specific. Hence, highly variable microsatellite primer sets available for both, the algal and the fungal symbionts of L. pulmonaria are now at our hands, which allow us to investigate so far unexplored biological processes of lichen symbionts, such as codispersal and coevolution. In a broader sense, our work evaluates and discusses the challenges in developing biont-specific molecular markers for fungi forming close associations with other organisms. PMID:20943165

  20. Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.).

    PubMed

    Yu, K; Park, S J; Poysa, V; Gepts, P

    2000-01-01

    Microsatellite or simple sequence repeat (SSR) markers have been successfully used for genomic mapping, DNA fingerprinting, and marker-assisted selection in many plant species. Here we report the first successful assignment of 15 SSR markers to the Phaseolus vulgaris molecular linkage map. A total of 37 SSR primer pairs were developed and tested for amplification and product-length polymorphism with BAT93 and Jalo EEP558, the parental lines of an F7 recombinant inbred (RI) population previously used for the construction of a common bean molecular linkage map. Sixteen of the SSRs polymorphic to the parental lines were analyzed for segregation and 15 of them were assigned to seven different linkage groups, indicating a widespread distribution throughout the bean genome. Map positions for genes coding for DNAJ-like protein, pathogenesis-related protein 3, plastid-located glutamine synthetase, endochitinase, sn-glycerol-3 phosphate acyltransferase, NADP-dependent malic enzyme, and protein kinase were determined for the first time. Addition of three SSR loci to linkage group B4 brought two separated smaller linkage groups together to form a larger linkage group. Analysis of allele segregation in the F7 RI population revealed that all 16 SSRs segregated in the expected 1:1 ratio. These SSR markers were stable and easy to assay by polymerase chain reaction (PCR). They should be useful markers for genetic mapping, genotype identification, and marker-assisted selection of common beans. PMID:11218079

  1. Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori.

    PubMed

    Nagaraja, G M; Mahesh, G; Satish, V; Madhu, M; Muthulakshmi, M; Nagaraju, J

    2005-08-01

    In the silkworm, Bombyx mori, the female is the heterogametic (ZW) sex and the male is homogametic (ZZ). The female heterogamety is a typical situation in the insect order Lepidoptera. Although the W chromosome in silkworm is strongly female determining, no W-linked gene for a morphological character has been found on it. The Z chromosome carries important traits of economic value as well as genes for various phenotypic traits, but only 2% of molecular information based on its relative size is known. Studies conducted so far indicate that the Z-linked genes are not dosage compensated. In the present study, we constructed a genetic map of randomly amplified polymorphic DNA fragments (RAPD), simple sequence repeats (SSR), and fluorescent intersimple sequence repeat PCR (FISSR) markers for the Z chromosome using a backcross mapping population. A total of 16 Z-linked markers were identified, characterized, and mapped using od, a recessive trait for translucent skin as an anchor marker yielding a total recombination map of 334.5 cM. The linkage distances obtained suggested that the markers were distributed throughout the Z chromosome. Four RAPD and four SSR markers that were linked to W chromosome were also identified. The proposed mapping approach should be useful to identify and map sex-linked traits in the silkworm. The economic and evolutionary significance of Z- and W-linked genes in silkworm, in particular, and lepidopterans, in general, is discussed. PMID:15931240

  2. Comparison of PM2.5 source apportionment using positive matrix factorization and molecular marker-based

    E-print Network

    Zheng, Mei

    Comparison of PM2.5 source apportionment using positive matrix factorization and molecular marker balance (CMB-MM) modeling on PM2.5 source contributions was conducted for particulate matter measurements 24-h PM2.5 samples collected in July 2001 and January 2002. While for PMF, with elements, ions, five

  3. USING CARBOHYDRATES AS MOLECULAR MARKERS TO DETERMINE THE CONTRIBUTION OF AGRICULTURAL SOIL TO AMBIENT FINE AND COURSE PM

    EPA Science Inventory

    Project research optimized the quantification technique for carbohydrates that also allows quantification of other non-polar molecular markers based on using an isotopically labeled internal standard (D-glucose-1,2,3,4,5,6,6-d7) to monitor extraction efficiency, extraction usi...

  4. Identification of candidate predictive and surrogate molecular markers for dasatinib in prostate cancer: rationale for patient selection and efficacy monitoring

    Microsoft Academic Search

    Xi-De Wang; Karen Reeves; Feng R Luo; Li-An Xu; Francis Lee; Edwin Clark; Fei Huang

    2007-01-01

    BACKGROUND: Dasatinib is a potent, multi-targeted kinase inhibitor that was recently approved for treatment of chronic myelogenous leukemia resistant to imatinib. To aid the clinical development of dasatinib in prostate cancer, we utilized preclinical models to identify potential molecular markers for patient stratification and efficacy monitoring. RESULTS: Using gene expression profiling, we first identified 174 genes whose expression was highly

  5. Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies

    Microsoft Academic Search

    Rebecca J. Case; Yan Boucher; Ingela Dahllof; Carola Holmstrom; W. Ford Doolittle; Staffan Kjelleberg

    2007-01-01

    Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to

  6. Identification of Genetic Factors Contributing to Heterosis in a Hybrid From Two Elite Maize Inbred Lines Using Molecular Markers

    Microsoft Academic Search

    Charles W. Stuber; Stephen E. Lincoln; David W. Wolff; Tim Helentjarisn; Eric S. Lander

    The use of molecular markers to identify quantitative trait loci (QTLs) affecting agriculturally important traits has become a key approach in plant genetics-both for understanding the genetic basis of these traits and to help design novel plant improvement programs. In the study reported here, we mapped QTLs (and evaluated their phenotypic effects) associated with seven major traits (including grain yield)

  7. Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

  8. Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations

    Microsoft Academic Search

    M. Heckenberger; M. Bohn; M. Frisch; H. P. Maurer; A. E. Melchinger

    2005-01-01

    Genetic similarities (GS) based on molecular markers have been proposed as a tool for identification of essentially derived varieties (EDVs). Nevertheless, scientifically reliable criteria for discrimination of EDVs and independently derived varieties with GS estimates are scanty, and implementation into practical breeding has not yet taken place. Our objectives were to (1) assess the influence of chromosome number and length,

  9. Molecular markers of early Parkinson's disease based on gene expression in blood

    PubMed Central

    Scherzer, Clemens R.; Eklund, Aron C.; Morse, Lee J.; Liao, Zhixiang; Locascio, Joseph J.; Fefer, Daniel; Schwarzschild, Michael A.; Schlossmacher, Michael G.; Hauser, Michael A.; Vance, Jeffery M.; Sudarsky, Lewis R.; Standaert, David G.; Growdon, John H.; Jensen, Roderick V.; Gullans, Steven R.

    2007-01-01

    Parkinson's disease (PD) progresses relentlessly and affects five million people worldwide. Laboratory tests for PD are critically needed for developing treatments designed to slow or prevent progression of the disease. We performed a transcriptome-wide scan in 105 individuals to interrogate the molecular processes perturbed in cellular blood of patients with early-stage PD. The molecular multigene marker here identified is associated with risk of PD in 66 samples of the training set comprising healthy and disease controls [third tertile cross-validated odds ratio of 5.7 (P for trend 0.005)]. It is further validated in 39 independent test samples [third tertile odds ratio of 5.1 (P for trend 0.04)]. Insights into disease-linked processes detectable in peripheral blood are offered by 22 unique genes differentially expressed in patients with PD versus healthy individuals. These include the cochaperone ST13, which stabilizes heat-shock protein 70, a modifier of ?-synuclein misfolding and toxicity. ST13 messenger RNA copies are lower in patients with PD (mean ± SE 0.59 ± 0.05) than in controls (0.96 ± 0.09) (P = 0.002) in two independent populations. Thus, gene expression signals measured in blood can facilitate the development of biomarkers for PD. PMID:17215369

  10. Molecular markers associated with outcome and metastasis in human pancreatic cancer

    PubMed Central

    2012-01-01

    Background Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous cancer in which differences in survival rates might be related to a variety in gene expression profiles. Although the molecular biology of PDAC begins to be revealed, genes or pathways that specifically drive tumour progression or metastasis are not well understood. Methods We performed microarray analyses on whole-tumour samples of 2 human PDAC subpopulations with similar clinicopathological features, but extremely distinct survival rates after potentially curative surgery, i.e. good outcome (OS and DFS?>?50?months, n?=?7) versus bad outcome (OS?molecular markers in pancreatic cancer as their expression seems to be related with prognosis. PMID:22925330

  11. Genotoxic effect of cadmium in okra seedlings: comparative investigation with population parameters and molecular markers.

    PubMed

    Aydin, Semra Soydam; Basaran, Esin; Cansaran-Duman, Demet; Aras, Sümer

    2013-11-01

    Plants are considered as good bioindicators because of their significant role in food chain transfer. They are also easy to grow, adaptable to environmental stresses and can be used for assaying a range of environmental conditions in different habitats. Thus, many plant species have been used as bioindicators. In order to evaluate the genotoxic effect of cadmium, okra (Abelmoschus esculontus L.) seedlings were treated with different concentrations (30, 60, 120 mg I(-1)) of cadmium and investigated for their population parameters such as inhibition of root growth; total soluble protein content, dry weight and also the impact of metal on the genetic material by RAPD analysis. Root growth and total soluble protein content in okra seedlings were reduced with increased Cd concentrations. RAPD analysis indicated formation of new bands mostly at 60 and 120 mg I(-1) Cd treatments. Altered DNA band patterns and population parameters after Cd treatments suggest that okra could be used as an indicator to reveal the effects of genotoxic agents. PMID:24555326

  12. Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.

    PubMed

    Öz, M H; Vurgun, H; Bakir, M; Büyük, ?; Yüksel, C; Ünlü, H M; Çukadar, K; Karado?an, B; Köse, Ö; Ergül, A

    2013-01-01

    We conducted SSR analyses of 59 accessions, including 29 traditional plum (Prunus domestica), 24 sweet cherry (Prunus avium), and 1 sour cherry (Prunus cerasus) selected from East Anatolian gene sources and 3 plum and 2 cherry reference accessions for molecular characterization and investigation of genetic relationships. Eight SSR loci [1 developed from the apricot (UDAp-404), 4 from the peach (UDP96-010, UDP96-001, UDP96-019, Pchgms1) and 3 from the cherry (UCD-CH13, UCD-CH17, UCD-CH31) genome] for plum accessions and 9 SSR loci [5 developed from the cherry (PS12A02, UCD-CH13, UCD-CH17, UCD-CH31, UCD-CH21), 3 from the peach (Pchgms1, UDP96-001, UDP96-005) and 1 from the plum (CPSCT010) genome] for cherry accessions were used for genetic identification. A total of 66 and 65 alleles were obtained in the genetic analyses of 31 plum and 28 cherry accessions, respectively. The number of alleles revealed by SSR analysis ranged from 4 to 14 alleles per locus, with a mean value of 8.25 in plum accessions, and from 5 to 10 alleles per locus with a mean value of 7.2 in cherry accessions. Only one case of synonym was identified among the cherry accessions, while no case of synonym was observed among the plum accessions. Genomic SSR markers used in discrimination of plum and cherry accessions showed high cross-species transferability in the Prunus genus. Because of their appreciable polymorphism and cross species transferability, the SSR markers that we evaluated in this study will be useful for studies involving fingerprinting of cherry and plum cultivars. PMID:24301792

  13. Genetic rearrangements of six wheat-agropyron cristatum 6P addition lines revealed by molecular markers.

    PubMed

    Han, Haiming; Bai, Li; Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

    2014-01-01

    Agropyron cristatum (L.) Gaertn. (2n?=?4x?=?28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat-A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat-A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

  14. Establishment of a proteome profile and identification of molecular markers for mouse spermatogonial stem cells

    PubMed Central

    Zhou, Quan; Guo, Yueshuai; Zheng, Bo; Shao, Binbin; Jiang, Min; Wang, Gaigai; Zhou, Tao; Wang, Lei; Zhou, Zuomin; Guo, Xuejiang; Huang, Xiaoyan

    2015-01-01

    Spermatogonial stem cells (SSCs) are undifferentiated cells that are required to maintain spermatogenesis throughout the reproductive life of mammals. Although SSC transplantation and culture provide a powerful tool to identify the mechanisms regulating SSC function, the precise signalling mechanisms governing SSC self-renewal and specific surface markers for purifying SSCs remain to be clearly determined. In the present study, we established a steady SSC culture according to the method described by Shinohara's lab. Fertile progeny was produced after transplantation of cultured SSCs into infertile mouse testis, and the red fluorescence exhibited by the culture cell membranes was stably and continuously transmitted to the offspring. Next, via advanced mass spectrometry and an optimized proteomics platform, we constructed the proteome profile, with 682 proteins expressed in SSCs. Furthermore bioinformatics analysis showed that the list contained several known molecules that are regulated in SSCs. Several nucleoproteins and membrane proteins were chosen for further exploration using immunofluorescence and RT-PCR. The results showed that SALL1, EZH2, and RCOR2 are possibly involved in the self-renewal mechanism of SSCs. Furthermore, the results of tissue-specific expression analysis showed that Gpat2 and Pld6 were uniquely and highly expressed in mouse testes and cultured SSCs. The cellular localization of PLD6 was further explored and the results showed it was primarily expressed in the spermatogonial membrane of mouse testes and cultured SSCs. The proteins identified in this study form the basis for further exploring the molecular mechanism of self-renewal in SSCs and for identifying specific surface markers of SSCs. PMID:25352495

  15. Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii

    PubMed Central

    Zhang, Shouan; Gao, Muqiang; Zaitlin, David

    2012-01-01

    Nicotiana langsdorffii is one of two species of Nicotiana known to express an incompatible interaction with the oomycete Peronospora tabacina, the causal agent of tobacco blue mold disease. We previously showed that incompatibility is due to the hypersensitive response (HR), and plants expressing the HR are resistant to P. tabacina at all stages of growth. Resistance is due to a single dominant gene in N. langsdorffii accession S-4-4 that we have named NlRPT. In further characterizing this unique host-pathogen interaction, NlRPT has been placed on a preliminary genetic map of the N. langsdorffii genome. Allelic scores for five classes of DNA markers were determined for 90 progeny of a “modified backcross” involving two N. langsdorffii inbred lines and the related species N. forgetiana. All markers had an expected segregation ratio of 1:1, and were scored in a common format. The map was constructed with JoinMap 3.0, and loci showing excessive transmission distortion were removed. The linkage map consists of 266 molecular marker loci defined by 217 amplified fragment length polymorphisms (AFLPs), 26 simple-sequence repeats (SSRs), 10 conserved orthologous sequence markers, nine inter-simple sequence repeat markers, and four target region amplification polymorphism markers arranged in 12 linkage groups with a combined length of 1062?cM. NlRPT is located on linkage group three, flanked by four AFLP markers and one SSR. Regions of skewed segregation were detected on LGs 1, 5, and 9. Markers developed for N. langsdorffii are potentially useful genetic tools for other species in Nicotiana section Alatae, as well as in N. benthamiana. We also investigated whether AFLPs could be used to infer genetic relationships within N. langsdorffii and related species from section Alatae. A phenetic analysis of the AFLP data showed that there are two main lineages within N. langsdorffii, and that both contain populations expressing dominant resistance to P. tabacina. PMID:22936937

  16. Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp.

    PubMed

    Latrofa, Maria S; Dantas-Torres, Filipe; Annoscia, Giada; Cantacessi, Cinzia; Otranto, Domenico

    2013-12-01

    The genus Rhipicephalus (Acari: Ixodidae) comprises a large number of vectors of pathogens of substantial medical and veterinary concern; however, species identification based solely on morphological features is often challenging. In the present study, genetic distance within selected Rhipicephalus species (i.e., Rhipicephalus bursa, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus), were investigated based on molecular and phylogenetic analyses of fragments of the mitochondrial 16S, 12S and cytochrome c oxidase subunit 1 (cox1) genes, as well as of the whole sequences of the ribosomal internal transcribed spacer-2 (ITS-2) region. Mean values of inter-specific genetic distance (e.g., up to 12.6%, 11.1% and 15.2%), as well as of intra-specific genetic distance (e.g., 0.9%, 0.9% and 1%), calculated using the Kimura-2 parameter substitution model with uniform rates among sites for 16S, 12S and cox1 genes, respectively, confirmed the differentiation of the rhipicephaline species herein examined. The molecular identification was also supported by the distinct separation of species-specific clades inferred from the phylogenetic analyses of all mitochondrial sequences. Conversely, little interspecific divergence was detected amongst ribosomal ITS-2 sequences (i.e., up to 2.8%) for species belonging to the R. sanguineus complex, which resulted in the ambiguous placement of selected R. sanguineus s.l. and R. turanicus sequences in the corresponding phylogenetic tree. Results from this study confirm the suitability of mtDNA markers for the reliable identification of ticks within the Rhipicephalus genus and provide a framework for future studies of taxonomy, speciation history and evolution of this group of ticks. PMID:24103336

  17. Genetic variability and geographic typicality of Italian former Prosecco grape variety using PCR-derived molecular markers.

    PubMed

    Meneghetti, Stefano; Costacurta, Angelo; Bavaresco, Luigi; Calo', Antonio

    2014-05-01

    This study uses PCR-derived marker systems to investigate the extent and distribution of genetic variability of 80 Italian Prosecco accessions coming from Prosecco DOC area (north-east area of Italy). The studied samples include genotypes from Veneto and Friuli Venezia Giulia region. In order to verify the varietal identity of the samples, analyses based on 22 SSR loci were performed, and two grape varieties were found: Prosecco tondo and Prosecco lungo. In addition to microsatellite analysis, intra-varietal variability study was performed using AFLP, SAMPL, ISSR, and M-AFLP molecular markers. This molecular approach could discriminate different Prosecco tondo accessions coming from Treviso hills, from Veneto plain, from Friuli Venezia Giulia region, and from Padua hills (Serprina samples). As concerning Prosecco lungo variety, it was possible to discriminate molecularly the accessions from Veneto region and those from Friuli Venezia Giulia region. The molecular analysis allowed a distinction of the Prosecco genotypes on the basis of their geographic origins with plant-specific markers able to differentiate all Prosecco accessions. In this paper, the studied grape variety is termed Prosecco and not Glera (which is the present name) because the sampled vineyards were established many years ago when the name of the variety was Prosecco. PMID:24347297

  18. Molecular markers and imaging tools to identify malignant potential in Barrett's esophagus

    PubMed Central

    Bennett, Michael; Mashimo, Hiroshi

    2014-01-01

    Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barrett’s esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barrett’s lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and surveillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of high-risk lesions in Barrett’s esophagus. PMID:25400987

  19. Molecular markers for identifying a new selected variety of Pacific white shrimp Litopenaeus vannamei

    NASA Astrophysics Data System (ADS)

    Yu, Yang; Zhang, Xiaojun; Liu, Jingwen; Li, Fuhua; Huang, Hao; Li, Yijun; Liu, Xiaolin; Xiang, Jianhai

    2015-01-01

    Selective breeding of the Pacific white shrimp Litopenaeus vannamei during the last decade has produced new varieties exhibiting high growth rates and disease resistance. However, the identification of new varieties of shrimps from their phenotypic characters is difficult. This study introduces a new approach for identifying varieties of shrimps using molecular markers of microsatellites and mitochondrial control region sequences. The method was employed to identify a new selected variety, Kehai No. 1 (KH-1), from three representative stocks (control group): Zhengda; Tongwei; and a stock collected from Fujian Province, which is now cultured in mainland China. By pooled genotyping of KH-1 and the control group, five microsatellites showing differences between KH-1 and the control group were screened out. Individual genotyping data confirmed the results from pooled genotyping. The genotyping data for the five microsatellites were applied to the assignment analysis of the KH-1 group and the control group using the partial Bayesian assignment method in GENECLASS2. By sequencing the mitochondrial control regions of individuals from the KH-1 and control group, four haplotypes were observed in the KH-1 group, whereas 14 haplotypes were obtained in the control group. By combining the microsatellite assignment analysis with mitochondrial control region analysis, the average accuracy of identification of individuals in the KH-1 group and control group reached 89%. The five selected microsatellite loci and mitochondrial control region sequences were highly polymorphic and could be used to distinguish new selected varieties of L. vannamei from other populations cultured in China.

  20. [Exploring genetic diversity in Dioscorea zingiberensis by amplified fragment length polymorphism molecular markers].

    PubMed

    Li, Yong-Hui; Li, Xiang-Min

    2007-08-01

    Amplified fragment length polymorphism (AFLP) was used to study 30 individuals from 5 wild populations of Dioscorea zingiberensis for the first time. A total of 14 698 bands were detected with 9 pairs of AFLP primers and 12 686 of them were polymorphic. On the average each primer combination could be used to detect 230 polymorphic bands and account for 85.92% of total genetic diversity at species level. Shannonos index of diversity (I) was 0.3656-/+0.1721, and Nei's gene diversity (H) was 0.2322-/+0.2200 at the species level. The result of genetic variance analysis showed the coefficient of genetic differentiation (Gst) was 0.4827 at species level, it indicated there were certain degree of genetic differentiation in five Dioscorea zingiberensis populations. The gene flow (Nm) among populations of D. zingiberensis was 0.5358. The data were analyzed using unweighted pair group method, basing on arithmetic averages (UPGMA) bootstrap analysis. Cluster analyses were performed by using NTSYSpc version 2.11F and Popgene 1.32 software. The results showed that the genetic differentiation of 5 wild populations of D. zingiberensis was abundant, and 5 wild populations of D. zingiberensis could be clustered by the distance of the position basically. The AFLP molecular marker was used to identify the genetic differences of different populations of Dioscorea zingiberensis. PMID:17675758

  1. Tracking neuronal marker expression inside living differentiating cells using molecular beacons

    PubMed Central

    Ilieva, Mirolyuba; Della Vedova, Paolo; Hansen, Ole; Dufva, Martin

    2013-01-01

    Monitoring gene expression is an important tool for elucidating mechanisms of cellular function. In order to monitor gene expression during nerve cell development, molecular beacon (MB) probes targeting markers representing different stages of neuronal differentiation were designed and synthesized as 2'-O-methyl RNA backbone oligonucleotides. MBs were transfected into human mesencephalic cells (LUHMES) using streptolysin-O-based membrane permeabilization. Mathematical modeling, simulations and experiments indicated that MB concentration was equal to the MB in the transfection medium after 10 min transfection. The cells will then each contain about 60,000 MBs. Gene expression was detected at different time points using fluorescence microscopy. Nestin and NeuN mRNA were expressed in approximately 35% of the LUHMES cells grown in growth medium, and in 80–90% of cells after differentiation. MAP2 and tyrosine hydroxylase mRNAs were expressed 2 and 3 days post induction of differentiation, respectively. Oct 4 was not detected with MB in these cells and signal was not increased over time suggesting that MB are generally stable inside the cells. The gene expression changes measured using MBs were confirmed using qRT-PCR. These results suggest that MBs are simple to use sensors inside living cell, and particularly useful for studying dynamic gene expression in heterogeneous cell populations. PMID:24431988

  2. Molecular Screening of Blast Resistance Genes in Rice using SSR Markers

    PubMed Central

    Singh, A. K.; Singh, P. K.; Arya, Madhuri; Singh, N. K.; Singh, U. S.

    2015-01-01

    Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1–24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106

  3. Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinobacteria speciation

    PubMed Central

    Hayward, Don; van Helden, Paul D; Wiid, Ian JF

    2009-01-01

    Background Although the gene encoding for glutamine synthetase (glnA) is essential in several organisms, multiple glnA copies have been identified in bacterial genomes such as those of the phylum Actinobacteria, notably the mycobacterial species. Intriguingly, previous reports have shown that only one copy (glnA1) is essential for growth in M. tuberculosis, while the other copies (glnA2, glnA3 and glnA4) are not. Results In this report it is shown that the glnA1 and glnA2 encoded glutamine synthetase sequences were inherited from an Actinobacteria ancestor, while the glnA4 and glnA3 encoded GS sequences were sequentially acquired during Actinobacteria speciation. The glutamine synthetase sequences encoded by glnA4 and glnA3 are undergoing reductive evolution in the mycobacteria, whilst those encoded by glnA1 and glnA2 are more conserved. Conclusion Different selective pressures by the ecological niche that the organisms occupy may influence the sequence evolution of glnA1 and glnA2 and thereby affecting phylogenies based on the protein sequences they encode. The findings in this report may impact the use of similar sequences as molecular markers, as well as shed some light on the evolution of glutamine synthetase in the mycobacteria. PMID:19245690

  4. A test of the maximum heterozygosity hypothesis using molecular markers in tetraploid potatoes.

    PubMed

    Bonierbale, M W; Plaisted, R L; Tanksley, S D

    1993-05-01

    It has been theorized that in cross-pollinated polyploid species hybrid vigor is maximized by the frequent occurrence of more than two alleles per chromosomal locus. In polyploid crops this condition of maximum heterozygosity has been reported to be associated with increased yield and optimum field performance. We report herein the first direct test of the maximum heterozygosity hypothesis. Molecular markers were used to examine the association between maximum heterozygosity and several components of yield in three different populations of tetraploid potatoes. The results indicate that the value of maximum heterozygosity is not universal but dependent on the genetic background of the material under evaluation. In a cross between adapted breeding lines, homozygosity was negatively correlated with tuber yield, and maximum heterozygosity was positively correlated with the proportion of tuber yield in the large-size fraction. In contrast, in crosses between adapted and unadapted parents, maximum heterozygosity had no detectable effect on any character. Quantitative trait locus (QTL) analysis of the three populations reveals that, regardless of the genetic background, additive genetic effects are more strongly correlated with the components of yield than are any measures of heterozygosity and that some common QTLs may be influencing yield in all three populations. PMID:24193596

  5. Molecular Screening of Blast Resistance Genes in Rice using SSR Markers.

    PubMed

    Singh, A K; Singh, P K; Arya, Madhuri; Singh, N K; Singh, U S

    2015-03-01

    Rice Blast is the most devastating disease causing major yield losses in every year worldwide. It had been proved that using resistant rice varieties would be the most effective way to control this disease. Molecular screening and genetic diversities of major rice blast resistance genes were determined in 192 rice germplasm accessions using simple sequence repeat (SSR) markers. The genetic frequencies of the 10 major rice blast resistance genes varied from 19.79% to 54.69%. Seven accessions IC337593, IC346002, IC346004, IC346813, IC356117, IC356422 and IC383441 had maximum eight blast resistance gene, while FR13B, Hourakani, Kala Rata 1-24, Lemont, Brown Gora, IR87756-20-2-2-3, IC282418, IC356419, PKSLGR-1 and PKSLGR-39 had seven blast resistance genes. Twenty accessions possessed six genes, 36 accessions had five genes, 41 accessions had four genes, 38 accessions had three genes, 26 accessions had two genes, 13 accessions had single R gene and only one accession IC438644 does not possess any one blast resistant gene. Out of 192 accessions only 17 accessions harboured 7 to 8 blast resistance genes. PMID:25774106

  6. Current Status of Molecular Markers for Early Detection of Sporadic Pancreatic Cancer

    PubMed Central

    Chakraborty, Subhankar; Baine, Michael J.; Sasson, Aaron R.; Batra, Surinder K.

    2010-01-01

    Pancreatic cancer (PC) is a highly lethal malignancy with near 100% mortality. This is in part due to the fact that most patients present with metastatic or locally advanced disease at the time of diagnosis. Significantly, in nearly 95% of PC patients there is neither an associated family history of PC nor of diseases known to be associated with an increased risk of PC. These groups of patients who comprise the bulk of PC cases are termed as “sporadic PC” in contrast to the familial PC cases that comprise only about 5% of all PCs. Given the insidious onset of the malignancy and its extreme resistance to chemo and radiotherapy, an abundance of research in recent years has focused on identifying biomarkers for the early detection of PC, specifically aiming at the sporadic PC cohort. However, while several studies have established that asymptomatic individuals with a positive family history of PC and those with certain heritable syndromes are candidates for PC screening, the role of screening in identifying sporadic PC is still an unsettled question. The present review attempts to assess this critical question by investigating the recent advances made in molecular markers with potential use in the early diagnosis of sporadic PC- the largest cohort of PC cases worldwide. It also outlines a novel yet simple risk-factor based stratification system that could be potentially employed by clinicians to identify those individuals who at an elevated-risk for the development of sporadic PC and therefore candidates for screening. PMID:20888394

  7. Correlation analysis of ultrasonic characteristics, pathological type, and molecular markers of thyroid nodules.

    PubMed

    Su, J J; Hui, L Z; Xi, C J; Su, G Q

    2015-01-01

    The present study was conducted to analyze the correlation between ultrasonic characteristics, pathological type, and molecular markers of thyroid-tumor-related genes as well as to evaluate the diagnosis and prognosis of thyroid nodules. The acoustic characteristics of 130 thyroid specimens were detected. Pathological sectioning and immunohistochemical detection were performed to determine the correlation between tumor gene expression and ultrasonic characteristics. Ultrasonic testing revealed that malignant nodules were normally accompanied by lymph nodes. Expression of the human telomerase reverse transcriptase, Ki67, vascular endothelial growth factor, Ret, and P53 genes exhibited statistically significant differences in malignant, benign, and normal tissues. The performance of thyroid malignant nodules showed different degrees of correlation with the expression of the human telomerase reverse transcriptase, Ki67, VEGF, Ret, and P53 genes. Color Doppler ultrasound is highly sensitive for thyroid nodules and is therefore effective for identifying thyroid nodules and early diagnosis of thyroid cancer. Color Doppler ultrasound can identify benign or malignant thyroid nodules based on 5 characteristic indicators. Tumor pathology and gene expression are associated with the sonographic features of thyroid cancer. Therefore, determining the pathological basis of ultrasonography would facilitate prognostic assessments of thyroid cancer. PMID:25729930

  8. Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers

    PubMed Central

    Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

    2014-01-01

    Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids. PMID:24977711

  9. Intensive Linkage Mapping in a Wasp (Bracon Hebetor) and a Mosquito (Aedes Aegypti) with Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers

    PubMed Central

    Antolin, M. F.; Bosio, C. F.; Cotton, J.; Sweeney, W.; Strand, M. R.; Black-IV, W. C.

    1996-01-01

    The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a diploid mosquito, Aedes aegypti. RAPD-SSCP analysis revealed segregation of codominant alleles at markers that appeared to segregate as dominant (band presence/band absence) markers or appeared invariant on agarose gels. Our SSCP protocol uses silver staining to detect DNA fractionated on large thin polyacrylamide gels and reveals more polymorphic markers than agarose gel electrophoresis. In B. hebetor, 79 markers were mapped with 12 RAPD primers in six weeks; in A. aegypti, 94 markers were mapped with 10 RAPD primers in five weeks. Forty-five percent of markers segregated as codominant loci in B. hebetor, while 11% segregated as codominant loci in A. aegypti. SSCP analysis of RAPD-PCR markers offers a rapid and inexpensive means of constructing intensive linkage maps of many species. PMID:8844159

  10. Characterization of alien chromosomes in backcross derivatives of Triticum aestivum × Elymus rectisetus hybrids by using molecular markers and sequential multicolor FISH/GISH.

    PubMed

    Dou, Quan-Wen; Lei, Yunting; Li, Xiaomei; Mott, Ivan W; Wang, Richard R-C

    2012-05-01

    Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Based on DNA sequences of genome-specific RAPD markers, sequence-tagged site (STS) markers specific for W and Y genomes have been obtained. Coupling with the use of genomic in situ hybridization, these STS markers enabled the identification of the W- and Y-genome chromosomes in backcross derivatives from hybrids of bread wheat Triticum aestivum L. (2n=42; AABBDD) and Elymus rectisetus (Nees in Lehm.) Á. Löve & Connor (2n=42; StStWWYY). The detection of six different alien chromosomes in five of these derivatives was ascertained by quantitative PCR of STS markers, simple sequence repeat markers, rDNA genes, and (or) multicolor florescence in situ hybridization. Disomic addition line 4687 (2n=44) has the full complement of 42 wheat chromosomes and a pair of 1Y chromosomes that carry genes for resistance to tan spot (caused by Pyrenophora tritici-repentis (Died.) Drechs.) and Stagonospora nodorum blotch (caused by Stagonospora nodorum (Berk.) Castellani and Germano). The disomic addition line 4162 has a pair of 1St chromosomes and 21 pairs of wheat chromosomes. Lines 4319 and 5899 are two triple substitution lines (2n=42) having the same chromosome composition, with 2A, 4B, and 6D of wheat substituted by one pair of W- and two pairs of St-genome chromosomes. Line 4434 is a substitution-addition line (2n=44) that has the same W- and St-genome chromosomes substituting 2A, 4B, and 6D of wheat as in lines 4319 and 5899 but differs by having an additional pair of Y-genome chromosome, which is not the 1Y as in line 4687. The production and identification of these alien cytogenetic stocks may help locate and isolate genes for useful agronomic traits. PMID:22494709

  11. Review of the molecular profile and modern prognostic markers for gastric lymphoma: How do they affect clinical practice?

    PubMed Central

    Alevizos, Leonidas; Gomatos, Ilias P.; Smparounis, Spyridon; Konstadoulakis, Manousos M.; Zografos, Georgios

    2012-01-01

    Primary gastric lymphoma is a rare cancer of the stomach with an indeterminate prognosis. Recently, a series of molecular prognostic markers has been introduced to better describe this clinical entity. This review describes the clinical importance of several oncogenes, apoptotic genes and chromosomal mutations in the initiation and progress of primary non-Hodgkin gastric lymphoma and their effect on patient survival. We also outline the prognostic clinical importance of certain cellular adhesion molecules, such as ICAM and PECAM-1, in patients with gastric lymphoma, and we analyze the correlation of these molecules with apoptosis, angiogenesis, tumour growth and metastatic potential. We also focus on the host–immune response and the impact of Helicobacter pylori infection on gastric lymphoma development and progression. Finally, we explore the therapeutic methods currently available for gastric lymphoma, comparing the traditional invasive approach with more recent conservative options, and we stress the importance of the application of novel molecular markers in clinical practice. PMID:22564515

  12. Efficient Molecular Marker Design Using the MaizeGDB Mo17 SNPs and Indels Track

    PubMed Central

    Settles, A. Mark; Bagadion, Alyssa M.; Bai, Fang; Zhang, Junya; Barron, Brady; Leach, Kristen; Mudunkothge, Janaki S.; Hoffner, Cassandra; Bihmidine, Saadia; Finefield, Erin; Hibbard, Jaime; Dieter, Emily; Malidelis, I. Alex; Gustin, Jeffery L.; Karoblyte, Vita; Tseung, Chi-Wah; Braun, David M.

    2014-01-01

    Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion–deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize. PMID:24747759

  13. Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track.

    PubMed

    Settles, A Mark; Bagadion, Alyssa M; Bai, Fang; Zhang, Junya; Barron, Brady; Leach, Kristen; Mudunkothge, Janaki S; Hoffner, Cassandra; Bihmidine, Saadia; Finefield, Erin; Hibbard, Jaime; Dieter, Emily; Malidelis, I Alex; Gustin, Jeffery L; Karoblyte, Vita; Tseung, Chi-Wah; Braun, David M

    2014-06-01

    Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion-deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize. PMID:24747759

  14. Rose germplasm identification and analysis with RAPD markers

    E-print Network

    Jan, Chih-Hui

    1996-01-01

    gigantea Collett, R. helenae Rehder & Wilson, R hugonis Hemsl. & Wils. , R laevigata Michx. , R Jara Retzius, R. luciae Franch. & Rochebr. , R moschata Herrmann, R. mulliganii Bouleng. , R. multibracteata Hemsley & Wilson, R multij7ora Thunb. , R primula... similar to the section Cassiorhodon, This agrees well with the report of Roberts (1977) that R koreana should be placed in section Cassiorhodon. Three species of the section Synsrylae, R luciae Franchet k Rochebrune, R multiflora Thunb. and R...

  15. Inheritance and development of molecular markers linked to angular leaf spot resistance genes in the common bean accession G10909

    Microsoft Academic Search

    George S. MahukuMaria; María Antonia Henríquez; Carmenza Montoya; Carlos Jara; Henry Teran; Stephen Beebe

    2011-01-01

    Angular leaf spot (ALS) is one of the major diseases of the common bean (Phaseolus vulgaris L.). Different sources of resistance have been identified but few have been characterized. Studies were conducted to elucidate\\u000a the inheritance of ALS resistance in the bean accession G10909 and to identify molecular markers linked to these genes. Evaluation\\u000a of parental genotypes, F1, F2 and

  16. Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea

    Microsoft Academic Search

    Federico Luis Iniguez-Luy; Lewis Lukens; Mark W. Farnham; Richard M. Amasino; Thomas C. Osborn

    2009-01-01

    Publicly available genomic tools help researchers integrate information and make new discoveries. In this paper, we describe\\u000a the development of immortal mapping populations of rapid cycling, self-compatible lines, molecular markers, and linkage maps\\u000a for Brassica rapa and B. oleracea and make the data and germplasm available to the Brassica research community. The B. rapa population consists of 160 recombinant inbred

  17. Temporal trends of molecular markers associated with artemether-lumefantrine tolerance\\/resistance in Bagamoyo district, Tanzania

    Microsoft Academic Search

    M. Malmberg; B. Ngasala; P. E. Ferreira; E. Larsson; I. Jovel; A. Hjalmarsson; M. Petzold; Z. Premji; J. P. Gil; A. Bjorkman; A. Martensson

    2013-01-01

    BACKGROUND: Development and spread of Plasmodium falciparum resistance to artemisinin-based combination therapy (ACT) constitutes a major threat to recent global malaria control achievements. Surveillance of molecular markers could act as an early warning system of ACT-resistance before clinical treatment failures are apparent. The aim of this study was to analyse temporal trends of established genotypes associated with artemether-lumefantrine tolerance\\/resistance before

  18. Predicting Quantitative Traits With Regression Models for Dense Molecular Markers and Pedigree

    PubMed Central

    de los Campos, Gustavo; Naya, Hugo; Gianola, Daniel; Crossa, José; Legarra, Andrés; Manfredi, Eduardo; Weigel, Kent; Cotes, José Miguel

    2009-01-01

    The availability of genomewide dense markers brings opportunities and challenges to breeding programs. An important question concerns the ways in which dense markers and pedigrees, together with phenotypic records, should be used to arrive at predictions of genetic values for complex traits. If a large number of markers are included in a regression model, marker-specific shrinkage of regression coefficients may be needed. For this reason, the Bayesian least absolute shrinkage and selection operator (LASSO) (BL) appears to be an interesting approach for fitting marker effects in a regression model. This article adapts the BL to arrive at a regression model where markers, pedigrees, and covariates other than markers are considered jointly. Connections between BL and other marker-based regression models are discussed, and the sensitivity of BL with respect to the choice of prior distributions assigned to key parameters is evaluated using simulation. The proposed model was fitted to two data sets from wheat and mouse populations, and evaluated using cross-validation methods. Results indicate that inclusion of markers in the regression further improved the predictive ability of models. An R program that implements the proposed model is freely available. PMID:19293140

  19. Sex determination in 58 bird species and evaluation of CHD gene as a universal molecular marker in bird sexing.

    PubMed

    Vucicevic, Milos; Stevanov-Pavlovic, Marija; Stevanovic, Jevrosima; Bosnjak, Jasna; Gajic, Bojan; Aleksic, Nevenka; Stanimirovic, Zoran

    2013-01-01

    The aim of this research was to test the CHD gene (Chromo Helicase DNA-binding gene) as a universal molecular marker for sexing birds of relatively distant species. The CHD gene corresponds to the aim because of its high degree of conservation and different lengths in Z and W chromosomes due to different intron sizes. DNA was isolated from feathers and the amplification of the CHD gene was performed with the following sets of polymerase chain reaction (PCR) primers: 2550F/2718R and P2/P8. Sex determination was attempted in 284 samples of 58 bird species. It was successful in 50 bird species; in 16 of those (Alopochen aegyptiacus, Ara severus, Aratinga acuticaudata, Bucorvus leadbeateri, Cereopsis novaehollandiae, Columba arquatrix, Corvus corax, C. frugilegus, Cyanoliseus patagonus, Guttera plumifera, Lamprotornis superbus, Milvus milvus, Neophron percnopterus, Ocyphaps lophotes, Podiceps cristatus, and Poicephalus senegalus), it was carried out for the first time using molecular markers and PCR. It is reasonable to assume that extensive research is necessary to define the CHD gene as a universal molecular marker for successful sex determination in all bird species (with exception of ratites). The results of this study may largely contribute to the aim. PMID:22553188

  20. Molecular markers of yolk sac fry development in nine families of lake trout.

    PubMed

    Vuori, Kristiina A; Paavilainen, Tiia; Nikinmaa, Mikko; Czesny, Sergiusz; Rinchard, Jacques

    2009-12-01

    Salmonids in certain areas of North America and northern Europe suffer from reproductive disturbances manifested through the death of yolk sac fry. These disturbances are referred to as early mortality syndrome (EMS) in the Great Lakes region and M74 in the Baltic Sea. Both of these syndromes have been associated with reduced concentrations of thiamine in affected females and their eggs. However, large variations in signs and mortality, both within and between the individual syndromes, have been reported. Yolk sac fry mortality (M74) in Atlantic salmon Salmo salar has been shown to be associated with reduced DNA binding of the hypoxia-inducible transcription factor 1 (HIF-1), reduced production of vascular endothelial growth factor (VEGF) protein, decreased capillary density, and down-regulation of adult-type globin gene transcription (which is responsible for the protein part of adult hemoglobin). One of the main effects of all of these changes is reduced oxygen transport to the tissues of affected fry. In this study, the developmental patterns of HIF-1 DNA binding, VEGF protein expression, and adult-type globin gene transcription were analyzed in nine family groups of Lake Michigan lake trout Salvelinus namaycush. The results indicate that HIF-1 DNA binding and globin gene transcription increase from hatch to the end of yolk sac stage. Interindividual and between-family biological variations were detected, especially in VEGF protein expression and globin gene transcription. Our results demonstrate the possibility of using these molecular markers in investigating the etiology of EMS and making comparisons between the mechanisms of different salmonid yolk sac fry mortalities. PMID:20218502

  1. Subtracted Diversity Array Identifies Novel Molecular Markers Including Retrotransposons for Fingerprinting Echinacea Species

    PubMed Central

    Olarte, Alexandra; Mantri, Nitin; Nugent, Gregory; Pang, Edwin C. K.

    2013-01-01

    Echinacea, native to the Canadian prairies and the prairie states of the United States, has a long tradition as a folk medicine for the Native Americans. Currently, Echinacea are among the top 10 selling herbal medicines in the U.S. and Europe, due to increasing popularity for the treatment of common cold and ability to stimulate the immune system. However, the genetic relationship within the species of this genus is unclear, making the authentication of the species used for the medicinal industry more difficult. We report the construction of a novel Subtracted Diversity Array (SDA) for Echinacea species and demonstrate the potential of this array for isolating highly polymorphic sequences. In order to selectively isolate Echinacea-specific sequences, a Suppression Subtractive Hybridization (SSH) was performed between a pool of twenty-four Echinacea genotypes and a pool of other angiosperms and non-angiosperms. A total of 283 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. Twenty-seven Echinacea genotypes including four that were not used in the array construction could be successfully discriminated. Interestingly, unknown samples of E. paradoxa and E. purpurea could be unambiguously identified from the cluster analysis. Furthermore, this Echinacea-specific SDA was also able to isolate highly polymorphic retrotransposon sequences. Five out of the eleven most discriminatory features matched to known retrotransposons. This is the first time retrotransposon sequences have been used to fingerprint Echinacea, highlighting the potential of retrotransposons as based molecular markers useful for fingerprinting and studying diversity patterns in Echinacea. PMID:23940565

  2. Molecular markers of trichloroethylene-induced toxicity in human kidney cells

    SciTech Connect

    Lash, Lawrence H. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)]. E-mail: l.h.lash@wayne.edu; Putt, David A. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Hueni, Sarah E. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States); Horwitz, Beth P. [Department of Pharmacology, Wayne State University School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201 (United States)

    2005-08-07

    Difficulties in evaluation of trichloroethylene (TRI)-induced toxicity in humans and extrapolation of data from laboratory animals to humans are due to the existence of multiple target organs, multiple metabolic pathways, sex-, species-, and strain-dependent differences in both metabolism and susceptibility to toxicity, and the lack or minimal amount of human data for many target organs. The use of human tissue for mechanistic studies is thus distinctly advantageous. The kidneys are one target organ for TRI and metabolism by the glutathione (GSH) conjugation pathway is responsible for nephrotoxicity. The GSH conjugate is processed further to produce the cysteine conjugate, S-(1,2-dichlorovinyl)-L-cysteine (DCVC), which is the penultimate nephrotoxic species. Confluent, primary cultures of human proximal tubular (hPT) cells were used as the model system. Although cells in log-phase growth, which are undergoing more rapid DNA synthesis, would give lower LD{sub 50} values, confluent cells more closely mimic the in vivo proximal tubule. DCVC caused cellular necrosis only at relatively high doses (>100 {mu}M) and long incubation times (>24 h). In contrast, both apoptosis and enhanced cellular proliferation occurred at relatively low doses (10-100 {mu}M) and early incubation times (2-8 h). These responses were associated with prominent changes in expression of several proteins that regulate apoptosis (Bcl-2, Bax, Apaf-1, Caspase-9 cleavage, PARP cleavage) and cellular growth, differentiation and stress response (p53, Hsp27, NF-{kappa}B). Effects on p53 and Hsp27 implicate function of protein kinase C, the mitogen activated protein kinase pathway, and the cytoskeleton. The precise pattern of expression of these and other proteins can thus serve as molecular markers for TRI exposure and effect in human kidney.

  3. Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium

    PubMed Central

    Pochon, Xavier; Putnam, Hollie M.; Burki, Fabien; Gates, Ruth D.

    2012-01-01

    Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available. PMID:22238660

  4. Cloning a DNA marker associated to wheat scab resistance

    Microsoft Academic Search

    Guihong YU; Hongxiang MA; Zhang XU; Lijian REN; Maoping ZHOU; Weizhong LU

    2004-01-01

    Wheat head blight caused mainly byFusariumgraminearum, is an important wheat disease, causing yield and quality losses. The breeding of resistant varieties is the key measure to control this disease, but the conventional breeding method is of low efficiency. The marker-assisted selection (MAS) can significantly improve the breed- ing efficiency. In this study, four RAPD (randomly amplified polymorphic DNA) markers linked

  5. MARKER-ASSISTED SELECTION FOR DISEASE RESISTANCE IN COMMON BEAN

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Marker-assisted selection (MAS) can provide an effective and efficient breeding tool for maintaining and enhancing disease resistance. For common bean, PCR-based RAPD and SCAR markers linked with more than 20 major genes conditioning resistance to angular leaf spot, anthracnose, ashy stem blight, be...

  6. MOLECULAR PHYLOGENY OF CUCUMIS SPECIES AS REVEALED BY CCSSR MARKER LENGTH AND SEQUENCE VARIATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Cucumis has been partitioned into two subgenera Cucumis (x = 7) and Melo (x = 12). Although the genetic relationships among species within this two subgenera have been well studied using nuclear genetic markers, recent development of chloroplast markers consensus chloroplast simple sequen...

  7. The First Sex-Specific Molecular Marker Discovered in the Moss Pseudocalliergon trifarium

    Microsoft Academic Search

    HELENA KORPELAINEN; I RENE BISANG; L ARS HEDENAS; JOHANNA KOLEHMAINEN

    2008-01-01

    Most dioecious plants do not exhibit discernible sexual dimorphism before sexual maturity. Therefore, it is impossible to address any sex-related questions during the prereproductive phase unless a genetic sex marker is available for gender determination. The aim of the present study was to develop a genetic sex marker for the moss Pseudocalliergon trifarium to allow gender and sex ratio determination

  8. A Molecular Marker-Based Linkage Map of Phaseolus vulgaris L

    Microsoft Academic Search

    C. Eduardo Vallejos; Ney S. Sakiyama; Christine D. Chase

    1992-01-01

    A seed and flower color marker (P), nine seed protein, nine isozyme and 224 restriction fragment length polymorphism marker loci were used to construct a linkage map of the common bean, Phaseolus vulgaris L. (n = 11). The mapping population consisted of a backcross progeny between the Mesoamerican breeding line 'XR-235-1-1' and the Andean cultivar 'Calima'; the former was used

  9. SYSTEMATICS, MORPHOLOGY AND PHYSIOLOGY Evaluation of the RAPD Profi les from Different Body Parts of Euglossa pleosticta Dressler Male Bees (Hymenoptera: Apidae, Euglossina)

    Microsoft Academic Search

    AMÁLIA N. T. PASCUAL; KAREN M. SUZUKI; FERNANDA S. ALMEIDA; LEDA M. K. SODRÉ; SILVIA H. SOFIA

    In the current literature, information is scarce on which part of the adult insect body is suitable for isolation of genomic DNA for genetic analysis based on DNA-markers. In this study, we evaluated RAPD profi les generated from total genomic DNA isolated from distinct body parts (head, legs, thorax + wings and abdomen) of 12 males of Euglossa pleosticta Dressler.

  10. Development of user-friendly functional molecular markers for VvDXS gene conferring muscat flavor in grapevine.

    PubMed

    Emanuelli, F; Sordo, M; Lorenzi, S; Battilana, J; Grando, M S

    2014-01-01

    High fruit and wine quality combined with good climatic adaptation and disease resistance are essential objectives of grape breeding. While several molecular markers are available for pyramiding resistance to fungal pathogens, molecular tools for predicting fruit composition are still scarce. Muscat flavor, caused by the accumulation of monoterpenoids in the berry, is an important target trait for breeding, sought after in both table grapes and wine. Four missense mutations in the VvDXS gene in grape germplasm have been shown to be tightly linked to muscat flavor. Here we present highly reproducible and breeder-friendly functional markers for each of the targeted polymorphisms developed by using either the multiplexed minisequencing SNaPshot™ method, the high-resolution melting (HRM) assay or the cleaved amplified polymorphic sequence system. A total of 242 grapevine accessions were analyzed to optimize these different genotyping methods and to provide allele-specific markers for accurate selection of muscat flavor at early stages of grape breeding programs. The HRM and the minisequencing SNaPshot multiplex assays allow for high-throughput automated screening and are suitable for large-scale breeding programs and germplasm characterization. PMID:24482604

  11. Characterization of the Miiuy Croaker (Miichthys miiuy) Transcriptome and Development of Immune-Relevant Genes and Molecular Markers

    PubMed Central

    Che, Rongbo; Sun, Yueyan; Sun, Dianqiao; Xu, Tianjun

    2014-01-01

    Background The miiuy croaker (Miichthys miiuy) is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. Principal Findings In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13%) were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs) and 8,510 putative single nucleotide polymorphisms (SNPs) were identified from the 69,071 unigenes. Conclusion The miiuy croaker (Miichthys miiuy) transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker. PMID:24714210

  12. Age-related degeneration of articular cartilage in the pathogenesis of osteoarthritis: molecular markers of senescent chondrocytes.

    PubMed

    Musumeci, Giuseppe; Szychlinska, Marta Anna; Mobasheri, Ali

    2015-01-01

    Aging is a natural process by which every single living organism approaches its twilight of existence in a natural way. However, aging is also linked to the pathogenesis of a number of complex diseases. This is the case for osteoarthritis (OA), where age is considered to be a major risk factor of this important and increasingly common joint disorder. Half of the world's population, aged 65 and older, suffers from OA. Although the relationship between the development of OA and aging has not yet been completely understood, it is thought that age-related changes correlate with other risk factors. The most prominent hypothesis linking aging and OA is that chondrocytes undergo premature aging due to several factors, such as excessive mechanical load or oxidative stress, which induce the so called "stress-induced senescent state", which is ultimately responsible for the onset of OA. This review focuses on molecular markers and mechanisms implicated in chondrocyte aging and the pathogenesis of OA. We discuss the most important age-related morphological and biological changes that affect articular cartilage and chondrocytes. We also identify the main senescence markers that may be used to recognize molecular alterations in the extracellular matrix of cartilage as related to senescence. Since the aging process is strongly associated with the onset of osteoarthritis, we believe that strategies aimed at preventing chondrocyte senescence, as well as the identification of new increasingly sensitive senescent markers, could have a positive impact on the development of new therapies for this severe disease. PMID:25010513

  13. Differences in the apportionment of molecular and morphological variation in North American strawberry and the consequences for genetic resource management

    Microsoft Academic Search

    Richard E. Harrison; James J. Luby; Glenn R. Furnier; James F. Hancock

    2000-01-01

    Variation for 24 morphological traits measured in a greenhouse environment and 36 randomly amplified polymorphic DNA (RAPD) markers was assessed among 318 wild octoploid strawberry (Fragariaspp.) genotypes from diverse habitats across the northern USA. RAPD marker frequencies and certain leaf and flower morphology traits (petiole color, leaf mass\\/area ratio, leaflet length and width, flower and receptacle diameter, petal width, flowers\\/inflorescence)

  14. Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers.

    PubMed

    Korshunov, Andrey; Ryzhova, Marina; Hovestadt, Volker; Bender, Sebastian; Sturm, Dominik; Capper, David; Meyer, Jochen; Schrimpf, Daniel; Kool, Marcel; Northcott, Paul A; Zheludkova, Olga; Milde, Till; Witt, Olaf; Kulozik, Andreas E; Reifenberger, Guido; Jabado, Nada; Perry, Arie; Lichter, Peter; von Deimling, Andreas; Pfister, Stefan M; Jones, David T W

    2015-05-01

    Pediatric glioblastoma (pedGBM) is amongst the most common malignant brain tumors of childhood and carries a dismal prognosis. In contrast to adult GBM, few molecular prognostic markers for the pediatric counterpart have been established. We, therefore, investigated the prognostic significance of genomic and epigenetic alterations through molecular analysis of 202 pedGBM (1-18 years) with comprehensive clinical annotation. Routinely prepared formalin-fixed paraffin-embedded tumor samples were assessed for genome-wide DNA methylation profiles, with known candidate genes screened for alterations via direct sequencing or FISH. Unexpectedly, a subset of histologically diagnosed GBM (n = 40, 20 %) displayed methylation profiles similar to those of either low-grade gliomas or pleomorphic xanthoastrocytomas (PXA). These tumors showed a markedly better prognosis, with molecularly PXA-like tumors frequently harboring BRAF V600E mutations and 9p21 (CDKN2A) homozygous deletion. The remaining 162 tumors with pedGBM molecular signatures comprised four subgroups: H3.3 G34-mutant (15 %), H3.3/H3.1 K27-mutant (43 %), IDH1-mutant (6 %), and H3/IDH wild-type (wt) GBM (36 %). These subgroups were associated with specific cytogenetic aberrations, MGMT methylation patterns and clinical outcomes. Analysis of follow-up data identified a set of biomarkers feasible for use in risk stratification: pedGBM with any oncogene amplification and/or K27M mutation (n = 124) represents a particularly unfavorable group, with 3-year overall survival (OS) of 5 %, whereas tumors without these markers (n = 38) define a more favorable group (3-year OS ~70 %).Combined with the lower grade-like lesions, almost 40 % of pedGBM cases had distinct molecular features associated with a more favorable outcome. This refined prognostication method for pedGBM using a molecular risk algorithm may allow for improved therapeutic choices and better planning of clinical trial stratification for this otherwise devastating disease. PMID:25752754

  15. Application of ISSR markers to analyze molecular relationships in Iranian jasmine (Jasminum spp.) accessions.

    PubMed

    Ghasemi Ghehsareh, Masood; Salehi, Hassan; Khosh-Khui, Morteza; Niazi, Ali

    2015-01-01

    There are many species of jasmines in different regions of Iran in natural or cultivated form, and there is no information about their genetic status. Therefore, inter-simple sequence repeat (ISSR) analysis was used to evaluate genetic variations of the 53 accessions representing eight species of Jasminum collected from different regions of Iran. A total of 21 ISSR primers were used which generated 981 bands of different sizes. Mean percentage of polymorphic bands was 90.64 %. Maximum resolving power, polymorphic information content average, and marker index values were 21.55, 0.35, and 14.42 for primers of 3, 4, and 3 respectively. The unweighted pair group method with arithmetic mean dendrogram based on Jaccard's coefficients indicated that 53 accessions were divided into two major clusters. The first major cluster was divided into two subclusters; the subcluster A included Jasminum grandiflorum L., J. officinale L., and J. azoricum L. and the subcluster B consisted of three forms of J. sambac L. (single, semi-double, and double flowers). The second major cluster was divided into two subclusters; the first subcluster (C) included J. humile L., J. primulinum Hemsl., J. nudiflorum Lindl. and the second subcluster (D) consisted of J. fruticans L. At the species level, the highest percentage of polymorphism (34.05 %), numbers of effective alleles (1.16), Shannon index (0.151), and Nei's genetic diversity (0.098) were observed in J. officinale. The lowest values of percentage polymorphism (0.011), number of effective alleles (1.009), Shannon index (0.007), and Nei's genetic diversity (0.005) were obtained for J. nudiflorum. Based on pairwise population matrix of Nei's unbiased genetic identity, the highest identity (0.85) was found between J.officinale and J. azoricum and the lowest identity (0.69) was between J. grandiflorum and J. perimulinum. Based on analysis of molecular variance, the amount of genetic variations among the eight populations was 83 %. This study demonstrated that the ISSR is an useful tool in jasmine genomic diversity studies and to detect their relationships. PMID:25189463

  16. Chromosomal origin of small ring marker chromosomes in man: characterization by molecular genetics.

    PubMed Central

    Callen, D F; Eyre, H J; Ringenbergs, M L; Freemantle, C J; Woodroffe, P; Haan, E A

    1991-01-01

    Ten cases of small ring chromosomes which did not stain with distamycinA/DAPI and did not possess satellite regions associated with nucleolus-organizing regions are described. In situ hybridization with a battery of biotinylated pericentric repeat probes specific either for individual chromosomes or for groups of chromosomes allowed the identification of the chromosomal origin of these marker chromosomes. There was one example of a marker derived from each of chromosomes 1, 3, 6, 14, 16, 18, 20, 13 or 21, and the X, and there were two examples of markers derived from chromosome 12. One case possessed two markers, one derived from chromosome 6, and one derived from the X. The mechanism of generation of ring marker chromosomes is discussed. Five of seven cases who could be phenotypically assessed were abnormal. Three of these--the first with a ring chromosome derived from chromosome 1; the second with two markers, one derived from chromosome 6 and the other from the X chromosome; and the third with a ring chromosome derived from chromosome 20--each possessed distinctive facies. Additional cases with identified rings may allow the delineation of new chromosomal syndromes. Images Figure 1 p776-a Figure 2 p778-a p779-a p780-a p781-a PMID:2014800

  17. Insights into the phylogeny of sporadotrichid ciliates (Protozoa, Ciliophora: Hypotricha) based on genealogical analyses of multiple molecular markers

    NASA Astrophysics Data System (ADS)

    Hu, Xiaoyan; Hu, Xiaozhong; Al-Rasheid, Khaled A. S.; Al-Farraj, Saleh A.; Song, Weibo

    2011-01-01

    The sporadotrichid ciliates are an especially diverse group. A number of investigators have studied the morphological, morphogenetic, and molecular relationships among members of this group. Despite this, a consistent classification is still lacking and several important questions about the phylogenetic relationships within this group remain unsolved. To improve our understanding of these relationships, we constructed phylogenetic trees using the nucleotide sequences of the small-subunit rRNA (SSrRNA) gene and amino acid sequences of actin I and ?-tubulin. Analyses of SSrRNA gene sequences indicated that: 1) the Sporadotrichida sensu Lynn (2008) and the Oxytrichidae are polyphyletic; 2) the Uroleptus species, which are classified to urostylids, formed a sister group with the oxytrichids; 3) Halteria grandinella, which is grouped morphologically with oligotrich species, clustered within the oxytrichids. These results are congruent with previous studies based on SSrRNA gene sequences. However, the amino acid sequences of actin I and ?-tubulin yielded different topologies. The main results are: 1) in all phylogenetic trees, the genus Oxytricha was paraphyletic; 2) Uroleptus was sister to a subset of Urostyla and Holosticha, albeit with low supporting values; 3) Halteria grandinella was separated distantly from the Oxytrichidae in trees inferred from actin I amino acid sequences but clustered with oligotrichids in the ?-tubulin analysis. The inconsistency among the trees inferred from these different molecular markers may be caused by rapidly accumulated genetic characterizations of ciliates. Further studies with additional molecular markers and sampling of more taxa are expected to better address the relationships among sporadotrichids.

  18. Transcript Profiling and Identification of Molecular Markers for Early Microspore Embryogenesis in Brassica napus1[W][OA

    PubMed Central

    Malik, Meghna R.; Wang, Feng; Dirpaul, Joan M.; Zhou, Ning; Polowick, Patricia L.; Ferrie, Alison M.R.; Krochko, Joan E.

    2007-01-01

    Isolated microspores of Brassica napus are developmentally programmed to form gametes; however, microspores can be reprogrammed through stress treatments to undergo appropriate divisions and form embryos. We are interested in the identification and isolation of factors and genes associated with the induction and establishment of embryogenesis in isolated microspores. Standard and normalized cDNA libraries, as well as subtractive cDNA libraries, were constructed from freshly isolated microspores (0 h) and microspores cultured for 3, 5, or 7 d under embryogenesis-inducing conditions. Library comparison tools were used to identify shifts in metabolism across this time course. Detailed expressed sequence tag analyses of 3 and 5 d cultures indicate that most sequences are related to pollen-specific genes. However, semiquantitative and real-time reverse transcription-polymerase chain reaction analyses at the initial stages of embryo induction also reveal expression of embryogenesis-related genes such as BABYBOOM1, LEAFY COTYLEDON1 (LEC1), and LEC2 as early as 2 to 3 d of microspore culture. Sequencing results suggest that embryogenesis is clearly established in a subset of the microspores by 7 d of culture and that this time point is optimal for isolation of embryo-specific expressed sequence tags such as ABSCISIC ACID INSENSITIVE3, ATS1, LEC1, LEC2, and FUSCA3. Following extensive polymerase chain reaction-based expression profiling, 16 genes were identified as unequivocal molecular markers for microspore embryogenesis in B. napus. These molecular marker genes also show expression during zygotic embryogenesis, underscoring the common developmental pathways that function in zygotic and gametic embryogenesis. The quantitative expression values of several of these molecular marker genes are shown to be predictive of embryogenic potential in B. napus cultivars (e.g. ‘Topas’ DH4079, ‘Allons,’ ‘Westar,’ ‘Garrison’). PMID:17384168

  19. Towards the Development of a Molecular Map in Switchgrass: I. Microsatellite Marker Development

    SciTech Connect

    Gunter, L.E.

    2001-08-23

    The long-term goal of the switchgrass breeding program is to improve regionally adapted varieties and increase biomass yield and feedstock quality. Although, to some extent, biomass yields are dependent on environmental constraints, increased yield can be achieved through the development of genotypes with improved seasonal adaptation, tolerance to unfavorable environmental conditions, and improved resistance to pest and disease. To date, improvement in switchgrass has relied on recurrent breeding strategies based on phenotypic or genotypic selection. Yield improvements have been modest by this method. If we expect to make significant increase in yields, we need tools that will allow us to map complex traits and uncover the genes that influence them. A genetic linkage map could be a powerful tool for accelerating switchgrass development through marker-assisted selection, breeding and recombination. This type of mapping requires the development of markers that can be associated with phenotypic traits in a population of known pedigree. The most commonly used markers for mapping include restriction fragment length polymorphisms (RFLP) and simple sequence repeats (SSR). At ORNL, we have been concentrating on the development of SSR markers, while our colleagues at the University of Georgia are developing RFLP markers in order to select parents to produce a mapping population and from there to create a framework map from {approx}100 F1 progeny.

  20. Sources of Bias in Specimens for Research About Molecular Markers for Cancer

    PubMed Central

    Ransohoff, David F.; Gourlay, Margaret L.

    2010-01-01

    Claims about the diagnostic or prognostic accuracy of markers often prove disappointing when “discrimination” found between cancers versus normals is due to bias, a systematic difference between compared groups. This article describes a framework to help simplify and organize current problems in marker research by focusing on the role of specimens as a source of bias in observational research and using that focus to address problems and improve reliability. The central idea is that the “fundamental comparison” in research about markers (ie, the comparison done to assess whether a marker discriminates) involves two distinct processes that are “connected” by specimens. If subject selection (first process) creates baseline inequality between groups being compared, then laboratory analysis of specimens (second process) may erroneously find positive results. Although both processes are important, subject selection more fundamentally influences the quality of marker research, because it can hardwire bias into all comparisons in a way that cannot be corrected by any refinement in laboratory analysis. An appreciation of the separateness of these two processes—and placing investigators with appropriate expertise in charge of each—may increase the reliability of research about cancer biomarkers. PMID:20038718

  1. Molecular characterization of Klebsiella pneumoniae isolated from renal transplanted patients: virulence markers, extended-spectrum ?-lactamases, and genetic relatedness.

    PubMed

    Calhau, Vera; Boaventura, Luísa; Ribeiro, Graça; Mendonça, Nuno; da Silva, Gabriela J

    2014-07-01

    The objective was to characterize virulence markers and ?-lactam resistance in Klebsiella pneumoniae isolates from renal transplant patients and to evaluate their genetic relatedness. Two main genetic lineages were detected: 1 carried bla(CTX-M-15) not associated to IncFIIA plasmid replicon, which was found on the other lineage not expressing CTX-M-type enzyme. PAI III(536) and PAI II(CFT073) were detected for the first time in K. pneumoniae in 1 clone, while the siderophore kfu was carried by the other, with only PAI IV(536). The molecular data indicate colonization before admission and fuel the discussion on implementation of antibiotherapy before surgery. PMID:24746826

  2. Overexpression of hMTH1 mRNA: a molecular marker of oxidative stress in lung cancer cells

    Microsoft Academic Search

    Christopher H Kennedy; Rafael Cueto; Steven A Belinsky; John F Lechner; William A Pryor

    1998-01-01

    Human MutT homologue (hMTH1) mRNA was overexpressed in SV-40-transformed non-tumorigenic human bronchial epithelial cells (BEAS-2B cells) and in 11 out of 12 human lung cancer cell lines relative to normal human bronchial epithelial cells. Expression levels of hMTH1 mRNA were inversely proportional to cellular levels of 8-oxo-deoxyguanosine. Together, these results suggest that hMTH1 gene expression may represent a molecular marker

  3. Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models

    E-print Network

    Borenstein, Elhanan

    Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models Genome 570 February, 2010 Week 6: Restriction sites, RAPDs, microsatellites, likelihood, hidden Markov models ­ p.1, likelihood, hidden Markov models ­ p.2/62 #12;Number of sequences in a restriction site location Nk = r k 3k

  4. Review article Using molecular tools for diagnosis

    E-print Network

    Paris-Sud XI, Université de

    are ribosomal DNA and RNA as well as fragments derived from RAPD (random amplified polymorphic DNA). The most studied protozoan genera have been: Eimeria, Babesia, Theileria, Trypanosoma and Cryptosporidium parasitology / molecular tool / polymerase chain reaction (PCR) I ran- dom amplified polymorphic DNA (RAPD

  5. Prevalence of molecular markers of Plasmodium falciparum drug resistance in Dakar, Senegal

    PubMed Central

    2012-01-01

    Background As a result of the widespread resistance to chloroquine and sulphadoxine-pyrimethamine, artemisinin-based combination therapy (ACT) (including artemether-lumefantrine and artesunate-amodiaquine) has been recommended as a first-line anti-malarial regimen in Senegal since 2006. Intermittent preventive treatments with anti-malarial drugs based on sulphadoxine-pyrimethamine are also given to children or pregnant women once per month during the transmission season. Since 2006, there have been very few reports on the susceptibility of Plasmodium falciparum to anti-malarial drugs. To estimate the prevalence of resistance to several anti-malarial drugs since the introduction of the widespread use of ACT, the presence of molecular markers associated with resistance to chloroquine and sulphadoxine-pyrimethamine was assessed in local isolates at the military hospital of Dakar. Methods The prevalence of genetic polymorphisms in genes associated with anti-malarial drug resistance, i.e., Pfcrt, Pfdhfr, Pfdhps and Pfmdr1, and the copy number of Pfmdr1 were evaluated for a panel of 174 isolates collected from patients recruited at the military hospital of Dakar from 14 October 2009 to 19 January 2010. Results The Pfcrt 76T mutation was identified in 37.2% of the samples. The Pfmdr1 86Y and 184F mutations were found in 16.6% and 67.6% of the tested samples, respectively. Twenty-eight of the 29 isolates with the 86Y mutation were also mutated at codon 184. Only one isolate (0.6%) had two copies of Pfmdr1. The Pfdhfr 108N/T, 51I and 59R mutations were identified in 82.4%, 83.5% and 74.1% of the samples, respectively. The double mutant (108N and 51I) was detected in 83.5% of the isolates, and the triple mutant (108N, 51I and 59R) was detected in 75.3%. The Pfdhps 437G, 436F/A and 613S mutations were found in 40.2%, 35.1% and 1.8% of the samples, respectively. There was no double mutant (437G and 540E) or no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E). The prevalence of the quadruple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G) was 36.5%. Conclusions Since 2004, the prevalence of chloroquine resistance had decreased. The prevalence of isolates with high-level pyrimethamine resistance is 83.5%. The prevalence of isolates resistant to sulphadoxine is 40.2%. However, no quintuple mutant (Pfdhfr 108N, 51I and 59R and Pfdhps 437G and 540E), which is associated with a high level of sulphadoxine-pyrimethamine resistance, has been identified to date. The resistance to amodiaquine remains moderate. PMID:22694921

  6. Conservation phylogenetics of helodermatid lizards using multiple molecular markers and a supertree approach

    Microsoft Academic Search

    Michael E. Douglas; Marlis R. Douglas; Gordon W. Schuett; Daniel D. Beck; Brian K. Sullivan

    2010-01-01

    We analyzed both mitochondrial (mt-) and nuclear (n) DNAs in a conservation phylogenetic framework to examine deep and shallow histories of the Beaded Lizard (Heloderma horridum) and Gila Monster (H. suspectum) throughout their geographic ranges in North and Central America. Both mtDNA and intron markers clearly partitioned each species. One intron and mtDNA further subdivided H. horridum into its four

  7. Development of nuclear gene-derived molecular markers linked to legume genetic maps

    Microsoft Academic Search

    Hong-Kyu Choi; Melissa A. Luckow; Jeff Doyle; Douglas R. Cook

    2006-01-01

    The systematic identification of the orthologous features of related organisms greatly facilitates comparative genomics, including research on genome evolution and comparative genetic mapping. In this study, we selected 274 unique gene sequences for the development of PCR-based genetic markers across fifteen legume genomes, representing six crop or model legume species from the phaseoloid and inverted repeat loss clades (IRLC). DNA

  8. A clinical, cytogenetic, FISH and molecular study of supernumerary marker 15 chromosomes

    SciTech Connect

    Dennis, N.R. [Princess Anne Hospital, Southampton (United Kingdom); Crolla, J.A.; Harvey, J.F. [Salisbury District Hospital (United Kingdom)

    1994-09-01

    We studied 17 patients with supernumerary marker chromosomes shown by fluorescent in situ hybridization (FISH) with the 15-centromere specific probe pTRA-25 to be 15-derived. Genetic constitution of the marker chromosomes was investigated using FISH, Southern blot analysis and PCR for proximal and distal loci on 15q as well as conventional cytogenetics. Eight of the 17 patients were mentally retarded. Six of the eight carried a de novo marker 15 containing one or two doses of loci known to be in or near the Prader-Willi/Angelman (PWS/AS) region, whereas none of the nine non-retarded patients had duplications of this region, and only two of the eight whose parents were available had a de novo marker. None of the mentally retarded patients had PWS or AS. In two retarded patients (one de novo, one familial) there was no duplication of the PWS/AS region. Uniparental disomy affecting the normal 15 homologs was excluded in 10 of the patients, including all eight with mental retardation.

  9. Molecular markers to determine ecological fate of Bacillus thuringiensis subsp. kurstaki

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacillus thuringiensis (“Bt”) is a ubiquitous soil bacterium with entomopathogenic properties. One strain, Bt subsp. kurstaki (“Btk”), is highly toxic to lepidopteran larvae and used in many commercial products for biological pest control. We designed a set of DNA markers that successfully identifi...

  10. A molecular marker-based linkage map of Phaseolus vulgaris L.

    PubMed

    Vallejos, C E; Sakiyama, N S; Chase, C D

    1992-07-01

    A seed and flower color marker (P), nine seed protein, nine isozyme and 224 restriction fragment length polymorphism marker loci were used to construct a linkage map of the common bean, Phaseolus vulgaris L. (n = 11). The mapping population consisted of a backcross progeny between the Mesoamerican breeding line 'XR-235-1-1' and the Andean cultivar 'Calima'; the former was used as the recurrent parent. A bean PstI genomic library enriched for single copy sequences (95%) was the source of DNA probes. Sixty percent of the probes tested detected polymorphisms between the parental genotypes with at least one of the four restriction enzymes used here (DraI, EcoRI, EcoRV and HindIII). The computer software Mapmaker was used to determine the linkage relationships and linear order of segregating markers. These markers assorted into 11 linkage groups covering 960 cM of the bean genome. Partial linkage data were used to estimate the total length of the genome at 1200 cM. This estimate and that for the physical size of the genome yield an average ratio of 530 kb/cM. The relatively small size of the genome makes this crop species a good candidate for the isolation of genes via chromosome walking techniques. PMID:1352759

  11. Molecular markers in circulating tumour cells from metastatic colorectal cancer patients

    PubMed Central

    Gazzaniga, Paola; Gradilone, Angela; Petracca, Arianna; Nicolazzo, Chiara; Raimondi, Cristina; Iacovelli, Roberto; Naso, Giuseppe; Cortesi, Enrico

    2010-01-01

    Abstract The prognosis of metastatic cancer patients is still largely affected by treatment failure, mainly due to drug resistance. The hypothesis that chemotherapy might miss circulating tumour cells (CTCs) and particularly a subpopulation of more aggressive, stem-like CTCs, characterized by multidrug resistance, has been recently raised. We investigated the prognostic value of drug resistance and stemness markers in CTCs from metastatic colorectal cancer patients treated with oxaliplatin (L-OHP) and 5-fluoruracil (5-FU) based regimens. Forty patients with metastatic colorectal cancer were enrolled. CTCs were isolated from peripheral blood and analysed for the expression of aldheyde dehydrogenase 1 (ALDH1), CD44, CD133 (used as markers of stemness), multidrug resistance related protein 5 (MRP5 used as marker of resistance to 5-FU and L-OHP) and survivin (used as a marker of apoptosis resistance). CTCs were found in 27/40 (67%) patients. No correlation was found between the expression of either CD44 and CD133 in CTCs and the outcome of patients, while a statistically significant shorter progression-free survival was found in patients with CTCs positive for the expression of ALDH1, survivin and MRP5. These results support the idea that isolating survivin and MRP5+ CTCs may help in the selection of metastatic colorectal cancer patients resistant to standard 5-FU and L-OHP based chemotherapy, for which alternative regimens may be appropriate. PMID:20597995

  12. Identification of molecular markers associated with low chill/heat tolerance in raspberry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New genetic markers were developed which are linked to cold and heat tolerant raspberries. Raspberry is a cool season crop, and as such, cannot tolerate the high temperatures of the South during the normal growing season. Expanding the commercial growth range of raspberry production to the southern...

  13. Molecular markers associated with resistance to Aspergillus flavus in maize: QTL and discriminant analyses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aflatoxin contamination of maize (Zea mays L.) grain caused by Aspergillus flavus is a serious health hazard to animals and humans. Resistance to infection by A. flavus is poorly understood. The objectives of this investigation were to identify potential candidate markers associated with resistance ...

  14. Molecular genetic characterization of lasquerella new industrial crop using DArTseq markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DArTseq, a new SNP-based marker platform, was developed and used to analyze the genetic diversity of the US germplasm collection of lesquerella. Lesquerella is a new oilseed crop in the Brassica family found native in the American Southwest. The potential of the species as a domestic source of indu...

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

    Microsoft Academic Search

    P. W. Skroch; J. Nienhuis

    1995-01-01

    Ten snap bean (Phaseolus vulgaris) genotypes were screened for polymorphism with 400 RAPD (random amplified polymorphic DNA) primers. Polymorphic RAPDs were scored and classified into three categories based on ethidium bromide staining intensity. An average of 5.19 RAPD bands were scored per primer for the 364 primers that gave scorable amplification products. An average of 2.15 polymorphic RAPDs were detected

  16. A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

    PubMed Central

    2013-01-01

    Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications. PMID:24377374

  17. Mitochondrial DNA variation and RAPD mark oleasters, olive and feral olive from Western and Eastern Mediterranean.

    PubMed

    De Caraffa, V. Bronzini; Maury, J.; Gambotti, C.; Breton, C.; Bervillé, A.; Giannettini, J.

    2002-05-01

    The study of genetic diversity within the olive-tree (cultivated and wild forms) may be useful to reveal agronomic traits in the wild germplasm and to try to understand the history of the olive-tree domestication. In this way, a study of nuclear and mitochondrial DNAs of cultivated and wild olives from two Corsican and Sardinian Mediterranean islands was performed using RAPD and RFLP markers. Our results show that most of the varieties and most of the oleasters were separated using the UPGMA dendrogram based on the Nei and Li similarity index. Most of oleasters carried either the MOM or MCK mitotype, characteristic of olives in the Western Mediterranean, whereas most of the varieties carried the ME1 mitotype, characteristic of olives in the East Mediterranean. The results indicate that the combination of mitotype and RAPD markers can be used as a powerful tool for differentiating two groups in the wild forms: the Western true oleasters and the feral forms. The true oleasters are characterized by a Western mitotype and a Western RAPD pattern. Feral forms originate either from varieties or from hybridisation between a variety and an oleaster. Consequently, as expected, some of them aggregated with the varieties from which they were derived. The other feral forms are clustered with the oleasters and were detected only by their mitotype determination. This study has also permitted us to differentiate two populations of cultivated olives in Corsica: one with close relationships with Italian varieties (influenced by the East) and one selected from local oleasters probably due to a better local adaptation than foreign varieties. PMID:12582632

  18. RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

    PubMed Central

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-01-01

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

  19. Genetic analysis of two Portuguese populations of Ruditapes decussatus by RAPD profiling

    NASA Astrophysics Data System (ADS)

    Pereira, Jorge C.; Chaves, Raquel; Leitão, Alexandra; Matias, Domitilia; Guedes-Pinto, Henrique

    2011-09-01

    The clam Ruditapes decussatus is commercially important in the south of Portugal. The random amplified polymorphic DNA (RAPD) technique was applied to assess the genetic diversity and population structure of two Portuguese populations occurring in the Ria Formosa (Faro) and the Ria de Alvor, respectively. Twenty-five individuals of each population were investigated by RAPD profiles. Genetic diversity within populations, measured by the percentage of polymorphic loci ( %P), varied between 68.57% (Alvor) and 73.88% (Faro). Shannon's information index ( H) and Nei's gene diversity ( h) were 0.281 and 0.176, respectively, for the Alvor population and 0.356 and 0.234 for the Faro population. Overall, genetic variation within R. decussatus populations was high. The total genetic diversity ( H T) was explained by a low variation between populations ( G ST = 0.145), which is consistent with high gene flow ( N m = 2.9). The analysis of molecular variance (AMOVA) showed that 65% of variability is within populations and 35% between populations (?PT = 0.345; P ? 0.001). The value of Nei's genetic distance was 0.0881, showing a low degree of population genetic distance, despite the different geographic origin. This is the first study on the population genetics of R. decussatus by RAPD technique. The results may be useful for restocking programs and aquaculture.

  20. Phylogenetic Relationship in Different Commercial Strains of Pleurotus nebrodensis Based on ITS Sequence and RAPD

    PubMed Central

    Alam, Nuhu; Shim, Mi Ja; Lee, Min Woong; Shin, Pyeong Gyun; Yoo, Young Bok

    2009-01-01

    The molecular phylogeny in nine different commercial cultivated strains of Pleurotus nebrodensis was studied based on their internal transcribed spacer (ITS) region and RAPD. In the sequence of ITS region of selected strains, it was revealed that the total length ranged from 592 to 614 bp. The size of ITS1 and ITS2 regions varied among the strains from 219 to 228 bp and 211 to 229 bp, respectively. The sequence of ITS2 was more variable than ITS1 and the region of 5.8S sequences were identical. Phylogenetic tree of the ITS region sequences indicated that selected strains were classified into five clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by RAPD with 20 arbitrary primers. Twelve primers were efficient to applying amplification of the genomic DNA. The sizes of the polymorphic fragments obtained were in the range of 200 to 2000 bp. RAPD and ITS analysis techniques were able to detect genetic variation among the tested strains. Experimental results suggested that IUM-1381, IUM-3914, IUM-1495 and AY-581431 strains were genetically very similar. Therefore, all IUM and NCBI gene bank strains of P. nebrodensis were genetically same with some variations. PMID:23983530

  1. Applications of molecular markers and DNA sequences in identifying fungal pathogens of cool season grain legumes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular techniques have now been widely applied in many disciplines of biological sciences including fungal identification in microbial ecology and plant pathology. In plant pathology, it is now common to use molecular techniques to identify and study plant pathogens of many agronomic and horticul...

  2. Identification of the IFITM Family as a New Molecular Marker in Human Colorectal Tumors

    Microsoft Academic Search

    Pauline Andreu; Sabine Colnot; Cecile Godard; Pierre Laurent-Puig; Dominique Lamarque; Axel Kahn; Christine Perret; Beatrice Romagnolo

    2006-01-01

    We analyzed the expression profiles of intestinal adenomas from a new murine familial adenomatous polyposis model (Apc#14\\/+) using suppression subtractive hybridization to identify novel diagnostic markers of colorectal carcinogenesis. We identified 18 candidate genes having increased expression levels in the adenoma. Subsequent Northern blotting, real- time reverse transcription-PCR, and in situ hybridization analysis confirmed their induction in B-catenin-activated epithelial cells

  3. Identification of Brassica oleracea monosomic alien chromosome addition lines with molecular markers reveals extensive gene duplication

    Microsoft Academic Search

    J. Mitchell McGrath; Carlos F. Quiros; John J. Harada; Benoit S. Landry

    1990-01-01

    Chromosomes of Brassica oleracea (2n=18) were dissected from the resynthesized amphidiploid B. napus Hakuran by repeated backcrosses to B. campestris (2n=20), creating a series of monosomic alien chromosome addition line plants (2n=21). Using morphological, isozyme and restriction fragment length polymorphism markers (RFLPs), 81 putative loci were identified. Of nine possible synteny groups, seven were represented in the 25 monosomic addition

  4. The utility of fast evolving molecular markers for studying speciation in the Antarctic benthos

    Microsoft Academic Search

    Christoph Held; Florian Leese

    2007-01-01

    The Southern Ocean is surprisingly rich in species that coexist in one of the most extreme environments on Earth yet the processes\\u000a leading to speciation in this ecosystem are not well understood. To remedy this, tools that measure the genetic connectedness\\u000a within a species are needed. Although useful for phylogenetic purposes, the readily available mitochondrial markers (e.g.\\u000a 16S, COI) suffer

  5. Detection by RAPD-PCR of polymorphism in populations of Bemisia tabaci (Genn.) collected on four host plants from Iran.

    PubMed

    Samih, M A; Izadi, H; Mahdian, K

    2006-01-01

    The sweetpotato whitefly, Bernisia tabaci (Genn.) (Hom: Aleyrodidae) is a major pest of field crops, vegetables and ornamentals in Iran. In this study, the infested leaves of cucumber (Cucurnis sativus L.) zucchini (Cucurbita pepo L.) eggplant (Solanum melongena L.) and cotton (Gossypium hirsutum L.) with whitefly nymphs and pupae were collected from Iran, and were transferred to the laboratory. The newly emerged males and females of each population were released separately into a large cage set on cotton plants. Experiments were carried out in a growth chamber on cotton, (Varamin 76 variety) at 24+/-20C, 55+/-3% RH and 16:8 h (L:D) photoperiod. The adults of every collected population after emergency were reared in the large cages (40x50x70) containing pots of cotton plants. In this study five decamer primers were used in the amplification reactions. All the primers produced polymorphisms. Totally, 71 RAPD markers were found. The amplified DNA fragments were 200 to 3000 bp. The Jaccards and Nies similarity coefficient and Euclidian distances were used to generate a dendrogram based on unweighted pair-group method with arithmetic averages (UPGMA). The clusters based on RAPD markers correlate fairly well with classification scheme based on biological traits. This study suggested that RAPD can be useful technique to study DNA polymorphism in Bemisia tabaci. PMID:17385530

  6. Generation of expressed sequence tags under cadmium stress for gene discovery and development of molecular markers in chickpea.

    PubMed

    Gaur, Rashmi; Bhatia, Sabhyata; Gupta, Meetu

    2014-07-01

    Chickpea is the world's third most important legume crop and belongs to Fabaceae family but suffered from severe yield loss due to various biotic and abiotic stresses. Development of modern genomic tools such as molecular markers and identification of resistant genes associated with these stresses facilitate improvement in chickpea breeding towards abiotic stress tolerance. In this study, 1597 high-quality expressed sequence tags (ESTs) were generated from a cDNA library of variety Pusa 1105 root tissue after cadmium (Cd) treatment. Assembly of ESTs resulted in a total of 914 unigenes of which putative homology was obtained for 38.8 % of unigenes after BLASTX search. In terms of species distribution, majority of sequences found similarity with Medicago truncatula followed by Glycine max, Vitis vinifera and Populus trichocarpa and Pisum sativum sequences. Functional annotation was assigned using Blast2Go, and the Gene Ontology (GO) terms were categorized into biological process, molecular function and cellular component. Approximately 10.83 % of unigenes were assigned at least one GO term. Moreover, in the distribution of transcripts into various biological pathways, 20 of the annotated transcripts were assigned to ten pathways in KEGG database. A majority of the genes were found to be involved in sulphur and nitrogen metabolism. In the quantitative real-time PCR analysis, five of the transcription factors and three of the transporter genes were found to be highly expressed after Cd treatment. Besides, the utility of ESTs was demonstrated by exploiting them for the development of 83 genic molecular markers including EST-simple sequence repeats and intron targeted polymorphism that would assist in tagging of genes related to metal stress for future prospects. PMID:24414095

  7. Influence of different colloids on molecular markers of haemostasis and platelet function in patients undergoing major abdominal surgery.

    PubMed

    Hüttner, I; Boldt, J; Haisch, G; Suttner, S; Kumle, B; Schulz, H

    2000-09-01

    Synthetic colloids have been reported to cause haemorrhagic complications. The effects of perioperative volume replacement with 4% gelatin (n = 20), 6% low-molecular weight (LMW) hydroxyethyl starch (HES) (Mw: 70,000 dalton; HES 70/0.5; n = 20) and 6% medium-molecular weight (MMW) HES (Mw: 200,000 dalton; HES 200/0.5; n = 20) on haemostasis were assessed in patients undergoing major abdominal surgery. Volume was administered to keep central venous pressure (CVP) between 10 and 14 mm Hg. Conventional global coagulation tests, molecular markers of coagulation, and platelet function (using a platelet function analyser (PFA-100) with ADP as inductor) were monitored prior to surgery (T0), at the end of surgery (T1), 4 h after the end of surgery (T2), and on the morning of the first postoperative day (T3). Significantly more gelatin (2900 (SD 320) ml) than HES 200 (2150 (312) ml) was given during the study period. Bleeding and the use of allogeneic blood-blood products were similar in all groups. Markers of thrombin generation (F1 + 2), of thrombin neutralization (TAT III complex), and of fibrin formation and its degradation (D-dimer) increased significantly during and after surgery without showing significant group differences. Factor VIII and von Willebrand factor (vWF) also increased in all groups beyond the normal range, showing the significantly highest increase in the gelatin-treated group (VIII: from 173 (36) to 266 (33) U dl-1; vWF: from 164(33) to 238 (31) U dl-1). Platelet function remained within the normal range and without group differences throughout the study period. We can conclude that all three solutions can be used safely in patients undergoing major abdominal surgery with regard to the haemostatic process. PMID:11103184

  8. A multi-molecular marker assessment of organic pollution in shore sediments from the Río de la Plata Estuary, SW Atlantic.

    PubMed

    Venturini, Natalia; Bícego, Márcia C; Taniguchi, Satie; Sasaki, Silvio T; García-Rodríguez, Felipe; Brugnoli, Ernesto; Muniz, Pablo

    2015-02-28

    Organic pollution was evaluated in surface sediments along the middle portion of the Río de la Plata Estuary, SW Atlantic. A multi-molecular marker approach was performed to identify major sources of organic compounds using diagnostic indices. The relative contribution of different sources of hydrocarbons was quantified by source apportionment employing Principal Component Analysis/Multiple Linear Regression (PCA/MLR) as chemometric technique. All molecular markers indicated high chronic organic pollution in the stations of Montevideo Bay. Main sources of aliphatic and polycyclic aromatic hydrocarbons were petroleum inputs and combustion, due to oil transport and refinement, harbour activities and vehicular emissions. Major sources of linear alkylbenzenes and steroids were industrial and domestic sewage. Although, significant anthropogenic inputs, a natural footprint of terrestrial higher plants contribution was recognized. Multi-molecular marker and comprehensive assessments can improve the establishment of more precise regulation actions to reduce pollution levels. PMID:25060626

  9. Improving the reliability of molecular sexing of birds using a W-specific marker

    Microsoft Academic Search

    DAIZABURO SHIZUKA; BRUCE E. LYON

    2008-01-01

    Molecular techniques for identifying sex of birds utilize length differences between CHD-Z and CHD-W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W-specific primer can be used in conjunction with a pre-existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American

  10. The bioenergetic signature of lung adenocarcinomas is a molecular marker of cancer diagnosis and prognosis.

    PubMed

    Cuezva, José M; Chen, Guoan; Alonso, Andrés M; Isidoro, Antonio; Misek, David E; Hanash, Samir M; Beer, David G

    2004-07-01

    The aim of this study was to investigate the mitochondrial bioenergetic signature of lung adenocarcinomas as a prognostic marker of cancer progression. For this purpose, a series of 90 lung adenocarcinomas and 10 uninvolved lung samples were examined for quantitative differences in protein expression using two-dimensional polyacrylamide gel electrophoresis. The beta subunit of the mitochondrial H(+)-ATP synthase (beta-F1-ATPase) and heat shock protein 60 (Hsp 60), and the glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH), used to define the bioenergetic cellular (BEC) index, were identified using mass spectrometry and specific antibodies. Correlations of the expression level of the protein markers and of the BEC index were established with the clinicopathological information of the tumors and the follow-up data of the patients. The expression of beta-F1-ATPase is significantly reduced in lung adenocarcinomas in the absence of significant changes in the expression of Hsp 60 and of a major GAPDH isoform. Cross-validation analysis using the beta-F1-ATPase/Hsp 60 ratio and GAPDH expression as predictor variables revealed a classification sensitivity of 97.3%. The beta-F1-ATPase/Hsp 60 ratio is significantly higher in well differentiated and bronchioloalveolar tumors than in moderate or poorly differentiated and in bronchial-derived tumors. The BEC index of T1 tumors was significantly higher than that of T2 tumors. Likewise, stage IA tumors had a higher BEC index than stage IB tumors. Kaplan-Meier survival analysis using the BEC index as predictor of survival revealed that within tumors of the same size or stage I or with no lymph node metastasis (N0) the patients bearing 'low' BEC index tumors had a significant worse prognosis. We conclude that the bioenergetic signature of lung adenocarcinomas is altered, further providing a relevant marker for the diagnosis and classification of lung adenocarcinomas, and for the prognosis of lung cancer patients. PMID:14963017

  11. [Incomplete congruence between morphobiological characters and sex-specific molecular markers in Pacific salmons: 1. Analysis of discrepancy in five species of the genus Oncorhynchus].

    PubMed

    Brykov, Vl A; Kukhlevski?, A D; Podlesnykh, A V

    2010-07-01

    The congruence between molecular markers, identifying the presence of the Y chromosome, and secondary sexual characters was examined in Asian populations of five Pacific salmon species: pink salmon (Oncorhynchus gorbuscha), chum salmon (O. keta), sockeye salmon (O. nerka), chinook salmon (O. tschawytsha), and sima (O. masou). It was demonstrated that in all species examined, the presence or absence of sex-specific molecular markers was to a considerable degree congruent with secondary sexual characters, but in some cases, an incongruence was found. These findings suggested that the mechanism underlying this phenomenon was similar or identical in all species examined. Possible genetic and physiological explanations of this phenomenon are discussed. PMID:20795502

  12. Activation loop phosphorylation of a protein kinase is a molecular marker of organelle size that dynamically reports flagellar length

    PubMed Central

    Cao, Muqing; Meng, Dan; Wang, Liang; Bei, Shuqing; Snell, William J.; Pan, Junmin

    2013-01-01

    Specification of organelle size is crucial for cell function, yet we know little about the molecular mechanisms that report and regulate organelle growth and steady-state dimensions. The biflagellated green alga Chlamydomonas requires continuous-length feedback to integrate the multiple events that support flagellar assembly and disassembly and at the same time maintain the sensory and motility functions of the organelle. Although several length mutants have been characterized, the requisite molecular reporter of length has not been identified. Previously, we showed that depletion of Chlamydomonas aurora-like protein kinase CALK inhibited flagellar disassembly and that a gel-shift–associated phosphorylation of CALK marked half-length flagella during flagellar assembly. Here, we show that phosphorylation of CALK on T193, a consensus phosphorylation site on the activation loop required for kinase activity, is distinct from the gel-shift–associated phosphorylation and is triggered when flagellar shortening is induced, thereby implicating CALK protein kinase activity in the shortening arm of length control. Moreover, CALK phosphorylation on T193 is dynamically related to flagellar length. It is reduced in cells with short flagella, elevated in the long flagella mutant, lf4, and dynamically tracks length during both flagellar assembly and flagellar disassembly in WT, but not in lf4. Thus, phosphorylation of CALK in its activation loop is implicated in the disassembly arm of a length feedback mechanism and is a continuous and dynamic molecular marker of flagellar length during both assembly and disassembly. PMID:23836633

  13. Sequence characterization, in silico mapping and cytosine methylation analysis of markers linked to apospory in Paspalum notatum.

    PubMed

    Podio, Maricel; Rodríguez, María P; Felitti, Silvina; Stein, Juliana; Martínez, Eric J; Siena, Lorena A; Quarin, Camilo L; Pessino, Silvina C; Ortiz, Juan Pablo A

    2012-12-01

    In previous studies we reported the identification of several AFLP, RAPD and RFLP molecular markers linked to apospory in Paspalum notatum. The objective of this work was to sequence these markers, obtain their flanking regions by chromosome walking and perform an in silico mapping analysis in rice and maize. The methylation status of two apospory-related sequences was also assessed using methylation-sensitive RFLP experiments. Fourteen molecular markers were analyzed and several protein-coding sequences were identified. Copy number estimates and RFLP linkage analysis showed that the sequence PnMAI3 displayed 2-4 copies per genome and linkage to apospory. Extension of this marker by chromosome walking revealed an additional protein-coding sequence mapping in silico in the apospory-syntenic regions of rice and maize. Approximately 5 kb corresponding to different markers were characterized through the global sequencing procedure. A more refined analysis based on sequence information indicated synteny with segments of chromosomes 2 and 12 of rice and chromosomes 3 and 5 of maize. Two loci associated with apomixis locus were tested in methylation-sensitive RFLP experiments using genomic DNA extracted from leaves. Although both target sequences were methylated no methylation polymorphisms associated with the mode of reproduction were detected. PMID:23271945

  14. Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.

    PubMed Central

    Alghamdi, Salem S.; Al-Faifi, Sulieman A.; Migdadi, Hussein M.; Khan, Muhammad Altaf; El-Harty, Ehab H.; Ammar, Megahed H.

    2012-01-01

    Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding. PMID:23211669

  15. Molecular mapping of restriction-site associated DNA markers in allotetraploid upland cotton.

    PubMed

    Wang, Yangkun; Ning, Zhiyuan; Hu, Yan; Chen, Jiedan; Zhao, Rui; Chen, Hong; Ai, Nijiang; Guo, Wangzhen; Zhang, Tianzhen

    2015-01-01

    Upland cotton (Gossypium hirsutum L., 2n = 52, AADD) is an allotetraploid, therefore the discovery of single nucleotide polymorphism (SNP) markers is difficult. The recent emergence of genome complexity reduction technologies based on the next-generation sequencing (NGS) platform has greatly expedited SNP discovery in crops with highly repetitive and complex genomes. Here we applied restriction-site associated DNA (RAD) sequencing technology for de novo SNP discovery in allotetraploid cotton. We identified 21,109 SNPs between the two parents and used these for genotyping of 161 recombinant inbred lines (RILs). Finally, a high dense linkage map comprising 4,153 loci over 3500-cM was developed based on the previous result. Using this map quantitative trait locus (QTLs) conferring fiber strength and Verticillium Wilt (VW) resistance were mapped to a more accurate region in comparison to the 1576-cM interval determined using the simple sequence repeat (SSR) genetic map. This suggests that the newly constructed map has more power and resolution than the previous SSR map. It will pave the way for the rapid identification of the marker-assisted selection in cotton breeding and cloning of QTL of interest traits. PMID:25894395

  16. Multivariate analysis of molecular markers in peripheral blood associated with recurrence and metastasis of hepatocellular carcinoma.

    PubMed

    Liu, X J; Wang, B; Jiang, W G; Li, Y J; Liu, J B; Zhang, M

    2015-01-01

    Invasion, metastasis, and recurrence are the most common causes of death in patients with hepatocellular carcinoma (HCC) and are therefore critical factors for both therapy and prognosis. Current methods for diagnosis of HCC rely mainly on serological markers such as alpha-fetoprotein and liver enzymes, together with physical assessment and imaging techniques. The availability of more accurate serum markers may facilitate screening and early diagnosis, which will improve prognosis. This retrospective cohort analysis included 50 consecutive patients with cirrhosis and single or multifocal HCC and 40 control subjects with no liver disease or risk factors for viral hepatitis. Expression of epidermal growth factor-like domain 7 (EGFL7), osteopontin (OPN), and prostaglandin E2 (PGE2) were detected using an enzyme-linked immunosorbent assay. The mean serum levels of EGFL7, OPN, and PGE2 in the HCC group were 132.11 pg/mL, 11.77 ng/mL, and 179.37 pg/mL, respectively, which were all significantly higher than the levels in the control group (23.03 pg/mL, 2.31 ng/mL, and 47.36 pg/mL, respectively; P < 0.001). Serum levels of EGFL7, OPN, and PGE2 levels may thus be useful for screening and surveillance of HCC among high-risk populations, and have the potential to improve prognosis of these patients. PMID:25730089

  17. A molecular marker associated with low-temperature induction of dormancy in red osier dogwood (Cornus sericea).

    PubMed

    Svendsen, Erl; Wilen, Ron; Stevenson, Robert; Liu, Rensong; Tanino, Karen K

    2007-03-01

    Dormancy induction in temperate deciduous plants is thought to be regulated by short photoperiods, but low temperature has been shown to eliminate the short photoperiod requirement in northern ecotypes. An F2 population (191 plants) red osier dogwood (Cornus sericea L.) derived from a polycross of an F1 population produced from reciprocal crosses of the parental clonal ecotypes, Northwest Territories (NWT, 62 degrees N) and Utah (42 degrees N), was examined to identify molecular markers of temperature-induced endodormancy. Dormancy induction curves were generated for each individual in the F2 population and a standard point prior to vegetative maturity (i-VM) was inferred from the change in slope of the dormancy acquisition curve. Under Saskatoon, Saskatchewan field conditions (52 degrees N), the NWT ecotype entered i-VM on average 5-6 weeks before the Utah ecotype. Two sub-populations of the F2 population were distinguishable based on VM acquisition on exposure to low temperature but not to short photoperiods. A sequence characterized amplified region (SCAR) marker was developed that correctly (> 92%) identified individual plants within the F2 subpopulation that were responsive to low-temperature induction of VM. Timing of bud break was strongly associated with the timing of VM in the geographical ecotypes but not in the F2 population, indicating that these are separate traits under genetic control. PMID:17241980

  18. Molecular diversity and relationships among Cymbidium goeringii cultivars based on inter-simple sequence repeat (ISSR) markers.

    PubMed

    Wang, Hui-Zhong; Wu, Zhen-Xing; Lu, Jiang-Jie; Shi, Nong-Nong; Zhao, Yan; Zhang, Zhi-Tao; Liu, Jun-Jun

    2009-07-01

    Spring orchid (Cymbidium goeringii) is a popular flowering plant species. There have been few molecular studies of the genetic diversity and conservation genetics on this species. An assessment of the level of genetic diversity in cultivated spring orchid would facilitate development of the future germplasm conservation for cultivar improvement. In the present study, DNA markers of intersimple sequence repeats (ISSR) were identified and the ISSR fingerprinting technique was used to evaluate genetic diversity in C. goeringii cultivars. Twenty-five ISSR primers were selected to produce a total of 224 ISSR loci for evaluation of the genetic diversity. A wide genetic variation was found in the 50 tested cultivars with Nei's gene diversity (H = 0.2241) and 93.75% of polymorphic loci. Fifty cultivars were unequivocally distinguished based on ISSR fingerprinting. Cultivar-specific ISSR markers were identified in seven of 50 tested cultivars. Unweighted pair-group mean analysis (UPGMA) and principal coordinates analysis (PCA) grouped them into two clusters: one composed the cultivars mainly from Japan, and the other contained three major subclusters mainly from China. Two Chinese subclusters were generally consistent with horticultural classification, and the third Chinese subcluster contained cultivars from various horticultural groups. Our results suggest that the ISSR technique provides a powerful tool for cultivar identification and establishment of genetic relationships of cultivars in C. goeringii. PMID:19085060

  19. Molecular Phylogeny of a tick, Ixodes granulatus (Acari: Ixodidae) based on cytochrome oxidase subunit I (COI) marker

    NASA Astrophysics Data System (ADS)

    Lah, Ernieenor Faraliana Che; Yaakop, Salmah; Ahamad, Mariana; George, Ernna; Nor, Shukor Md

    2014-09-01

    Identification of a local species of tick, Ixodes granulatus from the family Ixodidae is essential because it has potential to be vector for spotted fever group (SFG) rickettsia and tick thypus. The aim of this study is to portray the relationships among several populations of I. granulatus collected from different species of animal hosts and localities in Peninsular Malaysia. Polymerase Chain Reaction was conducted by amplifying mitochondrial DNA marker, namely cytochrome oxidase subunit I (COI) sequences from 15 individual ticks that attached to five different hosts caught from three different localities. Confirmation of the species identity was accomplished using BLAST program. Neighbor-joining (NJ) and Maximum Parsimony (MP) tree based on COI sequences were constructed by using PAUP 4.0b10 to identify the relationship among species. The result of this study showed a high genetic heterogeneity between I. granulatus and other species of the same genus (7.2-23.7%). Furthermore, a low intraspecific variation was observed among the species of I. granulatus collected from different localities (0-3.7%). This study produced the first establishment of molecular marker for clarifying genetic species variation and diversity of local I. granulatus tick which contribute to the control of tick-borne infections.

  20. Molecular identification and phylogenetic relationship of green algae, Spirogyra ellipsospora (Chlorophyta) using ISSR and rbcL markers.

    PubMed

    Wongsawad, Pheravut; Peerapornpisal, Yuwadee

    2014-11-01

    Spirogyra is found in a wide range of habitats, including small stagnant water bodies, rivers, and streams. Spirogyra ellipsospora is common in northern Thailand. Species identification of the Spirogyra species based only on morphological characteristics can be difficult. A reliable and accurate method is required to evaluate genetic variations. This study aims to apply molecular approaches for the identification of S. ellipsospora using microsatellites and rbcL markers. Based on DNA sequencing, the rbcL gene was sequenced and the data was analyzed using the BLAST (Basic Local Alignment Search Tool) program in the NCBI (National Center for Biotechnology Information) database. The sequence of S. ellipsospora from this study revealed definitive identity matches in the range of 99% for the consensus sequences of S. ellipsospora. The 10 primers of ISSR could be amplified by 92 amplification fragments. The DNA fragments and the rbcL sequence data grouped the Spirogyra specimens into two distinct clusters. PMID:25313288