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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 SEX CHROMOSOME MOLECULAR MARKERS USING RAPDS AND FLUORESCENT IN SITU HYBRIDIZATION IN RAINBOW TROUT

    EPA Science Inventory

    The goal of this work is to identify molecular markers associated with the sex chromosomes in rainbow trout to study the mode of sex determination mechanisms in this species. Using the RAPD assay and bulked segregant analysis, two markers were identified that generated polymorphi...

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

    PubMed

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

    2015-01-01

    The sequence-characterized amplified region (SCAR) is a valuable molecular technique for the genetic identification of any species. This method is mainly derived from the molecular cloning of the amplified DNA fragments achieved from the random amplified polymorphic DNA (RAPD). In this study, we collected DNA from 10 species of Ganoderma mushroom and amplified the DNA using an improved RAPD technique. The amplified fragments were then cloned into a T-vector, and positive clones were screened, indentified, and sequenced for the development of SCAR markers. After designing PCR primers and optimizing PCR conditions, 4 SCAR markers, named LZ1-4, LZ2-2, LZ8-2, and LZ9-15, were developed, which were specific to Ganoderma gibbosum (LZ1-4 and LZ8-2), Ganoderma sinense (LZ2-2 and LZ8-2), Ganoderma tropicum (LZ8-2), and Ganoderma lucidum HG (LZ9-15). These 4 novel SCAR markers were deposited into GenBank with the accession Nos. KM391935, KM391936, KM391937, and KM391938, respectively. Thus, in this study we developed specific SCAR markers for the identification and authentication of different Ganoderma species. PMID:26125765

  4. Molecular cloning and development of RAPD-SCAR markers for Dimocarpus longan variety authentication.

    PubMed

    Yang, Luquan; Fu, Shelly; Khan, Md Asaduzzaman; Zeng, Weimin; Fu, Junjiang

    2013-01-01

    As an edible fruit and source of traditional medicine, D. longan is grown in most areas of Southern China. Identification of D. longan cultivars by using molecular markers is important genetically. In this study, we cloned fragments from improved randomly amplified polymorphic DNA (RAPD), and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific RAPD bands of D. longan cultivars from Guangxi, with size ranging from 500 bp to 900 bp were gel-purified, cloned and sequenced. Four clones named LY2-1, LY4-7, LY4-8 and LY5-2 were identified. In order to investigate whether the fragments were specific for the species, four pairs of SCAR primers were then designed. PCR amplifications were conducted to analyze 18 samples including different D. longan cultivars and other species. The specific bands with expected sizes were amplified in five D. longan samples but not in others. To identify and characterize the difference between D. longan and D. confinis, PCR amplifications were performed again. The specific bands with expected sizes were found in D. longan but not in D. confinis by SCAR markers LY2-1, LY4-7 and LY5-2, respectively. These results showed that our developed SCAR markers could be very useful as a specific D. longan variety authentication. Therefore, our study provides an effective and precise PCR-based diagnostic method and markers to identify D. longan species. PMID:24130961

  5. [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

  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. Molecular characterization of RAPD and SCAR markers linked to the Tm-1 locus in tomato.

    PubMed

    Ohmori, T; Murata, M; Motoyoshi, F

    1996-02-01

    We have cloned and sequenced six RAPD fragments tightly linked to the Tm-1 gene which confers tomato mosaic virus (ToMV) resistance in tomato. The terminal ten bases in each of these clones exactly matched the sequence of the primer for amplifying the corresponding RAPD marker, except for one in which the 5'-endmost two nucleotides were different from those of the primer. These RAPD clones did not cross-hybridize with each other, suggesting that they were derived from different loci. From Southern-hybridization experiments, five out of the six RAPD clones were estimated to be derived from middle- or high-repetitive sequences, but not from any parts of the ribosomal RNA genes (rDNA), which are known to be tightly linked with the Tm-1 locus. The remaining clone appeared to be derived from a DNA family consisting of a few copies. These six RAPD fragments were converted to sequence characterized amplified region (SCAR) markers, each of which was detectable using a pair of primers having the same sequence as that at either end of the corresponding RAPD clone. All pairs of SCAR primers amplified distinct single bands whose sizes were the same as those of the RAPD clones. In four cases, the SCAR markers were present in the line with Tm-1 but absent in the line without it, as were the corresponding RAPD markers. In the two other cases, the products of the same size were amplified in both lines. When these SCAR products were digested with different restriction endonucleases which recognize 4-bp sequences, however, polymorphisms in fragment length were found between the two lines. These co-dominant markers are useful for differentiating heterozygotes from both types of homozygote. PMID:24166161

  8. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations

    PubMed Central

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express–in the form of dendrograms–the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  9. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations.

    PubMed

    Costa, Rita; Pereira, Graça; Garrido, Inmaculada; Tavares-de-Sousa, Manuel María; Espinosa, Francisco

    2016-01-01

    Three different DNA-based techniques, Random Amplified Polymorphic DNA (RAPD), Inter Simple Sequence Repeat (ISSR) and Amplified Fragment Length Polymorphism (AFLP) markers, were used for fingerprinting Dactylis glomerata genotypes and for detecting genetic variation between the three different subspecies. In this study, RAPD assays produced 97 bands, of which 40 were polymorphic (41.2%). The ISSR primers amplified 91 bands, and 54 showed polymorphism (59.3%). Finally, the AFLP showed 100 bands, of which 92 were polymorphic (92%). The fragments were scored as present (1) or absent (0), and those readings were entered in a computer file as a binary matrix (one for each marker). Three cluster analyses were performed to express-in the form of dendrograms-the relationships among the genotypes and the genetic variability detected. All DNA-based techniques used were able to amplify all of the genotypes. There were highly significant correlation coefficients between cophenetic matrices based on the genetic distance for the RAPD, ISSR, AFLP, and combined RAPD-ISSR-AFLP data (0.68, 0.78, 0.70, and 0.70, respectively). Two hypotheses were formulated to explain these results; both of them are in agreement with the results obtained using these three types of molecular markers. We conclude that when we study genotypes close related, the analysis of variability could require more than one DNA-based technique; in fact, the genetic variation present in different sources could interfere or combine with the more or less polymorphic ability, as our results showed for RAPD, ISSR and AFLP markers. Our results indicate that AFLP seemed to be the best-suited molecular assay for fingerprinting and assessing genetic relationship among genotypes of Dactylis glomerata. PMID:27070939

  10. A molecular linkage map of olive (Olea europaea L) based on RAPD, microsatellite, and SCAR markers.

    PubMed

    Wu, Shu-Biao; Collins, Graham; Sedgley, Margaret

    2004-02-01

    An integrated molecular linkage map of olive (Olea europaea L.) was constructed based on randomly amplified polymorphic DNA (RAPD), sequence characterized amplified region (SCAR), and microsatellite markers using the pseudo-testcross strategy. A mapping population of 104 individuals was generated from an F1 full-sib family of a cross between 'Frantoio' and 'Kalamata'. The hybridity of the mapping population was confirmed by genetic similarity and nonmetric multidimensional scaling. Twenty-three linkage groups were mapped for 'Kalamata', covering 759 cM of the genome with 89 loci and an average distance between loci of 11.5 cM. Twenty-seven linkage groups were mapped for 'Frantoio', covering 798 cM of the genome with 92 loci and an average distance between loci of 12.3 cM. For the integrated map, 15 linkage groups covered 879 cM of the genome with 101 loci and an average distance between loci of 10.2 cM. The size of the genomic DNA was estimated to be around 3000 cM. A sequence characterized amplified region marker linked to olive peacock disease resistance was mapped to linkage group 2 of the integrated map. These maps will be the starting point for studies on the structure, evolution, and function of the olive genome. When the mapping progeny pass through their juvenile phase and assume their adult characters, mapping morphological markers and identification of quantitative trait loci for adaptive traits will be the primary targets. PMID:15060599

  11. 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...

  12. Molecular and functional diversity of PGPR fluorescent Pseudomonads based on 16S rDNA-RFLP and RAPD markers.

    PubMed

    Singh, Bhim Pratap

    2015-09-01

    The genetic and functional diversity of plant growth promoting rhizobacterial (PGPR) fluorescent pseudomonads associated with chickpea (Cicer arietinum L.) rhizosphere was analyzed. In total, 34 isolates along with two reference isolates were screened for various plant growth promoting traits (phosphorous solubilization, ACC deaminase, HCN, IAA and siderophore productions) and antagonist activity against four fungal phytopathogens and three bacterial pathogens. Most of the isolates, that showed PGPR activity, also showed antagonistic activity against all the three fungal pathogens. The genetic relationship was assessed by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (16S rDNA-RFLP). Relationship between both the markers was analyzed based on mantel test and a negative correlation was observed. The study concluded that PGPR traits appeared to be strain specific rather than specific to any phylogenetic group. The study also reported that 16S rDNA based profiling differentiated PGPR fluorescent Pseudomonas on the basis of location rather than biological trait. RAPD profiling could be useful to differentiate among the closely related isolates. The genetic and functional diversity of fluorescent pseudomonads, associated with the chickpea rhizosphere, has useful ecological role and potential utilization in sustainable agriculture. PMID:26521562

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

    PubMed

    Lam, Kelly Y C; Chan, Gallant K L; Xin, Gui-Zhong; Xu, Hong; Ku, Chuen-Fai; Chen, Jian-Ping; Yao, Ping; Lin, Huang-Quan; Dong, Tina T X; Tsim, Karl W K

    2015-01-01

    Cordyceps sinensis is an endoparasitic fungus widely used as a tonic and medicinal food in the practice of traditional Chinese medicine (TCM). In historical usage, Cordyceps specifically is referring to the species of C. sinensis. However, a number of closely related species are named themselves as Cordyceps, and they are sold commonly as C. sinensis. The substitutes and adulterants of C. sinensis are often introduced either intentionally or accidentally in the herbal market, which seriously affects the therapeutic effects or even leads to life-threatening poisoning. Here, we aim to identify Cordyceps by DNA sequencing technology. Two different DNA-based approaches were compared. The internal transcribed spacer (ITS) sequences and the random amplified polymorphic DNA (RAPD)-sequence characterized amplified region (SCAR) were developed here to authenticate different species of Cordyceps. Both approaches generally enabled discrimination of C. sinensis from others. The application of the two methods, supporting each other, increases the security of identification. For better reproducibility and faster analysis, the SCAR markers derived from the RAPD results provide a new method for quick authentication of Cordyceps. PMID:26694332

  14. Development of RAPD-SCAR markers for Lonicera japonica (Caprifolicaceae) variety authentication by improved RAPD and DNA cloning.

    PubMed

    Yang, Luquan; Khan, Md Asaduzzaman; Mei, Zhiqiang; Yang, Manman; Zhang, Tiandan; Wei, Chunli; Yang, Weichan; Zhu, Li; Long, Yan; Fu, Junjiang

    2014-12-01

    Genetic diversity within a species is a common feature, which plays a vital role in its survival and adaptability, and is important for the identification and authentication of a species. Lonicera japonica is a traditionally used medicinal plant, which have been recently genetically characterized by an improved ran- dom amplified polymorphic DNA (RAPD) analysis. In this study, the molecular markers on the basis of these RAPD fragments have been developed to identify specific L. japonica variety. The DNAs were extracted from fresh young leaves of different samples of L. japonica collected from Shenzhen, Yichang, Leshan, Emei and Loudi, China. The DNA materials were amplified using improved RAPD PCR. Different RAPD bands were excised, cloned and developed for stable sequence-characterized amplified region (SCAR) markers with differ- ent species. Two SCAR markers, JYH3-3 and JYH4-3, have been successfully cloned from improved.RAPD fragments. The SCAR marker JYH3-3 was found specific for all of the L. japonica samples collected from the different regions, and another marker JYH 4-3 was strictly specific to the Shenzhen sample from Guangdong province, which is geographically distant from Hubei, Sichuan and Hunan Provinces (source of other L. japonica samples). The marker JYH3-3 was found as specific molecular marker for the identification of L. japonica, while JYH4-3 was found as molecular marker strictly specific for the Shenzhen sample. The developed SCAR markers might serve as more specific molecular markers for L. japonica variety authentication. The combination of improved RAPD analysis and SCAR marker development have resulted useful tools to study the genetic variety of any organism, which we have successfully applied here in L. japonica. PMID:25720194

  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. Screening and characterization of RAPD markers in viscerotropic Leishmania parasites.

    PubMed

    Mkada-Driss, Imen; Lahmadi, Ramzi; Chakroun, Ahmed S; 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

  17. Genetic relationships among Heliconia (Heliconiaceae) species based on RAPD markers.

    PubMed

    Marouelli, L P; Inglis, P W; Ferreira, M A; Buso, G S C

    2010-01-01

    The family Heliconiaceae contains a single genus, Heliconia, with approximately 180 species of Neotropical origin. This genus was formerly allocated to the family Musaceae, but today forms its own family, in the order Zingiberales. The combination of inverted flowers, a single staminode and drupe fruits is an exclusive characteristic of Heliconia. Heliconias are cultivated as ornamental garden plants, and are of increasing importance as cut flowers. However, there are taxonomic confusions and uncertainties about the number of species and the relationships among them. Molecular studies are therefore necessary for better understanding of the species boundaries of these plants. We examined the genetic variability and the phylogenetic relationships of 124 accessions of the genus Heliconia based on RAPD markers. Phenetic and cladistic analyses, using 231 polymorphic RAPD markers, demonstrated that the genus Heliconia is monophyletic. Groupings corresponding to currently recognized species and some subgenera were found, and cultivars and hybrids were found to cluster with their parents. RAPD analysis generally agreed with morphological species classification, except for the position of the subgenus Stenochlamys, which was found to be polyphyletic. PMID:20645261

  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. Study of genetic variation of eggplant cultivars by using RAPD-PCR molecular markers and the relationship with Phomopsis blight disease reaction.

    PubMed

    Asad, H A; Meah, M B; Begum, S N; Khalil, M I; Rafii, M Y; Latif, M A

    2015-01-01

    Disease susceptibility and genetic variability in 10 eggplant genotypes were studied after inoculating Phomopsis vexans under confined field conditions. Random amplified polymorphic DNA (RAPD) markers were used to assess genetic variation and relationships among eggplant genotypes. The disease index of leaves ranged 0.208-13.79%, while fruit infection ranged 2.15-42.76%. Two varieties, Dohazari G and Laffa S, were found to be susceptible, 6 were moderately resistant, 1 was moderately susceptible, and BAU Begun-1 was resistant to P. vexans. Amplification of genomic DNA by using 3 RAPD primers produced 20 bands: 14 (70%) were polymorphic and 6 (30%) were monomorphic. The highest intra-variety similarity indices values were found in ISD 006, Ishurdi L, Jessore L, and BAU Begun-1 (100%), while the lowest was in Dohazari G (90%). The lowest genetic distance (0.0513) and the highest genetic identity (0.9500) were observed between the ISD 006 and Ishurdi L combinations. A comparatively higher genetic distance (0.3724) and the lowest genetic identity (0.6891) were observed between the ISD 006 and Dohazari G combinations. A dendogram was constructed based on Nei's genetic distance, which produced 2 main clusters of the genotypes - Cluster I: ISD 006, Ishurdi L, Marich begun L, BAU Begun-1, Marich begun S, and Chega and Cluster 2: Laffa S, Dohazari G, Jessore L, and Singhnath. Genetic variation and its relationship with disease susceptibility were assessed using RAPD markers, to develop disease-resistant varieties and improve eggplant crops. PMID:26681048

  1. Diversity among populations of switchgrass based on RAPD markers

    SciTech Connect

    Gunter, L.E.; Tuskan, G.A.; Wullschleger, S.D.

    1996-07-01

    Information on the amount of genetic diversity in switchgrass (Panicum virgatum L.) is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. This study characterized and assessed genetic diversity by means of RAPD markers among 14 populations representing upland and lowland switchgrass ecotypes. Forty-five of 128 primers produced polymorphic markers among sets of genomic DNA pooled from individual genotypes of each population. Five primers were selected to amplify a total of 91 polymorphic loci among genotypes. The RAPD markers were scored for presence or absence of bands to generate distance matrices for cluster analysis. Overall similarity was 65% among population compared to 81% within populations. Blackwell and Caddo were the most similar populations (78%) based on RAPD markers, whereas Alamo and Forestburg were the most divergent (53%). Cluster analysis clearly segregated populations into two main groups (putatively based on ecotype) and united individual genotypes within a population into discrete groups within the larger clusters. Although the relationship between ploidy level and ecotype remained unclear, RAPD profiles can be used to identify switchgrass populations and may be useful in predicting relationship between experimental germplasm sources and released populations. 50 refs., 2 figs., 2 tabs.

  2. Confirmation of Clematis hybrids using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The hybrid origin of two progeny from reciprocal crosses of Clematis tubulosa and C. brevicaudata was investigated using molecular markers generated by randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and single nucleotide polymorphisms (SNPs). Morphologi...

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

    PubMed

    Zhao, Ya-E; Wu, Li-Ping

    2012-06-01

    For a long time, classification of Demodex mites has been mainly based on their hosts and phenotype characteristics. The study was the first to conduct molecular identification and genetic relationship analysis for six isolates of three Demodex species by random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) marker. Totally, 239 DNA fragments were amplified from six Demodex isolates with 10 random primers in RAPD, of which 165 were polymorphic. Using a single primer, at least five fragments and at most 40 in the six isolates were amplified, whereas within a single isolate, a range of 35-49 fragments were amplified. DNA fingerprints of primers CZ 1-9 revealed intra- and interspecies difference in six Demodex isolates, whereas primer CZ 10 only revealed interspecies difference. The genetic distance and dendrogram showed the intraspecific genetic distances were closer than the interspecific genetic distances. The interspecific genetic distances of Demodex folliculorum and Demodex canis (0.7931-0.8140) were shorter than that of Demodex brevis and D. canis (0.8182-0.8987). The RAPD-SCAR marker displayed primer CZ 10 could be applied to identify the three Demodex species. The 479-bp fragment was specific for D. brevis, and the 261-bp fragment was specific for D. canis. The conclusion was that the RAPD-SCAR multi-marker was effective in molecular identification of three Demodex species. The genetic relationship between D. folliculorum and D. canis was nearer than that between D. folliculorum and D. brevis. PMID:22205351

  4. 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

  5. Genetic Authentication of Gardenia jasminoides Ellis var. grandiflora Nakai by Improved RAPD-Derived DNA Markers.

    PubMed

    Mei, Zhiqiang; Zhou, Boxu; Wei, Chunli; Cheng, Jingliang; Imani, Saber; Chen, Hanchun; Fu, Junjiang

    2015-01-01

    The evergreen shrub, Gardenia jasminoides Ellis var. grandiflora Nakai is one of the most popular garden-plants, with significant ornamental importance. Here, we have cloned improved random amplified polymorphic DNA (RAPD) derived fragments into T-vector, and developed sequence-characterized amplified region (SCAR) markers. These markers have been deposited in GenBank database with the accession numbers KP641310, KP641311, KP641312 and KP641313 respectively. The BLAST search of database confirmed the novelty of these markers. The four SCAR markers, namely ZZH11, ZZH31, ZZH41 and ZZH51 can specifically recognize the genetic materials of G. jasminoides from other plant species. Moreover, SCAR marker ZZH31 can be used to distinguish G. jasminoides Ellis var. grandiflora Nakai from other G. jasminoides on the market. Together, this study has developed four stably molecular SCAR markers by improved RAPD-derived DNA markers for the genetic identification and authentication, and for ecological conservation of medicinal and ornamental plant G. jasminoides. PMID:26569205

  6. Genetic diversity analysis in Tunisian perennial ryegrass germplasm as estimated by RAPD, ISSR, and morpho-agronomical markers.

    PubMed

    Ghariani, S; Elazreg, H; Chtourou-Ghorbel, N; Chakroun, M; Trifi-Farah, N

    2015-01-01

    Tunisia is rich in diverse forage and pasture species including perennial ryegrass. In order to enhance forage production and improve agronomic performance of this local germplasm, a molecular analysis was undertaken. Random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR) and morpho-agronomical traits markers were used for genetic diversity estimation of ryegrass germplasm after screening 20 spontaneous accessions, including a local and an introduced cultivars. Same mean polymorphism information content values were obtained (0.37) for RAPD and ISSR suggesting that both marker systems were equally effective in determining polymorphisms. The average pairwise genetic distance values were 0.57 (morpho-agronomical traits), 0.68 (RAPD), and 0.51 (ISSR) markers data sets. A higher Shannon diversity index was obtained with ISSR marker (0.57) than for RAPD (0.54) and morpho-agronomical traits (0.36). The Mantel test based on genetic distances of a combination of molecular markers and morpho-agronomical data exhibited a significant correlation between RAPD and ISSR data, suggesting that the use of a combination of molecular techniques was a highly efficient method of estimating genetic variability levels among Tunisian ryegrass germplasm. In summary, results showed that combining molecular and morpho-agronomical markers is an efficient way in assessing the genetic variability among Tunisian ryegrass genotypes. In addition, the combined analysis provided an exhaustive coverage for the analyzed diversity and helped us to identify suitable accessions showed by Beja and Jendouba localities, which present large similarities with cultivated forms and can be exploited for designing breeding programmes, conservation of germplasm and management of ryegrass genetic resources. PMID:26782500

  7. Genetic variation among South Brazilian accessions of Lippia alba Mill. (Verbenaceae) detected by ISSR and RAPD markers.

    PubMed

    Manica-Cattani, M F; Zacaria, J; Pauletti, G; Atti-Serafini, L; Echeverrigaray, S

    2009-05-01

    Twenty-seven accessions of Lippia alba Mill. collected in Rio Grande do Sul state, Brazil, were analysed by ISSR and RAPD markers to evaluate their genetic variability and relationships. Six ISSR primers and four RAPD primers generated 120 amplified fragments, most of which were polymorphics. The overall genetic variability among accessions was very high when compared with other plant species. The hierarchical analysis of molecular data (UPGMA) showed low relationship between accessions, and no grouping between accessions of the same chemotype. Canonical functions allowed identifying some variables related with the chemical characteristics of the essential oils. Both ISSR and RAPD markers were efficient to address the genetic diversity of L. alba, and may contribute to the conservation and breeding of this increasingly important aromatic and medicinal species. PMID:19675941

  8. Genetic diversity of wild and cultivated genotypes of pigeonpea through RAPD and SSR markers.

    PubMed

    Walunjkar, Babasaheb C; Parihar, Akarsh; Singh, Nirbhay Kumar; Parmar, L D

    2015-03-01

    Eight wild and four cultivated pigeonpea genotypes were subjected to RAPD and microsatellite analysis, with 40 primers each. Out of these, eight RAPD and five SSR primers were found polymorphic. RAPD primers showed 100% polymorphism and produced a total of 517 DNA fragments, whereas SSR primers produced 67 fragments and they too showed 100% polymorphism. The RAPD markers revealed highest similarity co-efficient of 0.93 (GT-100 and ICPL-87), whereas the highest similarity co-efficient obtained with SSR markers was 1.00 (GTH-1 and GT-100). Average PIC value obtained with RAPD and SSR were 0.90 and 0.18, respectively. The arithmetic mean heterozygosity and marker index were 0.90 and 22.47 respectively with RAPD marker, whereas the corresponding values for SSR markers were 0.18 and 33.66. Moreover; the four wild genotypes (Cajanus scarabaeoides, Rhyncosia rufescence, Cajanus cajanifolius and Rhyncosia canna) and the four cultivars (GTH-1, GT-100, ICPL-87 and GT-1) grouped distinctly in the same subgroups of the dendrograms obtained with both RAPD and SSR analysis. Therefore, the findings of SSR supplement and validate the results obtained with RAPD analysis. PMID:25895271

  9. 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

  10. Identification of RAPD markers linked to genetic factors controlling the milling energy requirement of barley.

    PubMed

    Chalmers, K J; Barua, U M; Hackett, C A; Thomas; Waugh, R; Powell, W

    1993-11-01

    Doubled haploid (DH) populations of barley have been used in combination with PCR-based polymorphic-assay procedures to identify molecular markers linked to genes controlling the milling energy requirement of the grain. Milling energy (ME) is a quantitative trait and locating individual quantitative trait loci (QTLs) involved the construction of bulks by combining DNA from DH families representing the extreme members of the distribution for ME. In addition, the individuals had alternative alleles at theRrn2 locus that has previously been shown to be linked to an ME QTL. The DNA bulks were screened with Randomly Amplified Polymorphic DNA (RAPD) markers and polymorphic amplification products tested for linkage to genes influencing the expression of ME in a DH population. Several markers were identified which are linked to a QTL controlling ME and the recombination fraction determined by maximum likelihood procedures. The results indicate that DHs in combination with RAPDs and bulked segregant analysis provide an efficient method for locating QTLs in barely. Furthermore, this approach is applicable to mapping other QTLs in a range of organisms from which DH or recombinant inbred lines can be extracted. PMID:24190256

  11. Genetic diversity and genetic relationships in Hyacinthaceae in India using RAPD and SRAP markers.

    PubMed

    Jehan, Tabassum; Vashishtha, Amit; Yadav, S R; Lakhanpaul, Suman

    2014-01-01

    Genetic diversity and relationship among three genera namely Drimia, Dipcadi and Ledebouria of Hyacinthaceae in India was studied using RAPD and SRAP markers. Twenty one RAPD primers and nine SRAP were used for analyzing 41 accessions. RAPD gave an average 12.6 markers per primer, while SRAP generated 10.1 markers per primer pair. The family emerged very diverged with high polymorphism. The study resolved the three genera into monophyletic groups corresponding to three subfamilies; Urginoideae, Hyacinthoideae and Ornithogaloideae. Drimia wightii emerged a very distinct species and species specific markers were obtained with both marker systems. AMOVA analysis also revealed the genera to be quite well diverged. The two markers showed high correlation (r = 0.932) in Mantel matrix crresspondance test. The combined data also showed a very good correlation with the respective markers individually. PMID:24554844

  12. 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

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

    PubMed

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

    2015-01-01

    The purpose of this study was to analyze the effects of management on the genetic structure of natural populations of Attalea speciosa in the State of Piauí, Brazil, using random-amplified polymorphic DNA (RAPD) markers. Three babassu populations under different management systems were selected. Polymerase chain reactions were performed for 20 RAPD primers. A total of 146 bands were generated, 141 of which were polymorphic (96.58%), with a variation of 4 and 12 loci and an average of 7 bands per primer. A dendrogram revealed a clear separation between the three populations (0.57). Data reliability and node consistency were verified by bootstrap values and the cophenetic correlation coefficient (88.15%). Coefficients of similarity between pairs of genotypes ranged from 0.26 to 0.86, with a mean of 0.57. Nei's genetic diversity index (HE) value of the population sampled in Teresina was 0.212, of Esperantina it was 0.195, and of José de Freitas it was 0.207. After the HE was decomposed, the complete diversity was found to be 0.3213. Genetic differentiation between populations was 0.362, and the estimation of gene flow between populations was low (0.879). Analysis of molecular variance revealed that 59.52% of the variation was contained within populations, and 40.48% was between populations. RAPD markers were effective for genetic diversity analysis within and between natural babassu populations, and exhibited a high level of polymorphism. Genetic diversity was the highest within populations; variability was lower in the managed populations than in the undisturbed populations. PMID:26125813

  14. Genetic polymorphism between and within Meloidogyne species detected with RAPD markers.

    PubMed

    Castagnone-Sereno, P; Vanlerberghe-Masutti, F; Leroy, F

    1994-12-01

    Genetic analyses were conducted on root-knot nematode populations belonging to the four major species of the genus Meloidogyne and originating from many countries throughout the world. Discrete genetic markers used in this study were random genomic DNA sequences amplified by the polymerase chain reaction (RAPD). Primers of 17-30 nucleotides with 30-55% G + C content were tested. Five of them generated a total of 74 scorable markers that provided reliable polymorphisms both between and within species. Using RAPD patterns alone or in combination, all the Meloidogyne species and populations studied could be unambiguously discriminated. Based on the presence or absence of bands, maximum-parsimony analysis of the data resulted in clustering of species and populations congruent with previous isoenzymatic and molecular data. The resulting tree confirmed the early divergence of M. hapla from the other species and also that M. arenaria is closer to M. javanica than it is to M. incognita. The boot-strap analysis significantly supported most of the specific branching observed in the topology but did not identify the three M. arenaria populations as a monophyletic group. PMID:7828838

  15. RAPD and ISSR markers in the evaluation of genetic divergence among accessions of elephant grass.

    PubMed

    de Lima, R S N; Daher, R F; Gonçalves, L S A; Rossi, D A; do Amaral Júnior, A T; Pereira, M G; Lédo, F J S

    2011-01-01

    Considering the expected genetic variability of elephant grass (Pennisetum purpureum), due to its cultivation in different continents, we characterized and estimated the genetic divergences between 46 accessions of elephant grass with different edaphoclimatic adaptations, using RAPD and ISSR markers. We evaluated, comparatively, the consistency of the information achieved with these markers. Twenty-six RAPD and 25 ISSR primers were employed. The RAPD markers produced 185 bands, 72% of which were polymorphic, with a mean of 5.11 polymorphic bands per primer. The 25 ISSR starters produced 216 bands; 76% were polymorphic, with a mean of 6.56 polymorphic bands per primer. The correlation between the genetic distances achieved by the RAPD and ISSR markers was 0.76, which is highly significant by the Mantel test. Based on UPGMA grouping, considering the point of sudden change, five and six groups were formed for the data from the RAPD and ISSR markers, respectively. These markers provided partially concordant groups, indicating that these techniques can provide consistent information and consequently could be used in studies of genetic diversity among accessions. PMID:21751156

  16. Molecular cloning and characterization of a microsatellite locus found in an RAPD marker of a spider mite, Panonychus citri (Acari: Tetranychidae).

    PubMed

    Osakabe, M; Hinomoto, N; Toda, S; Komazaki, S; Goka, K

    2000-01-01

    Genetic markers were searched using PCR with 40 kinds of decanucleotide primers to investigate DNA polymorphism in Panonychus citri. A region consisting of a variable number of CT tandem repeats (microsatellite) was found in a fragment amplified with the OPB10 primer. The microsatellite differed in size by ca. 100bp among several P. citri populations screened and was derived from at least seven alleles. This region was characteristic of P. mori and P. osmanthi, but was lacking in P. ulmi. The flanking regions were highly conserved among these species. PMID:11156164

  17. 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....

  18. 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

  19. Application of ISSR, RAPD, and cytological markers to the certification of Picea mariana, P. glauca, and P. engelmannii trees, and their putative hybrids.

    PubMed

    Nkongolo, K K; Michael, P; Demers, T

    2005-04-01

    Picea glauca (white spruce) and P. engelmannii (Engelmann spruce) are so similar and integrated that it is impossible to distinguish between them and their hybrids using morphological characteristics. Although natural hybrids between P. glauca and P. mariana (black spruce) do not generally occur, even though the 2 species are sympatric in North America, a first-generation hybrid, called the Rosendahl spruce, has been reported in the literature. In this study, several inter-simple sequence repeat (ISSR) markers were developed, as were randomly amplified polymorphic DNA (RAPD) markers, to certify spruce trees and their hybrids. ISSR fingerprinting was more efficient than RAPD assay; it detected 70% polymorphic DNA markers among the spruce species analyzed, whereas RAPD fingerprinting detected only 53%. Species-diagnostic ISSR and RAPD markers differentiating P. glauca from P. engelmannii and P. mariana were cloned and sequenced. Molecular certification of the spruce samples analyzed confirmed that all the seeds from interior spruce populations were true hybrids of P. glauca and P. engelmannii. But the analysis of seeds derived from the putative Rosendahl spruce indicated that this tree is likely a pure P. glauca genotype, rather than a hybrid of P. glauca and P. mariana. These data were confirmed by cytological analyses. Further analysis, using a more sensitive DNA amplification method with designed primers flanking the species-diagnostic ISSR and RAPD markers, revealed that such sequences are not generally species-specific because they are present in other spruce species. PMID:15838553

  20. A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.

    PubMed

    Mehlenbacher, Shawn A; Brown, Rebecca N; Nouhra, Eduardo R; Gökirmak, Tufan; Bassil, Nahla V; Kubisiak, Thomas L

    2006-02-01

    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. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations. PMID:16498462

  1. Genetic map of the chicken Z chromosome using random amplified polymorphic DNA (RAPD) markers.

    PubMed

    Levin, I; Crittenden, L B; Dodgson, J B

    1993-04-01

    Commercially important traits of domestic animals have often been genetically linked to sex chromosomes, such as the Z chromosome of chickens. Using a backcross mapping population between two divergent, inbred lines and random-amplified polymorphic DNA (RAPD)-PCR markers, a genetic map of the chicken Z chromosome has been generated. Thirteen Z-linked RAPD markers were identified, mapped, and linked to two RFLPs and one phenotypic marker. The protocol used also generated RAPD markers for the W chromosome. The linkage distances obtained suggest that the RAPD markers are widely distributed throughout the Z chromosome and are likely to be linked to most or all traits of interest on this chromosome. The map provides a preliminary estimate of genetic to physical distance of about 0.5 Mb per centimorgan for the Z chromosome in chickens (male-specific recombination). A similar approach should be applicable to facilitate the mapping and analysis of sex-linked traits in other domestic animals. PMID:8486362

  2. 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 ...

  3. Genetic characterization of heat tolerant tomato (Solanum lycopersicon) genotypes by SRAP and RAPD markers.

    PubMed

    Comlekcioglu, N; Simsek, O; Boncuk, M; Aka-Kacar, Y

    2010-01-01

    We employed RAPD and sequence-related amplified polymorphism (SRAP) markers to evaluate polymorphisms in 15 tomato (Solanum lycopersicon) genotypes that were obtained from a tomato breeding program. Four local tomato genotypes selected from the Sanliurfa province (Southeastern Anatolia Region of Turkey), 10 heat-tolerant tomato genotypes, received from the Asian Vegetable Research and Development Center, and a sample of S. pimpinellifolium were genotyped with RAPD and SRAP markers. Eleven SRAP primer combinations were used and 66 bands were scored. The number of bands scored per primer combination ranged from three to 12, with a mean of six alleles per primer combination. All fragments scored for each primer combination were polymorphic. The percentage of polymorphic products ranged from 25 to 80%. The 15 tomato genotypes were screened for RAPD markers using 50 primers in a PCR-based DNA amplification procedure; 46 primers produced clear and good amplification. Ten of these 46 primers amplified monomorphic fragments in the tomato genotypes. A dendrogram was constructed by combining data from the RAPD and SRAP analyses. Similarity ratios of genotypes ranged from 0.87 to 0.99. The dendrogram was divided into two branches; the first main branch included only genotype CL 5915, and the second main branch included all the other genotypes. PMID:21128206

  4. A novel strategy for identification of 47 pomegranate (Punica granatum) cultivars using RAPD markers.

    PubMed

    Zhang, Y P; Tan, H H; Cao, S Y; Wang, X C; Yang, G; Fang, J G

    2012-01-01

    DNA marker can be used for precise plant cultivar identification. However, DNA markers have often not been used effectively for the identification of plant cultivars due to a lack of an effective analysis strategy. We used a novel strategy for effective identification of plant individuals based on a new way of recording DNA fingerprints of the genotyped plants; a cultivar identification diagram can be manually generated and used as key reference information for quick identification of plant and/or seed samples. Forty-seven pomegranate varieties popularly cultivated in various provinces of China were subjected to RAPD marker analysis. Using the cultivar identification diagram strategy, they were clearly separated by the fingerprints of 11 RAPD primers. The utility and accuracy of the cultivar identification diagram analysis results were confirmed by the identification of three randomly chosen groups of cultivars among the 47 varieties. PMID:22782622

  5. 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.

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

    PubMed

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

    2012-12-01

    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 F(2) 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 OPW16(905 bp) showed the most significant association with cocoon and shell weights, and its inheritance was confirmed in F(2) 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 16(826 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

  7. Rapid identification of white-Engelmann spruce species by RAPD markers.

    PubMed

    Khasa, P D; Dancik, B P

    1996-01-01

    Fragments of random amplified polymorphic DNA (RAPDs) were used as markers to distinguish Picea glauca (Moench) Voss (white spruce) and Picea engelmannii Parry (Engelmann spruce). These species and their putative hybrids are difficult to differentiate morphologically and are collectively known as interior spruce. Four oligodeoxynucleotide decamer primers showed species-specific amplification products between white spruce and Engelmann spruce. These fragments are highly conserved among seed lots and individual trees of each species from diverse geographic origins. The consistency and reproducibility of these species-specific amplification products were tested in more than two amplification reactions. Therefore, RAPD markers can provide genetic markers for easy and rapid identification of the specific genetic entry of these spruce species and their reported putative hybrids. According to the frequencies of the species-specific RAPD markers, it is possible to estimate the hybrid fraction, indicative of true introgression between the two species. These results are useful for quick identification of both species and their hybrid swarms at any stage in the sporophyte phase of the life cycle, for determining the occurrence and the magnitude of introgressive hybridization in an overlap zone between the two species, and for certification purposes in operational re-forestation and tree-improvement programs. PMID:24166115

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

    PubMed

    Jiang, Y; Liu, J-P

    2011-01-01

    Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) analysis were applied to 74 individual plants of Piper spp in Hainan Island. The results showed that the SRAP technique may be more informative and more efficient and effective for studying genetic diversity of Piper spp than the RAPD technique. The overall level of genetic diversity among Piper spp in Hainan was relatively high, with the mean Shannon diversity index being 0.2822 and 0.2909, and the mean Nei's genetic diversity being 0.1880 and 0.1947, calculated with RAPD and SRAP data, respectively. The ranges of the genetic similarity coefficient were 0.486-0.991 and 0.520-1.000 for 74 individual plants of Piper spp (the mean genetic distance was 0.505 and 0.480) and the within-species genetic distance ranged from 0.063 to 0.291 and from 0.096 to 0.234, estimated with RAPD and SRAP data, respectively. These genetic indices indicated that these species are closely related genetically. The dendrogram generated with the RAPD markers was topologically different from the dendrogram based on SRAP markers, but the SRAP technique clearly distinguished all Piper spp from each other. Evaluation of genetic variation levels of six populations showed that the effective number of alleles, Nei's gene diversity and the Shannon information index within Jianfengling and Diaoluoshan populations are higher than those elsewhere; consequently conservation of wild resources of Piper in these two regions should have priority. PMID:22179965

  9. RAPD markers linked to eastern filbert blight resistance in Corylus avellana.

    PubMed

    Mehlenbacher, S A; Brown, R N; Davis, J W; Chen, H; Bassil, N V; Smith, D C; Kubisiak, T L

    2004-02-01

    A total of 1,110 decamer primers were screened for RAPD markers linked to a dominant allele in hazelnut ( Corylus avellana) that confers resistance to eastern filbert blight caused by Anisogramma anomala. Twenty RAPD markers linked in coupling, and five markers linked in repulsion, were found. A seedling population was used to construct a linkage map of the region flanking the resistance locus. The map spans 46.6 cM, with 14 markers on one side of the resistance locus and eight on the other side. Eleven markers showed less than 3% recombination with resistance, including three that showed no recombination. Seven of these 11 markers are sufficiently robust to allow their use in marker-assisted selection. These include AA12(850) which shows no recombination, and six markers on one side of the resistance locus: 173(500), 152(800), 122(825), 275(1130), H19(650) and O16(1250). Marker 268(580), which flanks the resistance locus on the other side, is also suitable for use in marker-assisted selection, but shows 5.8% recombination with resistance. Other markers are less suitable for marker-assisted selection because of sensitivity to changes in primer or MgCl(2) concentration, or the long time required for electrophoresis to separate bands of similar size. The 16 markers closest to the resistance locus were cloned and sequenced. The W07(365) marker, which showed no recombination with the resistance locus but is difficult to score, includes a CT microsatellite repeat. The sequence information will allow the design of SCAR primers and eventual map-based cloning of the resistance allele. PMID:14569427

  10. The linkage maps of Dendrobium species based on RAPD and SRAP markers.

    PubMed

    Xue, Dawei; Feng, Shangguo; Zhao, Hongyan; Jiang, Hua; Shen, Bo; Shi, Nongnong; Lu, Jiangjie; Liu, Junjun; Wang, Huizhong

    2010-03-01

    Dendrobium plants are used commonly as tonic herbs and health food in many Asian countries, especially in China. Here we report the genetic map construction of two Dendrobium species with a double pseudo-testcross strategy using random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) markers. A F(1) mapping population of 90 individuals was developed from a cross between D. officinale and D. hercoglossum. A total of 307 markers, including 209 RAPD and 98 SRAP, were identified and used for genetic linkage group (LG) analysis. The D. officinale linkage map consisted of 11 major linkage groups and 3 doublets, which covered 629.4 cM by a total of 62 markers with an average locus distance of 11.2 cM between two adjacent markers. The D. hercoglossum linkage map contained 112 markers mapped on 15 major and 4 minor linkage groups, spanning a total length of 1,304.6 cM with an average distance of 11.6 cM between two adjacent markers. The maps constructed in this study covered 92.7% and 82.7% of the D. hercoglossum and D. officinale genomes respectively, providing an important basis for the mapping of horticultural and medicinal traits and for the application of marker-assisted selection in Dendrobium breeding program. PMID:20347829

  11. Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers.

    PubMed

    Ulloa, Odeth; Ortega, Fernando; Campos, Hugo

    2003-08-01

    Red clover is an important forage legume species for temperate regions and very little is known about the genetic organization of its breeding populations. We used random amplified polymorphic DNA (RAPD) genetic markers to address the genetic diversity and the distribution of variation in 20 breeding populations and cultivars from Chile, Argentina, Uruguay, and Switzerland. Genetic distances were calculated for all possible pairwise combinations. A high level of polymorphism was found and the proportion of polymorphic loci across populations was 74.2%. A population derived from a non-certified seedlot displayed a higher proportion of polymorphic loci than its respective certified seedlot. Gene diversity values and population genetics parameters suggest that the populations analyzed are diverse. An analysis of molecular variance (AMOVA) revealed that the largest proportion of variation (80.4%) resides at the within population level. RAPD markers are a useful tool for red clover breeding programs. A dendrogram based on genetic distances divided the breeding populations analyzed into three distinct groups. The amount and partition of diversity observed can be of value in identifying the populations that parents of synthetic cultivars are derived from and to exploit the variation available in the populations analyzed. PMID:12897860

  12. Evaluation of the extent of genetic variation in mahoganies (Meliaceae) using RAPD markers.

    PubMed

    Chalmers, K J; Newton, A C; Waugh, R; Wilson, J; Powell, W

    1994-10-01

    Despite the economic importance of mahoganies (Meliaceae) little is known of the pattern of genetic variation within this family of tropical trees. We describe the application of a polymerase chain reaction (PCR)-based polymorphic DNA assay procedure random amplified polymorphic DNAs (RAPDs) to assess the extent of genetic variation between eight mahogany species from four genera. Pronounced genetic differentiation was found between the species and genera. There was a clear separation of Cedrela odorata from the other species, with 95% of the variable amplification products differing, whereas Lovoa trichilioides, Khaya spp. and Swietenia spp. were more closely grouped. These results are consistent with the current taxonomic viewpoint. A number of markers were found to be diagnostic for particular species, which could be of value in determining the status of putative hybrids. The application of RAPDs to the study of genetic variation in mahoganies is discussed in the context of developing genetic conservation and improvement strategies for these species. PMID:24177901

  13. 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

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

    SciTech Connect

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

    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.

  15. Genetic Structure of the Endangered Plant Neolitsea sericea (Lauraceae) from the Zhoushan Archipelago Using RAPD Markers

    PubMed Central

    WANG, ZHONG-SHENG; AN, SHU-QING; LIU, HONG; LENG, XIN; ZHENG, JIAN-WEI; LIU, YU-HONG

    2004-01-01

    • Background and Aims The Zhoushan archipelago is the largest archipelago in China. It separated from the mainland about 9000 years ago due to rising sea levels and climate change. Because of the long-term influences of human activities, the original forest vegetation on the large islands has been badly damaged and its plant diversity reduced. • Methods Levels and patterns of genetic diversity in 114 individuals from six natural populations and four cultivated populations of the insular endangered plant Neolitsea sericea (Lauraceae) on the Zhoushan archipelago were assessed using random amplified polymorphic DNA (RAPD) markers. • Key Results A total of 99 discernible loci were obtained for all populations using ten primers, 50·5 % of which were polymorphic [percentage of polymorphic bands (PPB) = 50·5 %]. Despite being a woody, long-lived, perennial, outcrossing and insect-pollinated plant, N. sericea exhibited low levels of genetic variation. The cultivated populations (PPB = 18·9 %, HE = 0·060, S = 0·092) were genetically less diverse than the natural populations (PPB = 23·1 %, HE = 0·082, S = 0·123). Based on analysis of molecular variance, a high degree of among-population differentiation was revealed for both natural (0·387) and cultivated populations (0·598). • Conclusions Removal of plants from the wild for horticulture purposes has eroded the level of genetic variation of N. sericea. Low levels of genetic diversity and a high degree of population differentiation indicate that management strategies should include conservation of natural habitats occupied by all six wild populations, and sampling of germplasm resources from multiple seed sources. PMID:15546928

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

    PubMed

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

    2016-01-01

    Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs. PMID:26858551

  17. Analysis of a Detailed Genetic Linkage Map of Lactuca Sativa (Lettuce) Constructed from RFLP and Rapd Markers

    PubMed Central

    Kesseli, R. V.; Paran, I.; Michelmore, R. W.

    1994-01-01

    A detailed genetic map has been constructed from the F(2) population of a single intraspecific cross of Lactuca sativa (n = 9). It comprises 319 loci, including 152 restriction fragment length polymorphism (RFLP), 130 random amplified polymorphic DNA (RAPD), 7 isozyme, 19 disease resistance, and 11 morphological markers. Thirteen major, four minor linkage groups and several unlinked markers are identified for this genome which is estimated to be approximately 1950 cM. RFLP and RAPD markers show similar distributions throughout the genome and identified similar levels of polymorphism. RAPD loci were much quicker to identify but more difficult to order. Procedures for generating accurate genetic maps and their limitations are described. PMID:7912217

  18. RAPD and ISSR marker mediated genetic polymorphism of two mangroves Bruguiera gymnorrhiza and Heritiera fomes from Indian Sundarbans in relation to their sustainability.

    PubMed

    Dasgupta, Nirjhar; Nandy, Paramita; Sengupta, Chandan; Das, Sauren

    2015-07-01

    Increased salinity distresses some key species severely in Indian Sundarbans. Geomorphic characteristics coupled with demographic obligations have proven to be pivotal factor towards the prevalence of elevated salinity in this zone. Better adaptation to rapid changes in microclimate demands wide range of genetic polymorphism as well. RAPD and ISSR molecular markers were used for this genetic diversity study. Degree of polymorphism was found relatively higher in Bruguiera gymnorrhiza (26.43 % in RAPD and 24.36 % in ISSR) than the other taxa, Heritiera fomes (14.43 and 12.76 % respectively) in case of RAPD and ISSR. Dendrogram constructed based on the similarity matrix showed that for H. fomes, least saline and highest saline zones are positioned in the same clade; whereas in B. gymnorrhiza the higher saline areas were clustered together. Nei's gene diversity (h) as revealed from RAPD and ISSR analysis were found to be 0.0821, 0.0785 and 0.0647, 0.0592 in B. gymnorrhiza and H. fomes respectively. The higher degree of polymorphism as revealed from UPGMA Dendrogram and Nei's genetic diversity might be attributed towards the comfortable growth of B. gymnorrhiza all along the Indian Sundarbans. On the other hand the relatively lesser degree of genetic polymorphism of H. fomes might be attributed towards their precarious status in present days elevated salinity in Indian Sundarbans. PMID:26261402

  19. RAPD-based genetic linkage maps of Tribolium castaneum.

    PubMed Central

    Beeman, R W; Brown, S J

    1999-01-01

    A genetic map of the red flour beetle (Tribolium castaneum) integrating molecular with morphological markers was constructed using a backcross population of 147 siblings. The map defines 10 linkage groups (LGs), presumably corresponding to the 10 chromosomes, and consists of 122 randomly amplified polymorphic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total map length is 570 cM, giving an average marker resolution of 4.3 cM. The average physical distance per genetic distance was estimated at 350 kb/cM. A cluster of loci showing distorted segregation was detected on LG9. The process of converting RAPD markers to sequence-tagged site markers was initiated: 18 RAPD markers were cloned and sequenced, and single-strand conformational polymorphisms were identified for 4 of the 18. The map positions of all 4 coincided with those of the parent RAPD markers. PMID:10471716

  20. 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

  1. Molecular genetic differentiation of avian Escherichia coli by RAPD-PCR

    PubMed Central

    Salehi, Taghi Zahraei; Madani, Seyed Ahmad; Karimi, Vahid; Khazaeli, Fatemeh Arab

    2008-01-01

    Escherichia coli is one of the most important bacterial avian pathogens and a common inhabitant of the gastrointestinal tract of animals. Most pathogenic E. coli can not be differentiated biochemically or by classic microbiologic methods. Molecular typing methods, particularly PCR, facilitated epidemiological and ecological studies of bacteria. Here we describe the application of a random amplified polymorphic DNA- polymerase chain reaction (RAPD-PCR) for molecular genetic differentiation of E. coli isolates in Iran. In this study 58 E. coli isolates including 4 standard strains, 3 food originated isolates, 33 avian isolates, 8 isolates form diarrheic calves and 10 isolates from unweaned diarrheic lambs were analyzed by RAPD-PCR using primer 1247(5/-AAG AGC CCG T-3/). The RAPD analysis showed that these isolates could be grouped into 33 RAPD types and avian isolates were discriminated into 29 genotypes. It was shown that the primer could not differentiate E. coli isolated from lambs. Discriminatory index for entire isolates was 0.912 and for avian isolates was 0.990. We concluded that RAPD-PCR can be used as a method for molecular differentiation of E. coli isolates. PMID:24031252

  2. 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.) ...

  3. 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

  4. Genetic diversity of the bacterial wilt pathogen Ralstonia solanacearum using a RAPD marker.

    PubMed

    Nishat, Sayeda; Hamim, Islam; Khalil, M Ibrahim; Ali, Md Ayub; Hossain, Muhammed Ali; Meah, M Bahadur; Islam, Md Rashidul

    2015-11-01

    Bacterial wilt caused by Ralstonia solanacearum is a destructive disease of many economically important crop species. A significant variation in wilt incidence and severity in eggplant and potato was observed among the growing areas surveyed. R. solanacearum isolates obtained both from eggplant and potato belong to biovar III, while isolates from eggplant belong to race 1 and isolates obtained from potato belong to race 3. Random amplified polymorphic DNA (RAPD) technique was used as a tool for assessing genetic variation and relationship among seven isolate groups of R. solanacearum viz., RsB-1, RsB-2, RsB-3, RsP-1, RsP-2, RsP-3 and RsP-4, consisting in a total of 28 isolates. Out of the RAPD markers used, amplification with four decamer primers produced 70 bands with sizes ranging from 100 to 1400 bp. Out of 70 bands, 68 bands (97.06%) were polymorphic and two bands (2.94%) were monomorphic amongst the seven R. solanacearum isolates group. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei's genetic distance produced two main clusters of the seven isolates of R. solanacearum. The isolates RsB-1, RsB-2, RsB-3 and R-4 grouped in cluster І, while RsP-2, RsP-3 and RsP-4 grouped in cluster ІІ. The highest intra-variety similarity index (Si) was found in RsB-1 isolate (86.35%) and the lowest one in RsP-2 (56.59%). The results indicated that relatively higher and lower levels of genetic variation were found in RsP-3 and RsB-3, respectively. The coefficient of gene differentiation (G(st)) was 0.5487, reflecting the existence of a high level of genetic variations among seven isolates of R. solanacearum. Comparatively higher genetic distance (0.4293) and lower genetic identity (0.6510) were observed between RsB-2 and RsP-4 combinations. The lowest genetic distance (0.0357) and highest genetic identity (0.9650) were found in RsB-1 vs. RsB-2 pair. Thus, RAPD offers a potentially simple, rapid and reliable method to evaluate genetic diversity analysis in R. solanacearum. PMID:26302834

  5. Genetic structure of three orchid species with contrasting breeding systems using RAPD and allozyme markers.

    PubMed

    Sun, M; Wong, K C

    2001-12-01

    Zeuxine gracilis, Zeuxine strateumatica, and Eulophia sinensis are wild orchids with different breeding systems and colonizing abilities. Zeuxine gracilis is an outcrosser with restricted distribution, whereas S. strateumatica is an apomictic colonizer found only in newly available open habitats. Eulophia sinensis is an outcrossing colonizer. This study investigates the levels of genetic variation and patterns of population structure in these wild orchids to provide genetic information for the development of suitable conservation strategies. Lack of allozyme variation was characteristic of all three species, especially in populations of the two colonizing orchids, Z. strateumatica and E. sinensis. More variable markers, randomly amplified polymorphic DNAs (RAPDs), were further employed to characterize population structure of these species. Substantial genetic variation was found at the RAPD loci within populations of Z. gracilis (p = 21.65 ± 15.88%, A = 1.217 ± 0.159, and H = 0.076 ± 0.054) and E. sinensis (p = 17.82 ± 20.97%, A = 1.179 ± 0.209, and H = 0.070 ± 0.084), but little variation existed within populations of Z. strateumatica (p = 2.84 ± 2.58%, A = 1.029 ± 0.026, and H = 0.011 ± 0.011). Regardless of the breeding system, the total gene diversity at the species level was partitioned primarily between populations, as shown by high G(ST) values, in all three species. An extremely high level of population differentiation (G(ST) = 0.924) was found in the apomictic colonizer Z. strateumatica. The patterns of genetic variation in these wild orchids are apparently related to their differences in breeding system and colonizing ability. Different conservation strategies are needed for the long-term survival of these species. PMID:21669650

  6. Genetic Confirmation of Mungbean (Vigna radiata) and Mashbean (Vigna mungo) Interspecific Recombinants using Molecular Markers

    PubMed Central

    Abbas, Ghulam; Hameed, Amjad; Rizwan, Muhammad; Ahsan, Muhammad; Asghar, Muhammad J.; Iqbal, Nayyer

    2015-01-01

    Molecular confirmation of interspecific recombinants is essential to overcome the issues like self-pollination, environmental influence, and inadequacy of morphological characteristics during interspecific hybridization. The present study was conducted for genetic confirmation of mungbean (female) and mashbean (male) interspecific crosses using molecular markers. Initially, polymorphic random amplified polymorphic DNA (RAPD), universal rice primers (URP), and simple sequence repeats (SSR) markers differentiating parent genotypes were identified. Recombination in hybrids was confirmed using these polymorphic DNA markers. The NM 2006 × Mash 88 was most successful interspecific cross. Most of true recombinants confirmed by molecular markers were from this cross combination. SSR markers were efficient in detecting genetic variability and recombination with reference to specific chromosomes and particular loci. SSR (RIS) and RAPD identified variability dispersed throughout the genome. In conclusion, DNA based marker assisted selection (MAS) efficiently confirmed the interspecific recombinants. The results provided evidence that MAS can enhance the authenticity of selection in mungbean improvement program. PMID:26697053

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

    PubMed

    Lamare, Animos; Rao, Satyawada Rama

    2015-07-01

    North east India is considered as one of the major biodiversity hotspots worldwide and centre of origin of several plant species including Musa. Musa acuminata Colla is known to be one of the wild progenitors of cultivated bananas and plantains. Three single primer based DNA marker techniques viz., random amplified polymorphic DNA (RAPD), inter simple sequence repeat (ISSR) and directed amplification of minisatellites DNA (DAMD) were used for diversity diagnostics among 25 genotypes of wild M. acuminata collected from Meghalaya province of north east India. A total of 58 primers (26-RAPD, 21-ISSR, and11-DAMD) yielded 451 DNA fragments, of which 395 (87.58 %) were found to be polymorphic in nature. The polymorphic information content (PIC) values were almost identical for each marker system. The resolving power of the marker system was found to be highest in RAPD (3.96) whereas ISSR resolved highest marker index (16.39) in the study. Selected amplicon data obtained through single primer amplification reactions were utilized for determination of diversity within and among the populations of M. acuminata. Nei's genetic differentiation (Gst) value (0.451) indicated higher proportion of the genetic variation within the populations which is supported by the AMOVA analysis (88 %). The study provides insight into the efficacy of RAPD, ISSR and DAMD to analyse the genetic variation existing in the wild Musa germplasm, which can further be exploited for quality trait improvement and domestication of such important horticultural crops. The genetic diversity based population structure may shed light on the genetic basis of speciation and evolution of various species within the genus Musa. PMID:26261399

  8. Molecular fingerprinting of Helicanthus elastica (Desr.) Danser growing on five different hosts by RAPD

    PubMed Central

    Sunil Kumar, K.N.; Maruthi, K.R.; Alfarhan, A.H.; Rajakrishnan, R.; Thomas, J.

    2015-01-01

    Mistletoes are hemiparasitic plants growing on aerial parts of other host trees. Many of the mistletoes are reported to be medicinally important. The hemiparasitic nature of these plants makes their chemical composition dependent on the host on which it grows. They are shown to exhibit morphological dissimilarities also when growing on different hosts. Helicanthus elastica (Desr.) Danser (mango mistletoe) is one such less explored medicinal mistletoe found on almost every mango tree in India. Traditionally, the leaves of this plant are used for checking abortion and for removing stones in the kidney and urinary bladder while significant antioxidant and antimicrobial properties are also attributed to this species of mistletoe. The current study was undertaken to evaluate molecular differences in the genomic DNA of the plant while growing on five different host trees using four random markers employing random amplified polymorphic DNA (RAPD) followed by similarity matrix by Jaccard’s coefficient and distance matrix by hierarchal clustering analysis. Similarity and distance matrix data employing just 4 random markers, separately and the pooled data as well, revealed significant difference in the genomic DNA of H. elastica growing on five different hosts. Pooled data of similarity from all the 4 primers cumulatively showed similarity between 0.256 and 0.311. Distance matrix ranged from of 0.256 to 0.281 on pooling the data from all the four primers. The result employing a minimum number of primers could conclude that genomic DNA of H. elastica differs depending upon the host on which it grows, hence the host must be considered while studying or utilizing this mistletoe for medicinal purposes. PMID:27081357

  9. Molecular fingerprinting of Helicanthus elastica (Desr.) Danser growing on five different hosts by RAPD.

    PubMed

    Sunil Kumar, K N; Maruthi, K R; Alfarhan, A H; Rajakrishnan, R; Thomas, J

    2016-05-01

    Mistletoes are hemiparasitic plants growing on aerial parts of other host trees. Many of the mistletoes are reported to be medicinally important. The hemiparasitic nature of these plants makes their chemical composition dependent on the host on which it grows. They are shown to exhibit morphological dissimilarities also when growing on different hosts. Helicanthus elastica (Desr.) Danser (mango mistletoe) is one such less explored medicinal mistletoe found on almost every mango tree in India. Traditionally, the leaves of this plant are used for checking abortion and for removing stones in the kidney and urinary bladder while significant antioxidant and antimicrobial properties are also attributed to this species of mistletoe. The current study was undertaken to evaluate molecular differences in the genomic DNA of the plant while growing on five different host trees using four random markers employing random amplified polymorphic DNA (RAPD) followed by similarity matrix by Jaccard's coefficient and distance matrix by hierarchal clustering analysis. Similarity and distance matrix data employing just 4 random markers, separately and the pooled data as well, revealed significant difference in the genomic DNA of H. elastica growing on five different hosts. Pooled data of similarity from all the 4 primers cumulatively showed similarity between 0.256 and 0.311. Distance matrix ranged from of 0.256 to 0.281 on pooling the data from all the four primers. The result employing a minimum number of primers could conclude that genomic DNA of H. elastica differs depending upon the host on which it grows, hence the host must be considered while studying or utilizing this mistletoe for medicinal purposes. PMID:27081357

  10. Utilization of RAPD markers to assess genetic diversity of wild populations of North American ginseng (Panax quinquefolium).

    PubMed

    Lim, Wansang; Mudge, Kenneth W; Weston, Leslie A

    2007-01-01

    The Catskill Mountains of New York State are an important source of wild-collected American ginseng (Panax quinquefolium) and, increasingly, of woods-cultivated ginseng. The objective of this study was to assess genetic diversity among 9 different wild ginseng populations in and adjacent to the Catskill Mountain region of New York State and to compare these to wild populations from other states including Kentucky, Tennessee, North Carolina, Pennsylvania, and Virginia, and one cultivated population from Wisconsin. Randomly amplified polymorphic DNA (RAPD) markers were used to estimate the genetic distance among samples from the 15 populations. Pooled DNA from 10 plants of each of 8 New York populations was initially screened with 64 random primers; subsequently, the 15 primers that exhibited the greatest number of reproducible polymorphic markers were selected for further experimentation. Gel electrophoresis with the selected 15 primers produced 124 highly reproducible polymorphic bands. The ratio of discordant bands to total bands scored was used to estimate the genetic distance within and among populations. Multidimensional scaling (MDS) of the relation matrix showed distinctly separate clusters between New York and non-New York populations, indicating separation between these two groupings. The MDS analysis was confirmed using pooled chi-square tests for fragment homogeneity. This study shows that RAPD markers can be used as population-specific markers for Panax quinquefolium, and may eventually be utilized as markers for ginsenoside assessment. PMID:17315311

  11. 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

  12. 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

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

    PubMed

    Apostol, B L; Black, W C; Reiter, P; Miller, B R

    1996-04-01

    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 dominant alleles, (2) that genotypes at RAPD loci are in Hardy-Weinberg proportions, (3) identity in state (iis) among dominant amplified alleles and (4) iis among null alleles. The average genic heterozygosity was 0.354, more than twice the level detected in earlier allozyme surveys. Nested analysis of variance indicated extensive genetic differentiation among locations within cities. Effective migration rates (Nm) among cities were estimated from FST assuming an island model of migration. Estimates of Nm ranged from 9.7 to 12.2 indicating a high dispersal rate. The large number of polymorphisms revealed by RAPD-PCR allowed the distribution of FST and linkage disequilibrium to be examined among loci and demonstrated that small samples inflate FST and linkage disequilibrium. No linkage disequilibrium maintained through epistasis was detected among alleles at the 57 loci. PMID:8626220

  14. Molecular marker applications in plants.

    PubMed

    Hayward, Alice C; Tollenaere, Reece; Dalton-Morgan, Jessica; Batley, Jacqueline

    2015-01-01

    Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants. PMID:25373746

  15. Molecular typing of Staphylococcus aureus based on PCR-RFLP of coa gene and RAPD analysis.

    PubMed

    Karakulska, J; Pobucewicz, A; Nawrotek, P; Muszyńska, M; Furowicz, A J; Czernomysy-Furowicz, D

    2011-01-01

    The aim of this study was molecular identification of S. aureus strains isolated from mastitic milk samples and establishing the genetic relationship between strains isolated from cows belonging to the same herd. In all 43 isolated strains the gap gene (930 bp) was amplified, which enabled their affiliation to the Staphylococcus genus to be established. PCR-RFLP with AluI endonuclease of the gap gene as well as nuc (450 bp) and coa (1130 bp) gene amplification allowed precise S. aureus species identification. One hundred percent of the genetic relationship between strains was established via RAPD-PCR and coa-typing. PMID:21721416

  16. Haplorchis taichui, Witenberg, 1930: Development of a HAT-RAPD marker for the detection of minute intestinal fluke infection.

    PubMed

    Wongsawad, Chalobol; Wongsawad, Pheravut; Chai, Jong Yil; Anuntalabhochai, Somboon

    2009-10-01

    Specific primers to determine the presence of an intestinal fluke, Haplorchis taichui, were investigated using the high annealing temperature random amplified polymorphic DNA (HAT-RAPD) PCR, and 18 arbitrary primers (Operon Technologies), to generate different polymorphic DNA profiles. Thirteen kinds of parasites were used to compare fingerprints. A 256bp HAT-RAPD marker, generated from the OPP-11 primer, was found to be H. taichui-specific, and this marker was cloned, transformed, and sequenced. From the sequence data, a pair of primers were designed with Genetyx-MAC ver.11 and indicated as: Hap-t F 5'-GGC CAA CGC AAT CGT CAT CC-3' and Hap-t R 5'-GCG TCG GGT TTC AGA CAT GG-3'. These specific primers were tested for efficacy and specificity by amplifying them with all 13 parasites DNAs in PCR reaction. A 256bp amplicon was generated, which was shown to have a positive result, only for H. taichui DNA. It revealed no cross-reaction with any of the other tested parasite species. The minimum DNA template, needed for detection by PCR, was 0.1picogram (pg). The successful development of H. taichui-specific primers is expected to be beneficial for epidemiological studies and for prevention and control of these parasitic infections. PMID:19563805

  17. Molecular Identification of Clinical Isolates of Mycobacterium fortuitum by Random Amplified Polymorphic DNA (RAPD) Polymerase Chain Reaction and ERIC PCR

    PubMed Central

    Khosravi, Azar Dokht; Farahani, Abbas; Jamali, Hooshang

    2015-01-01

    Backgrounds Non tuberculous mycobacteria (NTM) are of importance now-a-days due to their increasing virulence outbreaks and emerging antibiotic resistance. Since the most common NTM in Iran is reportedly Mycobacterium fortuitum, the present study was designed with the aim of molecular identification of clinical isolates of M. foruitum to analyse their heterogeneity. Materials and Methods A total of 81 isolates of NTM isolated from various samples were collected. The clinical isolates were assigned to species M. fortuitum by using conventional and molecular methods. The DNA banding patterns of ERIC- PCR and RAPD- PCR were analysed by using Bionumeric 7.5 software. Results Out of 81 tested NTM, 36 strains of M. fortuitum were identified. 33 isolates were selected for molecular typing in this study. Based on RAPD and ERIC analysis, M. fortuitum isolates were divided into 3 and 6 clusters, respectively. Most of the isolates were distributed into types of II RAPD (20 members/ 60.6 %) and V (14 members/ 42.4% with sub cluster I & II) of ERIC. In RAPD analysis, the major fragments were 300 bp, followed by fragment 1000. In ERIC analysis, the major fragments were 280 bp followed by fragment 1200 bp. Conclusion In conclusion, though the results from this study represented higher discriminatory power of ERIC, however the combination of RAPD and ERIC analysis were able to sufficiently discriminate the genotypic diversity, infection control, and gain useful epidemiological information regarding M. fortuitum isolates. PMID:26816886

  18. 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

  19. Genetic variation at allozyme and RAPD markers in Pinus longaeva (Pinaceae) of the White Mountains, California.

    PubMed

    Lee, Seok-Woo; Ledig, F Thomas; Johnson, David R

    2002-04-01

    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 tree to determine whether they originated from multiple seed caches of the Clark's nutcracker. Despite the limited and fragmented distribution of bristlecone pine, its level of genetic diversity was comparable to that of other pines, but lower than that reported for eastern populations of Great Basin bristlecone pine. Twenty-six of 36 allozymes were polymorphic (p(95) = 38.9%; p = 63.0%), with observed heterozygosity (H(o)) of 0.122 and expected heterozygosity (H(e)) of 0.134. The proportion of the total variation among populations (G(ST)) was only 0.011. The high proportion of trees with multiple stems was not due to germination in seed caches; only six of 210 forked trees had multiple allozyme genotypes. Of the 42 RAPD loci scored, 27 were monomorphic. Genetic diversity for RAPDs was nearly the same as that for allozymes (p(95) = 34.1%, H(e) = 0.130). However, the estimates of diversity and differentiation were much higher (H(e) = 0.321, G(ST) = 0.039) after excluding monomorphic loci. PMID:21665657

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

    PubMed

    Grover, Atul; Sharma, P C

    2016-01-01

    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

  1. Molecular markers linked to the leaf rust resistance gene Lr24 in different wheat cultivars.

    PubMed

    Dedryver, F; Jubier, M F; Thouvenin, J; Goyeau, H

    1996-10-01

    The aim of this study was to find molecular markers (RAPD and SCAR) for the wheat leaf rust resistance gene Lr24. A backcross line, RL 6064, possessing a single resistance gene to leaf rust (Lr24) and its recurrent parent 'Thatcher' were used to find RAPD markers linked to the Lr24 gene. Among 125 RAPD primers tested, only one (OP-H5) detected an additional band in the resistant line RL 6064. The genetic linkage of this molecular marker to Lr24 was tested on a segregating F2 population derived from a cross between the leaf rust resistant line RL 6064 and the susceptible line 'Chinese Spring'. This marker showed complete linkage to the Lr24 resistance gene. A more reliable and specific marker for this resistance gene was made by converting it into a sequence characterized amplified region (SCAR). The presence of a single amplification product allowed direct detection of the gene in the test tube by the addition of ethidium bromide. This SCAR marker linked to the leaf rust resistance gene Lr24 could be used easily in a practical breeding program. PMID:8890515

  2. A genetic linkage map of marine shrimp Penaeus ( Fenneropenaeus) chinensis based on AFLP, SSR, and RAPD markers

    NASA Astrophysics Data System (ADS)

    Liu, Bo; Wang, Qingyin; Li, Jian; Liu, Ping; He, Yuying

    2010-07-01

    The Chinese shrimp Penaeus ( Fenneropaeneus) chinensis is an important species in marine fishery and aquaculture in China. A female Chinese shrimp Penaeus ( Fenneropaeneus) chinensis was captured from west coast of the Korean peninsula and mated with a “Yellow Sea No. 1” male to produce the first filial generation (F1) 100 F2 full-sib progeny from brother-sister crosses between F1 families was used for the mapping study. A genetic linkage map of the Chinese shrimp was constructed, based on 354 markers, including 300 amplified fragment length polymorphism (AFLP) markers, 42 microsatellite (SSR) markers, and 12 randomly amplified polymorphism (RAPD) markers. Forty-seven linkage groups (LGs) were identified. The total map length was 4 580.5 cM, with an average spacing of 11.3 cM, covering 75.8% of the estimated genome size. The construction of this genetic linkage map was part of a genetic breeding program. This linkage map will contribute to the discovery of genes and quantitative trait loci (QTLs) in Chinese shrimp.

  3. 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. PMID:25821599

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

    PubMed

    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. PMID:25821599

  5. Application of RAPD in genetic diversity study on Gracilaria lemaneiformis III. Phase and sex related markers

    NASA Astrophysics Data System (ADS)

    Li, Xiang-Feng; Sui, Zheng-Hong; Zhang, Xue-Cheng

    1998-03-01

    Random amplification of polymorphic DNA (RAPD) was conducted by using 10 random primers (P-1 to P-10) in Gracilaria lemaneiformis. Phase and sex specific bands were amplified by primers P-2, P-6, P-7 and P-8: for P-2 a 1.4 kb band was found in female gametophytes and tetrasporophytes, for P-6, a 0.6 kb band appeared in male gametophytes and tetrasporophytes; for P-7, a 0.76 kb band appeared in male gametophytes and tetrasporophytes; for P-7, a 0.72 kb band appeared in female gametophytes and tetrasporophytes; for P-8, a 0.73 kb band only appeared in male gametophytes.

  6. 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 μM 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 μM 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

  7. Randomly amplified polymorphic DNA (RAPD) and derived techniques.

    PubMed

    Babu, Kantipudi Nirmal; Rajesh, Muliyar Krishna; Samsudeen, Kukkumgai; Minoo, Divakaran; Suraby, Erinjery Jose; Anupama, Kallayan; Ritto, Paul

    2014-01-01

    Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selecting core collections, determination of genetic distances, genome analysis, developing molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest and cost-effective and can be performed in a moderate laboratory for most of its applications. In addition RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like AP-PCR, SCAR, DAF, SRAP, CAPS, RAMPO, and RAHM can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented. PMID:24415476

  8. A comparison of UP-PCR and RAPD markers to study genetic diversity of Fusicladium effusum (G. Winter, cause of pecan scab

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusicladium effusum is a plant pathogenic fungus that infects pecan causing yield loss. There is no information on the population genetics or genetic diversity of F. effusum, or the applicability of available molecular tools to study these aspects. The usefulness of RAPDs and Universally Primed (UP)...

  9. A composite genetic map of the parasitoid wasp Trichogramma brassicae based on RAPD markers.

    PubMed Central

    Laurent, V; Wajnberg, E; Mangin, B; Schiex, T; Gaspin, C; Vanlerberghe-Masutti, F

    1998-01-01

    Three linkage maps of the genome of the microhymenopteran Trichogramma brassicae were constructed from the analysis of segregation of random amplified polymorphic DNA markers in three F2 populations. These populations were composed of the haploid male progeny of several virgin F1 females, which resulted from the breeding of four parental lines that were nearly fixed for different random amplified polymorphic DNA markers and that were polymorphic for longevity and fecundity characters. As the order of markers common to the three mapping populations was found to be well conserved, a composite linkage map was constructed. Eighty-four markers were organized into five linkage groups and two pairs. The mean interval between two markers was 17.7 cM, and the map spanned 1330 cM. PMID:9725846

  10. Molecular markers associated with cold-hardiness in Camellia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sequence-characterized amplified region (SCAR) markers from expressed sequence tag-polymerase chain reaction (EST-PCR) and random amplified polymorphic DNA (RAPD) markers were developed with the goal to separate cold hardy camellias from non-cold hardy ones. A total of 28 cold hardy and non-cold h...

  11. Genetic variability and differentiation of Caragana microphylla populations as revealed by RAPD markers.

    PubMed

    Chen, X H; Gao, Y B

    2011-09-01

    Genetic variability in random amplified polymorphic DNA (RAPD) was studied in 90 individuals of Caragana microphylla, an outcrossing perennial shrub species, from five natural populations sampled in Inner Mongolia steppe of China on a small scale. Nineteen selected primers were used to amplify DNA samples, and totally 225 bands were detected. The percentage of polymorphic bands within populations ranged form 58.22% to 63.56%, with an average of 60% at the population level and 71.11% at the species level, indicating relatively high genetic variations in C. microphylla species. Shannon's information index (I) and Nei's gene diversity (h) showed the similar trend with each other. According to the analysis of Nei's gene diversity, the percentage of genetic variation among populations was 7.13%, indicating a low level of genetic differentiation among populations. There existed a strong gene flow (Nm = 3.26) among populations. Although AMOVA analysis also revealed most variation was within populations (phi(ST) = 4.1%), a significant proportion was observed among populations (P<0.001) in the present study, suggesting genetic differentiation occurred among populations at a certain extent. Based on Mantel's tests and the results of previous studies, the genetic structure pattern of C. microphylla accorded with the isolation-by-distance model on a very large scale, however, on a small scale, the significant genetic differentiation among populations might be enhanced by the micro-environmental divergence among the sampling sites, rather than by geographic factors. Analysis of the genetic variations of C. microphylla populations provided useful information for the adaptive strategy of Caragana species. PMID:22117404

  12. 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

  13. Inbreeding, outbreeding and RAPD markers studies of faba bean (Vicia faba L.) crop.

    PubMed

    Obiadalla-Ali, Hazem A; Mohamed, Naheif E M; Khaled, Abdelsabour G A

    2015-11-01

    Five faba bean genotypes (Vicia faba L.) were selfed for two cycles to produce S1 and S2 generations. A half-diallel cross was carried out among them in each level of inbreeding (S0, S1 and S2) to obtain 10 F1 hybrids. Parental materials as well as their respective F1s were evaluated during the winter season of 2012. All studied traits except total dry seed yield showed significant inbreeding depression after the first generation of selfing (S1). No further decrease was noticed at the S2 generation. In the S1 generation the degree of inbreeding depression was highest for No. of branches/plant (-14.0%) and the least for weight of 100-seeds (-2.7). Some parents showed inbreeding vigor i.e. positive difference between S2 and S1 for some traits in S2 generation. Most studied traits showed significant positive heterosis values over mid-parent. The highest value of heterosis over the mid-parent was detected for total dry seed yield (128.8) and the lowest value of hybrid vigor was shown by weight of 100-seeds (1.2%). Specific combination among the 5 parental genotypes showed the highest value for heterosis for example cross Misr 2 × Giza 429 was the best cross for total dry seed yield, cross Giza 429 × Misr 1 for No. of branches/plant. Giza 429 is the best general combiner for most traits. Some crosses showed heterosis depression i.e. negative heterosis value in some traits. Hybridization among parental genotypes is recommended to be at the S1 or S2 generation. Twelve arbitrary primers produced different degrees of genetic polymorphism among the parental genotypes. A total of 65 amplification products were scored polymorphic. The percentage of polymorphic bands detected ranged from 33% to 100% with an average of 66.47%. The average of amplified bands was 5.42 polymorphic bands per primer. A positive, but non-significant, correlation (r = 0.085) between Euclidean distance and RAPD distance was observed. PMID:26644923

  14. 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 μM 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 μM 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

  15. 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

  16. Identification of RAPD markers, in situ DNA content and structural chromosomal diversity in some legumes of the mangrove flora of Orissa.

    PubMed

    Jena, S; Sahoo, P; Mohanty, S; Das, A B

    2004-11-01

    Randomly amplified polymorphic DNA (RAPD) markers, karyotypes and 4C DNA content were analyzed in five legume mangroves belonging to the sub-family Papilinoideae (Dalbergia spinosa, Derris heterophylla and D. indica) and Caesalpinioideae (Caesalpinia crista, Cynometra ramiflora) of the family Fabaceae to establish the genetic variability and phylogenetic affinities. Somatic chromosome numbers were reported for the first time in D. spinosa (2n = 20), C. ramiflora (2n = 26) and D. heterophylla (2n = 24) with reconfirmation of the somatic chromosome number in D. indica (2n = 22) and C. crista (2n = 24). Significant intergeneric and interspecific variation of 4C DNA content was observed and that varied from 8.970 pg in C. ramiflora to 28.730 pg in D. indica. From the RAPD analysis, the dendogram showed clustering of Caesalpinia crista and Cynomitra ramiflora into one group (81.80). In the second groups Derris indica and Derris heterophylla were more similar (83.10) than Dalbergia spinosa (85.80). Species-specific DNA markers (900 bp) obtained in D. spinosa from OPN15; 700 and 2000 bp in C. ramiflora from OPN4 and 400 and 800 bp in D. heterophylla and 500 bp DNA fragment in C. crista obtained from OPN-11 were found characteristic RAPD markers of these species. C. crista found more closer affinity to C. ramiflora of the sub-family Caesalpinioideae [genetic distance (1-F) = 0.847]. Derris indica showed closer genetic relation with D. heterophylla [genetic distance (1-F) = 0.856] than D. spinosa [genetic distance (1-F) = 0.876] where Derris and Dalbergia belongs to the sub-family Papilionoideae. By employing these markers the present study has helped to resolve the relationship between the taxonomically diverse leguminous mangroves and study their ability to coexist with mangroves that would shed light on the evolution of mangroves from terrestrial species. PMID:15609544

  17. A GENETIC MAP OF MOLECULAR MARKERS IN TRITICOSECALE WITTMACK

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A genetic map of triticale produced with polymorphic markers based on PCR technology (RAPD, RAMP, AFLP and SSR) is reported. These revealed levels of polymorphism of 7.6%, 6.2%, 7.9% and 28.4%, respectively. The plant materials employed were two hexaploid triticale cultivars, 'Torote' and 'Presto', ...

  18. Assessment of genetic variation in lucerne (Medicago sativa L.) using protease inhibitor activities and RAPD markers.

    PubMed

    Chandra, Amaresh; Pandey, Krishna Chandra

    2011-09-01

    The aim of the present study is to identify and characterize lucerne lines resistance to weevil infestation. After three years of field screening for resistance to weevil infestation, 13 lines of lucerne were selected to assess the genotypic variations for lucerne weevil (Hypera postica Gyll.) at biochemical and molecular levels. Total phenols varied from 0.15 to 0.91 mg g (DM) in these genotypes. The highest trypsin (11.11 unit mg(-1) protein) and chymotrypsin (93.0 unit mg(-1) protein) inhibitors activities were recorded in G-1-02 and B-4-03 lines respectively, whereas highest alpha-amylases inhibitor activity (14.2 unit mg(-1) protein) in C-6-01. Zymogram patterns for trypsin inhibitor activity showed quantitative variations among the lines. In total 262 DNA fragments were generated when 45 deca-mer random primers were employed. Genetic variation in terms of genetic distance ranged from 0.65 to 0.85. Sequential Agglomerative Hierarchical and Nested (SAHN) clustering using the Un-weighted Pair Group Method with Arithmetic mean (UPGMA) algorithm yielded two clusters (cluster I and II) which converged at 72% similarity level. Cluster I contained most of the lines having low level of weevil infestation. High bootstrap values (>40) indicated the significance of nodes embodied in these two clusters. However, SDS-PAGE analysis of the leaf proteins of these 13 lines showed no major variations except minor difference in the protein bands of molecular weights between 14 to 20 kD. PMID:22319869

  19. Molecular markers for rust and pyricularia leaf spot disease resistance in pearl millet.

    PubMed

    Morgan, R N; Wilson, J P; Hanna, W W; Ozias-Akins, P

    1998-03-01

    Pearl millet [Pennisetum glaucum (L.) R.Br.] is a warm-season grass used for food, feed, fodder and forage, primarily in countries of Africa and India but grown around the world. The two most-destructive diseases to pearl millet in the United States are rust (caused by Puccinia substriata var. indica) and pyricularia leaf spot (caused by Pyricularia grisea). Genes for disease resistance to both pathogens have been transferred into agronomically acceptable forage and grain cultivars. A study was undertaken to identify molecular markers for three rust loci and one pyricularia resistance locus. Three segregating populations were screened for RAPDs using random decamer primers and for RFLPs using a core set of probes detecting single-copy markers on the pearl millet map. The rust resistance gene Rr 1 from the pearl millet subspecies P. glaucum ssp. monodii was linked 8.5 cM from the RAPD OP-G8350. The linkage of two RFLP markers, Xpsm108 (15.5 cM) and Xpsm174 (17.7 cM), placed the Rr 1 gene on linkage-group 3 of the pearl millet map. Rust resistance genes from both Tift 89D2 and ICMP 83506 were placed on linkage-group 4 by determining genetic linkage to the RFLP marker Xpsm716 (4.9 and 0.0 cM, respectively). Resistance in ICMP 83506 was also linked to the RFLP marker Xpsm306 (10.0 cM), while resistance in Tift 89D2 was linked to RAPD markers OP-K19350 (8.8 cM) and OP-O8350 (19.6 cM). Fragments from OP-K19 and OP-O8 in the ICMP 83506 population, and Xpsm306 in the Tift 89D2 population, were monomorphic. Only one RAPD marker (OP-D11700, 5.6 cM) was linked to pyricularia leaf spot resistance. Attempts to detect polymorphisms with rice RFLP probes linked to rice blast resistance (Pyricularia oryzae; syn=P. grisea) were unsuccessful. PMID:24710880

  20. 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...

  1. 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...

  2. (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...

  3. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  5. [Characterization of the genetic diversity of the fish Brycon henni (Characiformes: Characidae) in central Colombia with RAPD markers].

    PubMed

    Pineda Santis, Hermes; Arboleda Chacón, Lucy; Echeverry Echavarria, Amparo; Urcuqui Inchima, Silvio; Pareja Molina, Diego; Olivera Angel, Martha; Builes Gómez, Juan

    2007-01-01

    Knowledge on the genetic diversity of wild fish species is essential for conservation and appropriate management of individuals in repopulation programs. In Colombia, Brycon henni has been reported in the Magdalena and Cauca river basins, but the population and range have diminished as a consequence of anthropic activities. In this study, the Random Amplified Polymorphic DNA (RAPD) was used to estimate the actual genetic structure in this species. For the purpose, six sample sites located in the department of Antioquia (Central Chain Mountains of Colombia) were used. Thirty five primers (87.5%), out of forty used, yielded 1 466 reliable and consistent fragments; 417 were considered as unique fragments able to discriminate among the Magdalena (Humarada-1 and Humarada-2) and Cauca (Piedras, La Clara y Guaracfi) river basins samples, suggesting that each is a discrete unit. This diversity suggests that anthropic effects of over fishing, dam building, deforestation and water pollution, have contributed to the isolation of these fish groups on the high mountains. Brycon moorei and Colossoma macropomum, as an interspecific control groups, were placed out of the B. henni general group, confirming their taxonomic classification through morphologic data. The RAPD technique was useful to know the genetic diversity and to discriminate among B. henni populations from different geographic origins, as a basis for an appropriate plan of repopulation, conservation and wildlife management. PMID:19086404

  6. Molecular markers in pediatric neuro-oncology

    PubMed Central

    Ichimura, Koichi; Nishikawa, Ryo; Matsutani, Masao

    2012-01-01

    Pediatric molecular neuro-oncology is a fast developing field. A multitude of molecular profiling studies in recent years has unveiled a number of genetic abnormalities unique to pediatric brain tumors. It has now become clear that brain tumors that arise in children have distinct pathogenesis and biology, compared with their adult counterparts, even for those with indistinguishable histopathology. Some of the molecular features are so specific to a particular type of tumors, such as the presence of the KIAA1549-BRAF fusion gene for pilocytic astrocytomas or SMARCB1 mutations for atypical teratoid/rhabdoid tumors, that they could practically serve as a diagnostic marker on their own. Expression profiling has resolved the existence of 4 molecular subgroups in medulloblastomas, which positively translated into improved prognostication for the patients. The currently available molecular markers, however, do not cover all tumors even within a single tumor entity. The molecular pathogenesis of a large number of pediatric brain tumors is still unaccounted for, and the hierarchy of tumors is likely to be more complex and intricate than currently acknowledged. One of the main tasks of future molecular analyses in pediatric neuro-oncology, including the ongoing genome sequencing efforts, is to elucidate the biological basis of those orphan tumors. The ultimate goal of molecular diagnostics is to accurately predict the clinical and biological behavior of any tumor by means of their molecular characteristics, which is hoped to eventually pave the way for individualized treatment. PMID:23095836

  7. Study of the genetic diversity and structure of a natural population of Nectandra megapotamica (Spreng.) Mez. using RAPD markers.

    PubMed

    Costa, L S; Reiniger, L R S; Heinzmann, B M; Amaral, L P; Serrote, C M L

    2015-01-01

    Nectandra megapotamica (Spreng.) Mez. is a tree species that naturally occurs in the Atlantic Forest, Brazil. The aim of this study was to evaluate the genetic diversity and structure of a natural population of 12 N. megapotamica individuals using random amplified polymorphic DNA markers. Eleven primers were used in this study, producing 81 bands, of which 98.99% were polymorphic. Analysis using STRUCTURE defined three different clusters (K = 3), results that were consistent with those of principal coordinates analysis. Both Nei's genetic diversity (h = 0.33) and Shannon's diversity index (I = 0.49) were relatively high. Analysis of molecular variance indicated that 24.89% of the genetic variability was among clusters, while the remaining 75.11% was within clusters. The Mantel test showed a weak correlation between genetic and geographic distances (r = 0.25, P = 0.105). Overall, the results revealed high levels of genetic diversity within clusters and high genetic differentiation among clusters without any spatial pattern of genetic variability. In addition, gene flow was independent of the geographical distribution and was compatible with the hierarchical island model. PMID:26782488

  8. NABIC marker database: A molecular markers information network of agricultural crops

    PubMed Central

    Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

    2013-01-01

    In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. Availability The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/ PMID:24250118

  9. Genetic variability in the natural populations of Lasioderma serricorne (F.) (Coleoptera: Anobiidae), detected by RAPD markers and by esterase isozymes.

    PubMed

    Coelho-Bortolo, T; Mangolin, C A; Lapenta, A S

    2016-02-01

    Lasioderma serricorne (F.) is a small cosmopolitan beetle regarded as a destructive pest of several stored products such as grains, flour, spices, dried fruit and tobacco. Chemical insecticides are one of the measures used against the pest. However, intensive insecticide use has resulted in the appearance of resistant insect populations. Therefore, for the elaboration of more effective control programs, it is necessary to know the biological aspects of L. serricorne. Among these aspects, the genetic variability knowledge is very important and may help in the development of new control methods. The objective of this study was to evaluate the genetic variability of 11 natural populations of L. serricorne collected respectively in three and four towns in the states of Paraná and São Paulo, Brazil, using 20 primers random amplified polymorphic DNA (RAPD) and polymorphisms of esterases. These primers produced 352 polymorphic bands. Electrophoretic analysis of esterases allowed the identification of four polymorphic loci (Est-2, Est-4, Est-5 and Est-6) and 18 alleles. Results show that populations are genetically differentiated and there is a high level of genetic variability within populations. The high degree of genetic differentiation is not directly correlated to geographical distance. Thus, our data indicate that movement of infested commodities may contribute to the dissemination of L. serricorne, facilitating gene flow. PMID:26459013

  10. 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 μM) and α-naphthalene acetic acid (NAA, 2.6 μM) in addition to antioxidants. Shoot elongation was obtained on MS medium containing BA (4.4 μM) + phloroglucinol (PG, 3.9 μM). Elongated shoots were transferred to half strength MS medium containing indole-3-butyric acid (IBA, 2.5 μM) 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

  11. Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers.

    PubMed

    Gulsen, Osman; Sever-Mutlu, Songul; Mutlu, Nedim; Tuna, Metin; Karaguzel, Osman; Shearman, Robert C; Riordan, Terrance P; Heng-Moss, Tiffany M

    2009-05-01

    Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars. PMID:19229513

  12. Estimation of pairwise relatedness with molecular markers.

    PubMed

    Lynch, M; Ritland, K

    1999-08-01

    Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears. PMID:10430599

  13. Estimation of pairwise relatedness with molecular markers.

    PubMed Central

    Lynch, M; Ritland, K

    1999-01-01

    Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears. PMID:10430599

  14. 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

  15. 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...

  16. Metabolite profiles of essential oils and molecular markers analysis to explore the biodiversity of Ferula communis: Towards conservation of the endemic giant fennel.

    PubMed

    Rahali, Fatma Zohra; Lamine, Myriam; Gargouri, Mahmoud; Rebey, Iness Bettaieb; Hammami, Majdi; Sellami, Ibtissem Hamrouni

    2016-04-01

    Giant fennel (Ferula communis L.) is well known in folk medicine for the treatment of various organ disorders. The biological importance of members of genus Ferula prompted us to investigate the leaves of the endangered Tunisian medicinal plant F. communis L. not previously investigated. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Thus, four F. communis populations were RAPD fingerprinted (63 RAPD markers generated by 7 primers) and the composition of their leaf essential oils (EO) (134 EO compounds) was characterized by GC-MS. Cluster analysis based on the leaf volatiles chemical composition of F. communis accessions defined three chemotypes according to main compounds have been distinguished: α-eudesmol/β-eudesmol/γ-terpinene; α-eudesmol/α-pinene/caryophyllene oxide and chamazulene/α-humulene chemotypes. A high genetic diversity within population and high genetic differentiation among them, based on RAPDs, were revealed (Hpop=0.320 and GST=0.288) caused both by the habitat fragmentation, the low size of most populations and the low level of gene flow among them. The RAPD dendrogram showed separation of three groups. Populations dominated by individuals from the β-eudesmol/γ-terpinene; chemotype showed the lowest gene diversity (H=0.104), while populations with exclusively α-pinene/caryophyllene oxide chemotype showed the highest value (H=0.285). The UPGMA dendrogram and PCA analysis based on volatiles yielded higher separation among populations, indicated specific adaptation of populations to the local environments. Correlation analysis showed a non-significant association between the distance matrices based on the genetic markers (RAPD) and chemical compounds of essential oil (P>0.05) indicating no influence of genetic background on the observed chemical profiles. These results reinforce the use of both volatile compounds and RAPD markers as a starting point for in situ conservation. The analysis of chemical constitution of oil of the populations from a specific region revealed predominance of specific constituents indicating possibility of their collection/selection for specific end uses like phytomedicines. Sufficient molecular and biochemical diversity detected among natural populations of this species will form the basis for the future improvement. The correlation between matrices of RAPD and essential oils was not significant. The conservation strategies of populations should be made according to their level of genetic and chemical diversity in relation to geographic location of populations. Our results give some insights into the characterization of this as yet little investigated plant. PMID:26826740

  17. 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

  18. 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

  19. Developmnent of molecular markers for powdery mildew resistance in grapevines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have been used as a tool for plant breeding for two decades. Markers linked to disease resistance can be used to pyramid resistance genes for improved durability and to improve the efficiency of evaluation. To develop molecular markers linked to resistance to grape powdery mildew ...

  20. RAPD MARKERS AS A MOLECULAR TOOL FOR ADDRESSING THE SPECIES PROBLEM IN CORALS. (R825158)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  1. RAPD MARKERS AS A MOLECULAR TOOL FOR ADDRESSING THE SPECIES PROBLEM IN CORALS. (R828008)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  2. Isolation and identification of Escherichia coli O157:H7 using different detection methods and molecular determination by multiplex PCR and RAPD.

    PubMed

    Kim, Ji-Yeon; Kim, So-Hyun; Kwon, Nam-Hoon; Bae, Won-Ki; Lim, Ji-Youn; Koo, Hye-Cheong; Kim, Jun-Man; Noh, Kyoung-Min; Jung, Woo-Kyung; Park, Kun-Taek; Park, Yong-Ho

    2005-03-01

    Escherichia coli O157:H7 is recognized as a significant food-borne pathogen, so rapid identification is important for food hygiene management and prompt epidemiological investigations. The limited prevalence data on Shiga toxin-producing E. coli (STEC) and E. coli O157:H7 in foods and animals in Korea made an assessment of the risks difficult, and the options for management and control unclear. The prevalence of the organisms was examined by newly developed kit-E. coli O157:H7 Rapid kit. For the isolation of E. coli O157:H7, conventional culture, immunomagnetic separation, and E. coli O157:H7 Rapid kit were applied, and multiplex PCR and randomly amplified polymorphic DNA (RAPD) were performed for the molecular determination. There was high molecular relatedness among 11 Korean isolates and 17 U.S. strains at 63% level. Additionally, distinct differentiation between pig and cattle isolates was determined. It implied that RAPD had a capacity to distinguish strains with different sources, however it could not discriminate among isolates according to their differences in the degree of virulence. In antimicrobial susceptibility tests, 45.5% of isolates showed antibiotic resistance to two or more antibiotics. Unlike the isolates from other countries, domestic isolates of E. coli O157:H7 was mainly resistant to ampicillin and tetracyclines. In summary, the application of E. coli O157:H7 Rapid kit may be useful to detect E. coli O157:H7 due to its sensitivity and convenience. Moreover, combinational analysis of multiplex PCR together with RAPD can aid to survey the characteristics of isolates. PMID:15785118

  3. 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 α-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

  4. 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.

  5. Clones identification of Sequoia sempervirens (D. Don) Endl. in Chile by using PCR-RAPDs technique.

    PubMed

    Toral Ibañez, Manuel; Caru, Margarita; Herrera, Miguel A; Gonzalez, Luis; Martin, Luis M; Miranda, Jorge; Navarro-Cerrillo, Rafael M

    2009-02-01

    A protocol of polymerase chain reaction-random amplified polymorphic DNAs (PCR-RAPDs) was established to analyse the gene diversity and genotype identification for clones of Sequoia sempervirens (D. Don) Endl. in Chile. Ten (out of 34) clones from introduction trial located in Voipir-Villarrica, Chile, were studied. The PCR-RAPDs technique and a modified hexadecyltrimethylammonium bromide (CTAB) protocol were used for genomic DNA extraction. The PCR tests were carried out employing 10-mer random primers. The amplification products were detected by electrophoresis in agarose gels. Forty nine polymorphic bands were obtained with the selected primers (BG04, BF07, BF12, BF13, and BF14) and were ordered according to their molecular size. The genetic similarity between samples was calculated by the Jaccard index and a dendrogram was constructed using a cluster analysis of unweighted pair group method using arithmetic averages (UPGMA). Of the primers tested, 5 (out of 60) RAPD primers were selected for their reproducibility and high polymorphism. A total of 49 polymorphic RAPD bands were detected out of 252 bands. The genetic similarity analysis demonstrates an extensive genetic variability between the tested clones and the dendrogram depicts the genetic relationships among the clones, suggesting a geographic relationship. The results indicate that the RAPD markers permitted the identification of the assayed clones, although they are derived from the same geographic origin. PMID:19235269

  6. Construction of a genetic linkage map of black gram, Vigna mungo (L.) Hepper, based on molecular markers and comparative studies.

    PubMed

    Gupta, S K; Souframanien, J; Gopalakrishna, T

    2008-08-01

    A genetic linkage map of black gram, Vigna mungo (L.) Hepper, was constructed with 428 molecular markers using an F9 recombinant inbred population of 104 individuals. The population was derived from an inter-subspecific cross between a black gram cultivar, TU94-2, and a wild genotype, V. mungo var. silvestris. The linkage analysis at a LOD score of 5.0 distributed all 428 markers (254 AFLP, 47 SSR, 86 RAPD, and 41 ISSR) into 11 linkage groups. The map spanned a total distance of 865.1 cM with an average marker density of 2 cM. The largest linkage group spanned 115 cM and the smallest linkage group was of 44.9 cM. The number of markers per linkage group ranged from 11 to 86 and the average distance between markers varied from 1.1 to 5.6 cM. Comparison of the map with other published azuki bean and black gram maps showed high colinearity of markers, with some inversions. The current map is the most saturated map for black gram to date and will provide a useful tool for identification of QTLs and for marker-assisted selection of agronomically important characters in black gram. PMID:18650952

  7. Novel Molecular Markers for Breast Cancer

    PubMed Central

    Inoue, Kazushi; Fry, Elizabeth A.

    2016-01-01

    The use of molecular biomarkers assures that breast cancer (BC) patients receive optimal treatment. Established biomarkers, such as estrogen receptor, progesterone receptor, HER2, and Ki67, have been playing significant roles in the subcategorization of BC to predict the prognosis and decide the specific therapy to each patient. Antihormonal therapy using 4-hydroxytamoxifen or aromatase inhibitors have been employed in patients whose tumor cells express hormone receptors, while monoclonal antibody to HER2 has been administered to HER2-positive BCs. Although new therapeutic agents have been developed in the past few decades, many patients still die of the disease due to relapse; thus, novel molecular markers that predict therapeutic failure and those that can be targets for specific therapy are expected. We have chosen four of such molecules by reviewing recent publications, which are cyclin E, B-Myb, Twist, and DMP1β. The oncogenicity of these molecules has been demonstrated in vivo and/or in vitro through studies using transgenic mice or siRNAs, and their expressions have been shown to be associated with shortened overall or disease-free survival of BC patients. The former three molecules have been shown to accelerate epithelial–mesenchymal transition that is often associated with cancer stem cell-ness and metastasis; all these four can be novel therapeutic targets as well. Thus, large prospective studies employing immunohistochemistry will be needed to establish the predictive values of these molecules in patients with BC. PMID:26997872

  8. Glioblastoma: pathology, molecular mechanisms and markers.

    PubMed

    Aldape, Kenneth; Zadeh, Gelareh; Mansouri, Sheila; Reifenberger, Guido; von Deimling, Andreas

    2015-06-01

    Recent advances in genomic technology have led to a better understanding of key molecular alterations that underlie glioblastoma (GBM). The current WHO-based classification of GBM is mainly based on histologic features of the tumor, which frequently do not reflect the molecular differences that describe the diversity in the biology of these lesions. The current WHO definition of GBM relies on the presence of high-grade astrocytic neoplasm with the presence of either microvascular proliferation and/or tumor necrosis. High-throughput analyses have identified molecular subtypes and have led to progress in more accurate classification of GBM. These findings, in turn, would result in development of more effective patient stratification, targeted therapeutics, and prediction of patient outcome. While consensus has not been reached on the precise nature and means to sub-classify GBM, it is clear that IDH-mutant GBMs are clearly distinct from GBMs without IDH1/2 mutation with respect to molecular and clinical features, including prognosis. In addition, recent findings in pediatric GBMs regarding mutations in the histone H3F3A gene suggest that these tumors may represent a 3rd major category of GBM, separate from adult primary (IDH1/2 wt), and secondary (IDH1/2 mut) GBMs. In this review, we describe major clinically relevant genetic and epigenetic abnormalities in GBM-such as mutations in IDH1/2, EGFR, PDGFRA, and NF1 genes-altered methylation of MGMT gene promoter, and mutations in hTERT promoter. These markers may be incorporated into a more refined classification system and applied in more accurate clinical decision-making process. In addition, we focus on current understanding of the biologic heterogeneity and classification of GBM and highlight some of the molecular signatures and alterations that characterize GBMs as histologically defined. We raise the question whether IDH-wild type high grade astrocytomas without microvascular proliferation or necrosis might best be classified as GBM, even if they lack the histologic hallmarks as required in the current WHO classification. Alternatively, an astrocytic tumor that fits the current histologic definition of GBM, but which shows an IDH mutation may in fact be better classified as a distinct entity, given that IDH-mutant GBM are quite distinct from a biological and clinical perspective. PMID:25943888

  9. 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...

  10. APPLICATION OF MOLECULAR MARKERS FOR CUCUMBER IMPROVEMENT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The historicity of marker development, map construction, and the utility of marker-assisted selection is presented. Experimental results indicate that the identification of marker-trait associations will continue to be extremely expensive and time consuming, but will likely pay large dividends for ...

  11. 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

  12. [Comparative genome analysis in pea Pisum sativum L. varieties and lines with chromosomal and molecular markers].

    PubMed

    Samatadze, T E; Zelenina, D A; Shostak, N G; Volkov, A A; Popov, K V; Rachinskaia, O V; Borisov, A Iu; Tikhonovich, I A; Zelenin, A V; Muravenko, O V

    2008-12-01

    C banding, Ag-NOR staining, FISH with pTa71 (45S rDNA) and pTa794 (5S rDNA), and RAPD-PCR analysis were used to study the genome and chromosome polymorphism in four varieties (Frisson, Sparkle, Rondo, and Finale) and two genetic lines (Sprint-2 and SGE) of pea Pisum sativum L. A comparison of the C-banding patterns did not reveal any polymorphism within the varieties. The most significant between-variety differences were observed for the size of C bands on satellite chromosomes 4 and 7. All grain pea varieties (Frisson, Sparkle, and Rondo) had a large C band in the satellite of chromosome 4 and a medium C band in the region adjacent to the satellite thread on chromosome 7. C bands were almost of the same size in the genetic lines and vegetable variety Finale. In all accessions, 45S rDNA mapped to the secondary constriction regions of chromosomes 1, 3, and 5. The signal from chromosome 5 in the lines was more intense than in the varieties. Ag-NOR staining showed that the transcriptional activity of the 45S rRNA genes on chromosome 7 was higher than on chromosome 4 in all accessions. No more than four Ag-NOR-positive nucleoli were observed in interphase nuclei. Statistical analysis of the total area of Ag-NOR-stained nucleoli did not detect any significant difference between the accessions examined. RAPD-PCR analysis revealed high between-variety and low within-variety genomic polymorphism. Chromosomal and molecular markers proved to be promising for genome identification in pea varieties and lines. PMID:19178083

  13. Molecular and morphological markers for rapid distinction between 2 Colletotrichum species.

    PubMed

    Pileggi, Sônia Alvim Veiga; Vieira de Oliveira, Sarah Franco; Andrade, Caroline Waculicz; Vicente, Vânia Aparecida; Dalzoto, Patrícia do Rocio; Kniphoff da Cruz, Gerson; Gabardo, Juarez; Massola, Nelson Sidnei; Tozze, Hugo José; Pileggi, Marcos; Kava-Cordeiro, Vanessa; Galli-Terasawa, Lygia Vitória; Pimentel, Ida Chapaval; Stringari, Danyelle; Glienke, Chirlei

    2009-09-01

    Endophytic microorganisms reside asymptomatically within plants and are a source of new bioactive products for use in medicine, agriculture, and industry. Colletotrichum (teleomorph Glomerella) is a fungus widely cited in the literature as a producer of antimicrobial substances. Identification at the species level, however, has been a problem in this type of study. Several authors have reported the presence of endophytic fungi from the medicinal plant Maytenus ilicifolia ("espinheira-santa") in Brazil that has antimicrobial activity against various pathogens. Therefore, Colletotrichum strains were isolated from M. ilicifolia and identified based on morphology, RAPD markers, sequence data of the internal transcribed spacer regions (ITS-1 and ITS-2), the 5.8S gene, and species-specific PCR. The analyses suggested the presence of 2 species, Colletotrichum gloeosporioides and Colletotrichum boninense. Two morphological markers were characterized to allow C. gloeosporioides and C. boninense to be distinguished quickly and accurately. The molecular diagnosis of C. boninense was confirmed by using Col1 and ITS4 primers. This species of Colletotrichum is reported for the first time in M. ilicifolia. PMID:19898550

  14. Random amplified marker technique for plants rich in polyphenols.

    PubMed

    Jhang, Tripta; Shasany, Ajit Kumar

    2012-01-01

    More than 10,000 publications using the random amplified polymorphic DNA (RAPD) or related arbitrary marker techniques have been published in two decades of its inception in 1990. Despite extensive use, RAPD technique has also attracted some criticisms, mainly for lack of reproducibility. In the light of its widespread applications, the objective of this chapter is to (1) provide a protocol for RAPD assay, (2) identify the potential factors affecting the optimization of the RAPD assays, and (3) provide proper statistical analysis to avoid false positives. It is suggested that after proper optimization, the RAPD is a reliable, sensitive, and reproducible assay having the potential to detect a wide range of DNA variations. Analyses of the relevant fragments generated in RAPD profile allow not only to identify some of the molecular events implicated in the genomic instability but also to discover genes playing key roles in genetic evolution and gene mapping. RAPD markers will continue to be boon for genetic studies of those organisms where yet no sequence information or scanty information is available. PMID:22419489

  15. 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...

  16. Phylogenetic analysis, genetic diversity and relationships between the recently segregated species of Corynandra and Cleoserrata from the genus Cleome using DNA barcoding and molecular markers.

    PubMed

    Tamboli, Asif Shabodin; Patil, Swapnil Mahadeo; Gholave, Avinash Ramchandra; Kadam, Suhas Kishor; Kotibhaskar, Shreya Vijaykumar; Yadav, Shrirang Ramchandra; Govindwar, Sanjay Prabhu

    2016-01-01

    Cleome is the largest genus in the family Cleomaceae and it is known for its various medicinal properties. Recently, some species from the Cleome genus (Cleome viscosa, Cleome chelidonii, Cleome felina and Cleome speciosa) are split into genera Corynandra (Corynandra viscosa, Corynandra chelidonii, Corynandra felina), and Cleoserrata (Cleoserrata speciosa). The objective of this study was to obtain DNA barcodes for these species for their accurate identification and determining phylogenetic relationships. Out of 10 screened barcoding regions, rbcL, matK and ITS1 regions showed higher PCR efficiency and sequencing success. This study added matK, rbcL and ITS1 barcodes for the identification of Corynandra chelidonii, Corynandra felina, Cleome simplicifolia and Cleome aspera species in existing barcode data. Corynandra chelidonii and Corynandra felina species belong to the Corynandra genus, but they are not grouped with the Corynandra viscosa species, however clustered with the Cleome species. Molecular marker analysis showed 100% polymorphism among the studied plant samples. Diversity indices for molecular markers were ranged from He=0.1115-0.1714 and I=0.2268-0.2700, which indicates a significant amount of genetic diversity among studied species. Discrimination of the Cleome and Corynandra species from Cleoserrata speciosa was obtained by two RAPD primers (OPA-4 and RAPD-17) and two ISSR primers (ISSR-1 and ISSR-2). RAPD and ISSR markers are useful for the genetic characterization of these studied species. The present investigation will be helpful to understand the relationships of Cleome lineages with Corynandra and Cleoserrata species. PMID:27032370

  17. Molecular markers and strategies to control aflatoxin in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Methods of isolation of molecular markers and software developed in ARS for finding the most informative markers will be presented. Also, two different approaches being used at the NPRL to reduce aflatoxin in peanut will be discussed. One is the development of phytoalexin-detoxification enzyme inh...

  18. DEVELOPMENT OF SIMPLE SEQUENCE REPEAT (SSR) MOLECULAR MARKERS IN STRAWBERRY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Simple sequence repeat, SSR, molecular markers have been shown to be repeatable, co-dominant, highly polymorphic, technically simple to use, and well distributed within the genomes of many plant and animal species. SSR markers have shown great utility for many applications including genetic fingerpr...

  19. Molecular Markers Predictive of Chemotherapy Response in Colorectal Cancer

    PubMed Central

    Shiovitz, Stacey; Grady, William M.

    2015-01-01

    Recognition of the molecular heterogeneity of colorectal cancer (CRC) has led to the classification of CRC based on a variety of clinical and molecular characteristics. Although the clinical significance of the majority of these molecular alterations is still being ascertained, it is widely anticipated that these characteristics will improve the accuracy of our ability to determine the prognosis and therapeutic response of CRC patients. A few of these markers, such as microsatellite instability and the CpG island methylator phenotype (CIMP), show promise as predictive markers for cytotoxic chemotherapy. KRAS is a validated biomarker for EGFR-targeted therapy, while NRAS and PI3KCA are evolving markers for targeted therapies. Multiple new actionable drug targets are being identified on a regular basis, but most are not ready for clinical use at this time. This review focuses on key molecular features of CRCs and the application of these molecular alterations as predictive biomarkers for CRC. PMID:25663616

  20. Molecular marker database for efficient use in agricultural breeding programs

    PubMed Central

    Kim, Chang-Kug; Lee, Gang-Seob; Mo, Ji-Su; Bae, Seon-Hwa; Lee, Tae-Ho

    2015-01-01

    The National Agricultural Biotechnology Information Center (NABIC) constructed a web-based molecular marker database to provide information about 7,847 sequence-tagged site (STS) markers identified in the 11 species using a next generation sequencing (NGS) technologies. The database consists of three major functional categories: keyword search, detailed viewer and download function. The molecular marker annotation table provides detailed information such as ownership information, basic information, and STS-related characterization information. Availability The database is available for free at http://nabic.rda.go.kr/Molecularmarker PMID:26527854

  1. Evaluation of genetic homogeneity in tissue culture regenerates of Jatropha curcas L. using flow cytometer and DNA-based molecular markers.

    PubMed

    Rathore, Mangal S; Yadav, P; Mastan, Shaik G; Prakash, Ch R; Singh, A; Agarwal, Pradeep K

    2014-01-01

    The present investigation aimed to evaluate the reliability of in vitro propagation methods for elite genotypes of Jatropha curcas L., that maintain genetic integrity of tissue culture (TC) regenerates among two regeneration systems developed through direct shoot bud regeneration using nodal/apical shoot segments (protocol-A) and in vitro-derived leaves (protocol-B) as explants. Random amplified polymorphic DNA (RAPD), intersimple sequence repeat (ISSR), simple sequence repeat (SSR) molecular markers, and flow cytometery (FCM) were employed to evaluate genetic homogeneity in TC-regenerates at different passages of subcultures. RAPD markers showed genetic homogeneity in fifth-generation TC-regenerates of both protocols. ISSR markers showed genetic stability of leaf regenerates (protocol-B) at 10th generation. FCM analysis of TC-regenerates at 10th generation in protocol-B and at 20th generation in both protocols, showed stability of ploidy level. SSR assessment of TC-regenerates at 20th generation in both protocols confirmed genetic homogeneity. The results confirmed the genetic stability of the TC-regenerates and demonstrated the reliability of the regeneration systems developed so far using explants of two different origins, for large-scale multiplication of elite genotypes of Jatropha. PMID:24078186

  2. 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

  3. A SCAR marker for the analysis of chloroplast DNA from different cultivars of Cornus officinalis.

    PubMed

    Zhang, L; Liu, R X; Wang, J; Zhang, T; Li, J; Shi, J H; Kang, B Y; Chen, S Q

    2015-01-01

    The aims of this study were to establish a random amplified polymorphic DNA (RAPD) fingerprint database of chloroplast DNA (cpDNA) from different cultivars of Cornus officinalis and to convert RAPD markers to sequence characterized amplified regions (SCAR) markers. A method of extraction was established that was suitable for obtaining cpDNA from samples rapidly dried in silicone; an RAPD fingerprint database was built; and the genetic distance between samples was used as statistical clustering variables for calculating DICE genetic similarity coefficients and for building a kinship tree chart. RAPD markers were converted to SCAR markers to design specific primers, and samples from C. officinalis cultivars, plants of the same family, and its adulterants, were used for amplification and identification. Fifteen amplified primers with stable polymorphisms were screened for amplification of 130 copies of materials. In total, 57 sites were achieved, 40 of which were polymorphic, and the polymorphic rate was up to 70.18%. A genetic tree was built based on seven cultivars. SCAR markers of C. officinalis cpDNA were successfully converted into RAPD markers. cpDNA samples from hawthorn, C. officinalis, Cornus wood, and grape were used for SCAR amplification, and their bands were distinctly different. In conclusion, SCAR markers and cpDNA may be used for research on C. officinalis and its adulterants, and the results may provide a basis for identifying germplasm and screening fine varieties at a molecular level. PMID:26681064

  4. Molecular markers in medicinal plant biotechnology: past and present.

    PubMed

    Sarwat, Maryam; Nabi, Gowher; Das, Sandip; Srivastava, Prem Shankar

    2012-03-01

    Plant based medicines have gained popularity worldwide due to their almost negligible side effects. In India, the three traditional medicinal systems, namely homeopathy, Ayurveda and Siddha rely heavily on plants for medicinal formulations. To prevent the indiscriminate collection of these valuable medicinal plants and for their proper authentication and conservation, it is imperative to go for sustained efforts towards proper germplasm cataloguing and devising conservation strategies. For this purpose, molecular markers have a significant role, as they provide information ranging from diversity at nucleotide level (single nucleotide polymorphisms) to gene and allele frequencies (genotype information), the extent and distribution of genetic diversity, and population structure. Over the past twenty years, the molecular marker field has completely transformed the meaning of conservation genetics which has emerged from a theory-based field of population biology to a full-fledged pragmatic discipline. In this review, we have explored the transition and transformation of molecular marker technologies throughout these years. PMID:21649550

  5. Genetic diversity within and among Lepidium draba populations from Eastern Anatolia based on RAPD analysis.

    PubMed

    Aksakal, Ozkan; Sunar, Serap; Kaya, Yusuf; Agar, Guleray

    2010-08-01

    Genetic variation and structure of six natural populations of Lepidium draba L. from Eastern Anatolia were assessed using random amplified polymorphic DNA (RAPD) markers. For RAPD analysis, 12 primers generated 218 reproducible bands across the six populations analyzed, of which 73 bands (33.3%) were polymorphic. The mean Nei's gene diversity value for all six populations was 0.1771. Shannon's information index varied with population (0.2278-0.3082), averaging 0.2608. Analysis of molecular variance (AMOVA) showed that genetic diversity was greater within populations (58.66%) than among populations (30.68%). In addition, the variation between groups was 10.33%. The genetic differentiation among populations (G (ST)) was 0.3210, indicating that most genetic diversity occurs within populations. Gene flow (Nm) was low, at only 0.5288. PMID:20496111

  6. Characterization and genetic variability of feed-borne and clinical animal/human Aspergillus fumigatus strains using molecular markers.

    PubMed

    Pena, Gabriela A; Coelho, Irene; Reynoso, María M; Soleiro, Carla; Cavaglieri, Lilia R

    2015-09-01

    Aspergillus fumigatus, the major etiological agent of human and animal aspergillosis, is a toxigenic fungus largely regarded as a single species by macroscopic and microscopic features. However, molecular studies have demonstrated that several morphologically identified A. fumigatus strains might be genetically distinct. This work was aimed to apply PCR-restriction length fragment polymorphisms (PCR-RFLP) and random amplification of polymorphic DNA (RAPD) molecular markers to characterize a set of feed-borne and clinical A. fumigatus sensu lato strains isolated from Argentina and Brazil and to determine and compare their genetic variability. All A. fumigatus strains had the same band profile and those typical of A. fumigatus sensu stricto positive controls by PCR-RFLP. Moreover, all Argentinian and Brazilian strains typified by RAPD showed similar band patterns to each other and to A. fumigatus sensu stricto reference strains regardless of their isolation source (animal feeds or human/animal clinical cases) and geographic origin. Genetic similarity coefficients ranged from 0.61 to 1.00, but almost all isolates showed 78% of genetic similarly suggesting that genetic variability was found at intraspecific level. Finally, benA sequencing confirmed its identification as A. fumigatus sensu stricto species. These results suggest that A. fumigatus sensu stricto is a predominant species into Aspergillus section Fumigati found in animal environments as well as in human/animal clinical cases, while other species may be rarely isolated. The strains involved in human and animal aspergillosis could come from the environment where this fungus is frequently found. Rural workers and animals would be constantly exposed. PMID:26129892

  7. Molecular Genetic Markers in Acute Myeloid Leukemia

    PubMed Central

    Yohe, Sophia

    2015-01-01

    Genetics play an increasingly important role in the risk stratification and management of acute myeloid leukemia (AML) patients. Traditionally, AML classification and risk stratification relied on cytogenetic studies; however, molecular detection of gene mutations is playing an increasingly important role in classification, risk stratification, and management of AML. Molecular testing does not take the place of cytogenetic testing results, but plays a complementary role to help refine prognosis, especially within specific AML subgroups. With the exception of acute promyelocytic leukemia, AML therapy is not targeted but the intensity of therapy is driven by the prognostic subgroup. Many prognostic scoring systems classify patients into favorable, poor, or intermediate prognostic subgroups based on clinical and genetic features. Current standard of care combines cytogenetic results with targeted testing for mutations in FLT3, NPM1, CEBPA, and KIT to determine the prognostic subgroup. Other gene mutations have also been demonstrated to predict prognosis and may play a role in future risk stratification, although some of these have not been confirmed in multiple studies or established as standard of care. This paper will review the contribution of cytogenetic results to prognosis in AML and then will focus on molecular mutations that have a prognostic or possible therapeutic impact. PMID:26239249

  8. Use of molecular markers and flow cytometry to preserve ancient Annurca apple germplasm.

    PubMed

    Iannaccone, Marco; Palumbo, Daniela; Ventimiglia, Ilaria; Patocchi, Andrea; Spigno, Paola; Capparelli, Rosanna

    2007-02-01

    The old Annurca apple cultivar (Malus domestica), particularly appreciated for its peculiar flavor and crispy flesh, was studied in order to preserve its ancient germplasm. Twelve clones of Annurca were analyzed using random amplified polymorphic DNA (RAPD) and simple-sequence repeat (SSR) markers. Two out of 30 RAPD primers and nine out of ten SSR primers were able to discriminate all the clones analyzed. Data were confirmed by measuring DNA content using flow cytometry. The results provide a good procedure to improve germplasm field management, in order to removing redundant material in the Annurca collection. This represents an efficient way to create a data bank in order to preserve the genetic variability of the Annurca cultivar. PMID:17120090

  9. 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...

  10. 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

  11. 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...

  12. Pilocytic astrocytoma: pathology, molecular mechanisms and markers.

    PubMed

    Collins, V Peter; Jones, David T W; Giannini, Caterina

    2015-06-01

    Pilocytic astrocytomas (PAs) were recognized as a discrete clinical entity over 70 years ago. They are relatively benign (WHO grade I) and have, as a group, a 10-year survival of over 90%. Many require merely surgical removal and only very infrequently do they progress to more malignant gliomas. While most show classical morphology, they may present a spectrum of morphological patterns, and there are difficult cases that show similarities to other gliomas, some of which are malignant and require aggressive treatment. Until recently, almost nothing was known about the molecular mechanisms involved in their development. The use of high-throughput sequencing techniques interrogating the whole genome has shown that single abnormalities of the mitogen-activating protein kinase (MAPK) pathway are exclusively found in almost all cases, indicating that PA represents a one-pathway disease. The most common mechanism is a tandem duplication of a ≈2 Mb-fragment of #7q, giving rise to a fusion between two genes, resulting in a transforming fusion protein, consisting of the N-terminus of KIAA1549 and the kinase domain of BRAF. Additional infrequent fusion partners have been identified, along with other abnormalities of the MAP-K pathway, affecting tyrosine kinase growth factor receptors at the cell surface (e.g., FGFR1) as well as BRAF V600E, KRAS, and NF1 mutations among others. However, while the KIAA1549-BRAF fusion occurs in all areas, the incidence of the various other mutations identified differs in PAs that develop in different regions of the brain. Unfortunately, from a diagnostic standpoint, almost all mutations found have been reported in other brain tumor types, although some retain considerable utility. These molecular abnormalities will be reviewed, and the difficulties in their potential use in supporting a diagnosis of PA, when the histopathological findings are equivocal or in the choice of individualized therapy, will be discussed. PMID:25792358

  13. Confirmation of hybrid origin in Arisaema (Araceae) using molecular markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A population of hybrids between Arisaema triphyllum subsp. stewardsonii and A. dracontium was investigated using molecular markers to document the hybrid origin. Total genomic DNA was extracted from A. triphyllum, A. dracontium, and the hybrids, and subjected to sequence analysis of various regions...

  14. Acceleration of peanut breeding programs by molecular marker assisted selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peanut breeding has played a significant role in yield increases and disease control. Conventional breeding focuses on field selection and phenotypic analysis and it typically takes 12-15 years before a new cultivar can be released. Molecular markers developed from sequencing data can be of great ...

  15. Clinical Relevance of Prognostic and Predictive Molecular Markers in Gliomas.

    PubMed

    Siegal, Tali

    2016-01-01

    Sorting and grading of glial tumors by the WHO classification provide clinicians with guidance as to the predicted course of the disease and choice of treatment. Nonetheless, histologically identical tumors may have very different outcome and response to treatment. Molecular markers that carry both diagnostic and prognostic information add useful tools to traditional classification by redefining tumor subtypes within each WHO category. Therefore, molecular markers have become an integral part of tumor assessment in modern neuro-oncology and biomarker status now guides clinical decisions in some subtypes of gliomas. The routine assessment of IDH status improves histological diagnostic accuracy by differentiating diffuse glioma from reactive gliosis. It carries a favorable prognostic implication for all glial tumors and it is predictive for chemotherapeutic response in anaplastic oligodendrogliomas with codeletion of 1p/19q chromosomes. Glial tumors that contain chromosomal codeletion of 1p/19q are defined as tumors of oligodendroglial lineage and have favorable prognosis. MGMT promoter methylation is a favorable prognostic marker in astrocytic high-grade gliomas and it is predictive for chemotherapeutic response in anaplastic gliomas with wild-type IDH1/2 and in glioblastoma of the elderly. The clinical implication of other molecular markers of gliomas like mutations of EGFR and ATRX genes and BRAF fusion or point mutation is highlighted. The potential of molecular biomarker-based classification to guide future therapeutic approach is discussed and accentuated. PMID:26508407

  16. Biological (molecular and cellular) markers of toxicity

    SciTech Connect

    Shugart, L.R.

    1990-10-01

    The overall objective of this study is to evaluate the use of the small aquarium fish, Japanese Medaka (Oryzias latipes), 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). Because of the often long latent period between initial contact with certain chemical and physical agents in our environment and subsequent expression of deleterious health or ecological impact, the development of sensitive methods for detecting and estimating early exposure is needed so that necessary interventions can ensue. A promising biological endpoint for detecting early exposure to damaging chemicals is the interaction of these compounds with cellular macromolecules such as Deoxyribonucleic acids (DNA). This biological endpoint assumes significance because it can be one of the critical early events leading eventually to adverse effects (neoplasia) in the exposed organism.

  17. Molecular markers predictive of chemotherapy response in colorectal cancer.

    PubMed

    Shiovitz, Stacey; Grady, William M

    2015-02-01

    Recognition of the molecular heterogeneity of colorectal cancer (CRC) has led to the classification of CRC based on a variety of clinical and molecular characteristics. Although the clinical significance of the majority of these molecular alterations is still being ascertained, it is widely anticipated that these characteristics will improve the accuracy of our ability to determine the prognosis and therapeutic response of CRC patients. A few of these markers, such as microsatellite instability and the CpG island methylator phenotype (CIMP), show promise as predictive markers for cytotoxic chemotherapy. KRAS is a validated biomarker for epidermal growth factor receptor (EGFR)-targeted therapy, while NRAS and PI3KCA are evolving markers for targeted therapies. Multiple new actionable drug targets and potential response biomarkers are being identified on a regular basis, but most are not ready for clinical use at this time. This review focuses on key molecular features of CRCs and the application of these molecular alterations as predictive biomarkers for CRC. PMID:25663616

  18. Genetic diversity analysis with RAPD linked to sex identification in the sugar cane borer Diatraea saccharalis.

    PubMed

    Heideman, C; Munhoz, R E F; Pattaro Júnior, J R; Fernandez, M A

    2010-01-01

    Diatraea saccharalis is an insect that causes considerable losses in the sugar cane crop. Our aim was to contribute to the knowledge of the biology of D. saccharalis, with the report of DNA fragments involved in the differentiation between the male and female of this species using the RAPD sex molecular marker GyakuU-13, which is specific for the W chromosome of Bombyx mori. Another point evaluated in this study was the genetic diversity of a D. saccharalis population maintained by inbreeding in a laboratory culture. The profile of sex-specific fragments was analyzed, and the genetic variability of this population was estimated. An analysis of the molecular markers showed only one fragment, of approximately 700 bp, that could be considered as a female sex marker in D. saccharalis. PMID:21128215

  19. Competition as a source of errors in RAPD analysis.

    PubMed

    Halldén, C; Hansen, M; Nilsson, N O; Hjerdin, A; Säll, T

    1996-12-01

    We have used artificial 1∶1 DNA mixtures of all pairwise combinations of four doubled haploid Brassica napus lines to test the ability of RAPDs to function as reliable dominant genetic markers. In situations where a specific RAPD band is present in one homozygous line but absent in the other, the band is expected in the artificial heterozygote, i.e. in the 1∶1 DNA mixture. In 84 of all 613 heterozygous situations analysed, the expected band failed to amplify in the RAPD reaction. Thus, RAPD markers will lead to an erroneous genetic interpretation in 14% of all cases. In contrast, the formation of non-parental heteroduplex bands was found at a frequency of only 0.2%. Analysis of 1∶ 1 mixtures using (1) a different set of optimized reaction conditions and (2) a material with low genomic complexity (Bacillus cereus) gave identical results. Serial dilutions of one genome into another, in steps of 10%, showed that all of the polymorphic bands decreased in intensity as a linear function of their respective proportion in the mixture. In dilutions with water no differences in band intensity were detected. Thus, competition occurs in the amplification of all RAPD fragments and is a major source of genotyping errors in RAPD analysis. PMID:24162529

  20. Study Of Genetic Diversity Between Grasspea Landraces Using Morphological And Molecular Marker

    NASA Astrophysics Data System (ADS)

    Sedehi, Abbasali Vahabi; Lotfi, Asefeh; Solooki, Mahmood

    2008-01-01

    Grass pea is a beneficial crop to Iran since it has some major advantageous such as high grain and forage quality, high drought tolerance and medium level of salinity tolerance and a good native germplasm variation which accessible for breeding programs. This study was carried out to evaluate morphological traits of the grass pea landraces using a randomized complete block design with 3 replications at Research Farm of Isfahan University of Technology. To evaluate genetic diversity of 14 grass pea landraces from various locations in Iran were investigated using 32 RAPD & ISJ primers at Biocenter of University of Zabol. Analysis of variance indicated a highly significant differences among 14 grass pea landrace for the morphological traits. Average of polymorphism percentage of RAPD primer was 73.9%. Among used primer, 12 random primers showed polymorphism and a total of 56 different bands were observed in the genotypes. Jafar-abad and Sar-chahan genotypes with similarity coefficient of 66% and Khoram-abad 2 and Khoram-abad 7 genotypes with similarity coefficient of 3% were the most related and the most distinct genotypes, respectively. Fourteen primers out of 17 semi random primers produced 70 polymorphic bands which included 56% of the total 126 produced bands. Genetic relatedness among population was investigated using Jacard coefficient and unweighted pair group mean analysis (UPGMA) algorithm. The result of this research verified possibility of use of RAPD & ISJ markers for estimation of genetic diversity, management of genetic resources and determination of repetitive accessions in grass pea.

  1. [Molecular markers for transitional cell carcinoma of bladder].

    PubMed

    Kleinmann, Judy; Siegel, Yoram I; Zisman, Amnon

    2003-07-01

    Superficial transitional cell carcinoma (TCC) has significant rates of recurrence and progression, therefore accurate urinary makers for early diagnosis and follow-up are essential. Urine cytology is the oldest marker, constantly used clinically and considered the "gold standard". In this review we will summarize the properties of different molecular markers for TCC and their yield compared to cytology. Briefly, the older markers--BTA stat, BTA TRAK and NMP22 are more sensitive than cytology, but their specificity is lower, especially in patients with underlying urologic pathologies. FDP (fibrinogen degradation products) analysis is rapid and the test is available clinically. It's sensitivity is higher than cytology for low grade tumors, but specificity is low. Of the newer markers, telomerase has a high sensitivity, and a specificity similar to urine cytology, but also has an increased rate of false positive results. HA-HAase (Hyaluronidase) and CK20 have promising sensitivity and specificity, but are still unavailable for clinical use. CK20 has the additional advantage of being able to detect premalignant conditions as well as predicting recurrence. The role of urinary markers in replacing cystoscopy and urine sediment cytology in the follow-up of TCC and in hematuria work up is still uncertain. It is possible that urinary markers in different panel arrays will have a role in the future for those indications and perhaps in the screening of populations at risk, such as smokers and workers exposed to occupational hazards. PMID:12908389

  2. DNA marker applications to molecular genetics and genomics in tomato

    PubMed Central

    Shirasawa, Kenta; Hirakawa, Hideki

    2013-01-01

    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

  3. DNA marker applications to molecular genetics and genomics in tomato.

    PubMed

    Shirasawa, Kenta; Hirakawa, Hideki

    2013-03-01

    Tomato is an important crop and regarded as an experimental model of the Solanaceae family and of fruiting plants in general. To enhance breeding efficiency and advance the field of genetics, tomato has been subjected to DNA marker studies as one of the earliest targets in plants. The developed DNA markers have been applied to the construction of genetic linkage maps and the resultant maps have contributed to quantitative trait locus (QTL) and gene mappings for agronomically important traits, as well as to comparative genomics of Solanaceae. The recently released whole genome sequences of tomato enable us to develop large numbers of DNA markers comparatively easily, and even promote new genotyping methods without DNA markers. In addition, databases for genomes, DNA markers, genetic linkage maps and other omics data, e.g., transcriptome, proteome, metabolome and phenome information, will provide useful information for molecular breeding in tomatoes. The use of DNA marker technologies in conjunction with new breeding techniques will promise to advance tomato breeding. PMID:23641178

  4. Genetic diversity of two Portuguese populations of the pullet carpet shell Venerupis senegalensis, based on RAPD markers: contribution to a sustainable restocking program

    NASA Astrophysics Data System (ADS)

    Joaquim, Sandra; Pereira, Jorge; Leitão, Alexandra; Matias, Domitília; Chaves, Raquel; Guedes-Pinto, Henrique; Chícharo, Luís; Gaspar, Miguel

    2010-12-01

    The pullet carpet shell Venerupis senegalensis (= V. pullastra) is a commercially important species in Portugal, Spain, France, and Italy. In Portugal, this species was once abundant in the Ria Formosa (southern Portugal). However, in the early 1980s, its abundance declined dramatically due to overfishing. In order to reverse this negative trend, the genetic sustainable management of the wild stocks of V. senegalensis should be performed by promoting successful restocking actions and the development of an aquaculture commercial production program of this species. In order to find the best broodstock for aquaculture purposes and therefore minimize the deleterious effects of hatchery practices, we analyzed the genetic diversity of the natural population to be restocked (Ria Formosa) but also of another potential genetically close population (Ria de Aveiro) by RAPD. Similar and substantive percentage of polymorphic loci, effective number of alleles, Nei’s gene diversity, and Shannon’s diversity index was found within both populations. This high genetic variability within populations suggests that they might have a gene pool with sufficient genetic plasticity to support changes in the environmental conditions. Analyses of population genetic structure also revealed a small genetic differentiation between the two populations. The high genetic variability of the natural population to be restocked makes it the preferential broodstock for aquaculture purposes. However, the Ria de Aveiro population could also be a viable alternative, due to its genetic plasticity and the genetic similarity of both populations. The results of this study can be useful to the sustainable management of wild stocks as well as in promoting successful restocking actions based on aquaculture production.

  5. STRENGTHS AND WEAKNESSES OF MOLECULAR MARKERS FOR STUDIES OF DIVERSITY IN GENEBANK HOLDINGS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular markers have many potential advantages over morphological or other marker types to characterize within- and between-species diversity, useful for management of genebank holdings. These include greater number (potentially unlimited) of markers, freedom from pleiotropic effects, greater ease...

  6. Molecular markers in oral lichen planus: A systematic review

    PubMed Central

    Sagari, Shitalkumar; Sanadhya, Sudhanshu; Doddamani, Mallikarjun; Rajput, Rajan

    2016-01-01

    Oral lichen planus (OLP) is a chronic inflammatory mucosal disease that is usually detected in 0.5–2.2% of the human population. Among these, only 0.5–2.9% of the lesions progress to carcinoma. However, there are no prognostic markers available presently to recognize the increased risk in malignant transformation of the lesions. Selected markers for cell proliferation, adhesion, apoptosis and lymphocytic infiltration were analyzed by immunohistochemistry in addition to static cytometry for DNA content. The concept linking OLP and oral squamous cell carcinoma states that chronic inflammation results in crucial DNA damage, which further progresses to development of carcinoma. Even though in the past decade, enormous information has been accumulated on malignant potential of OLP, its transformation still remains unclear. Hence, the purpose of this article was to review cellular and molecular markers to understand the pathogenesis of OLP and its progression toward malignancy. PMID:27194873

  7. Molecular markers for breast cancer: prediction on tumor behavior.

    PubMed

    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

  8. Molecular markers and sentinel organisms for environmental monitoring.

    PubMed

    Graczyk, T K; Conn, D B

    2008-09-01

    Molecular methods are useful for both to monitor anthropogenic viral, bacterial, and protozoan enteropathogens, and to track pathogen specific markers in a complex environment in order to reveal sources of these pathogens. Molecular genetic markers for fecal viruses, bacteria, and protozoans hold promise for monitoring environmental pollution and water quality. The demand for microbiologically safe waters grows exponentially due to the global demographic rise of the human population. Economically important shellfish, such as oysters, which are harvested commercially and preferentially consumed raw can be of public health importance if contaminated with human waterborne pathogens. However, feral molluscan shellfish which do not have an apparent economic value serve as indicators in monitoring aquatic environments for pollution with human waterborne pathogens and for sanitary assessment of water quality. Current technology allows for multiplexed species-specific identification, genotyping, enumeration, viability assessment, and source-tracking of human enteropathogens which considerably enhances the pathogen source-tracking efforts. PMID:18814723

  9. Clinical Applications of Molecular Markers in Bone Tumors.

    PubMed

    Hameed, Meera

    2015-11-01

    Pathologic diagnosis of primary bone neoplasms can be challenging primarily due to rarity of the disease entities, overlapping imaging and histologic findings, and lack of tumor-specific immunohistochemical stains. Although slow to evolve, in recent years there has been a rapid advance in the discovery of new and novel molecular markers in primary bone neoplasms, which has enhanced diagnostic accuracy and has shed light into their pathogenesis. Modern technological approaches such as next-generation sequencing including RNA sequencing are serving as "rapid discovery platforms" for new and novel mutations and translocations with diagnostic, prognostic, and possible therapeutic applicability. As next-generation sequencing technologies are finding their place in clinical laboratories, one could envision routine testing for mutations spanning across a gene or translocations with multiple breakpoints and partner genes. This review will focus on the clinical relevance and applicability of molecular markers in primary bone neoplasms with examples. PMID:26452209

  10. Molecular authentication of Gynostemma pentaphyllum through development and application of random amplification polymorphic DNA sequence-characterized amplified region marker.

    PubMed

    Zhou, J; Wu, Y S; Zhao, R Q; Jiang, J F; Luo, Y; Ma, C T; Qian, J Y

    2015-01-01

    Due to the morphological similarities of aerial parts, it is difficult to distinguish Gynostemma pentaphyllum from Cayratia japonica, which is usually an adulterant of the former. To develop a reliable method for the identification and authentication of G. pentaphyllum, a combination of random amplification polymorphic DNA (RAPD) technique with sequence-characterized amplified region (SCAR) markers was studied. Twenty-five samples of G. pentaphyllum and two samples of C. japonica were collected from different regions in Guangxi or bought from different provinces in China. Through the RAPD analysis, significant genetic polymorphism was observed among the intraspecies samples of G. pentaphyllum. Furthermore, a specific marker, J-750, was obtained for authentication. Therefore, the SCAR marker for G. pentaphyllum (359 bp) was developed from the RAPD amplicon. With PCR amplification using the SCAR primers, a specific band of 359 bp was distinctly visible for all tested samples of G. pentaphyllum, but was absent in the samples of C. japonica. Furthermore, the results revealed that the SCAR marker was useful for the identification and authentication of G. pentaphyllum irrespective of whether samples were fresh, dry, or of commercial origin. The SCAR marker obtained in this study successfully authenticated G. pentaphyllum through an integrated PCR system containing SCAR and control primer combinations of two pairs. In addition, it was also used for simultaneous discrimination of G. pentaphyllum from C. japonica. PMID:26662413

  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. Molecular markers in prostate cancer. Part I: predicting lethality

    PubMed Central

    Agrawal, Sachin; Dunsmuir, William D.

    2009-01-01

    Assessing the lethality of 'early,' potentially organ-confined prostate cancer (PCa) is one of the central controversies in modern-day urological clinical practice. Such cases are often considered for radical 'curative' treatment, although active surveillance may be equally appropriate for many men. Moreover, the balance between judicious intervention and overtreatment can be difficult to judge. The patient's age, comorbidities, family history and philosophy of self-health care can be weighed against clinical features such as the palpability of disease, the number and percentage of biopsy cores involved with the disease, histological grade, presenting prostate-specific antigen (PSA) and possible previous PSA kinetics. For many years, scientists and physicians have sought additional molecular factors that may be predictive for disease stage, progression and lethality. Usually, claims for a 'new' unique marker fall short of true clinical value. More often than not, such molecular markers are useful only in multivariate models. This review summarizes relevant molecular markers and models reported up to and including 2008. PMID:19050690

  13. Molecular typing by random amplification of polymorphic DNA (RAPD) and detection of virulence genes of Salmonella enterica subspecies enterica serovar Gallinarum biovar gallinarum.

    PubMed

    Jin, Ji-Dong; Lee, Dong-Seok; Shin, Eun-Kyung; Kim, Sun-Joong; Jung, Rose; Hahn, Tae-Wook

    2006-12-01

    Salmonella enterica subspecies enterica serovar Gallinarum biovar Gallinarum is the causative agent of fowl typhoid in chickens, outbreaks of which have devastated poultry populations in Korea since 1992. In order to identify genetic differences among S. Gallinarum isolates, bacteria were examined using the random amplified polymorphic DNA (RAPD) method. Of 13 arbitrary primers screened initially, the primer designated as universal rice primer-6 (URP-6) was selected for subsequent typing assays because it produced a distinctive and reproducible DNA fingerprint for a S. Gallinarum reference strain. URP-6-based RAPD analysis assigned 30 S. Gallinarum isolates into 6 types, with 26 isolates (86.6%) belonging to 2 major RAPD types. The distribution of virulence genes in S. Gallinarum isolates was examined by Southern hybridization. All tested isolates had the invasion gene, invA, the virulence plasmid gene, spvB, and the S. Enteritidis fimbrial gene, sefC. The distribution of virulence genes among S. Gallinarum isolates did not correlate with any specific RAPD type. PMID:17213701

  14. Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis.

    PubMed

    Barua, U M; Chalmers, K J; Hackett, C A; Thomas, W T; Powell, W; Waugh, R

    1993-08-01

    Three hundred random sequence 10-mer primers were used to screen a pair of near-isogenic lines of barley and their donor parent for markers linked to genes conferring resistance to Rhynchosporium secalis. One primer was identified which reproducibly generated a product, SC10-65-H400, from the donor parent and the Rhynchosporium-resistant near-isogenic line but not from the recurrent parent. Segregation analysis on a barley doubled haploid population and examination of a further three near-isogenic lines, their donor and recurrent parents confirmed that this marker was linked to the Rhynchosporium resistance locus (Rh) on chromosome 3L. The presence or absence of SC10-65-H400 was subsequently used along with the resistance phenotype to identify two groups of individuals in the doubled haploid population which possessed alternative alleles at both loci and defined a genetic interval between these two markers. Based on that information two bulked DNA samples were constructed by combining equal amounts of DNA from five individuals from each group. The two bulks and doubled haploid parental lines were screened with 700 10-mer primers. Seven products were identified which were present in the 'resistant' bulk and parent and were absent in the susceptible samples. Segregation analysis established their association with Rh. In addition co-segregation of the linked markers with a set of chromosome arm specific RFLPs confirmed the location of the Rh locus on the long arm of barley chromosome 3. PMID:8376177

  15. 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...

  16. New molecular markers in resistant B-CLL.

    PubMed

    Bouley, Julien; Deriano, Ludovic; Delic, Jozo; Merle-Béral, Hélène

    2006-05-01

    B-chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course which has long remained a stumbling block for clinicians. This variability appears to arise from complex molecular alterations identified in malignant cells from patient subsets. Recent studies have focused in particular on identifying new molecular markers to help predict the most effective and adapted treatments. In addition to the mutation status of immunoglobulin variable heavy-chain region (IgVH) genes, which is a well-established predictive factor in B-CLL, these new markers include defects of cell factors involved in the maintenance of genome stability, such as telomere function, DNA repair, ATM and p53. Other predictive factors, such as tyrosine kinase Zap-70 and soluble factors found in patient sera, may be associated with B-cell receptor signal transduction. Interestingly, an alteration of these factors fits closely, though not strikingly, with the absence of somatic mutations in IgVH genes, suggesting that the latter may be due either to epigenetic events leading to an unstable genome or to an inherited defect in the immune response of malignant B-cells. Recent lessons from Zap-70 expression/phosphorylation suggest that some of these markers may reflect the defective pathways in B-CLL cells rather than being markers of cell malignancy per se. Furthermore, specific subsets of markers are found in patient cells resistant to treatment. Current studies on gene expression profiling and proteomic analyses should soon lead to a better understanding of how these pathways are affected, especially in multi-drug resistant B-CLL. PMID:16753863

  17. 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

  18. 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

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

    PubMed

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

    2015-01-01

    The artichoke (Cynara scolymus L.) is an important food and medicinal crop that is cultivated in Mediterranean countries. Morphological characteristics, such as head shape and diameter, leaf shape, and bract shape, are mainly affected by environmental conditions. A molecular marker approach was used to analyze the degree of polymorphism between artichoke hybrid lines. The degree of genetic difference among three artichoke hybrids was evaluated using random amplified polymorphic DNA-PCR (RAPD-PCR). In this study, the DNA fingerprints of three artichoke lines (A13-010, A11-018, and A12-179) were generated, and a total of 10 decamer primers were applied for RAPD-PCR analyses. Polymorphism  (16.66 to 62.50%) was identified using eight arbitrary decamers and total genomic DNA extracted from the hybrids. Of the 59 loci detected, there were 25 polymorphic and 34 monomorphic loci. Jaccard's similarity index (JSI) ranged between 1.0 and 0.84. Based on the unweighted pair group method with arithmetic mean (UPGMA) similarity matrix and dendrogram, the results indicated that two hybrids (A13-010 and A11-018) were closely related to each other, and the A12-179 line showed more divergence. When identifying correct accessions, consideration of the genetic variation and genetic relationships among the genotypes are required. The RAPD-PCR fingerprinting of artichoke lines clearly showed that it is possible to analyze the RAPD patterns for correlation between genetic means and differences or resemblance between close accessions (A13-010 and A11- 018) at the genomic level. PMID:26782491

  20. 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 (δ(13)C) and radiocarbon ((14)C) isotope methods. PMID:25084061

  1. 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

  2. Genetic diversity in Tunisian populations of faba bean (Vicia faba L.) based on morphological traits and molecular markers.

    PubMed

    Backouchi, I Z; Aouida, M; Khemiri, N; Jebara, M

    2015-01-01

    Genetic diversity within Vicia faba L. is key to the genetic improvement of this important species. In this study, morphological traits and RAPD molecular markers were used to assess the levels of polymorphism across 12 Tunisian populations, three major and nine minor from different locations. Analysis of morphological traits indicated that the three major populations showed significant differences and the nine minor populations exhibited considerable variation for most traits. The grain yield of the Alia population could be increased by inoculation. Of the seven primers tested, it was clear that the Cs12 primer would be recommend for genetic diversity analysis of V. faba.Within population genetic diversity exhibited 94% of total diversity. Intra-population genetic diversity (HS) was 0.16, which was clearly higher than between population genetic diversity (DST = 0.06) UPG-MA showed a high level of genetic variation between major and minor populations of V. faba L. Particularly the minor populations showed a high level of diversity and was divided into two subclusters. Ltaifia was separated from the other populations. In addition to a high grain yield, these populations showed the lowest Nei and Shannon indices (H = 0.08 and I = 0.13) justifying their homogeneity. For these reasons, these cultivars can be considered a selected population. However, the Takelsa population showed the highest Nei and Shannon indices (H = 0.13 and I = 0.21), indicating that this population was the most heterogeneous, which is interesting for breeding programs. PMID:26214437

  3. 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.

  4. 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

  5. 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

  6. Tagging QTLs for maximum root length in rainfed lowland rice (Oryza sativa L.) using molecular markers.

    PubMed

    Toorchi, Mahmoud; Shashidhar, H E; Sharma, Naveen; Hittalmani, Shailaja

    2002-01-01

    A number of morphological, physiological and phenological traits are known to improve the performance of rice challenged by drought. Root morphological traits and stress-induced response form important components of drought tolerance. Enhancing grain yield remains the principal objective of most breeding programs. Interaction between primary traits poses a formidable challenge while dealing with grain yield under stress. The evaluation of root morphology at three different growth stages and grain yield along with related characteristics under contrasting moisture regimes was made using nine backcrosses along with their parent and standard checks. The backcrosses invoved transgressant double haploid lines derived from IR64 and Azucena with IR64. Marked genotypic differences were observed for all root morphology as well as grain yield related characteristics across the sampling dates as revealed by individual and combined ANOVA. Among the nine backcrosses studied in this experiment, the BC1F2 population of P124 x IR64 were evaluated for forwarding based on their performance with respect to maximum root length and grain yield under both well-watered and low-moisture stress conditions. Sixty-nine plants - ten percent of the backcross population - were selectively genotyped using RAPD primers. Under well-watered conditions two RAPD markers showed strong linkage to QTLs for maximum root length evaluated under ww conditions. Two other markers could explain the considerable amount of variation in MRL under LMS. One of the markers identified under low-moisture stress conditions was also able to explain variability in maximum root length in the mean environment. PMID:12378237

  7. 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.

  8. Random amplified polymorphic DNA (RAPD) analysis of Mycobacterium tuberculosis strains in India.

    PubMed

    Singh, J P; Verma, Rishendra; Chaudhuri, P

    2006-06-01

    The usefulness of random amplification of polymorphic DNA (RAPD) analysis for typing Indian strains of M. tuberculosis was investigated. M. tuberculosis H37Rv, M. tuberculosis DT and 42 clinical isolates of M. tuberculosis were subjected to RAPD-PCR using 7 random decamer primers. All 7 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for M. tuberculosis. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers. RAPD analysis provided a rapid and easy means of identifying polymorphism in M. tuberculosis isolates, and it was found to be a valuable alternative epidemiological tool. In addition, the results of the present study showed heterogeneity in the M. tuberculosis strains in the population studied. PMID:16645345

  9. Genetic distances between popcorn populations based on molecular markers and correlations with heterosis estimates made by diallel analysis of hybrids.

    PubMed

    Munhoz, R E F; Prioli, A J; Amaral, A T; Scapim, C A; Simon, G A

    2009-01-01

    Diallel analysis was used to obtain information on combining ability, heterosis, estimates of genetic distances by random amplified polymorphic DNA (RAPD) and on their correlations with heterosis, for the popcorn varieties RS 20, UNB2, CMS 43, CMS 42, Zélia, UEM J1, UEM M2, Beija-Flor, and Viçosa, which were crossed to obtain all possible combinations, without reciprocals. The genitors and the 36 F(1) hybrids were evaluated in field trials in Maringá during two growing seasons in a randomized complete block design with three replications. Based on the results, strategies for further studies were developed, including the construction of composites by joining varieties with high general combining ability for grain yield (UNB2 and CMS 42) with those with high general combining ability for popping expansion (Zélia, RS 20 and UEM M2). Based on the RAPD markers, UEM J1 and Zélia were the most genetically distant and RS 20 and UNB2 were the most similar. The low correlation between heterosis and genetic distances may be explained by the random dispersion of the RAPD markers, which were insufficient for the exploitation of the popcorn genome. We concluded that an association between genetic dissimilarity and heterosis based only on genetic distance is not expected without considering the effect of dominant loci. PMID:19731196

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

    SciTech Connect

    Huuskonen, Hannele . 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.

  11. Efficient detection of DNA polymorphisms by fluorescent RAPD analysis.

    PubMed

    Corley-Smith, G E; Lim, C J; Kalmar, G B; Brandhorst, B P

    1997-04-01

    A method is presented for the analysis of fluorescently labeled random amplified polymorphic DNA (FRAPD) fragments. A DNA sequencer and collection and analysis software were used to estimate the sizes of DNA fragments based on their mobilities relative to in-lane size markers. This allowed confident identification and comparison of FRAPD markers both within and between polyacrylamide gels. In comparison with analysis of RAPD products using ethidium bromide-stained agarose gels, fluorescent analysis improved the sensitivity, resolution and precision of sizing of RAPD products of about 50-2100 bp. FRAPD fragments produced from amplification of zebrafish DNA are informative as genetic markers that segregate with Mendelian inheritance. FRAPD analysis was found to be very efficient for identifying new DNA polymorphisms. PMID:9105621

  12. 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...

  13. RAPD MARKER VARIATION AMONG SMOOTH BROMEGRASS CULTIVARS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The level of genetic diversity within and among smooth bromegrass (Bromus inermis Leyss.) cultivars and land races is unknown. The objective of this study was to investigate and characterize genetic diversity of smooth bromegrass cultivars and selected populations based on randomly amplified polymo...

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

    SciTech Connect

    Theodorakis, C.W.; Shugart, L.R.

    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.

  15. 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

  16. Biogeographic pattern of genetic diversity detected by RAPD and ISSR analysis in Gypsophila (Caryophyllaceae) species from Turkey.

    PubMed

    Korkmaz, M; Dogan, N Y

    2015-01-01

    Gypsophila L. is the 3rd-largest genus of Caryophyllaceae in Turkey, a country that includes 60 taxa belonging to 56 species of the 126 recognized in the genus. A total of 35 taxa are endemic to Turkey, with an approximately 60% endemism ratio. In this study, the genetic diversity of 14 Gypsophila species from Turkey was analyzed using random amplification of polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Sixteen RAPD and 6 ISSR primers produced 132 polymorphic bands. RAPD, ISSR, and RAPD + ISSR primers for the 14 species showed 92.7, 93.8, and 92.9% polymorphism, respectively. Our results indicate that RAPD and ISSR markers are reliable and effective for assessing the genetic diversity of Gypsophila species. Gypsophila species studied were separated into 2 clusters. Our analysis shows that the clusters correlated with geographic and phytogeographic regions. PMID:26345814

  17. Comparison of RAPD, AFLP, and EF-1α Sequences for the Phylogenetic Analysis of Fusarium oxysporum and Its formae speciales in Korea

    PubMed Central

    Park, Jae-Min; Kim, Gi-Young; Lee, Song-Jin; Kim, Mun-Ok; Huh, Man-Kyu; Lee, Tae-Ho

    2006-01-01

    Although Fursarium oxysporum causes diseases in economically important plant hosts, identification of F. oxysporum formae speciales has been difficult due to confusing phenotypic classification systems. To resolve these complexity, we evaluated genetic relationship of nine formae speciales of F. oxysporum with random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and translation elongation factor-1 alpha (EF-1α) gene. In addition, the correlation between mycotoxin content of fusaric acid and isolates based on molecular marker data was evaluated using the modified Mantel's test. According to these result, these fusaric acid-producing strains could not identify clearly, and independent of geographic locations and host specificities. However, in the identification of F. oxysporum formae speciales, especially, AFLP analysis showed a higher discriminatory power than that of a the RAPD and EF-1α analyses, all three techniques were able to detect genetic variability among F. oxysporum formae speciales in this study. PMID:24039470

  18. Genetic diversity analysis of common beans based on molecular markers

    PubMed Central

    Gill-Langarica, Homar R.; Muruaga-Martínez, José S.; Vargas-Vázquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-01-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation. PMID:22215964

  19. 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...

  20. 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.

  1. ZIP4 is a novel molecular marker for glioma

    PubMed Central

    Lin, Yi; Chen, Yong; Wang, Yongzhi; Yang, Jingxuan; Zhu, Vivian F.; Liu, Yulun; Cui, Xiaobo; Chen, Leon; Yan, Wei; Jiang, Tao; Hergenroeder, Georgene W.; Fletcher, Stephen A.; Levine, Jonathan M.; Kim, Dong H.; Tandon, Nitin; Zhu, Jay-Jiguang; Li, Min

    2013-01-01

    Background Dysregulated zinc transport has been observed in many cancers. However, the status of zinc homeostasis and the expression profile of zinc transporters in brain and brain tumors have not been reported. Methods The gene profiles of 14 zinc importers (ZIPs) and 10 zinc exporters (ZnTs) in patients with glioma were studied by investigating the association between the zinc transporters and brain tumor characteristics (tumor grade and overall survival time). Three independent cohorts were analyzed to cross-validate the findings: the Chinese Glioma Genome Atlas (CGCA) cohort (n = 186), the US National Cancer Institute Repository for Molecular Brain Neoplasia Data (REMBRANDT) cohort (n = 335), and The University of Texas (UT) cohort (n = 34). Results The expression of ZIP3, 4, 8, 14, ZnT5, 6, and 7 were increased, and the expression of ZnT10 was decreased in grade IV gliomas, compared with grade II gliomas. Among all 24 zinc transporters, ZIP4 is most significantly associated with tumor grade and overall survival; this finding is consistent across 2 independent cohorts (CGCA and REMBRANDT) and is partially validated by the third cohort (UT). High ZIP4 expression was significantly associated with higher grade of gliomas and shorter overall survival (hazard ratio = 1.61, 95% confidence interval = 1.02–2.53, P = .040 in CGCA cohort; hazard ratio = 1.32, 95% confidence interval = 1.08–1.61, P = .007 in REMBRANDT cohort). Conclusions Dysregulated expression of zinc transporters is involved in the progression of gliomas. Our results suggest that ZIP4 may serve as a potential diagnostic and prognostic marker for gliomas. PMID:23595627

  2. Molecular markers for leaf rust resistance genes in wheat.

    PubMed

    Chełkowski, J; Stepień, L

    2001-01-01

    Over 100 genes of resistance to rust fungi: Puccinia recondita f. sp. tritici, (47 Lr - leaf rust genes), P. striiformis (18 Yr - yellow rust genes) and P. graminis f. sp. tritici (41 Sr - stripe rust genes) have been identified in wheat (Triticum aestivum L.) and its wild relatives according to recent papers. Sixteen Lr resistance genes have been mapped using restriction fragments length polymorphism (RFLP) markers on wheat chromosomes. More than ten Lr genes can be identified in breeding materials by sequence tagged site (STS) specific markers. Gene Lrk 10, closely linked to gene Lr 10, has been cloned and its function recognized. Available markers are presented in this review. The STS, cleaved amplified polymorphic sequence (CAPS) and sequence characterized amplified regions (SCAR) markers found in the literature should be verified using Triticum spp. with different genetic background. Simple sequence repeats (SSR) markers for Lr resistance genes are now also available. PMID:14564046

  3. 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 tissuesmarkers 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

  4. Genetic variability of Brazilian isolates of Alternaria alternata detected by AFLP and RAPD techniques

    PubMed Central

    Dini-Andreote, Francisco; Pietrobon, Vivian Cristina; Andreote, Fernando Dini; Romão, Aline Silva; Spósito, Marcel Bellato; Araújo, Welington Luiz

    2009-01-01

    The Alternaria brown spot (ABS) is a disease caused in tangerine plants and its hybrids by the fungus Alternaria alternata f. sp. citri which has been found in Brazil since 2001. Due to the recent occurrence in Brazilian orchards, the epidemiology and genetic variability of this pathogen is still an issue to be addressed. Here it is presented a survey about the genetic variability of this fungus by the characterization of twenty four pathogenic isolates of A. alternata f. sp. citri from citrus plants and four endophytic isolates from mango (one Alternaria tenuissima and three Alternaria arborescens). The application of two molecular markers Random Amplified Polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP) had revealed the isolates clustering in distinct groups when fingerprintings were analyzed by Principal Components Analysis (PCA). Despite the better assessment of the genetic variability through the AFLP, significant modifications in clusters components were not observed, and only slight shifts in the positioning of isolates LRS 39/3 and 25M were observed in PCA plots. Furthermore, in both analyses, only the isolates from lemon plants revealed to be clustered, differently from the absence of clustering for other hosts or plant tissues. Summarizing, both RAPD and AFLP analyses were both efficient to detect the genetic variability within the population of the pathogenic fungus Alternaria spp., supplying information on the genetic variability of this species as a basis for further studies aiming the disease control. PMID:24031413

  5. Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes.

    PubMed

    Kazan, K; Manners, J M; Cameron, D F

    1993-02-01

    The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping. PMID:8458572

  6. Development of new candidate gene and EST-based molecular markers for Gossypium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New source of molecular markers accelerates 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 expressed sequence tag (EST) sequences, and validated them through amplification, ge...

  7. 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...

  8. 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

  9. 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

  10. PlantMarkers—a database of predicted molecular markers from plants

    PubMed Central

    Rudd, Stephen; Schoof, Heiko; Mayer, Klaus

    2005-01-01

    Molecular markers are required in a broad spectrum of gene screening approaches, ranging from gene-mapping within traditional ‘forward’-genetics approaches through QTL identification studies to genotyping and haplotyping studies. As we enter the post-genomics era, the need for genetic markers does not diminish, even in the species with fully sequenced genomes. PlantMarkers is a genetic marker database that contains a comprehensive pool of predicted molecular markers. We have adopted contemporary techniques to identify putative single nucleotide polymorphism (SNP), simple sequence repeat (SSR) and conserved orthologue set markers. A systematic approach to identify as broad a range of putative markers has been undertaken by screening the available openSputnik unigene consensus sequences from over 50 plant species. A web presence at http://markers.btk.fi provides functionality so that a user may search for species-specific markers on the basis of many specific criteria not limited to non-synonymous SNPs segregating between different varieties or measured polymorphic SSRs. Feedback forms are provided with all sequence entries to enable inclusion of, for example, map location for markers validated by the research community. PMID:15608276

  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. 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...

  13. 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…

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Wang, Tiegu; Huang, Qunce; Feng, Weisen

    2007-10-01

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

  16. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects.

    PubMed

    Chenuil, Anne; Anne, Chenuil

    2006-05-01

    The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique. PMID:16850217

  17. 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 ...

  18. DNA markers in molecular diagnostics for hepatocellular carcinoma

    PubMed Central

    Su, Ying-Hsiu; Lin, Selena Y; Song, Wei; Jain, Surbhi

    2015-01-01

    Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40–50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening. PMID:25098554

  19. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica

    PubMed Central

    Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

    2015-01-01

    Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

  20. Molecular breeding in Brassica for salt tolerance: importance of microsatellite (SSR) markers for molecular breeding in Brassica.

    PubMed

    Kumar, Manu; Choi, Ju-Young; Kumari, Nisha; Pareek, Ashwani; Kim, Seong-Ryong

    2015-01-01

    Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the "candidate genes" and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops. PMID:26388887

  1. 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

  2. Clinical aspects on molecular probes, markers and metabolism.

    PubMed

    Rydberg, U

    1994-01-01

    Though today techniques utilizing molecular methods are emphasized, we must not neglect to put the molecular data into a clinical context. Extrapolations should be handled with great care. The knowledge on alcohol has many levels, and facts are often taken out of context. For a proper report of a clinical state or situation, validity lies both in the precision of clinical descriptions and in the accuracy of the molecular parameter. Alcohol as a medical risk factor is often disregarded, and there is often a communication gap. PMID:8032144

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

    PubMed Central

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

    2013-01-01

    The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccards similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program. PMID:24600309

  4. 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

  5. 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.

  6. Molecular markers associated with seed weight in two soybean populations.

    PubMed

    Mian, M A; Bailey, M A; Tamulonis, J P; Shipe, E R; Carter, T E; Parrott, W A; Ashley, D A; Hussey, R S; Boerma, H R

    1996-11-01

    Seed weight (SW) is a component of soybean, Glycine max (L.) Merr., seed yield, as well as an important trait for food-type soybeans. Two soybean populations, 120 F4-derived lines of 'Young'xPI416937 (Pop1) and 111 F2-derived lines of PI97100x'Coker 237' (Pop2), were mapped with RFLP makers to identify quantitative trait loci (QTLs) conditioning SW across environments and populations. The genetic map of Pop1 consisted of 155 loci covering 973 cM, whereas Pop2 involved 153 loci and covered 1600 cM of map distance. For Pop1, the phenotypic data were collected from Plains, GA., Windblow, N.C., and Plymouth, N.C., in 1994. For Pop2, data were collected from Athens, GA., in 1994 and 1995, and Blackville, S.C., in 1995. Based on single-factor analysis of variance (ANOVA), seven and nine independent loci were associated with SW in Pop1 and Pop2, respectively. Together the loci explained 73% of the variability in SW in Pop1 and 74% in Pop2. Transgressive segregation occurred among the progeny in both populations. The marker loci associated with SW were highly consistent across environments and years. Two QTLs on linkage group (LG) F and K were located at similar genomic regions in both populations. The high consistency of QTLs across environments indicates that effective marker-assisted selection is feasible for soybean SW. PMID:24162474

  7. Molecular Prognostic and Predictive Markers in Colorectal Cancer: Current Status

    PubMed Central

    Lee, Jeffrey K.

    2011-01-01

    In parallel with our growing understanding of the molecular pathways underlying colorectal neoplasia, significant advances have been made in the treatment of colorectal cancer (CRC). For the past few decades, 5-fluorouracil-based therapy has been the cornerstone of adjuvant therapy. More recently, additional cytotoxic drugs and molecular-targeted therapies have provided additional clinical benefit in certain patient populations. Unfortunately, overall survival remains about 45%. Notably, our understanding of why certain patients do or do not respond to treatment remains limited. Thus, as therapeutic options for CRC continue to expand, there is now an even greater imperative to identify reliable biomarkers that have the potential to predict prognosis as well as response to chemotherapy. In this review, we will summarize the current status of such molecular prognostic and predictive biomarkers in CRC and assess their usefulness in tailoring therapeutic options. PMID:21572547

  8. Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques

    PubMed Central

    2014-01-01

    Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor κB and its ligand, chemokine receptors, vascular cell adhesion molecule-1, αVβ3 integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein. PMID:25099015

  9. Predictive and prognostic molecular markers for cancer medicine

    PubMed Central

    Mehta, Sunali; Shelling, Andrew; Muthukaruppan, Anita; Lasham, Annette; Blenkiron, Cherie; Laking, George; Print, Cristin

    2010-01-01

    Over the last 10 years there has been an explosion of information about the molecular biology of cancer. A challenge in oncology is to translate this information into advances in patient care. While there are well-formed routes for translating new molecular information into drug therapy, the routes for translating new information into sensitive and specific diagnostic, prognostic and predictive tests are still being developed. Similarly, the science of using tumor molecular profiles to select clinical trial participants or to optimize therapy for individual patients is still in its infancy. This review will summarize the current technologies for predicting treatment response and prognosis in cancer medicine, and outline what the future may hold. It will also highlight the potential importance of methods that can integrate molecular, histopathological and clinical information into a synergistic understanding of tumor progression. While these possibilities are without doubt exciting, significant challenges remain if we are to implement them with a strong evidence base in a widely available and cost-effective manner. PMID:21789130

  10. Molecular Characterization of Entomopathogenic Fungi Using Microsatellite Markers.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Identification of entomopathogenic fungi isolated from their arthropod hosts or other sources can be cumbersome when certain morphological features are not clear or time consuming when the organism needs to reach a certain growth stage for proper identification. Molecular tools can be handy and offe...

  11. Separation of DNA for molecular markers analysis from leaves of the Vitis vinifera.

    PubMed

    Nazhad, Nafiseh Rigi; Solouki, Mahmood

    2008-06-01

    In the present study, three DNA extraction procedures were examined to determine which might yield DNA from Grape leaves suitable for molecular analysis for RAPD, SSR. AFLP and etc analysis. The three methods examined were: the miniprep procedure and the modified CTAB for difficult species and protocol CTAB. Only the modified CTAB method consistently yielded DNA suitable for Polymerase Chain Reaction (PCR) amplification, regardless of plant growing conditions or leaf age. The quality and quantity of extracted genomic DNA gained from these methods are deliberated by means UV biophotometer, electrophoresis in 1.2% agarose gel and PCR. In this regard, application chosen for young and mature leaves, the most value of qualified DNA, is extracted from fully expanded leave when PVP was added to the extraction buffer. This same procedure also yielded PCR-amplifiable DNA from various other perennial, woody species and from other fruit species such as apple (Malus domestica), cherry (Prunus avium), peach (Prunuspersica), plum (Prunus domestica). DNA yield from this procedure is high (up to 1 mg g(-1) of leaf tissue). DNA is completely digestible with restriction endonucleases and amplifiable in the Polymerase Chain Reaction (PCR). PMID:18817243

  12. Phylogenetic relationships among pufferfish of genus Takifugu by RAPD analysis

    NASA Astrophysics Data System (ADS)

    Song, Lin-Sheng; Liu, Bao-Zhong; Wang, Zai-Zhao; Li, Hong-Lei; Xiang, Jian-Hai; Qian, Pei-Yuan

    2001-06-01

    Amplifications with 300 10-base primers under predetermined optimal reaction yielded 2762 reproducible amplified fragments ranging from 200 to 3000 bp. Genetic distances among five species of Takifugu and Lagocephalus spadiceus as outgroup were calculated based on the presence/absence of the amplified fragments. Topological phylogenic trees of the 5 species of Takifugu and the outgroup were generated by Parsimony and Neighbor-Joining analysis based on RAPD data set. The genetic distance between T. rubripes and T. pseudommus was almost the same as that between individuals within each species, but was much smaller than that among T. rubripes, T. pseudommus and the other species. The molecular data from RAPD analysis convincingly showed that T. rubripes and T. pseudommus should be the same species.

  13. Ultrasound-based Measurement of Molecular Marker Concentration in Large Blood Vessels: A Feasibility Study

    PubMed Central

    Wang, Shiying; Mauldin, F. William; Klibanov, Alexander L.; Hossack, John A.

    2014-01-01

    Ultrasound molecular imaging has demonstrated efficacy in pre-clinical studies for cancer and cardiovascular inflammation. However, these techniques often require lengthy protocols due to waiting periods or additional control microbubble injections. Moreover, they are not capable of quantifying molecular marker concentration in human tissue environments that exhibit variable attenuation and propagation path lengths. Our group recently investigated a modulated Acoustic Radiation Force (ARF)-based imaging sequence, which was demonstrated to detect targeted adhesion independent of control measurements. In the present study, this sequence was tested against various experimental parameters to determine feasibility for quantitative measurements of molecular marker concentration. Results demonstrated that measurements obtained from the sequence (residual-to-saturation ratio, Rresid) were independent of acoustic pressure and attenuation (p> 0.13, n = 10)when acoustic pressures were sufficiently low. The Rresid parameter exhibited a linear relationship with measured molecular marker concentration (R2> 0.94). Consequently, feasibility was demonstrated in vitro, for quantification of molecular marker concentration in large vessels using a modulated ARF-based sequence. Moreover, these measurements were independent of absolute acoustic reflection amplitude and used short imaging protocols(3 min) without control measurements. PMID:25308943

  14. Ultrasound-based measurement of molecular marker concentration in large blood vessels: a feasibility study.

    PubMed

    Wang, Shiying; Mauldin, F William; Klibanov, Alexander L; Hossack, John A

    2015-01-01

    Ultrasound molecular imaging has demonstrated efficacy in pre-clinical studies for cancer and cardiovascular inflammation. However, these techniques often require lengthy protocols because of waiting periods or additional control microbubble injections. Moreover, they are not capable of quantifying molecular marker concentration in human tissue environments that exhibit variable attenuation and propagation path lengths. Our group recently investigated a modulated acoustic radiation force-based imaging sequence, which was found to detect targeted adhesion independent of control measurements. In the present study, this sequence was tested against various experimental parameters to determine its feasibility for quantitative measurements of molecular marker concentration. Results indicated that measurements obtained from the sequence (residual-to-saturation ratio, Rresid) were independent of acoustic pressure and attenuation (p > 0.13, n = 10) when acoustic pressures were sufficiently low. The Rresid parameter exhibited a linear relationship with measured molecular marker concentration (R(2) > 0.94). Consequently, feasibility was illustrated in vitro, for quantification of molecular marker concentration in large vessels using a modulated acoustic radiation force-based sequence. Moreover, these measurements were independent of absolute acoustic reflection amplitude and used short imaging protocols (3 min) without control measurements. PMID:25308943

  15. Molecular Markers of Secondary Organic Aerosol in Mumbai, India.

    PubMed

    Fu, Pingqing; Aggarwal, Shankar G; Chen, Jing; Li, Jie; Sun, Yele; Wang, Zifa; Chen, Huansheng; Liao, Hong; Ding, Aijun; Umarji, G S; Patil, R S; Chen, Qi; Kawamura, Kimitaka

    2016-05-01

    Biogenic secondary organic aerosols (SOA) are generally considered to be more abundant in summer than in winter. Here, polar organic marker compounds in urban background aerosols from Mumbai were measured using gas chromatography-mass spectrometry. Surprisingly, we found that concentrations of biogenic SOA tracers at Mumbai were several times lower in summer (8-14 June 2006; wet season; n = 14) than in winter (13-18 February 2007; dry season; n = 10). Although samples from less than 10% of the season are extrapolated to the full season, such seasonality may be explained by the predominance of the southwest summer monsoon, which brings clean marine air masses to Mumbai. While heavy rains are an important contributor to aerosol removal during the monsoon season, meteorological data (relative humidity and T) suggest no heavy rains occurred during our sampling period. However, in winter, high levels of SOA and their day/night differences suggest significant contributions of continental aerosols through long-range transport together with local sources. The winter/summer pattern of SOA loadings was further supported by results from chemical transport models (NAQPMS and GEOS-Chem). Furthermore, our study suggests that monoterpene- and sesquiterpene-derived secondary organic carbon (SOC) were more significant than those of isoprene- and toluene-SOC at Mumbai. PMID:27045808

  16. Application of molecular markers to detect DNA damage caused by environmental pollutants in lichen species.

    PubMed

    Cansaran-Duman, D; Altunkaynak, E; Aslan, A; Byk, I; Aras, S

    2015-01-01

    Pseudevernia furfuracea L. (Zopf), Peltigera praetextata (Flrke ex Sommerf.) Zopf, Lobaria pulmonaria (L.) Hoffm., and Usnea longissima Ach. lichen species were used as bioindicators to assess the genotoxicity of air pollutants. In the present study, we examined significant environmetal pollutants and investigate how changes may lead to damage in DNA structure using RAPD markers. In the study area (Erzurum, Turkey), poor-quality lignite, which generates a large amount of sulfur dioxide, nitrogen oxides, and particle matter, is used for domestic heating, and vehicles also contribute to air pollution. Control lichen samples were collected far from large urban and industrial settlements and transplanted to four polluted sites for 4, 8, or 12 months. The total soluble protein content of the examined four lichen species did not significantly change with exposure time (P < 0.05). The four lichen samples exposed to the pollutants for 8 months had the highest ratio of DNA changes. The ratio of band differences in P. praetextata was higher than that in the other three lichen species, possibly because it has broad leaves that accumulated more pollutants. The average incidences of polymorphism were 64.14, 54.58, 65.76, and 43.06% for P. furfuracea, P. praetextata, L. pulmonaria, and U. longissima, respectively. The genomic template stability (GTS) significantly decreased following exposure to pollutants. GTS ratios revealed that the highest value (98.36%) belonged to U. longissima samples from Site 1 (10 m) after 4 months of exposure, and the lowest values belonged to P. praetextata (73.58%) from Site 3 (100 m) after 8 months of exposure. Based on our findings, we recommend the use of P. praetextata as an indicator of genotoxicity. PMID:25966238

  17. Standardization for transcriptomic molecular markers to screen human colon cancer.

    PubMed

    Ahmed, Farid E; Vos, Paul W; Ijames, Stephanie; Lysle, Donald T; Flake, Gordon; Sinar, Dennis R; Naziri, Wade; Marcuard, Stephan P

    2007-01-01

    Establishing test performance criteria for a transcriptomic colon cancer marker approach must be carried out in a standardized fashion in order tso ensure that the test will perform the same way in any laboratory, anywhere. Condition of sample preservation and shipping prior to total RNA extraction is critical, and we recommend preserving stool samples in an appropriate preservative and shipping them in cold packs so as to keep stools at 4 degrees C. It is not necessary to isolate colonocytes to obtain adequate RNA for testing. It is, however, important to obtain samples from both mucin-rich and non-mucin rich to have a good representation of both left- and right-side colon cancers. Employing a commercial total RNA extraction kit that contains an RLT buffer from Qiagen Corporation (Valencia, CA, USA) removes bacterial RNA from stool preparations and results in a high yield of undegraded RNA of human origin. Genes selected based on the enormous resources of NCI's Cancer Genome Anatomy project give good results. Primers for PCR should span more than one exon. Use of semiquantitative PCR, preferably with several reference housekeeping genes of various copy numbers, depending on tested genes, should enhance confidence in the quantitative results. Having standardized the testing conditions in our ongoing work, it is now imperative that a larger prospective randomized clinical study utilizing stool and tissue samples derived from several control and colon cancer patients, to allow for statistically valid analyses, be conducted in order to determine the true sensitivity and specificity of the transcriptomic screening approach for this cancer whose incidence is on the rise worldwide. PMID:18204205

  18. Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting

    NASA Astrophysics Data System (ADS)

    Thiel, Volker; Peckmann, Jörn; Seifert, Richard; Wehrung, Patrick; Reitner, Joachim; Michaelis, Walter

    1999-12-01

    We propose that organic compounds found in a Miocene limestone from Marmorito (Northern Italy) are source markers for organic matter present in ancient methane vent systems (cold seeps). The limestone contains high concentrations of the tail-to-tail linked, acyclic C 20 isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), a C 25 homolog 2,6,10,15,19-pentamethylicosane (PME), and a distinctive glycerol ether lipid containing 3,7,11,15-tetramethylhexadecyl (phytanyl-) moieties. The chemical structures of these biomarkers indicate a common origin from archaea. Their extremely 13C-depleted isotope compositions (δ 13C ≈ -108 to -115.6‰ PDB) suggest that the respective archaea have directly or indirectly introduced isotopically depleted, methane-derived carbon into their biomass. We postulate that a second major cluster of biomarkers showing heavier isotope values (δ 13C ≈ -88‰) is derived from sulfate-reducing bacteria (SRB). The observed biomarkers sustain the idea that methanogenic bacteria, in a syntrophic community with SRB, are responsible for the anaerobic oxidation of methane in marine sediments. Marmorito may thus represent a conceivable ancient scenario for methane consumption performed by a defined, two-membered bacterial consortium: (1) archaea that perform reversed methanogenesis by oxidizing methane and producing CO 2 and H 2; and (2) SRB that consume the resulting H 2. Furthermore, the respective organic molecules are, unlike other compounds, tightly bound to the crystalline carbonate phase. The Marmorito carbonates can thus be regarded as "cold seep microbialites" rather than mere "authigenic" carbonates.

  19. Molecular markers for oocyte competence in bovine cumulus cells.

    PubMed

    Kussano, N R; Leme, L O; Guimarães, A L S; Franco, M M; Dode, M A N

    2016-04-01

    This study aimed to quantify the expression of candidate genes in cumulus cells (CCs) from cumulus-oocyte complexes (COCs) with high and low potential for in vitro development up to the blastocyst stage. First, the effects of individual culture and biopsy on embryo development were evaluated. Individuals cultured using the well of the well system were compared with individuals cultured in 20 μL droplets (microdroplets) and those cultured in groups (control). Blastocyst rates were lower for the individual culture systems (P < 0.05; well of the well = 17.9%, n = 95; microdrop = 26.3%, n = 95) than for the control group (45.0%, n = 209). Second, the effects of biopsy on embryo production were compared between the control and microdroplet cultures, and no effects (P > 0.05) were observed for either group. Finally, the expression profiles of glypican 4 (GPC4), IGF4-binding protein, follicle-stimulating hormonereceptor, growth hormone receptor, epidermal growth factor receptor, fibroblast growth factor 11, solute carrier family 2 member 1, solute carrier family 2 member 3,sprouty homolog 1, versican, and keratin protein 8 in CCs obtained by biopsy were quantified by real-time polymerase chain reaction. Cumulus cells were categorized on the basis of the fates of the COCs: expanded blastocyst, cleaved and arrested, and uncleaved. The GPC4 gene was overexpressed (P = 0.007) in CCs from oocytes that formed embryos compared with those that produced cleaved and arrested embryos. We concluded that individual culture reduced blastocyst production; however, biopsy did not affect embryo development. The profile of GPC4 expression can be used as a marker to distinguish COCs with potential for embryo development from those with limited developmental potential. PMID:26792377

  20. 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.

  1. Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting

    SciTech Connect

    Thiel, V.; Peckmann, J.; Seifert, R.; Wehrung, P.; Reitner, J.; Michaelis, W.

    1999-12-01

    The authors propose that organic compounds found in a Miocene limestone from Marmorito (Northern Italy) are source markers for organic matter present in ancient methane vent systems (cold seeps). The limestone contains high concentrations of the tail-to-tail linked, acyclic C{sub 20} isoprenoid 2,6,11,15-tetramethylhexadecane (crocetane), a C{sub 25} homolog 2,6,10,15,19-pentamethylicosane (PME), and a distinctive glycerol ether lipid containing 3,7,11,15-tetramethylhexadecyl (phytanyl-) moieties. The chemical structures of these biomarkers indicate a common origin from archaea. Their extremely {sup 13}C-depleted isotope compositions ({delta}{sup 13}C {approximately} {minus}108 to {minus}115.6% PDB) suggest that the respective archaea have directly or indirectly introduced isotopically depleted, methane-derived carbon into their biomass. The authors postulate that a second major cluster of biomarkers showing heavier isotope values ({delta}{sup 13}C {approximately} {minus}88%) is derived from sulfate-reducing bacteria (SRB). The observed biomarkers sustain the idea that methanogenic bacteria, in a syntrophic community with SRB, are responsible for the anaerobic oxidation of methane in marine sediments. Marmorito may thus represent a conceivable ancient scenario for methane consumption performed by a defined, two-membered bacterial consortium: (1) archaea that perform reversed methanogenesis by oxidizing methane and producing CO{sub 2} and H{sub 2}; and (2) SRB that consume the resulting H{sub 2}. Furthermore, the respective organic molecules are, unlike other compounds, tightly bound to the crystalline carbonate phase. The Marmorito carbonates can thus be regarded as cold seep microbialites rather than mere antigenic carbonates.

  2. 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 (5α-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

  3. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis.

    PubMed

    Sudheer Pamidimarri, D V N; Reddy, Muppala P

    2014-05-01

    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity. PMID:24469734

  4. [PSM2 and POLR2J gene families as molecular markers of the higher primate evolution].

    PubMed

    Shematorova, E K; Shpakovski?, D G; Shpakovski?, G V

    2010-09-01

    We have studied the molecular evolution of two gene families specific for primates: POLR2J of the transcription system and PMS2 of the MMR repair system. The appearance and improvement of the genetic structure in each of the families was shown to strongly correlate with the main stages of the higher primates biological evolution. Our results indicate that the PSM2 and POLR2J genes can serve as helpful and reliable molecular markers of anthropogenesis. PMID:21061629

  5. 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...

  6. RiceCAP: Development of molecular markers associated with long grain milling yield

    Technology Transfer Automated Retrieval System (TEKTRAN)

    U.S. rice breeders are focused on developing new cultivars that have high yield and high milling quality. Using traditional breeding methods, it takes approximately ten years to develop a new cultivar. Development of molecular markers that are closely linked to traits of economic value will increase...

  7. 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...

  8. QUANTITATION, DETECTION AND MEASUREMENT PRECISION OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    EPA Science Inventory

    This work focuses on analysis of organic molecular markers in airborne particulate matter (PM) by Gas Chromatography/Ion Trap Mass Spectrometry (GC/IT MS). The particulate samples used in the method development were collected as PM10 in metropolitan Philadelphia during...

  9. A novel molecular marker for the study of Neotropical cichlid phylogeny.

    PubMed

    Fabrin, T M C; Gasques, L S; Prioli, S M A P; Prioli, A J

    2015-01-01

    The use of molecular markers has contributed to phylogeny and to the reconstruction of species' evolutionary history. Each region of the genome has different evolution rates, which may or may not identify phylogenetic signal at different levels. Therefore, it is important to assess new molecular markers that can be used for phylogenetic reconstruction. Regions that may be associated with species characteristics and are subject to selective pressure, such as opsin genes, which encode proteins related to the visual system and are widely expressed by Cichlidae family members, are interesting. Our aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system. We used Bayesian inference and maximum likelihood analysis to support the use of the nuclear opsin LWS gene in the phylogeny of eight Neotropical cichlid species. Their use concatenated to the mitochondrial gene COI was also tested. The LWS gene fragment comprised the exon 2-4 region, including the introns. The LWS gene provided good support for both analyses up to the genus level, distinguishing the studied species, and when concatenated to the COI gene, there was a good support up to the species level. Another benefit of utilizing this region, is that some polymorphisms are associated with changes in spectral properties of the LWS opsin protein, which constitutes the visual pigment that absorbs red light. Thus, utilization of this gene as a molecular marker to study the phylogeny of Neotropical cichlids is promising. PMID:26782460

  10. 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...

  11. [Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

    PubMed

    Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

    2014-01-01

    Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis. PMID:25510798

  12. Cloning and characterization of resistance gene candidate sequences and molecular marker development in gerbera (Gerbera hybrida)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving disease resistance has become an important breeding objective in gerbera, one of the most important floricultural crops in the world. Development and application of molecular markers are expected to assist selection of gerberas with improved disease resistance. The availability of resistan...

  13. SEASONAL ABUNDANCE OF ORGANIC MOLECULAR MARKERS IN URBAN PARTICULATE MATTER FROM PHILADELPHIA, PA

    EPA Science Inventory

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundances of key tracer compounds together with their dominant sources. Daily PM10...

  14. Improving a Lecture-Size Molecular Model Set by Repurposing Used Whiteboard Markers

    ERIC Educational Resources Information Center

    Dragojlovic, Veljko

    2015-01-01

    Preparation of an inexpensive model set from whiteboard markers and either HGS molecular model set or atoms made of wood is described. The model set is relatively easy to prepare and is sufficiently large to be suitable as an instructor set for use in lectures.

  15. New DNA Markers for High Molecular Weight Glutenin Subunits in Wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    End-use quality is one of the priorities of modern wheat breeding. Even though quality is a complex trait, high molecular weight (HMW) glutenins play a major role in determining the bread making quality of wheat. DNA markers developed from the sequences of HMW glutenin genes were reported in several...

  16. 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…

  17. 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...

  18. 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

  19. 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

  20. Molecular markers and cotton genetic improvement: current status and future prospects.

    PubMed

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

    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 global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan.

    PubMed

    Chang, C S; Chen, C F; Berthouly-Salazar, C; Chazara, O; Lee, Y P; Chang, C M; Chang, K H; Bed'Hom, B; Tixier-Boichard, M

    2012-04-01

    Molecular and phenotypic data have been combined to characterize the genetic diversity of six local chicken breeds maintained with a long-term conservation programme. Hua-Tung, Hsin-Yi, Ju-Chi and Quemoy originated from Taiwan, Shek-Ki is from South China, and Nagoya is from Japan. Molecular tools included 24 microsatellite markers, melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) (MC1R), the LEI0258 marker located within the major histocompatibility complex (MHC), and mitochondrial DNA. Performance was recorded on the same individuals for body weight, panting rate in summer and antibody response (antigens: Newcastle disease virus and sheep red blood cells). A multivariate method previously proposed for taxonomy was used to combine the different data sets. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) and the MCW330 marker contributed the most to the first axis of the multiple coinertia analysis of molecular markers. Melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) showed evidence of selection, probably related to its effect on feather colour. The MHC exhibited a large diversity, with 16 alleles of the LEI0258 marker. Immune response traits contributed the most to the principal component analysis of phenotypic data. Eight mitochondrial DNA haplotypes related to clades A, B, C and E were distributed across breeds and revealed an important contribution of Indian and European breeds to Ju-Chi, Quemoy and Hsin-Yi. Phenotypic data contributed less than molecular data to the combined analysis, and two markers, LEI0258 and LEI0228, contributed the most. The combined analysis could clearly discriminate all breeds, except Ju-Chi, which was similar to Quemoy for many criteria, except immune response. PMID:22404353

  2. Assessing the germplasm of Laminaria (phaeophyceae) with random amplified polymorphic DNA (RAPD) method

    NASA Astrophysics Data System (ADS)

    He, Yingjun; Zou, Yuping; Wang, Xiaodong; Zheng, Zhiguo; Zhang, Daming; Duan, Delin

    2003-06-01

    Eighteen gametophytes including L. japonica, L. ochotensis and L. longissima, were verified with random amplified polymorphic DNA (RAPD) technique. Eighteen ten-base primers were chosen from 100 primers selected for final amplification test. Among the total of 205 bands amplified, 181 (88.3%) were polymorphic. The genetic distance among different strains ranged from 0.072 to 0.391. The dendrogram constructed by unweighted pair-group method with arithmetic (UPGMA) method showed that the female and male gametophytes of the same cell lines could be grouped in pairs respectively. It indicated that RAPD analysis could be used not only to distinguish different strains of Laminaria, but also to distinguish male and female gametophyte within the same cell lines. There is ambiguous systematic relationship if judged merely by the present data. It seems that the use of RAPD marker is limited to elucidation of the phylogenetic relationship among the species of Laminaria.

  3. MOLECULAR VARIATION AMONG ISOLATES OF THE MITE PATHOGENIC FUNGI NEOZYGITES TANAJOAE AND N. FLORIDANA: DEVELOPMENT OF RAPD, AFLP AND SCAR MARKERS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    NEOZYGITES TANAJOAE is a key natural enemy of cassava green mite in Brazil that was experimentally released in cassava fields in Benin (W. Africa) in 1988/1999. N. FLORIDANA closely resembles N. TANAJOAE but is a widespread pathogen of tetranychid mites in temperate and tropical regions. Genetic var...

  4. 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...

  5. 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...

  6. Evaluation of genetic diversity in Chinese kale (Brassica oleracea L. var. alboglabra Bailey) by using rapid amplified polymorphic DNA and sequence-related amplified polymorphism markers.

    PubMed

    Zhang, J; Zhang, L G

    2014-01-01

    Chinese kale is an original Chinese vegetable of the Cruciferae family. To select suitable parents for hybrid breeding, we thoroughly analyzed the genetic diversity of Chinese kale. Random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) molecular markers were used to evaluate the genetic diversity across 21 Chinese kale accessions from AVRDC and Guangzhou in China. A total of 104 bands were detected by 11 RAPD primers, of which 66 (63.5%) were polymorphic, and 229 polymorphic bands (68.4%) were observed in 335 bands amplified by 17 SRAP primer combinations. The dendrogram showed the grouping of the 21 accessions into 4 main clusters based on RAPD data, and into 6 clusters based on SRAP and combined data (RAPD + SRAP). The clustering of accessions based on SRAP data was consistent with petal colors. The Mantel test indicated a poor fit for the RAPD and SRAP data (r = 0.16). These results have an important implication for Chinese kale germplasm characterization and improvement. PMID:24615113

  7. Intestinal microflora molecular markers of spleen-deficient rats and evaluation of traditional Chinese drugs

    PubMed Central

    Peng, Ying; Wang, Zhuo; Lu, Yuan; Wu, Chun-Fu; Yang, Jing-Yu; Li, Xiao-Bo

    2009-01-01

    AIM: To find a rapid and efficient analysis method of gastrointestinal microflora in Pi-deficient (spleen-deficient) rats and to evaluate traditional Chinese drugs. METHODS: Enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) based assay was performed to examine changes of intestinal microflora in two Pi-deficienct animal models and to evaluate the efficacy of four traditional Chinese drugs as well as a probiotic recipe and another therapy in Pi-deficient rats. RESULTS: A molecular marker was identified for Pi-deficiency in rats. The pharmacodynamic evaluation system, including identified molecular markers (net integral area and abundance of DNA bands), Shannon’s index for diversity of intestinal microflora, and Sorenson’s pairwise similarity coefficient, was established. The four major clinical recipes of traditional Chinese drugs for Pi-deficiency in rats, especially at their medium dose (equivalence to the clinical dose), produced more pronounced recovery activities in Pi-deficient rats, while higher doses of these recipes did not show a better therapeutic effect but some toxic effects such as perturbation deterioration of intestinal microflora. CONCLUSION: Both fingerprint analysis and identified marker can show Pi-deficiency in rats and its difference after treatment. The identified molecular marker may be applied in screening for the active compounds both in relative traditional Chinese drugs and in pharmacodynamic study of Pi-deficiency in rats. PMID:19437561

  8. 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

  9. Molecular marker development and genetic diversity exploration by RNA-seq in Platycodon grandiflorum.

    PubMed

    Kim, Hyun Jung; Jung, Jungsu; Kim, Myung-Shin; Lee, Je Min; Choi, Doil; Yeam, Inhwa

    2015-10-01

    Platycodon grandiflorum, generally known as the bellflower or balloon flower, is the only species in the genus Platycodon of the family Campanulaceae. Platycodon plants have been traditionally used as a medicinal crop in East Asia for their antiphlogistic, antitussive, and expectorant properties. Despite these practical uses, marker-assisted selection and molecular breeding in platycodons have lagged due to the lack of genetic information on this genus. In this study, we performed RNA-seq analysis of three platycodon accessions to develop molecular markers and explore genetic diversity. First, genic simple sequence repeats (SSRs) were retrieved and compared; dinucleotide motifs were the most abundant repeats (39%-40%) followed by trinucleotide (25%-31%), tetranucleotide (1.5%-1.9%), and pentanucleotide (0.3%-1.0%) repeats. The result of in silico SSR analysis, three SSR markers were detected and showed possibility to distinguish three platycodon accessions. After several filtering procedures, 180 single nucleotide polymorphisms (SNPs) were used to design 40 cleaved amplified polymorphic sequence (CAPS) markers. Twelve of these PCR-based markers were validated as highly polymorphic and utilized to investigate genetic diversity in 21 platycodon accessions collected from various regions of South Korea. Collectively, the 12 markers yielded 35 alleles, with an average of 3 alleles per locus. Polymorphism information content (PIC) values ranged from 0.087 to 0.693, averaging 0.373 per locus. Since platycodon genetics have not been actively studied, the sequence information and the DNA markers generated from our research have the potential to contribute to further genetic improvements, genomic studies, and gene discovery in this genus. PMID:26501479

  10. 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.

  11. 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

  12. How do molecular marker patterns of BC change at increasing age of chars?

    NASA Astrophysics Data System (ADS)

    Schneider, M. P. W.; Hilf, M.; Schmidt, M. W. I.

    2009-04-01

    Black carbon (BC) is considered to be a relatively stable form of organic carbon. However, previous results have shown that the physical and chemical properties of BC can vary considerably with formation temperature. Thus, to understand the long-term carbon sink potential of BC there is increasing interest to gain more information about i) the conditions under which BC was formed, and ii) the resulting degradability of BC under natural conditions. In a first step, we synthesised chars from two different sources of biomass (chestnut wood, rice straw) under well-defined conditions as model substances to analyse the changes in their molecular structure at increasing formation temperature. Results are presented obtained from a set of laboratory produced char samples pyrolysed at increasing temperatures with a high resolution between 200 and 1000 °C. The chars were characterized by a molecular marker method for pyrogenic carbon quantification, which additionally provides information about the degree of condensation of chars. At temperatures between 275 and 500°C, which typically are observed during wildfires and thus are relevant for natural char formation, the molecular marker pattern of the chars remains almost constant. In a next step, we analysed changes in the molecular marker patterns of chars from a chronosequence, with BC deposited between 0 and 100 years ago. Based on the data obtained from the laboratory char series, we compare changes in the molecular marker patterns of the chars from the chronosequence over time. These results show if less condensed forms of BC are degraded preferentially and more condensed, aromatic backbone of BC becomes enriched in the soils with time of degradation. Our results provide information about the fate of BC in the environment, which has important implications in the context of carbon sequestration strategies.

  13. [Developing waxy wheat with backcrossing approach and molecular markers-assisted selection].

    PubMed

    Shu, Shou-Gui; Wang, Tao

    2006-05-01

    A series of Chinese Spring Wx loci near-isogenic lines were used to identify the specific bands of 6 STS markers and 1 CAPS marker of Wx genes. After optimizing PCR amplification and separation of PCR products, 3 co-dominant and dominant STS-markers were identified at the Wx-A1, Wx-D1 loci and Wx-B1 loci, respectively, which were used in molecular markers-assisted selection of waxy wheat in our breeding program. A cross between waxy wheat "98Y1441" and variety "Chuanyu 12" was made, and I2-KI dying method was used to select full waxy genotype individual from F2 seeds. The full waxy genotype individual was crossed with recurrent parent "Chuanyu 12". After 5 generations of self-cross and backcross, BC5F2 segregating population was obtained. Using the markers above, 8 Wx genotypes were developed from the BC5F2 population, which follows Mendelian segregation. Among them, there were 2 aabbdd waxy plants whose amylose content in the BC5F3 seeds were 1.81% and 0.82%, respectively. In addition, there were partial waxy plants (AAbbdd and aabbDD) whose amylose content in the BC5F3 seeds were 15.24 % and 17.57%, respectively. Most agricultural traits of the BC5F2 segregating population resembled those of the recurrent parent "Chuanyu 12", and superior to waxy wheat parent "98Y1441". This shows that backcross approach in combination with molecular markers-assisted selection of waxy genes is helpful to develop partial and full waxy wheat with good traits in the waxy wheat breeding program. PMID:16735236

  14. Evaluation of the random amplified polymorphic DNA (RAPD) assay for the detection of DNA damage and mutations.

    PubMed

    Atienzar, Franck A; Venier, Paola; Jha, Awadhesh N; Depledge, Michael H

    2002-11-26

    The random amplified polymorphic DNA (RAPD) assay and related techniques like the arbitrarily primed polymerase chain reaction (AP-PCR) have been shown to detect genotoxin-induced DNA damage and mutations. The changes occurring in RAPD profiles following genotoxic treatments include variation in band intensity as well as gain or loss of bands. However, the interpretation of the molecular events responsible for differences in the RAPD patterns is not an easy task since different DNA alterations can induce similar type of changes. In this study, we evaluated the effects of a number of DNA alterations on the RAPD profiles. Genomic DNA from different species was digested with restriction enzymes, ultrasonicated, treated with benzo[a]pyrene (B[a]P) diol epoxide (BPDE) and the resulting RAPD profiles were evaluated. In comparison to the enzymatic DNA digestions, sonication caused greater changes in the RAPD patterns and induced a dose-related disappearance of the high molecular weight amplicons. A DNA sample substantially modified with BPDE caused very similar changes but amplicons of low molecular weight were also affected. Appearance of new bands and increase in band intensity were also evident in the RAPD profiles generated by the BPDE-modified DNA. Random mutations occurring in mismatch repair-deficient strains did not cause any changes in the banding patterns whereas a single base change in 10-mer primers produced substantial differences. Finally, further research is required to better understand the potential and limitations of the RAPD assay for the detection of DNA damage and mutations. PMID:12438012

  15. Use of molecular markers to compare Fusarium verticillioides pathogenic strains isolated from plants and humans.

    PubMed

    Chang, S C; Macêdo, D P C; Souza-Motta, C M; Oliveira, N T

    2013-01-01

    Fusarium verticillioides is a pathogen of agriculturally important crops, especially maize. It is considered one of the most important pathogens responsible for fumonisin contamination of food products, which causes severe, chronic, and acute intoxication in humans and animals. Moreover, it is recognized as a cause of localized infections in immunocompetent patients and disseminated infections among severely immunosuppressed patients. Several molecular tools have been used to analyze the intraspecific variability of fungi. The objective of this study was to use molecular markers to compare pathogenic isolates of F. verticillioides and isolates of the same species obtained from clinical samples of patients with Fusarium mycoses. The molecular markers that we used were inter-simple sequence repeat markers (primers GTG5 and GACA4), intron splice site primer (primer EI1), random amplified polymorphic DNA marker (primer OPW-6), and restriction fragment length polymorphism-internal transcribed spacer (ITS) from rDNA. From the data obtained, clusters were generated based on the UPGMA clustering method. The amplification products obtained using primers ITS4 and ITS5 and loci ITS1-5.8-ITS2 of the rDNA yielded fragments of approximately 600 bp for all the isolates. Digestion of the ITS region fragment using restriction enzymes such as EcoRI, DraI, BshI, AluI, HaeIII, HinfI, MspI, and PstI did not permit differentiation among pathogenic and clinical isolates. The inter-simple sequence repeat, intron splice site primer, and random amplified polymorphic DNA markers presented high genetic homogeneity among clinical isolates in contrast to the high variability found among the phytopathogenic isolates of F. verticillioides. PMID:24065642

  16. Identification of molecular markers of bipolar cells in the murine retina

    PubMed Central

    Kim, Douglas S; Ross, Sarah E; Trimarchi, Jeffrey M; Aach, John; Greenberg, Michael E; Cepko, Constance L

    2008-01-01

    Retinal bipolar neurons serve as relay interneurons that connect rod and cone photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies essential for correct routing of photoreceptor cell signals to specific postsynaptic amacrine and ganglion cells. The development and physiology of these interneurons have not been completely defined molecularly. Despite previous identification of genes expressed in several bipolar cell subtypes, molecules that mark each bipolar cell type still await discovery. In this report, novel genetic markers of murine bipolar cells were found. Candidates were initially generated by using microarray analysis of single bipolar cells and mining of retinal serial analysis of gene expression (SAGE) data. These candidates were subsequently tested for expression in bipolar cells by RNA in situ hybridization. Ten new molecular markers were identified, five of which are highly enriched in their expression in bipolar cells within the adult retina. Double-labeling experiments using probes for previously characterized subsets of bipolar cells were performed to identify the subtypes of bipolar cells that express the novel markers. Additionally, the expression of bipolar cell genes was analyzed in Bhlhb4 knockout retinas, in which rod bipolar cells degenerate postnatally, to delineate further the identity of bipolar cells in which novel markers are found. From the analysis of Bhlhb4 mutant retinas, cone bipolar cell gene expression appears to be relatively unaffected by the degeneration of rod bipolar cells. Identification of molecular markers for the various subtypes of bipolar cells will lead to greater insights into the development and function of these diverse interneurons. PMID:18260140

  17. Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.).

    PubMed

    Peng, Ze; Gallo, Maria; Tillman, Barry L; Rowland, Diane; Wang, Jianping

    2016-02-01

    Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in genotyping peanut germplasm and breeding materials. PMID:26362763

  18. A note on the rationale for estimating genealogical coancestry from molecular markers

    PubMed Central

    2011-01-01

    Background Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature. Methods We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators. Results The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation. Conclusions Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift. PMID:21749687

  19. 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

  20. Genetic variation in the vulnerable and endemic Monkey Puzzle tree, detected using RAPDs.

    PubMed

    Bekessy, Sarah A; Allnutt, T R; Premoli, A C; Lara, A; Ennos, R A; Burgman, M A; Cortes, M; Newton, A C

    2002-04-01

    Araucaria araucana (Monkey Puzzle), a southern South American tree species of exceptional cultural and economic importance, is of conservation concern owing to extensive historical clearance and current human pressures. Random amplified polymorphic DNA (RAPD) markers were used to characterise genetic heterogeneity within and among 13 populations of this species from throughout its natural range. Extensive genetic variability was detected and partitioned by analysis of molecular variance, with the majority of variation existing within populations (87.2%), but significant differentiation was recorded among populations (12.8%). Estimates of Shannon's genetic diversity and percent polymorphism were relatively high for all populations and provide no evidence for a major reduction in genetic diversity from historical events, such as glaciation. All pairwise genetic distance values derived from analysis of molecular variance (Phi(ST)) were significant when individual pairs of populations were compared. Although populations are geographically divided into Chilean Coastal, Chilean Andes and Argentinean regions, this grouping explained only 1.77% of the total variation. Within Andean groups there was evidence of a trend of genetic distance with increasing latitude, and clustering of populations across the Andes, suggesting postglacial migration routes from multiple refugia. Implications of these results for the conservation and use of the genetic resource of this species are discussed. PMID:11920130

  1. Plasmodium falciparum kelch 13: a potential molecular marker for tackling artemisinin-resistant malaria parasites.

    PubMed

    Mita, Toshihiro; Tachibana, Shin-Ichiro; Hashimoto, Muneaki; Hirai, Makoto

    2016-01-01

    Although artemisinin combination therapies have been deployed as a first-line treatment for uncomplicated malaria in almost all endemic countries, artemisinin-resistant parasites have emerged and have gradually spread across the Greater Mekong subregions. There is growing concern that the resistant parasites may migrate to or emerge indigenously in sub-Saharan Africa, which might provoke a global increase in malaria-associated morbidity and mortality. Therefore, development of molecular markers that enable identification of artemisinin resistance with high sensitivity is urgently required to combat this issue. In 2014, a potential artemisinin-resistance responsible gene, Plasmodium falciparum kelch13, was discovered. Here, we review the genetic features of P. falciparum kelch13 and discuss its related resistant mechanisms and potential as a molecular marker. PMID:26535806

  2. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review.

    PubMed

    Chen, Chih-Ping; Chen, Ming; Su, Yi-Ning; Huang, Jian-Pei; Chern, Schu-Rern; Wu, Peih-Shan; Su, Jun-Wei; Chang, Shun-Ping; Chen, Yu-Ting; Lee, Chen-Chi; Chen, Li-Feng; Pan, Chen-Wen; Wang, Wayseen

    2013-10-15

    We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case. PMID:23933412

  3. The prognostic value of molecular marker analysis in patients treated with trimodality therapy for esophageal cancer.

    PubMed

    Harpole, D H; Moore, M B; Herndon, J E; Aloia, T; D'Amico, T A; Sporn, T; Parr, A; Linoila, I; Allegra, C

    2001-03-01

    The purpose of this study was to define the prognostic value of a group of molecular tumor markers in a well-staged population of patients treated with trimodality therapy for esophageal cancer. The original pretreatment paraffin-embedded endoscopic esophageal tumor biopsy material was obtained from 118 patients treated with concurrent cisplatin + 5-fluorouracil (5-FU) + 45 Gy radiation followed by resection from 1986 until 1997 at the Duke University Comprehensive Cancer Center. Three markers of possible platinum chemotherapy association [metallothionein (MT), glutathione S-transferase-pi (GST-pi), P-glycoprotein (P-gp or multidrug resistance)] and one marker of possible 5-FU association [thymidylate synthase (TS)] were measured using immunohistochemistry. The median cancer-free survival was 25.0 months, with a significantly improved survival for the 38 patients who had a complete response (P < 0.001). High-level expression of GST-pi, P-gp, and TS were associated with a decreased survival. MT was not significant in this population. Multivariate analysis identified high-level expression in two of the platinum markers (GST-pi and P-gp) and the 5-FU marker TS as independent predictors of early recurrence and death. In conclusion, this investigation measured three possible markers associated with platinum and one possible marker associated with 5-FU in a cohort of esophageal cancer patients. Independent prognostic significance was observed, which suggests that it may be possible to predict which patients may benefit most from trimodality therapy. These data need to be reproduced in a prospective investigation. PMID:11297249

  4. Chromatographic measurement of molecular markers of sources of atmospheric aerosol particles.

    PubMed

    Veltkamp, P R; Hansen, K J; Barkley, R M; Sievers, R E

    1996-06-01

    Various organic compounds in aerosol particles in ambient air near a coniferous forest fire in Boulder, Colorado were identified as molecular markers of wood burning and forest fires. Particle samples were collected by filtering small volumes of air. The samples were analysed using thermal desorption followed by gas chromatographic separation and detection, a highly sensitive analytical method. Several compounds unique to softwood combustion were identified in the samples. Additionally, a predominance of odd-carbon-numbered n-alkanes over the corresponding even-carbon-numbered n-alkanes was observed. This predominance is a well-documented molecular pattern indicative of epicutical waxes in plants. PMID:24194378

  5. Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers.

    PubMed

    Almeida, I G; Ianella, P; Faria, M T; Paiva, S R; Caetano, A R

    2013-01-01

    Arapaima gigas (Osteoglossidae) is one of the largest fish species in the Amazon Basin, attaining lengths of over 2.5 m and weights of over 100 kg. Its flesh is prized, and it has great potential for production in aquaculture systems. However, live pirarucu cannot be reliably sexed visually, even after sexual development, since this species does not have clear external sexual dimorphism. Simple and inexpensive methods for sexing immature pirarucu based on DNA markers would facilitate production of this species in commercial operations. We analyzed A. gigas male and female DNA pools with 566 RAPD primers, generating 2609 fragments, with an estimated 1341 segregating polymorphic markers, and an estimated average spacing of 714 kb, which corresponds to less than 0.1% of the species' genome. Two putative sex-specific fragments were initially identified in bulked samples; but they were not confirmed in a study of individual male and female samples. We suggest that A. gigas has developed a non-chromosomal system of sex determination or, alternatively, that the species has undergone a recent loss of the chromosome carrying the sex-determining locus. PMID:24338425

  6. 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

  7. 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...

  8. 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

  9. Evaluation of Pakistan wheat germplasms for stripe rust resistance using molecular markers.

    PubMed

    Sobia, Tabassum; Muhammad, Ashraf; Chen, XianMing

    2010-09-01

    Wheat production in Pakistan is seriously constrained due to rust diseases and stripe rust (yellow) caused by Puccinia striiformis f. sp. tritici, which could limit yields. Thus development and cultivation of genetically diverse and resistant varieties is the most sustainable solution to overcome these diseases. The first objective of the present study was to evaluate 100 Pakistan wheat cultivars that have been grown over the past 60 years. These cultivars were inoculated at the seedling stage with two virulent stripe rust isolates from the United States and two from Pakistan. None of the wheat cultivars were resistant to all tested stripe rust isolates, and 16% of cultivars were susceptible to the four isolates at the seedling stage. The data indicated that none of the Pakistan wheat cultivars contained either Yr5 or Yr15 genes that were considered to be effective against most P. striiformis f. sp. tritici isolates from around the world. Several Pakistan wheat cultivars may have gene Yr10, which is effective against isolate PST-127 but ineffective against PST-116. It is also possible that these cultivars may have other previously unidentified genes or gene combinations. The second objective was to evaluate the 100 Pakistan wheat cultivars for stripe rust resistance during natural epidemics in Pakistan and Washington State, USA. It was found that a higher frequency of resistance was present under field conditions compared with greenhouse conditions. Thirty genotypes (30% of germplasms) were found to have a potentially high temperature adult plant (HTAP) resistance. The third objective was to determine the genetic diversity in Pakistan wheat germplasms using molecular markers. This study was based on DNA fingerprinting using resistance gene analog polymorphism (RGAP) marker analysis. The highest polymorphism detected with RGAP primer pairs was 40%, 50% and 57% with a mean polymorphism of 36%. A total of 22 RGAP markers were obtained in this study. RGAP, simple sequence repeat (SSR) and sequence tagged site (STS) markers were used to determine the presence and absence of some important stripe rust resistance genes, such as Yr5, Yr8, Yr9, Yr15 and Yr18. Of the 60 cultivars analyzed, 17% of cultivars showed a RGAP marker band for Yr9 and 12% of cultivars exhibited the Yr18 marker band. No marker band was detected for Yr5, Yr8 and Yr15, indicating a likely absence of these genes in the tested Pakistan wheat cultivars. Cluster analysis based on molecular and stripe rust reaction data is useful in identifying considerable genetic diversity among Pakistan wheat cultivars. The resistant germplasms identified with 22 RGAP markers and from the resistance evaluations should be useful in developing new wheat cultivars with stripe rust resistance. PMID:21104373

  10. The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: a critical review.

    PubMed

    Atienzar, Franck A; Jha, Awadhesh N

    2006-01-01

    More than 9000 papers using the random amplified polymorphic DNA (RAPD) or related techniques (e.g. the arbitrarily primed polymerase chain reaction (AP-PCR)) have been published from 1990 to 2005. The RAPD method has been initially used to detect polymorphism in genetic mapping, taxonomy and phylogenetic studies and later in genotoxicity and carcinogenesis studies. Despite their extensive use, these techniques have also attracted some criticisms, mainly for lack of reproducibility. In the light of their widespread applications, the objectives of this review are to (1) identify the potential factors affecting the optimisation of the RAPD and AP-PCR assays, (2) critically describe and analyse these techniques in genotoxicity and carcinogenesis studies, (3) compare the RAPD assay with other well used methodologies, (4) further elucidate the impact of DNA damage and mutations on the RAPD profiles, and finally (5) provide some recommendations/guidelines to further improve the applications of the assays and to help the identification of the factors responsible for the RAPD changes. It is suggested that after proper optimisation, the RAPD is a reliable, sensitive and reproducible assay, has the potential to detect a wide range of DNA damage (e.g. DNA adducts, DNA breakage) as well as mutations (point mutations and large rearrangements) and therefore can be applied to genotoxicity and carcinogenesis studies. Nevertheless, the interpretation of the changes in RAPD profiles is difficult since many factors can affect the generation of RAPD profiles. It is therefore important that these factors are identified and taken into account while using these assays. On the other hand, further analyses of the relevant bands generated in RAPD profile allow not only to identify some of the molecular events implicated in the genomic instability but also to discover genes playing key roles, particularly in the initiation and development of malignancy. Finally, to elucidate the potential genotoxic effects of environmental contaminants, a powerful strategy could be firstly to use the RAPD assay as a screening method and secondly to apply more specific methods measuring for instance DNA adducts, gene mutations or cytogenetic effects. It is also envisaged that these assays (i.e. RAPD and related techniques), which reflect effects at whole genome level, would continue to complement the use of emerging technologies (e.g. microarrays which aim to quantify expression of individual genes). PMID:16979375

  11. 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

  12. Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)

    PubMed Central

    Douaihy, Bouchra; Sobierajska, Karolina; Jasińska, Anna Katarzyna; Boratyńska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratyński, 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

  13. A sex-associated sequence identified by RAPD screening in gynogenetic individuals of turbot (Scophthalmus maximus).

    PubMed

    Vale, Luis; Dieguez, Rebeca; Sánchez, Laura; Martínez, Paulino; Viñas, Ana

    2014-03-01

    Understanding the genetic basis of sex determination mechanisms is essential for improving the productivity of farmed aquaculture fish species like turbot (Scophthalmus maximus). In culture conditions turbot males grow slower than females starting from eight months post-hatch, and this differential growth rate is maintained until sexual maturation is reached, being mature females almost twice as big as males of the same age. The goal of this study was to identify sex-specific DNA markers in turbot using comparative random amplified polymorphism DNA (RAPD) profiles in males and females to get new insights of the genetic architecture related to sex determination. In order to do this, we analyzed 540 commercial 10-mer RAPD primers in male and female pools of a gynogenetic family because of its higher inbreeding, which facilitates the detection of associations across the genome. Two sex-linked RAPD markers were identified in the female pool and one in the male pool. After the analysis of the three markers on individual samples of each pool and also in unrelated individuals, only one RAPD showed significant association with females. This marker was isolated, cloned and sequenced, containing two sequences, a microsatellite (SEX01) and a minisatellite (SEX02), which were mapped in the turbot reference map. From this map position, through a comparative mapping approach, we identified Foxl2, a relevant gene related to initial steps of sex differentiation, and Wnt4, a gene related with ovarian development, close to the microsatellite and minisatellite markers, respectively. The position of Foxl2 and Wnt4 was confirmed by linkage mapping in the reference turbot map. PMID:24415295

  14. Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

    PubMed Central

    Liu, Yaling; Zhang, Pengfei; Song, Meiling; Hou, Junling; Qing, Mei; Wang, Wenquan; Liu, Chunsheng

    2015-01-01

    Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice. PMID:26571372

  15. Progesterone 5β-reductase genes of the Brassicaceae family as function-associated molecular markers.

    PubMed

    Munkert, J; Costa, C; Budeanu, O; Petersen, J; Bertolucci, S; Fischer, G; Müller-Uri, F; Kreis, W

    2015-11-01

    This study aimed to define progesterone 5β-reductases (P5βR, EC 1.3.99.6, enone 1,4-reductases) as function-associated molecular markers at the plant family level. Therefore cDNAs were isolated from 25 Brassicaceae species, including two species, Erysimum crepidifolium and Draba aizoides, known to produce cardiac glycosides. The sequences were used in a molecular phylogeny study. The cladogram created is congruent to the existing molecular analyses. Recombinant His-tagged forms of the P5βR cDNAs from Aethionema grandiflorum, Draba aizoides, Nasturtium officinale, Raphanus sativus and Sisymbrium officinale were expressed in E. coli. Enone 1,4-reductase activity was demonstrated in vitro using progesterone and 2-cyclohexen-1-one as substrates. Evidence is provided that functional P5βRs are ubiquitous in the Brassicaceae. The recombinant P5βR enzymes showed different substrate preferences towards progesterone and 2-cyclohexen-1-one. Sequence comparison of the catalytic pocket of the P5βR enzymes and homology modelling using Digitalis lanata P5βR (PDB ID: 2V6G) as template highlighted the importance of the hydrophobicity of the binding pocket for substrate discrimination. It is concluded that P5βR genes or P5βR proteins can be used as valuable function-associated molecular markers to infer taxonomic relationship and evolutionary diversification from a metabolic/catalytic perspective. PMID:26108256

  16. Development of a novel and efficient strategy for practical identification of Pyrus spp (Rosaceae) cultivars using RAPD fingerprints.

    PubMed

    Lin, J; Wang, X C; Chang, Y H; Fang, J G

    2011-01-01

    Accurate and reliable cultivar identification of crop species is essential to guarantee plant material identity for purposes of registration, cultivar protection and production. To facilitate identification of plant cultivars, we developed a novel strategy for efficient recording of DNA molecular fingerprints in genotyped plant individuals. These fingerprints can be used as efficient referential information for quick plant identification. We made a random amplified polymorphic DNA (RAPD) marker analysis of 68 pear cultivars. All pear genotypes could be distinguished by a combination of eight 11-mer primers. The efficiency of the method was further verified by correct identification of four cultivars randomly chosen from the initial 68. The advantages of this identification include use of fewer primers and ease of cultivar separation by the corresponding primers marked on the cultivar identification diagram. The cultivar identification diagram can efficiently serve for pear cultivar identification by readily providing the information needed to separate cultivars. To the best of our knowledge, this is the most efficient strategy for identification of plant varieties using DNA markers; it could be employed for the development of the pear industry and for the utilization of DNA markers to identify other plant species. PMID:21644210

  17. Seasonal abundance of organic molecular markers in urban particulate matter from Philadelphia, PA

    NASA Astrophysics Data System (ADS)

    Li, Min; McDow, Stephen R.; Tollerud, David J.; Mazurek, Monica A.

    Organic molecular markers were measured in airborne particulate matter (PM10) from the City of Philadelphia North Broad Street air quality monitoring site to identify the seasonal abundance of key tracer compounds together with their dominant sources. Daily PM10 samples were collected seasonally in 2000 for four 2-week periods (January, April, August, and October). The North Broad Street site is within a heavily populated location in Philadelphia, PA. A suite of 52 individual organic marker compounds was monitored in the PM10 samples. Molecular markers, homologous compound series, and nonpolar and polar organic compounds were detected at ng m -3 ambient concentrations using gas chromatography/ion trap mass spectrometry (GC/IT MS). Organic diacids (C 3-C 9) and monoacids (C 10-C 30) had seasonal mass concentrations ranging from 91.0 (winter) to 261.8 ng m -3 (summer). Total n-alkanes (C 25-C 33) ranged from 25.9 (spring) to 49.5 ng m -3 (fall), total PAHs from 2.1 ng m -3 (summer) to 4.1 ng m -3 (winter), and total hopanes ranged from 4.0 ng m -3 (winter) to 7.4 ng m -3 (fall). The molecular marker ambient mass concentrations were normalized by the annual average mass of PM10 elemental carbon (EC) for the central Philadelphia area. The ambient mass concentrations to EC and OC ratios ranged from 2.6×10 -3 for total PAHs to EC to 115.3×10 -3 for total n-alkanoic acids to EC, 0.5×10 -3 for total PAHs to OC to 23.8×10 -3 for total n-alkanoic acids to OC. Ambient concentrations of individual markers are similar to other reported levels for metropolitan Los Angeles, CA and Atlanta, GA. Seasonal and daily variations of marker compounds are consistent with motor vehicle exhaust, particularly in winter. Summer concentration patterns indicate the importance of secondary organic aerosol to the PM10 ambient mass.

  18. Prospective molecular markers for the identification of illegally traded angelsharks (Squatina) and dolphin (Sotalia guianensis).

    PubMed

    Falco, 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

  19. Prediction of Genetic Values of Quantitative Traits in Plant Breeding Using Pedigree and Molecular Markers

    PubMed Central

    Crossa, José; Campos, Gustavo de los; Pérez, Paulino; Gianola, Daniel; Burgueño, Juan; Araus, José Luis; Makumbi, Dan; Singh, Ravi P.; Dreisigacker, Susanne; Yan, Jianbing; Arief, Vivi; Banziger, Marianne; Braun, Hans-Joachim

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection (GS) for plant breeding. However, the evaluation of models for GS in real plant populations is very limited. This article evaluates the performance of parametric and semiparametric models for GS using wheat (Triticum aestivum L.) and maize (Zea mays) data in which different traits were measured in several environmental conditions. The findings, based on extensive cross-validations, indicate that models including marker information had higher predictive ability than pedigree-based models. In the wheat data set, and relative to a pedigree model, gains in predictive ability due to inclusion of markers ranged from 7.7 to 35.7%. Correlation between observed and predictive values in the maize data set achieved values up to 0.79. Estimates of marker effects were different across environmental conditions, indicating that genotype × environment interaction is an important component of genetic variability. These results indicate that GS in plant breeding can be an effective strategy for selecting among lines whose phenotypes have yet to be observed. PMID:20813882

  20. Recent trends and perspectives of molecular markers against fungal diseases in wheat

    PubMed Central

    Goutam, Umesh; Kukreja, Sarvjeet; Yadav, Rakesh; Salaria, Neha; Thakur, Kajal; Goyal, Aakash K.

    2015-01-01

    Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40–60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases. PMID:26379639

  1. Recent trends and perspectives of molecular markers against fungal diseases in wheat.

    PubMed

    Goutam, Umesh; Kukreja, Sarvjeet; Yadav, Rakesh; Salaria, Neha; Thakur, Kajal; Goyal, Aakash K

    2015-01-01

    Wheat accounts for 19% of the total production of major cereal crops in the world. In view of ever increasing population and demand for global food production, there is an imperative need of 40-60% increase in wheat production to meet the requirement of developing world in coming 40 years. However, both biotic and abiotic stresses are major hurdles for attaining the goal. Among the most important diseases in wheat, fungal diseases pose serious threat for widening the gap between actual and attainable yield. Fungal disease management, mainly, depends on the pathogen detection, genetic and pathological variability in population, development of resistant cultivars and deployment of effective resistant genes in different epidemiological regions. Wheat protection and breeding of resistant cultivars using conventional methods are time-consuming, intricate and slow processes. Molecular markers offer an excellent alternative in development of improved disease resistant cultivars that would lead to increase in crop yield. They are employed for tagging the important disease resistance genes and provide valuable assistance in increasing selection efficiency for valuable traits via marker assisted selection (MAS). Plant breeding strategies with known molecular markers for resistance and functional genomics enable a breeder for developing resistant cultivars of wheat against different fungal diseases. PMID:26379639

  2. Inhibitory neurons in the anterior piriform cortex of the mouse: classification using molecular markers.

    PubMed

    Suzuki, Norimitsu; Bekkers, John M

    2010-05-15

    The primary olfactory cortex (or piriform cortex, PC) is attracting increasing attention as a model system for the study of cortical sensory processing, yet little is known about inhibitory neurons in the PC. Here we provide the first systematic classification of GABA-releasing interneurons in the anterior PC of mice, based on the expression of molecular markers. Our experiments used GAD67-GFP transgenic mice, in which gamma-aminobutyric acid (GABA)-containing cells are labeled with green fluorescent protein (GFP). We first confirmed, using paired whole-cell recordings, that GFP(+) neurons in the anterior PC of GAD67-GFP mice are functionally GABAergic. Next, we performed immunolabeling of GFP(+) cells to quantify their expression of every possible pairwise combination of seven molecular markers: calbindin, calretinin, parvalbumin, cholecystokinin, neuropeptide Y, somatostatin, and vasoactive intestinal peptide. We found that six main categories of interneurons could be clearly distinguished in the anterior PC, based on the size and laminar location of their somata, intensity of GFP fluorescence, patterns of axonal projections, and expression of one or more of the seven markers. A number of rarer categories of interneurons could also be identified. These data provide a road map for further work that examines the functional properties of the six main classes of interneurons. Together, this information elucidates the cellular architecture of the PC and provides clues about the roles of GABAergic interneurons in olfactory processing. PMID:20235162

  3. 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...

  4. Pulsatilla tongkanensis, a natural hybrid population hybridized with P. Koraiensis based on RAPD and SNPs of Chloroplast DNA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new putative species of Pulsatilla, P. tongkangensis, growing in calcified rock cavities was discovered along the Donggang, Jeongseon Kun, Kangwon Province, Korea. Accessions of P. tongkangensis and P. koreana were characterized with randomly amplified polymorphic DNA (RAPD) markers and single n...

  5. Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

    PubMed Central

    Dziewit, Lukasz; Pyzik, Adam; Romaniuk, Krzysztof; Sobczak, Adam; Szczesny, Pawel; Lipinski, Leszek; Bartosik, Dariusz; Drewniak, Lukasz

    2015-01-01

    Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia. PMID:26217325

  6. Cerebrospinal fluid tau levels are a marker for molecular subtype in sporadic Creutzfeldt-Jakob disease.

    PubMed

    Karch, André; Hermann, Peter; Ponto, Claudia; Schmitz, Matthias; Arora, Amandeep; Zafar, Saima; Llorens, Franc; Müller-Heine, Annika; Zerr, Inga

    2015-05-01

    The molecular subtype of sporadic Creutzfeldt-Jakob disease (sCJD) is an important prognostic marker for patient survival. However, subtype determination is not possible during lifetime. Because the rate of disease progression is associated with the molecular subtype, this study aimed at investigating if total tau, a marker of neuronal death, allows premortem diagnosis of molecular subtype when codon 129 genotype is known. Two hundred ninety-six sCJD patients were tested for their cerebrospinal fluid total tau level at the time of diagnosis and were investigated for their sCJD subtype postmortem. There was a significant association between tau levels and the prion protein type in patients with codon 129 MM (p < 0.001), MV (p = 0.004), and VV (p = 0.001) genotype. Receiver operating characteristic analyses showed values of area under the curve of 0.76-0.80 for the different genotypes indicating a good diagnostic validity of the test. Total tau can be used as a diagnostic test for the assessment of prion protein type when codon 129 genotype is known. It provides valuable information for physicians and next of kin about the further course of disease. PMID:25749129

  7. [Molecular Prognostic Markers and Their Clinical Relevance in Chronic Lymphocytic Leukemia].

    PubMed

    Navrkalová, V; Kantorová, B; Jarošová, M; Pospíšilová, Š

    2015-01-01

    Chronic lymphocytic leukemia is the most common leukemia in Western countries affecting particularly elderly adults. Despite the constantly improving therapy options, chronic lymphocytic leukemia is still an incurable disease owing to considerable clinical and bio-logical heterogeneity. Pathogenesis of chronic lymphocytic leukemia is not fully understood; however, aberrant antigenic stimulation, apoptosis deregulation and microenvironmental interactions play a crucial role in disease development. The most important molecular prognostic markers with clinical relevance include mutation status of heavychain immunoglobulin genes (IGHV), presence of cytogenetic aberrations and TP53 and ATM gene mutations. Recent implementation of next generation sequencing technologies has enabled more accurate analysis of both wellestablished and novel potential prognostic markers. The most relevant candidates are mutations in SF3B1, NOTCH1 and BIRC3 genes, which are now intensively studied with respect to their clinical importance. The other examined molecular mechanisms of chronic lympho-cytic leukemia pathogenesis include deregulation of B cell receptor signalization and abnormal regulation of gene expression by microRNA. The precise characterization of molecular abnormalities improves the risk stratification of chronic lymphocytic leukemia patients, which could possibly benefit from new treatment approaches. PMID:26489496

  8. Molecular marker approaches for tracking redox damage and protection in keratins.

    PubMed

    Dyer, Jolon M; Cornellison, Charisa D; Grosvenor, Anita J; Clerens, Stefan; Deb-Choudhury, Santanu

    2014-01-01

    There is increasing awareness of the importance of reductive and oxidative (redox) protein damage in protein-based materials including, hair, wool, nails, and skin. Light-induced damage to protein-based materials is of particular concern because of its impact on age-related degradation and product life spans. Consequently, cosmetic applications frequently target hair and skin restoration, where the integrity of the constituent filamentous proteins is essential to a healthy appearance. The keratins constitute an important subset of the structural proteins within skin, hair, and wool. We will introduce a means to assess damage to this important group of proteins at the molecular level, utilizing proteomic techniques to track the formation or degradation of sensitive peptides within intermediate filament proteins. The degradation of three molecular markers of redox damage, the peptides SFGYR, LASDDFR, and DVEEWYIR, along with the formation of their oxidized products, is demonstrated after exposure to ultraviolet A, ultraviolet B, and blue light. The method is shown to be suitable for evaluating the protective effect of treatments, as lower levels of oxidative markers were observed after the application of a protective fiber treatment. Molecular-level redox tracking will allow more targeted design and evaluation of protection and repair treatments for protein systems. PMID:24602820

  9. A comparison analysis of Listeria monocytogenes isolates recovered from chicken carcasses and human by using RAPD PCR

    PubMed Central

    Zeinali, Tayebeh; Jamshidi, Abdolah; Rad, Mehrnaz; Bassami, Mohammadreza

    2015-01-01

    Chicken meat is a valuable source of protein and consumption of it continues to rise day to day. The aim of the present study was to evaluate the genetic homogeneity of Listeria monocytogenes (L. monocytogenes) isolates obtained from chicken carcasses and human. Random Amplification of Polymorphic DNA (RAPD) PCR with three different primers were used to analyze the 31 L. monocytogenes isolates recovered from human and chicken carcasses. Primers were D8635, HLWL74, and OPM01. Scanned images of RAPD-PCR products were analyzed using Photocap software. The data were analyzed by SPSS software using Jaccard distance matrix and Ward’s hierarchical cluster technique, isolates were clustered and displayed in dendrogram form. Molecular serotyping of the isolate was done. Most of the isolates were grouped into two serogroup IIb and IIa. However some of them were serotyped as IVb serogroup. In the RAPD assay, all of the primers gave amplified bands. Among these three primers, OPM01 had the most discriminatory power due to producing polymorph bands. Totally, 75 different bands with sizes ranging from 150 bp to 3300 bp, were produced. The dendrogram for Listeria monocytogenes isolates from chicken and human showed five different clusters (designed as A to E). In this study, there wasn’t any association between food and human isolates of L. monocytogenes. RAPD has more discriminatory power than serotyping. On the other hand, there were different RAPD profiles among isolates of the same serotype and also, similar RAPD profile among different serotypes were observed. PMID:26309714

  10. 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.

  11. Mitochondrial DNA and RAPD polymorphisms in the haploid mite Brevipalpus phoenicis (Acari: Tenuipalpidae).

    PubMed

    Rodrigues, J C V; Gallo-Meagher, M; Ochoa, R; Childers, C C; Adams, B J

    2004-01-01

    Brevipalpus phoenicis (Geijskes) (Acari: Tenuipalpidae) is recognized as the vector of citrus leprosis virus that is a significant problem in several South American countries. Citrus leprosis has been reported from Florida in the past but no longer occurs on citrus in North America. The disease was recently reported in Central America, suggesting that B. phoenicis constitutes a potential threat to the citrus industries of North America and the Caribbean. Besides B. phoenicis, B. obovatus Donnadieu, and B. californicus (Banks) have been incriminated as vectors of citrus leprosis virus and each species has hundreds of host plants. In this study, Brevipalpus mite specimens were collected from different plants, especially citrus, in the States of Florida (USA) and São Paulo (Brazil), and reared on citrus fruit under standard laboratory conditions. Mites were taken from these colonies for DNA extraction and for morphological species identification. One hundred and two Random Amplified Polymorphic DNA (RAPD) markers were scored along with amplification and sequencing of a mitochondrial cytochrome oxidase subunit I gene fragment (374 bp). Variability among the colonies was detected with consistent congruence between both molecular data sets. The mites from the Florida and Brazilian colonies were morphologically identified as belonging to B. phoenicis, and comprise a monophyletic group. These colonies could be further diagnosed and subdivided geographically by mitochondrial DNA analysis. PMID:15651525

  12. TMED6-COG8 is a novel molecular marker of TFE3 translocation renal cell carcinoma.

    PubMed

    Xu, Yongcan; Rao, Qiu; Xia, Qiuyuan; Shi, Shanshan; Shi, Qunli; Ma, Henghui; Lu, Zhenfeng; Chen, Hui; Zhou, Xiaojun

    2015-01-01

    TFE3 translocation renal cell carcinoma is a highly aggressive malignancy which often occurs primarily in children and young adults. The pathognomonic molecular lesion in this subtype is a translocation event involving the TFE3 transcription factor at chromosome Xp11.2. Hence, the pathological diagnosis of an Xp11.2 translocation RCC is based upon morphology, TFE3 immunohistochemistry, or genetic analyses. However, due to the false-positive immunoreactivity for TFE3 IHC and expensive for TFE3 break-apart FISH assay, additional molecular markers are necessary to help provide early diagnose and individualization treatment. Owing to recent advances in microarray and RNA-Seq, Pflueger et al. have discovered that TMED6-COG8 is dramatically increased in TFE3 translocation RCCs, compared with clear cell RCCs and papillary RCCs, implying that TMED6-COG8 might be a new molecular tumor marker of TFE3 translocation RCCs. To extend this observation, we firstly validated the TMED6-COG8 expression level by qRT-PCR in RCCs including Xp11.2 translocation RCCs (n=5), clear cell RCCs (n=7) and papillary RCCs (n=5). Then, we also examined the expression level of TMED6-COG8 chimera in Xp11.2 translocation alveolar soft part sarcoma. We found that TMED6-COG8 chimera expression level was higher in Xp11.2 translocation RCCs than in ASPS (P<0.05). What's more, the expression levels of TMED6-COG8 chimera in esophagus cancers (n=32), gastric cancers (n=11), colorectal cancers (n=12), hepatocellular carcinomas (n=10) and non-small-cell lung cancers (n=12) were assessed. Unexpectedly, TMED6-COG8 chimera was decreased in these five human types. Therefore, our observations from this study indicated that TMED6-COG8 chimera might act as a novel diagnostic marker in Xp11.2 translocation RCCs. PMID:26045774

  13. Molecular Markers Predict Distant Metastases After Adjuvant Chemoradiation for Rectal Cancer

    SciTech Connect

    Kim, Jun Won; Kim, Yong Bae; Choi, Jun Jeong; Koom, Woong Sub; Kim, Hoguen; Kim, Nam-Kyu; Ahn, Joong Bae; Lee, Ikjae; Cho, Jae Ho; Keum, Ki Chang

    2012-12-01

    Purpose: The outcomes of adjuvant chemoradiation for locally advanced rectal cancer are nonuniform among patients with matching prognostic factors. We explored the role of molecular markers for predicting the outcome of adjuvant chemoradiation for rectal cancer patients. Methods and Materials: The study included 68 patients with stages II to III rectal adenocarcinoma who were treated with total mesorectal excision and adjuvant chemoradiation. Chemotherapy based on 5-fluorouracil and leucovorin was intravenously administered each month for 6-12 cycles. Radiation therapy consisted of 54 Gy delivered in 30 fractions. Immunostaining of surgical specimens for COX-2, EGFR, VEGF, thymidine synthase (TS), and Raf kinase inhibitor protein (RKIP) was performed. Results: The median follow-up was 65 months. Eight locoregional (11.8%) and 13 distant (19.1%) recurrences occurred. Five-year locoregional failure-free survival (LRFFS), distant metastasis-free survival (DMFS), disease-free survival (DFS), and overall survival (OS) rates for all patients were 83.9%, 78.7%, 66.7%, and 73.8%, respectively. LRFFS was not correlated with TNM stage, surgical margin, or any of the molecular markers. VEGF overexpression was significantly correlated with decreased DMFS (P=.045), while RKIP-positive results were correlated with increased DMFS (P=.025). In multivariate analyses, positive findings for COX-2 (COX-2+) and VEGF (VEGF+) and negative findings for RKIP (RKIP-) were independent prognostic factors for DMFS, DFS, and OS (P=.035, .014, and .007 for DMFS; .021, .010, and <.0001 for DFS; and .004, .012, and .001 for OS). The combination of both COX-2+ and VEGF+ (COX-2+/VEGF+) showed a strong correlation with decreased DFS (P=.007), and the combinations of RKIP+/COX-2- and RKIP+/VEGF- showed strong correlations with improved DFS compared with the rest of the patients (P=.001 and <.0001, respectively). Conclusions: Molecular markers can be valuable in predicting treatment outcome of adjuvant chemoradiation for rectal cancer patients.

  14. Oral keratinocyte stem/progenitor cells: specific markers, molecular signaling pathways and potential uses.

    PubMed

    Calenic, Bogdan; Greabu, Maria; Caruntu, Constantin; Tanase, Cristiana; Battino, Maurizio

    2015-10-01

    Oral keratinocyte stem cells reside in the basal layers of the oral epithelium, representing a minor population of cells with a great potential to self-renew and proliferate over the course of their lifetime. As a result of the potential uses of oral keratinocyte stem cells in regenerative medicine and the key roles they play in tissue homeostasis, inflammatory conditions, wound healing and tumor initiation and progression, intense scientific efforts are currently being undertaken to identify, separate and reprogram these cells. Although currently there is no specific marker that can characterize and isolate oral keratinocyte stem cells, several suggestions have been made. Thus, different stem/progenitor-cell subpopulations have been categorized based on combinations of positive and/or negative membrane-surface markers, which include integrins, clusters of differentiation and cytokeratins. Important advances have also been made in understanding the molecular pathways that govern processes such as self-renewal, differentiation, proliferation, wound healing and programmed cell death. A thorough understanding of stem-cell biology and the molecular players that govern cellular fate is paramount in the quest for using stem-cell-derived therapies in the treatment of various oral pathologies. The current review focuses on recent advances in understanding the molecular signaling pathways coordinating the behavior of these cells and in identifying suitable markers used for their isolation and characterization. Special emphasis will also be placed on the roles played by oral keratinocyte stem and progenitor cells in normal and diseased oral tissues and on their potential uses in the fields of general medicine and dentistry. PMID:26252402

  15. Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations.

    PubMed

    Heckenberger, M; Bohn, M; Frisch, M; Maurer, H P; Melchinger, A E

    2005-08-01

    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, marker density, and distribution, as well as the degree of polymorphism between the parental inbreds on the distribution of GS between parental inbreds and their progenies [GS(P1,O)] derived from F2 and different backcross populations and (2) evaluate these factors with regard to the power for distinguishing F2- versus BC1- and BC1- versus BC2-derived lines with molecular markers. We developed an approach based on statistical test theory for the identification of EDVs with molecular markers. Standard deviations and overlaps of distributions of GS(P1,O) of F2-, BC1-, and BC2-derived lines were smaller with (1) increasing chromosome number and length, (2) increasing marker density, and (3) uniformly instead of randomly distributed markers, approaching a lower boundary determined by the genetic parameters. The degree of polymorphism between the parental inbreds influenced the power only if the remaining number of polymorphic markers was low. Furthermore, suggestions are made for (1) determining the number of markers required to ascertain a given power and (2) EDV identification procedures. PMID:15918007

  16. [Molecular-biological markers as prognostic factors in breast cancer of I-IIA stage].

    PubMed

    Stepanova, E V; Zagrekova, E I; Ermilova, V D; Turbin, A D; Petrovichev, N N; Vysotskaia, I V; Dbar, Zh N; Pashchenko, N V; Baryshnikov, A Iu; Lichinitser, M R

    2003-01-01

    The study of molecular-biological markers for prediction of recurrence-free survival in breast cancer stage I-IIA demonstrates that high expression of thymidilate synthetase and high maximal density of microvessels are prognostically effective and that the prognosis is influenced by expression of both Bcl-2 and Bax. Low recurrence-free survival was observed in Bcl-2-/Bax patients (31%, median 44 months) while such survival was high in Bcl-2+/Bax patients (86%, median was not reached). The findings can be used for prognostication of a breast cancer clinical course. PMID:12879604

  17. Molecular Markers for Prostate Cancer in Formalin-Fixed Paraffin-Embedded Tissues

    PubMed Central

    García, Marta; Montes, Melania; Oliván, Mireia; Rigau, Marina; Colás, Eva; de Torres, Inés; Morote, Juan; Reventós, Jaume

    2013-01-01

    Prostate cancer (PCa) is the most frequently diagnosed type of cancer in developed countries. The decisive method of diagnosis is based on the results of biopsies, morphologically evaluated to determine the presence or absence of cancer. Although this approach leads to a confident diagnosis in most cases, it can be improved by using the molecular markers present in the tissue. Both miRNAs and proteins are considered excellent candidates for biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues, due to their stability over long periods of time. In the last few years, a concerted effort has been made to develop the necessary tools for their reliable measurement in these types of samples. Furthermore, the use of these kinds of markers may also help in establishing tumor grade and aggressiveness, as well as predicting the possible outcomes in each particular case for the different treatments available. This would aid clinicians in the decision-making process. In this review, we attempt to summarize and discuss the potential use of microRNA and protein profiles in FFPE tissue samples as markers to better predict PCa diagnosis, progression, and response to therapy. PMID:24371818

  18. Population structure and genotypic variation of Crataegus pontica inferred by molecular markers.

    PubMed

    Rahmani, Mohammad-Shafie; Shabanian, Naghi; Khadivi-Khub, Abdollah; Woeste, Keith E; Badakhshan, Hedieh; Alikhani, Leila

    2015-11-01

    Information about the natural patterns of genetic variability and their evolutionary bases are of fundamental practical importance for sustainable forest management and conservation. In the present study, the genetic diversity of 164 individuals from fourteen natural populations of Crataegus pontica K.Koch was assessed for the first time using three genome-based molecular techniques; inter-retrotransposon amplified polymorphism (IRAP); inter-simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism. IRAP, ISSR and SCoT analyses yielded 126, 254 and 199 scorable amplified bands, respectively, of which 90.48, 93.37 and 83.78% were polymorphic. ISSR revealed efficiency over IRAP and SCoT due to high effective multiplex ratio, marker index and resolving power. The dendrograms based on the markers used and combined data divided individuals into three major clusters. The correlation between the coefficient matrices for the IRAP, ISSR and SCoT data was significant. A higher level of genetic variation was observed within populations than among populations based on the markers used. The lower divergence levels depicted among the studied populations could be seen as evidence of gene flow. The promotion of gene exchange will be very beneficial to conserve and utilize the enormous genetic variability. PMID:26143753

  19. 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

  20. Multigene assays and molecular markers in breast cancer: systematic review of health economic analyses.

    PubMed

    Rouzier, Roman; Pronzato, Paolo; Chéreau, Elisabeth; Carlson, Josh; Hunt, Barnaby; Valentine, William J

    2013-06-01

    Breast cancer is the most common female cancer and is associated with a significant clinical and economic burden. Multigene assays and molecular markers represent an opportunity to direct chemotherapy only to patients likely to have significant benefit. This systematic review examines published health economic analyses to assess the support for adjuvant therapy decision making. Literature searches of PubMed, the Cochrane Library, and congress databases were carried out to identify economic evaluations of multigene assays and molecular markers published between 2002 and 2012. After screening and data extraction, study quality was assessed using the Quality of Health Economic Studies instrument. The review identified 29 publications that reported evaluations of two assays: Oncotype DX(®) and MammaPrint. Studies of both tests provided evidence that their routine use was cost saving or cost-effective versus conventional approaches. Benefits were driven by optimal allocation of adjuvant chemotherapy and reduction in chemotherapy utilization. Findings were sensitive to variation in the frequency of chemotherapy prescription, chemotherapy costs, and patients' risk profiles. Evidence suggests that multigene assays are likely cost saving or cost-effective relative to current approaches to adjuvant therapy. They should benefit decision making in early-stage breast cancer in a variety of settings worldwide. PMID:23722312

  1. Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori

    PubMed Central

    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 830.81050bp was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.51950bp and 825.9710bp showed significant association with floss content and TLD. These markers were segregated in F2 generation and Chi-square test confirmed (χ2 = ~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

  2. DNA variation and polymorphism in Tunisian plum species (Prunus spp): contribution of flow cytometry and molecular markers.

    PubMed

    Ben Tamarzizt, H; Walker, D; Ben Mustapha, S; Abdallah, D; Baraket, G; Salhi Hannachi, A; Zehdi Azzouzi, S

    2015-01-01

    Plums (Prunus spp) are among the most important stone fruit crops in the world. European (Prunus domestica) and Japanese (Prunus salicina) plums are characterized by different levels of ploidy. Because genetic variability is the prerequisite for any plant-breeding program, we aimed to establish the taxonomic status of Tunisian plums and study their genetic variability. The nuclear DNA content of 45 wild and cultivated Tunisian plums was determined by flow cytometry. Two arbitrary primers (AD10, AD17) were used to elaborate SCAR markers useful to identify plum species. Three wild trees, Zenou 1, Zenou 6, and Zenou 3, which had 2C nuclear DNA contents of 1.99, 2.05, and 2.13 pg, were shown to be hexaploid (2n = 6x = 48), whereas the others were diploid (2n = 2x = 16). These results suggest that the three hexaploid wild plums belong to Prunus insititia, and the others belong to Prunus salicina. No SCAR markers were revealed using the AD10 and AD17 RAPD primers in relation to the ploidy of plums. We note also that AD17 primer appears to be the most informative concerning the genetic diversity. Morphological and pomological traits revealed similarity between introduced and Tunisian plum cultivars. Despite the significant morphological differences found, all the cultivars studied belong to P. salicina. The information obtained in this analysis provided on local plum genetic resources will be helpful to establish a core collection, to evaluate genetic diversity, and to initiate an improvement and selection program. PMID:26782451

  3. Genetic molecular analysis of Coffea arabica (Rubiaceae) hybrids using SRAP markers.

    PubMed

    Mishra, Manoj Kumar; Suresh, Narayana; Bhat, Asha M; Suryaprakash, Nayani; Kumar, Saya Satheesh; Kumar, Anil; Jayarama

    2011-06-01

    In Coffea arabica (arabica coffee), the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP) is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. PMID:21717853

  4. 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

  5. Molecular markers define progressing stages of phosphorus limitation in the nitrogen-fixing cyanobacterium, Crocosphaera.

    PubMed

    Pereira, Nicole; Shilova, Irina N; Zehr, Jonathan P

    2016-04-01

    Crocosphaera watsonii is a marine cyanobacterium that frequently inhabits low phosphate environments in oligotrophic oceans. While C. watsonii has the ability to fix atmospheric nitrogen, its growth may be limited by availability of phosphorus. Biomarkers that indicate cellular phosphorus status give insight into how P-limitation can affect the distribution of nitrogen-fixing cyanobacterial populations. However, adaptation to phosphorus stress is complex and one marker may not be sufficient to determine when an organism is P-limited. In this study, we characterized the transcription of key genes, activated during phosphorus stress in C. watsonii WH8501, to determine how transcription changed during the phosphorus stress response. Transcription of pstS, which encodes a high-affinity phosphate binding protein, was discovered to be quickly up-regulated in phosphorus-depleted cells as an immediate stress response; however, its transcription declined after a period of phosphorus starvation. In addition, diel regulation of pstS in C. watsonii WH8501 complicates the interpretation of this marker in field applications. Transcription of the gene coding for the arsenite efflux protein, arsB, was upregulated after pstS in phosphorus limited cells, but it remained upregulated at later stages of phosphorus limitation. These results demonstrate that a single molecular marker does not adequately represent the entire phosphorus stress response in C. watsonii WH8501. Using both markers, the variations in transcriptional response over a range of degrees of phosphorus limitation may be a better approach for defining cellular phosphorus status. PMID:27037592

  6. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers.

    PubMed

    Ammar, Megahed H; Alghamdi, Salem S; Migdadi, Hussein M; Khan, Muhammad A; El-Harty, Ehab H; Al-Faifi, Sulieman A

    2015-05-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010-11 and 2011-12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  7. The interrelationship of biological marker maturity parameters and molecular yields during contact metamorphism

    NASA Astrophysics Data System (ADS)

    Bishop, A. N.; Abbott, G. D.

    1993-08-01

    Jurassic siltstone samples were collected, on a centimetre scale, as a function of increasing distance from a dolerite dyke (Isle of Skye, northwest Scotland). The constant origin and type of the organic matter in this single lithological horizon is indicated by organic petrological observations as well as organic geochemical analyses. Therefore, changes in biological marker distributions, with distance from the dyke contact, can be unequivocally correlated with the thermal influence of the intrusion. The vitrinite reflectance ( R0 Average) values of these samples increase gradually from 0.35% to 3.60% as the dyke contact is approached. Four classical biological marker maturity parameters ( 20S/(20S + 20R), TA/(TA + MA), C 20/(C 20 + C 28) , and 22S/(22S + 22R)). have been measured from GCMS analyses of the sample extracts. Changes in these molecular parameters were compared with changes in the concentrations of the individual biological marker compounds, expressed relative to mass of rock extracted. This comparison revealed that these molecular parameters are not governed by the conventional productreactant relationships (chiral isomerisation, aromatisation or side-chain cracking reactions) operating solely in the free saturated or aromatic hydrocarbon structures. Release/formation from macromolecular and/or functionalised moieties (hydrocarbon or non-hydrocarbon) followed by compound loss provide an alternative paradigm in all four cases in this particular thermal regime. Direct chiral isomerisation in the free sterane or homohopane cannot, however, be completely ruled out as a contributor to an admixture of processes. Similarly, aromatisation in the free hydrocarbon fraction may account for a proportion of the triaromatic steroids.

  8. 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

  9. Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers

    PubMed Central

    Ammar, Megahed H.; Alghamdi, Salem S.; Migdadi, Hussein M.; Khan, Muhammad A.; El-Harty, Ehab H.; Al-Faifi, Sulieman A.

    2015-01-01

    Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010–11 and 2011–12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5 cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8 g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r = 0.01, p > 0.54 and r = 0.26, p < 0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels. PMID:25972757

  10. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers

    PubMed Central

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8–27.6% and 9.5–23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5–26.5% and 7.5%–15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48–49% and 30.5–45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321–0.854 and 0.299–0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  11. Molecular Assortment of Lens Species with Different Adaptations to Drought Conditions Using SSR Markers.

    PubMed

    Singh, Dharmendra; Singh, Chandan Kumar; Tomar, Ram Sewak Singh; Taunk, Jyoti; Singh, Ranjeet; Maurya, Sadhana; Chaturvedi, Ashish Kumar; Pal, Madan; Singh, Rajendra; Dubey, Sarawan Kumar

    2016-01-01

    The success of drought tolerance breeding programs can be enhanced through molecular assortment of germplasm. This study was designed to characterize molecular diversity within and between Lens species with different adaptations to drought stress conditions using SSR markers. Drought stress was applied at seedling stage to study the effects on morpho-physiological traits under controlled condition, where tolerant cultivars and wilds showed 12.8-27.6% and 9.5-23.2% reduction in seed yield per plant respectively. When juxtaposed to field conditions, the tolerant cultivars (PDL-1 and PDL-2) and wild (ILWL-314 and ILWL-436) accessions showed 10.5-26.5% and 7.5%-15.6% reduction in seed yield per plant, respectively under rain-fed conditions. The reductions in seed yield in the two tolerant cultivars and wilds under severe drought condition were 48-49% and 30.5-45.3% respectively. A set of 258 alleles were identified among 278 genotypes using 35 SSR markers. Genetic diversity and polymorphism information contents varied between 0.321-0.854 and 0.299-0.836, with mean value of 0.682 and 0.643, respectively. All the genotypes were clustered into 11 groups based on SSR markers. Tolerant genotypes were grouped in cluster 6 while sensitive ones were mainly grouped into cluster 7. Wild accessions were separated from cultivars on the basis of both population structure and cluster analysis. Cluster analysis has further grouped the wild accessions on the basis of species and sub-species into 5 clusters. Physiological and morphological characters under drought stress were significantly (P = 0.05) different among microsatellite clusters. These findings suggest that drought adaptation is variable among wild and cultivated genotypes. Also, genotypes from contrasting clusters can be selected for hybridization which could help in evolution of better segregants for improving drought tolerance in lentil. PMID:26808306

  12. Combustion inputs into a terrestrial archive over 265 years as evidenced by BPCA molecular markers

    NASA Astrophysics Data System (ADS)

    Hanke, Ulrich M.; Eglinton, Timothy I.; Wiedemeier, Daniel B.; Schmidt, Michael W. I.

    2015-04-01

    Pyrogenic organic matter (PyOM) such as char and soot is produced during the incomplete combustion of biomass and fossil fuel. It is composed of condensed aromatic structures and can resist degradation processes, maybe over long periods of time. Land-use changes, industrial activity and its transport by wind and water affect the fluxes of PyOM from the source to its sedimentary archive. Investigating environmental PyOM with the molecular marker benzene polycarboxylic acid (BPCA) method provides various information about quantity, quality (BPCA distribution pattern) and about its isotopic composition (13C and 14C). Assessing PyOM quality can indicate whether it is mostly combustion condensate (soot) or combustion residue (charcoal) and potentially allow source apportionment. Our study area is the Pettaquamscutt River catchment area (35 km2), Rhode Island, U.S.A. It is located down-wind of industrial areas recording deposition of long-distance atmospheric transport as well as local catchment inputs, both from natural and anthropogenic sources. We investigated 50 samples of a sediment record over a time span of 265 years (1733-1998 AD). Previous investigations provided information on the age of deposition, the content of polycyclic aromatic hydrocarbons (PAH) as well as of the radiocarbon contents of total organic carbon (TOC) and PAH (Lima, 2004). We used the BPCA molecular marker method to quantify and characterize PyOM in the same record. First results show that quantity and quality of PyOM change over 265 years. Our investigation aims at understanding how different sources of PyOM are reflected in terrestrial archives by comparing the results of BPCA with radiocarbon-dated TOC and PAH records. Among other aspects, the PAH record reflects the Great Depression and the 1970s oil embargo in North America. We interpret the BPCA distribution patterns regarding the simultaneous shift of dominant fuels including wood, coal, petroleum and gas. Future work will include compound-specific radiocarbon analysis of BPCA molecular markers to improve our understanding of the sources and residence time of PyOM. References Lima, A.L.C., 2004. Molecular and Isotopic Records of Combustion Inputs to the Environment Over the Last 250 Years, doctoral dissertation, Massachusetts Institute of Technology/Woods Hole Oceanographic Institution (MIT/WHOI).

  13. Source apportionment of primary and secondary organic aerosols using positive matrix factorization (PMF) of molecular markers

    NASA Astrophysics Data System (ADS)

    Zhang, YuanXun; Sheesley, Rebecca J.; Schauer, James J.; Lewandowski, Michael; Jaoui, Mohammed; Offenberg, John H.; Kleindienst, Tadeusz E.; Edney, Edward O.

    Monthly average ambient concentrations of more than eighty particle-phase organic compounds, as well as total organic carbon (OC) and elemental carbon (EC), were measured from March 2004 through February 2005 in five cities in the Midwestern United States. A multi-variant source apportionment receptor model, positive matrix factorization (PMF), was applied to explore the average source contributions to the five sampling sites using molecular markers for primary and secondary organic aerosols (POA, SOA). Using the molecular makers in the model, POA and SOA were estimated for each month at each site. Three POA factors were derived, which were dominated by primary molecular markers such as EC, hopanes, steranes, and polycyclic aromatic hydrocarbons (PAHs), and which represented the following POA sources: urban primary sources, mobile sources, and other combustion sources. The three POA sources accounted for 57% of total average ambient OC. Three factors, characterized by the presence of reaction products of isoprene, α-pinene and β-caryophyllene, and displaying distinct seasonal trends, were consistent with the characteristics of SOA. The SOA factors made up 43% of the total average measured OC. The PMF-derived results are in good agreement with estimated SOA concentrations obtained from SOA to tracer yield estimates obtained from smog chamber experiments. A linear regression comparing the smog chamber yield estimates and the PMF SOA contributions had a regression slope of 1.01 ± 0.07 and an intercept of 0.19 ± 0.10 μg OC m -3 (adjusted R2 of 0.763, n = 58).

  14. 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

  15. Molecular Characterization of Invasive and Noninvasive Campylobacter jejuni and Campylobacter coli Isolates

    PubMed Central

    Carvalho, Alexandro C. T.; Ruiz-Palacios, Guillermo M.; Ramos-Cervantes, Pilar; Cervantes, Luz-Elena; Jiang, Xi; Pickering, Larry K.

    2001-01-01

    Campylobacter jejuni is one of the most common causes of bacterial diarrhea worldwide and is the primary bacterial cause of food-borne illness. Adherence to and invasion of epithelial cells are the most important pathogenic mechanisms of Campylobacter diarrhea. Molecular characterization of invasive and noninvasive Campylobacter isolates from children with diarrhea and symptom-free children was performed by random amplified polymorphic DNA techniques (RAPD). A distinct RAPD profile with a DNA band of 1.6 kb was observed significantly more frequently among invasive (63%) than among noninvasive (16%) Campylobacter isolates (P = 0.000005). The 1.6-kb band was named the invasion-associated marker (IAM). Using specifically designed primers, a fragment of 518 bp of the iam locus was amplified in 85% of invasive and 20% of noninvasive strains (P = 0.0000000). Molecular typing with a PCR-restriction fragment length polymorphism assay which amplified the entire iam locus showed a HindIII restriction fragment polymorphism pattern associated mainly with invasive strains. Although cluster analysis of the RAPD fingerprinting showed genetic diversity among strains, two main clusters were identified. Cluster I comprised significantly more pathogenic and invasive isolates, while cluster II grouped the majority of nonpathogenic, noninvasive isolates. These data indicate that most of the invasive Campylobacter strains could be differentiated from noninvasive isolates by RAPD analysis and PCR using specific primers that amplify a fragment of the iam locus. PMID:11283056

  16. 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

  17. Differentiation of beauveria bassiana isolates from the darkling beetle, alphitobius diaperinus, using isozyme and RAPD analyses

    PubMed

    Castrillo; Brooks

    1998-11-01

    Two natural genetic markers, isozymes and RAPD, were utilized to differentiate 24 strains of Beauveria bassiana (Deuteromycotina: Hyphomycetes) collected from the darkling beetle, Alphitobius diaperinus (Coleoptera: Tenebrionidae), from poultry houses in North Carolina and West Virginia. Nine enzyme systems were screened, of which alkaline phosphatase, alpha- and beta-esterase, and glucose phosphate isomerase gave well-resolved, scorable bands. A total of 26 isozyme bands was generated by these four enzymes which partitioned the 24 strains into 14 classes. Three classes were shared by two or more strains while the rest of the strains had distinct electrophoretic profiles. Ten RAPD primers, selected from 72 that were screened, produced 141 bands from the 24 strains and separated each as a unique class. While both systems were able to detect variation present among the 24 strains from different regions in North Carolina and West Virginia, RAPD markers provided better resolution of the differences between strains. Variation was detected not only within and among strains from different regions but also among strains collected from a given insect host. Copyright 1998 Academic Press. PMID:9784340

  18. A slippery molecular assembly allows water as a self-erasable security marker

    PubMed Central

    Thirumalai, Rajasekaran; Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Ajayaghosh, Ayyappanpillai

    2015-01-01

    Protection of currency and valuable documents from counterfeit continues to be a challenge. While there are many embedded security features available for document safety, they are not immune to forgery. Fluorescence is a sensitive property, which responds to external stimuli such as solvent polarity, temperature or mechanical stress, however practical use in security applications is hampered due to several reasons. Therefore, a simple and specific stimuli responsive security feature that is difficult to duplicate is of great demand. Herein we report the design of a fluorescent molecular assembly on which water behaves as a self-erasable security marker for checking the authenticity of documents at point of care. The underlying principle involves the disciplined self-assembly of a tailor-made fluorescent molecule, which initially form a weak blue fluorescence (λem = 425 nm, Φf = 0.13) and changes to cyan emission (λem = 488 nm,Φf = 0.18) in contact with water due to a reversible molecular slipping motion. This simple chemical tool, based on the principles of molecular self-assembly and fluorescence modulation, allows creation of security labels and optically masked barcodes for multiple documents authentication. PMID:25940779

  19. Targeted pathways in breast cancer: molecular and protein markers guiding therapeutic decisions.

    PubMed

    Kourea, Helen P; Zolota, Vassiliki; Scopa, Chrisoula D

    2014-01-01

    Breast carcinoma is currently considered as a group of diseases, differing not only in histopathologic phenotype, as indicated by histologic type and grade, but also in their protein, genetic and epigenetic molecular profile. The standard of care indicates that the core information for patient management includes data on Estrogen Receptor (ER), Progesterone Receptor (PgR) and Human Epidermal Growth Factor Receptor 2 (HER2), while there is an emerging role for the proliferation marker Ki67. These indices can be provided even in low resource settings and are indispensable for prognostication and therapeutic patient management. With the progress in molecular and translational research, there is a growing body of information on the molecular subtypes of breast carcinoma and their significance, and multigene signature assays are used to dictate prognosis and guide therapeutics in high resource settings. In addition, several cellular pathways involved in tumor growth and spread are dissected and targeted in clinical trials. Among these are the p53, RB, PI3K/Akt/mTOR and Ras/MAPK pathways, alterations associated with genetic instability and epigenetic alterations including histone methylation and acetylation, DNA methylation and microRNAs expression. The tumor immune microenvironment, including the tumor infiltrating lymphocytes (TILs) is attracting significant research interest. This review summarizes the mechanisms of function of the above factors in breast tumorigenesis with emphasis on their prognostic and predictive value and their use as therapeutic targets. PMID:25563853

  20. Association of molecular markers with cold tolerance and green period in zoysiagrass (Zoysia Willd.).

    PubMed

    Guo, Hai-Lin; Xuan, Ji-Ping; Liu, Jian-Xiu; Zhang, Yuan-Ming; Zheng, Yi-Qi

    2012-12-01

    Cold tolerance and the green period are key traits in the breeding of zoysiagrass (Zoysia Willd.). Identification of molecular markers associated with cold tolerance and the green period of zoysiagrass will contribute to efficient selection of elite cultivars. These two traits were measured in 96 zoysiagrass accessions in 2004 and 2005-2006, respectively. The mapping population was screened with 29 pairs of simple sequence repeat (SSR) primers and 54 pairs of sequence-related amplified polymorphism (SRAP) primers. A multi-loci in silico mapping approach implemented with an empirical Bayes method was applied for association mapping of cold tolerance and green period. We detected 254 SSR polymorphic loci and 338 SRAP polymorphic loci, among which three SSR loci (Xgwm131-3B-187, Xgwm469-6D-194 and Xgwm234-5B-244) and one SRAP locus (Me11Em7-406) were significantly associated with cold tolerance with effect values of 57.83%, 38.05%, 36.92% and 37%, respectively. Three SSR loci (Xgwm132-6B-225, Xgwm111-7D-34 and Xgwm102-2D-97) and two SRAP loci (Me19Em5-359 and Me16Em8-483) were significantly associated with the green period with effect values of 79.54%, 62.59%, 99.04%, 49.01% and 82.57%. These markers will be useful for genetic improvement of the cold tolerance and green period of zoysiagrass by marker-assisted breeding. PMID:23341745

  1. Molecular analysis of soybean varying in water use efficiency using SSRs markers.

    PubMed

    Kumar, Mithlesh; Lal, S K

    2015-07-01

    A set of 91 soybean germplasm lines, collected from different parts of the world, were screened for Water Use Efficiency (WUE) using Carbon Isotope Discrimination (CID) technique and were characterized for 10 quantitative traits. After screening under field condition, 44 soybean genotypes showed variations in WUE. Molecular diversity of these 44 diverse soybean lines was carried out with 26 Simple Sequence Repeats (SSRs) markers, of which 10 were polymorphic (38.47% polymorphism). 28 alleles were observed which were distributed over 10 loci, with an average of 2.8 alleles per locus. Polymorphism Information Content (PIC) value of 10 polymorphic markers ranged from 0.40 (locus Satt460) to 0.67 (locus satt260), with an average of 0.46. Pair-wise genetic similarity value, as calculated by simple matching coefficient, ranged from 0.99 to 0.40, with an average of 0.70. Genotypes were clustered using NTSYS-pc software employing unweighted paired group method using arithmetic averages to generate the dendrogram. Dendrogram exhibited 8 distinct clusters with a similarity coefficient of 0.69. Genotypes having low to medium and medium to high CID value were clustered in distant groups indicating usefulness of these polymorphic SSRs markers for differentiating genotypes on the basis of their CID value. The findings of this study indicate the need for broadening genetic base of the present Indian soybean cultivars through use of exotic sources of variation towards WUE. Thus, diverse genotypes identified in this study would be beneficial to soybean breeders to develop mapping population to identify QTLs for WUE. PMID:26364483

  2. De novo Transcriptome Analysis and Molecular Marker Development of Two Hemarthria Species

    PubMed Central

    Huang, Xiu; Yan, Hai-Dong; Zhang, Xin-Quan; Zhang, Jian; Frazier, Taylor P.; Huang, De-Jun; Lu, Lu; Huang, Lin-Kai; Liu, Wei; Peng, Yan; Ma, Xiao; Yan, Yan-Hong

    2016-01-01

    Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa “Yaan” and H. altissima “1110.” Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for “Yaan” and “1110,” respectively. In addition, a total of 86,731 “Yaan” and 48,645 “1110” unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were identified in 8330 unigenes. To validate the identified markers, high quality PCR primers were designed for both SNPs and SSRs. We randomly tested 16 of the SNP primers and 54 of the SSR primers and found that the majority of these primers successfully amplified the desired PCR product. In addition, high cross-species transferability (61.11–87.04%) of SSR markers was achieved for four other Poaceae species. The amount of RNA sequencing data that was generated for these two Hemarthria species greatly increases the amount of genomic information available for Hemarthria and the SSR and SNP markers identified in this study will facilitate further advancements in genetic and molecular studies of the Hemarthria genus. PMID:27148320

  3. 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-γ– 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

  4. Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari)

    PubMed Central

    Gil, Zulma Nancy; Benavides, Pablo; Souza, Og De; Acevedo, Flor Edith; Lima, Eraldo

    2015-01-01

    The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was Y^=αβXi, being Y^ the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. PMID:26078300

  5. Molecular markers as a method to evaluate the movement of Hypothenemus hampei (Ferrari).

    PubMed

    Gil, Zulma Nancy; Benavides, Pablo; De Souza, Og; Acevedo, Flor Edith; Lima, Eraldo

    2015-01-01

    The objective of this research was to develop a methodology to describe the movement of the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae) in the field through: (i) the evaluation of allele variation of a microsatellite marker on polymorphic Colombian H. hampei populations; (ii) the invention of a device for releasing H. hampei adults; (iii) the standardization of a release-recapture technique for H. hampei populations; (iv) the estimation of the flight distance of the insect; and (v) the calculation of a mathematical expression that describes the movement of H. hampei in space over time. The results indicated that: (i) the microsatellite molecular marker HHK.1.6 was exclusively present in a population from Guapotá-Santander, was dominant and allows the evaluation of H. hampei movement for several generations; (ii) a device that released 88.8% of H. hampei adults in 2 s was designed; (iii) this device was used as H. hampei populations containing HHK.1.6 marker release strategy, and coffee seeds as recapture strategy; (iv) it was estimated that H. hampei adults flew as far as 65 m, however, 90% were recovered in a radius of <40 m. Finally, (v) the mathematical expression that described the movement of H. hampei in space over time was [Formula: see text], being [Formula: see text] the average number of borer beetles recaptured per tree, and x the distance in meters. This method will allow to determine the movement of H. hampei from different environmental and ecological scenarios. PMID:26078300

  6. Molecular markers in colorectal cancer: genetic bases for a customised treatment.

    PubMed

    Casado, E; De Castro, J; Belda-Iniesta, C; Cejas, P; Feliu, J; Sereno, M; González-Barón, M

    2007-09-01

    Colorectal cancer (CRC) is the second leading cause of cancer death in Western countries. CRC treatment is based on the employment of three chemotherapeutic drugs, including 5-fluorouracil, oxaliplatin and irinotecan, and the use of recently incorporated targeted agents directed to vascular endothelial growth factor (VEGF) and epidermal growth factor receptor (EGFR). The approval of these biologicals and of others to come holds great promise for the improvement of patient outcome. The molecular bases for this lethal disease have been extensively investigated, laying the foundations for a rational and customised treatment approach, expanding the therapeutic index of current drugs and easing the incorporation of new molecules. Individual markers have been mainly investigated based on drug targets and metabolism. Also, the increasing availability of highthroughput technologies has prompted the opportunity for blind studies capable of screening new markers and of identifying the specific oncogenic pathways responsible for drug resistance in a given patient. An updated review of the field is presented in this article. PMID:17921101

  7. Photosynthetic and molecular markers of CO₂-mediated photosynthetic downregulation in nodulated alfalfa.

    PubMed

    Sanz-Sáez, Alvaro; Erice, Gorka; Aranjuelo, Iker; Aroca, Ricardo; Ruíz-Lozano, Juan Manuel; Aguirreolea, Jone; Irigoyen, Juan José; Sanchez-Diaz, Manuel

    2013-08-01

    Elevated CO₂ leads to a decrease in potential net photosynthesis in long-term experiments and thus to a reduction in potential growth. This process is known as photosynthetic downregulation. There is no agreement on the definition of which parameters are the most sensitive for detecting CO₂ acclimation. In order to investigate the most sensitive photosynthetic and molecular markers of CO₂ acclimation, the effects of elevated CO₂, and associated elevated temperature were analyzed in alfalfa plants inoculated with different Sinorhizobium meliloti strains. Plants (Medicago sativa L. cv. Aragón) were grown in summer or autumn in temperature gradient greenhouses (TGG). At the end of the experiment, all plants showed acclimation in both seasons, especially under elevated summer temperatures. This was probably due to the lower nitrogen (N) availability caused by decreased N₂-fixation under higher temperatures. Photosynthesis measured at growth CO₂ concentration, rubisco in vitro activity and maximum rate of carboxylation were the most sensitive parameters for detecting downregulation. Severe acclimation was also related with decreases in leaf nitrogen content associated with declines in rubisco content (large and small subunits) and activity that resulted in a drop in photosynthesis. Despite the sensitivity of rubisco content as a marker of acclimation, it was not coordinated with gene expression, possibly due to a lag between gene transcription and protein translation. PMID:23480453

  8. Molecular marker analysis as a guide to the sources of fine organic aerosols

    SciTech Connect

    Rogge, W.F.; Cass, G.R.; Hildemann, L.M.; Mazurek, M.A.; Simoneit, B.R.T.

    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.

  9. Molecular marker analysis as a guide to the sources of fine organic aerosols

    SciTech Connect

    Rogge, W.F.; Cass, G.R. ); Hildemann, L.M. . Dept. of Civil Engineering); Mazurek, M.A. ); Simoneit, B.R.T. 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.

  10. 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.

  11. Polycyclic aromatic hydrocarbons, black carbon, and molecular markers in soils of Switzerland.

    PubMed

    Bucheli, Thomas D; Blum, Franziska; Desaules, Andr; Gustafsson, Orjan

    2004-09-01

    Polycyclic aromatic hydrocarbons (PAH) were analysed in 23 soil samples (0-10 cm layer) from the Swiss soil monitoring network (NABO) together with total organic carbon (TOC) and black carbon (BC) concentration, as well as some PAH source diagnostic ratios and molecular markers. The concentrations of the sum of 16 EPA priority PAHs ranged from 50 to 619 microg/kg dw. Concentrations increased from arable, permanent and pasture grassland, forest, to urban soils and were 21-89% lower than median numbers reported in the literature for similar Swiss and European soils. NABO soils contained BC in concentrations from 0.4 to 1.8 mg/g dw, except for two sites with markedly higher levels. These numbers corresponded to 1-6% of TOC and were comparable to the limited published BC data in soil and sediments obtained with comparable analytical methods. The various PAH ratios and molecular markers pointed to a domination of pyrogenically formed PAHs in Swiss soils. In concert, the gathered data suggest the following major findings: (1) gas phase PAHs (naphthalene to fluorene) were long-range transported, cold-condensated at higher altitudes, and approaching equilibrium with soil organic matter (OM); (2) (partially) particle-bound PAHs (phenanthrene to benzo[ghi]perylene) were mostly deposited regionally in urban areas, and not equilibrated with soil OM; (3) Diesel combustion appeared to be a major emission source of PAH and BC in urban areas; and (4) wood combustion might have contributed significantly to PAH burdens in some soils of remote/alpine (forest) sites. PMID:15276719

  12. A better surgical resectability of WHO grade II gliomas is independent of favorable molecular markers.

    PubMed

    Cordier, Dominik; Goz, Catherine; Schdelin, Sabine; Rigau, Valrie; Mariani, Luigi; Duffau, Hugues

    2015-01-01

    A higher extent of resection (EOR) in WHO grade II gliomas (GIIG) is correlated with longer survival. However, the molecular markers also feature prognostic relevance. Here, we examined whether maximal EOR was related to the genetic profile. We retrospectively investigated the predictive value of 1p19q, IDH1, 53 expression and Ki67 index for the EOR in 200 consecutive GIIGs (2007-2013). Data were modeled in a linear model. The analysis was performed with two statistical methods (arcsin-sqrt and Beta-regression model with logit link). There was no deletion 1p19q in 118 cases, codeletion 1p19q (57 cases), single deletion 1p (4 cases) or19q (16 cases). 155 patients had a mutation of IDH1. p53 was graded in 4 degrees (0:92 cases, 1:52 cases, 2:31 cases, 3:8 cases). Mean Ki67 index was 5.2 % (range 1-20 %). Mean preoperative tumor volume was 60.8 cm(3) (range 3.3-250 cm(3)) and mean EOR was 0.917 (range 0.574-1). The statistical analysis was significant for a lower EOR in patients with codeletion 1p19q (OR 0.738, p = 0.0463) and with a single deletion 19q (OR 0.641, p = 0.0168). There was no significant correlation between IDH1 or p53 and the EOR. Higher Ki67 was marginally associated with higher EOR (p = 0.0603). The study demonstrates in a large cohort of GIIG that a higher EOR is not attributable to favorable genetic markers. This original result supports maximal surgical resection as an important therapeutic factor per se to optimize prognosis, independently of the molecular pattern. PMID:25261925

  13. Investigation of Molecular Marker Lipids in Alpine Ice Cores Via Stir Bar Sorptive Extraction

    NASA Astrophysics Data System (ADS)

    Makou, M. C.; Eglinton, T. I.; Thompson, L. G.; Hughen, K. A.

    2005-12-01

    Recently developed analytical techniques were employed to identify and quantify organic molecular markers trapped in high-altitude ice. While various compounds represent potentially useful proxies for biomass burning, vegetation type, atmospheric circulation, and anthropogenic activity, prior attempts to measure organic compounds in ice cores have typically required large volumes of sample material that are incompatible with generation of high-resolution paleoclimate records. We employed stir bar sorptive extraction (SBSE) and thermal desorption (TD), coupled with gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), to examine the organic content of small quantities (≤ 30 ml) of ice. To test the utility of the approach, post-industrial ice core samples from the Huascarán and Sajama sites (Andes), the Dasuopu and Puruogangri sites (Tibetan Plateau), and Mt. Kilimanjaro (east Africa) were tested. n-Alkanes, n-alkanoic acids, n-alkyl amides and nitriles, polycyclic aromatic hydrocarbons (PAHs), and various diterpenoids were identified in this suite of cores. These marker compounds suggest inputs from biomass burning, fresh vascular plant material, and anthropogenic activities such as fossil fuel combustion. Differences in distributions of the alkyl amide and nitrile homologues between the different sites suggest a predominantly local or regional supply of organic matter. Pre-industrial samples from the Sajama and Puruogangri ice cores were also analyzed in order to assess the character of biomarker assemblages in the absence of anthropogenic contributions and investigate changes in inputs over time. PAHs and diterpenoids, which may result from biomass burning and were observed in the modern Sajama samples, occurred in two Holocene Sajama samples, but not in a last glacial sample. Enhanced inputs of terrestrial vegetation combustion biomarkers were consistent with periods of enhanced aridity in both cores. This study demonstrates the utility of SBSE, TD, and GC/TOF-MS for isolating organic compounds from small amounts of alpine ice and paves the way for development of high-resolution molecular stratigraphic records from tropical ice cores.

  14. Altered Expression of Retinal Molecular Markers in the Canine RPE65 Model of Leber Congenital Amaurosis

    PubMed Central

    Hernández, Maria; Pearce-Kelling, Susan E.; Rodriguez, F. David; Aguirre, Gustavo D.; Vecino, Elena

    2010-01-01

    Purpose. Leber congenital amaurosis (LCA) is a group of childhood-onset retinal diseases characterized by severe visual impairment or blindness. One form is caused by mutations in the RPE65 gene, which encodes the retinal pigment epithelium (RPE) isomerase. In this study, the retinal structure and expression of molecular markers for different retinal cell types were characterized, and differences between control and RPE65 mutant dogs during the temporal evolution of the disease were analyzed. Methods. Retinas from normal and mutant dogs of different ages were examined by immunofluorescence with a panel of 16 different antibodies. Results. Cones and rods were preserved in the mutant retinas, and the number of cones was normal. However, there was altered expression of cone arrestin and delocalization of rod opsin. The ON bipolar cells showed sprouting of the dendritic arbors toward the outer nuclear layer (ONL) and retraction of their axons in the inner nuclear layer (INL). A decreased expression of GABA, and an increased expression of intermediate filament glial markers was also found in the mutant retinas. These changes were more evident in the adult than the young mutant retinas. Conclusions. The structure of the retina is well preserved in the mutant retina, but several molecular changes take place in photoreceptors and in bipolar and amacrine cells. Some of these changes are structural, whereas others reflect a change in localization of the examined proteins. This study provides new information that can be applied to the interpretation of outcomes of retinal gene therapy in animal models and humans. PMID:20671290

  15. Characterization of Pyricularia grisea in the United States Using Independent Genetic and Molecular Markers.

    PubMed

    Correll, J C; Harp, T L; Guerber, J C; Zeigler, R S; Liu, B; Cartwright, R D; Lee, F N

    2000-12-01

    ABSTRACT A total of 540 isolates of Pyricularia grisea from rice in the United States were examined for vegetative compatibility, MGR586 DNA fingerprint diversity, and mating type based on hybridization with the mat1-1 and mat1-2 sexual mating type alleles. The collections contained both archived and contemporary field isolates representative of the known MGR586 lineages and races that occur throughout the United States. Complementary nitrate nonutilizing (nit) or sulfate nonutilizing (sul) mutants were used to assess vegetative compatibility in P. grisea. There was a complete correspondence between vegetative compatibility groups (VCGs), MGR586 lineage, and mating type among 527 contemporary isolates (collected between 1991 and 1997) from Arkansas, Louisiana, Missouri, Mississippi, and Texas; all isolates in MGR586 lineages A, B, C, and D belonged to VCGs US-01, US-02, US-03, and US-04, respectively. In addition, all isolates tested in VCGs US-01 and US-04 had the mat1-1 mating type allele whereas those in VCGs US-02 and US-03 had the mat1-2 allele. The strict association of independent markers during this sample period was consistent with a strictly asexual mode of reproduction. However, examination of archived isolates collected in the 1970s and 1980s and contemporary isolates revealed an incongruent relationship between the independent markers. MGR586 C and E isolates were vegetatively compatible which indicated that multiple robust MGR586 delineated lineages could be nested within certain VCGs. Although isolates in lineages C and E were vegetatively compatible, they were of opposite mating type. Several hypotheses, including recombination, could account for the incongruence between the various markers. Among the eight MGR586 lineages (A through H) that occur in the United States, all isolates in lineages A, D, E, G, and H had the mat1-1 allele, whereas isolates in lineages B, C, and F had the mat1-2 allele. Nit mutants can be recovered relatively easy from P. grisea and should allow large numbers of individuals within a population to be assessed for vegetative compatibility. VCGs may prove to be an effective multilocus marker in P. grisea. Thus, VCGs should be a useful means for characterizing genetic structure in populations of the rice blast fungus worldwide, provide a useful genetic framework to assist in interpreting molecular population data, and may provide insight into potential sexual or asexual recombination events. PMID:18943382

  16. SCAR Marker for Identification and Discrimination of Commiphora wightii and C. myrrha.

    PubMed

    Sairkar, Pramod Kumar; Sharma, Anjana; Shukla, N P

    2016-01-01

    Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR) markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052) was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species. PMID:27069687

  17. SCAR Marker for Identification and Discrimination of Commiphora wightii and C. myrrha

    PubMed Central

    Sairkar, Pramod Kumar; Sharma, Anjana; Shukla, N. P.

    2016-01-01

    Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR) markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052) was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species. PMID:27069687

  18. [The effectiveness of molecular markers for the identification of Lr28, Lr35, and Lr47 genes in common wheat].

    PubMed

    Gul'tiaeva, E I; Orina, A S; Gannibal, F B; Mitrofanova, O P; Odintsova, I G; Laĭkova, L I

    2014-02-01

    The effectiveness of molecular markers for the identification of leaf rust resistance genes Lr28, Lr35, Lr47 transferred to common wheat was assessed the using samplesof Triticum spp. and Aegilops spp. from Ae. speltoides. Markers Sr39F2/R3, BCD260F1/35R2 of gene Lr35 and PS10 of Lr47 gene were characterized by high efficiency and were revealed in a line of common wheat containing these genes, and samples of Ae. speltoides (their donor). Marker SCS421 of Lr28gene and markers Sr39#22r, Sr39#50s, BE500705 of Lr35/Sr39 genes turned out to be less specific. Marker SCS421 was amplified in the samples of the T. timopheevii species, and markers Sr39#22r, Sr39#50s--in the Ae. speltoides, Ae. tauschii, T. timopheevii, line KS90WRC010 (Lr41), the sort of common wheat In Memory of Maistrenko, obtained using synthetic hexaploid T. timopheevii x Ae. tauschii and introgressive lines obtained using Ae. speltoides. Marker BE500705, which indicates the absence of Lr35/Sr39 genes, was not revealed in lines TcLr35 and MqSr39, in Ae. speltoides, Ae. tauschii and T. boeoticum (kk-61034, 61038). Analysis of the nucleotide sequences of amplification products obtained with the markers SCS421 and Sr39#22r indicated their low homology with TcLr28 and TcLr35. Using molecular markers, we showed a different distribution of Lr28 (77%), Lr35 (100%) and Lr47 (15%) genes in 13 studied samples ofAe. speltoides. In introgressive lines derived from Ae. speltoides, contemporary Russian sorts of common wheat and triticale variants Lr28, Lr35, Lr47 genes were not revealed. PMID:25711022

  19. Transcriptomic molecular markers for screening human colon cancer in stool and tissue.

    PubMed

    Ahmed, Farid E; Vos, Paul; iJames, Stephanie; Lysle, Donald T; Allison, Ron R; Flake, Gordon; Sinar, Dennis R; Naziri, Wade; Marcuard, Stefan P; Pennington, Rodney

    2007-01-01

    There is a need for sensitive and specific diagnostic molecular markers that can be used to monitor early patterns of gene expression in non-invasive exfoliated colonocytes shed in the stool, and in situ in adenoma-carcinoma epithelium of the colon. RNA-based detection methods are more comprehensive than either DNA-, protein- or methylation-based screening methods. By routinely and systematically being able to perform quantitative gene expression studies on these samples using less than ten colon cancer genes selected by the enormous resources of the National Cancer Institute's Cancer Genome Anatomy Project, we were able to monitor changes at various stages in the neoplastic process, allowing for reliable diagnostic screening of colon cancer particularly at the early, pre-malignant stages. Although the expression of some of the genes tested in tissue showed less variability in normal or cancerous patients than in stool, the stool by itself is suitable for screening. Thus, a transcriptomic approach using stool or tissue samples promises to offer more sensitivity and specificity than currently used molecular screening methods for colon cancer. A larger prospective clinical study utilizing stool and tissue samples derived from many control and colon cancer patients, to allow for a statistically valid analysis, is now urgently required to determine the true sensitivity and specificity of the transcriptomic screening approach for this preventable cancer. PMID:17726236

  20. Widespread utility of highly informative AFLP molecular markers across divergent shark species.

    PubMed

    Zenger, Kyall R; Stow, Adam J; Peddemors, Victor; Briscoe, David A; Harcourt, Robert G

    2006-01-01

    Population numbers of many shark species are declining rapidly around the world. Despite the commercial and conservation significance, little is known on even the most fundamental aspects of their population biology. Data collection that relies on direct observation can be logistically challenging with sharks. Consequently, molecular methods are becoming increasingly important to obtain knowledge that is critical for conservation and management. Here we describe an amplified fragment length polymorphism method that can be applied universally to sharks to identify highly informative genome-wide polymorphisms from 12 primer pairs. We demonstrate the value of our method on 15 divergent shark species within the superorder Galeomorphii, including endangered species which are notorious for low levels of genetic diversity. Both the endangered sand tiger shark (Carcharodon taurus, N = 18) and the great white shark (Carcharodon carcharias, N = 7) displayed relatively high levels of allelic diversity. A total of 59 polymorphic loci (H(e) = 0.373) and 78 polymorphic loci (H(e) = 0.316) were resolved in C. taurus and C. carcharias, respectively. Results from other sharks (e.g., Orectolobus ornatus, Orectolobus sp., and Galeocerdo cuvier) produced remarkably high numbers of polymorphic loci (106, 94, and 86, respectively) from a limited sample size of only 2. A major constraint to obtaining much needed genetic data from sharks is the time-consuming process of developing molecular markers. Here we demonstrate the general utility of a technique that provides large numbers of informative loci in sharks. PMID:17150982

  1. [Genetic polymorphism of flax Linum usitatissimum based on use of molecular cytogenetic markers].

    PubMed

    Rachinskaia, O A; Lemesh, V A; Muravenko, O V; Iurkevich, O Iu; Guzenko, E V; Bol'sheva, N L; Bogdanova, M V; Samatadze, T E; Popov, K V; Malyshev, S V; Shostak, N G; Heller, K; Khotyleva, L V; Zelenin, A V

    2011-01-01

    Using a set of approaches based on the use of molecular cytogenetic markers (DAPI/C-banding, estimation of the total area of DAPI-positive regions in prophase nuclei, FISH with 26S and 5S rDNA probes) and the microsatellite (SSR-PCR) assay, we studied genomic polymorphism in 15 flax (Linum usitatissimum L.) varieties from different geographic regions belonging to three directions of selection (oil, fiber, and intermediate flaxes) and in the k-37 x Viking hybrid. All individual chromosomes have been identified in the karyotypes of these varieties on the basis of the patterns of differential DAPI/C-banding and the distribution of 26S and 5S rDNA, and idiograms of the chromosomes have been generated. Unlike the oil flax varieties, the chromosomes in the karyotypes of the fiber flax varieties have, as a rule, pericentromeric and telomeric DAPI-positive bands of smaller size, but contain larger intercalary regions. Two chromosomal rearrangements (chromosome 3 inversions) were discovered in the variety Luna and in the k-37 x Viking hybrid. In both these forms, no colocalization of 26S rDNA and 5S rDNA on the satellite chromosome was detected. The SSR assay with the use of 20 polymorphic pairs of primers revealed 22 polymorphic loci. Based on the SSR data, we analyzed genetic similarity of the flax forms studied and constructed a genetic similarity dendrogram. The genotypes studied here form three clusters. The oil varieties comprise an independent cluster. The genetically related fiber flax varieties Vita and Luna, as well as the landrace Lipinska XIII belonging to the intermediate type, proved to be closer to the oil varieties than the remaining fiber flax varieties. The results of the molecular chromosomal analysis in the fiber and oil flaxes confirm their very close genetic similarity. In spite of this, the combined use of the chromosomal and molecular markers has opened up unique possibilities for describing the genotypes of flax varieties and creating their genetic passports. PMID:21446184

  2. 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

  3. Molecular marker characterization and source appointment of particulate matter and its organic aerosols.

    PubMed

    Choi, Jong-Kyu; Ban, Soo-Jin; Kim, Yong-Pyo; Kim, Yong-Hee; Yi, Seung-Muk; Zoh, Kyung-Duk

    2015-09-01

    This study was carried out to identify possible sources and to estimate their contribution to total suspended particle (TSP) organic aerosol (OA) contents. A total of 120 TSP and PM2.5 samples were collected simultaneously every third day over a one-year period in urban area of Incheon, Korea. High concentration in particulate matters (PM) and its components (NO3(-), water soluble organic compounds (WSOCs), and n-alkanoic acids) were observed during the winter season. Among the organics, n-alkanes, n-alkanoic acids, levoglucosan, and phthalates were major components. Positive matrix factorization (PMF) analysis identified seven sources of organic aerosols including combustion 1 (low molecular weight (LMW)-polycyclic aromatic hydrocarbons (PAHs)), combustion 2 (high molecular weight (HMW)-PAHs), biomass burning, vegetative detritus (n-alkane), secondary organic aerosol 1 (SOA1), secondary organic aerosol 2 (SOA2), and motor vehicles. Vegetative detritus increased during the summer season through an increase in biogenic/photochemical activity, while most of the organic sources were prominent in the winter season due to the increases in air pollutant emissions and atmospheric stability. The correlation factors were high among the main components of the organic carbon (OC) in the TSP and PM2.5. The results showed that TSP OAs had very similar characteristics to the PM2.5 OAs. SOA, combustion (PAHs), and motor vehicle were found to be important sources of carbonaceous PM in this region. Our results imply that molecular markers (MMs)-PMF model can provide useful information on the source and characteristics of PM. PMID:26022138

  4. Ribosomal DNA as molecular markers and their applications in the identification of fish parasites (Platyhelminthes: Monogenea) from India

    PubMed Central

    Chaudhary, Anshu; Verma, Chandni; Singh, Hridaya Shanker

    2014-01-01

    The development of molecular techniques for taxonomic analysis of monogenean parasites has led to a great increase for proper identification and factualness. These molecular techniques, in particular the use of molecular markers, have been used to identify and validate the monogenean parasites. Although, improvements in marker detection systems particularly of elements of rDNA like 18S, ITS and 28S used in monogeneans parasites have enabled great advances to be made in recent years in India. However, the molecular sequence analysis and phylogenetic relationships among the parasitic helminthes is unconventional in India. Many workers have been always questioned the validity of Indian species of monogeneans and emphasized the need to ascertain the status of species from Indian fish. Here we would like to provide additional resolution for the interpretation of use of molecular markers in study of monogeneans in India. This review provides an overview of current stage of studies in India that have been used in applying molecular techniques to monogenean.

  5. 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...

  6. Evaluation of molecular markers for discriminating Gonatocerus morrilli (Hymenoptera: Mymaridae): a biological control agent for Homalodisca vitripennis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We tested the utility of molecular markers for distinguishing between two closely related species, Gonatocerus morrilli (Howard) and G. walkerjonesi, S. Triapitsyn, to evaluate whether post-release G. morrilli specimens could be discriminated in the field. Initially, post-release specimens from Cal...

  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. Molecular markers linked to the blast resistance gene Pi-z in rice for use in marker-assisted selection.

    PubMed

    Conaway-Bormans, C A; Marchetti, M A; Johnson, C W; McClung, A M; Park, W D

    2003-10-01

    Rice blast, caused by the fungal pathogen Pyricularia grisea, is a serious disease affecting rice-growing regions around the world. Current methods for identification of blast-resistant germplasm and progeny typically utilize phenotypic screening. However, phenotypic screens are influenced by environmental conditions and the presence of one resistance gene can sometimes phenotypically mask other genes conferring resistance to the same blast race. Pi-z is a dominant gene located on the short arm of chromosome 6 that confers complete resistance to five races of blast. Using sequence data found in public databases and degenerate primer pairs based on the P-loop, nucleotide binding sites and kinase domain motifs of previously cloned resistance genes, we have developed PCR-based DNA markers that cosegregate with the gene. These markers are polymorphic in a wide range of germplasm, including the narrow crosses characteristic of applied rice-breeding programs. They can now be used as a low cost, high-throughput alternative to conventional phenotypic screening for direct detection of blast resistance genes, allowing rapid introgression of genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more-durable blast resistance. PMID:12955204

  9. 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

  10. Molecular analysis of East Anatolian traditional plum and cherry accessions using SSR markers.

    PubMed

    Öz, M H; Vurgun, H; Bakir, M; Büyük, İ; Yüksel, C; Ünlü, H M; Çukadar, K; Karadoğan, 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

  11. Genetic Rearrangements of Six Wheat–Agropyron cristatum 6P Addition Lines Revealed by Molecular Markers

    PubMed Central

    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

  12. Molecular Assay for Detection of Genetic Markers Associated with Decreased Susceptibility to Cephalosporins in Neisseria gonorrhoeae

    PubMed Central

    Peterson, S. W.; Martin, I.; Demczuk, W.; Bharat, A.; Hoang, L.; Wylie, J.; Allen, V.; Lefebvre, B.; Tyrrell, G.; Horsman, G.; Haldane, D.; Garceau, R.; Wong, T.

    2015-01-01

    The incidence of antimicrobial-resistant Neisseria gonorrhoeae continues to rise in Canada; however, antimicrobial resistance data are lacking for approximately 70% of gonorrhea infections that are diagnosed directly from clinical specimens by nucleic acid amplification tests (NAATs). We developed a molecular assay for surveillance use to detect mutations in genes associated with decreased susceptibility to cephalosporins that can be applied to both culture isolates and clinical samples. Real-time PCR assays were developed to detect single nucleotide polymorphisms (SNPs) in ponA, mtrR, penA, porB, and one N. gonorrhoeae-specific marker (porA). We tested the real-time PCR assay with 252 gonococcal isolates, 50 nongonococcal isolates, 24 N. gonorrhoeae-negative NAAT specimens, and 34 N. gonorrhoeae-positive NAAT specimens. Twenty-four of the N. gonorrhoeae-positive NAAT specimens had matched culture isolates. Assay results were confirmed by comparison with whole-genome sequencing data. For 252 N. gonorrhoeae strains, the agreement between the DNA sequence and real-time PCR was 100% for porA, ponA, and penA, 99.6% for mtrR, and 95.2% for porB. The presence of ≥2 SNPs correlated with decreased susceptibility to ceftriaxone (sensitivities of >98%) and cefixime (sensitivities of >96%). Of 24 NAAT specimens with matched cultures, the agreement between the DNA sequence and real-time PCR was 100% for porB, 95.8% for ponA and mtrR, and 91.7% for penA. We demonstrated the utility of a real-time PCR assay for sensitive detection of known markers for the decreased susceptibility to cephalosporins in N. gonorrhoeae. Preliminary results with clinical NAAT specimens were also promising, as they correlated well with bacterial culture results. PMID:25878350

  13. Development and evaluation of robust molecular markers linked to disease resistance in tomato for distinctness, uniformity and stability testing.

    PubMed

    Arens, Paul; Mansilla, Carmen; Deinum, Daniël; Cavellini, Laetitia; Moretti, André; Rolland, Sophie; van der Schoot, Hanneke; Calvache, David; Ponz, Fernando; Collonnier, Cécile; Mathis, René; Smilde, Diederik; Caranta, Carole; Vosman, Ben

    2010-02-01

    Molecular markers linked to phenotypically important traits are of great interest especially when traits are difficult and/or costly to be observed. In tomato where a strong focus on resistance breeding has led to the introgression of several resistance genes, resistance traits have become important characteristics in distinctness, uniformity and stability (DUS) testing for Plant Breeders Rights (PBR) applications. Evaluation of disease traits in biological assays is not always straightforward because assays are often influenced by environmental factors, and difficulties in scoring exist. In this study, we describe the development and/or evaluation of molecular marker assays for the Verticillium genes Ve1 and Ve2, the tomato mosaic virus Tm1 (linked marker), the tomato mosaic virus Tm2 and Tm2 ( 2 ) genes, the Meloidogyne incognita Mi1-2 gene, the Fusarium I (linked marker) and I2 loci, which are obligatory traits in PBR testing. The marker assays were evaluated for their robustness in a ring test and then evaluated in a set of varieties. Although in general, results between biological assays and marker assays gave highly correlated results, marker assays showed an advantage over biological tests in that the results were clearer, i.e., homozygote/heterozygote presence of the resistance gene can be detected and heterogeneity in seed lots can be identified readily. Within the UPOV framework for granting of PBR, the markers have the potential to fulfil the requirements needed for implementation in DUS testing of candidate varieties and could complement or may be an alternative to the pathogenesis tests that are carried out at present. PMID:19855951

  14. Molecular markers of biomass burning, fungal spores and biogenic SOA in the Taklimakan desert aerosols

    NASA Astrophysics Data System (ADS)

    Fu, Pingqing; Zhuang, Guoshun; Sun, Yele; Wang, Qiongzhen; Chen, Jing; Ren, Lujie; Yang, Fan; Wang, Zifa; Pan, Xiaole; Li, Xiangdong; Kawamura, Kimitaka

    2016-04-01

    Biogenic primary organic aerosols (POA) and secondary organic aerosols (SOA) are important organic constituents of atmospheric particulate matter (PM). In order to better understand the atmospheric abundances, molecular compositions and sources of the desert aerosols, biomass-burning tracers (e.g. levoglucosan), primary saccharides including fungal spore tracers, and SOA tracers from the oxidation of biogenic volatile organic compounds (e.g. isoprene, monoterpenes and sesquiterpene) have been studied in ambient aerosols from the Taklimakan desert, using gas chromatography-mass spectrometry. Results showed that the total concentrations of biomass-burning tracers at Hetian (177-359 ng m-3, mean 233 ng m-3 in PM2.5) in the south rim of the desert were much higher than those at Tazhong (1.9-8.8 ng m-3 in PM2.5 and 5.9-32 ng m-3 in TSP) in the central Taklimakan desert. Molecular markers of fungal spores were also detected in all the desert aerosols, highlighting the importance of primary bioaerosols in the Asian dust particles. A specific pattern of the dominance of 2-methylglyceric acid over 2-methyltetrols and C5-alkene triols was found in the Taklimakan desert aerosols, especially during the dust storm events, which is different from the 2-methyltetrols-dominated pattern in other ambient aerosols. Our results provide direct evidence on the biogenic POA and SOA tracers in the Taklimakan desert region, which help to better understand their impact on the aerosol chemistry in the down-wind regions.

  15. Molecular characterization of sour orange (Citrus aurantium) accessions and their relatives using SSR and SRAP markers.

    PubMed

    Polat, I; Kacar, Y A; Yesiloglu, T; Uzun, A; Tuzcu, O; Gulsen, O; Incesu, M; Kafa, G; Turgutoglu, E; Anil, S

    2012-01-01

    Citrus production with its many varieties is of importance since it provides economically important products for Turkish exports. Sour orange is a rootstock commonly used for propagating the different scion varieties. Knowledge of the genetic diversity of the rootstock accessions would be useful in order to improve citrus breeding programs. We studied genetic relationships and diversity of 51 accessions of sour orange (Citrus aurantium) and their relatives using SSR (simple sequence repeat) and SRAP (sequence-related amplified polymorphism) molecular markers. Twenty-one SRAP primer combinations were tested on these accessions and relatives, producing 167 polymorphic fragments, with a mean of 8.0 and a mean polymorphism information content value of 0.47. Seventeen SSR primers also produced 30 polymorphic fragments, with a mean of 1.4 per primer and a mean polymorphism information content value of 0.39. The unweighted pair-group method with arithmetic average analysis using combined SSR and SRAP data showed a similarity range from 0.71 to 1.00 among the accessions. In the cluster analysis, sour orange relatives were indicated as a separate group from sour orange. 'Macrophylla' and 'Mexican lime' were the accessions most distinct (0.71) from the others. We conclude that genetic diversity in these sour orange accessions is lower and some of them were identical. PMID:23079821

  16. 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

  17. Tumor Heterogeneity: Mechanisms and Bases for a Reliable Application of Molecular Marker Design

    PubMed Central

    Diaz-Cano, Salvador J.

    2012-01-01

    Tumor heterogeneity is a confusing finding in the assessment of neoplasms, potentially resulting in inaccurate diagnostic, prognostic and predictive tests. This tumor heterogeneity is not always a random and unpredictable phenomenon, whose knowledge helps designing better tests. The biologic reasons for this intratumoral heterogeneity would then be important to understand both the natural history of neoplasms and the selection of test samples for reliable analysis. The main factors contributing to intratumoral heterogeneity inducing gene abnormalities or modifying its expression include: the gradient ischemic level within neoplasms, the action of tumor microenvironment (bidirectional interaction between tumor cells and stroma), mechanisms of intercellular transference of genetic information (exosomes), and differential mechanisms of sequence-independent modifications of genetic material and proteins. The intratumoral heterogeneity is at the origin of tumor progression and it is also the byproduct of the selection process during progression. Any analysis of heterogeneity mechanisms must be integrated within the process of segregation of genetic changes in tumor cells during the clonal expansion and progression of neoplasms. The evaluation of these mechanisms must also consider the redundancy and pleiotropism of molecular pathways, for which appropriate surrogate markers would support the presence or not of heterogeneous genetics and the main mechanisms responsible. This knowledge would constitute a solid scientific background for future therapeutic planning. PMID:22408433

  18. Pink berry grape (Vitis vinifera L.) characterization: Reflectance spectroscopy, HPLC and molecular markers.

    PubMed

    Rustioni, Laura; De Lorenzis, Gabriella; Hr?a, Monica; Failla, Osvaldo

    2016-01-01

    Color has a fundamental role for the qualitative evaluation and cultivar characterization of fruits. In grape, a normally functional pigment biosynthesis leads to the accumulation of a high quantity of anthocyanins. In this work, 28 Vitis vinifera L. cultivars accumulating low anthocyanins in berries were studied to characterize the biosynthetic dysfunctions in both a phenotypic and genotypic point of view. Reflectance spectroscopy, HPLC profiles and molecular markers related to VvMybA1 and VvMybA2 genes allowed a detailed description of the pigment-related characteristics of these cultivars. Data were consistent concerning the heterozygosity of the non-functional allele in both investigated genes, resulting in a low colored phenotype as described by reflectance. However, the variability in berry colour among our samples was not fully explained by MybA locus, probably due to specific interferences among the biosynthetic pathways, as suggested by the anthocyanin profile variations detected among our samples. The results presented in this work confirmed the importance of the genetic background: grapes accumulating high levels of cyanidin-3-O-glucosides (di-substituted anthocyanin) are generally originated by white cultivar retro-mutations and they seem to preserve the anomalies in the flavonoid hydroxylases enzymes which negatively affect the synthesis of tri-substituted anthocyanins. PMID:26687319

  19. Peptides, specific proteolysis products, as molecular markers of allergenic proteins - in silico studies.

    PubMed

    Dziuba, Marta; Minkiewicz, Piotr; Dąbek, Marianna

    2013-01-01

    The objective of this study was to analyse allergenic proteins by identifying their molecular biomarkers for detection in food using bioinformatics tools. The protein and epitope sequences were from BIOPEP database, proteolysis was simulated using BIOPEP program and UniProt database screening via BLAST and FASTA programs. The biomarkers of food proteins were proposed: for example for whey proteins - TPEVDDEALEKFDKALKALPMHIR (β-Lg: fragment 141-164), chicken egg - AAVSVDCSEYPKPDCTAEDRPL (ovomucoid: 156-177), wheat - KCNGTVEQVESIVNTLNAGQIASTDVVEVVVSPPY (triose phosphate isomerase: 12-46) and peanuts - QARQLKNNNPFKFFVPPFQQSPRAVA (arachin: 505-530). The results are annotated in the BIOPEP database of allergenic proteins and epitopes, available at http://www.uwm.edu.pl/biochemia. The epitope-receptor interactions are attributed to the epitope's sequence and suggest that in silico proteolysis products showing the highest degree of sequence identity with an epitope or its part are characteristic of a given protein or a group of cross-reactive homologs. The protein markers from basic food groups were proposed based on the above assumption. PMID:24584870

  20. The phylogenetic relationship between Astigmata and Oribatida (Acari) as indicated by molecular markers.

    PubMed

    Domes, Katja; Althammer, Max; Norton, Roy A; Scheu, Stefan; Maraun, Mark

    2007-01-01

    Astigmata comprise a diverse group of acariform mite species with a remarkable range of life histories, most of which involve parasitic or commensal relationships with other organisms. Several authors have suggested that Astigmata evolved as a paedomorphic clade from within Oribatida, and both morphology and gland-chemistry strongly suggest that their sister-clade is within the oribatid subgroup Desmonomata. The biologies of these groups contrast greatly, since oribatid mites are mostly soil-living detritivores and fungivores, and have life cycles that are much longer than those in Astigmata. We tested the hypothesis that Astigmata evolved from within Desmonomata using two molecular markers, the ribosomal 18S region (18S) and the nuclear elongation factor 1 alpha (ef1alpha) gene. Representative acariform mites included 28 species of Oribatida, eight of Astigmata, two of Prostigmata and two of Endeostigmata; outgroups included members of Opilioacariformes, Parasitiformes and Ricinulei. To minimize the possibility of long-branch attraction artifacts, we limited highly variable sites by removing gaps (18S) and third codon positions (ef1alpha) from the sequences. Maximum parsimony, neighbor-joining and Bayesian algorithms formed trees that consistently placed Astigmata outside monophyletic Oribatida, usually as sister-group of the endeostigmatid mite Alicorhagia sp. Analyses with and without outgroups resulted in similar topologies, showing no evidence for long-branch artifacts and leaving the conflict with morphological and biochemical data unexplained. PMID:17611803

  1. Genetic diversity analysis of Croton antisyphiliticus Mart. using AFLP molecular markers.

    PubMed

    Oliveira, T G; Pereira, A M S; Coppede, J S; França, S C; Ming, L C; Bertoni, B W

    2016-01-01

    Croton antisyphiliticus Mart. is a medicinal plant native to Cerrado vegetation in Brazil, and it is popularly used to treat urogenital tract infections. The objective of the present study was to assess the genetic variability of natural C. antisyphiliticus populations using AFLP molecular markers. Accessions were collected in the states of Minas Gerais, São Paulo, and Goiás. The genotyping of individuals was performed using a LI-COR® DNA Analyzer 4300. The variability within populations was found to be greater than the variability between them. The FST value was 0.3830, which indicated that the populations were highly structured. A higher percentage of polymorphic loci (92.16%) and greater genetic diversity were found in the population accessions from Pratinha-MG. Gene flow was considered restricted (Nm = 1.18), and there was no correlation between genetic and geographic distances. The populations of C. antisyphiliticus exhibited an island-model structure, which demonstrates the vulnerability of the species. PMID:26909989

  2. 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.

  3. Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells.

    PubMed

    Wang, Denong; Liu, Shaoyi; Trummer, Brian J; Deng, Chao; Wang, Aili

    2002-03-01

    We describe here the development of a carbohydrate-based microarray to extend the scope of biomedical research on carbohydrate-mediated molecular recognition and anti-infection responses. We have demonstrated that microbial polysaccharides can be immobilized on a surface-modified glass slide without chemical conjugation. With this procedure, a large repertoire of microbial antigens (approximately 20,000 spots) can be patterned on a single micro-glass slide, reaching the capacity to include most common pathogens. Glycoconjugates of different structural characteristics are shown here to be applicable for microarray fabrication, extending the repertoires of diversity and complexity of carbohydrate microarrays. The printed microarrays can be air-dried and stably stored at room temperature for long periods of time. In addition, the system is highly sensitive, allowing simultaneous detection of a broad spectrum of antibody specificities with as little as a few microliters of serum specimen. Finally, the potential of carbohydrate microarrays is demonstrated by the discovery of previously undescribed cellular markers, Dex-Ids. PMID:11875429

  4. Identification of molecular markers for DNA barcoding in the Aphidiinae (Hym. Braconidae).

    PubMed

    Derocles, Stephane A P; LE Ralec, Anne; Plantegenest, Manuel; Chaubet, Bernard; Cruaud, Corinne; Cruaud, Astrid; Rasplus, Jean-Yves

    2012-03-01

    Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphid-parasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphid-parasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A. microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae. PMID:22004100

  5. Intraspecific chromosomal and genetic polymorphism in Brassica napus L. detected by cytogenetic and molecular markers.

    PubMed

    Amosova, Alexandra V; Zemtsova, Lyudmila V; Grushetskaya, Zoya E; Samatadze, Tatiana E; Mozgova, Galina V; Pilyuk, Yadviga E; Volovik, Valentina T; Melnikova, Natalia V; Zelenin, Alexandr V; Lemesh, Valentina A; Muravenko, Olga V

    2014-04-01

    The application of DNA intercalator 9-aminoacridine allowed us to increase the resolution of chromosome C-banding and DAPI-banding patterns and to investigate chromosomal polymorphism in karyotypes of seven spring and six winter rape varieties. It was shown that the pericentromeric and intercalary C-bands of most of the chromosomes in spring rape were smaller in size and less polymorphic than those of winter rape. More 26S and 5S rDNA sites were found in the winter rape karyotypes than the spring varieties. Separate or colocalized 26S and 5S rDNA sites were revealed on chromosomes 4, 5, 6, 8, 10, 14, 15, 16 and 18. Intervarietal and intravarietal polymorphism of the number and chromosomal localization of rDNA sites were detected. The generalized idiogram of chromosomes of 13 Brassica napus varieties with account of all possibilities of C-banding patterns as well as localization of 26S and 5S rDNA sites were constructed. Polymorphism of the examined molecular and cytogenetic markers as well as the heterozygosis level of FAE1.1 gene controlling erucic acid synthesis in rapeseed was higher in the winter varieties than in the spring ones. The obtained data were in a atisfactory agreement with increased tolerance to environmental stress conditions of winter rape. PMID:24840830

  6. Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans

    PubMed Central

    Sharp, Frank R; Jickling, Glen C; Stamova, Boryana; Tian, Yingfang; Zhan, Xinhua; Liu, DaZhi; Kuczynski, Beth; Cox, Christopher D; Ander, Bradley P

    2011-01-01

    Whole genome expression microarrays can be used to study gene expression in blood, which comes in part from leukocytes, immature platelets, and red blood cells. Since these cells are important in the pathogenesis of stroke, RNA provides an index of these cellular responses to stroke. Our studies in rats have shown specific gene expression changes 24 hours after ischemic stroke, hemorrhage, status epilepticus, hypoxia, hypoglycemia, global ischemia, and following brief focal ischemia that simulated transient ischemic attacks in humans. Human studies show gene expression changes following ischemic stroke. These gene profiles predict a second cohort with >90% sensitivity and specificity. Gene profiles for ischemic stroke caused by large-vessel atherosclerosis and cardioembolism have been described that predict a second cohort with >85% sensitivity and specificity. Atherosclerotic genes were associated with clotting, platelets, and monocytes, and cardioembolic genes were associated with inflammation, infection, and neutrophils. These gene profiles predicted the cause of stroke in 58% of cryptogenic patients. These studies will provide diagnostic, prognostic, and therapeutic markers, and will advance our understanding of stroke in humans. New techniques to measure all coding and noncoding RNAs along with alternatively spliced transcripts will markedly advance molecular studies of human stroke. PMID:21505474

  7. Treatment Outcome and Prognostic Molecular Markers of Supratentorial Primitive Neuroectodermal Tumors

    PubMed Central

    Shim, Kyu-Won; Han, Jung Woo; Choi, Junjeong; Kim, Dong-Seok; Lyu, Chuhl Joo; Kim, Jun Won; Suh, Chang-Ok

    2016-01-01

    Background To identify prognostic factors and define the optimal management of patients with supratentorial primitive neuroectodermal tumors (sPNETs), we investigated treatment outcomes and explored the prognostic value of specific molecular markers. Methods A total of 47 consecutive patients with pathologically confirmed sPNETs between May 1985 and June 2012 were included. Immunohistochemical analysis of LIN28, OLIG2, and Rad51 expression was performed and correlated with clinical outcome. Results With a median follow-up of 70 months, 5-year overall survival (OS) and progression-free survival (PFS) was 55.5% and 40%, respectively, for all patients. Age, surgical extent, and radiotherapy were significant prognostic factors for OS and PFS. Patients who received initially planned multimodal treatment without interruption (i.e., radiotherapy and surgery (≥subtotal resection), with or without chemotherapy) showed significantly higher 5-year OS (71.2%) and PFS (63.1%). In 29 patients with available tumor specimens, tumors with high expression of either LIN28 or OLIG2 or elevated level of Rad51 were significantly associated with poorer prognosis. Conclusions We found that multimodal treatment improved outcomes for sPNET patients, especially when radiotherapy and ≥subtotal resection were part of the treatment regimen. Furthermore, we confirmed the prognostic significance of LIN28 and OLIG2 and revealed the potential role of Rad51 in sPNETs. PMID:27074032

  8. A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes

    PubMed Central

    Steinberger-Levy, Ida; Shifman, Ohad; Zvi, Anat; Ariel, Naomi; Beth-Din, Adi; Israeli, Ofir; Gur, David; Aftalion, Moshe; Maoz, Sharon; Ber, Raphael

    2016-01-01

    Standard antimicrobial susceptibility tests used to determine bacterial susceptibility to antibiotics are growth dependent and time consuming. The long incubation time required for standard tests may render susceptibility results irrelevant, particularly for patients infected with lethal bacteria that are slow growing on agar but progress rapidly in vivo, such as Yersinia pestis. Here, we present an alternative approach for the rapid determination of antimicrobial susceptibility, based on the quantification of the changes in the expression levels of specific marker genes following exposure to growth-inhibiting concentrations of the antibiotic, using Y. pestis and ciprofloxacin as a model. The marker genes were identified by transcriptomic DNA microarray analysis of the virulent Y. pestis Kimberley53 strain after exposure to specific concentrations of ciprofloxacin for various time periods. We identified several marker genes that were induced following exposure to growth-inhibitory concentrations of ciprofloxacin, and we confirmed the marker expression profiles at additional ciprofloxacin concentrations using quantitative RT-PCR. Eleven candidate marker transcripts were identified, of which four mRNA markers were selected for a rapid quantitative RT-PCR susceptibility test that correctly determined the Minimal Inhibitory Concentration (MIC) values and the categories of susceptibility of several Y. pestis strains and isolates harboring various ciprofloxacin MIC values. The novel molecular susceptibility test requires just 2 h of antibiotic exposure in a 7-h overall test time, in contrast to the 24 h of antibiotic exposure required for a standard microdilution test.

  9. Validation of molecular markers associated with boron tolerance, powdery mildew resistance and salinity tolerance in field peas

    PubMed Central

    Javid, Muhammad; Rosewarne, Garry M.; Sudheesh, Shimna; Kant, Pragya; Leonforte, Antonio; Lombardi, Maria; Kennedy, Peter R.; Cogan, Noel O. I.; Slater, Anthony T.; Kaur, Sukhjiwan

    2015-01-01

    Field pea (Pisum sativum L.) is an important grain legume consumed both as human food and animal feed. However, productivity in low rainfall regions can be significantly reduced by inferior soils containing high levels of boron and/or salinity. Furthermore, powdery mildew (PM) (Erysiphe pisi) disease also causes significant yield loss in warmer regions. Breeding for tolerance to these abiotic and biotic stresses are major aims for pea breeding programs and the application of molecular markers for these traits could greatly assist in developing improved germplasm at a faster rate. The current study reports the evaluation of a near diagnostic marker, PsMlo, associated with PM resistance and boron (B) tolerance as well as linked markers associated with salinity tolerance across a diverse set of pea germplasm. The PsMlo1 marker predicted the PM and B phenotypic responses with high levels of accuracy (>80%) across a wide range of field pea genotypes, hence offers the potential to be widely adapted in pea breeding programs. In contrast, linked markers for salinity tolerance were population specific; therefore, application of these markers would be suitable to relevant crosses within the program. Our results also suggest that there are possible new sources of salt tolerance present in field pea germplasm that could be further exploited. PMID:26579164

  10. Transport of sewage molecular markers through saturated soil column and effect of easily biodegradable primary substrate on their removal.

    PubMed

    Foolad, Mahsa; Ong, Say Leong; Hu, Jiangyong

    2015-11-01

    Pharmaceutical and personal care products (PPCPs) and artificial sweeteners (ASs) are emerging organic contaminants (EOCs) in the aquatic environment. The presence of PPCPs and ASs in water bodies has an ecologic potential risk and health concern. Therefore, it is needed to detect the pollution sources by understanding the transport behavior of sewage molecular markers in a subsurface area. The aim of this study was to evaluate transport of nine selected molecular markers through saturated soil column experiments. The selected sewage molecular markers in this study were six PPCPs including acetaminophen (ACT), carbamazepine (CBZ), caffeine (CF), crotamiton (CTMT), diethyltoluamide (DEET), salicylic acid (SA) and three ASs including acesulfame (ACF), cyclamate (CYC), and saccharine (SAC). Results confirmed that ACF, CBZ, CTMT, CYC and SAC were suitable to be used as sewage molecular markers since they were almost stable against sorption and biodegradation process during soil column experiments. In contrast, transport of ACT, CF and DEET were limited by both sorption and biodegradation processes and 100% removal efficiency was achieved in the biotic column. Moreover, in this study the effect of different acetate concentration (0-100mg/L) as an easily biodegradable primary substrate on a removal of PPCPs and ASs was also studied. Results showed a negative correlation (r(2)>0.75) between the removal of some selected sewage chemical markers including ACF, CF, ACT, CYC, SAC and acetate concentration. CTMT also decreased with the addition of acetate, but increasing acetate concentration did not affect on its removal. CBZ and DEET removal were not dependent on the presence of acetate. PMID:26210019

  11. Population structure of the banana weevil, an introduced pest in the Canary Islands, studied by RAPD analysis.

    PubMed

    Magaña, C; Beroiz, B; Hernández-Crespo, P; Montes de Oca, M; Carnero, A; Ortego, F; Castañera, P

    2007-12-01

    The banana weevil (BW), Cosmopolites sordidus (Coleoptera: Curculionidae), is one of the most important insect pests of bananas and plantains. The mobility and the origin of BW infestations at the Canary Islands (Tenerife, La Gomera and La Palma) have been analysed using Random Amplified Polymorphic DNA (RAPD) as molecular markers. Populations from Costa Rica, Colombia, Uganda and Madeira were also included for comparison. One hundred and fifteen reproducible bands from eight primers were obtained. The level of polymorphism in the populations from the Canary Islands (40-62%) was in the range of those found in other populations. Nei's genetic distances, pair-wise fixation index (FST) values indicate that the closest populations are Tenerife populations among themselves (Nei's genetic distance=0.054-0.100; FST=0.091-0.157) and Costa Rica and Colombia populations (Nei's genetic distance=0.049; FST=0.113). Our results indicate the existence of BW local biotypes with limited gene flow and affected by genetic drift. These results are compatible with a unique event of colonization at Tenerife; whereas, the outbreaks in La Gomera and La Palma may come from independent introductions. The Madeira population is phylogenetically and geographically closer to the Canary Islands populations, suggesting that it is the most likely source of the insects introduced in the Canary Islands. PMID:17997871

  12. Dynamics of molecular markers linked to the resistance loci in a mosquito-Plasmodium system.

    PubMed Central

    Yan, Guiyun; Severson, David W

    2003-01-01

    Models on the evolution of resistance to parasitism generally assume fitness tradeoffs between the costs of being parasitized and the costs associated with resistance. This study tested this assumption using the yellow fever mosquito Aedes aegypti and malaria parasite Plasmodium gallinaceum system. Experimental mosquito populations were created by mixing susceptible and resistant strains in equal proportions, and then the dynamics of markers linked to loci for Plasmodium resistance and other unlinked neutral markers were determined over 12 generations. We found that when the mixed population was maintained under parasite-free conditions, the frequencies of alleles specific to the susceptible strain at markers closely linked to the loci for resistance (QTL markers) as well as other unlinked markers increased significantly in the first generation and then fluctuated around equilibrium frequencies for all six markers. However, when the mixed population was exposed to an infected blood meal every generation, allele frequencies at the QTL markers for resistance were not significantly changed. Small population size caused significant random fluctuations of allele frequencies at all marker loci. Consistent allele frequency changes in the QTL markers and other unlinked markers suggest that the reduced fitness in the resistant population has a genome-wide effect on the genetic makeup of the mixed population. Continuous exposure to parasites promoted the maintenance of alleles from the resistant Moyo-R strain in the mixed population. The results are discussed in relation to the proposed malaria control strategy through genetic disruption of vector competence. PMID:12807772

  13. Genetic diversity and relationships detected by ISSR and RAPD analysis among Aethionema species growing in Eastern Anatolia (Turkey).

    PubMed

    Sunar, Serap; Yildirim, Nalan; Sengul, Meryem; Agar, Guleray

    2016-01-01

    In this study, Random amplified polymorphic DNA (RAPD) and Inter-Simple Sequence Repeat (ISSR) analysis were used to examine the genetic relationships among eight Aethionema species (Aethionema caespitosum, A. arabicum, A. cordatum, A. fimnraitum, A. armenum, A. speciosum supsp. speciosum, A. memraneceum, A. grandiflorum var. grandiflorum) growing in the wild in Eastern Anatolia, Turkey. Fourteen RAPD primers and 7 ISSR primers were used. The UPGMA cluster was constructed using a combination of data from RAPD and ISSR markers. The Aethionema species were classified into two major groups. The similarity matrix values of between 0.182 (A. cordatum, A. speciosum supsp. speciosum) and 0.927 (A. grandiflorum var. grandiflorum, A. cordatum). High genetic variations among Aethionema species growing in the wild in Eastern Anatolia, Turkey may reveal differences in their origin. The present study suggests that both RAPD and ISSR analysis are useful for the differentiation of the Aethionema species. PMID:27012533

  14. Molecular Linkage Mapping and Marker-Trait Associations with NlRPT, a Downy Mildew Resistance Gene in Nicotiana langsdorffii.

    PubMed

    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

  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. 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

  17. Evaluation of the use of SCAR markers for screening genetic diversity of Lentinula edodes strains.

    PubMed

    Liu, Jing-Yu; Ying, Zheng-He; Liu, Fang; Liu, Xin-Rui; Xie, Bao-Gui

    2012-04-01

    In this study, three molecular marker systems including sequence related amplified polymorphism (SRAP), random amplified polymorphic DNA (RAPD), and inter-simple sequence repeats (ISSR) were screened to select polymorphisms of 24 main commercial strains of Lentinula edodes cultivated widely in China. Twenty-nine sequence characterized amplified region (SCAR) markers were developed to set up a dendrogram using UPMGA based on nucleotide sequences of some SRAP, RAPD, and ISSR polymorphic fragments. The grouping showed that the 24 strains were apparently clustered into five groups at a level of 0.68 similarity coefficient, and those that have similar breeding background clustered preferentially into the same subgroup. Results also revealed that the 24 strains had a low level of genetic diversity, and the breeding source of L. edodes should be broadened by exploiting wild types and introducing exotic strains. In addition, the tested strains of L. edodes could be clearly distinguished and identified from others by using different combinations of SCAR primers. Thus, results of this work demonstrated that SCAR was an excellent genetic marker system to characterize and investigate genetic diversity of L. edodes. Furthermore, this provided an alternative method to identify the genetic relationship of different strains of other fungi. PMID:22218569

  18. Mating type genes and genetic markers to decipher intraspecific variability among Fusarium udum isolates from pigeonpea.

    PubMed

    Kashyap, Prem Lal; Rai, Shalini; Kumar, Sudheer; Srivastava, Alok Kumar; Anandaraj, M; Sharma, Arun Kumar

    2015-07-01

    To ascertain the variability in Fusarium udum (Fu) isolates associated with pigeonpea wilt is a difficult task, if based solely on morphological and cultural characters. In this respect, the robustness of five different genetic marker viz., random amplified polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus (ERIC), BOX elements, mating type locus, and microsatellite markers were employed to decipher intra-specific variability in Fu isolates. All techniques yielded intra-specific polymorphism, but different levels of discrimination were obtained. RAPD-PCR was more discriminatory, enabling the detection of thirteen variants among twenty Fu isolates. By microsatellite, ERIC- and BOX-PCR fingerprinting, the isolates were categorized in seven, five, and two clusters, respectively. Cluster analysis of the combined data also showed that the Fu isolates were grouped into ten clusters, sharing 50-100% similarity. The occurrence of both mating types in Fu isolates is reported for the first time in this study. All examined isolates harbored one of the two mating-type idiomorphs, but never both, which suggests a heterothallic mating system of sexual reproduction among them. Information obtained from comparing results of different molecular marker systems should be useful to organize the genetic variability and ideally, will improve disease management practices by identifying sources of inoculum and isolate characteristics. PMID:25639472

  19. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich.

    PubMed

    Marubodee, Rusama; Ogiso-Tanaka, Eri; Isemura, Takehisa; Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  20. Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich

    PubMed Central

    Chankaew, Sompong; Kaga, Akito; Naito, Ken; Ehara, Hiroshi; Tomooka, Norihiko

    2015-01-01

    Vigna vexillata (L.) A. Rich. (tuber cowpea) is an underutilized crop for consuming its tuber and mature seeds. Wild form of V. vexillata is a pan-tropical perennial herbaceous plant which has been used by local people as a food. Wild V. vexillata has also been considered as useful gene(s) source for V. unguiculata (cowpea), since it was reported to have various resistance gene(s) for insects and diseases of cowpea. To exploit the potential of V. vexillata, an SSR-based linkage map of V. vexillata was developed. A total of 874 SSR markers successfully amplified single DNA fragment in V. vexillata among 1,336 SSR markers developed from Vigna angularis (azuki bean), V. unguiculata and Phaseolus vulgaris (common bean). An F2 population of 300 plants derived from a cross between salt resistant (V1) and susceptible (V5) accessions was used for mapping. A genetic linkage map was constructed using 82 polymorphic SSR markers loci, which could be assigned to 11 linkage groups spanning 511.5 cM in length with a mean distance of 7.2 cM between adjacent markers. To develop higher density molecular linkage map and to confirm SSR markers position in a linkage map, RAD markers were developed and a combined SSR and RAD markers linkage map of V. vexillata was constructed. A total of 559 (84 SSR and 475 RAD) markers loci could be assigned to 11 linkage groups spanning 973.9 cM in length with a mean distance of 1.8 cM between adjacent markers. Linkage and genetic position of all SSR markers in an SSR linkage map were confirmed. When an SSR genetic linkage map of V. vexillata was compared with those of V. radiata and V. unguiculata, it was suggested that the structure of V. vexillata chromosome was considerably differentiated. This map is the first SSR and RAD marker-based V. vexillata linkage map which can be used for the mapping of useful traits. PMID:26398819

  1. 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

  2. Monitoring disease activity by stool analyses: from occult blood to molecular markers of intestinal inflammation and damage.

    PubMed

    Foell, D; Wittkowski, H; Roth, J

    2009-06-01

    It is a common experience that gastrointestinal symptoms urge us to differentiate inflammatory bowel disease (IBD) from functional disorders. Furthermore, in patients with proven IBD the disease activity has to be accurately monitored. Faecal markers of neutrophil influx into the mucosa are promising indicators of intestinal inflammation. Some neutrophil-derived proteins may be linked to the pathogenesis of IBD due to their functions as damage-associated molecular pattern molecules (DAMPs). Phagocyte-specific DAMPs of the S100 family are released from neutrophils or monocytes, followed by pro-inflammatory activation of pattern recognition receptors. The complex of S100A8/S100A9 was termed "calprotectin" and has been in use as a faecal marker for 10 years. More recently, faecal S100A12 has been reported to be an even more accurate faecal marker of inflammation. We review the biology of this novel group of molecules which can be used as surrogate markers directly linked to the molecular mechanisms of gut inflammation. PMID:19136508

  3. Molecular cytogenetic analysis of wheat-barley hybrids using genomic in situ hybridization and barley microsatellite markers.

    PubMed

    Malysheva, L; Sjakste, T; Matzk, F; Röder, M; Ganal, M

    2003-04-01

    In the present investigation, genomic in situ hybridization (GISH) and barley microsatellite markers were used to analyse the genome constitution of wheat-barley hybrids from two backcross generations (BC1 and BC2). Two BC1 plants carried 3 and 6 barley chromosomes, respectively, according to GISH data. Additional chromosomal fragments were detected using microsatellites. Five BC2 plants possessed complete barley chromosomes or chromosome segments and six BC2 plants did not preserve barley genetic material. Molecular markers revealed segments of the barley genome with the size of one marker only, which probably resulted from recombination between wheat and barley chromosomes. The screening of backcrossed populations from intergeneric hybrids could be effectively conducted using both genomic in situ hybridization and molecular microsatellite markers. GISH images presented a general overview of the genome constitution of the hybrid plants, while microsatellite analysis revealed the genetic identity of the alien chromosomes and chromosomal segments introgressed. These methods were complementary and provided comprehensive information about the genomic constitution of the plants produced. PMID:12723047

  4. Molecular characterization of Brazilian equid herpesvirus type 1 strains based on neuropathogenicity markers

    PubMed Central

    Mori, Enio; Lara, Maria do Carmo C.S.H.; Cunha, Elenice M.S.; Villalobos, Eliana M.C.; Mori, Claudia M.C.; Soares, Rodrigo M.; Brandão, Paulo E.; Fernandes, Wilson R.; Richtzenhain, Leonardo J.

    2015-01-01

    Partial nucleotide sequences of ORF72 (glycoprotein D, gD), ORF64 (infected cell protein 4, ICP4) and ORF30 (DNA polymerase) genes were compared with corresponding sequences of EHV-1 reference strains to characterize the molecular variability of Brazilian strains. Virus isolation assays were applied to 74 samples including visceral tissue, total blood, cerebrospinal fluid (CSF) and nasal swabs of specimens from a total of 64 animals. Only one CSF sample (Iso07/05 strain) was positive by virus isolation in cell culture. EHV-1 Iso07/05 neurologic strain and two abortion visceral tissues samples (Iso11/06 and Iso33/06) were PCR-positive for ORF33 (glycoprotein B, gB) gene of EHV-1. A sequence analysis of the ORF72, ORF64 and ORF30 genes from three EHV-1 archival strains (A3/97, A4/72, A9/92) and three clinical samples (Iso07/05, Iso11/06 and Iso33/06) suggested that among Brazilian EHV-1 strains, the amplified region of the gD gene sequence is highly conserved. Additionally, the analysis of ICP4 gene showed high nucleotide and amino acid identities when compared with genotype P strains, suggesting that the EHV-1 Brazilian strains belonged to the same group. All the EHV-1 Brazilian strains were classified as non-neuropathogenic variants (N752) based on the ORF30 analysis. These findings indicate a high conservation of the gD-, ICP4- and ORF30-encoding sequences. Different pathotypes of the EHV-1 strain might share identical genes with no specific markers, and tissue tropism is not completely dependent on the gD envelope, immediate-early ICP4 and DNA polymerase proteins. PMID:26273275

  5. Molecular markers of trichloroethylene-induced toxicity in human kidney cells

    SciTech Connect

    Lash, Lawrence H. . E-mail: l.h.lash@wayne.edu; Putt, David A.; Hueni, Sarah E.; Horwitz, Beth P.

    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.

  6. Cryptic Diversity within the Major Trypanosomiasis Vector Glossina fuscipes Revealed by Molecular Markers

    PubMed Central

    Choi, Kwang-Shik; Darby, Alistair C.; Causse, Sandrine; Kapitano, Berisha; Hall, Martin J. R.; Steen, Keith; Lutumba, Pascal; Madinga, Joules; Torr, Steve J.; Okedi, Loyce M.; Lehane, Michael J.; Donnelly, Martin J.

    2011-01-01

    Background The tsetse fly Glossina fuscipes s.l. is responsible for the transmission of approximately 90% of cases of human African trypanosomiasis (HAT) or sleeping sickness. Three G. fuscipes subspecies have been described, primarily based upon subtle differences in the morphology of their genitalia. Here we describe a study conducted across the range of this important vector to determine whether molecular evidence generated from nuclear DNA (microsatellites and gene sequence information), mitochondrial DNA and symbiont DNA support the existence of these taxa as discrete taxonomic units. Principal Findings The nuclear ribosomal Internal transcribed spacer 1 (ITS1) provided support for the three subspecies. However nuclear and mitochondrial sequence data did not support the monophyly of the morphological subspecies G. f. fuscipes or G. f. quanzensis. Instead, the most strongly supported monophyletic group was comprised of flies sampled from Ethiopia. Maternally inherited loci (mtDNA and symbiont) also suggested monophyly of a group from Lake Victoria basin and Tanzania, but this group was not supported by nuclear loci, suggesting different histories of these markers. Microsatellite data confirmed strong structuring across the range of G. fuscipes s.l., and was useful for deriving the interrelationship of closely related populations. Conclusion/Significance We propose that the morphological classification alone is not used to classify populations of G. fuscipes for control purposes. The Ethiopian population, which is scheduled to be the target of a sterile insect release (SIT) programme, was notably discrete. From a programmatic perspective this may be both positive, given that it may reflect limited migration into the area or negative if the high levels of differentiation are also reflected in reproductive isolation between this population and the flies to be used in the release programme. PMID:21858237

  7. Detection of chloroquine and artemisinin resistance molecular markers in Plasmodium falciparum: A hospital based study

    PubMed Central

    Ramani, S; Parija, Subhash Chandra; Mandal, Jharna; Hamide, Abdoul; Bhat, Vishnu

    2016-01-01

    Introduction: Emergence of chloroquine (CQ) resistance in Plasmodium falciparum has increased the morbidity and mortality of falciparum malaria worldwide. Artemisinin-based combination therapies are now recommended by the World Health Organization as the first line treatment for falciparum malaria. Numerous molecular markers have been implicated in the CQ and artemisinin resistance. Materials and Methods: A total of 26 confirmed cases of falciparum malaria (by giemsa stained thick and thin smear, quantitative buffy coat, immunochromatographic test, or polymerase chain reaction [PCR]) were included in the study. About 5 ml of ethylenediaminetetraacetic acid blood sample was collected and stored at −20°C till use. Plasmodium DNA was extracted using QIAamp whole blood DNA extraction kit. PCR was done to amplify pfcrt, pfmdr1, pfserca, and pfmrp1 genes and the amplicons obtained were sequenced by Macrogen, Inc., Korea. Single nucleotide polymorphism (SNP) analysis was done using Bio-Edit Sequence Alignment Editor. Results: Out of the four genes targeted, we noted a SNP in the pfcrt gene alone. This SNP (G > T) was noted in the 658th position of the gene, which was seen in 13 patients. The pfmdr1 and pfserca genes were present in 9 and 14 patients respectively. But we could not find any SNPs in these genes. This SNP in pfcrt gene was not significantly associated with any adverse outcome and neither altered disease progression. Conclusion: Presence of a single SNP may not be associated with any adverse clinical outcome. As the sample size was small, we may have not been able to detect any other known or unknown polymorphisms. PMID:26998436

  8. Characterizing the transcriptome and molecular markers information for roach, Rutilus rutilus.

    PubMed

    Chi, Wei; Ma, Xufa; Niu, Jiangong; Zou, Ming

    2016-03-01

    Rutilus rutilus (roach) is native to most of Europe and western Asia, and the Irtysh River basin in Sinkiang, northwest China is the marginal area of their natural distribution. The wide distribution and unique characteristic of this species makes it an ideal model for analysing ecological and comparative genomics. However, the limited genome sequences available for this species have hindered these investigations. Transcriptomes from the brains and livers of five individuals collected from the Irtysh River basin were sequenced using Illumina paired-end sequencing technology. A collection of 132,289 unigenes for this species were obtained using a de novo assembly method based on nearly 120 million clean reads encompassing more than 14 Gb data. Approximately 37.5% (49,656), 27.1% (35,867) and 21.2% (27,987) of the transcriptome had homologues deposited in Nt, Nr and Swiss-Prot, respectively; 12.3% (16,328) were assigned to eukaryotic orthologous groups of proteins classifications, and 21.5% (28,429) harboured Interpro domains. On the basis of the assembled transcriptome, we detected 177,493 single-nuc leotide variation resident in 39.3% (52,029) of the sequences and 20.8% (27,497) of the sequences harbouring 36,639 simple sequence repeats. The identified molecular markers are a basis for further ecological analysis, and the transcriptome reported here allows for more extensive evolutionary analyses of the Cyprinidae, the most species-rich family of freshwater fishes. PMID:27019431

  9. Molecular markers indicate different dynamics of leaves and roots during litter decomposition

    NASA Astrophysics Data System (ADS)

    Altmann, Jens; Jansen, Boris; Palviainen, Marjo; Kalbitz, Karsten

    2010-05-01

    Up to now there is only a poor understanding of the sources contributing to organic carbon in forest soils, especially the contribution of leaves and roots. Studies of the last 2 decades have shown that methods like pyrolysis and CuO oxidation are suitable tools to trace back the main contributors of organic matter in water, sediments and soils. Lignin derived monomers, extractable lipids, cutin and suberin derived compounds have been used frequently for identification of plant material. However, for the selection of suitable biomarker the decomposition patterns and stability of these compounds are of high importance but they are only poorly understood. In this study we focused on following questions: (I) Which compounds are characteristic to identify certain plant parts and plant species? (II) How stable are these compounds during the first 3 years of litter decomposition? We studied the chemical composition of samples from a 3-year litterbag decomposition experiment with roots and leaves of spruce, pine and birch which was done in Finland. Additionally to mass loss, carbon and nitrogen contents, free lipids were extracted; by alkaline hydrolysis non extractable lipids were gained. The extracts were analyzed afterwards by GC-MS, the insoluble residues were analyzed by curie-point Pyrolysis GC-MS. In addition to the identification and quantification of a variety of different compounds and compound ratios we used statistical classification methods to get deeper insights into the patterns of leaf and root-derived biomarkers during litter decomposition. The mass loss was largely different between the litter species and we always observed larger mass loss for leaf-derived litter in comparison to root derived litter. This trend was also observed by molecular analysis. The increase of the ratio of vanillic acid to vanillin was correlated to the mass loss of the samples over time. This shows that the degree of decomposition of plant material was linked with the degree of lignin degradation. Preliminary results show, that we were able to distinguish the different species and plant parts using various approaches, e.g., abundance and patterns of different substances and different ratios of compounds. The polyesters suberin and cutin were particularly useful to differentiate between roots and leaves. We conclude that knowledge of the decomposition patterns of molecular markers will largely improve the identification power of organic matter sources in soils.

  10. A conservative region of the mercuric reductase gene (mera) as a molecular marker of bacterial mercury resistance

    PubMed Central

    Sotero-Martins, Adriana; de Jesus, Michele Silva; Lacerda, Michele; Moreira, Josino Costa; Filgueiras, Ana Luzia Lauria; Barrocas, Paulo Rubens Guimarães

    2008-01-01

    The most common bacterial mercury resistance mechanism is based on the reduction of Hg(II) to Hg0, which is dependent of the mercuric reductase enzyme (MerA) activity. The use of a 431 bp fragment of a conservative region of the mercuric reductase (merA) gene was applied as a molecular marker of this mechanism, allowing the identification of mercury resistant bacterial strains. PMID:24031221

  11. Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus.

    PubMed

    Ferri, D V; Munhoz, C F; Neves, P M O; Ferracin, L M; Sartori, D; Vieira, M L C; Fungaro, M H P

    2012-12-01

    The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field. PMID:24293712

  12. Diversity of Rhodopirellula and related planctomycetes in a North Sea coastal sediment employing carB as molecular marker.

    PubMed

    Žure, Marina; Munn, Colin B; Harder, Jens

    2015-09-01

    Rhodopirellula is an abundant marine member of the bacterial phylum Planctomycetes. Cultivation studies revealed the presence of several closely related Rhodopirellula species in European coastal sediments. Because the 16S rRNA gene does not provide the desired taxonomic resolution to differentiate Rhodopirellula species, we performed a comparison of the genomes of nine Rhodopirellula strains and six related planctomycetes and identified carB, coding for the large subunit of carbamoylphosphate synthetase, as a suitable molecular marker. In this study, we investigated the diversity of Rhodopirellula in coastal intertidal surface sediments of Sylt island, North Sea, using the 16S rRNA and carB genes as molecular markers. The carB clone and pyrosequencing libraries revealed the presence of 12 species of Rhodopirellula and of 66 species in closely related undescribed genera, a diversity that was not detected with a 16S rRNA gene library. This study demonstrates that the carB gene is a powerful molecular marker for detecting Rhodopirellula species in the environment and may be used for the taxonomic evaluation of new strains. PMID:26253575

  13. Direct Analysis of Low-Volatile Molecular Marker Extract from Airborne Particulate Matter Using Sensitivity Correction Method.

    PubMed

    Irei, Satoshi

    2016-01-01

    Molecular marker analysis of environmental samples often requires time consuming preseparation steps. Here, analysis of low-volatile nonpolar molecular markers (5-6 ring polycyclic aromatic hydrocarbons or PAHs, hopanoids, and n-alkanes) without the preseparation procedure is presented. Analysis of artificial sample extracts was directly conducted by gas chromatography-mass spectrometry (GC-MS). After every sample injection, a standard mixture was also analyzed to make a correction on the variation of instrumental sensitivity caused by the unfavorable matrix contained in the extract. The method was further validated for the PAHs using the NIST standard reference materials (SRMs) and then applied to airborne particulate matter samples. Tests with the SRMs showed that overall our methodology was validated with the uncertainty of ~30%. The measurement results of airborne particulate matter (PM) filter samples showed a strong correlation between the PAHs, implying the contributions from the same emission source. Analysis of size-segregated PM filter samples showed that their size distributions were found to be in the PM smaller than 0.4 μm aerodynamic diameter. The observations were consistent with our expectation of their possible sources. Thus, the method was found to be useful for molecular marker studies. PMID:27127511

  14. Direct Analysis of Low-Volatile Molecular Marker Extract from Airborne Particulate Matter Using Sensitivity Correction Method

    PubMed Central

    Irei, Satoshi

    2016-01-01

    Molecular marker analysis of environmental samples often requires time consuming preseparation steps. Here, analysis of low-volatile nonpolar molecular markers (5-6 ring polycyclic aromatic hydrocarbons or PAHs, hopanoids, and n-alkanes) without the preseparation procedure is presented. Analysis of artificial sample extracts was directly conducted by gas chromatography-mass spectrometry (GC-MS). After every sample injection, a standard mixture was also analyzed to make a correction on the variation of instrumental sensitivity caused by the unfavorable matrix contained in the extract. The method was further validated for the PAHs using the NIST standard reference materials (SRMs) and then applied to airborne particulate matter samples. Tests with the SRMs showed that overall our methodology was validated with the uncertainty of ~30%. The measurement results of airborne particulate matter (PM) filter samples showed a strong correlation between the PAHs, implying the contributions from the same emission source. Analysis of size-segregated PM filter samples showed that their size distributions were found to be in the PM smaller than 0.4 μm aerodynamic diameter. The observations were consistent with our expectation of their possible sources. Thus, the method was found to be useful for molecular marker studies. PMID:27127511

  15. 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 (ΦPT = 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.

  16. 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

  17. Genetic polymorphism and taxonomic infrastructure of the Pleurotus eryngii species-complex as determined by RAPD analysis, isozyme profiles and ecomorphological characters.

    PubMed

    Zervakis, G I; Venturella, G; Papadopoulou, K

    2001-11-01

    The Pleurotus eryngii species-complex includes populations of choice edible mushrooms, growing in the greater Mediterranean area in close association with different genera of plants of the family Apiaceae. Their distinct host-specialization served as the principal criterion for the discrimination of several taxa; however, the genetic relationships among the various P. eryngii ecotypes remain ambiguous. In the present study, 46 Pleurotus strains with a wide range of geographical origins were isolated from Eryngium spp., Ferula communis, Cachrys ferulacea, Thapsia garganica and Elaeoselinum asclepium subsp. asclepium, and were subjected to isozyme and random amplified polymorphic DNA-PCR (RAPD) analysis. The 16 enzyme activities tested were controlled by 28 loci, 11 of which were monomorphic. Host-exclusive zymograms for the Aph (acid phosphatase) and Phe-1 (dopa-phenoloxidase) loci were obtained from Pleurotus strains associated with C. ferulacea. Allele frequencies, genetic diversity and mean diversity were high for isolates from Eryngium spp. and Ferula communis. In RAPD analysis, the use of five primers allowed the production of 45 (out of 48) polymorphic bands, while four molecular markers specific for the identification of Pleurotus strains growing on E. asclepium subsp. asclepium and C. ferulacea were obtained. The Pleurotus strains produced 35 distinct electrophoretic types and 42 RAPD patterns, which independently permitted the separation of the fungal populations into five clusters in accordance with their host-specificity. In addition, the evaluation of the principal ecological and morphological characters provided further evidence for discriminating between P. nebrodensis growing on C. ferulacea and the rest of the host-associated populations. The latter represent taxa at the varietal level: P. eryngii var. eryngii, P. eryngii var. ferulae and P. eryngii var. elaeoselini. The position of taxa of dubious validity, such as P. hadamardii and P. fossulatus, is discussed in relation to the new findings. All Mediterranean Pleurotus populations growing on umbellifers seem to have recently diverged through a sympatric speciation process, that is based on both intrinsic reproductive barriers and extrinsic ecogeographical factors. PMID:11700370

  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. User-friendly markers linked to Fusarium wilt race 1 resistance Fw gene for marker-assisted selection in pea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium wilt is one of the most widespread diseases of pea. Resistance to Fusarium wilt race 1 was reported as a single gene, Fw, located on linkage group III. The previously reported AFLP and RAPD markers linked to Fw have limited usage in marker-assisted selection due to their map distance and l...

  20. Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

    PubMed

    Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

    2015-01-01

    Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection. PMID:26125744

  1. [Molecular genetic markers in evaluating risk of cardiovascular diseases in coal miners of Ukraine].

    PubMed

    Kundiev, Iu I; Basanets, A V; Andrushchenko, T A; Dolinchuk, L V

    2014-01-01

    Left ventricle hypertrophy increases risk of cardiac failure and influences life expectancy. The authors demonstrated diagnostic reliability of genetic markers in evaluating left ventricle hypertrophy formation and their advantages over clinical signs, as outlines prognosis of diseases development on preclinical stage. Through genetic markers analysis with consideration of echo-cardiographic values of left ventricle myocardial weight, the authors determined genotypes associated with left ventricle hypertrophy development. PMID:25335421

  2. Investigation and Analysis of Genetic Diversity of Diospyros Germplasms Using SCoT Molecular Markers in Guangxi

    PubMed Central

    He, Xinhua; Luo, Cong; Chen, Hu; Qin, Zhenshi

    2015-01-01

    Background Knowledge about genetic diversity and relationships among germplasms could be an invaluable aid in diospyros improvement strategies. Methods This study was designed to analyze the genetic diversity and relationship of local and natural varieties in Guangxi Zhuang Autonomous Region of China using start codon targeted polymorphism (SCoT) markers. The accessions of 95 diospyros germplasms belonging to four species Diospyros kaki Thunb, D. oleifera Cheng, D. kaki var. silverstris Mak, and D. lotus Linn were collected from different eco-climatic zones in Guangxi and were analyzed using SCoT markers. Results Results indicated that the accessions of 95 diospyros germplasms could be distinguished using SCoT markers, and were divided into three groups at similarity coefficient of 0.608; these germplasms that belong to the same species were clustered together; of these, the degree of genetic diversity of the natural D. kaki var. silverstris Mak population was richest among the four species; the geographical distance showed that the 12 natural populations of D. kaki var. silverstris Mak were divided into two groups at similarity coefficient of 0.19. Meanwhile, in order to further verify the stable and useful of SCoT markers in diospyros germplasms, SSR markers were also used in current research to analyze the genetic diversity and relationship in the same diospyros germplasms. Once again, majority of germplasms that belong to the same species were clustered together. Thus SCoT markers were stable and especially useful for analysis of the genetic diversity and relationship in diospyros germplasms. Discussion The molecular characterization and diversity assessment of diospyros were very important for conservation of diospyros germplasm resources, meanwhile for diospyros improvement. PMID:26317414

  3. Semi-volatile organic compounds as molecular markers for atmospheric and ecosystem transport

    NASA Astrophysics Data System (ADS)

    Genualdi, Susan

    The use of semi-volatile organic compounds (SOCs) as molecular markers to identify the contributions of regional and long-range atmospheric transport, as well as current and historic sources, and contaminant deposition in remote ecosystems of the Western U.S. was investigated. Trans-Pacific air masses influenced by Siberian biomass burning events had elevated concentrations of polycyclic aromatic hydrocarbons (PAHs) and the historic use pesticides dieldrin and alpha-HCH, while air masses influenced by regional fires in the Pacific Northwestern U.S. had enhanced concentrations of PAHs and the current-use pesticides dacthal and endosulfan. This suggests that previously deposited SOCs, such as pesticides, revolatilize to the atmosphere during forest fires. In addition, forest soils collected from a burned area in the Pacific Northwestern U.S. had significantly lower SOC concentrations (34 to 100 %) than soils collected from an unburned area separated only by a two lane road. This confirms that SOCs re-volatilize and/or degrade from soils and vegetation during the burning process. The chiral signatures of alpha-HCH in air masses at three sites in the Pacific Northwestern U.S. indicated that the boundary layer has a non-racemic alpha-HCH signature likely due to re-volatilization of alpha-HCH from the Pacific Ocean and that the free troposphere is a source of racemic alpha-HCH. Racemic alpha-HCH was also associated with Asian and trans-Pacific air masses. Racemic cis and trans-chlordane in Pacific Northwestern U.S. air masses indicated that U.S. urban areas continue to be a source of chlordane to the atmosphere. The deposition of non-racemic alpha-HCH in seasonal snowpack in continental Western U.S. national park high elevation ecosystems reflected regional transport, while the high latitude, Alaskan national parks were influenced by long-range atmospheric transport of racemic alpha-HCH. The chiral signature of alpha-HCH in fish collected from high elevation and high latitude ecosystems in Western U.S. national parks reflected the chiral signature of the seasonal snowpack in the lake catchment. This indicates that the fish in these ecosystems do not enantioselectively biotransform alpha-HCH. Racemic cis-chlordane was measured in seasonal snowpack and lake sediments in Sequoia National Park due to the high population density surrounding the park and the past use of chlordane as a termiticide in urban areas. Non-racemic cis-chlordane was measured in sediment collected from Rocky Mountain National Park because this park receives chlordane due to re-volatilization from regional agricultural soil.

  4. Emerging concepts in biomarker discovery; the US-Japan Workshop on Immunological Molecular Markers in Oncology.

    PubMed

    Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Hervé; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M

    2009-01-01

    Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions. PMID:19534815

  5. Emerging concepts in biomarker discovery; The US-Japan workshop on immunological molecular markers in oncology

    PubMed Central

    Tahara, Hideaki; Sato, Marimo; Thurin, Magdalena; Wang, Ena; Butterfield, Lisa H; Disis, Mary L; Fox, Bernard A; Lee, Peter P; Khleif, Samir N; Wigginton, Jon M; Ambs, Stefan; Akutsu, Yasunori; Chaussabel, Damien; Doki, Yuichiro; Eremin, Oleg; Fridman, Wolf Hervé; Hirohashi, Yoshihiko; Imai, Kohzoh; Jacobson, James; Jinushi, Masahisa; Kanamoto, Akira; Kashani-Sabet, Mohammed; Kato, Kazunori; Kawakami, Yutaka; Kirkwood, John M; Kleen, Thomas O; Lehmann, Paul V; Liotta, Lance; Lotze, Michael T; Maio, Michele; Malyguine, Anatoli; Masucci, Giuseppe; Matsubara, Hisahiro; Mayrand-Chung, Shawmarie; Nakamura, Kiminori; Nishikawa, Hiroyoshi; Palucka, A Karolina; Petricoin, Emanuel F; Pos, Zoltan; Ribas, Antoni; Rivoltini, Licia; Sato, Noriyuki; Shiku, Hiroshi; Slingluff, Craig L; Streicher, Howard; Stroncek, David F; Takeuchi, Hiroya; Toyota, Minoru; Wada, Hisashi; Wu, Xifeng; Wulfkuhle, Julia; Yaguchi, Tomonori; Zeskind, Benjamin; Zhao, Yingdong; Zocca, Mai-Britt; Marincola, Francesco M

    2009-01-01

    Supported by the Office of International Affairs, National Cancer Institute (NCI), the "US-Japan Workshop on Immunological Biomarkers in Oncology" was held in March 2009. The workshop was related to a task force launched by the International Society for the Biological Therapy of Cancer (iSBTc) and the United States Food and Drug Administration (FDA) to identify strategies for biomarker discovery and validation in the field of biotherapy. The effort will culminate on October 28th 2009 in the "iSBTc-FDA-NCI Workshop on Prognostic and Predictive Immunologic Biomarkers in Cancer", which will be held in Washington DC in association with the Annual Meeting. The purposes of the US-Japan workshop were a) to discuss novel approaches to enhance the discovery of predictive and/or prognostic markers in cancer immunotherapy; b) to define the state of the science in biomarker discovery and validation. The participation of Japanese and US scientists provided the opportunity to identify shared or discordant themes across the distinct immune genetic background and the diverse prevalence of disease between the two Nations. Converging concepts were identified: enhanced knowledge of interferon-related pathways was found to be central to the understanding of immune-mediated tissue-specific destruction (TSD) of which tumor rejection is a representative facet. Although the expression of interferon-stimulated genes (ISGs) likely mediates the inflammatory process leading to tumor rejection, it is insufficient by itself and the associated mechanisms need to be identified. It is likely that adaptive immune responses play a broader role in tumor rejection than those strictly related to their antigen-specificity; likely, their primary role is to trigger an acute and tissue-specific inflammatory response at the tumor site that leads to rejection upon recruitment of additional innate and adaptive immune mechanisms. Other candidate systemic and/or tissue-specific biomarkers were recognized that might be added to the list of known entities applicable in immunotherapy trials. The need for a systematic approach to biomarker discovery that takes advantage of powerful high-throughput technologies was recognized; it was clear from the current state of the science that immunotherapy is still in a discovery phase and only a few of the current biomarkers warrant extensive validation. It was, finally, clear that, while current technologies have almost limitless potential, inadequate study design, limited standardization and cross-validation among laboratories and suboptimal comparability of data remain major road blocks. The institution of an interactive consortium for high throughput molecular monitoring of clinical trials with voluntary participation might provide cost-effective solutions. PMID:19534815

  6. Bladder tumor markers: from hematuria to molecular diagnostics--where do we stand?

    PubMed

    Shirodkar, Samir P; Lokeshwar, Vinata B

    2008-07-01

    Bladder cancer is a common malignancy in the USA. Currently, the detection of initial tumors and recurrent disease is based on evaluation of voided urinary specimens, often followed by cystoscopy. With the high rate of recurrence, cystoscopies are regularly repeated with the aim of halting progression of the disease. For patients, this process is fraught with anxiety, pain and high cost. As a result, intense work is being done in the field of bladder tumor markers with the goal of identifying bladder cancer earlier, both in the initial diagnosis and in recurrences of known tumor. The possibility of identifying a marker that could noninvasively differentiate benign and malignant causes of hematuria, and identify recurrences prior to their pathologic progression is the objective of this area of research. Currently, a large number of tumor markers exist, each scrutinized in both the laboratory and in clinical trials. Here we present many of the most widely used and tested markers. Background details are provided as to the mechanism of detection of malignant cells, the results of recent trials and future directions of study. Some novel modalities for tumor detection are also presented. The next few years will no doubt bring newer markers and lead to the elimination of others. Studies continue to refine the role of these markers in clinical practice, but their ultimate efficacy will need to be borne out in large-scale clinical trials in a multitude of settings. PMID:18588456

  7. [Kohonen network study of the results of RAPD and ISSR analyses of genomic polymorphism in the genus Capsicum L].

    PubMed

    Ruanet, V V; Kochieva, E Z; Ryzhova, N N

    2005-02-01

    The results of studies based on multilocus molecular analyses, including random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and amplified fragment length polymorphism (AFLP) analyses, are usually presented in the form of images (electrophoregrams, photographs, etc.). The interpretation of this information is complicated, labor-consuming, and subjective. Artificial neural networks (ANNs), which are ideal "image processors," may be useful when solving such tasks. The possibility of using ANNs for the treatment of the results of RAPD and ISSR analyses has been studied. The RAPD and ISSR spectra have been studied in fragments of DNA of plants from the genus Capsicum L. (peppers). The results of clustering the accessions studied by means of the unweighted pair-group method with arithmetic averages (UPGMA), which is often used for phylogenetic constructions based on RAPD and ISSR data, serve as expert estimates. Fundamentally new methods of genetic polymorphism estimation using ANN technologies, namely, self-organizing feature maps (SOFMs) have been developed. The results show that the clusters obtained with the use of UPGMA and SOFM coincide by more than 90%; taking into account that ANNs can deal with high noise levels and incomplete or contradictory data, the approach proposed may prove to be efficient. PMID:15810617

  8. 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

  9. The comparison between allozyme and RAPD makers for the population genetic structure analysis of scallop Chlamys farreri

    NASA Astrophysics Data System (ADS)

    Liu, Baozhong; You, Feng; Dong, Bo; Xiang, Jianhai

    2006-09-01

    To compare genetic markers for population genetics analysis, allozyme electrophoresis and random amplified polymorphic DNA (RAPD) were used to detect the genetic structure of scallop Chlamys farreri population. Thirteen enzymes (MDH, ME, IDH, GPI, PGM, PEP-LG, PEP-PP, ACP, AK, PK, AAT, SOD, EST) in three buffer systems (TC, Ph6.9; TMME, Ph 7.4; and EBT, pH8.9) were selected and 22 loci were used for the analysis, among them 7 loci (Gpi, Pgm, Pep-LG-1, Pep-PP Aat-2, Est-2, Est-3) were polymorphic which attributed 31.82% to the total. The average of heterozygosity was 0.113 and most of the studied loci showed heterozygote deficiencies. The same specimens were investigated using 10 arbitrarily selected primers (10-base). Twenty two of 54 RAPD fragments were polymorphic with average heterozygosity of 0.194. The result indicated that the two types of markers reflected a consistent trend in the parameter values of genetic diversity of the population, but RAPD revealed more information of genetic variation than allozyme electrophoresis.

  10. Molecular diversity and population structure of the forage grass Hemarthria compressa (Poaceae) in south China based on SRAP markers.

    PubMed

    Huang, L-K; Zhang, X-Q; Xie, W-G; Zhang, J; Cheng, L; Yan, H D

    2012-01-01

    Hemarthria compressa is one of the most important and widely utilized forage crops in south China, owing to its high forage yield and capability of adaptation to hot and humid conditions. We examined the population structure and genetic variation within and among 12 populations of H. compressa in south China using sequence-related amplified polymorphism (SRAP) markers. High genetic diversity was found in these samples [percentage polymorphic bands (PPB) = 82.21%, Shannon's diversity index (I) = 0.352]. However, there was relatively low level of genetic diversity at the population level (PPB = 29.17%, I = 0.155). A high degree of genetic differentiation among populations was detected based on other measures and molecular markers (Nei's genetic diversity analysis: G(ST) = 54.19%; AMOVA analysis: F(ST) = 53.35%). The SRAP markers were found to be more efficient than ISSR markers for evaluating population diversity. Based on these findings, we propose changes in sampling strategies for appraising and utilizing the genetic resources of this species. PMID:22653675

  11. Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids.

    PubMed

    Villano, Clizia; Miraglia, Valeria; Iorizzo, Massimo; Aversano, Riccardo; Carputo, Domenico

    2016-03-01

    In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques. PMID:26663623

  12. 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

  13. Laboratory studies of oxidation of primary emissions: Oxidation of organic molecular markers and secondary organic aerosol production

    NASA Astrophysics Data System (ADS)

    Weitkamp, Emily A.

    Particulate matter (PM) is solid particles and liquid droplets of complex composition suspended in the atmosphere. In 1997, the National Ambient Air Quality Standards (NAAQS) for PM was modified to include new standards for fine particulate (particles smaller than 2.5mum, PM2.5) because of their association with adverse health effects, mortality and visibility reduction. Fine PM may also have large impacts on the global climate. Chemically, fine particulate is a complex mixture of organic and inorganic material, from both natural and anthropogenic sources. A large fraction of PM2.5 is organic. The first objective was to investigate heterogeneous oxidation of condensed-phase molecular markers for two major organic source categories, meat-cooking emissions and motor vehicle exhaust. Effective reaction rate constants of key molecular markers were measured over a range of atmospherically relevant experimental conditions, including a range of concentrations and relative humidities, and with SOA condensed on the particles. Aerosolized meat grease was reacted with ozone to investigate the oxidation of molecular markers for meat-cooking emissions. Aerosolized motor oil, which is chemically similar to vehicle exhaust aerosol and contains the molecular markers used in source apportionment, was reacted with the hydroxyl radical (OH) to investigate oxidation of motor vehicle molecular markers. All molecular markers of interest - oleic acid, palmitoleic acid, and cholesterol for meat-cooking emissions, and hopanes and steranes for vehicle exhaust - reacted at rates that are significant for time scales on the order of days assuming typical summertime oxidant concentrations. Experimental conditions influenced the reaction rate constants. For both systems, experiments conducted at high relative humidity (RH) had smaller reaction rate constants than those at low RH. SOA coating slowed the reaction rate constants for meat-cooking markers, but had no effect on the oxidation of vehicle markers. Aerosol composition is a key influence on reaction rate constants, perhaps more significant than external influences. Alkenoic acid concentrations in the meat grease particles appear to influence cholesterol oxidation rates. Also, the reaction rate constants for new motor oil were faster than those of the more viscous used motor oil. The measured reaction rate constants were used to oxidize source profiles that were subsequently run in the Chemical Mass Balance (CMB) model. Oxidizing the molecular markers in the meat-cooking profile led to unrealistically high meat-cooking aerosol contributions to the total organic carbon (OC), often more than 100%. This suggests that there is either unaccounted for sources of meat-cooking molecular markers in the ambient samples, or there is some property of atmospheric aerosols that significantly inhibits reaction that was not captured in this study. Oxidation of motor vehicle profiles led to both higher estimates of total vehicle OC and a quadrupling of gasoline OC, while the diesel contribution changed very little. The increase in gasoline OC changes gasoline vehicle emissions from a relatively minor source to a major one. Thus, oxidation of molecular markers can have a significant impact on receptor model predictions. The second objective was to investigate SOA formation from the photo-oxidation of whole diesel exhaust. Diluted exhaust from a diesel engine was photo-oxidized in a smog chamber to investigate SOA production. Photochemical oxidation rapidly produced significant SOA, almost doubling the organic aerosol contribution of primary emissions after several hours of processing. Less than 10% of the SOA mass could be explained using a SOA model and the measured oxidation of known precursors, such as light aromatics. However, the ultimate yield of SOA is uncertain because it is sensitive to treatment of particle and vapor losses to the chamber walls. Aerosol Mass Spectrometer (AMS) mass spectra reveal that the organic aerosol becomes progressively more oxidized throughout the experiments. The data provide strong evidence that oxidation of a wide array of precursors that are currently not accounted for in existing models contribute to ambient SOA formation. Results from this study have the potential to influence the way organic aerosols are treated in models. We provide evidence that two key assumptions used in models - that POA is non-reactive and that SOA is formed primarily from high volatility precursors - may not be valid. These assumptions can lead to the underestimation of important sources of OC. For example, assuming POA is non-reactive can lead to an underestimation of source contributions in receptor models, and assuming SOA is formed primarily from high-volatility precursors may overlook a major source of SOA. Our improved understanding of organic aerosol can be used to improve model estimates and better regulate emission sources.

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

    PubMed

    Palmieri, Darío A; Bechara, Marcelo D; Curi, Rogério A; Monteiro, Jomar P; Valente, Sérgio E S; Gimenes, Marcos A; Lopes, Catalina R

    2010-01-01

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

  15. 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.

  16. Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R.

    PubMed

    Pérez, Paulino; de Los Campos, Gustavo; Crossa, José; Gianola, Daniel

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression) implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO) in a unifi ed framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed. PMID:21566722

  17. Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

    PubMed Central

    Pérez, Paulino; de los Campos, Gustavo; Crossa, José; Gianola, Daniel

    2010-01-01

    The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression) implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO) in a unifi ed framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed. PMID:21566722

  18. A molecular approach towards the taxonomy of fresh water prawns Macrobrachium striatum and M. equidens (Decapoda, Palaemonidae) using mitochondrial markers.

    PubMed

    Jose, Deepak; Nidhin, B; Anil Kumar, K P; Pradeep, P J; Harikrishnan, M

    2016-07-01

    Genus Macrobrachium includes freshwater prawns which inhabit most diverse habitats ranging from low saline areas to inland hill streams and impounded water bodies. Being morphologically conserved, this genus has been exposed to severe disputes related to their taxonomy, systematics and phylogeny. Macrobrachium striatum and M. equidens represent two morphologically related congeneric species within this genus. Earlier, M. striatum was considered as a striped form of M. equidens. Though these species are now well-described morphologically and differentiated into two species, no molecular level investigation has been carried out in support of their speciation. We report a study on M. striatum and M. equidens with emphasis to their molecular data through mitochondrial markers (16S ribosomal RNA and cytochrome oxidase subunit I). Results obtained from developed molecular markers of the two species revealed considerable genetic differentiation between them. Phylogram generated using Minimum evolution and Neighbour joining analyses differentiated M. striatum and M. equidens as two independent species. Genetic distance data showed high interspecific divergence (ranging from 3.9% to 17.0% for 16S rRNA sequences and 13.8% to 21.0% for COI sequences) between M. striatum and M. equidens confirming the findings of phylogram. Hence, it could be delineated that M. striatum and M. equidens represent two distinct species within genus Macrobrachium with emphasis to their morphology and genetics. PMID:26119113

  19. Genetic stability assessment of plants regenerated from cryopreserved embryogenic tissues of Dioscorea bulbifera l. Using RAPD, biochemical and morphological analysis.

    PubMed

    Dixit, Sonali; Mandal, B B; Ahuja, Sangeeta; Srivastava, P S

    2003-01-01

    Embryogenic tissues of Dioscorea bulbifera were cryopreserved using the encapsulation-dehydration technique. Genetic stability of plants regenerated from cryopreserved embryogenic tissues was assessed using molecular, biochemical and morphological analysis. The random amplified polymorphic DNA (RAPD) analysis of 60 cryopreserved-derived and 20 in vitro grown (control) plantlets showed that 10 primers produced 62 clear reproducible DNA fragment profiles. The amplification products were monomorphic for all the plantlets except one. A total of 4960 DNA fragments were obtained from this study showing no variation in RAPD profiles. The diosgenin content of cryopreserved-derived plants, analyzed using HPLC, was similar to that of control plants. Morphology and the ability to form microtuber were also found to be unaltered in cryopreserved embryo-derived plantlets. Thus, the D. bulbifera plants regenerated from cryopreserved embryogenic tissues were genetically stable at the molecular, biochemical and morphological levels. PMID:12819828

  20. 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

  1. [Genetic relationships among Far Eastern species of the family Araliacea inferred by RAPD analysis].

    PubMed

    Zhuravlev, Iu N; Artiukova, E V; Kozyrenko, M M; Reunova, G D

    2003-01-01

    A molecular genetic study of Far Eastern species of the family Araliaceae by means of RAPD analysis was conducted. Using 21 primers we assessed variability at 595 loci. Based on matrices of genetic distances D, dendrograms of genetic relationships among eleven species of six genera of this family were constructed. Our results suggest that Acanthopanax sessiliflorus and Eleutherococcus senticosus belong to different genera, Aralia cordata and A. continentalis are different species, and A. elata and A. mandshurica probably cannot be regarded as distinct species. Genetic similarity of Far Eastern A. cordata and American A. hispida is shown. PMID:12624934

  2. GLOBAL EXPRESSION PROFILING AS A ROOL TO DEVELOP MOLECULAR MARKERS LINKED TO HERBICIDE STRESS IN ARABIDOPSIS

    EPA Science Inventory

    Herbicide drift (unintentional physical movement from target to off-target plants) is a cause of crop loss in US. Low-dose, high-potency herbicides that have short environmental persistence times constrain efforts to develop or identify metabolite or biochemical markers of exposu...

  3. A Molecular Marker-Based Linkage Map of Phaseolus Vulgaris L

    PubMed Central

    Vallejos, C. E.; Sakiyama, N. S.; Chase, C. D.

    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 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 betwen 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

  4. 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...

  5. 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...

  6. Molecular phylogeny of Lathyrus species: insights from sequence-related amplified polymorphism markers.

    PubMed

    Marghali, S; Touati, A; Gharbi, M; Sdouga, D; Trifi-Farah, N

    2016-01-01

    Sequence-related amplified polymorphism (SRAP) markers were used to evaluate the intra- and interspecific variation among 40 Lathyrus genotypes (four species) (Fabaceae). Ten SRAP primer combinations resulted in a total of 94 bands, and they exhibited high interspecific variability. The genetic differentiation among Lathyrus, estimated using AMOVA, was highly significant. The results indicated that 58% of the total genetic variation existed among species, and 42% of the differentiation was within species. This was explained by the high level of genome conservation of these species as well as the recent and slow evolution of this genus. These results were confirmed by the topology of the neighbor-joining cladogram and the results of the principal coordinate analysis. Our data support previous results based on seed protein diversity. These results make SRAP markers choice markers for the study of functional polymorphism that is directly related to the transcriptomic data. The SRAP markers used in this study provide an accurate picture of the population structure within Lathyrus germplasm, which is critically important information for the design of genetic diversity and structure analyses. Moreover, further extensive studies are necessary to fully examine other Lathyrus species and tests that adopt the SRAP technique to enrich the Lathyrus library for next-generation sequencing, thus providing a potent protocol for the study of polymorphism. PMID:27051021

  7. Molecular characterization of the marker chromosome associated with cat eye syndrome

    SciTech Connect

    Mears, A.J.; McDermid, H.E. ); Duncan, A.M.V. ); Budarf, M.L.; Emanuel, B.S.; Sellinger, B. ); Siegel-Bartelt, J. ); Greenberg, C.R. )

    1994-07-01

    Cat eye syndrome (CES) is associated with a supernumerary bisatellited marker chromosome which is derived from duplicated regions of 22pter-22q11.2. In this study the authors have used dosage and RFLP analyses on 10 CES patients with marker chromosomes, by using probes to five loci mapped to 22q11.2. The sequences recognized by the probes D22S9, D22S43, and D22S57 are in four copies in all patients, but the sequences at the more distal loci, D22S36 and D22S75, are duplicated only in some individuals. D22S36 is present in three copies in some individuals, and D22S75 is present in two copies in the majority of cases. Only three individuals have a duplication of the most distal locus examined (D22S75), and these individuals have the largest marker chromosomes identified in this study. From the dosage analysis it was found that the marker chromosomes are variable in size and can be asymmetric in nature. There is no obvious correlation between the severity of the phenotype and the size of the duplication. The distal boundary of the CES critical region (D22S36) is proximal to that of DiGeorge syndrome, a contiguous-gene-deletion syndrome of 22q11.2. 35 refs., 3 figs., 2 tabs.

  8. Molecular characterization of peach [Prunus persica (L.) Batsch] germplasm in the United States using microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peach [Prunus persica (L.) Batsch] is an important medicinal fruit with immense health benefits and antioxidant activity. In this study, microsatellite markers were used as DNA fingerprinting tools for the identification and characterization of peach germplasm in the United States. Eleven microsatel...

  9. 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 ...

  10. Identification of Single-Copy Orthologous Genes between Physalis and Solanum lycopersicum and Analysis of Genetic Diversity in Physalis Using Molecular Markers

    PubMed Central

    Wei, Jingli; Hu, Xiaorong; Yang, Jingjing; Yang, Wencai

    2012-01-01

    The genus Physalis includes a number of commercially important edible and ornamental species. Its high nutritional value and potential medicinal properties leads to the increased commercial interest in the products of this genus worldwide. However, lack of molecular markers prevents the detailed study of genetics and phylogeny in Physalis, which limits the progress of breeding. In the present study, we compared the DNA sequences between Physalis and tomato, and attempted to analyze genetic diversity in Physalis using tomato markers. Blasting 23180 DNA sequences derived from Physalis against the International Tomato Annotation Group (ITAG) Release2.3 Predicted CDS (SL2.40) discovered 3356 single-copy orthologous genes between them. A total of 38 accessions from at least six species of Physalis were subjected to genetic diversity analysis using 97 tomato markers and 25 SSR markers derived from P. peruviana. Majority (73.2%) of tomato markers could amplify DNA fragments from at least one accession of Physalis. Diversity in Physalis at molecular level was also detected. The average Nei’s genetic distance between accessions was 0.3806 with a range of 0.2865 to 0.7091. These results indicated Physalis and tomato had similarity at both molecular marker and DNA sequence levels. Therefore, the molecular markers developed in tomato can be used in genetic study in Physalis. PMID:23166835

  11. Molecular Diversity in Ukrainian Melon Collection as Revealed by AFLP and Microsatellite Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty-eight melon accessions, which are of primary breeding importance in the Ukraine, were analyzed for diversity. These collections represent a major non-US and non-west Europe source of melon germplasm that have not yet been subjected to molecular characterization. Molecular diversity was esti...

  12. 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...

  13. Anastomosis groups and molecular variation in Pseudocercospora griseola.

    PubMed

    Damasceno-Silva, K J; Souza, E A; Freire, C N S; Ishikawa, F H

    2015-01-01

    The fungus Pseudocercospora griseola is the causal agent of angular leaf spot, a common bean (Phaseolus vulgaris L.) disease. The successful development of angular leaf spot-resistant cultivars depends on understanding the levels of variability in pathogen populations. P. griseola shows great pathogenic and genetic variation using inoculation on differential bean cultivars and molecular markers. Nevertheless, how this variability develops is not clearly understood. Parasexuality has been presented as a mechanism used by asexual fungi to increase variation. Hyphal fusion is the first step for the parasexual cycle, and it can be considered an additional trait for population studies. The aim of this study was to identify hyphal fusion (anastomosis) among P. grisola isolates and to evaluate the variability of isolates using analyses of anastomosis groups and RAPD markers. Hyphal anastomosis was observed in all isolates. Three isolates showed 85.0% compatibility and were compatible with 17 isolates. This is the first report of the occurrence of anastomosis between P. griseola isolates. Sixteen anastomosis groups were observed and only one group was formed by five isolates (Pg-01, Pg-02, Pg-07, Pg-08, and Pg-12). There was a large number of anastomosis groups and absence of clustering among isolates for hyphal fusion, demonstrating the existence of genetic variability for loci involved in the control of this trait. High genotypic variability by RAPD markers was detected, but there was no relationship between genotype and anastomosis group. More studies are necessary to elucidate further the process of asexual recombination in this phytopathogen. PMID:26214422

  14. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics

    PubMed Central

    Harper, Andrea L.; McKinney, Lea Vig; Nielsen, Lene Rostgaard; Havlickova, Lenka; Li, Yi; Trick, Martin; Fraser, Fiona; Wang, Lihong; Fellgett, Alison; Sollars, Elizabeth S. A.; Janacek, Sophie H.; Downie, J. Allan; Buggs, Richard. J. A.; Kjær, Erik Dahl; Bancroft, Ian

    2016-01-01

    Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback. PMID:26757823

  15. Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.

    PubMed

    Harper, Andrea L; McKinney, Lea Vig; Nielsen, Lene Rostgaard; Havlickova, Lenka; Li, Yi; Trick, Martin; Fraser, Fiona; Wang, Lihong; Fellgett, Alison; Sollars, Elizabeth S A; Janacek, Sophie H; Downie, J Allan; Buggs, Richard J A; Kjær, Erik Dahl; Bancroft, Ian

    2016-01-01

    Tree disease epidemics are a global problem, impacting food security, biodiversity and national economies. The potential for conservation and breeding in trees is hampered by complex genomes and long lifecycles, with most species lacking genomic resources. The European Ash tree Fraxinus excelsior is being devastated by the fungal pathogen Hymenoscyphus fraxineus, which causes ash dieback disease. Taking this system as an example and utilizing Associative Transcriptomics for the first time in a plant pathology study, we discovered gene sequence and gene expression variants across a genetic diversity panel scored for disease symptoms and identified markers strongly associated with canopy damage in infected trees. Using these markers we predicted phenotypes in a test panel of unrelated trees, successfully identifying individuals with a low level of susceptibility to the disease. Co-expression analysis suggested that pre-priming of defence responses may underlie reduced susceptibility to ash dieback. PMID:26757823

  16. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus

    SciTech Connect

    Darvasi, A.; Soller, M.

    1994-12-01

    Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: {open_quotes}selective DNA pooling{close_quotes}) takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F{sub 2} and half-sib designs, the power of selective DNA pooling for detecting genes with large effect can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. 25 refs., 3 figs., 3 tabs.

  17. Molecular identification and genetic variation of varieties of Styphnolobium japonicum (Fabaceae) using SRAP markers.

    PubMed

    Sun, R X; Zhang, C H; Zheng, Y Q; Zong, Y C; Yu, X D; Huang, P

    2016-01-01

    Thirty-four Styphnolobium japonicum varieties were analyzed using sequence-related amplified polymorphism (SRAP) markers, to investigate genetic variation and test the effectiveness of SRAP markers in DNA fingerprint establishment. Twelve primer pairs were selected from 120 primer combinations for their reproducibility and high polymorphism. We found a total of 430 amplified fragments, of which 415 fragments were considered polymorphic with an average of 34.58 polymorphic fragments for each primer combination. The percentage of polymorphic fragments was 96.60%, and four primer pairs showed 100% polymorphism. Moreover, simple matched coefficients ranged between 0.68 and 0.89, with an average of 0.785, indicating that the genetic variation among varieties was relatively low. This could be because of the narrow genetic basis of the selected breeding material. Based on the similarity coefficient value of 0.76, the varieties were divided into four major groups. In addition, abundant and clear SRAP fingerprints were obtained and could be used to establish DNA fingerprints. In the DNA fingerprints, each variety had its unique pattern that could be easily distinguished from others. The results demonstrated that 34 varieties of S. japonicum had a relatively narrow genetic variation. Hence, a broadening of the genetic basis of breeding material is necessary. We conclude that establishment of DNA fingerprint is feasible by means of SRAP markers. PMID:27173318

  18. Molecular markers for species identification of Hessian fly males caught on sticky pheromone traps.

    PubMed

    Chen, Ming-Shun; Wheeler, Shanda; Davis, Holly; Whitworth, R Jeff; Knutson, Allen; Giles, Kristopher L; Royer, Tom A; Skinner, Margaret

    2014-06-01

    Pheromone traps have been widely used to monitor insect population activity. However, sticky pheromone traps for the Hessian fly (Mayetiola destructor), one of the most destructive pests of wheat, have been used only in recent years. Hessian fly male adults are small and fragile, and preserving specimens during sorting of sticky pheromone traps is a challenge when intact specimens are often required to visually distinguish them from related insects such as fungus gnats. In this study, we have established a quick and reliable method based on polymerase chain reaction markers to correctly distinguish Hessian fly males from other closely related insects. Two Hessian fly-specific markers were established, one based on the trypsin gene MDP-10 and the other based on a gene encoding the salivary gland protein SSGP31-5. Both markers provided > 98% identification success of 110 Hessian fly samples prepared from single insects. The method should provide a useful tool to allow for identification of Hessian fly individuals on sticky pheromone traps or in other situations when Hessian fly eggs, larvae, pupae, and adults are difficult to distinguish from other insects. PMID:25026671

  19. Selective DNA Pooling for Determination of Linkage between a Molecular Marker and a Quantitative Trait Locus

    PubMed Central

    Darvasi, A.; Soller, M.

    1994-01-01

    Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: ``selective DNA pooling'') takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F(2) and half-sib designs, the power of selective DNA pooling for detecting genes with large effect, can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. PMID:7896115

  20. Identification of a novel mitochondrial genome type and development of molecular markers for cytoplasm classification in radish (Raphanus sativus L.).

    PubMed

    Kim, Sunggil; Lim, Heerae; Park, Suhyung; Cho, Kang-Hee; Sung, Soon-Kee; Oh, Dae-Geun; Kim, Ki-Taek

    2007-11-01

    Plant mitochondrial genomes have complex configurations resulting from the multipartite structures and highly rearranged substoichiometric molecules created by repetitive sequences. To expedite the reliable classification of the diverse radish (Raphanus sativus L.) cytoplasmic types, we have developed consistent molecular markers within their complex mitochondrial genomes. orf138, a gene responsible for Ogura male-sterility, was detected in normal cultivars in the form of low-copy-number substoichiometric molecules. In addition to the dominant orf138-atp8 Ogura mitochondrial DNA (mtDNA) organization, three novel substoichiometric organizations linked to the atp8 gene were identified in this study. PCR amplification profiles of seven atp8- and atp6-linked sequences were divided into three groups. Interestingly, the normal cytoplasm type, which had previously been considered a single group, showed two patterns by PCR amplification. The most prominent difference between the two normal mtDNAs was size variation within four short-repeat sequences linked to the atp6 gene. This variation appeared to be the result of a double crossover, mediated by these homologous, short-repeat sequences. Specific PCR amplification profiles reflecting the stoichiometry of different mtDNA fragments were conserved within cultivars and across generations. Therefore, the specific sequences detected in these profiles were used as molecular markers for the classification of diverse radish germplasm. Using this classification system, a total of 90 radish cultivars, or accessions, were successfully assigned to three different mitotypes. PMID:17828522

  1. 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

  2. Integration of the Classical and Molecular Linkage Maps of Tomato Chromosome 6

    PubMed Central

    Weide, R.; van-Wordragen, M. F.; Lankhorst, R. K.; Verkerk, R.; Hanhart, C.; Liharska, T.; Pap, E.; Stam, P.; Zabel, P.; Koornneef, M.

    1993-01-01

    In the past, a classical map of the tomato genome has been established that is based on linkage data from intraspecific Lycopersicon esculentum crosses. In addition, a high density molecular linkage map has recently been constructed using a L. esculentum X L. pennellii cross. As the respective maps only partially match, they provide limited information about the relative positions of classical and molecular markers. In this paper we describe the construction of an integrated linkage map of tomato chromosome 6 that shows the position of cDNA-, genomic DNA- and RAPD markers relative to 10 classical markers. Integration was achieved by using a L. esculentum line containing an introgressed chromosome 6 from L. pennellii in crosses to a variety of L. esculentum marker lines. In addition, an improved version of the classical linkage map is presented that is based on a combined analysis of new linkage data for 16 morphological markers and literature data. Unlike the classical map currently in use, the revised map reveals clustering of markers into three major groups around the yv, m-2 and c loci, respectively. Although crossing-over rates are clearly different when comparing intraspecific L. esculentum crosses with L. esculentum X L. pennellii crosses, the clusters of morphological markers on the classical map coincide with clusters of genomic- and cDNA-markers on the molecular map constructed by Tanksley and coworkers. PMID:7905845

  3. Identification of Diploid Stylosanthes seabrana accessions from existing germplasm of S. scabra utilizing genome-specific STS markers and flow cytometry, and their molecular characterization.

    PubMed

    Chandra, Amaresh; Kaushal, Pankaj

    2009-07-01

    Stylosanthes seabrana (Maass and 't Mannetje) (2n = 2x = 20), commonly known as Caatinga stylo, is an important tropical perennial forage legume. In nature, it largely co-exist with S. scabra, an allotetraploid (2n = 4x = 40) species, sharing a very high similarity for morphological traits like growth habit, perenniality, fruit shape and presence of small appendage at the base of the pod or loment. This makes the two species difficult to distinguish morphologically, leading to chances of contamination in respective germplasm collections. In present study, 10 S. seabrana accessions were discovered from the existing global germplasm stock of S. scabra represented by 48 diverse collections, utilizing sequence-tagged-sites (STS) genome-specific markers. All the newly identified S. seabrana accessions displayed STS phenotypes of typical diploid species. Earlier reports have conclusively indicated S. seabrana and S. viscosa as two diploid progenitors of allotetraploid S. scabra. With primer pairs SHST3F3/R3, all putative S. seabrana yielded single band of approximately 550 bp and S. viscosa of approximately 870 bp whereas both of these bands were observed in allotetraploid S. scabra. Since SHST3F3/R3 primer pairs are known to amplify single or no band with diploid and two bands with tetraploid species, the amplification patterns corroborated that all newly identified S. seabrana lines were diploid in nature. Flow cytometric measurement of DNA content of the species, along with distinguishing morphological traits such as flowering time and seedling vigour, which significantly differ from S. scabra, confirmed all identified lines as S. seabrana. These newly identified lines exhibited high level of similarity among themselves as revealed by RAPD and STS markers (>92% and 80% respectively). Along with the enrichment in genetic resources of Stylosanthes, these newly identified and characterized accessions of S. seabrana can be better exploited in breeding programs targeted to quality. PMID:19214807

  4. Cancer Associated Fibroblasts in Stage I-IIIA NSCLC: Prognostic Impact and Their Correlations with Tumor Molecular Markers

    PubMed Central

    Kilvaer, Thomas K.; Khanehkenari, Mehrdad Rakaee; Hellevik, Turid; Al-Saad, Samer; Paulsen, Erna-Elise; Bremnes, Roy M.; Busund, Lill-Tove

    2015-01-01

    Background Cancer Associated Fibroblasts (CAFs) are thought to regulate tumor growth and metastasis. Fibroblast Activating Protein 1 (FAP-1) is a marker for fibroblast activation and by many recognized as the main marker of CAFs. Alpha Smooth Muscle Actin (α-SMA) is a general myofibroblast marker, and can be used to identify CAFs. This study investigates the prognostic impact of FAP-1 and α-SMA in non-small cell lung cancer (NSCLC) patients and correlates their expression to 105 proteins investigated in the same cohort. Methods Tumor specimens from 536 NSCLC patients were obtained and tissue micro-arrays were constructed. Immunohistochemistry was used to evaluate the expression of FAP-1 and α-SMA and explore their impact on survival and association with other tumor molecular markers in NSCLC patients. Results High expression of FAP-1, but not α-SMA, in squamous cell carcinoma (SCC, P = 0.043, HR = 0.63 95% CI 0.40–0.99) was significantly associated with increased disease-specific survival. FAP-1 and α-SMA were not significantly correlated to each other. Analyses of FAP-1 and α-SMA associated with other tumor-related proteins revealed histotype-specific correlation patterns. Conclusion The presence of FAP-1 expressing CAFs is an indicator of positive outcome for NSCLC-SCC patients. In addition, correlation analyses suggest FAP-1 and α-SMA to label different subsets of fibroblasts and their associations with other tumor-related proteins diverge according to histological subtype. PMID:26252379

  5. Molecular and immunocytochemical characterization of primary neuronal cultures from adult rat brain: Differential expression of neuronal and glial protein markers.

    PubMed

    Ray, Balmiki; Bailey, Jason A; Sarkar, Sumit; Lahiri, Debomoy K

    2009-11-15

    Neurobiological studies using primary neuronal cultures commonly employ fetal-derived neurons, but much less often adult brain-derived neurons. Our goal is to perform morphological and molecular characterization of primary neuronal cultures from adult rat brain, including the relative expression of neuronal and glial cell markers at different time points. We tested the hypothesis that long-term neuronal viability is compatible with glial proliferation in adult neuron culture. We examined neuron culture from adult rat brain, which was maintained at steady state up to 24 days, and characterized them on the basis of cellular, molecular and biochemical properties at different time points of the culture. We identified neuronal and glial cells by both immunocytochemical and western immunoblotting techniques using NSE and Tau as neuronal markers and GFAP as glial protein marker, which revealed the presence of predominantly neuronal cells in the initial phase of the culture and a rise in glial cells from day 12 onwards. Notably, neuronal cells were preserved in the culture along with the glial cells even at day 24. Transfection of the cultured cells with a GFP expression vector and plasmids containing a luciferase reporter gene under the control of two different gene promoters demonstrated DNA transfectability. Taken together, these results suggest a differential expression of neuronal and glial cells at different time points and long-term neuronal viability in the presence of glial proliferation. Such adult neurons serve as a suitable system for the application of neurodegeneration models and for drug target discovery in various brain disorders including Alzheimer's disease. PMID:19720084

  6. Molecular and immunocytochemical characterization of primary neuronal cultures from adult rat brain: differential expression of neuronal and glial protein markers

    PubMed Central

    Ray, Balmiki; Bailey, Jason A.; Sarkar, Sumit; Lahiri, Debomoy K

    2010-01-01

    Neurobiological studies using primary neuronal cultures commonly employ fetal-derived neurons, but much less often adult brain-derived neurons. Our goal is to perform morphological and molecular characterization of primary neuronal cultures from adult rat brain, including the relative expression of neuronal and glial cell markers at different time points. We tested the hypothesis that long-term neuronal viability is compatible with glial proliferation in adult neuron culture. We examined neuron culture from adult rat brain, which was maintained at steady state up to 24 days, and characterized them on the basis of cellular, molecular and biochemical properties at different time points of the culture. We identified neuronal and glial cells by both immunocytochemical and western immunoblotting techniques using NSE and Tau as neuronal markers and GFAP as glial protein marker, which revealed the presence of predominantly neuronal cells in the initial phase of the culture and a rise in glial cells from day 12 onwards. Notably, neuronal cells were preserved in the culture along with the glial cells even at day 24. Transfection of the cultured cells with a GFP expression vector and plasmids containing a luciferase reporter gene under control of two different gene promoters demonstrated DNA transfectability. Taken together, these results suggest a differential expression of neuronal and glial cells at different time points and long-term neuronal viability in the presence of glial proliferation. Such adult neurons serve as a suitable system for the application of neurodegenaration models and for drug target discovery in various brain disorders including Alzheimer’s disease. PMID:19720084

  7. RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae)

    PubMed Central

    Lin, Yu-Shium; Chang, Chia-Hung; Chiang, Yu-Chung; Chou, Chang-Hung

    2015-01-01

    Background The moth orchid (Phalaenopsis species) is an ornamental crop that is highly commercialized worldwide. Over 30,000 cultivars of moth orchids have been registered at the Royal Horticultural Society (RHS). These cultivars were obtained by artificial pollination of interspecific hybridization. Therefore, the identification of different cultivars is highly important in the worldwide market. Methods/Results We used Illumina sequencing technology to analyze an important species for breeding, Phalaenopsis aphrodite subsp. formosana and develop the expressed sequence tag (EST)-simple sequence repeat (SSR) markers. After de novo assembly, the obtained sequence covered 29.1 Mb, approximately 2.2% of the P. aphrodite subsp. formosana genome (1,300 Mb), and a total of 1,439 EST-SSR loci were detected. SSR occurs in the exon region, including the 5’ untranslated region (UTR), coding region (CDS), and 3’UTR, on average every 20.22 kb. The di- and tri-nucleotide motifs (51.49% and 35.23%, respectively) were the two most frequent motifs in the P. aphrodite subsp. formosana. To validate the developed EST-SSR loci and to evaluate the transferability to the genus Phalaenopsis, thirty tri-nucleotide motifs of the EST-SSR loci were randomly selected to design EST-SSR primers and to evaluate the polymorphism and transferability across 22 native Phalaenopsis species that are usually used as parents for moth orchid breeding. Of the 30 EST-SSR loci, ten polymorphic and transferable SSR loci across the 22 native taxa can be obtained. The validated EST-SSR markers were further proven to discriminate 12 closely related Phalaenopsis cultivars. The results show that it is not difficult to obtain universal SSR markers by transcriptome deep sequencing in Phalaenopsis species. Conclusions This study supported that transcriptome analysis based on deep sequencing is a powerful tool to develop SSR loci in non-model species. A large number of EST-SSR loci can be isolated, and about 33.33% EST-SSR loci are universal markers across the Phalaenopsis breeding germplasm after preliminary validation. The potential universal EST-SSR markers are highly valuable for identifying all of Phalaenopsis cultivars. PMID:26523377

  8. Molecular markers discriminate closely related species Encarsia diaspidicola and Encarsia berlesei (Hymenoptera: Aphelinidae): biocontrol candidate agents for white peach scale in Hawaii.

    PubMed

    De León, Jesse H; Neumann, Gabor; Follett, Peter A; Hollingsworth, Robert G

    2010-06-01

    We genetically characterized Encarsia diapsidicola Silvestri and Encarsia berlesei Howard (Hymenoptera: Aphelinidae) by two molecular methods: phylogenetic analysis of the cytochrome oxidase subunit I gene (COI) and intersimple sequence repeat-polymerase chain reaction (ISSR-PCR) DNA fingerprinting. These two closely related endoparasitoids are candidate biological control agents for the white peach scale, Pseudaulacaspis pentagona Targioni-Tozetti (Hemiptera: Diaspididae), in Hawaii. We developed species-specific COI molecular markers that discriminated the two species, and we tested the utility of the E. diaspidicola-specific COI marker to detect parasitism of white peach scale. The COI sequence data uncovered 46-bp differences between the two Encarsia spp. The level of COI genetic divergence between the two species was 9.7%, and the two clustered into their own clade on a parismonious phylogram. ISSR-PCR readily discriminated the two Encarsia spp. because each was observed with fixed species-specific banding patterns. The COI molecular markers were specific for each species because cross-reactivity was not observed with nontarget species. The E. diaspidicola-specific COI markers were successful at detecting parasitism of white peach scale by E. diaspidicola by 24 h. Both molecular marker types successfully discriminated the two Encarsia spp., whereas the COI markers will be useful as tools to assess levels of parasitism in the field and to study competitive interactions between parasitoids. PMID:20568638

  9. The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

    PubMed

    Damasceno, L S; Leitão, T M J S; Taylor, M L; Muniz, M M; Zancopé-Oliveira, R M

    2016-01-01

    Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations. PMID:26589702

  10. Identification of fish species using random amplified polymorphic DNA (RAPD).

    PubMed

    Partis, L; Wells, R J

    1996-12-01

    The random amplified polymorphic DNA (RAPD) method was investigated as a potential fish species identification method. One hundred and sixteen specimens from eight species of fish were analysed. The eight species tested were barramundi, Nile perch, john dory, mirror dory, silver dory, spikey oreo, warty oreo and smooth oreo. The predominant species tested was barramundi; 80 specimens of this species were analysed. Of these samples, 42 had been individually verified by independent sources. The RAPD profiles generated were consistent within this group. The remaining samples were retail purchased and consisted of 24 imports and eight local whole small barramundi and six fillets. All of the whole barramundi, including the imported fish, generated profiles which agreed with the verified samples. Four of the six fillets purchased did not match the typical barramundi profile, three profiles, however, were consistent with those generated for Nile perch. Species-specific profiles were also generated for the other seven species analysed by RAPD. One john dory, from five fillets tested, did not comply with the six authenticated sample. All of the RAPD profiles were resolved by agarose gel electrophoresis. Forty nine RAPD profiles including those that did not match were also confirmed by native polyacrylamide gel electrophoresis (PAGE) on a DNA sequencer. PMID:9025081

  11. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis.

    PubMed

    Walter, Stephanie; Ali, Sajid; Kemen, Eric; Nazari, Kumarse; Bahri, Bochra A; Enjalbert, Jérôme; Hansen, Jens G; Brown, James K M; Sicheritz-Pontén, Thomas; Jones, Jonathan; de Vallavieille-Pope, Claude; Hovmøller, Mogens S; Justesen, Annemarie F

    2016-05-01

    Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2. PMID:27066253

  12. Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water.

    PubMed

    Ahmed, W; Staley, C; Sadowsky, M J; Gyawali, P; Sidhu, J P S; Palmer, A; Beale, D J; Toze, S

    2015-10-01

    In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. PMID:26231650

  13. Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

    PubMed Central

    Staley, C.; Sadowsky, M. J.; Gyawali, P.; Sidhu, J. P. S.; Palmer, A.; Beale, D. J.; Toze, S.

    2015-01-01

    In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. PMID:26231650

  14. 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 α-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 α-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 α-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.

  15. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

    PubMed

    Bhandari, Vaibhav; Naushad, Hafiz S; Gupta, Radhey S

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies. PMID:22919687

  16. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution

    PubMed Central

    Bhandari, Vaibhav; Naushad, Hafiz S.; Gupta, Radhey S.

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. Th