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1

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...

2

Molecular characterization of ten cultivars of Canna lilies (Canna Linn.) using PCR based molecular markers (RAPDs and ISSRs)  

Microsoft Academic Search

Molecular markers like RAPD and ISSR were used to study the genomic affinity among 10 cultivars of Canna lilies (Canna linn.). 15 numbers of decamer oligonucleotide primers produced a total of 103 bands out of which 20 were monomorphic and among the polymorphic bands there were 16 unique bands. Three ISSR primers produced 27 bands among which there were 21

Biswabijayinee Patra; Laxmikanta Acharya; Arup Kumar Mukherjee; Manoj Kumar Panda; Pratap Chandra Panda

3

Isolation of molecular markers for tomato ( L. esculentum ) using random amplified polymorphic DNA (RAPD)  

Microsoft Academic Search

A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (“RAPD mapping”). We have now adapted the

R. M. Klein-Lankhorst; A. Vermunt; R. Weide; T. Liharska; P. Zabel

1991-01-01

4

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

Microsoft Academic Search

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

Greg J. Hunt; Robert E. Page

1992-01-01

5

Molecular identification of tropical tasar silkworm (Antheraea mylitta) ecoraces with RAPD and SCAR markers.  

PubMed

The tropical tasar silkworm, Antheraea mylitta, has several ecoraces, 10 of which are commercially exploited for the production of tasar silk. These ecoraces are identified by morphological markers that are greatly influenced by photoperiod, humidity, altitude, and host plants. The DNA markers, random amplification of polymorphic DNA (RAPD), and sequence-characterized amplified region (SCAR) are identified to complement the existing morphological markers. Seven RAPD bands are selected that identify 8 of the 10 ecoraces. These identified RAPD fragments are sequenced and primers are designed for SCAR markers. Of the seven sets of primers, a single primer pair produced polymorphic SCAR bands that diagnose 5 of the 10 ecoraces. All 10 ecoraces are identified by the use of RAPD and SCAR markers together. PMID:16648996

Saha, Monalee; Kundu, S C

2006-04-29

6

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

PubMed

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

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

2009-04-06

7

Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L. using RAPD, AFLP and SSR markers.  

PubMed

Jatropha curcas L., a multipurpose shrub has acquired significant economic importance for its seed oil which can be converted to biodiesel, is emerging as an alternative to petro-diesel. The deoiled seed cake remains after oil extraction is toxic and cannot be used as a feed despite having best nutritional contents. No quantitative and qualitative differences were observed between toxic and non-toxic varieties of J. curcas except for phorbol esters content. Development of molecular marker will enable to differentiate non-toxic from toxic variety in a mixed population and also help in improvement of the species through marker assisted breeding programs. The present investigation was undertaken to characterize the toxic and non-toxic varieties at molecular level and to develop PCR based molecular markers for distinguishing non-toxic from toxic or vice versa. The polymorphic markers were successfully identified specific to non-toxic and toxic variety using RAPD and AFLP techniques. Totally 371 RAPD, 1,442 AFLP markers were analyzed and 56 (15.09%) RAPD, 238 (16.49%) AFLP markers were found specific to either of the varieties. Genetic similarity between non-toxic and toxic verity was found to be 0.92 by RAPD and 0.90 by AFLP fingerprinting. In the present study out of 12 microsatellite markers analyzed, seven markers were found polymorphic. Among these seven, jcms21 showed homozygous allele in the toxic variety. The study demonstrated that both RAPD and AFLP techniques were equally competitive in identifying polymorphic markers and differentiating both the varieties of J. curcas. Polymorphism of SSR markers prevailed between the varieties of J. curcas. These RAPD and AFLP identified markers will help in selective cultivation of specific variety and along with SSRs these markers can be exploited for further improvement of the species through breeding and Marker Assisted Selection (MAS). PMID:18642099

Sudheer Pamidimarri, D V N; Singh, Sweta; Mastan, Shaik G; Patel, Jalpa; Reddy, Muppala P

2008-07-19

8

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

PubMed

Lentil (Lens culinaris ssp. culinaris), is a self-pollinating diploid (2n = 2x = 14), cool-season legume crop and is consumed worldwide as a rich source of protein (~24.0%), largely in vegetarian diets. Here we report development of a genetic linkage map of Lens using 114 F(2) plants derived from the intersubspecific cross between L 830 and ILWL 77. RAPD (random amplified polymorphic DNA) primers revealed more polymorphism than ISSR (intersimple sequence repeat) and SSR (simple sequence repeat) markers. The highest proportion (30.72%) of segregation distortion was observed in RAPD markers. Of the 235 markers (34 SSR, 9 ISSR and 192 RAPD) used in the mapping study, 199 (28 SSRs, 9 ISSRs and 162 RAPDs) were mapped into 11 linkage groups (LGs), varying between 17.3 and 433.8 cM and covering 3843.4 cM, with an average marker spacing of 19.3 cM. Linkage analysis revealed nine major groups with 15 or more markers each and two small LGs with two markers each, and 36 unlinked markers. The study reported assigning of 11 new SSRs on the linkage map. Of the 66 markers with aberrant segregation, 14 were unlinked and the remaining 52 were mapped. ISSR and RAPD markers were found to be useful in map construction and saturation. The current map represents maximum coverage of lentil genome and could be used for identification of QTL regions linked to agronomic traits, and for marker-assisted selection in lentil. PMID:23271013

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

2012-12-01

9

Use of RAPD and ITE molecular markers in studying the genetic structure of the Crimean population of T. boeoticum Boiss  

Microsoft Academic Search

The influence of ecological factors on variation of random PCR markers (RAPD and inter-MITE polymorphism (IMP) primers) was\\u000a evaluated in two wild Triticum boeoticum populations with contrasting climatic conditions in Crimea. The proportion of variation that undergoes natural selection\\u000a was compared for these two types of molecular markers. The Sapun Mountain and Baidar Valley populations differed significantly\\u000a in 24.7% of

D. Sh. Mallabaeva; A. N. Ignatov; I. A. Sheiko; V. P. Isikov; V. P. Gelyuta; N. G. Boiko; A. A. Seryapin; D. B. Dorokhov

2007-01-01

10

Molecular characterization of eight Indian Snakehead species (Pisces: Perciformes Channidae) using RAPD markers  

Microsoft Academic Search

Murrels (Perciformes; Channidei; Channidae) are unique group of freshwater air breathing fishes having a confined distribution\\u000a to African and Asian continents. The phylogenetic relationship among eight Channid species viz.\\u000a Channa aurantimaculata, Channa bleheri, Channa diplogramma, Channa gachua, Channa marulius, Channa punctatus, Channa stewartii and Channa striatus were investigated using RAPD markers. Eight random oligodecamers viz. OPAC03, OPAC05, OPAC07, OPAC09, OPAC19,

Ajaz Ali Bhat; M. A. Haniffa; P. R. Divya; A. Gopalakrishnan; M. James Milton; Raj Kumar; Bilal Ahmad Paray

11

Genetic diversity in Hemileia vastatrix based on RAPD markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust iso- lates with different virulence spectra and from dif- ferent hosts and geographical regions were ana- lyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstruc- tured variability of

M. M. C. Gouveia; A. Ribeiro; V. M. P. Varzea; C. J. Rodrigues

2005-01-01

12

Molecular characterization of some Egyptian date palm germplasm using RAPD and ISSR markers  

Microsoft Academic Search

The genetic variability and relationships among 14 date palm (Phoenix dactylifera L.) accessions representing six Egyptian cultivars were assayed using 27 RAPD and 10 ISSR primers. The level of polymorphism among the 14 accessions as revealed by RAPD and ISSR was 25.2% and 28.6%, respectively. These low levels of polymorphism reflect the narrow genetic background of these accessions. The genetic

Ebtissam H. A. Hussein; Sami S. Adawy; Samer E. M. E. Ismail; Hanaiya A. El-Itriby

13

Análisis de dos poblaciones de gallinas criollas (Gallus domesticus) utilizando RAPDs como marcadores moleculares An analysis of two native poultry populations (Gallus domesticus) using RAPD's as molecular markers  

Microsoft Academic Search

México has a great variety of native poultry but knowledge about its diversity is minimal. In this study, twenty individuals belonging to two populations of native hens (Gallus domesticus) were analyzed. They were chosen by egg production, through polymorphism identification generated by DNA random amplification (RAPD's). Amplification generated products show different sizes between 0.2 to 1.1 kb. Polymorphism was detected

Irma Morelia Soto Huipe; Guadalupe Zavala Páramoa; Horacio Cano Camacho; Joel E. López Meza

14

Identification of apple cultivars using RAPD markers  

Microsoft Academic Search

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

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

1993-01-01

15

Microorganism screening for limonene bioconversion and correlation with RAPD markers.  

PubMed

The use of microorganisms for biotransformations of monoterpenes has stimulated the biotechnological market. Aiming at the highest efficiency in the process of strains screening, the application of molecular biology techniques have been proposed. Based on these aspects, the objective of this work was to select different strains able to convert limonene using fermentative process and random amplified polymorphic DNA (RAPD) markers. The results obtained in the fermentative screening, from 17 strains tested, pointed out that four microorganisms were able to convert limonene into oxygenated derivatives. The RAPD study showed a polymorphism of 96.02% and a similarity from 16.02 to 51.51%. Based on this it was possible to observe a high genetic diversity, even among strains of same species, concluding that the RAPD was not able to correlate the genetic characteristics of the microorganism with the results obtained from the biotransformation process. PMID:16915709

Toniazzo, Geciane; Lerin, Lindomar; de Oliveira, Débora; Dariva, Claudio; Cansian, Rogério L; Padilha, Francine Ferreira; Antunes, Octávio A C

2006-01-01

16

Efficiency of Arbitrarily Amplified Dominant Markers (SCOT, ISSR and RAPD) for Diagnostic Fingerprinting in Tetraploid Potato  

Microsoft Academic Search

Three molecular markering techniques: start codon targeted (SCOT), inter-simple sequence repeat (ISSR) and random amplified\\u000a polymorphic DNA (RAPD) markers were compared for fingerprinting of 24 varieties and a segregating population of tetraploid\\u000a potato. The number of scoreable and polymorphic bands produced using the SCOT, ISSR and RAPD primers for varieties was more\\u000a than that of genotypes. SCOTs markers were more

Ahmad Mousapour Gorji; Peter Poczai; Zsolt Polgar; Janos Taller

2011-01-01

17

The use of RAPD markers for detecting genetic diversity, relationship and molecular identification of Chinese elite tea genetic resources [ Camellia sinensis (L.) O. Kuntze] preserved in a tea germplasm repository  

Microsoft Academic Search

The genetic diversity, relationship and molecular identification of 15 well known, widely planted traditional Chinese elite tea genetic resources [Camellia sinensis (L.) O. Kuntze] preserved in the China National Germplasm Hangzhou Tea Repository in the Tea Research Institute of the Chinese Academy of Agricultural Sciences located in Zhejiang province, China, were investigated using RAPD markers. A total of 1050 bands

Liang Chen; Qi-kang Gao; Da-ming Chen; Chang-jie Xu

2005-01-01

18

RAPDs as molecular markers for the detection of Aegilops markgrafii chromatin in addition and euploid introgression lines of hexaploid wheat  

Microsoft Academic Search

Aegilops markgrafii contains resistance genes to powdery mildew, leaf rust and stripe rust, and also has high crude protein and lysine contents,\\u000a which can be useful for wheat improvement. These important traits are localized on different chromosomes. Disomic Triticum aestivum-Ae. markgrafii addition lines and euploid introgression lines showing leaf-rust and powdery mildew resistance were screened with RAPDs to\\u000a detect chromosome-specific

A. Peil; V. Schubert; E. Schumann; W. E. Weber

1997-01-01

19

Variation in Capsicum annuum revealed by RAPD and AFLP markers  

Microsoft Academic Search

Genetic relationships were examined among thirty-four pepper (Capsicum annuum) cultivars of different types. Two types of\\u000a PCR-based markers were used, RAPD and AFLP, and their relative effectiveness was compared. A dendrogram based on RAPD markers\\u000a separated the large-fruited sweet cultivars from the small-fruited pungent peppers, and the former group showed less divergence\\u000a than the latter. The percentage of polymorphic markers

Ilan Paran; Ester Aftergoot; Chen Shifriss

1998-01-01

20

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

PubMed Central

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.

2009-01-01

21

Molecular markers derived from RAPD, SCAR, and the conserved 18S rDNA sequences for classification and identification in Pyrus pyrifolia and P . communis  

Microsoft Academic Search

We generated RAPD, SCAR, and conserved 18S rDNA markers for classifying and identifying cultivars of Pyrus pyrifolia (Japanese pear) and P. communis (European pear). PCR amplification with selected specific primers—LCH327UP and LCH327DOWN—was performed using DNA extracted from 25 P. pyrifolia and P. communis cultivars. The 1,380-bp fragment was amplified from P. communis cvs. Beurre Giffard, Cascade, Conference, Clapp’s Favorite, Packhams Triumph,

G. P. Lee; C. H. Lee; C. S. Kim

2004-01-01

22

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

PubMed

The genetic diversity of Cistus ladanifer ssp. ladanifer (Cistaceae) growing on ultramafic and non-ultramafic (basic and schists) soils in the NE of Portugal was studied in order to identify molecular markers that could distinguish the metal-tolerant ecotypes of this species. Random Amplified Polymorphic DNA (RAPD) markers were used in order to estimate genetic variation and differences between populations. The RAPD dataset was analysed by means of a cluster analysis and an analysis of molecular variance (AMOVA). Our results indicate a significant partitioning of molecular variance between ultramafic and non-ultramafic populations of Cistus ladanifer, although the highest percentage of this variance was found at the intra-population level. Mantel's test showed no relationship between inter-population genetic and geographic distances. A series of RAPD bands that could be related to heavy metal tolerance were observed. The identification of such markers will enable the use of Cistus ladanifer in phytoremediation procedures. PMID:15948588

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

23

Molecular Markers for Identification of Stellantchasmus falcatus and a Phylogenic Study using the HAT-RAPD Method  

PubMed Central

Stellantchasmus falcatus is a minute intestinal fluke in the family Heterophyidae. Metacercariae, the infective stage, were reported in a marine fish, mullet Liza subviridis, and a fresh water fish, Dermogenus pusillus, in Thailand. Adults were found in chicks, rats, cats, and humans. Morphological studies were done for comparing Stellantchasmus sp. worms found in 2 different fish hosts; their shapes and organ arrangements were very similar except for the prepharynx length. Therefore, the present study aimed to compare their DNA fingerprints using the HAT-RAPD method for both types of Stellantchasmus and several other related species. Ten arbitrarily selected primers (OPA-04, OPA-09, OPN-02, OPN-03, OPN-09, OPN-12, OPP-11, OPR-15, OPX-13, and OPAD-01) were used. It was found that OPA-09, OPN-03, and OPAD-01 were able to generate S. falcatus specific fragments in mullets which consisted of 200, 760, and 280 bp, respectively. In addition, the results of morphologic, DNA fingerprinting, and phylogenetic analyses strongly suggest that the fresh water and marine specimens of Stellantchamus may be different species.

Wongsawad, Pheravut

2010-01-01

24

Genetic diversity in Hemileia vastatrix based on RAPD markers.  

PubMed

Random amplified polymorphic DNA (RAPD) was used to assess the genetic structure of Hemileia vastatrix populations. Forty-five rust isolates with different virulence spectra and from different hosts and geographical regions were analyzed. Out of 45 bands, generated with three RAPD primers, 35 (78%) were polymorphic and scored as molecular markers. Cluster analysis exhibits unstructured variability of this pathogen with regard to physiological race, geographical origin or host. The genotypic diversity (H') inferred from Shannon's index was higher than gene diversity (Ht), suggesting that diversity is distributed among clonal lineages. Estimates of gene diversity in Africa and Asia populations were higher in total (Ht) as compared to within population diversity (Hs). Genetic differentiation was considerable among coffee rust isolates from Africa (Gst = 0.865) and Asia (Gst = 0.768) but not among isolates from South America (Gst = 0.266). We concluded that genetic diversity in H. vastatrix was moderately low and that the genetic differentiation among populations shows that asexual reproduction is likely to play an important role in the population biology of this fungus. This should be taken into account for the development of breeding programs. PMID:16396347

Gouveia, M Manuela C; Ribeiro, Ana; Várzea, Vítor M P; Rodrigues, Carlos J

25

Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers.  

PubMed

Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F(2) progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism. The OPB12/OPH08 primer gave the highest effective number of alleles (N(E)), and the largest Shannon index (I), Nei's genetic diversity (H), and polymorphism information content (PIC) values. Some RAPD bands were present in the parental genotypes but were absent in their hybrids. Ten ISSR primers produced 206 reproducible bands, with 49.4% polymorphism. The UBC807 locus gave the highest N(E), I, H, and PIC values. Some ISSR bands occurred only in the parental genotype, while others were only present in the hybrid genotypes. Four microsatellite loci produced 12 alleles, ranging from 181 to 236 bp, with 54% polymorphism. The TMB1421 locus, with a monomorphic allele, was digested with three restriction enzymes (CAP-microsatellite) to evaluate sequence variations among samples. Association analysis between molecular markers and agronomic data revealed a significant correlation between ISSR-UBC807-1500 and yield. The Mantel test performed among the genetic distance matrices obtained from RAPD, ISSR and SSR showed a non-significant regression between RAPD versus ISSR and ISSR versus SSR, while RAPD versus SSR showed a significant regression; regression for ISSR and RAPD+ISSR+SSR combined data was also significant. Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies. Among the molecular markers, ISSR revealed more genetic variation among the genotypes. However, using all three types of molecular markers provided a better overall view of cotton genome polymorphism. PMID:23408413

Noormohammadi, Z; Hasheminejad-Ahangarani Farahani, Y; Sheidai, M; Ghasemzadeh-Baraki, S; Alishah, O

2013-01-30

26

Identification of RAPD and ISSR markers for drought tolerance in wheat (Triticum aestivum L.).  

PubMed

Drought tolerance is the essential trait that needs to be incorporated in cereal crops, particularly those grown under the rainfed cultivation. Drought tolerance being contributed by several regions of the genome requires identification of these regions, using suitable molecular markers. Therefore, present investigation was aimed at analyzing the genetic diversity present among the cultivars of rainfed and the irrigated areas with respect to the drought tolerant trait. In all, 14 RAPD and 90 ISSR markers were used to identify these genomic regions. Out of 14 RAPD markers, one RAPD primer exhibited polymorphic banding pattern with 18.6 % polymorphism, clearly separating drought tolerant and drought susceptible genotypes. Out of 90 ISSR primers, only 3 ISSR primers revealed polymorphism in relation to the drought tolerance trait exhibiting 21.38 % polymorphism. PMID:23573046

Deshmukh, Reena; Tomar, Nawab Singh; Tripathi, Niraj; Tiwari, Sharad

2011-12-09

27

Characterization of white sapote ( Casimiroa edulis Llave & Lex.) germplasm using floral morphology, RAPD and AFLP markers  

Microsoft Academic Search

Floral morphology, random amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) were used to characterize and verify genetic diversity within a white sapote cultivar collection and to develop molecular markers for germplasm identification. On the basis of floral morphology, the cultivars were classified into three types: type I included 23 cultivars with large ovaries and small anthers; type

Yoshimi Yonemoto; Abul Kashem Chowdhury; Hidenori Kato; Mustad Malid Macha; Hitoshi Okuda

2007-01-01

28

Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach  

Microsoft Academic Search

The identification of molecular markers linked to economically important traits for use in crop improvement is very important in long-lived perennial species. Three-hundred-and-sixty RAPD primers were used with bulked segregant analysis to identify markers linked to loci of specific interest in peach [(Prunus persica) L. Batch] and peach x almond [(Prunus dulcis) Batch] crosses. The traits analyzed included flesh color,

M. L. Warburton; V. L. Becerra-Velásquez; J. C. Goffreda; F. A. Bliss

1996-01-01

29

Assessment of natural and induced genetic variation in Alstroemeria using random amplified polymorphic DNA (RAPD) markers  

Microsoft Academic Search

We have used random amplified polymorphic DNA (RAPD) markers to study genetic variation in Alstroemeria. The first objective was to examine the discriminatory power of RAPD markers in different genotypes of Alstroemeria obtained by traditional breeding. All genotypes examined, including commercial Alstroemeria varieties, could be distinguished on the basis of their RAPD profiles. Progeny plants could be distinguished from their

E. Anastassopoulos; M. Keil

1996-01-01

30

Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers.  

PubMed

We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2 n = 2 x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between two genotypes from a previously designed cross. Consequently, both parents are fullsibs. The same proportion of bi-parental markers (heterozygotic in both parents) and pseudo-testcross markers (heterozygotic in one parent and null in the other), mono-parental markers, have been obtained. A total of 383 RAPD markers were analysed within the 89 F1 plants. Out of these markers, 257 were mapped into 28 linkage groups which spanned a total map length of around 1,074.5 cM with an average density of 4.2 cM per marker. Out of 257 mapped markers, 62 were inherited from F1.1 (P1), 63 from F1.7 (P7) and 132 were bi-parental markers. The contribution to the map was equal from both parents. This map provides a useful tool for genetic analyses of agronomically interesting characters in M. sinensis such as flowering, yield, plant height, stem diameter and mineral constitution. The offspring cross mapping strategy is proposed to obtain a higher efficiency in developing integrated maps including both parents. PMID:12582920

Atienza, G.; Satovic, Z.; Petersen, K.; Dolstra, O.; Martín, A.

2002-06-19

31

RAPD MARKERS LINKED TO EASTERN FILBERT BLIGHT RESISTANCE IN CORYLUS AVELLANA  

Technology Transfer Automated Retrieval System (TEKTRAN)

A total of 1420 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 additional markers linked in repulsion were fou...

32

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

Microsoft Academic Search

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

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

1995-01-01

33

Analysis of genetic diversity in Larix gmelinii (Pinaceae) with RAPD and ISSR markers.  

PubMed

Dahurian larch (Larix gmelinii), a deciduous conifer, is the northernmost tree, native to eastern Siberia and nearby regions of China. We used growth traits and molecular markers to assess genetic variation in different L. gmelinii growing regions; 105 individual samples were collected from seven regions of the Qingshan Forestry Centre, Heilongjiang Province, China. The greatest genetic regional variation was seen in the Youhao area, based on coefficients of variation for tree height, diameter and volume (14.73, 28.25, and 55.27%, respectively). Analysis using molecular markers showed rich genetic diversity. The RAPD and ISSR methods both indicated that most variation came from within populations. The seven regions were divided into two groups (Daxing'an and Xiaoxing'an Mountain ranges) by RAPD cluster analysis: Tianchi, Xiaojiuya, Yuanjiang, and Taiping regions were placed in the first group at a genetic distance of 0.08; while the other regions were in the second group. The correlation between RAPD markers and geographical distance was significant, with a correlation coefficient of 0.752. PMID:23408406

Zhang, L; Zhang, H G; Li, X F

2013-01-24

34

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

PubMed

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

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

2013-03-11

35

A comparison of RAPD versus microsatellite DNA markers in population studies of the massasauga rattlesnake.  

PubMed

We compared genetic differentiation among populations of the threatened massasauga rattlesnake (Sistrurus c. catenatus) using two types of nuclear molecular markers: randomly amplified polymorphic DNA (RAPD) markers and microsatellites. Analyses of molecular variance (AMOVA) and G(ST) and F(ST) analyses indicated that levels of among-population differentiation between regional populations (>100 km) were comparable for both markers. However, microsatellites were superior in population assignment tests and at discerning fine-scale genetic differentiation between subpopulations separated by tens of kilometers. These results argue that both types of markers are suitable for defining broad-scale genetic structures in snake populations and can provide important inputs into conservation initiatives of focal taxa. However, our analyses suggest that microsatellites 3re better for detecting structure at limited spatial scales. PMID:11218083

Lougheed, S C; Gibbs, H L; Prior, K A; Weatherhead, P J

36

Use of RAPD markers for the study of microbial community similarity from termite mounds and tropical soils  

Microsoft Academic Search

In this study, we test the use of the RAPD (Random Amplified Polymorphic DNA) molecular markers as a way to estimate the similarity of the microbial communities in various termite mounds and soils. In tropical ecosystems, termite activities induce changes in the chemical and physical properties of soil. The question then arises as to whether or not termites affect the

M Harry; N Jusseaume; B Gambier; E Garnier-Sillam

2001-01-01

37

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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

38

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

Microsoft Academic Search

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

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

1995-01-01

39

Genetic Linkage Maps of the Guppy ( Poecilia reticulata ): Assignment of RAPD Markers to Multipoint Linkage Groups  

Microsoft Academic Search

Genetic linkage maps of the guppy ( Poecilia reticulata) were constructed from independent crosses between the Tuxedo strain and a feral line (Wildtype). Segregation patterns of random amplified polymorphic DNA (RAPD) markers and phenotypic markers were investigated in F 2 offspring of Tuxedo ?? × Wildtype ?? and Wildtype ?? × Tuxedo ?? crosses. Among the 300 and 276 RAPD

Gideon Khoo; Meng Huat Lim; Haridas Suresh; Damien K. Y. Gan; Kok Fang Lim; Fan Chen; Woon-Khiong Chan; Tit Meng Lim; Violet P. E. Phang

2003-01-01

40

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

Microsoft Academic Search

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

Greg J. Hunt; Robert E. Page

1995-01-01

41

[Construction of silkworm RAPD molecular linkage map].  

PubMed

In this research, a RAPD linkage map of Bombyx mori was constructed with Dazao/C108 and their F2 generation. The map consists of 182 RAPD loci, of which 103 loci come from Dazao and from the first 23 linkage groups and the other 79 loci come from C108 and form the second 16 linkage groups. This map covered a total genetic distance of over 1,148.3 cM (centimorgan). It could be integrated with the SADF map of the same materials constructed in our laboratory and the corresponding RFLP linkage map. PMID:10887679

Li, B; Lu, C; Zhou, Z Y; Xiang, Z H

2000-01-01

42

RAPD markers reveal polymorphism among some Iranian pomegranate ( Punica granatum L.) genotypes  

Microsoft Academic Search

In this study RAPD markers were used to determine the diversity level among 24 Iranian pomegranate genotypes. One hundred decamer random primers were used for PCR reactions, among which 16 showed reliable polymorphic patterns. These primers produced 178 bands, of which 102 were polymorphic. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Jaccard's

A. Sarkhosh; Z. Zamani; R. Fatahi; A. Ebadi

2006-01-01

43

Random amplified polymorphic DNA (RAPD) markers readily distinguish cryptic mosquito species (Diptera: Culicidae: Anopheles )  

Microsoft Academic Search

The usefulness of random amplified polymorphic DNA (RAPD) was examined as a potential tool to differen- tiate cryptic mosquito species. It proved to be a quick, effective means of finding genetic markers to separate two laboratory populations of morphologically indis- tinguishable African malaria vectors, Anopheles gam- biae and An. arabiensis. In an initial screening of fifty- seven RAPD primers, 377

R. C. Wilkerson; T. J. Parsons; D. G. Albright; T. A. Klein; M. J. Braun

1993-01-01

44

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

Microsoft Academic Search

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

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

1994-01-01

45

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

Microsoft Academic Search

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

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

1997-01-01

46

Classification of Iranian Garlic (Allium sativum L.) Ecotypes Using RAPD Marker  

Microsoft Academic Search

Background: Garlic is a valuable medicinal plant with variability in desirable morphological and physiological characteristics. The analysis of genetic diversity plays an important role in breeding programs. The RAPD technique could be very effective in detecting genetic variation in garlic. Objective: The objective of the present work was to detect molecular polymorphism among Iranian garlic ecotypes by RAPD technique. Methods:

Baghalian K

2009-01-01

47

RAPD marker polymorphism among commercial winery yeast strains  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) analysis was employed to characterize commercial winery yeast strains currently used in Brazilian industries and to examine the relationship between them. Sixteen strains were subjected to RAPD analysis using eight primers, selected from the 40 primers of the kits B and X of Operon Techn. From the total of 93 scorable bands, 39 (41.9%) were

S. Echeverrigaray; S. Paese-Toresan; J. L. Carrau

2000-01-01

48

Identification of white truffle species using RAPD markers  

Microsoft Academic Search

Morphologically very similar species of white truffle were analyzed by the random amplified polymorphic DNA (RAPD) technique. Species-specific RAPD fragments were selected and pairs of primers were designed on their sequences. Sequence-characterized amplified regions were developed and applied to identify these species throughout their entire life cycle: fruit body, mycelium, ectomycorrhiza. This procedure provides an unambiguous and rapid tool for

I. Rossi; B. Bartolacci; L. Potenza; L. Bertini; E. Barbieri; V. Stocchi

2000-01-01

49

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

PubMed

Until now, neither phenotypic nor molecular approaches have been used to characterize the landraces of Palestine faba beans (Vicia faba). We used PCR-based RAPD markers to determine the genetic diversity and relatedness among 26 Palestinian faba bean landraces (traditional farmers' varieties) from 8 localities in the West Bank, Palestine. In tests with 37 primers, 14 generated no polymorphic bands, 12 exhibited weak and unclear products, and 11 primers produced good amplification products with high intensity and pattern stability. Ninety-four DNA fragments (loci) were detected, with an average of 8.54 loci per primer and size ranging from 160 to 1370 bp. A minimum of 4 and a maximum of 14 DNA fragments were obtained using (OPA-05 and OPA-09) and (BC-261) primers, respectively. The maximum percentage of polymorphic markers was 71.4 (BC-298) and the minimum was 50.0 (OPA-05, -09, -16). The 11 primers exhibited relatively high collective resolving power (Rp) values of 26.316, and varied from 0.154 for the OPA-09 primer to 5.236 for the BC-261, with an overall mean of 2.392. The primers BC-261, -322, and -298 were found to be the most useful RAPD primers to assess the genetic diversity of Palestinian faba beans, as they revealed relatively high Rp rates (5.236, 3.618, and 3.150, respectively). Based on the Jaccard coefficient, the genetic distance ranged from 0.358 to 0.069, with a mean of 0.213. We conclude that the RAPD technique is useful for determining genetic diversity and for developing suitable fingerprints for faba bean landraces grown in Palestine. PMID:24065673

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

2013-09-03

50

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

Microsoft Academic Search

We carried out four separate studies using random amplified polymorphic DNA (RAPD) markers to analyse samples of Eucalyptus supplied by several different organisations. The objective was to examine the reproducibility of the RAPD technique and its ability to discriminate between individual genotypes for verification of clonal identities. We found that RAPD profiles that are unique to a genotype can be

M. Keil; A. R. Griffin

1994-01-01

51

[Polymorphism of RAPD, ISSR and AFLP markers of the Panax ginseng C. A. Meyer (Araliaceae) genome].  

PubMed

The genus Panax (Araliaceae) is world-famous because many its members have important medicinal properties. Panax ginseng C. A. Meyer is more popular than other species of the genus because remedies prepared from this plant stimulate immunity, help to prevent diseases, and have antistress effects. In addition, the ginseng root extract is traditionally used as a means against aging. At present, this species is found in the wild only in Primorsky krai, Russia, but its populations are extremely exhausted and need to be restored. In this study, effectiveness of molecular DNA markers in detecting genetic variation and differentiation of the ginseng populations was tested. Genetic variation of ginseng, identified using RAPD (P = 4%; H(pop) = 0.0130) and ISSR (P = 9.3%; H(pop) = 0.0139) markers was low. The AFLP* approach, according to which amplicons are separated in polyacrylamide gel and visualized by means of silver staining, showed somewhat higher variability (P = 21.8%; H(pop) = 0.0509), while its effectiveness in population differentiation was as low as that of RAPD and ISSR. The AFLP** technique, which included analysis of the fragments using genetic analyzer, revealed high genetic differentiation of ginseng (P = 94.4%; H(pop) = 0.3246). All populations examined using the AFLP** markers were statistically significantly differentiated based on the AMOVA results. Our result suggest effectiveness of AFLP** markers for characterization of the genetic structure and genetic relationships of the ginseng populations. These markers are recommended for use in large-scale population genetic studies of this species to develop measures of its conservation. PMID:20873202

Reunova, G D; Kats, I L; Muzarok, T I; Zhuravlev, Iu N

2010-08-01

52

Advance of molecular marker application in the tobacco research  

Microsoft Academic Search

Tobacco (Nicotiana spp.) is one of the most important commercial crops in the world. During the last two decades, molecular markers have entered the scene of genetic improvement in different fields of agricultural research. The principles and characteristics of several molecular markers such as RFLP, RAPD, AFLP, microsatellites and minisatellites applied in tobacco genetics and breeding were reviewed. The application

X. Z. Liu; H. Y. Zhang

53

Genetic diversity of a Coffea Germplasm Collection assessed by RAPD markers  

Microsoft Academic Search

Genetic diversity and relationships within and among nine species of Coffea, one species of Psilanthus and the Piatã hybrid from the Coffee Germplasm Collection of Instituto Agronômico de Campinas (IAC), Brazil were assessed\\u000a using RAPD markers. Genetic diversity and relationships were evaluated by proportion of polymorphic loci (P), Shannon’s genetic index (H? and G?ST) and clustering analysis. The overall RAPD

Milene Silvestrini; Mirian P. Maluf; Maria B. Silvarolla; Oliveiro Guerreiro-Filho; Herculano P. Medina-Filho; Marina M. T. Vanini; Adalgisa S. Oliveira; Cristiana de Gaspari-Pezzopane; Luiz C. Fazuoli

2008-01-01

54

Correspondence of ISSR and RAPD markers for comparative analysis of genetic diversity among different apricot genotypes from cold arid deserts of trans-Himalayas.  

PubMed

The phylogenetic relationships of 36 locally grown Prunus armeniaca genotypes which are collected from nine sampling sites from two valleys viz. Nubra (9,600 ft) and Leh (11,500 ft) of trans-Himalayan region were analyzed using 31 PCR markers (20 RAPDs and 11 ISSRs). This is the first report of molecular genetic diversity studies in apricot from this region of the world. RAPD analysis yielded 139 fragments, of which 136 were polymorphic, with an average of 6.8 polymorphic fragments per primer. ISSR analysis produced 58 bands, of which 56 were polymorphic, with an average of 5.09 polymorphic fragments per primer. The primers based on (CT)n produced maximum number of bands (nine) while, (AT)n and many other motifs gave no amplification. RAPD markers were found more efficient with regards to polymorphism detection, as they detected 97.84 % as compared to 96.5 % for ISSR markers. Clustering of genotypes within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the genotypes remained more or less the same in RAPD and combined data of RAPD + ISSR. The results of PCA analysis were comparable to the cluster analysis. These analyses, allowed us to identify the groups corresponding to the two apricot collection sites. PMID:23572932

Kumar, Meetul; Mishra, Gyan P; Singh, Raghwendra; Kumar, Jitendra; Naik, Pradeep K; Singh, Shashi Bala

2009-10-28

55

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

PubMed Central

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.

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

2012-01-01

56

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....

57

Identification of a major gene and RAPD markers for yellow seed coat colour in Brassica napus.  

PubMed

The development of yellow-seeded Brassica napus for improving the canola-meal quality characteristics of lower fibre content and higher protein content has been restricted because no yellow-seeded forms of B. napus exist, and their conventional development requires interspecific introgression of yellow seed coat colour genes from related species. A doubled-haploid (DH) population derived from the F1 generation of the cross 'Apollo' (black-seeded) x YN90-1016 (yellow-seeded) B. napus was analysed via bulked segregant analysis to identify molecular markers associated with the yellow-seed trait in B. napus for future implementation in marker-assisted breeding. A single major gene (pigment 1) flanked by eight RAPD markers was identified co-segregating with the yellow seed coat colour trait in the population. This gene explained over 72% of the phenotypic variation in seed coat colour. Further analysis of the yellow-seeded portion of this DH population revealed two additional genes favouring 'Apollo' alleles, explaining 11 and 8.5%, respectively, of the yellow seed coat colour variation. The data suggested that there is a dominant, epistatic interaction between the pigment I locus and the two additional genes. The potential of the markers to be implemented in plant breeding for the yellow-seed trait in B. napus is discussed. PMID:11768211

Somers, D J; Rakow, G; Prabhu, V K; Friesen, K R

2001-12-01

58

The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin.  

PubMed

The potential of bulk analyses of RAPD and ISSR-PCR markers for fingerprinting purposes was evaluated using ten RAPD and ten ISSR primers. The phylogenetic relationships of 16 barley cultivars from different countries, and all having a known pedigree, were analysed using 353 PCR markers (125 RAPDs and 228 ISSRs). The band profiles generated were reproducible in spite of the different DNA extractions, PCR techniques, electrophoretic methods and gel scorings used. The RAPD primer S10 and four ISSR primers (811, 820, 835 and 881) were both able to distinguish all cultivars. A strong and quite linear relationship was observed between Resolving Power (Rp) of a primer and its ability to distinguish genotypes. The dendrograms obtained using these two molecular markers are in agreement with their known origin, showing clusters that separate very well the spring/winter and six-rows/two-rows cultivars. Thus, bulk analyses of RAPD and ISSR PCR markers provides a quick, reliable and highly informative system for DNA fingerprinting and also permit to establish genetic relationships which agree with, by other means, known origin of the cultivars. PMID:12582645

Fernández, E.; Figueiras, M.; Benito, C.

2002-02-01

59

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

PubMed

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

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

2011-12-14

60

Relationships between an Italian Strawberry Ecotype and its Ancestor using RAPD Markers  

Microsoft Academic Search

Random-amplified polymorphic DNA (RAPD) markers were used to evaluate genetic variability among populations of an Italian strawberry ecotype, and to determinate genetic relationships between genotypes and their putative ancestor. A total of 65 selections and one cultivar ‘Madame Moutot’ (MM), were analysed to evaluate genetic variability present in Etna mountain area and to confirm as MM was one of the

Luigi Milella; Danilo Saluzzi; Mauro Lapelosa; Giuseppe Bertino; Piero Spada; Ivana Greco; Giuseppe Martelli

2006-01-01

61

Identification of a RAPD marker linked to sex determination in Pistacia vera using bulked segregant analysis  

Microsoft Academic Search

The Random Amplified Polymorphic DNA (RAPD) technique was used to amplify DNA segments, with the objective of finding markers linked to sex determination in the dioecious species, Pistacia vera. Progenies from two female parents pollinated by a common male parent were studied. Two bulks of DNA were made in each cross, one from males and one from females, by pooling

J. I. Hormaza; L. Dollo; V. S. Polito

1994-01-01

62

DIVERSITY ANALYSIS OF MOROCCAN CAROB (CERATONIA SILIQUA L.) ACCESSIONS USING PHENOTYPIC TRAITS AND RAPD MARKERS  

Microsoft Academic Search

SUMMARY. Diversity analysis of moroccan carob (Ceratonia siliqua L.) accessions using phenotypic traits and RAPD markers. The carob (Ceratonia siliqua L.) is a perennial leguminous (Caesalpinioideae) that grows as an evergreen shrub or tree. It's an important component of the Mediterranean vegetation and its adaptation in marginal soils of the Mediterranean regions is important environmentally and economically. Phenotypic and genetic

Ibrahim KONATÉ; Abdelkarim FILALI-MALTOUF; El Bekkay BERRAHO

63

RAPD analysis in the parasitoid wasp Psyttalia concolor reveals Mediterranean population structure and provides SCAR markers  

Microsoft Academic Search

Psyttalia concolor (Szepligeti) (Hymenoptera: Braconidae) is a parasitic wasp reared and released for the biological control of the olive fruit fly Bactrocera oleae (Gmelin) (Diptera: Tephritidae). We used RAPD (Random Amplified Polymorphic DNA) markers to assess the level of genetic differentiation in and between 11 introduced (“wild”) Mediterranean populations (nine from South Italy, and two from the Middle East). The

N. Karam; C. R. Guglielmino; S. Bertin; L. M. Gomulski; A. Bonomi; F. Baldacchino; V. Simeone; A. R. Malacrida

2008-01-01

64

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

Microsoft Academic Search

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

Vijay Rani; Ajay Parida; S. N. Raina

1995-01-01

65

The role of RAPD markers in breeding for disease resistance in common bean  

Microsoft Academic Search

Diseases are regarded as the leading constraint to increased common bean (Phaseolus vulgaris L.) production worldwide. The range in variability and complexity among bean pathogens can be controlled with different single gene and quantitative resistance sources. Combining these resistance sources into commercial cultivars is a major challenge for bean breeders. To assist breeders, a major effort to identify RAPD markers

James D. Kelly; Phillip N. Miklas

1998-01-01

66

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

Microsoft Academic Search

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

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

1995-01-01

67

Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR markers  

Microsoft Academic Search

Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence\\u000a repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic;\\u000a and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR

W. Qian; S. Ge; D.-Y. Hong

2001-01-01

68

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

Microsoft Academic Search

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

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

2002-01-01

69

Comparison of RAPD and ISSR markers for assessment of genetic diversity among endangered rare Dalbergia oliveri (Fabaceae) genotypes in Vietnam.  

PubMed

Dalbergia oliveri is a leguminous tree of the Fabaceae family. This species is popular and valuable in Vietnam and is currently listed on the Vietnam Red List and on the IUCN Red List as endangered. Two PCR techniques using RAPD and inter-simple sequence repeat (ISSR) markers were used to make a comparative analysis of genetic diversity in this species. Fifty-six polymorphic primers (29 RAPD and 27 ISSR) were used. The RAPD primers produced 63 bands across 35 genotypes, of which 24 were polymorphic. The number of amplified bands varied from one to four, with a size range from 250 to 1400 bp. The percentage polymorphism ranged from 0 to 75. Amplification of genomic DNA of the 35 genotypes, using ISSR analysis, yielded 104 fragments, of which 63 were polymorphic. The number of amplified fragments using ISSR primers ranged from one to nine and varied in size from 250 to 1500 bp. The percentage polymorphism ranged from 0 to 100. ISSR markers were relatively more efficient than RAPDs. The mental test between two Jaccard's similarity matrices gave r ?0.802, showing good fit correlation between ISSRs and RAPDs. Clustering of isolates remained more or less the same for RAPDs compared to combined RAPD and ISSR data. The similarity coefficient ranged from 0.785 to 1.000, 0.698 to 0.956 and 0.752 to 0.964 with RAPD, ISSR, and the combined RAPD-ISSR dendrogram, respectively. PMID:22002131

Phong, D T; Hien, V T T; Thanh, T T V; Tang, D V

2011-10-06

70

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

PubMed

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

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

2012-10-02

71

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

PubMed

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

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

2009-08-18

72

Molecular DNA Markers in Phylogeny and Systematics  

Microsoft Academic Search

The review considers data on the use of the main evolutionary markers (ribosomal, mitochondrial, and RAPD markers; dispersed and tandem repeats). Some circumstances impending analysis of these data are discussed.

V. V. Grechko

2002-01-01

73

Assessment of genetic fidelity of micropropagated date palm (Phoenix dactylifera L.) plants by RAPD and ISSR markers assay.  

PubMed

RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter-Simple Sequence Repeats) markers assay were employed to validate the genetic stability of date palm (Phoenix dactylifera L.) plants multiplied through somatic embryogenesis with upto forty two in vitro subcultures. Out of the 160 RAPD and 21 ISSR primers screened, 30 RAPD and 12 ISSR primers produced a total of 347 (246 RAPDs + 101 ISSRs) clear, distinct and reproducible amplicons, which were monomorphic across all micropropagated plants (27) studied. Thus, a total 8592 bands (number of plants analysed x number of amplicons with all the primers) were generated which exhibited homogeneous banding patterns with both RAPD and ISSR markers. These results indicate that the micropropagation protocol developed by us for rapid in vitro multiplication is appropriate and suitable for clonal propagation of date palm and corroborated the fact that somatic embryogenesis can also be used as one of the safest modes for production of true-to-type plants. PMID:23572971

Kumar, Nitish; Modi, Arpan R; Singh, Amritpal S; Gajera, Bhavesh B; Patel, Armi R; Patel, Mukesh P; Subhash, Naraynan

2010-09-05

74

MOLECULAR MARKERS FOR SEX DETERMINATION IN PAPAYA (CARICA PAPAYA L.)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers tightly linked to Sex1, the gene that determines plant sex in papaya (Carica papaya L.), were developed. Three RAPD products have been cloned and a portion of their DNA sequenced. Based on these sequences SCAR primers were synthesized. SCAR T12 and SCAR W11 produce products in h...

75

COMPARISON OF AFLPS, RAPD MARKERS, AND ISOZYMES FOR DIVERSITY ASSESSMENT OF GARLIC AND DETECTION OF PUTATIVE DUPLICATES IN GERMPLASM COLLECTIONS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Garlic (Allium sativum L.) is an asexually propagated crop that displays much morphological diversity. Studies which have assessed garlic diversity with isozymes and RAPD markers generally agreed with the morphological observations but sometimes failed to discriminate clones. To discriminate among...

76

Genetic diversity among Texas bluegrass genotypes (Poa arachnifera Torr.) revealed by AFLP and RAPD markers  

Microsoft Academic Search

Texas bluegrass Poa arachnifera Torr., is a vigorous sod-forming perennial, dioecious grass, tolerant to heat. It is native to the Southern Great Plains. Genetic\\u000a relationships existing among 28 Texas bluegrass genotypes were investigated using amplified fragment length polymorphism (AFLP)\\u000a and randomly amplified polymorphic DNA (RAPD). A total of 3756 AFLP markers were generated on the 28 genotypes of Texas bluegrass.

K. Renganayaki; J. C. Read; A. K. Fritz

2001-01-01

77

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

Microsoft Academic Search

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

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

1997-01-01

78

A new citrus linkage map based on SRAP, SSR, ISSR, POGP, RGA and RAPD markers  

Microsoft Academic Search

Sequence-related amplified polymorphism (SRAP), simple sequence repeats (SSR), inter-simple sequence repeat (ISSR), peroxidase\\u000a gene polymorphism (POGP), resistant gene analog (RGA), randomly amplified polymorphic DNA (RAPD), and a morphological marker,\\u000a Alternaria brown spot resistance gene of citrus named as Cabsr caused by (Alternaria alternata f. sp. Citri) were used to establish genetic linkage map of citrus using a population of 164

Osman Gulsen; Aydin Uzun; Ihsan Canan; Ubeyit Seday; Ercan Canihos

2010-01-01

79

Genetic diversity of Pistachio ( Pistacia vera , Anacardiaceae) Germplasm based on Randomly Amplified Polymorphic DNA (RAPD) markers  

Microsoft Academic Search

We used Randomly Amplified Polymorphic DNA (RAPD) markers to examine patterns of relatedness among 29 pistachio (Pistacia\\u000a vera L.) cultivars and accessions. These included 13 cultivars that we had previously described, and an additional 16 items\\u000a from the USDA National Clonal Germplasm Repository\\/Davis comprising cultivars and land races originating further east of the\\u000a cultivars described previously, and material from wild

J. I. Hormaza; K. Plnney; V. S. Polito

1998-01-01

80

An improved genetic linkage map for cowpea (Vigna unguiculata L.) combining AFLP, RFLP, RAPD, biochemical markers, and biological resistance traits.  

PubMed

An improved genetic linkage map has been constructed for cowpea (Vigna unguiculata L. Walp.) based on the segregation of various molecular markers and biological resistance traits in a population of 94 recombinant inbred lines (RILs) derived from the cross between 'IT84S-2049' and '524B'. A set of 242 molecular markers, mostly amplified fragment length polymorphism (AFLP), linked to 17 biological resistance traits, resistance genes, and resistance gene analogs (RGAs) were scored for segregation within the parental and recombinant inbred lines. These data were used in conjunction with the 181 random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), AFLP, and biochemical markers previously mapped to construct an integrated linkage map for cowpea. The new genetic map of cowpea consists of 11 linkage groups (LGs) spanning a total of 2670 cM, with an average distance of 6.43 cM between markers. Astonishingly, a large, contiguous portion of LG1 that had been undetected in previous mapping work was discovered. This region, spanning about 580 cM, is composed entirely of AFLP markers (54 in total). In addition to the construction of a new map, molecular markers associated with various biological resistance and (or) tolerance traits, resistance genes, and RGAs were also placed on the map, including markers for resistance to Striga gesnerioides races 1 and 3, CPMV, CPSMV, B1CMV, SBMV, Fusarium wilt, and root-knot nematodes. These markers will be useful for the development of tools for marker-assisted selection in cowpea breeding, as well as for subsequent map-based cloning of the various resistance genes. PMID:11908660

Ouédraogo, J T; Gowda, B S; Jean, M; Close, T J; Ehlers, J D; Hall, A E; Gillaspie, A G; Roberts, P A; Ismail, A M; Bruening, G; Gepts, P; Timko, M P; Belzile, F J

2002-02-01

81

MOLECULAR CHARACTERIZATION OF EGYPTIAN DATE PALM: 11.RAPD FINGERPRINTS  

Microsoft Academic Search

RAPD fingerprints were performed on DNA extracted trom the internal leaves of the offshoots of five date palm cultivars (Samanie, Seaweae, Hyeane, Amhat and Zaghlool). Two random primers (OPC2 and OPD16) out of ten were selected on the basis of the number and frequency of polymorphic bands produced. Distinguishable RAPD fingerprints among the different varieties were obtainable if suitable primers

Mahmoud M. Saker; Hamdy A. Moursy

82

Linkage among isozyme, RFLP and RAPD markers in Vicia faba  

Microsoft Academic Search

Segregating allozyme and DNA polymorphisms were used to construct a preliminary linkage map for faba bean. Two F2 populations were analyzed, the most informative of which was segregating for 66 markers. Eleven independently assorting linkage groups were identified in this population. One of the groups contained the 45s ribosomal array and could be assigned to the large metacentric chromosome I

A. M. Torres; N. F. Weeden; A. Martín

1993-01-01

83

Molecular distinction amongst varieties of Mulberry using RAPD and DAMD profiles  

PubMed Central

Background Mulberry trees are the most important host for rearing mulberry silkworms in sericulture. Improved varieties of mulberry tree have been developed through traditional breeding procedures. Not much work, however, has been carried out on the molecular characterization of these varieties. Random Amplified Polymorphic DNA (RAPD) and Directed Amplification of Minisatellite DNA (DAMD) methods based on Polymerase Chain Reaction are important tools to analyze genetic diversity of mulberries. These have been used to determine variation amongst nine varieties of Morus spp. maintained at Banthra Research Station of National Botanical Research Institute, Lucknow. Results and Discussion The varieties were analyzed using 23 arbitrary sequence decamer primers for RAPD, and 3 minisatellite core sequence primers for DAMD reactions. The RAPD and DAMD band data, (a total of 200 bands), were used to determine the pair wise distances according to Jaccard's algorithm. From these distance values Neighbour Joining (NJ) analyses were carried out separately for the RAPD and the DAMD data. The triploid varieties were found to be most similar to each other using RAPD analysis, while the varieties S13 and S34 were more similar using DAMD analysis. Nearly 85% of the RAPD bands and 91% of the DAMD bands were polymorphic across the nine varieties. Conclusions The mulberry varieties could be distinguished by their RAPD and DAMD profiles. As many as five RAPD primers and one DAMD primer generated profiles that can together differentiate all the nine varieties in terms of unique bands.

Bhattacharya, Esha; Ranade, Shirish Anand

2001-01-01

84

RAPD markers associated with drought tolerance in bread wheat (Triticum aestivum L.).  

PubMed

Randomly Amplified Polymorphic DNAs (RAPDs) were used to search genetic diversity and markers associated with drought tolerance in 20 bread wheat cultivars. These cultivars are extensively being used by farmers in Iran, 6 of them are known as drought tolerant. Initial screens involved growing 10 cultivars at seedling stage under drought conditions (-5 and -8 bar) exerted by PEG 6000 in a hydroponic experiment. These tests confirmed the tolerance of the 6 above mentioned cultivars. Thirty 10-mer RAPD primers were used for fingerprinting of the cultivars of which primers P6 (TCGGCGGTTC) and P7 (CTGCATCGTG) produced respectively a 920 and a 750 bp band present in drought tolerant (absent in others) cultivars. These bands may be associated with drought tolerance in bread wheat. PMID:19090135

Pakniyat, H; Tavakol, E

2007-09-15

85

Phylogenetic relationships among Portuguese rye based on isozyme, RAPD and ISSR markers.  

PubMed

The phylogenetic relationships of 10 rye landraces and cultivars from the north of Portugal and from Brazil were analysed using 20 isozyme loci, and a total of 511 PCR markers (342 ISSRs and 169 RAPDs). The isozymes were analysed in at least 100 plants of each population/cultivar and, therefore, we have data about intra and inter population/cultivar genetic variability. However, the analyses with ISSRs and RAPDs were obtained using a mix of 25 plants of each population. Therefore, each population/cultivar was reduced to one tube and we have no data about intra genetic variability. As expected in a cross pollinated crop we found genetic diversity and a larger variation within than among the populations using isozymes. Somewhat unexpectedly, however, we found that the breeding cultivars have the same level of heterozygosity as the landraces. The phylogenetic relationships obtained using isozymes among the landraces, synthetic cultivar and the cultivars from breeding programs do not reflect their origin. Moreover, the cultivar from Brazil is not separated from the remaining populations/cultivars studied. However, the data observed using RAPDs and ISSRs are in agreement with their known origin. The populations maintained by the farmers in the north of Portugal are grouped in a cluster in the phenogram and the C902591 (from Brazil), the Alvão (synthetic variety) and Larouco (a hybrid between Montalegre and Brazil) are in a different cluster. The ISSRs and RAPDs provide a rapid method for the production of polymorphic markers, which appear to correspond to known pedigree information. PMID:11833286

Matos, M; Pinto-Carnide, O; Benito, C

2001-01-01

86

Genetic Diversity and Taxonomic Implication of Cordyceps sinensis as Revealed by RAPD Markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) markersare used to investigate genetic variation andevolutionary relationships of 29 samples of Cordycepssinensis from different geographical populations on theQinghai–Tibet plateau. Out of 137 RAPDbands scored, 100 are polymorphic. A correlation isrevealed between geographical distance and geneticdistance. The molecular phylogenetic tree suggests thatthe 29 samples are divided into three notableclusters, corresponding to the geographical populations,i.e., the

Yongjiu Chen; Ya-Ping Zhang; Yuexiong Yang; Darong Yang

1999-01-01

87

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

Microsoft Academic Search

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

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

88

Application of random amplified polymorphic DNA (RAPD) markers to evaluate intraspecific genetic variation in red mullet (Mullus barbatus)  

Microsoft Academic Search

The random amplified polymorphic DNA (RAPD) technique was used to evaluate genetic affinities among eight red mullet (Mullus barbatus L., 1758) samples from the Mediterranean Sea. Twenty-nine random primers were used. Despite the variability which was found\\u000a within samples, no specific RAPD marker for the discrimination of the populations was detected. The data analysis revealed\\u000a that the genetic diversity among

Z. Mamuris; A. P. Apostolidis; A. J. Theodorou; C. Triantaphyllidis

1998-01-01

89

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

SciTech Connect

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.

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

1995-03-01

90

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

PubMed

The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability. PMID:21174261

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

2010-12-21

91

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

PubMed

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

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

2012-06-29

92

RAPD-based genetic linkage maps of Tribolium castaneum.  

PubMed Central

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.

Beeman, R W; Brown, S J

1999-01-01

93

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

PubMed

The prawn genus Macrobrachium belongs to the family Palaemonidae. Its species are widely distributed in lakes, reservoirs, floodplains, and rivers in tropical and subtropical regions of South America. Globally, the genus Macrobrachium includes nearly 210 known species, many of which have economic and ecological importance. We analyzed three species of this genus (M. jelskii, M. amazonicum and M. brasiliense) using RAPD-PCR to assess their genetic variability, genetic structure and the phylogenetic relationship between them and to look for molecular markers that enable separation of M. jelskii and M. amazonicum, which are closely related syntopic species. Ten different random decamer primers were used for DNA amplification, yielding 182 fragments. Three of these fragments were monomorphic and exclusive to M. amazonicum or M. jelskii and can be used as specific molecular markers to identify and separate these two species. Similarity indices and a phylogenetic tree showed that M. amazonicum and M. jelskii are closest to each other, while M. brasiliense was the most differentiated species among them; this may be attributed to the different habitat conditions to which these species have been submitted. This information will be useful for further studies on these important crustacean species. PMID:21128212

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

2010-11-30

94

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

PubMed Central

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

Grattapaglia, D.; Sederoff, R.

1994-01-01

95

Identification and genetic variation among Hibiscus species (Malvaceae) using RAPD markers.  

PubMed

Germplasm identification and characterization is an important link between the conservation and utilization of plant genetic resources. Traditionally, species or cultivars identification has relied on morphological characters like growth habit or floral morphology like flower colour and other characteristics of the plant. Studies were undertaken for identification and determination of genetic variation within the two species of Hibiscus and 16 varieties of Hibiscus rosa-sinensis L. through random amplified polymorphic (RAPD) markers. Primer screening was made by using the DNA of variety "Prolific". Genetic analysis was made by using ten selected decamer primers. A total of 79 distinct DNA fragments ranging from 0.3 to 2.5 kb were amplified by using ten selected random decamer primers. The genetic similarity was evaluated on the basis of presence or absence of bands. The cluster analysis indicated that the 16 varieties and two species formed one cluster. The first major cluster consisted of three varieties and a second major cluster consisted of two species and 13 varieties. The genetic distance was very close within the varieties and also among the species. Thus, these RAPD markers have the potential for identification of species/varieties and characterization of genetic variation within the varieties. This is also helpful in Hibiscus breeding programs and provides a major input into conservation biology. PMID:16610229

Barik, Suvakanta; Senapati, Sunil Kumar; Aparajita, Subhashree; Mohapatra, Anuradha; Rout, Gyana Ranjan

96

Mapping Co , a gene controlling the columnar phenotype of apple, with molecular markers  

Microsoft Academic Search

The columnar phenotype is a very valuable genetic resource for apple breeding because of its compact growth form determined by the dominant gene Co. Using bulked segregant analysis combined with several DNA molecular marker techniques to screen the F1 progeny of Spur Fuji × Telamon (heterozygous for Co), 9 new DNA markers (6 RAPD, 1 AFLP and 2 SSRs) linked

Yi-Ke Tian; Cai-Hong Wang; Ji-Shu Zhang; Celia James; Hong-Yi Dai

2005-01-01

97

Genetic variation in the endemic and endangered Rosmarinus tomentosus Huber-Morath & Maire (Labiatae) using RAPD markers  

Microsoft Academic Search

Rosmarinus tomentosus Huber-Morath & Maire, an endemic species of southern Spain, is critically endangered as a consequence of habitat destruction by anthropogenic activities. Random amplified polymorphic DNA (RAPD) markers were used for initial evaluation of genetic variation in this species; among zones, among populations (within zones and independently of zones), and among individuals (within populations and zones). The eight primers

Juan Pedro Martín; J Esteban Hernández Bermejo

2000-01-01

98

Analysis of genetic diversity in early introduced clones of rubber tree (Hevea brasiliensis) using RAPD and microsatellite markers  

Microsoft Academic Search

Genetic analysis in 53 early introduced clones of rubber tree (Hevea brasiliensis) collected from different areas in Southern Thailand was performed using RAPD (Random Amplified Polymorphic DNA) and microsatellite markers. Seven- teen cultivated clones (34 samples) were also included to compare DNA patterns. DNA was isolated from leaf samples using CTAB buffer. One hundred and ninety two 10-base oligonucleotide primers

Korakot Nakkanong; Charassri Nualsri; Sayan Sdoodee

2008-01-01

99

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

Microsoft Academic Search

The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20490 tightly linked (no recombinants) in coupling phase and OAE19890 linked in repulsion phase

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

1995-01-01

100

Use of sequence characterised amplified region and RAPD markers in the identification of the white truffle Tuber magnatum Pico  

Microsoft Academic Search

Isolates of white truffles were identified as Tuber magnatum Pico species using a pair of primers selected from a sequence characterised amplified region (SCAR) and a specific random amplified polymorphic DNA (RAPD) marker. The present study reveals that PCR-fragment-pattern polymorphisms, the construction of probes and couples of primers from one or more of these polymorphic fragments may provide a useful

Antonella Amicucci; Ismaela Rossi; Lucia Potenza; Deborah Agostini; Vilberto Stocchi

1997-01-01

101

Genetic variation and population structure of endemic yellow catfish, Horabagrus brachysoma (Bagridae) among three populations of Western Ghat region using RAPD and microsatellite markers  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) and microsatellite markers were applied to evaluate the genetic variation in endemic\\u000a and endangered yellow catfish, Horabagrus\\u000a brachysoma sampled from three geographic locations of Western Ghat, South India river systems. In RAPD, of 32 10-mer RAPD primers screened\\u000a initially, 10 were chosen and used in a comparative analysis of H. brachysoma collected from Meenachil, Chalakkudy

P. M. Abdul Muneer; A. Gopalakrishnan; K. K. Musammilu; Vindhya Mohindra; K. K. Lal; V. S. Basheer; W. S. Lakra

2009-01-01

102

Comparative analysis of genetic diversity in Indian bitter gourd ( Momordica charantia L.) using RAPD and ISSR markers for developing crop improvement strategies  

Microsoft Academic Search

A genetic analysis of 38 diverse Indian bitter gourd (Momordicacharantia var. charantia, and var. muricata) accessions was performed using 29 RAPD and 15 ISSR markers. RAPD primers yielded 208 amplicons of which 76 (36.5%) were polymorphic providing an average of 2.6 amplicons per primer. RAPD amplicons per primer ranged from 3 (OPE-19, OPW-09) to 15 (OPW-05), and varied in size

T. K. Behera; A. K. Singh; Jack. E. Staub

2008-01-01

103

RAPD-Based Genetic Linkage Maps of Tribolium castaneum  

Microsoft Academic Search

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 polymor- phic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total

Richard W. Beeman; Susan J. Brown

104

Gene flow from wheat (Triticum aestivum L.) to jointed goatgrass (Aegilops cylindrica Host.), as revealed by RAPD and microsatellite markers  

Microsoft Academic Search

In order to estimate the potential of gene flow between wheat (Triticum ?stivum L.) and jointed goatgrass (Aegilops cylindrica Host.), we carried out mixed pollinations in experimental and natural conditions. A set of species-specific RAPD (random\\u000a amplified polymorphic DNA) and microsatellite markers were used to detect the presence of parental markers in the progeny\\u000a of the plants used in these

R. Guadagnuolo; D. Savova-Bianchi; F. Felber

2001-01-01

105

Implications of ITS sequences and RAPD markers for the taxonomy and biogeography of the Oxytropis campestris and O. arctica (Fabaceae) complexes in Alaska.  

PubMed

Taxonomic consensus is lacking on the Oxytropis arctica and O. campestris species complexes, two polyploid complexes found in the interior and arctic areas of Alaska. One classification has emphasized flower size, whereas flower color is considered a key diagnostic character in another classification. Our analyses of internal transcribed spacer (ITS) sequences and random amplified polymorphic DNA (RAPD) markers provided no support for either classification system. The trees generated from ITS sequences and the phenogram derived from RAPD markers suggest that most recognized taxa in the two complexes are probably polyphyletic, including O. arctica var. barnebyana, which is listed as threatened in Alaska. The only consistent pattern detected by both types of molecular markers was a geographic split dividing the northeastern arctic populations from most other populations (48.60-55.03% in AMOVA analyses). This genetic subdivision probably reflects a Pleistocene barrier formed by the northern coastal ice shield. Our molecular data, in conjunction with the previously reported variation of ploidy levels in these groups, suggest a scenario of recent and multiple origins of polyploidy. It is possible that most Alaskan populations of these two complexes are best referred to as a single taxonomic species despite morphological differentiation within the complexes. PMID:21659099

Jorgensen, Janet L; Stehlik, Ivana; Brochmann, Christian; Conti, Elena

2003-10-01

106

Molecular characterization of Desmodium species--an important ingredient of 'Dashmoola' by RAPD analysis.  

PubMed

Identification of medicinal plants by their molecular signature is a fast growing tool. The identification of Desmodium gangeticum (L.) DC. (Shalparni, a constituent of Ayurvedic formulation "Dashmoolarishtha") was carried out using genomic approach. Authentic samples of D. gangeticum(L.) DC., D. velutinum (Willd.) DC. and D. triflorum (L.) DC. were analyzed and compared to commercial samples of various origin. Within twenty primers used, eleven gave 223 RAPD fragments. RAPD profiles of three species showed very low similarity index (0.21-0.39), whereas market samples showed high similarity of 0.82-0.89 with authenticated D. gangeticum. PMID:19100816

Irshad, Saba; Singh, Jyotsna; Kakkar, Poonam; Mehrotra, Shanta

2008-11-28

107

Molecular characterization of Vigna radiata (L.) Wilczek genotypes based on nuclear ribosomal DNA and RAPD polymorphism.  

PubMed

Mungbean germplasm characterization, evaluation and improvement are fundamentally based on morpho-agronomic traits. The lack of break-through in mungbean production has been due to non-availability of genetic variability for high yield potential. Forty-four genotypes of mungbean [Vigna radiata (L.)Wilczek] were subjected to random amplified polymorphic DNA (RAPD) analysis to assess the genetic diversity and relationships among the genotypes. Multilocus genotyping by twelve RAPD primers generated 166 markers and detected an average of intraspecific variation amounting to 82% polymorphism in banding patterns. Dendrogram obtained from cluster analysis delineated all the 44 genotypes into six clusters. Higher values of Nei's gene diversity (h) and Shannon information index (i) and genetic distance analysis validate existence of wide genetic diversity among mungbean genotypes tested. Besides internal transcribed spacer (ITS) length variations, single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELS) were detected at number of sites in nuclear rDNA region and the sequences of representatives of each sub-cluster and all distinct genotypes have been submitted to NCBI database and assigned Gen accession numbers HQ 148136-148147. Multiple sequence alignment revealed further lineages of distinct genotypes with main RAPD clusters. The measures of relative genetic distances among the genotypes of mungbean did not completely correlate the geographical places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among mungbean genotypes studied. RMG-62, RMG-976, and NDM-56 have been identified as potential source of parents for crop improvement. RAPD primers, OPA-9 and OPA-2 as polymorphic genetic markers and number of pods/plant and number of seeds/plant as dependable phenotypic markers have been identified for improving yield potentials. This genetic diversity will be of significance in developing intraspecific crosses in mungbean crop improvement programme. PMID:21667105

Raturi, Aparna; Singh, S K; Sharma, Vinay; Pathak, Rakesh

2011-06-11

108

Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis.  

PubMed

Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used for RAPD to generate DNA fingerprints from the Salmonella isolates. REP-PCR method showed greater discriminatory power in differentiating closely related strains of the related strains of Salmonella and produced more complex banding patterns as compared with RAPD. A dendogram was constructed with both sets of profiles using SPSS Version 13.0 computer software and showed that most human isolates were separately clustered from the non-human isolates. Two of the human isolates were closely related to some of the non-human isolates. A good correlation was also observed between the serogrouping of the O antigen and the molecular profiles obtained from REP-PCR and RAPD data of the Salmonella isolates. The results of a principal coordinate analysis (PCA) corresponded to the clustering in the dendrogram. PMID:18243815

Albufera, U; Bhugaloo-Vial, P; Issack, M I; Jaufeerally-Fakim, Y

2007-12-23

109

Identification of RAPD and SCAR markers linked to northern leaf blight resistance in waxy corn ( Zea mays var. ceratina )  

Microsoft Academic Search

Exserohilum turcicum causes northern corn leaf blight (NCLB), an important disease occurring in maize producing areas throughout the world. Currently,\\u000a the development of cultivars resistant to E. turcicum seems to be the most efficient method to control NCLB damage. Marker-assisted selection (MAS) enables breeders to improve\\u000a selection efficiency. The objective of this work was to identify random amplified polymorphic DNA (RAPD)

Juthaporn Khampila; Kamol Lertrat; Weerasak Saksirirat; Jirawat Sanitchon; Nooduan Muangsan; Piyada Theerakulpisut

2008-01-01

110

Random amplified polymorphic DNA (RAPD) markers reveal genetic homogeneity in the endangered Himalayan species Meconopsis paniculata and M. simplicifolia  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) marker-based analysis was carried out to study the extent of genetic polymorphism between populations of the two endangered Himalayan poppy species, Meconopsis paniculata and M. Simplicifolia. Of the 90 primers tested, 38 revealed marked inter-species genetic polymorphism between individuals of the two species from geographically isolated populations. However, intra-species genetic homogeneity was also evident with

Irshad M. Sulaiman; Seyed E. Hasnain

1996-01-01

111

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

Microsoft Academic Search

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

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

1998-01-01

112

Identification and localization of molecular markers linked to the Lr 9 leaf rust resistance gene of wheat  

Microsoft Academic Search

Near-isogenic lines (NILs) for the leaf rust resistance gene Lr9 were screened for polymorphisms at the molecular level. RAPD (random amplified polymorphic DNA) primers as well as RFLP (restriction fragment length polymorphism) markers were used. Out of 395 RAPD primers tested, three showed polymorphisms between NILs, i.e., an additional band was found in resistant lines. One of these polymorphic bands

G. Schachermayr; H. Siedler; M. D. Gale; H. Winzeler; M. Winzeler; B. Keller

1994-01-01

113

Molecular characterization of Salmonella isolates by REP-PCR and RAPD analysis  

Microsoft Academic Search

Eighteen Salmonella isolates from both human and food (non-human) sources (fish, meat, and poultry) were characterized using conventional culture methods, biochemical, serological, and molecular analyses. REP-PCR and RAPD produced DNA profiles for differentiation purposes. Enterobacterial repetitive intergenic consensus (ERIC), repetitive extragenic palindronic (REP) and BOXAIR primers were selected for REP-PCR and two arbitrary primers, namely OPP-16 and OPS-11 were used

U. Albufera; P. Bhugaloo-Vial; M. I. Issack; Y. Jaufeerally-Fakim

2009-01-01

114

[Genetic diversity of the house mouse Mus musculus and geographic distribution of its subspecies-specific RAPD markers on the territory of Russia].  

PubMed

Genetic diversity and geographic distribution of taxon-specific RAPD markers was examined in ten local populations of the house mouse Mus musculus (n = 42). The house mice were generally characterized by moderate genetic variation: polymorphism P99 = 60%, P95 = 32.57%; heterozygosity H = 0.12; the observed allele number n(a) = 1.6; the effective allele number n(e) = 1.18; the within-population differentiation Theta = 0.388; and Shannon index I = 0.19. The degree of genetic isolation of individual local populations was greatly variable. The genetic subdivision index G(st) varied from 0.162 to 0.770 at the gene flow of Nm = 2.58-0.149, while the among-population distances D(N) varied from 0.026 to 0.178. of the largest part of the genetic diversity was found among the populations (H(T) = 0.125), while the within-population diversity was twice lower (H(S) = 0.06). The samples examined were well discriminated relative to the sets of RAPD markers. The character distribution pattern provided conditional subdivision of the mice into the "western" and the "eastern" groups with the putative boarder along the Baikal Lake. The first group was characterized by the prevalence of the markers typical of M. m. musculus and M. m. domesticus. The second group was characterized by the prevalence of the markers typical of M. m. musculus, M. m. gansuensis, M. m. castaneus, M. m. domesticus, and m. m. wagneri. The genotype of the nominative subspecies M. m. musculus was background for all populations. In the populations examined some of earlier described subspecies-specific molecular markers were found at different frequencies, pointing to the involvement of several subspecies of M. musculus in the process of hybridization. PMID:18672801

Spiridonova, L N; Korobitsina, K V; Iakimenko, L V; Bogdanov, A S

2008-05-01

115

[Discrimination of interspecific hybrids in natural populations of Amur sturgeon fishes using multilocus RAPD-PCR markers].  

PubMed

RAPD-PCR analysis of 46 individuals of sturgeons from Amur River has been carried out. Genetic status of Amur sturgeon Acipenser schrenckii Brandt, 1869 and kaluga Huso dauricus Georgi, 1775 native populations has been estimated. Genetic evidences of hybrid origin for two phenotypical hybrids were obtained; estimations of genetic distances between species and hybrids appeared to be at interspecific level. The exact test for differentiation of populations (Exact test) and multidimensional scaling (MDS) analysis were estimated to be the most effective for species and hybrid discrimination, respectively. According to data obtained populations of sturgeon fishes which inhabit Amur River maintained an essential level of genetic variability; the presence of hybrids is regarded as one of risk factors. Multilocus RAPD-PCR markers admit as the convenient and reliable tool for genetic monitoring of Amur River sturgeons to preserve their gene pool. PMID:19140442

Chelomina, G N; Rozhkovan, K V; Ivanov, S A

116

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

Microsoft Academic Search

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

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

2007-01-01

117

Genetic diversity of bitter gourd ( Momordica charantia L.) genotypes revealed by RAPD markers and agronomic traits  

Microsoft Academic Search

Bitter gourd or bitter melon (Momordica charantia L.) is considered as minor cucurbitaceous vegetable in spite of having considerable nutritional and medicinal properties. Although some reports on genetic diversity based on morphological characterization are available, no work has been conducted to estimate genetic diversity using molecular markers in this crop. In the present study, 38 genotypes of M. charantia including

S. S. Dey; A. K. Singh; D. Chandel; T. K. Behera

2006-01-01

118

Identification of a RAPD marker linked to the oat stem rust gene Pg3  

Microsoft Academic Search

The feasibility of identifying molecular markers linked to disease resistance genes in oats was investigated utilizing random primers in conjunction with polymerase chain reaction technology. A pair of near-isogenic oat lines were screened for polymorphic DNA fragments linked to the stem rust resistance gene Pg3. Two primers were identified which amplified DNA fragments that were polymorphic between the lines analyzed.

G. A. Penner; J. Chong; M. Lévesque-Lemay; S. J. Molnar; G. Fedak

1993-01-01

119

Genetic polymorphism in exotic safflower (Carthamus tinctorious L.) using RAPD markers  

Microsoft Academic Search

Safflower is a drought tolerant annual oil crop and this gives it an advantage over the other crops in the drier parts of Kenya. It is valued worldwide as a source of high quality vegetable oil. In the past, characterization of safflower using molecular markers has been limited. The objective of this study was to evaluate the degree of polymorphism

120

RAPD, ISSR AND AFLP MARKERS REPRESENTING VARIOUS LINKAGE REGIONS OF A WATERMELON GENETIC MAP ARE POLYMORPHIC AMONG CLOSELY RELATED WATERMELON CULTIVARS  

Technology Transfer Automated Retrieval System (TEKTRAN)

A genetic linkage map was previously constructed for watermelon using a wide testcross population {[Griffin 14113 (C. lanatus var. citroides) x New Hampshire Midget; NHM (C. lanatus var. lanatus)] x U.S. PI 386015 (C. colocynthis)}. Most markers (44 RAPD, 15 ISSR and 48 AFLP markers) unique to NHM a...

121

CARACTERIZAÇÃO MOLECULAR DE BUTIAZEIRO POR MARCADORES RAPD1  

Microsoft Academic Search

RESUMO- O grupo botânico Arecaceae é de extremo interesse por compreender plantas em extinção e por apresentar um grande potencial de exploração econômica. O butiazeiro (Butia capitata (Mart.) Becc.) ocorre naturalmente no Sul do Brasil. Sua caracterização molecular é de extremo interesse para futuros trabalhos de melhoramento genético. Assim sendo, verificou-se a variabilidade genética existente entre vinte e dois genótipos

ADRISE MEDEIROS NUNES; VALMOR JOÃO BIANCHI; JOSÉ CARLOS FACHINELLO; ALEXANDRE ZANARDO DE CARVALHO; GUILHERME CARDOSO

122

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

PubMed

Almond shoots produced by axillary branching from clone VII derived from a seedling of cultivar Boa Casta were evaluated for somaclonal variation using randomly amplified polymorphic DNA (RAPD) and inter-simple sequence repeats (ISSR) analysis. To verify genetic stability we compared RAPD and ISSR patterns of plantlets obtained after 4 and 6 years of in vitro multiplication. A total of 64 RAPD and 10 ISSR primers gave 326 distinct and reproducible band classes, monomorphic across all 22 plantlets analysed. Thus, a total of 7,172 bands were generated, exhibiting homogeneous RAPD and ISSR patterns for the plantlets tested. These results suggest that the culture conditions used for axillary branching proliferation are appropriate for clonal propagation of almond clone VII, as they do not seem to interfere with the integrity of the regenerated plantlets. These results allowed us to establish the use of axillary branching plantlets (mother-plants) as internal controls for the analysis of somaclonal variation of shoots regenerated from other in vitro culture processes performed with clone VII (adventitious regeneration, regeneration from meristem culture, virus sanitation programs and genetic engineering). PMID:15372197

Martins, M; Sarmento, D; Oliveira, M M

2004-09-15

123

Random amplified polymorphic DNA (RAPD) markers for genetic analysis in Allium  

Microsoft Academic Search

RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative

Susan E. Wilkie; Peter G. Isaac; Robert J. Slater

1993-01-01

124

Genetic diversity in European and Mediterranean faba bean germ plasm revealed by RAPD markers  

Microsoft Academic Search

Broadening of the genetic base and systematic exploitation of heterosis in faba bean requires reliable information on the genetic diversity in the germ plasm. Three groups of faba bean inbred lines were examined by means of RAPDs (random amplified polymorphic DNAs) assays: 13 European small-seeded lines, 6 European large-seeded lines, and 9 Mediterranean lines. Out of 59 primers, 35 were

W. Link; C. Dixkens; M. Schwall; A. E. Melchinger

1995-01-01

125

Microsatellite Markers for Molecular Breeding  

Microsoft Academic Search

Microsatellites are tandem repeats of short sequence motifs that occur ubiquitously in eukaryotic genomes. A key feature of this class of repetitive DNA is an extraordinarily high level of variation among taxa, mainly expressed as a variable copy number of tandem repeats. A multitude of techniques were described that exploit microsatellite variability as molecular markers. Basically, these approaches can be

Kurt Weising; Peter Winter; Bruno Hüttel; GüNter Kahl

1997-01-01

126

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR HOMALODISCA SHARPSHOOTERS PRESENT IN CALIFORNIA TO AID IN THE IDENTIFICATION OF KEY PREDATORS  

Technology Transfer Automated Retrieval System (TEKTRAN)

The aim of the present study was to develop molecular diagnostic markers to identify key predators of Homalodisca sharpshooter species present in California, H coagulata (Glassy-winged Sharpshooter, GWSS) and H liturata (Smoke-tree Sharpshooter, STSS). RAPD-PCR DNA fmgerprinting of several sharpshoo...

127

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

PubMed

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

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

2010-03-24

128

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

Microsoft Academic Search

The aim of the present study was to determine the effect of nickel on shoot regeneration in tissue culture as well as to identify\\u000a polymorphisms induced in leaf explants exposed to nickel through random amplified polymorphic DNA (RAPD). In vitro leaf explants\\u000a of Jatropha curcas were grown in nickel amended Murashige and Skoog (MS) medium at four different concentrations (0,

Tanmoy Sarkar; K. G. Vijay Anand; M. P. Reddy

2010-01-01

129

Potential of Molecular Markers in Plant Biotechnology  

Microsoft Academic Search

During the last few decades, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in plant biotechnology and their genetics studies. There are different types of markers viz. morphological, biochemical and DNA based molecular markers. These DNA based markers are differentiates in two types first non PCR based (RFLP) and second is

P. Kumar; V. K. Gupta; A. K. Misra; D. R. Modi; B. K. Pandey

2009-01-01

130

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

PubMed

Genetic relationships among 52 Eleusine coracana (finger millet) genotypes collected from different districts of Uttarakhand were investigated by using randomly amplified polymorphic DNA (RAPD), simple sequence repeat (SSR) and cytochrome P450 gene based markers. A total of 18 RAPD primers, 10 SSR primers, and 10 pairs of cytochrome P450 gene based markers, respectively, revealed 49.4%, 50.2% and 58.7% polymorphism in 52 genotypes of E. coracana. Mean polymorphic information content (PIC) for each of these marker systems (0.351 for RAPD, 0.505 for SSR and 0.406 for cyt P450 gene based markers) suggested that all the marker systems were effective in determining polymorphisms. Pair-wise similarity index values ranged from 0.011 to 0.999 (RAPD), 0.010 to 0.999 (SSR) and 0.001 to 0.998 (cyt P450 gene based markers) and mean similarity index value of 0.505, 0.504 and 0.499, respectively. The dendrogram developed by RAPD, SSR and cytochrome P450 gene based primers analyses revealed that the genotypes are grouped in different clusters according to high calcium (300-450 mg/100 g), medium calcium (200-300 mg/100 g) and low calcium (100-200 mg/100 g). Mantel test employed for detection of goodness of fit established cophenetic correlation values above 0.95 for all the three marker systems. The dendrograms and principal coordinate analysis (PCA) plots derived from the binary data matrices of the three marker systems are highly concordant. High bootstrap values were obtained at major nodes of phenograms through WINBOOT software. Comparison of RAPD, SSR and cytochrome P450 gene based markers, in terms of the quality of data output, indicated that SSRs and cyt P450 gene based markers are particularly promising for the analysis of plant genome diversity. The genotypes of finger millet collected from different districts of Uttarakhand constitute a wide genetic base and clustered according to calcium contents. The identified genotypes could be used in breeding programmes and amajor input into conservation biology of cereal crops. PMID:20861563

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

2010-08-01

131

An improved genetic linkage map for cowpea ( Vigna unguiculata L.) Combining AFLP, RFLP, RAPD, biochemical markers, and biological resistance traits  

Microsoft Academic Search

An improved genetic linkage map has been constructed for cowpea (Vigna unguiculata L. Walp.) based on the segregation of various molecular markers and biological resistance traits in a population of 94 recombinant inbred lines (RILs) derived from the cross between 'IT84S-2049' and '524B'. A set of 242 molecular markers, mostly ampli- fied fragment length polymorphism (AFLP), linked to 17 biological

J. T. Ouédraogo; B. S. Gowda; M. Jean; T. J. Close; J. D. Ehlers; A. E. Hall; A. G. Gillaspie; P. A. Roberts; A. M. Ismail; G. Bruening; P. Gepts; M. P. Timko; F. J. Belzile

2002-01-01

132

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

PubMed

The inheritance of shoot regeneration through shoot-tip meristem culture derived from maize seedling was evaluated, and the markers (RAPD and SSR) associated with this regeneration character were identified both in a group of North American maize inbreds and a crossing population. A discrete distribution of percent regeneration and no. of shoots per explant was observed in the inbred group and the F(2) population. The results suggested that this regenerable trait was controlled by several major genes. Five RAPD markers were identified to be relevant to percent regeneration in maize shoot-tip culture system. One RAPD marker and three SSR markers were associated with no. of shoot per explant and its relevant traits. Of them marker BC603-1600 explained 18% of the variation for no. of shoot per explant and 16% of the variation for callus size. The BC603-1600 was sequenced and assigned in linkage group 7 based on a NCBI blast search. The information provided here should benefit to determine the genetic mechanisms involved in the maize regeneration response related to shoot meristem culture pathway and benefit to select high regenerable germplasm by using marker assisted selection. PMID:14586503

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

2003-10-30

133

Genetic characterization of fig tree mutants with molecular markers.  

PubMed

The fig (Ficus carica L.) is a fruit tree of great world importance and, therefore, the genetic improvement becomes an important field of research for better crops, being necessary to gather information on this species, mainly regarding its genetic variability so that appropriate propagation projects and management are made. The improvement programs of fig trees using conventional procedures in order to obtain new cultivars are rare in many countries, such as Brazil, especially due to the little genetic variability and to the difficulties in obtaining plants from gamete fusion once the wasp Blastophaga psenes, responsible for the natural pollinating, is not found in Brazil. In this way, the mutagenic genetic improvement becomes a solution of it. For this reason, in an experiment conducted earlier, fig plants formed by cuttings treated with gamma ray were selected based on their agronomic characteristics of interest. We determined the genetic variability in these fig tree selections, using RAPD and AFLP molecular markers, comparing them to each other and to the Roxo-de-Valinhos, used as the standard. For the reactions of DNA amplification, 140 RAPD primers and 12 primer combinations for AFLP analysis were used. The selections did not differ genetically between themselves and between them and the Roxo-de-Valinhos cultivar. Techniques that can detect polymorphism between treatments, such as DNA sequencing, must be tested. The phenotypic variation of plants may be due to epigenetic variation, necessitating the use of techniques with methylation-sensitive restriction enzymes. PMID:22911583

Rodrigues, M G F; Martins, A B G; Desidério, J A; Bertoni, B W; Alves, M C

2012-08-06

134

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

PubMed Central

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

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

2010-01-01

135

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

NASA Astrophysics Data System (ADS)

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.

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

1998-03-01

136

Application of molecular markers in predicting production quality of cultivated Cistanche deserticola.  

PubMed

We developed a set of molecular markers in Cistanche deserticola Y. C. MA to evaluate the production quality of cultivated C. deserticola individuals. This application utilizes the inter-simple-sequence repeat (ISSR) polymerase chain reaction (PCR) and random amplified polymorphic DNA (RAPD) PCR as molecular markers to determine the echinacoside content in cultivated C. deserticola individuals. The unweighted pair-group method using arithmetic average clustering (UPGMA) confirmed that the combined ISSR and RAPD data could categorize all C. deserticola individuals into three groups according to their respective echinacoside content. The stepwise multiple regression analysis (SMRA) revealed six potential markers associated with echinacoside accumulation in C. deserticola and produced 18 echinacoside-marker prediction models, four of which were successfully used to predict the quality of C. deserticola from Neimenggu. Both clustering and SMRA showed a correlation between the echinacoside content and molecular markers in cultivated C. deserticola. The relative average deviation of prediction (RADP) of the prediction models could be improved by simplifying and adjusting the model. It was found that the RADP value could reach 2.6% after adjustment and the simplified prediction models could successfully predict the quality of cultivated C. deserticola individuals. PMID:20118564

Wu, Yan; Shi, Hai Ming; Bao, Zhong; Wang, Meng Yue; Tu, Peng Fei; Li, Xiao Bo

2010-01-01

137

A RAPD-PCR derived marker can differentiate between pathogenic and non-pathogenic Sarcocystis species of sheep  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD)-PCR was used to differentiate among four cyst-forming coccidia of sheep,Sarcocystis tenella,Sarcocystis gigantea,Sarcocystis arieticanis, andToxoplasma gondii. Genomic DNA of the four parasite species was amplified using RAPD-PCR and the DNA fragments were separated on agarose gels. A RAPD-PCR band derived fromS. tenellawas isolated from the gel and subcloned into pUC18. The insert was sequenced and found

A. Joachim; A. M. Tenter; A. C. Jeffries; A. M. Johnson

1996-01-01

138

Genetic diversity of Amaranthus species from the Indo-Gangetic plains revealed by RAPD analysis leading to the development of ecotype-specific SCAR marker.  

PubMed

Genetic diversity and relationships among 6 Amaranthus species from 8 phytogeographic regions of the Indo-Gangetic plains were analyzed using a random amplified polymorphic DNA (RAPD) marker. RAPD primers yielded a total of 262 amplicons, ranging from approximately 250 to approximately 3000 bp in size with an average of 13.1 amplicons per primer, of which 254 amplicons (96.94%) were polymorphic. The genetic similarity coefficient among all the Amaranthus species ranged from 0.16 to 0.97 with a mean similarity coefficient of 0.56, indicating that variation existed in the genetic diversity of different populations. In the unweighted pair group method with arithmetic average dendrogram, populations of the same species clustered together. A unique 1371-bp RAPD band specific for Amaranthus gangeticus (syn. tricolor) of a particular phytogeographic region was converted to a sequenced characterized amplified region (SCAR) marker. The translated marker sequence showed homology with hemagglutinin protein. This SCAR marker is potentially useful for germplasm conservation and identification of amaranth ecotype. PMID:19060233

Ray, Tui; Roy, Satyesh Chandra

2008-12-05

139

Genetic variability of Fusarium wilt pathogen isolates of chickpea (Cicer arietinum L.) assessed by molecular markers.  

PubMed

Genetic variability among 43 isolates of Fusarium oxysporum f.sp. ciceri, the chickpea wilt pathogen, collected from nine states of India including the four well-characterized races of the pathogen were assessed using the molecular markers, RAPDs and AFLP. Principal coordinate analysis of the similarity index data generated from the molecular marker studies mostly gave three different clusters: Of these two clusters represented race-1 and race-2, and the third cluster consisted of race-3 and race-4 pathogen isolates. In RAPDs a fourth cluster was seen which did not go with any of the four races of the pathogen. The molecular markers established the distinctness of race-1 and race-2 pathogen isolates and the close similarity of pathogen isolates of race-3 with that of race-4. AFLP was found to be more informative as it differentiated more number of the pathogen isolates with the known races with minimum of outliers. The high levels of DNA polymorphism observed with the molecular markers suggest the rapid evolution of new recombinants of the pathogen in the chickpea growing fields. PMID:12617504

Sivaramakrishnan, S; Kannan, Seetha; Singh, S D

2002-01-01

140

Molecular Marker Discovery and Genetic Map Visualisation  

Microsoft Academic Search

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

Chris Duran; David Edwards; Jacqueline Batley

141

A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference.  

PubMed

AFLPs (and to a lesser extent ISSRs and RAPDs) are increasingly being used for phylogenetic inference among closely related species. Presence/absence characters for each AFLP allele treat all absences as homologous to one another. With three or more alleles, terminals are grouped by their shared absence of alleles in character-based phylogenetic-inference methods in a manner that is not redundant with their shared presence of an alternative allele. We conducted simulations to quantify how severe the negative effect of using presence/absence characters of individual bands is for phylogenetic inference relative to standard multistate characters. We examined alternative tree topologies, relative branch lengths, numbers of characters, rates of evolution, and numbers of alternative alleles, using both parsimony and Nei-and-Li distance analyses. Multistate parsimony generally outperformed presence/absence parsimony, which in turn outperformed Nei-and-Li distance. Increasing the character-state space (i.e., the number of alternative character states available) was found to be advantageous for all three methods of analysis examined, but was most advantageous for multistate parsimony. However, the advantage of multistate parsimony relative to Nei-and-Li distance decreased when applied to more divergent characters. More parsimony-informative variation generally alleviated the problem associated with scoring multistate characters as presence/absence characters. The ensemble consistency index was lower for presence/absence characters relative to multistate characters. PMID:16997581

Simmons, Mark P; Zhang, Li-Bing; Webb, Colleen T; Müller, Kai

2006-08-22

142

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

PubMed Central

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.

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

1998-01-01

143

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

PubMed

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

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

144

Estimation of the number of full sibling families at an oviposition site using RAPD-PCR markers: applications to the mosquito Aedes aegypti  

Microsoft Academic Search

There are many species in which groups of individuals encountered in the field are known to consist of mixtures of full-sibling families. We describe a statistical technique, based on the use of random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) markers, that allows for the estimation of the number of families contained in these groups. We test the technique on full-sibling

B. L. Apostol; W. C. Black; B. R. Miller; P. Reiter; B. J. Beaty

1993-01-01

145

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

Microsoft Academic Search

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

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

2003-01-01

146

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

Microsoft Academic Search

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

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

2005-01-01

147

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

Microsoft Academic Search

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

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

2003-01-01

148

Molecular markers linked to genes for specific rust resistance and indeterminate growth habit in common bean  

Microsoft Academic Search

Bulked segregant analysis was utilized to identify random amplified polymorphic DNA (RAPD) markers linked to genes for specific resistance to a rust pathotype and indeterminate growth habit in an F2 population from the common bean cross PC-50 (resistant to rust and determinate growth habit) × Chichara 83-109 (susceptible to rust and indeterminate growth habit). Six RAPD markers were mapped in

Soon O. Park; Dermot P. Coyne; James M. Bokosi; James R. Steadman

1999-01-01

149

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

PubMed

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

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

2004-08-12

150

Harmonizing Molecular Marker Analyses of Organic Aerosols  

Microsoft Academic Search

Analysis of molecular markers in aerosol samples using GC-MS has become widely used in air pollution studies. There is considerable variability in the analytical details of molecular marker analyses across different research and regulatory groups. These discrepancies result in the use of different methods for the interpretation of source and ambient measurements used in source apportionment and atmospheric particulate studies.

Yuan Xun Zhang; James Jay Schauer; Elizabeth Anne Stone; Yuanhang Zhang; Min Shao; Yongjie Wei; Xianlei Zhu

2009-01-01

151

Prognostic molecular markers in cancer - quo vadis?  

PubMed

Despite the tremendous number of studies of prognostic molecular markers in cancer, only a few such markers have entered clinical practise. The lack of clinical prognostic markers clearly reflects limitations in or an inappropriate approach to prognostic studies. This situation should be of great concern for the research community, clinicians and patients. In the present review, we evaluate immunohistochemical prognostic marker studies in oral squamous cell carcinomas (OSCC) from 2006 to 2012. We comment upon general issues such as study design, assay methods and statistical methods, applicable to prognostic marker studies irrespective of cancer type. The three most frequently studied markers in OSCC are reviewed. Our analysis revealed that most new molecular markers are reported only once. To draw conclusions of clinical relevance based on the few markers that appeared in more than one study was problematic due to between-study heterogeneity. Currently, much valuable tissue material, time and money are wasted on irrelevant studies. PMID:23837466

Søland, Tine M; Brusevold, Ingvild J

2013-07-09

152

Molecular identification of lizard by RAPD & FINS of mitochondrial 16s rRNA gene  

Microsoft Academic Search

In the present study, we identified the structure-less skeleton suspected to be of house lizard present in jaggery, consumption of which caused mass food poisoning using, RAPD (Random Amplification of Polymorphic DNA) with random primers and FINS (Forensically Informative Nucleotide Sequencing) with mitochondrial 16s rRNA gene. The NJ tree dendogram based on distance calculated from RAPD bands clearly identified the

Saurav Guha; V. K. Kashyap

2006-01-01

153

Molecular marker analysis of European Setosphaeria turcica populations  

Microsoft Academic Search

Setosphaeria turcica is the causal agent of northern corn leaf blight, a foliar maize disease of worldwide economic importance. In Europe, its severity increases. To investigate the pathogen's population-genetic structure in central Europe, a total of 80 isolates was sampled in Germany, Switzerland, France, Austria, and Hungary and investigated with 52 random amplified polymorphic DNA (RAPD) markers. The mating type

Dorothea S. Borchardt; H. Günter Welz; Hartwig H. Geiger

1998-01-01

154

Genetic diversity and relationships among Lablab purpureus genotypes evaluated using RAPD as markers  

Microsoft Academic Search

Genetic variation in 40 accessions of Lablab purpureus was evaluated using random amplified polymorphic DNA as markers. A high level of genetic variation in this species was detected but this was mainly restricted to the difference between cultivated and wild forms. Of the cultivated genotypes, genetic variation among Asian collections was significantly higher than that among African collections. The three

C. J. Liu

1996-01-01

155

Molecular characterization and relatedness of Haematobia irritans (horn fly) populations, by RAPD-PCR.  

PubMed

Haematobia irritans is a hematophagous parasite of cattle that causes significant economic losses in many parts of the world, including Brazil. In the present work, one American and four Brazilian populations of this species were studied by Random Amplified Polymorpht DNA (RAPD) to assess basically genetic variability within and between populations. Ten different decamer random primers were employed in the genomic DNA amplification, yielding 117 fragments in the five H. irritans populations. In Drosophila prosaltans, used as an outgroup, 81 fragments were produced. Forty-three of these fragments were shared by both species. Among the H. irritans samples, that from Rio Branco (Acre State, Brazil) produced the smallest numbers of fragments and polymorphic bands. This high genetic homogenity may be ascribed to its geographic origin (in the Northwest of Brazil), which causes high isolation and low gene flow, unlike the other Brazilian populations, from the South Central region, in which cattle trade is very intensive. Marker fragments (exclusive bands) detected in every sample enabled the population origin to be characterized, but they are also potentially useful for further approaches such as the putative origin of Brazilian populations from North America. Similarity indices [Nei & Li, 1979, Proc. Natl. Acad. Sci. USA 76: 5269-5273] and phylogenetic trees, rooted by using the outgroup and produced by the Phylogenetic Analysis using Parsimony (PAUP 4.0-Swofford, 2001) program showed the closest relationships between flies from Sao Jose do Rio Preto and Turúba (both from São Paulo State, Brazil) while flies from the geographically distant Rio Branco showed the greatest differentiation relative to the others. PMID:16010999

Castiglioni, Lilian; de Campos Bicudo, Hermione Elly Melara

2005-05-01

156

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

PubMed Central

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.

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

2010-01-01

157

Identification of molecular markers linked to Pm13, an Aegilops longissima gene conferring resistance to powdery mildew in wheat  

Microsoft Academic Search

RFLP, RAPD, STS and DDRT-PCR techniques were applied to find molecular markers linked to Pm13, an Aegilops longissima gene conferring resistance to powdery mildew in wheat. The experimental strategy was based on the differential comparison\\u000a of DNAs from common wheat and from common wheat\\/Ae. longissima recombinant lines carrying short segments of the 3S\\u000a l\\u000a S chromosome arm containing the Pm13

A. Cenci; R. D’Ovidio; O. A. Tanzarella; C. Ceoloni; E. Porceddu

1999-01-01

158

Genetic relation of Coffea and Indian Psilanthus species as revealed through RAPD and ISSR markers  

Microsoft Academic Search

Coffee plants belong to the genus Coffea and Psilanthus of the tribe Coffeeae in the family Rubiaceae and are mostly distributed in tropical and sub-tropical regions. Over a period of time, Psilanthus was considered as a section Paracoffea under Coffea but recent taxonomic reports favor Psilanthus as separate genera. However, biochemical and molecular studies indicate close genome similarity of Psilanthus

S Ananda Kumar; J Sudisha; H L Sreenath

159

(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...

160

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...

161

Analysis of population genetic structure and variability using RAPD markers in the endemic and endangered Limonium dufourii (Plumbaginaceae).  

PubMed

Limonium dufourii (Plumbaginaceae) is a triploid species, with apomictic reproduction, endemic to the east mediterranean coast of Spain, where it is present in only six populations with a few individuals in most of them. L. dufourii is included in the Red List of Endangered Species by the IUCN. Genetic variation and population structure in this species has been studied using RAPDs. Twelve different primers provided 124 reliable bands of which 33 were polymorphic among the 165 individuals analysed. Those polymorphic bands were able to define 44 different patterns, of which all but six were present in only one population. Several methods for statistical evaluation have been used for intra- and interpopulation analysis of genetic variability. Relationships among patterns have led to the identification of four main clusters. Two of them show a perfect correspondence to the population of origin of those individuals that present them (Cullera and Torreblanca), and the other two (Groups A and B) include patterns found in individuals coexisting in the same populations (Marjal del Moro populations) and in El Saler. Most of the variation found in this species is due to differences among populations as shown by the analysis of molecular variance. This agrees with the expectation for an apomictic species such as L. dufourii. The analysis of homogeneity of variance shows that substantial differences in the amount of genetic variability present in the six populations exist. These results have been used to understand the evolutionary and demographic history of L. dufourii, which is a requisite in order to establish efficient conservation measures for this species. PMID:9421917

Palacios, C; González-Candelas, F

1997-12-01

162

SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean  

Microsoft Academic Search

Anthracnose, caused by the fungusColletotrichum lindemuthianum, is a severe disease of common bean (Phaseolus vulgaris L.) controlled, in Europe, by a single dominant gene,Are. Four pairs of near-isogenic lines (NILs) were constructed, in which theAre gene was introgressed into different genetic backgrounds. These pairs of NILs were used to search for DNA markers linked to the resistance gene. Nine molecular

A. F. Adam-Blondon; M. Sévignac; H. Bannerot; M. Dron

1994-01-01

163

RAPD markers for identifying oil palm ( Elaeis guineensis Jacq.) parental varieties (dura & pisifera ) and the hybrid tenera  

Microsoft Academic Search

Random amplification of polymorphic DNA (RAPD) analysis was done by arbitrary primers for determining the DNA polymorphism among the oil palm ( Elaeis guineensis ) varieties dura , pisifera and tenera , and monitoring the specificity of the primers for identifying each genotype. The three varieties were evaluated using thirty, 10-mer primers. Of the 30 primers, 26 yielded significant polymorphic

D K Sathish; C Mohankumar

164

[Identification of molecular markers linked to the fertility restoring gene for the CMS Capsicum annuum L].  

PubMed

Bulked segregant analysis method was used to identify random amplified polymorphic DNA (RAPD) markers linked to the fertility restoring gene for the cytoplasmic male sterility (CMS) capsicum annum L. Totally 336 random primers were screened on the DNA samples of restorer and sterile bulks. Primer S418 produced a special band in restorer line. It was about 3000 bp, including two fragments 1515 bp and 1162 bp. Fluorescence in situ hybridization(FISH) indicated the fragment of 1515 bp only existed in restorer line.It was designed to S418(1515). Analysis of the sequence indicated S418(1515) was unknown before. The homology of blastn was less than 40%, however the homology of tBlastx indicated this sequence was high homologous with the part sequences of rice which were distributed on 2,4,7,10 chromosomes. It suggested this sequence might have the similar function with them. This result offered a good foundation to research the molecular mechanism of fertility restoration for CMS capsicum. Based on the sequence, special primers were designed to transform the RAPD marker to PCR marker. The result indicated that these primers could be used to screen the restorer lines from a large quantitive of candidate lines. PMID:16044916

Chang, Cai Tao; Wang, Chun Guo; Chen, Cheng Bin; Wu, Feng; Sun, De Ling

2005-06-01

165

Assessing Genetic Structure with Multiple Classes of Molecular Markers: A Case Study Involving the Introduced Fire Ant Solenopsis invicta  

Microsoft Academic Search

We used 30 genetic markers of 6 different classes to describe hierarchical genetic structure in introduced populations of the fire ant Solenopsis invicta. These included four classes of presumably neutral nuclear loci (allozymes, co- dominant random amplified polymorphic DNAs (RAPDs), microsatellites, and dominant RAPDs), a class comprising two linked protein-coding nuclear loci under selection, and a marker of the mitochondrial

Kenneth G. Ross; D. DeWayne Shoemaker; Michael J. B. Krieger; Christopher J. DeHeer; Laurent Keller

166

Assessment of genetic diversity and genetic relationships among 29 populations of Azadirachta indica A. Juss. using RAPD markers  

Microsoft Academic Search

Randomly amplified polymorphic DNA (RAPD) analysis was employed to assess genetic divergence among 29 neem accessions collected from two agro-ecological regions of India (11 agro-climatic sub-zones), which cover three states, Punjab, Haryana and Rajasthan. Out of 24, 10-mer random primers used for studying genetic divergence, 14 were polymorphic, generating a total of 73 amplification products with an average of 5.21

R. P. Singh Deshwal; Rakesh Singh; Kanika Malik; G. J. Randhawa

2005-01-01

167

Effect of radiation on regeneration of Chinese narcissus and analysis of genetic variation with AFLP and RAPD markers  

Microsoft Academic Search

The aim of our study was to establish an efficient in vitro propagation protocol for Chinese narcissus (Narcissus tazetta var. chinensis) to obtain variants of this species using ?-radiation treatment and evaluate the effectiveness of this system for variant\\u000a induction using amplification fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) analysis.\\u000a Various doses (5–100 Gy) of gamma rays were

Gang Lu; Xiaoying Zhang; Yijing Zou; Qingcheng Zou; Xun Xiang; Jiashu Cao

2007-01-01

168

Discrimination of interspecific hybrids in natural populations of Amur sturgeon fish by means of multilocus RAPD-PCR markers  

Microsoft Academic Search

A RAPD-PCR analysis of a sample of Amur sturgeon fish (46 individuals) is performed. An estimate of the genetic state of native\\u000a populations of Amur sturgeon Acipenser schrenckii (Brandt, 1869) and kaluga fish Huso dauricus (Georgi, 1775) is given. Genetic evidence for the hybrid origin of two phenotypical hybrids is obtained. Estimates of the\\u000a genetic distances between the species and

G. N. Chelomina; K. V. Rozhkovan; S. A. Ivanov

2008-01-01

169

Construction of a linkage map and QTL analysis of horticultural traits for watermelon [Citrullus lanatus (THUNB.) MATSUM & NAKAI] using RAPD, RFLP and ISSR markers.  

PubMed

We have been constructing linkage maps for watermelon ( Citrullus lanatus) on the basis of random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), inter-simple sequence repeats (ISSRs) and isozymes using an F(2) population derived from a crossing between a cultivated inbred line (H-7; C. lanatus) and an African wild form (SA-1; C. lanatus). A total of 120 F(2) plants was used for construction of a linkage map using 477 RAPDs, 53 RFLPs, 23 ISSRs and one isozyme markers. Linkage analysis revealed that 554 loci could be mapped to 11 linkage groups that extended for 2,384 centimorgans (cM). While a BC(1) population [(H-7 x SA-1) x H-7] consisting of 60 individuals was grown and scored for quantitative traits. Another linkage map with a total length of 1,729 cM was constructed in the BC(1) using genetic markers found to segregate in the F(2) population. A QTL analysis was applied by means of interval mapping for locating such agronomic traits as hardness of rind, Brix of flesh juice, flesh color (red and yellow) and rind color. The relative order of markers in the BC(1) map was essentially the same as that on the linkage map in the F(2). A total of five QTLs for four agronomic traits was detected. The QTL for hardness of rind was mapped on group 4. The linkage group 8 contained the QTL for sugar content of the flesh as expressed in Brix of the juice. The QTL for red flesh color was detected on groups 2 and 8. The QTL for rind color mapped on the group 3. The present map and QTL analysis may provide a useful tool for breeders by introducing valuable wild watermelon genes to cultivars. PMID:12647050

Hashizume, T; Shimamoto, I; Hirai, M

2003-02-07

170

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)

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.

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

2011-03-01

171

Combining molecular-marker and chemical analysis of Capparis decidua (Capparaceae) in the Thar Desert of Western Rajasthan (india).  

PubMed

The Thar Desert, a very inhospitable place, accommodates only plant species that survive acute drought, unpredictable precipitation, and those can grow in the limited moisture of sandy soils. Capparis decidua is among one of the few plants able to grow well under these conditions. This species is highly exploited and has been naturally taken, as local people use it for various purposes like food, timber and fuel, although, no management or conservation efforts have been established. The present study was conducted in this arid area of Western Rajasthan (India) with the aim to obtain preliminary molecular information about this group of plants. We evaluated diversity among 46 samples of C. decidua using chemical parameters and random amplified polymorphic DNA (RAPD) markers. Fourteen chemical parameters and eight minerals (total 22 variables) of this species fruits were estimated. A total of 14 RAPD primers produced 235 band positions, of which 81.27% were polymorphic. Jaccard's similarity coefficients for RAPD primers ranged from 0.34 to 0.86 with a mean genetic similarity of 0.50. As per observed coefficient of variation, NDF (Neutral Detergent Fiber) content was found to be the most variable trait followed by starch and soluble carbohydrate. The Manhattan dissimilarity coefficient values for chemical parameters ranged between 0.02-0.31 with an average of 0.092. The present study revealed a very low correlation (0.01) between chemical parameters and RAPD-based matrices. The low correlation between chemical- and RAPD-based matrices indicated that the two methods were different and highly variable. The chemical-based diversity will assist in selection of nutritionally rich samples for medicinal purpose, while genetic diversity to face natural challenges and find sustainable ways to promote conservation for future use. PMID:23894984

Kumar, Sushil; Sharma, Ramavtar; Kumar, Vinod; Vyas, Govind K; Rathore, Abhishek

2013-03-01

172

Fecal Molecular Markers for Colorectal Cancer Screening  

PubMed Central

Despite multiple screening techniques, including colonoscopy, flexible sigmoidoscopy, radiological imaging, and fecal occult blood testing, colorectal cancer remains a leading cause of death. As these techniques improve, their sensitivity to detect malignant lesions is increasing; however, detection of precursor lesions remains problematic and has generated a lack of general acceptance for their widespread usage. Early detection by an accurate, noninvasive, cost-effective, simple-to-use screening technique is central to decreasing the incidence and mortality of this disease. Recent advances in the development of molecular markers in faecal specimens are encouraging for its use as a screening tool. Genetic mutations and epigenetic alterations that result from the carcinogenetic process can be detected by coprocytobiology in the colonocytes exfoliated from the lesion into the fecal matter. These markers have shown promising sensitivity and specificity in the detection of both malignant and premalignant lesions and are gaining popularity as a noninvasive technique that is representative of the entire colon. In this paper, we summarize the genetic and epigenetic fecal molecular markers that have been identified as potential targets in the screening of colorectal cancer.

Kanthan, Rani; Senger, Jenna-Lynn; Kanthan, Selliah Chandra

2012-01-01

173

Molecular markers of gliomas: a clinical approach.  

PubMed

Over the last decade, the knowledge on the molecular genetic background of gliomas has dramatically increased. This information provides the basis for the molecular target therapies and molecular tests serve to complement the subjective nature of histopathologic criteria and add useful data regarding response to treatments and prognosis. In particular, the use of loss of heterozygosity (LOH) and methylation specific polymerase chain reaction (PCR) (MSP) based testing of gliomas is already in place and used clinically in several centers. This paper provides a brief overview of these molecular genetic aberrations and discusses the clinical utility, as well as the advantages and disadvantages of such approach. Newly developed molecular techniques, such as LOH testing, fluorescence in situ hybridization (FISH), DNA sequencing and MSP, are currently being employed in assessment of gliomas in some laboratories. However, the clinical use of some markers and the context in which the information obtained should be used are still not entirely understood. Therefore, this paper will focus on validation and implementation of molecular testing in gliomas, with emphasis on LOH on chromosomes 1p, 19q, 17p and 10q and O(6)-methylguanine-DNA methyltransferase (MGMT) methylation status. PMID:16808886

Eoli, M; Silvani, A; Pollo, B; Bianchessi, D; Menghi, F; Valletta, L; Broggi, G; Boiardi, A; Bruzzone, M G; Finocchiaro, G

2006-07-01

174

Molecular and clinical markers of pancreas cancer.  

PubMed

Pancreas cancer has the worst prognosis of any solid tumor but is potentially treatable if it is diagnosed at an early stage. Thus there is critical interest in delineating clinical and molecular markers of incipient disease. The currently available biomarker, CA 19-9, has an inadequate sensitivity and specificity to achieve this objective. Diabetes mellitus, tobacco use, and chronic pancreatitis are associated with pancreas cancer. However, screening is currently only recommended in those with hereditary pancreatitis and genetic syndromes which predispose to cancer. Ongoing work to identify early markers of pancreas cancer consists of high throughput discovery methods including gene arrays and proteomics as well as hypothesis driven methods. While several promising candidates have been identified none has yet been convincingly proven to be better than CA 19-9. New methods including endoscopic ultrasound are improving detection of pancreas cancer and are being used to acquire tissue for biomarker discovery. PMID:21068484

Buxbaum, James L; Eloubeidi, Mohamad A

2010-11-09

175

Molecular characterization of the SCAR markers tightly linked to the Tm2 locus of the genus Lycopersicon  

Microsoft Academic Search

The Tm-2 gene and its alleles conferring tomato mosaic virus resistance in tomato originate from Lycopersicon peruvianum, a wild relative of tomato. DNA fragments of several RAPD markers tightly linked with the Tm-2 locus in tomato were successfully cloned and sequenced. Subsequently, the 24-mer oligonucleotide primer pairs of the SCAR\\u000a markers corresponding to the RAPD markers were designed based on

Sobir; T. Ohmori; M. Murata; F. Motoyoshi

2000-01-01

176

Confirmation of cross-fertilization using molecular markers in ornamental passion flower hybrids.  

PubMed

Several interspecific Passiflora hybrids are produced in the northern hemisphere for the ornamental plant market. In Brazil, production of passion flower hybrids is limited to the introgression of genes into the main cultivated species, yellow passion fruit, to be used as rootstocks. Confirmation of hybridization in the initial developmental stage is important for breeding perennial and sub-perennial plants, such as passion flowers, reducing time and costs in plant stock maintenance. In order to obtain F? hybrids with ornamental potential, four species of Passiflora (P. alata, P. gardneri, P. gibertii, and P. watsoniana) from the Active Germplasm Bank at UESC were hybridized. Flower buds, in pre-anthesis, of the genitors were previously protected, and the female buds were emasculated. To confirm hybridization, the genomic DNA of the genitor species and the supposed hybrids was extracted and RAPD primers were used to obtain molecular markers and select passion flower interspecific hybrids. Eight primers were used to confirm hybrids derived from P. gardneri with P. alata, P. watsoniana with P. alata, P. watsoniana with P. gardneri, and P. gardneri with P. gibertii; 75, 50, 45, and 46% of the informative bands, respectively, confirmed the hybrid nature of these plants. The RAPD technique was effective in the early identification of hybrids; this will be useful for development of hybrid Passiflora progeny. PMID:21264815

Conceição, L D H C S; Belo, G O; Souza, M M; Santos, S F; Cerqueira-Silva, C B M; Corrêa, R X

2011-01-11

177

A sex-averaged genetic linkage map in coastal Douglas-fir (Pseudotsuga menziesii[Mirb.] Franco var ‘menziesii’) based on RFLP and RAPD markers  

Microsoft Academic Search

We have constructed a sex-averaged genetic linkage map in coastal Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco var ‘menziesii’) using a three-generation outcrossed pedigree and molecular markers. Our research objectives are to learn about genome organization\\u000a and to identify markers associated with adaptive traits. The map reported here is comprised of 141 markers organized into\\u000a 17 linkage groups and covers 1,062 centiMorgans

K. D. Jermstad; D. L. Bassoni; N. C. Wheeler; D. B. Neale

1998-01-01

178

Molecular Marker Systems for Oenothera Genetics  

PubMed Central

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

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

2008-01-01

179

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

Microsoft Academic Search

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

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

2010-01-01

180

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

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.

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

1991-12-15

181

Molecular markers and their use in environmental organic geochemistry  

Microsoft Academic Search

Molecular markers are organic substances that carry information about sources of organic matter or contamination. The source\\/marker relation can be used to indicate the presence of a given source material (qualitative), or, under appropriate conditions, to estimate the amount of a source material (quantitative source apportionment) in the environment. Assemblages of markers can also be used as process probes. In

Robert P. Eganhouse

2004-01-01

182

Genetic variation in a wild population of the 'sleep' passion fruit (Passiflora setacea) based on molecular markers.  

PubMed

Little is known about the molecular genetic diversity of most Passiflora species. We used RAPD markers to evaluate the genetic diversity of 24 genotypes of the 'sleep' passion fruit (Passiflora setacea). Twelve primers generated 95 markers, 88% of which were polymorphic. The genetic distance estimated by the complement of the Dice index ranged from 0.29 (among accessions Ps-G1 and Ps-G13) to 0.69 (among accessions Ps-G21 and Ps-G23). Genotype grouping based on the UPGMA algorithm showed considerable variability among genotypes. We conclude that P. setacea has a broad genetic base that could be exploited in breeding programs. PMID:22576831

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

2012-03-22

183

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 ...

184

Genetics of resistance to anthracnose and identification of AFLP and RAPD markers linked to the resistance gene in PI 320937 germplasm of lentil ( Lens culinaris Medikus)  

Microsoft Academic Search

Anthracnose, caused by Colletotrichum truncatum, is a major disease problem and production constraint of lentil in North America. The research was conducted to examine the resistance to anthracnose in PI 320937 lentil and to identify molecular markers linked to the resistance gene in a recombinant inbred line (RIL) population developed from a cross of Eston lentil, the susceptible parent, and

A. Tullu; L. Buchwaldt; T. Warkentin; B. Taran; A. Vandenberg

2003-01-01

185

Screening of Resistance Genes to Fusarium Root Rot and Fusarium wilt Diseases in F3 family Lines of Tomato (Lycopersicon esculentum) using RAPD and CAPs Markers  

Microsoft Academic Search

Fusarium diseases constitute most of the loss in tomato production worldwide, because it spread on all geographic fields that it is so hard to find a place without Fusarium infestation. Thus, the best way to produce tomato is developing resistant cultivars against Fusarium species. In cultivar developing, molecular marker assisted techniques replaced traditional breeding techniques which are high cost and

Cengiz Akkale; Bahattin Tanyolaç

186

Linkage mapping of the Mediterranean cypress, Cupressus sempervirens, based on molecular and morphological markers.  

PubMed

Gene mapping for a Cupressus species is presented for the first time. Two linkage maps for the Mediterranean cypress (Cupressus sempervirens) varieties, C. sempervirens var. horizontalis and C. sempervirens var. pyramidalis, were constructed following the pseudo-testcross mapping strategy and employing RAPD, SCAR and morphological markers. A total of 427 loci (425 RAPDs, two SCARs) representing parents and F(1) progeny were screened for polymorphism with 32 random decamer and two SCAR primers. A morphological marker defined as "crown form" was also included. Of 274 polymorphic loci, the 188 that presented Mendelian inheritance formed the mapping dataset. Of these loci, 30% were mapped into seven linkage groups for the horizontalis (maternal) and four linkage groups for the pyramidalis (paternal) map. The putative "crown form" locus was included in a linkage group of both maps. The horizontalis and the pyramidalis maps covered 160.1 and 144.5 cM, respectively, while genome length was estimated to be 1696 cM for the former variety and 1373 cM for the latter. The four RAPD markers most tightly linked to crown form were cloned and converted to SCARs. Each of the cloned RAPD markers yielded two to three different sequences behaving as co-migrating fragments. Two SCAR markers, SC-D05(432) and SC-D09(667), produced amplified bands of the expected sizes and maintained linkage with the appropriate phenotype, but to a lesser extent compared to their original RAPD counterparts. These linkage maps represent a first step towards the localization of QTLs and genes controlling crown form and other polygenic traits in cypress. PMID:21948752

Manescu, C; Hamamouch, N; Maios, C; Harfouche, A; Doulis, A G; Aravanopoulos, F A

2011-08-30

187

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

PubMed

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

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

2013-01-06

188

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

PubMed Central

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.

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

2009-01-01

189

Molecular Serum Markers of Liver Fibrosis  

PubMed Central

Fibrosis is a hallmark histologic event of chronic liver diseases and is characterized by the excessive accumulation and reorganization of the extracellular matrix (ECM). The gold standard for assessment of fibrosis is liver biopsy. As this procedure has various limitations, including risk of patient injury and sampling error, a non-invasive serum marker for liver fibrosis is desirable. The increasing understanding of the pathogenesis of hepatic fibrosis has suggested several markers which could be useful indicators of hepatic fibrogenesis and fibrosis. These markers include serum markers of liver function, ECM synthesis, fibrolytic processes, ECM degradation and fibrogenesis related cytokines. Recently, neo-epitopes, which are post-translational modifications of proteins, have been successfully used in bone and cartilage diseases which are characterized by extensive ECM remodeling. Increasing numbers of studies are being undertaken to identify neo-epitopes generated during liver fibrosis, and which ultimately might be useful for diagnosing and monitoring fibrogenesis. To date, the metalloproteinases generated fragment of collagen I, III, IV and VI have been proven to be elevated in two rat models of fibrosis. This review summarizes the recent efforts that have been made to identify potentially reliable non-invasive serum markers. We used the recently proposed BIPED (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) system to characterize potential serum markers and neo-epitope markers that have been identified to date.

Liu, Tianhui; Wang, Xiaoming; Karsdal, Morten A.; Leeming, Diana J.; Genovese, Federica

2012-01-01

190

Authentication of the medicinal plant Sennaangustifolia by RAPD profiling  

PubMed Central

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

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

2011-01-01

191

A genetic map of potato ( Solanum tuberosum ) integrating molecular markers, including transposons, and classical markers  

Microsoft Academic Search

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female

J. M. E. Jacobs; H. J. Van Eek; P. F. P. Arens; B. Verkerk-Bakker; B. te Lintel Hekkert; H. J. M. Bastiaanssen; A. El-Kharbotly; A. Pereira; E. Jacobsen; W. J. Stiekema

1995-01-01

192

DETERMINACIÓN DEL MÉTODO DE EXTRACCIÓN DE ADN ÓPTIMO PARA EL DESARROLLO DE LA TÉCNICA RAPD EN MEGAGAMETOFITOS DE Pinus hartwegii Lindl  

Microsoft Academic Search

Molecular markers represent nowaday an important tool in forest genetic breeding; among them it was standed out the utility of the Random Amplified Polymorphism DNA (RAPD) technique in genetic studies of different forest species. So it was developed the present work as a part of a study, which are performing to examine the genetic variability present in Pinus hartwegii Lindl.

Lourdes G. Iglesias Andreu; Mauricio Luna Rodríguez; Rocío López Domínguez

2003-01-01

193

Characterisation of Phoma tracheiphila by RAPD-PCR, microsatellite-primed PCR and ITS rDNA sequencing and development of specific primers for in planta PCR detection  

Microsoft Academic Search

Thirty six isolates of Phoma tracheiphila from Italy, the causal agent of the mal secco disease on Citrus species, were characterised by different molecular tools in comparison with representative isolates of other phytopathogenic Phoma species. These included analysis of the distribution of RAPD and microsatellite markers and sequencing of the internal transcribed spacer (ITS) region of the nuclear rRNA genes.

Virgilio Balmas; Barbara Scherm; Stefano Ghignone; Ali Ould Mohamed Salem; Santa Olga Cacciola; Quirico Migheli

2005-01-01

194

Summary statement: utility of molecular marker testing in thyroid cancer.  

PubMed

The use of molecular markers for thyroid cancer diagnosis, prognosis, and surveillance have been an exciting area of study and change. Recent investigative focus on promising new markers will very likely lead to improvements in the diagnostic utility of fine needle aspiration biopsy (FNAB) in predicting malignancy, as well as provide more accurate prognostic information pre- and postoperatively. The 2010 Annual Meeting of the American Association for Endocrine Surgeons featured a symposium dedicated to molecular marker testing in thyroid cancer and its potential clinical applicability. PMID:21134567

Yip, Linwah; Kebebew, Electron; Milas, Mira; Carty, Sally E; Fahey, Thomas J; Parangi, Sareh; Zeiger, Martha A; Nikiforov, Yuri E

2010-12-01

195

RAPD mapping in a doubled haploid population of rice (Oryza sativa L.).  

PubMed

To examine the distribution and genome coverage of RAPDs, a total of 242 Random Amplified Polymorphic DNA (RAPD) markers generated by 73 random decamer primers were mapped onto 12 rice chromosomes by linkage analysis using a doubled haploid population, developed from an indica x japonica cross. The RAPD markers were derived from both parents equally and were well distributed over the rice genome. Furthermore, multiple RAPD markers generated from the same primer were dispersed over different chromosomes rather than clustered. The RAPD technique provided improved marker coverage on a previously developed RFLP map. A set of primers producing reproducible markers originating from either parent and equally spaced over all the 12 chromosomes were selected for application in marker-assisted backcross breeding. The RAPD analysis as a realistic and practical alternative to RFLP and their usefulness in anchoring the identified BAC contigs directly to chromosomes is discussed. PMID:10364828

Subudhi, P K; Huang, N

1999-01-01

196

Molecular Markers in Hereditary Breast Cancer.  

National Technical Information Service (NTIS)

We are entering a new era of medicine where genetic markers are going to be used to make clinical management. decisions My long term career goal is to further our understanding of the genetic alterations which characterize human breast cancer in a way tha...

O. I. Olopade

2002-01-01

197

Comparative assessment of DNA fingerprinting techniques (RAPD, ISSR and AFLP) for genetic analysis of cashew (Anacardium occidentale L.) accessions of India.  

PubMed

Nineteen cashew accessions were analysed with 50 random primers, 12 ISSR primers and 6 AFLP primer pairs to compare the efficiency and utility of these techniques for detecting variation in cashew germplasm. Each marker system could discriminate between all of the accessions, albeit with varied efficiency of polymorphism detection. AFLP exhibited maximum discrimination efficiency with a genotype index of 1. The utility of each molecular marker technique, expressed as marker index, was estimated as a function of average band informativeness and effective multiplex ratio. Marker index was calculated to be more than 10 times higher in AFLP than in RAPD and ISSR. Similarity matrices were determined based on the data generated by molecular and morphometric analyses, and compared for congruency. AFLP displayed no correspondence with RAPD and ISSR. Correlation between ISSR and RAPD similarity matrices was low but significant (r = 0.63; p < 0.005). The similarity matrix based on morphometric markers exhibited no correlation with any of the molecular markers. AFLP, with its superior marker utility, was concluded to be the marker of choice for cashew genetic analysis. PMID:12834051

Archak, S; Gaikwad, A B; Gautam, D; Rao, E V V B; Swamy, K R M; Karihaloo, J L

2003-06-01

198

Molecular markers linked to white rust resistance in mustard Brassica juncea  

Microsoft Academic Search

White rust, caused by Albugo candida (Pers.) Kuntze, is an economically important disease of Brassica juncea (L.) Czern. and Coss mustard, particularly in India. The most efficient and cost-effective way of protecting mustard plants\\u000a from white rust disease is through genetic resistance. The objective of this study was to identify RAPD markers for white\\u000a rust resistance in an F1-derived doubled-haploid

K. V. Prabhu; D. J. Somers; G. Rakow; R. K. Gugel

1998-01-01

199

Genetic diversity of wild coffee ( Coffea arabica L.) using molecular markers  

Microsoft Academic Search

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre\\u000a of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica\\u000a and Bourbon, spread in the 18th century, which gave rise to the most currently grown

F. Anthony; B. Bertrand; O. Quiros; A. Wilches; P. Lashermes; J. Berthaud; A. Charrier

2001-01-01

200

[Assessment of genetic diversity of Rehmannia glutinosa germplasm detected by RAPDs and ISSRs].  

PubMed

RAPD and ISSR markers were used to assess the germplasm genetic diversity among 10 individuals of Rehmannia glutinosa, including 8 cultivars and 2 virus-free lines micropropagated by tip tissue culture. 17 RAPD primers and 10 ISSR primers, with polymorphic and informative patterns, were selected from a total of 80 RAPD ones and 44 ISSR ones to determine these individuals' genetic diversity. The 17RAPD primers and 10 ISSR primers generated 177RAPDfragments and 110 fragments, respectively. The number of effective loci, the percentage of polymorphic loci, Shannon's Information index (I) and effective number of alleles (Ne) is in turn109, 61.58%, 0.3135, 1.3641 for RAPD makers, and 79, 71.82 %, 0.3577 and 1.4037 for ISSR markers; Jaccard's genetic similarity matrice and dendrograms for the 10 individuals were formed based on RAPD and ISSR-generated polymorphic bands. In dendrograms, they could be divided into two groups: one group containing six individuals such as Zupei 85.5, Datian 85.5, jinzhuangyuan, Jinbai, Zupei 9302 and Datian9302; the other composed of 4 ones such as Beijing No.1, Dahongpao, Dihuang 9104 and wild dihuang; the correlation coefficient of 0.649 between RAPD and ISSR markers GSs indicated that these two markers were significantly correlated. The results revealed that RAPD and ISSR markers were suitable for assessment of germplasm genetic diversity of Rehmannia glutinosa, and ISSR marker was superior to RAPD marker. PMID:15640128

Zhou, Yan-Qing; Jing, Jian-Zhou; Li, Zhen-Yong; Zhang, Bao-Hua; Jia, Jing-Fen

2004-11-01

201

Genetic diversity in wild species of passion fruit (Passiflora trintae) based on molecular markers.  

PubMed

In spite of the importance of and the considerable variability observed in Passiflora (Passifloraceae), little is known about the genetic diversity of most of the species of this genus. We evaluated the genetic diversity by RAPD markers in 18 genotypes of Passiflora trintae. The 15 primers generated 112 markers, 84% of which were polymorphic. The genetic distance estimated by the complement of the Dice index (average dissimilarity = 0.30) and genotype grouping based on the UPGMA algorithm showed low variability among genotypes. More attention should be given to the study and conservation of the biodiversity of this economically important genus. PMID:21038298

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

2010-10-26

202

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 ...

203

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

PubMed Central

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

2012-01-01

204

Biological (molecular and cellular) markers of toxicity  

SciTech Connect

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.

Shugart, L.R.

1990-10-01

205

Molecular analyses on the genetic diversity and inheritance of (?)-?-bisabolol and chamazulene content in tetraploid chamomile ( Chamomilla recutita (L.) Rausch.)  

Microsoft Academic Search

The study aims to analyse (i) the genetic diversity of cultivated chamomile germplasm, (ii) to possibly discriminate chemotypes and (iii) to develop molecular markers for the (?)-?-bisabolol and chamazulene content by using RAPD and AFLP marker analysis.By analysing di- and tetraploid chamomile (Chamomilla recutita (L.) Rausch.) accessions using 18 RAPD primers and 16 EcoRI+3\\/MseI+3 AFLP primer combinations genetic similarity (GSD)

Carola Wagner; Wolfgang Friedt; Richard A. Marquard; Frank Ordon

2005-01-01

206

Molecular marker-mediated validation of morphologically defined landraces of Pejibaye ( Bactris gasipaes ) and their phylogenetic relationships  

Microsoft Academic Search

RAPD markers were used to evaluate the genetic variability and structure of seven morphologically defined landraces of pejibaye (Bactris gasipaes Kunth, Palmae) to determine their validity and phylogenetic relationships. Two hundred and twenty plants of four Amazonian and three Central American landraces of var.gasipaes (the domesticate) and 30 plants of var.chichagui (H. Karsten) Henderson (the crop ancestor) maintained at the

Doriane P. Rodrigues; Spartaco Astolfi Filho; Charles R. Clement

2005-01-01

207

Reviewing and updating the major molecular markers for stem cells.  

PubMed

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

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

2013-01-22

208

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

Microsoft Academic Search

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

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

1995-01-01

209

DNA marker applications to molecular genetics and genomics in tomato  

PubMed Central

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.

Shirasawa, Kenta; Hirakawa, Hideki

2013-01-01

210

New genetic map of rye composed of PCR-based molecular markers and its alignment with the reference map of the DS2 x RXL10 intercross.  

PubMed

A new genetic map of rye, developed by using the 541 x Ot1-3 F2 intercross, consists of 148 marker loci, including 99 RAPDs, 18 SSRs, 14 STSs, 9 SCARs and 7 ISSRs, and spans the distance of 1401.4 cM. To the 7 rye chromosomes, 8 linkage groups were assigned and compared with the reference map of the DS2 x RXL10 F2 intercross by using 24 common markers. The 2 combined maps contain altogether 611 marker loci (70-109 per chromosome) and constitute a substantial source of information useful for further genomic studies in rye. From 21 to 37 RAPD marker loci are distributed randomly along each chromosome length and their total number for all 7 rye chromosomes is 177. This abundance of RAPD marker loci in the rye genetic map can be exploited for development of SCARs in regions containing important genes or QTL. PMID:17272857

Milczarski, Pawe?; Banek-Tabor, Aneta; Lebiecka, Karolina; Stoja?owski, Stefan; My?ków, Beata; Masoj?, Piotr

2007-01-01

211

Molecular Methods for Detection of Tumor Markers in Glioblastomas  

Microsoft Academic Search

\\u000a Glioblastoma (grade IV\\/IV astrocytoma), the most malignant type of brain tumor, occurs in all age groups with the highest\\u000a incidence in older patients. Novel therapeutic strategies and molecular assays to follow treatments of suppressible targets\\u000a are urgently needed. Surveys of large numbers of genes in the initial phase of tumor marker identification are currently being\\u000a performed in multi-center studies. Queries

Marie E. Beckner; Mary L. Nordberg

212

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

NASA Astrophysics Data System (ADS)

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.

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

2008-01-01

213

Molecular markers in prostate cancer. Part I: predicting lethality  

PubMed Central

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.

Agrawal, Sachin; Dunsmuir, William D.

2009-01-01

214

Discriminating ability of molecular markers and morphological characterization in the establishment of genetic relationships in cultivated genotypes of almond and related wild species  

Microsoft Academic Search

A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare\\u000a the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP)\\u000a and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related\\u000a wild species. SSRs presented a high level of

Karim Sorkheh; Behrouz Shiran; Soghra Kiani; Nazanin Amirbakhtiar; Sadegh Mousavi; Vahid Rouhi; Shahram Mohammady-D; Thomas M. Gradziel; Lyudmyla V. Malysheva-Otto; Pedro Martínez-Gómez

2009-01-01

215

Molecular phylogenetic study of the Iranians based on polymorphic markers.  

PubMed

The application of polymorphic markers in construction of phylogenetic trees has been documented. Five polymorphic markers located in the PAH gene region including PAH-BglII, PAH-PvuII(A), PAH-EcoRI, PAH-MspI and PAH-STR were selected for analysis of phylogenetic relationships of the Iranians with 15 other populations of the world. The lowest genetic distance was observed between the Iranians and populations residing in Adygei (an ethnic group of the Russian Caucasus), Russia and Druze (a Middle Eastern group). However, East Asian populations including Han, Japanese and Cambodians, Khmer or the Oceanians (Melanesian, Nasioi) showed high genetic distance with the Iranians. The data suggested that the Iranians might have relatively close evolutionary history with the populations residing in Russia rather than East Asian populations. This study provided the first new molecular insight into the evolutionary history of the Iranian population. PMID:23073556

Fazeli, Zahra; Vallian, Sadeq

2012-10-13

216

The application of LTR retrotransposons as molecular markers in plants.  

PubMed

Retrotransposons are a major agent of genome evolution. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The key methods, SSAP, IRAP, REMAP, RBIP, and ISBP, all detect the sites at which the retrotransposon DNA, which is conserved between families of elements, is integrated into the genome. Marker systems exploiting these methods can be easily developed and inexpensively deployed in the absence of extensive genome sequence data. They offer access to the dynamic and polymorphic, nongenic portion of the genome and thereby complement methods, such as gene-derived SNPs, that target primarily the genic fraction. PMID:22367869

Schulman, Alan H; Flavell, Andrew J; Paux, Etienne; Ellis, T H Noel

2012-01-01

217

Genetic fidelity of long-term micropropagated shoot cultures of vanilla (Vanilla planifolia Andrews) as assessed by molecular markers.  

PubMed

Occurrence of genetic variants during micropropagation is occasionally encountered when the cultures are maintained in vitro for long period. Therefore, the micropropagated multiple shoots of Vanilla planifolia Andrews developed from axillary bud explants established 10 years ago were used to determine somaclonal variation using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats markers (ISSR). One thousand micro-plants were established in soil of which 95 plantlets (consisting of four phenotypes) along with the mother plant were subjected to genetic analyses using RAPD and ISSR markers. Out of the 45 RAPD and 20 ISSR primers screened, 30 RAPD and 7 ISSR primers showed 317 clear, distinct and reproducible band classes resulting in a total of 30 115 bands. However, no difference was observed in banding patterns of any of the samples for a particular primer, indicating the absence of variation among the micropropagated plants. Our results allow us to conclude that the micropropagation protocol that we have used for in vitro proliferation of vanilla plantlets for the last 10 years might be applicable for the production of clonal plants over a considerable period of time. PMID:17427995

Sreedhar, Reddampalli V; Venkatachalam, Lakshmanan; Bhagyalakshmi, Neelwarne

2007-08-01

218

Molecular markers of endometrial carcinoma detected in uterine aspirates.  

PubMed

Endometrial cancer (EC) is the most frequent of the invasive tumors of the female genital tract. Although usually detected in its initial stages, a 20% of the patients present with advanced disease. To date, no characterized molecular marker has been validated for the diagnosis of EC. In addition, new methods for prognosis and classification of EC are needed to combat this deadly disease. We thus aimed to identify new molecular markers of EC and to evaluate their validity on endometrial aspirates. Gene expression screening on 52 carcinoma samples and series of real-time quantitative PCR validation on 19 paired carcinomas and normal tissue samples and on 50 carcinoma and noncarcinoma uterine aspirates were performed to identify and validate potential biomarkers of EC. Candidate markers were further confirmed at the protein level by immunohistochemistry and Western blot. We identified ACAA1, AP1M2, CGN, DDR1, EPS8L2, FASTKD1, GMIP, IKBKE, P2RX4, P4HB, PHKG2, PPFIBP2, PPP1R16A, RASSF7, RNF183, SIRT6, TJP3, EFEMP2, SOCS2 and DCN as differentially expressed in ECs. Furthermore, the differential expression of these biomarkers in primary endometrial tumors is correlated to their expression level in corresponding uterine fluid samples. Finally, these biomarkers significantly identified EC with area under the receiver-operating-characteristic values ranging from 0.74 to 0.95 in uterine aspirates. Interestingly, analogous values were found among initial stages. We present the discovery of molecular biomarkers of EC and describe their utility in uterine aspirates. These findings represent the basis for the development of a highly sensitive and specific minimally invasive method for screening ECs. PMID:21207424

Colas, Eva; Perez, Cristina; Cabrera, Silvia; Pedrola, Nuria; Monge, Marta; Castellvi, Josep; Eyzaguirre, Fernando; Gregorio, Jesus; Ruiz, Anna; Llaurado, Marta; Rigau, Marina; Garcia, Marta; Ertekin, Tugçe; Montes, Melania; Lopez-Lopez, Rafael; Carreras, Ramon; Xercavins, Jordi; Ortega, Alicia; Maes, Tamara; Rosell, Elisabet; Doll, Andreas; Abal, Miguel; Reventos, Jaume; Gil-Moreno, Antonio

2011-04-08

219

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)

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.

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

2010-12-01

220

Identification of early molecular markers for breast cancer  

PubMed Central

Background The ductal carcinoma in situ (DCIS) of the mammary gland represents an early, pre-invasive stage in the development of invasive breast carcinoma. Since DCIS is a curable disease, it would be highly desirable to identify molecular markers that allow early detection. Mice transgenic for the WAP-SV40 early genome region were used as a model for DCIS development. Gene expression profiling was carried out on DCIS-bearing mice and control animals. Additionally, a set of human DCIS and invasive mammary tumors were analyzed in a similar fashion. Enhanced expression of these marker genes in human and murine samples was validated by quantitative RT-PCR. Besides, marker gene expression was also validated by immunohistochemistry of human samples. Furthermore in silico analyses using an online microarray database were performed. Results In DCIS-mice seven genes were identified that were significantly up-regulated in DCIS: DEPDC1, NUSAP1, EXO1, RRM2, FOXM1, MUC1 and SPP1. A similar up-regulation of homologues of the murine genes was observed in human DCIS samples. Enhanced expression of these genes in DCIS and IDC (invasive ductal carcinoma) was validated by quantitative RT-PCR and immunohistochemistry. Conclusions By comparing murine markers for the ductal carcinoma in situ (DCIS) of the mammary gland with genes up-regulated in human DCIS-samples we were able to identify a set of genes which might allow early detection of DCIS and invasive carcinomas in the future. The similarities between gene expression in DCIS and invasive carcinomas in our data suggest that the early detection and treatment of DCIS is of utmost relevance for the survival of patients who are at high risk of developing breast carcinomas.

2011-01-01

221

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

Microsoft Academic Search

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

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

2000-01-01

222

Interspecific hybridization in vanilla and molecular characterization of hybrids and selfed progenies using RAPD and AFLP markers  

Microsoft Academic Search

Vanilla, Vanilla planifolia Andrews, is native to Mexico and Central America, but is now cultivated in other parts of the tropics. Continuous clonal propagation has resulted in very little variability for crop improvement programmes in vanilla. In this study, an attempt has been made to increase the spectrum of variation by interspecific hybridization with Vanilla aphylla, an Indian species which

Minoo Divakaran; K. Nirmal Babu; P. N. Ravindran; K. V. Peter

2006-01-01

223

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

Microsoft Academic Search

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

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

2004-01-01

224

Identification and validation of molecular markers linked to the leaf rust resistance gene Lr19 in wheat  

Microsoft Academic Search

A leaf rust resistance gene Lr19 on the chromosome 7DL of wheat derived from Agropyron elongatum was tagged with random amplified polymorphic DNA (RAPD) and microsatellite markers. The F2 population of 340 plants derived from a cross between the leaf rust resistant near-isogenic line (NIL) of Thatcher (Tc + Lr19) and leaf rust susceptible line Agra Local that segregated for dominant monogenic

Sudhir Kumar Gupta; Ashwini Charpe; Kumble Vinod Prabhu; Qazi Mohammad Rizwanul Haque

2006-01-01

225

Molecular markers as a tool for population and evolutionary studies of stingless bees  

Microsoft Academic Search

Molecular markers are widely used in biology to address questions related to ecology, genetics and evolution. In bees, molecular studies addressing those issues have focused on Apis and Apis mellifera. Here we describe examples where molecular markers from mtDNA and microsatellite analyses were applied to stingless bees species. The data obtained, although in some cases preliminary, have already proven useful

Maria Cristina Arias; Rute Magalhães Brito; Flávio de Oliveira Francisco; Geraldo Moretto; Favízia Freitas de Oliveira; Daniela Silvestre; Walter Steven Sheppard

2006-01-01

226

Prophage Carriage as a Molecular Epidemiological Marker in Streptococcus pneumoniae  

PubMed Central

The great majority of clinical isolates of Streptococcus pneumoniae carry prophages that may be identified through their hybridization with a DNA probe specific for the pneumococcal lytA gene (M. Ramirez, E. Severina, and A. Tomasz, J. Bacteriol. 181:3618–3625, 1999). We now show that the lytA hybridization pattern of chromosomal SmaI digests is stable for a given strain during extensive serial culturing in the laboratory; the pattern is specific for the strain’s clonal type, as defined by pulsed-field gel electrophoretis (PFGE) pattern, and variations in PFGE subtypes may be explained by changes in the number and chromosomal localization of this prophage(s). These observations indicate that the lytA hybridization pattern may be used as a molecular epidemiological marker that offers additional resolution of the genetic background of S. pneumoniae strains.

Severina, Elena; Ramirez, Mario; Tomasz, Alexander

1999-01-01

227

Mitochondrial DNA as a marker of molecular diversity: a reappraisal.  

PubMed

Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome. PMID:19821901

Galtier, N; Nabholz, B; Glémin, S; Hurst, G D D

2009-10-09

228

Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers  

PubMed Central

Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-?B, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression.

Koedrith, Preeyaporn; Seo, Young Rok

2011-01-01

229

Molecular typing of, and distribution of genetic markers among, Burkholderia cepacia complex isolates from Brazil.  

PubMed

PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone. PMID:12958239

Detsika, Maria G; Corkill, John E; Magalhães, Marcelo; Glendinning, Kerry J; Hart, C Anthony; Winstanley, Craig

2003-09-01

230

Molecular Typing of, and Distribution of Genetic Markers among, Burkholderia cepacia Complex Isolates from Brazil  

PubMed Central

PCR tests were used to assign genomovar status to 39 non-cystic fibrosis (non-CF) and 11 CF Burkholderia cepacia complex isolates from patients in hospitals in Recife, Brazil. Non-CF isolates were assigned to genomovar IIIA (71.8%), genomovar I (15.4%), B. vietnamiensis (7.7%), and B. multivorans (5.1%). CF isolates were assigned to genomovar IIIA (18.2%), B. vietnamiensis (18.2%), and genomovar I (9.1%). Six CF isolates sharing recA PCR-restriction fragment length polymorphism (RFLP) and randomly amplified polymorphic DNA (RAPD) patterns could not be assigned to a genomovar. 16S rDNA sequence obtained from these isolates indicated a closest relationship to B. anthina, but the recA sequence was equally divergent from several genomovars. PCR screening indicated the presence of cblA in only two isolates, whereas the B. cepacia epidemic strain marker was found in 22 of 28 genomovar IIIA isolates. A type III secretion gene was detected in all but genomovar I isolates. RAPD and PCR-RFLP assays, targeting both recA and fliC, indicated a large amount of genetic variability among the isolates, with many novel patterns being observed. Nine genomovar IIIA isolates from different non-CF patients and clinical sources had identical genotypes, indicating the presence of a common clone.

Detsika, Maria G.; Corkill, John E.; Magalhaes, Marcelo; Glendinning, Kerry J.; Hart, C. Anthony; Winstanley, Craig

2003-01-01

231

Differentiation of Setaria digitata and Setaria labiatopapillosa using molecular markers.  

PubMed

5S rRNA intergenic regions of Setaria digitata and Setaria labiatopapillosa were PCR amplified with primers designed from the 5S rRNA gene of Brugia malayi. The ladder-like banding patterns obtained for the amplifications were distinctly different for the two species. Four amplified products were cloned into the pBS vector and completely sequenced. DNA clones from two individual samples of S. digitata, Sd4 and Sd6, showed 97% sequence homology to each other. All sequenced clones showed the presence of the spliced leader (SL) RNA gene with a 22 nucleotide spliced leader sequence. The phylogenetic tree constructed using these data and the 5S rRNA intergenic regions of several other filarial nematodes showed the Setaria species sharing a branch with Dirofilaria. RAPD-PCR analyses identified 107 bands of which 86 were polymorphic (80%). A dendrogram constructed for S. digitata and S. labiatopapillosa separated the two species into two distinct clusters. The polymorphic loci identified by the RAPD-PCR analyses can be studied further to develop species-specific probes/PCR primers for the identification of each species. PMID:12573602

Jayasinghe, D R; Wijesundera, W S S

2003-03-01

232

Development of Random Amplified Polymorphic DNA markers for authentification of Cissus repanda vahl.  

PubMed

Cissus repanda Vahl. belongs to the family Vitaceae, commonly known in Hindi as "Panivel," is a large climber distributed all over India. The crushed or powder of root is prescribed by tribal people and traditional medical practitioners of Orissa for its healing properties in cases of bone fracture, cuts and wounds, swellings, and so on. In spite of its reputation, its leaves have not been investigated scientifically. The present study deals with pharmacognostical and molecular characterization by Random Amplified Polymorphic DNA (RAPD) markers and their role in laying down standardization and pharmacopoeial parameters. Genomic isolation of DNA from fresh leaves was amplified by RAPD markers. The diagnostic characters are mucilage, calcium oxalate rosette crystals, spiral vessels, and fibers. The unique bands obtained in Polymerase Chain Reaction (PCR) amplification clearly discriminated having, many bright and light bands indicating the genuinity of the plant. RAPD may serve as a complementary tool in quality control of many herbal sources. PMID:23559804

Harisha, C R; Acharya, Rabinarayan; Chauhan, Maltiben G

2012-04-01

233

Development of Random Amplified Polymorphic DNA markers for authentification of Cissus repanda vahl.  

PubMed Central

Cissus repanda Vahl. belongs to the family Vitaceae, commonly known in Hindi as “Panivel,” is a large climber distributed all over India. The crushed or powder of root is prescribed by tribal people and traditional medical practitioners of Orissa for its healing properties in cases of bone fracture, cuts and wounds, swellings, and so on. In spite of its reputation, its leaves have not been investigated scientifically. The present study deals with pharmacognostical and molecular characterization by Random Amplified Polymorphic DNA (RAPD) markers and their role in laying down standardization and pharmacopoeial parameters. Genomic isolation of DNA from fresh leaves was amplified by RAPD markers. The diagnostic characters are mucilage, calcium oxalate rosette crystals, spiral vessels, and fibers. The unique bands obtained in Polymerase Chain Reaction (PCR) amplification clearly discriminated having, many bright and light bands indicating the genuinity of the plant. RAPD may serve as a complementary tool in quality control of many herbal sources.

Harisha, C. R.; Acharya, Rabinarayan; Chauhan, Maltiben G.

2012-01-01

234

World Antimalarial Resistance Network (WARN) III: Molecular markers for drug resistant malaria  

Microsoft Academic Search

Molecular markers for drug resistant malaria represent public health tools of great but mostly unrealized potential value. A key reason for the failure of molecular resistance markers to live up to their potential is that data on the their prevalence is scattered in disparate databases with no linkage to the clinical, in vitro and pharmacokinetic data that are needed to

Christopher V Plowe; Cally Roper; John W Barnwell; Christian T Happi; Hema H Joshi; Wilfred Mbacham; Steven R Meshnick; Kefas Mugittu; Inbarani Naidoo; Ric N Price; Robert W Shafer; Carol H Sibley; Colin J Sutherland; Peter A Zimmerman; Philip J Rosenthal

2007-01-01

235

Molecular Markers of Hemostatic Activation: Applications in the Diagnosis of Thrombosis and Vascular and Thrombotic Disorders  

Microsoft Academic Search

The recognition of molecular marker events leading to hemostatic and thrombotic disorders and technologic advances in molecular biology and immunology has added a new dimension in the diagnosis of bleeding and thrombotic disorders. Pathophysiologic activation of coagulation, fibrinolysis, kallikrein-kinin system, vascu— lar stress, and intercellular interactions result in the generation of cell\\/process specific markers of a pathophysiologic event. It has

Jawed Fareed; Rodger L. Bick; Debra A. Hoppensteadt; Edward W. Bermes

1995-01-01

236

Molecular markers of endocrine disruption in aquatic organisms.  

PubMed

A wide range of organic contaminant compounds prevalent in the aquatic environment has been shown to exhibit hormone-disrupting activity. The actual potency of such compounds are low compared with endogenous hormones, such as 17beta-estradiol, but may still produce detrimental biological effects. Induced hormone levels are routinely measured using commercial testing kits, though these fail to relate to actual effects. Field and laboratory studies on the biological effects of environmental estrogens have, in the past, largely relied on assays of vitellogenin (vtg) induction in male fish, reduced growth in testes formation, and intersex incidence. Here, we critically review the current and potential application of molecular techniques in assessing the adverse biological reproductive effects of endocrine-disrupting chemicals in aquatic organisms. The role of fish (estrogen, androgen, and progestogen) hormone receptors and invertebrate (ecdysone) hormone receptor, egg production (vtg and chorion) proteins, steroid biosynthesis enzymes (aromatase, sulfotransferase, and hydroxysteroid dehydrogenase), DNA damage, apoptosis, and their potential development as biomarkers are discussed in turn. In each case, the sequences characterized are presented and homologies across species are highlighted. Molecular methods of gauging vtg and zona radiata (ZR) expression and protein concentrations have included immunoassay and reverse transcription polymerase chain reaction (RT-PCR). Suggestions for the isolation for key gene expression products (aromatase, ZR, and vtg, for instance), from a wider range of fish species using degenerate primers, are given. Endocrine disruption in invertebrates has received less attention compared with fish, partly because the knowledge regarding invertebrate endocrinology is limited. Here we review and suggest alternate isolation strategies for key players in the imposex induction process: vitellin (Vn), aromatase, and Ala-Pro-Gly-Trp (APGW) amide neurohormone. Current molecular-level techniques rely on ligand-binding assays, enzyme-linked immunosorbent assay (ELISA), and, more recently, gene expression. In the future, more reliance will be placed on the development of gene expression assays using reporter systems combined with cross-species PCR-based or polyclonal antibody-based assays. We discuss the use of recombinant receptors as a means of primary screening of environmental samples for estrogenicity and antiestrogenicity, which avoids species and seasonal variation in receptor response to ligand binding, a recognized problem of earlier bioassays. Most exciting is the potential that microarray and proteomics approaches have to offer. Such techniques are now used routinely in medical research to identify specific genes and proteins affected by treatment with endocrine disruptors, including estradiol. The technique has yet to be used to screen aquatic organisms, but it has the potential to implicate previously unsuspected estradiol-sensitive genes that may later become molecular markers of endocrine disruption. PMID:12888444

Rotchell, Jeanette M; Ostrander, Gary K

237

APPLICATION OF MOLECULAR MARKER TECHNOLOGIES ON CEREAL CROPS IMPROVEMENT  

Technology Transfer Automated Retrieval System (TEKTRAN)

The use of PCR-based DNA markers has greatly improved the efficiency in mapping agronomic traits. One such DNA marker is SSR or microsatellite. It is multiallelic and capable of detecting higher levels of polymorphism. At the moment, SSR is the most extensively used marker system in both wheat an...

238

Genetic diversity analysis of common beans based on molecular markers.  

PubMed

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

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

2011-10-01

239

Genetic diversity analysis of common beans based on molecular markers  

PubMed Central

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.

Gill-Langarica, Homar R.; Muruaga-Martinez, Jose S.; Vargas-Vazquez, M.L. Patricia; Rosales-Serna, Rigoberto; Mayek-Perez, Netzahualcoyotl

2011-01-01

240

Molecular characterization and identification of markers for toxic and non-toxic varieties of Jatropha curcas L. using RAPD, AFLP and SSR markers  

Microsoft Academic Search

Jatropha curcas L., a multipurpose shrub has acquired significant economic importance for its seed oil which can be converted to biodiesel,\\u000a is emerging as an alternative to petro-diesel. The deoiled seed cake remains after oil extraction is toxic and cannot be used\\u000a as a feed despite having best nutritional contents. No quantitative and qualitative differences were observed between toxic\\u000a and

D. V. N. Sudheer Pamidimarri; Sweta Singh; Shaik G. Mastan; Jalpa Patel; Muppala P. Reddy

2009-01-01

241

Molecular Markers of Lung Cancer in MAYAK Workers  

SciTech Connect

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.

Steven A. Belinsky, PhD

2007-02-15

242

Molecular Markers of Radiation-related Normal Tissue Toxicity  

PubMed Central

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

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

2009-01-01

243

A pseudoautosomal random amplified polymorphic DNA marker for the sex chromosomes of Silene dioica.  

PubMed Central

The segregation pattern of an 810-bp random amplified polymorphic DNA (RAPD) band in the F1 and backcross generations of a Silene dioica (L.) Clairv. family provides evidence that this molecular marker is located in the pseudoautosomal region (PAR) of the X and Y chromosomes. The marker was found through a combination of bulked segregant analysis (BSA) and RAPD techniques. Recombination rates between this pseudoautosomal marker and the differentiating portion of the Y chromosome are 15% in both generations. Alternative explanations involving nondisjunction or autosomal inheritance are presented and discussed. Chromosome counts provide evidence against the nondisjunction hypothesis, and probability calculations argue against the possibility of autosomal inheritance. This constitutes the first report of a pseudoautosomal DNA marker for plant sex chromosomes.

Di Stilio, V S; Kesseli, R V; Mulcahy, D L

1998-01-01

244

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...

245

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

Microsoft Academic Search

Detailed gas chromatographic\\/mass spectrometric analyses have been applied to sediment samples of the Havel and Spree River, tributaries to the Elbe River, in order to identify specific molecular markers of anthropogenic activities. Despite a wide variety of lipophilic organic compounds from diffuse anthropogenic contamination, a local emission of an industrial point source was reflected by specific markers including halogenated compounds

M. Ricking; J. Schwarzbauer; S. Franke

2003-01-01

246

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

Microsoft Academic Search

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

Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen

2002-01-01

247

Association between molecular markers for beef tenderness and growth traits in Argentinian angus cattle.  

PubMed

Molecular markers for beef tenderness are classic examples of the contribution of genome technology to animal breeding through marker-assisted selection (MAS). Markers on the ?-calpain (CAPN1) and calpastatin (CAST) genes have been extensively evaluated for their association with tenderness. However, little is known about their potential effect on other economically important traits. In this work, the association of molecular markers for beef tenderness with growth traits was evaluated in Angus cattle of Argentina. Expected progeny differences were extracted from the 2008 Angus Sire Summary of Argentina. Information corresponding to 268 influential bulls that had been genotyped for two markers in CAPN1 and two markers in CAST was provided by the Argentine Angus Association. Genotype probabilities were assigned, by segregation analysis, to those bulls in the Sire Summary that had no marker information. Expected progeny differences of 1365 sires were regressed on the number of alleles favouring tenderness at each locus. There was a significant effect of markers on expected progeny differences of birth weight, weaning weight (direct), weight at 18 months and rib eye area. In general, there was a negative effect of alleles favouring tenderness on growth traits. These correlated responses should be taken into account when molecular markers are used in selection schemes that aim to improve beef tenderness. PMID:21554351

Pintos, D; Corva, P M

2011-02-06

248

Molecular linkage maps of the Populus genome.  

PubMed

We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification. PMID:12033623

Yin, Tongming; Zhang, Xinye; Huang, Minren; Wang, Minxiu; Zhuge, Qiang; Tu, Shengming; Zhu, Li-Huang; Wu, Rongling

2002-06-01

249

Identification of tumor markers and differentiation markers for molecular diagnosis of lung adenocarcinoma  

Microsoft Academic Search

To identify tumor markers and differentiation markers for lung adenocarcinoma (AdC), we analysed expression profiles of 14 500 genes against three cases of type II alveolar epithelial cells, bronchiolar epithelial cells, and bronchial epithelial cells, respectively, and 10 cases of AdC cells isolated by laser capture microdissection. Hierarchical clustering analysis indicated that AdC cells and noncancerous lung epithelial cells are

N Nakamura; K Kobayashi; M Nakamoto; T Kohno; H Sasaki; Y Matsuno; J Yokota

2006-01-01

250

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

Microsoft Academic Search

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

Patrícia J. Faria; Cristina Y. Miyaki

2006-01-01

251

Analysis of plant diversity with retrotransposon-based molecular markers  

PubMed Central

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.

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

2011-01-01

252

Advances in the Use of Molecular Markers for Source Apportionment of Atmospheric Organic Aerosols  

NASA Astrophysics Data System (ADS)

Over the past decade, there has been significant effort directed at measuring particle-phase organic compounds in air pollution emission sources and in the atmosphere. A subset of these organic compounds are relatively unique to the emissions from specific air pollution source categories and are believed to be stable enough in the atmosphere to be used as source tracers. To date, studies have been conducted in North America, Asia and Europe in both remote and urbanized locations that have used these organic compound tracers, also called molecular markers, for source attribution studies. The major short-comings of these studies are the uncertainties associated with developing site and season specific molecular marker source profiles and the absence of source fingerprints for secondary organic aerosol. Recent advances in molecular marker chemical analysis methods has lead to two key advances for molecular marker source apportionment efforts: 1) sufficiently large data sets of molecular marker measures have been generated that now allow multivariate receptor models to be used in parallel with chemical mass balance (CMB) models, and 2) compounds that are believed to be predominately associated with secondary organic aerosol (SOA) have been identified and can be routinely analyzed in organic aerosol samples. Given these advances, data sets have been generated that can be used to apportion atmospheric organic aerosols to both primary and secondary organic aerosols without the use of source profiles. Background on molecular markers will be presented along with recent organic aerosol source apportionment results that were obtained using multivariate receptor models to analyze molecular marker data sets obtained in the Midwestern United States. These data sets include a daily time series of molecular marker concentration data from the Midwest Supersite in East St. Louis that spans two years and a monthly average tracer data for a year that were simultaneously obtained in St. Louis, Chicago, Detroit, Indianapolis, Cincinnati, and Bondville. The results of these studies will be presented along with a comparison of the molecular marker source profiles derived from a multivariate receptor models and source testing activities. Such analyses provide insight into the atmospheric stability of these molecular markers and their uniqueness to source categories.

Schauer, J. J.; Sheesley, R. J.; Jaeckels, J. M.

2006-12-01

253

[Non-small cell lung cancer. Subtyping and predictive molecular marker investigations in cytology].  

PubMed

The diagnosis and treatment of non-small cell lung cancer (NSCLC) have been revolutionized over the last few years. Requirements for cytopathologists in lung cancer diagnosis have therefore changed. The general diagnostic category of NSLC is no longer sufficient. In addition cytological specimens need to be evaluated for adequacy regarding predictive marker analyses. Accurate NSCLC subtyping with a distinction of adenocarcinoma from squamous cell carcinoma is crucial for treatment decisions as the subtype will decide on the chemotherapy regimen and the choice of predictive marker analyses for targeted treatment. In the majority of cases, the subtype can be diagnosed by morphology alone. Cytology is equally well suited as biopsy specimens for the assessment of molecular predictive markers. The best results are achieved when both cytology and biopsy specimens are compared to choose the most appropriate specimen for morphological subtyping and molecular testing. In this paper, we discuss special issues of NSCLC subtyping and currently recommended predictive molecular marker analyses. PMID:22711372

Savic, S; Bihl, M P; Bubendorf, L

2012-07-01

254

MYOSIN ISOENZYMES AS MOLECULAR MARKERS FOR MUSCLE PHYSIOLOGY  

Microsoft Academic Search

SUMMARY Myosin is a major component of skeletal muscle and it plays a central role in determining the physiological performance of adult tissue. Developing muscles contain myosin molecules which are different from the adult forms, and these isoenzymes have been found to be characteristic markers of the diverse physiological and pathological states of muscle tissue. The differences between these isoenzymes

ROBERT G. WHALEN

255

Fingerprinting fission yeast: polymorphic markers for molecular genetic analysis of Schizosaccharomyces pombe strains  

Microsoft Academic Search

The fission yeast Schizosaccharomyces pombe is widely used as a model eukaryote for cell and molecular studies but little is known of natural genetic variation in this species. In order to obtain informative molecular markers, imperfect tandem repeats, identified through bioinformatic methods, were tested for length polymorphism in six wild-type strains of Sch. pombe isolated from different substrates and geographical

Ann-Marie Patch; Stephen J. Aves

2007-01-01

256

Development and use of molecular markers to accelerate peanut cultivar development  

Technology Transfer Automated Retrieval System (TEKTRAN)

Close cooperation between conventional plant breeders and molecular geneticists will be needed to efficiently and effectively utilize modern genetic tools in the development of peanut cultivars. We have used this approach at Tifton to develop molecular markers for resistance to the peanut root-knot...

257

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 ...

258

Genetic mutations, molecular markers and future directions in research.  

PubMed

Recent molecular studies have described a number of abnormalities associated with the pathogenesis of thyroid carcinoma. These distinct molecular events are often associated with specific stages of tumor development and may serve as prognostic factors and therapeutic targets. A better understanding of the mechanisms involved in thyroid cancer pathogenesis, will hopefully help translate these discoveries to improved patient care. PMID:23602255

Patel, Kepal N

2013-04-17

259

Biodiversity in Date Palm: Molecular Markers as Indicators  

Microsoft Academic Search

\\u000a Date palm, a tree known only as cultivated and under domestication for thousands of years with a wide range of distinct morphological\\u000a diversity, has been a target of considerable research work, including, e.g. studies on both phenotypic and genetic diversity.\\u000a Most research has focused on cultivar identification, where both types of markers – phenotypic and genetic – have been utilized.

S. Elshibli; H. Korpelainen

260

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

PubMed Central

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.

Dini-Andreote, Francisco; Pietrobon, Vivian Cristina; Andreote, Fernando Dini; Romao, Aline Silva; Sposito, Marcel Bellato; Araujo, Welington Luiz

2009-01-01

261

Relative efficiency of morphological characters and molecular markers in the establishment of an apricot core collection.  

PubMed

In order to optimize the management of genetic resources, in most cases a representative sample of the germplasm collections needs to be developed. The establishment of a core collection is thus of major importance either to minimize the cost associated with the management of the associated germplasm or to apply analysis onto representative bases. In order to select a representative core collection among the Tunisian apricot germplasm of 110 accessions large, the Maximization strategy algorithm was used. This algorithm was shown to be the most convenient when using both morphological traits and molecular markers. Three core collections based on morphological characters, molecular markers or the combined data were compared. Our data indicate that both the molecular and the morphological markers have to be considered to obtain a core collection that represents the global diversity of the 110 accessions. Using this method, a subset of 34 selected accessions was found to represent accurately the 110 accessions present in the whole collection (75 to 100% for the morphological characters and 97% of the molecular markers). These results show that the combination of molecular and morphological markers is an efficient way to characterize the apricot core collection and provides an exhaustive coverage for the analyzed diversity on morphological and genetic bases. PMID:23121327

Krichen, L; Audergon, J M; Trifi-Farah, N

2012-09-21

262

Inheritance of RAPDs in F 1 hybrids of corn  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) markers were analyzed in materials from a partial diallel, including 16 corn F1 hybrids (with five reciprocals) and their five parental inbreds. Using 21 primers, we scored a total of 140 different fragments for their presence\\/absence and intensity variation, where appropriate. When all 21 genotypes were taken into consideration, 20.7% of these fragments were nonpolymorphic,

M. Heun; T. Helentjaris

1993-01-01

263

Markers  

ERIC Educational Resources Information Center

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…

Healthy Schools Network, Inc., 2011

2011-01-01

264

Genetic Diversity and Molecular Markers of Cupped Oysters (Genera Crassostrea, Saccostrea, and Striostrea ) in Thailand Revealed by Randomly Amplified Polymorphic DNA Analysis  

Microsoft Academic Search

:   Genetic diversity and species-diagnostic markers of 5 oysters in Thailand, Crassostrea belcheri (Sowerby, 1871), Crassostrea iredalei (Faustino, 1932), Saccostrea cucullata (Born, 1778), Saccostrea forskali (Gmelin, 1791), and Striostrea (Parastriostrea) mytiloides (Lamarck, 1819), were investigated by randomly amplified polymorphic DNA (RAPD) analysis. In a total, 135, 127, and 108 genotypes\\u000a were observed from primers OPA09, OPB01, and OPB08 (Operon Technologies

S. Klinbunga; P. Ampayup; A. Tassanakajon; P. Jarayabhand; W. Yoosukh

2001-01-01

265

Saffron is a monomorphic species as revealed by RAPD, ISSR and microsatellite analyses  

PubMed Central

Background Saffron (Crocus sativus) is considered the world's most expensive spice. Used mainly as a colorant for foodstuffs, it is highly appreciated for its aromatic and flavouring properties. Since no molecular markers for this species have been found in the literature, the objective of this study was to determine whether phenotypical differences found in C. sativus were supported by molecular analyses. Findings Thirty primers from Operon Technologies were used in random amplified polymorphic DNA (RAPD) analysis, forty eight primers were screened using intersimple sequence repeats (ISSR) method and fifteen primers derived from a microsatellites library flanking sequences with repeat motifs were assayed in forty three isolates of C. sativus from eleven different countries and a C. kotschyanus isolate was used as outgroup. No polymorphic bands were detected in any of the accessions combining the different approaches used in this study. Conclusion According to our findings, all accessions appear identical clones, not only because morphological characters but also at a molecular level. These data strongly suggested that C. sativus is a monomorphic species. Thus, genome sequencing is needed to find molecular markers for saffron.

Rubio-Moraga, Angela; Castillo-Lopez, Raquel; Gomez-Gomez, Lourdes; Ahrazem, Oussama

2009-01-01

266

Genotypic diversity, molecular markers and spatial distribution of genets in clonal plants, a literature survey  

Microsoft Academic Search

We present a literature survey of studies using molecular markers to investigate genet diversity and structure in clonal plants.\\u000a The data from 40 studies comprised 45 species of which only two were studied by DNA methods, the rest by isozyme markers.\\u000a Less than one third of the studies provided information about the spatial distribution of individual genets within populations,\\u000a and

Björn Widén; Nils Cronberg; Marie Widén

1994-01-01

267

Predictive and prognostic molecular markers for cancer medicine  

PubMed Central

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.

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

2010-01-01

268

Development of novel diagnostic and prognostic molecular markers for sporadic colon cancer.  

PubMed

Gene expression studies are informative about changes in colon cancer, increase understanding of the biology of tumorigenesis and aid in developing diagnostic and prognostic markers. In this review, expression techniques used to examine the multistage process of colon cancer are discussed. Many genes have been found to differ in expression between normal and tumorigenic states, as early as the seemingly normal colonic crypts. The clinical usefulness of markers varies with stage, ethnicity and anatomic location of colon cancer. Thus, combinations of markers can be used to develop an approach to molecularly screen and follow the progression of this prevalent cancer. PMID:15934812

Ahmed, Farid E

2005-05-01

269

Use of molecular markers to differentiate between commercial strains of the button mushroom Agaricus bisporus.  

PubMed

Agaricus bisporus is an edible basidiomycete cultivated industrially for food production. Different spawn and mushroom producers use genetically related A. bisporus strains frequently marketed as different products. In this paper we show that the use of suitable molecular markers reveals the high level of genetic homology of commercial strains of A. bisporus, and allows, at the same time, to distinguish between them. In the course of this work, a molecular marker potentially linked to the agronomic character 'mushroom weight' has been identified by bulked segregant analysis. PMID:11325552

Ramírez, L; Muez, V; Alfonso, M; García Barrenechea, A; Alfonso, L; Pisabarro, A G

2001-04-20

270

Genetic Relationship of Curcuma Species from Northeast India Using PCR-Based Markers  

Microsoft Academic Search

Molecular genetic fingerprints of nine Curcuma species from Northeast India were developed using PCR-based markers. The aim involves elucidating there intra- and inter-specific\\u000a genetic diversity important for utilization, management, and conservation. Twelve random amplified polymorphic DNA (RAPD),\\u000a 19 Inter simple sequence repeats (ISSRs), and four amplified fragment length polymorphism (AFLP) primers produced 266 polymorphic\\u000a fragments. ISSR confirmed maximum polymorphism of

Archana Das; Vigya Kesari; Vinod M. Satyanarayana; Ajay Parida; Latha Rangan

2011-01-01

271

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

PubMed Central

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

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

2011-01-01

272

Highly isotopically depleted isoprenoids: Molecular markers for ancient methane venting  

SciTech Connect

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.

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

1999-12-01

273

[Molecular markers of hemostasis activation in children with nephrotic syndrome].  

PubMed

Vein and arterial thrombosis is a rather rare but potentially life-threatening complication of nephrotic syndrome (n.s.). None of the specific markers of hypercoagulability state in n.s. have been identified. The aim of the study was to estimate plasma parameters of prothrombic state in children with n.s. Ten children aged from 3 to 10 yrs (mean 5.7 +/- 2.5) with recurrence of n.s. and 10 healthy controls matched for age and sex were studied. In all children with n.s. prothrombin fragments F 1+2, D-dimers (D-d), thrombin-antithrombin III complexes (TAT) and whole blood clotting time thrombin time, prothrombin time, plasma fibrinogen and platelet count were determined in the hypovolemic state (before therapy was started), in the normovolemic state (after plasma expander was used) and in the course of anticoagulation treatment (two week dicumarol therapy). In comparison with healthy controls all children with recurrence of n.s. in the hypovolemic state showed a significant (p < 0.05) increase of D-d (910 vs 500 ng/ml), TAT (14.26 vs 2.6 ng/ml), F 1+2 (5.68 vs 0.79 nmol/l), plasma fibrinogen (592 vs 272 mg/dl), platelet count (632 vs 275 x 10(9)/l) and shortening of WBCT (30.0 vs 35 s). Plasma volume expansion produced by dekstran was followed by a moderate decrease of all parameters. Two-week anticoagulant treatment had no impact on estimated haemostasis parameters. PMID:8649942

Ksiazek, J; Cichocka, E; Lukasiewicz, H; Tekli?ska, E; Wyszy?ska, T

1995-12-01

274

Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs.  

PubMed

The implications of transitioning to single nucleotide polymorphism (SNPs) from microsatellite markers (MSs) have been investigated in a number of population genetics studies, but the effect of genomic location on the amount of information each type of marker reveals has not been explored in detail. We developed novel SNP markers flanking 1 kb regions of 13 genic (within gene or <1 kb away from gene) and 13 nongenic (>10 kb from annotated gene) MSs in the threespine stickleback genome to obtain comparable data for both types of markers. We analysed patterns of genetic diversity and divergence on various geographic scales after converting the SNP loci within each genomic region into haplotypes. Marker type (SNP haplotype or MS) and location (genic or nongenic) significantly affected most estimates of population diversity and divergence. Between-lineage divergence was significantly higher in SNP haplotypes (genic and nongenic), however, within-lineage divergence was similar between marker types. Most divergence and diversity measures were uncorrelated between markers, except for population differentiation which was correlated between MSs and SNP haplotypes (both genic and nongenic). Broad-scale population structure and assignment were similarly resolved by both marker types, however, only the MSs were able to delimit fine-scale population structuring, particularly when genic and nongenic markers were combined. These results demonstrate that estimates of genetic variability and differentiation among populations can be strongly influenced by marker type, their genomic location in relation to genes and by the interaction of these two factors. This highlights the importance of having an awareness of the inherent strengths and limitations associated with different molecular tools to select the most appropriate methods for accurately addressing various ecological and evolutionary questions. PMID:23356957

DeFaveri, Jacquelin; Viitaniemi, Heidi; Leder, Erica; Merilä, Juha

2013-01-29

275

Identifying molecular markers associated with classification of genotypes by External Logistic Biplots  

Microsoft Academic Search

For characterization of genetic diversity in genotypes several mo- lecular techniques, usually resulting in a binary data matrix, have been used. Despite the fact that in Cluster Analysis and Principal Coordinates Analysis the interpretation of the variables responsible for grouping is not straightforward, these methods are commonly used to classify genotypes using DNA molecular markers. In this paper, we present

J. R. Demey; José L. Vicente-villardón; M. P. Galindo-villardón; A. Y. Zambrano

2008-01-01

276

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

Microsoft Academic Search

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

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

2006-01-01

277

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...

278

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

ERIC Educational Resources Information Center

|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…

Helms, T. C.; Doetkott, C.

2007-01-01

279

Use of molecular markers to differentiate between commercial strains of the button mushroom Agaricus bisporus  

Microsoft Academic Search

Agaricus bisporus is an edible basidiomycete cultivated industrially for food production. Different spawn and mushroom producers use genetically related A. bisporus strains frequently marketed as different products. In this paper we show that the use of suitable molecular markers reveals the high level of genetic homology of commercial strains of A. bisporus, and allows, at the same time, to distinguish

Luc??a Ram??rez; V??ctor Muez; Mikel Alfonso; Alberto Garc??a Barrenechea; Leopoldo Alfonso; Antonio G. Pisabarro

2001-01-01

280

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

Microsoft Academic Search

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

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

2004-01-01

281

Study of genetic diversity in Chamomile ( Matricaria chamomilla) based on morphological traits and molecular markers  

Microsoft Academic Search

Chamomile is one of the most important medicinal plants in the world trade that has many applications in drug and sanitary industrials. In order to evaluate the genetic diversity of different chamomile landraces based on morphological and molecular markers, 20 landraces were collected from different area of Iran. In addition to that, five populations imported from European were examined. The

M. Solouki; H. Mehdikhani; H. Zeinali; A. A. Emamjomeh

2008-01-01

282

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

PubMed

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

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

2004-06-01

283

Identification of Turkish and standard apple rootstocks by morphological and molecular markers  

Microsoft Academic Search

Two local (Vezir-1 and Vezir-2) and two standard (M9 and MM106) clonal apple rootstocks were compared using both mor- phological and molecular markers. International Union for the Protec- tion of New Varieties of Plants criteria were used for morphological evaluation, which did not clearly separate these rootstocks. We tested 47 random decamer primers for random amplified polymorphic DNA analysis; 15

A. Koc; M. Akbulut; E. Orhan; Z. Celik; S. Bilgener; S. Ercisli

2009-01-01

284

A general mixture model for mapping quantitative trait loci by using molecular markers  

Microsoft Academic Search

In a segregating population a quantitative trait may be considered to follow a mixture of (normal) distributions, the mixing proportions being based on Mendelian segregation rules. A general and flexible mixture model is proposed for mapping quantitative trait loci (QTLs) by using molecular markers. A method is discribed to fit the model to data. The model makes it possible to

R. C. Jansen

1992-01-01

285

Efficacy, Safety, and Selection of Molecular Markers of Drug Resistance by Two ACTs in Mali  

Microsoft Academic Search

We conducted a randomized single-blinded trial comparing the efficacy and safety of artesunate (AS) + amodiaquine (AQ, 3 days) versus AS (3 days) + sulfadoxine-pyrimethamine (SP, single dose) versus AS monotherapy (5 days) in Southern Mali. Uncomplicated malaria cases were followed for 28 days. Molecular markers of drug resistance were determined. After identification of recrudescences by genotyping, both artemisinin-based combination

Abdoulaye A. Djimdé; Bakary Fofana; Issaka Sagara; Bakary Sidibe; Sekou Toure; Demba Dembele; Souleymane Dama; Dinkorma Ouologuem; Alassane Dicko; Ogobara K. Doumbo

2008-01-01

286

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

EPA Science Inventory

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

287

QTL mapping and molecular marker analysis for the resistance of rice to ozone.  

PubMed

The resistance of rice to ozone (O3) is a quantitative trait controlled by nuclear genes. The identification of quantitative trait loci (QTL) and analysis of molecular markers of O3 resistance is important for increasing the resistance of rice to O3 stress. QTL associated with the O3 resistance of rice were mapped on chromosomes 1, 7 and 11 using 164 recombinant inbred (RI) lines from a cross between 'Milyang 23' and 'Gihobyeo'. The quantitative trait loci were tightly linked to the markers RG109, C507 and RG1094 and were detected in each of three replications. The association between these markers and O3 resistance in 26 rice cultivars and doubled haploid (DH) populations was analysed. The markers permit the screening of rice germplasm for O3 resistance and the introduction of resistance into elite lines in breeding programs. PMID:15055542

Kim, Kyung-Min; Kwon, Yong-Sham; Lee, Jong-Jun; Eun, Moo-Young; Sohn, Jae-Keun

2004-02-29

288

MOLECULAR MARKERS FOR IDENTIFICATION OF THE HYPERPARASITOIDS DENDROCERUS CARPENTERI AND ALLOXYSTA XANTHOPIS IN LYSIPHLEBUS TESTACEIPES PARASITIZING CEREAL APHIDS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Molecular markers have been developed to detect the presence of primary parasitoids in cereal aphids for use in estimating parasitism rates. However, the presence of secondary parasitoids (hyperparasitoids) may lead to underestimates of primary parasitism rates. Therefore, molecular markers to det...

289

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...

290

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

NASA Astrophysics Data System (ADS)

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.

Wang, Tiegu; Huang, Qunce; Feng, Weisen

2007-10-01

291

Development of new molecular markers for the Colletotrichum genus using RetroCl1 sequences.  

PubMed

A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant differences among the populations divided according to race, indicating that they are structured according to pathotype. No clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus. PMID:22805830

Dos Santos, Leandro Vieira; de Queiroz, Marisa Vieira; Santana, Mateus Ferreira; Soares, Marcos Antônio; de Barros, Everaldo Gonçalves; de Araújo, Elza Fernandes; Langin, Thierry

2011-10-01

292

Genetic diversity in cultivated carioca common beans based on molecular marker analysis  

PubMed Central

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm.

Kupper Cardoso Perseguini, Juliana Morini; Chioratto, Alisson Fernando; Zucchi, Maria Imaculada; Colombo, Carlos Augusto; Carbonell, Sergio Augusto Moraes; Costa Mondego, Jorge Mauricio; Gazaffi, Rodrigo; Franco Garcia, Antonio Augusto; de Campos, Tatiana; de Souza, Anete Pereira; Rubiano, Luciana Benchimol

2011-01-01

293

Immune Response to Mycobacterium tuberculosis and Identification of Molecular Markers of Disease  

PubMed Central

The complex molecular events that occur within the host during the establishment of a Mycobacterium tuberculosis infection are poorly defined, thus preventing identification of predictive markers of disease progression and state. To identify such molecular markers during M. tuberculosis infection, global changes in transcriptional response in the host were assessed using mouse whole genome arrays. Bacterial load in the lungs, the lesions associated with infection, and gene expression profiling was performed by comparing normal lung tissue to lungs from mice collected at 20, 40, and 100 days after aerosol infection with the H37Rv strain of M. tuberculosis. Quantitative, whole lung gene expression identified signature profiles defining different signaling pathways and immunological responses characteristic of disease progression. This includes genes representing members of the interferon-associated gene families, chemokines and cytokines, MHC, and NOS2, as well as an array of cell surface markers associated with the activation of T cells, macrophages, and dendritic cells that participate in immunity to M. tuberculosis infection. More importantly, several gene transcripts encoding proteins that were not previously associated with the host response to M. tuberculosis infection, and unique molecular markers associated with disease progression and state, were identified.

Gonzalez-Juarrero, Mercedes; Kingry, Luke C.; Ordway, Diane J.; Henao-Tamayo, Marcela; Harton, Marisa; Basaraba, Randall J.; Hanneman, William H.; Orme, Ian M.; Slayden, Richard A.

2009-01-01

294

Immune response to Mycobacterium tuberculosis and identification of molecular markers of disease.  

PubMed

The complex molecular events that occur within the host during the establishment of a Mycobacterium tuberculosis infection are poorly defined, thus preventing identification of predictive markers of disease progression and state. To identify such molecular markers during M. tuberculosis infection, global changes in transcriptional response in the host were assessed using mouse whole genome arrays. Bacterial load in the lungs, the lesions associated with infection, and gene expression profiling was performed by comparing normal lung tissue to lungs from mice collected at 20, 40, and 100 days after aerosol infection with the H37Rv strain of M. tuberculosis. Quantitative, whole lung gene expression identified signature profiles defining different signaling pathways and immunological responses characteristic of disease progression. This includes genes representing members of the interferon-associated gene families, chemokines and cytokines, MHC, and NOS2, as well as an array of cell surface markers associated with the activation of T cells, macrophages, and dendritic cells that participate in immunity to M. tuberculosis infection. More importantly, several gene transcripts encoding proteins that were not previously associated with the host response to M. tuberculosis infection, and unique molecular markers associated with disease progression and state, were identified. PMID:18787176

Gonzalez-Juarrero, Mercedes; Kingry, Luke C; Ordway, Diane J; Henao-Tamayo, Marcela; Harton, Marisa; Basaraba, Randall J; Hanneman, William H; Orme, Ian M; Slayden, Richard A

2008-09-11

295

Molecular characterization of Aspergillus flavus and aflatoxin contamination of wheat grains from Saudi Arabia.  

PubMed

Twelve species belonging to six fungal genera were found to be associated with wheat (Triticum aestivum L.) grain samples collected from three main regions in Saudi Arabia. The most common genera (average frequency) were Aspergillus (14.3%), Fusarium (29.1%), Penicillium (9.3%), and Alternaria (8.2%). Nineteen isolates of Aspergillus flavus were screened for their ability to produce aflatoxins using HPLC. Thirteen isolates produced aflatoxins ranging from 0.5 to 2.6 µg/kg. Inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) molecular markers were used, with the aim of genetically characterizing strains of A. flavus to discriminate between aflatoxigenic and non-aflatoxigenic isolates. RAPD and ISSR analysis revealed a high level of genetic diversity in the A. flavus population, useful for genetic characterization. Clustering based on RAPD and ISSR dendograms was unrelated to geographic origin. RAPD and ISSR markers were not suitable to discriminate aflatoxigenic and non-aflatoxigenic isolates, but ISSR primers were better compared to RAPD. PMID:24065675

Al-Wadai, A S; Al-Othman, M R; Mahmoud, M A; Abd El-Aziz, A R M

2013-09-03

296

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

PubMed Central

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.

2011-01-01

297

Molecular characterization of primary gene pool of chickpea based on ISSR markers.  

PubMed

Genetic diversity and relationships within and among members of the primary gene pool of chickpea, including 38 accessions of Cicer arietinum, six of C. reticulatum,, and four of C. echinospermum, were investigated using 31 ISSR markers. The study revealed moderate diversity, detecting 141 fragments, of which 79 (56%) were polymorphic. Averages were 0.125 for polymorphic information content, 0.350 for marker index, and 0.715 for resolving power. The UPGMA dendrogram and the principal coordinate analysis revealed a clear differentiation between wild and cultivated accessions. The clustering pattern did not strictly follow the grouping of accessions by geographic origin but was in good agreement with the pedigree data and the seed type. The study demonstrates that ISSRs provide promising marker tools in revealing genetic diversity and relationships in chickpea and can contribute to efficient identification, conservation, and utilization of germplasm for plant improvement through conventional as well as molecular breeding approaches. PMID:23329257

Choudhary, Pooja; Khanna, Suruchi M; Jain, Pradeep K; Bharadwaj, Chellapilla; Kumar, Jitendra; Lakhera, Pramesh C; Srinivasan, Ramamurthy

2013-01-18

298

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

PubMed

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

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

2013-08-12

299

Molecular and histological markers in urothelial carcinomas of the upper urinary tract.  

PubMed

Urothelial cell carcinomas (UCCs) are one of the most common types of malignancies. Recently, different mechanisms of carcinogenesis, as well as discrepancies in the natural history of urothelial cancers of the bladder and of the upper urinary tract (UUT), have been identified. As a result several teams have focused on specific markers in UUT-UCCs, a very rare type of cancer. This review gives a brief overview on the current markers of interest. Microsatellite instabilities (MSI) are independent molecular makers for prognosis. In addition, MSI can help detect a germline mutation and therefore allows for the detection of possible hereditary cancers. The loss of proteins of the mismatch repair system can also facilitate the detection of a germline mutation but should be followed by DNA sequencing. Epithelial cadherin has been shown to be an independent marker of prognosis, as well as hypoxia-inducible factor-1alpha (HIF-1alpha) and telomerase RNA component. Furthermore HIF-1alpha is significantly associated with the grade and pattern of growth and the telomerase RNA component could possibly also be used in diagnosis. The active form of the L-type amino acid transporter 1 (LAT1) was a significant prognostic marker in univariate analysis only. There are contrasting studies on the significances of p27 and Ki-67 as prognostic markers in UUT-UCCs. MET is a factor that correlates with vascular invasion of invasive cancer and bcl-2 oncoprotein correlates with stage. The ongoing identification of these markers might help to find specific treatments tailored to the molecular pattern of each tumour. Therefore a subgroup of patients with a higher risk of recurrence could be identified as well as patients that could benefit from minimal invasive surgery. PMID:18384628

Eltz, Stephanie; Comperat, Eva; Cussenot, Olivier; Rouprêt, Morgan

2008-04-02

300

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

PubMed

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 the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 P. granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He=0.245; Ho=0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a pomegranate core-collection without plant material duplication and for sustainable management of pomegranate landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies. PMID:22123180

Hasnaoui, Nejib; Buonamici, Anna; Sebastiani, Federico; Mars, Messaoud; Zhang, Dapeng; Vendramin, Giovanni G

2011-11-20

301

Identification of candidate molecular markers of nasopharyngeal Carcinoma by tissue microarray and in situ hybridization  

Microsoft Academic Search

To scan differentially expressed genes and to identify candidate molecular markers in nasopharyngeal carcinoma (NPC), we analyzed\\u000a cDNA microarray data by GenMAPP to find specifically expressed genes in NPC and used tissue microarray and in situ hybridization\\u000a techniques to confirm our microarray results. Our cDNA microarray results showed that TSPAN-1 and DPP10 genes were down-expressed\\u000a in NPC, and COX7B and

Shilong XiongQian; Qian Wang; Lei Zheng; Feng Gao; Junling Li

302

Characterization of molecular markers in smoke from residential coal combustion in China  

Microsoft Academic Search

The organic constituents and distributions of molecular markers emitted from a residential coal-stove burning honeycomb coal briquettes were determined in this study. The major organic components emitted directly in smoke particles were polycyclic aromatic hydrocarbons (PAHs), with abundant hydroxy-polycyclic aromatic hydrocarbons (OH-PAHs), i.e., thermally altered derivative compounds from coal combustion, UCM (unresolved complex mixture of branched and cyclic compounds), n-alkanes

Xinhui Bi; Bernd R. T. Simoneit; Guoying Sheng; Jiamo Fu

2008-01-01

303

The GCP molecular marker toolkit , an instrument for use in breeding food security crops  

Microsoft Academic Search

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate\\u000a the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number\\u000a of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access,\\u000a particularly those in developing countries. This situation separates them

Veerle Van Damme; Humberto Gómez-Paniagua; M. Carmen de Vicente

304

?H2AX: a sensitive molecular marker of DNA damage and repair  

Microsoft Academic Search

Phosphorylation of the Ser-139 residue of the histone variant H2AX, forming ?H2AX, is an early cellular response to the induction of DNA double-strand breaks. Detection of this phosphorylation event has emerged as a highly specific and sensitive molecular marker for monitoring DNA damage initiation and resolution. Further, analysis of ?H2AX foci has numerous other applications including, but not limited to,

L-J Mah; A El-Osta; T C Karagiannis

2010-01-01

305

Functionally associated molecular genetic marker map construction in perennial ryegrass ( Lolium perenne L.)  

Microsoft Academic Search

A molecular marker-based map of perennial ryegrass (Lolium perenne L.) has been constructed through the use of polymorphisms associated with expressed sequence tags (ESTs). A pair-cross between genotypes from a North African ecotype and the cultivar Aurora was used to generate a two-way pseudo-testcross population. A selection of 157 cDNAs assigned to eight different functional categories associated with agronomically important

M. J. Faville; A. C. Vecchies; M. Schreiber; M. C. Drayton; L. J. Hughes; E. S. Jones; K. M. Guthridge; K. F. Smith; T. Sawbridge; G. C. Spangenberg; G. T. Bryan; J. W. Forster

2004-01-01

306

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

PubMed

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

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

2013-08-07

307

PCR markers distinguish Plantago major subspecies  

Microsoft Academic Search

Plantago major plants from several Scottish and Dutch locations were surveyed for their genetic variation using PCR markers, namely RAPD\\u000a analysis, anchored inter-SSR PCR, and chloroplast PCR followed by RFLP analysis. The RAPD and inter-SSR markers showed a differentiation\\u000a between the two subspecies of P. major. These results are discussed in relation to earlier results using allozyme electrophoresis, DNA fingerprinting,

K. Wolff; M. Morgan-Richards

1998-01-01

308

Genetic homogeneity in the seagrass Cymodocea nodosa at its northern Atlantic limit revealed through RAPD  

Microsoft Academic Search

Random amplified polymorphic DNA (RAPD) markers were used to analyse the genetic variability of the dioecious seagrass Cymodocea nodosa Ucria (Ascherson) in the Ria Formosa lagoon, Portugal, the species' northern limit in the Atlantic. Three individuals from each of 6 meadows were genotyped with 28 primers. Meadows described previ- ously as having flower marks were compared with meadows where flowers

Filipe Alberto; Leonardo Mata; Rui Santos

2001-01-01

309

Application of random amplified polymorphic DNA (RAPD) to detect genetic variation in Norway spruce  

Microsoft Academic Search

Die RAPD Methode, ein Schnelltest für die genetische Variation, wurde für die europäische Fichte getestet, wo viele Aspekte der Biologie der Baumart damit untersucht werden könnten. Das Protokoll wurde optimiert, und genetische Stabilität in Klonen, besonders aus Gewebekultur, die genetische Variation in einer Samenprobe und die Mendel-konforme Aufspaltung in haploiden Megagametophyten wurde untersucht. Zahlreiche genetische Marker konnten gefunden werden, wodurch

B. Heinze; R. Westcott; J. Schmidt; J. Glössl

1996-01-01

310

APPLICATION OF RAPD TECHNIQUE FOR THE CONSERVATION OF AN ISOLATED POPULATION OF Capparis decidua  

Microsoft Academic Search

Capparis decidua is a rangeland plant species growi ng in isolated regions in Saudi Arabia. The populat ion in Rawdhat Khuraim was noticed to suffer from lack of new regeneration, in addition to excessive grazing which may reduce the size of the population and reduce the ge netic variability. RAPD markers were used to study genetic diversity in this population

A. L. Abdel-Mawgood; A. M. Assaeed; T. I. Al-Abdallatif

311

RAPD analysis of somaclonal variants derived from embryo callus cultures of peach  

Microsoft Academic Search

Peach [Prunus persica (L.) Batsch] regenerants from cv ‘Sunhigh’ embryo no. 156, regenerants obtained from cv ‘Redhaven’ embryo no. 30, and two peach cultivars ‘Sunhigh’ and ‘Redhaven’, were screened for polymorphic RAPD (Random Amplified Polymorphic DNA) markers with up to 60 10-mer primers. Although 35 primers produced results with scoreable bands, only 10 of the primers revealed polymorphism for regenerants

G. Hashmi; R. Huettel; R. Meyer; L. Krusberg; F. Hammerschlag

1997-01-01

312

Multilocus microsatellite signature and identification of specific molecular markers for Leishmania aethiopica  

PubMed Central

Background Leishmaniasis is a clinically and epidemiologically diverse zoonotic disease caused by obligatory, intracellular protozoan parasites of the genus Leishmania. Cutaneous leishmaniasis is the most widely distributed form of the disease characterized by skin lesions. Leishmania aethiopica is considered the predominant etiological agent in Ethiopia. The current study was aimed at developing multilocus microsatellite markers for L. aethiopica isolated from human cutaneous leishmaniasis patients in Ethiopia. Results L. aethiopica parasites for the study were obtained from Ethiopia and laboratory analysis was conducted at The Ohio State University. DNA was extracted from cultured parasites and an internal transcribed spacer located at the ribosomal region of L. aethiopica genomic DNA was PCR amplified for species identification. Microsatellite markers were identified using multilocus microsatellite typing. We generated an enriched genomic library, and using Primer3 software, designed PCR primers to amplify sequences flanking the detected microsatellites. Subsequent screening of the amplified markers for length variations was performed by gel electrophoresis. Using a variety of molecular methods, 22 different microsatellite markers were identified and tested for typing L. aethiopica strains using a number of clinical isolates. Of the 22 markers tested, 5 were polymorphic and showed distinctive multilocus genotypes, classifying them into four clusters. One marker was found to be specific for L. aethiopica, discriminating it from other species of Leishmania. Conclusion Multilocus microsatellite typing using the markers developed in this study could be useful for epidemiological and population genetic studies of strains of L. aethiopica in order to investigate the structure and dynamics of the corresponding natural foci. It could also help to answer specific clinical questions, such as the occurrence of local and diffuse lesions, strain correlates of parasite persistence after subclinical infection and lesion comparisons from patients suffering from L. aethiopica infections.

2013-01-01

313

Phylogenetic relationships among pufferfish of genus Takifugu by RAPD analysis  

NASA Astrophysics Data System (ADS)

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.

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

2001-06-01

314

An improved micropropagation of Arnebia hispidissima (Lehm.) DC. and assessment of genetic fidelity of micropropagated plants using DNA-based molecular markers.  

PubMed

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

Phulwaria, Mahendra; Rai, Manoj K; Shekhawat, N S

2013-05-05

315

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...

316

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

PubMed Central

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.

Douaihy, Bouchra; Sobierajska, Karolina; Jasinska, Anna Katarzyna; Boratynska, Krystyna; Ok, Tolga; Romo, Angel; Machon, Nathalie; Didukh, Yakiv; Bou Dagher-Kharrat, Magda; Boratynski, Adam

2012-01-01

317

Molecular genetic marker-based approaches to the verification of lilac Syringa vulgaris L. in vitro germplasm collections  

Microsoft Academic Search

RAPD analysis was used to verify the varieties in an in vitro germplasm collection of lilac Syringa vulgaris L. RAPD patterns were obtained with 16 decanucleotide primers for 46 accessions (microclones and corresponding reference\\u000a varieties). The RAPD patterns of a microclone and the corresponding reference variety often differed in composition; consequently,\\u000a it was infeasible to verify the accessions by direct

N. V. Melnikova; E. V. Borhert; S. P. Martynov; I. B. Okuneva; O. I. Molkanova; V. P. Upelniek; A. M. Kudryavtsev

2009-01-01

318

Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for oxyuroid species (Nematoda).  

PubMed

Random amplified DNA markers (RAPD; Williams et al., 1990) were used to obtained specific RAPD fragments characterising different species of oxyuroids. We tested six species of worms parasitizing vertebrates or invertebrates: Passalurus ambiguus Rudolphi, 1819, parasite of Leporids; Syphacia obvelata (Rudolphi, 1802) Seurat, 1916, a parasite of rodents; Blatticola blattae (Graeffe, 1860) Chitwood, 1932 parasite of the cockroach Blattella germanica; Hammerschmidtiella diesingi (Hammerschmidt, 1838) Chitwood, 1932 and Thelastoma bulhoesi (Magalhaes, 1990) Travassos, 1929, parasites of the cockroach Periplaneta americana, and an undescribed parasite species of a passalid insect from New Caledonia. Among 15 oligonucleotides tested, nine produced several specific bands allowing the interspecific discrimination. PMID:9754296

Jobet, E; Bougnoux, M E; Morand, S; Rivault, C; Cloarec, A; Hugot, J P

1998-03-01

319

Development of molecular diagnostic markers for sharpshooters Homalodisca coagulata and Homalodisca liturata for use in predator gut content examinations  

Microsoft Academic Search

To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter, Homalodisca coagulata (Say), and smoke-tree sharpshooter, Homalodisca liturata (Ball) (Homoptera: Cicadellidae). Two different types of markers were compared, those targeting single-copy sequence characterized amplified regions (SCAR) and mitochondrial markers targeting the multicopy cytochrome oxidase subunit genes

Jesse H. de Leon; Valerie Fournier; James R. Hagler; Kent M. Daane

2006-01-01

320

Map order and linkage distances of molecular markers close to the supernodulation ( nts-1 ) locus of soybean  

Microsoft Academic Search

The molecular characteristics of markers in the chromosome region surrounding the supernodulation gene (nts-1) of soybean (Glycine max L. Merr.) were investigated in 187 F2 plants from a cross of G. max cv. Bragg (nts) and G. soja PI468.397 (wild-type nodulation). RFLP marker pUTG-132a, linked tightly (0.7±0.5 cM) to nts-1, was converted to a PCR marker. The polymorphism resides within

A. Kolchinsky; D. Landau-Ellis; P. M. Gresshoff

1997-01-01

321

[Molecular genetic marker-based approaches to the verification of lilac Syringa vulgaris L. in in vitro collections].  

PubMed

RAPD analysis was used to verify the varieties in an in vitro germplasm collection of lilac Syringa vulgaris L. RAPD patterns were obtained with 16 decanucleotide primers for 46 accessions (microclones and corresponding reference varieties). The RAPD patterns of a microclone and the corresponding reference variety often differed in composition; consequently, it was infeasible to verify the accessions by direct comparison of the RAPD patterns. Hence, evaluation of the relative genetic distances between accessions (microclones) and known varieties was proposed as a method to verify lilac in vitro germplasm collections. PMID:19239103

Mel'nikova, N V; Borkhert, E V; Martynov, S P; Okuneva, I B; Molkanova, O I; Upelniek, V P; Kudriavtsev, A M

2009-01-01

322

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...

323

DNA marker technologies and their applications in aquaculture genetics  

Microsoft Academic Search

The development of DNA-based genetic markers has had a revolutionary impact on animal genetics. With DNA markers, it is theoretically possible to observe and exploit genetic variation in the entire genome. Popular genetic markers in the aquaculture community include allozymes, mitochondrial DNA, RFLP, RAPD, AFLP, microsatellite, SNP, and EST markers. The application of DNA markers has allowed rapid progress in

Z. J. Liu; J. F. Cordes

2004-01-01

324

Association between DNA Markers and Loci Controlling Avocado Traits  

Microsoft Academic Search

The detection of association between DNA markers and traits of interest in an outbred population is complicated and requires highly polymorphic markers. A genetic linkage map of avocado (Persea americana Mill.) recently generated consists of simple sequence repeat (SSR) markers as well as DNA fingerprint (DFP) and randomly amplified polymorphic DNA (RAPD) markers. These markers were used to detect putative

Dror Sharon; Jossi Hillel; Samir Mhameed; Perry B. Cregan; Emanuel Lahav; Uri Lavi

1998-01-01

325

Variability and structure of natural populations of Hordelymus europaeus (L.) Jess. ex Harz and Leymus arenarius (L.) Hochst. as revealed by morphology and DNA markers  

Microsoft Academic Search

Seven populations of Hordelymus europaeus and four populations of Leymus arenarius from Poland were subjected to examination of 36 morphological characters. This study showed that both species are relatively\\u000a uniform and that morphological variation of their populations represents a continuum. Of those, three populations of either\\u000a species were selected for analysis with molecular markersRAPDs and AFLPs. These populations

M. Mizianty; L. Frey; W. Bieniek; P. Boro?; M. Szklarczyk

2007-01-01

326

Clonal relationships among Escherichia coli serogroup O6 isolates based on RAPD.  

PubMed

The genetic diversity in a group of Escherichia coli strains belonging to serogroup O6 but expressing different H antigens was investigated by random amplification of polymorphic DNA (RAPD). Isolates of serotypes H16, H1, H31, and non-motile (NM) strains were typed using a set of 3 primers with different G + C contents. The amplified band arrays allowed the identification of 3 main clonal clusters corresponding to each O:H serotype analyzed. Based on their RAPD profiles NM strains could be assigned to either H1 or H31 serotypes. The results indicate that the flagellar antigen and the RAPD fingerprint represent reliable clonal markers in this E. coli group. PMID:9084154

Pacheco, A B; Guth, B E; Soares, K C; de Almeida, D F; Ferreira, L C

1997-03-15

327

Molecular markers for cancer prognosis and treatment: have we struck gold?  

PubMed

The last decade has witnessed an emerging role for molecular or biochemical markers indicating a specific cellular mechanism or tissue function, often called 'biomarkers'. Biomarkers such as altered DNA, proteins and inflammatory cytokines are critical in cancer research and strategizing treatment in the clinic. In this review we look at the application of biological indicators to cancer research and highlight their roles in cancer detection and treatment. With technological advances in gene expression, genomic and proteomic analysis, biomarker discovery is expanding fast. We focus on some of the predominantly used markers in different types of malignancies, their advantages, and their limitations. Finally we conclude by looking at the future of biomarkers, their utility in the tumorigenic studies, and the progress towards personalized treatment strategies. PMID:22120674

Nowsheen, Somaira; Aziz, Khaled; Panayiotidis, Mihalis I; Georgakilas, Alexandros G

2011-11-25

328

Genetic modulation in Be-78 and Y Trypanosoma cruzi strains after long-term infection in Beagle dogs revealed by molecular markers.  

PubMed

The genetic profile of Trypanosoma cruzi was evaluated in parasite populations isolated from Beagle dogs experimentally infected with Be-78 and Y strains that present distinct biological and genetic characteristics. Molecular characterization of the isolates obtained 30days and 2years after infection was carried out. For typing MLEE, sequence polymorphisms of the mitochondrial cytochrome oxidase subunit II gene (COII) and RAPD profiles were used. The profiles of MLEE were the same for the parental Be-78 strains as their respective isolates. However, changes of MLEE profile were observed in two T. cruzi isolates from dogs inoculated with Y strain. Changes in the mitochondrial DNA (COII) and RAPD profiles of the Y strain were also observed. The dendogram constructed by UPGMA with RAPD results indicated two major branches. Global data show that the genetic modulation in polyclonal strains during the long-term infection occurred and was strain-dependent. This study still suggests that each host (here each dog) harbors a determinate T. cruzi population that may change or be modulated throughout long-term infection. This might to hinder the observation of correlation between the genetics of T. cruzi and their biological properties and behavior in different host species due to the complexity of the parasite-host interaction in which probably the genetic background of both should be considered. PMID:22554652

Veloso, Vanja Maria; Guedes, Paulo Marcos da Matta; de Lana, Marta; Martins, Helen Rodrigues; Carneiro, Cláudia Martins; da Câmara, Antônia Cláudia Jácome; D'Ávila, Daniella Alchaar; Caldas, Ivo Santana; Galvão, Lúcia Maria da Cunha; Chiari, Egler; Bahia, Maria Terezinha

2012-03-28

329

Using molecular markers to characterize productivity in chinese hamster ovary cell lines.  

PubMed

Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp ) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction. PMID:24146795

Edros, Raihana Z; McDonnell, Susan; Al-Rubeai, Mohamed

2013-10-17

330

The Important Molecular Markers on Chromosome 17 and Their Clinical Impact in Breast Cancer  

PubMed Central

Abnormalities of chromosome 17 are important molecular genetic events in human breast cancers. Several famous oncogenes (HER2, TOP2A and TAU), tumor suppressor genes (p53, BRCA1 and HIC-1) or DNA double-strand break repair gene (RDM1) are located on chromosome 17. We searched the literature on HER2, TOP2A, TAU, RDM1, p53, BRCA1 and HIC-1 on the Pubmed database. The association of genes with chromosome 17, biological functions and potential significance are reviewed. In breast cancer, the polysomy 17 (three or more) is the predominant numerical aberration. HER2 amplification is widely utilized as molecular markers for trastuzumab target treatment. Amplified TOP2A, TAU and RDM1 genes are related to a significant response to anthracycline-based chemotherapy, taxane or cisplatin, respectively. In contrast, p53, BRCA1 and HIC-1 are important tumor suppressor genes related to breast carcinogenesis. This review focused on several crucial molecular markers residing on chromosome 17. The authors consider the somatic aberrations of chromosome 17 and associated genes in breast cancer.

Zhang, Wei; Yu, Yingyan

2011-01-01

331

Using Molecular Markers to Characterize Productivity in Chinese Hamster Ovary Cell Lines  

PubMed Central

Selection of high producing cell lines to produce maximum product concentration is a challenging and time consuming task for the biopharmaceutical industry. The identification of early markers to predict high productivity will significantly reduce the time required for new cell line development. This study identifies candidate determinants of high productivity by profiling the molecular and morphological characteristics of a panel of six Chinese Hamster Ovary (CHO) stable cell lines with varying recombinant monoclonal antibody productivity levels ranging between 2 and 50 pg/cell/day. We examined the correlation between molecular parameters and specific productivity (qp) throughout the growth phase of batch cultures. Results were statistically analyzed using Pearson correlation coefficient. Our study revealed that, overall, heavy chain (HC) mRNA had the strongest association with qp followed by light chain (LC) mRNA, HC intracellular polypeptides, and intracellular antibodies. A significant correlation was also obtained between qp and the following molecular markers: growth rate, biomass, endoplasmic reticulum, and LC polypeptides. However, in these cases, the correlation was not observed at all-time points throughout the growth phase. The repeated sampling throughout culture duration had enabled more accurate predictions of productivity in comparison to performing a single-point measurement. Since the correlation varied from day to day during batch cultivation, single-point measurement was of limited use in making a reliable prediction.

Edros, Raihana Z.; McDonnell, Susan; Al-Rubeai, Mohamed

2013-01-01

332

Molecular Markers of Epithelial-to-Mesenchymal Transition Are Associated with Tumor Aggressiveness in Breast Carcinoma  

PubMed Central

BACKGROUND: Epithelial-to-mesenchymal transition (EMT) is a transient process occurring during developmental stages and carcinogenesis, characterized by phenotypic and molecular alterations, resulting in increased invasive and metastatic capabilities of cancer cells and drug resistance. Moreover, emerging evidence suggests that EMT is associated with increased enrichment of cancer stem-like cells in neoplastic tissues. We interrogated the molecular alterations occurring in breast cancer using proposed EMT markers such as E-cadherin, vimentin, epidermal growth factor receptor (EGFR), platelet-derived growth factor (PDGF) D, and nuclear factor ?B (NF-?B) to decipher their roles in the EMT and breast cancer progression. METHODS: Fifty-seven invasive ductal adenocarcinomas of the breast were assessed for the expression of E-cadherin, vimentin, EGFR, NF-?B, and PDGF-D using immunohistochemical analysis. Tumors were categorized into three groups: A (ER+, and/or PR+, HER-2/neu-), B (ER+, and/or PR+, HER-2/neu+), and C (triple-negative: ER-, PR-, and HER-2/neu-). Immunostained slides were microscopically evaluated and scored using intensity (0, 1+, 2+, and 3+) and percentage of positive cells, and data were statistically analyzed. RESULTS: Membranous E-cadherin was positive in all 57 cases (100%), whereas cytoplasmic E-cadherin was predominantly positive in groups B and C compared with group A (21%, 7%, and 0%, respectively). All group A cases were negative for vimentin and EGFR. There was statistically significant increased expression of vimentin (P < .0002), EGFR (P < .0001), and NF-?B (P < .02) in triple-negative cases when compared with groups A and B. CONCLUSIONS: Vimentin, EGFR, and NF-?B were significantly increased in triple-negative tumors, which is consistent with the aggressiveness of these tumors. These markers could be useful as markers for EMT in breast cancers and may serve as predictive markers for designing customized therapy in the future.

Sethi, Seema; Sarkar, Fazlul H; Ahmed, Quratulain; Bandyopadhyay, Sudeshna; Nahleh, Zeina A; Semaan, Assaad; Sakr, Wael; Munkarah, Adnan; Ali-Fehmi, Rouba

2011-01-01

333

Evaluation of pharmaceuticals and personal care products as water-soluble molecular markers of sewage.  

PubMed

We examined the utility of 13 pharmaceuticals and personal care products (PPCPs) as molecular markers of sewage contamination in riverine, groundwater, and coastal environments. The PPCPs were crotamiton, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid, thymol, triclosan, propyphenazone, carbamazepine, diethyltoluamide, ethenzamide, and caffeine. Measurements in 37 Japanese rivers showed positive correlations of riverine flux of crotamiton (r2 = 0.85), carbamazepine (r2 = 0.84), ibuprofen (r2 = 0.73), and mefenamic acid (r2 = 0.67) with the population in the catchments. In three surveys in the Tamagawa estuary, crotamiton, carbamazepine, and mefenamic acid behaved conservatively across seasons within a salinity range of 0.4-29 per thousand, suggesting their utility as molecular markers in coastal environments. Removal of ketoprofen and naproxen in the estuary was ascribed to photodegradation. Ibuprofen and thymol were removed from estuarine waters in summer by microbial degradation. Triclosan was removed by a combination of microbial degradation, photodegradation, and adsorption. These results were consistent with those of river water incubated for 8 d at 25 degrees C in the dark in order to examine the effects of biodegradation and photodegradation. Crotamiton was detected in groundwater from the Tokyo metropolitan area (12 out of 14 samples), suggesting wastewater leakage from decrepit sewers. Carbamazepine, ketoprofen, and ibuprofen (5/14), caffeine (4/14), and diethyltoluamide (3/14) were also detected in the groundwater, whereas the other carboxylic and phenolic PPCPs were not detected and were thought to be removed during their passage through soil. All the data demonstrated the utility of crotamiton and carbamazepine as conservative markers in freshwater and coastal environments. We recommend combining these conservative markers with labile PPCPs to detect inputs of poorly treated sewage. PMID:18800500

Nakada, Norihide; Kiri, Kentaro; Shinohara, Hiroyuki; Harada, Arata; Kuroda, Keisuke; Takizawa, Satoshi; Takada, Hideshige

2008-09-01

334

Molecular-marker analysis of quantitative traits for growth and development in juvenile apple trees  

Microsoft Academic Search

Random amplified polymorphic DNAs (RAPDs) were used in combination with a double pseudo-testcross mapping strategy to estimate\\u000a the position and effects of quantitative trait loci (QTLs) for traits influencing juvenile tree growth and development in\\u000a two apple cultivars. The mapping population consisted of 172 F1 trees from a cross between the columnar mutant ‘Wijcik McIntosh’ and a standard form disease-resistant

P. J. Conner; S. K. Brown; N. F. Weeden

1998-01-01

335

Cyclin D1, a Novel Molecular Marker of Minimal Residual Disease, in Metastatic Neuroblastoma  

PubMed Central

Accurate monitoring of minimal residual disease (MRD) is critical for the management of metastatic neuroblastoma (NB). We evaluated cyclin D1 (CCND1), a cell-cycle control gene, as a novel MRD marker of NB. Using quantitative reverse transcriptase-polymerase chain reaction, we studied CCND1 expression in 133 solid tumors of different histological types, including 39 NB tumors, and examined its potential clinical utility as an early response marker in the bone marrows before and after treatment of 118 stage 4 patients enrolled after induction chemotherapy in an immunotherapy protocol. Based on 40 normal marrow and peripheral blood samples, a CCND1 transcript value greater than the mean + 2 SD was defined as positive. Sensitivity of this assay was one NB cell in 106 normal mononuclear cells. CCND1 transcript levels were high in NB, breast cancer, and Ewing family tumors. Among the NB patients evaluated, early (2.5 months from protocol entry) marrow response was strongly associated with both progression-free (P = 0.0001) and overall survival (P = 0.0006). CCND1 response remained predictive of survival among a subset of 66 patients who had no histological evidence of marrow disease before immunotherapy. We conclude that CCND1 has potential clinical utility as a novel molecular marker of MRD in the bone marrow of patients with metastatic NB.

Cheung, Irene Y.; Feng, Yi; Vickers, Andrew; Gerald, William; Cheung, Nai-Kong V.

2007-01-01

336

Identification of candidate molecular markers of nasopharyngeal carcinoma by tissue microarray and in situ hybridization.  

PubMed

To scan differentially expressed genes and to identify candidate molecular markers in nasopharyngeal carcinoma (NPC), we analyzed cDNA microarray data by GenMAPP to find specifically expressed genes in NPC and used tissue microarray and in situ hybridization techniques to confirm our microarray results. Our cDNA microarray results showed that TSPAN-1 and DPP10 genes were down-expressed in NPC, and COX7B and RFC2 genes were over-expressed in NPC. Real-time quantitative reverse transcription-PCR and in situ hybridization (ISH) techniques confirmed that TSPAN-1 and DPP10 genes had only 40.72 and 40.70% positive expression in NPC, but had high positive expression in chronic inflammation of nasopharyngeal mucosa (P < 0.01). However, COX7B and RFC2 genes were high positive rate in NPC (84.24 and 64.53%, respectively) than in normal control tissues. The data suggested that TSPAN-1, DPP10, COX7B and RFC2 genes might be the putative molecular markers of NPC. PMID:21057896

Xiong, Shilong; Wang, Qian; Zheng, Lei; Gao, Feng; Li, Junling

2010-11-05

337

Molecular phylogenetics of New Caledonian Diospyros (Ebenaceae) using plastid and nuclear markers.  

PubMed

To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK-matK and trnS-trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9million years ago. The oldest species are around 7million years old and the youngest ones probably much less than 1million years. PMID:23850609

Turner, Barbara; Munzinger, Jérôme; Duangjai, Sutee; Temsch, Eva M; Stockenhuber, Reinhold; Barfuss, Michael H J; Chase, Mark W; Samuel, Rosabelle

2013-07-12

338

Molecular Marker Differences Relate to Developmental Position and Subsets of Mesodiencephalic Dopaminergic Neurons  

PubMed Central

The development of mesodiencephalic dopaminergic (mdDA) neurons located in the substantia nigra compacta (SNc) and ventral tegmental area (VTA) follow a number of stages marked by distinct events. After preparation of the region by signals that provide induction and patterning, several transcription factors have been identified, which are involved in specifying the neuronal fate of these cells. The specific vulnerability of SNc neurons is thought to root in these specific developmental programs. The present study examines the positions of young postmitotic mdDA neurons to relate developmental position to mdDA subset specific markers. MdDA neurons were mapped relative to the neuromeric domains (prosomeres 1-3 (P1-3), midbrain, and hindbrain) as well as the longitudinal subdivisions (floor plate, basal plate, alar plate), as proposed by the prosomeric model. We found that postmitotic mdDA neurons are located mainly in the floorplate domain and very few in slightly more lateral domains. Moreover, mdDA neurons are present along a large proportion of the anterior/posterior axis extending from the midbrain to P3 in the diencephalon. The specific positions relate to some extent to the presence of specific subset markers as Ahd2. In the adult stage more of such subsets specific expressed genes are present and may represent a molecular map defining molecularly distinct groups of mdDA neurons.

Smits, Simone M.; von Oerthel, Lars; Hoekstra, Elisa J.; Burbach, J. Peter H; Smidt, Marten P.

2013-01-01

339

Transcriptome profiling and molecular marker discovery in red pepper, Capsicum annuum L. TF68.  

PubMed

Transcriptome from high throughput sequencing-by-synthesis is a good resource of molecular markers. In this study, we present utility of massively parallel sequencing by synthesis for profiling the transcriptome of red pepper (Capsicum annuum L. TF68) using 454 GS-FLX pyrosequencing. Through the generation of approximately 30.63 megabases (Mb) of expressed sequence tag (EST) data with the average length of 375 base pairs (bp), 9,818 contigs and 23,712 singletons were obtained by raw reads assembly. Using BLAST alignment against NCBI non-redundant and a UniProt protein database, 30% of the tentative consensus sequences were assigned to specific function annotation, while 24% returned alignments of unknown function, leaving up to 46% with no alignment. Functional classification using FunCat revealed that sequences with putative known function were distributed cross 18 categories. All unigenes have an approximately equal distribution on chromosomes by aligning with tomato (Solanum lycopersicum) pseudomolecules. Furthermore, 1,536 high quality single nucleotide discrepancies were discovered using the Bukang mature fruit cDNA collection (dbEST ID: 23667) as a reference. Moreover, 758 simple sequence repeat (SSR) motif loci were mined from 614 contigs, from which 572 primer sets were designed. The SSR motifs corresponded to di- and tri- nucleotide motifs (27.03 and 61.92%, respectively). These molecular markers may be of great value for application in linkage mapping and association mapping research. PMID:21706160

Lu, Fu-Hao; Cho, Myeong-Cheoul; Park, Yong-Jin

2011-06-25

340

Noninvasive Detection and Imaging of Molecular Markers in Live Cardiomyocytes Derived from Human Embryonic Stem Cells  

PubMed Central

Raman microspectroscopy (RMS) was used to detect and image molecular markers specific to cardiomyocytes (CMs) derived from human embryonic stem cells (hESCs). This technique is noninvasive and thus can be used to discriminate individual live CMs within highly heterogeneous cell populations. Principal component analysis (PCA) of the Raman spectra was used to build a classification model for identification of individual CMs. Retrospective immunostaining imaging was used as the gold standard for phenotypic identification of each cell. We were able to discriminate CMs from other phenotypes with >97% specificity and >96% sensitivity, as calculated with the use of cross-validation algorithms (target 100% specificity). A comparison between Raman spectral images corresponding to selected Raman bands identified by the PCA model and immunostaining of the same cells allowed assignment of the Raman spectral markers. We conclude that glycogen is responsible for the discrimination of CMs, whereas myofibril proteins have a lesser contribution. This study demonstrates the potential of RMS for allowing the noninvasive phenotypic identification of hESC progeny. With further development, such label-free optical techniques may enable the separation of high-purity cell populations with mature phenotypes, and provide repeated measurements to monitor time-dependent molecular changes in live hESCs during differentiation in vitro.

Pascut, Flavius C.; Goh, Huey T.; Welch, Nathan; Buttery, Lee D.; Denning, Chris; Notingher, Ioan

2011-01-01

341

Molecular Markers in Patients with Chronic Wounds to Guide Surgical Debridement  

PubMed Central

Chronic wounds, such as venous ulcers, are characterized by physiological impairments manifested by delays in healing, resulting in severe morbidity. Surgical debridement is routinely performed on chronic wounds because it stimulates healing. However, procedures are repeated many times on the same patient because, in contrast to tumor excision, there are no objective biological/molecular markers to guide the extent of debridement. To develop bioassays that can potentially guide surgical debridement, we assessed the pathogenesis of the patients’ wound tissue before and after wound debridement. We obtained biopsies from three patients at two locations, the nonhealing edge (prior to debridement) and the adjacent, nonulcerated skin of the venous ulcers (post debridement), and evaluated their histology, biological response to wounding (migration) and gene expression profile. We found that biopsies from the nonhealing edges exhibit distinct pathogenic morphology (hyperproliferative/hyperkeratotic epidermis; dermal fibrosis; increased procollagen synthesis). Fibroblasts deriving from this location exhibit impaired migration in comparison to the cells from adjacent nonulcerated biopsies, which exhibit normalization of morphology and normal migration capacity. The nonhealing edges have a specific, identifiable, and reproducible gene expression profile. The adjacent nonulcerated biopsies have their own distinctive reproducible gene expression profile, signifying that particular wound areas can be identified by gene expression profiling. We conclude that chronic ulcers contain distinct subpopulations of cells with different capacity to heal and that gene expression profiling can be utilized to identify them. In the future, molecular markers will be developed to identify the nonimpaired tissue, thereby making surgical debridement more accurate and more efficacious.

Brem, Harold; Stojadinovic, Olivera; Diegelmann, Robert F; Entero, Hyacinth; Lee, Brian; Pastar, Irena; Golinko, Michael; Rosenberg, Harvey; Tomic-Canic, Marjana

2007-01-01

342

Application of molecular methods to classification and identification of bacteria of the genus Bifidobacterium  

Microsoft Academic Search

The molecular methods currently used in the classification and identification of bifidobacteria are reviewed. The sequencing\\u000a of the 16S rRNA gene and some other genes considered to be phylogenetic markers is a universal and effective approach for\\u000a taxonomic characterization of members of the genus Bifidobacterium and to reliable identification of new isolates. Various techniques of obtaining DNA fingerprints (PFGE, RAPD,

A. V. Sidarenka; G. I. Novik; V. N. Akimov

2008-01-01

343

At3g08030 transcript: a molecular marker of seed ageing  

PubMed Central

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.

Garza-Caligaris, Luz Elena; Avendano-Vazquez, Aida Odette; Alvarado-Lopez, Sandra; Zuniga-Sanchez, Esther; Orozco-Segovia, Alma; Perez-Ruiz, Rigoberto V.; Gamboa-deBuen, Alicia

2012-01-01

344

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

SciTech Connect

Jurassic siltstone samples were collected, on a centimeter 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 (R[sub 0] 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[sub 20]/(C[sub 20] + C[sub 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 product-reactant relationships (chiral isomerization, aromatization or side-chain cracking reactions) operating solely in the free saturated or aromatic hydrocarbon structures. Release/formation from macromolecular and/or functionalized moieties (hydrocarbon or non-hydrocarbon) followed by compound loss provide an alternative paradigm in all four cases in this particularly thermal regime. Direct chiral isomerization in the free sterane or homohopane cannot, however, be completely ruled out as a contributor to an admixture of processes. Similarly, aromatization in the free hydrocarbon fraction may account for a proportion of the triaromatic steroids. 31 refs., 7 figs.

Bishop, A.N.; Abbott, G.D. (The University, Newcastle upon Tyne (United Kingdom))

1993-08-01

345

Status of potential PfATP6 molecular markers for artemisinin resistance in Suriname  

PubMed Central

Background Polymorphisms within the PfATP6 gene have been indicated as potential molecular markers for artemisinin efficacy. Since 2004, the use of artemisinin combination therapy (ACT) was introduced as first-line treatment of the uncomplicated malaria cases in Suriname. The aim of this research was to determine changes in Suriname in the status of the polymorphic markers in the PfATP6 gene before and after the adoption of the ACT-regimen, particularly of the S769N mutation, which was reported to be associated with in vitro Artemether resistance in the neighboring country French Guiana. Methods The PfATP6 gene from Plasmodium falciparum parasites in Suriname was investigated in 28 samples using PCR amplification and restriction enzyme analysis, to assess and determine the prevalence of potentially interesting single nucleotide polymorphisms. The polymorphisms [L263E; A623E; S769N], which may be associated with the artemisinin resistant phenotype were characterized in parasites from three endemic regions before and after the adoption of the ACT-regimen. In addition, the status of these molecular markers was compared in paired P. falciparum isolates from patients with recurring malaria after controlled ACT. Results All the investigated samples exhibit the wild-type genotype at all three positions; L263, A623, S769. Conclusion All investigated isolates before and after the adoption of the ACT-regimen and independent of endemic region harbored the wild-type genotype for the three investigated polymorphisms. The study revealed that decreased artemisinin susceptibility could occur independent from PfATP6 mutations, challenging the assumption that artemisinin resistance is associated with these mutations in the PfATP6 gene.

2012-01-01

346

Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone.  

PubMed

Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization-related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows (Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD-based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter- and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered. PMID:10652072

Hardig, T M; Brunsfeld, S J; Fritz, R S; Morgan, M; Orians, C M

2000-01-01

347

Comparison of anonymous and targeted molecular markers for the estimation of genetic diversity in ex situ conserved Lactuca.  

PubMed

The anonymous marker systems microsatellites (simple sequence repeats), amplified fragment length polymorphisms and sequence-specific amplified polymorphisms were compared with the targeted marker systems sequence-related amplified polymorphisms, target region amplification polymorphisms and nucleotide binding site profiling for their ability to describe the genetic diversity in a selected set of 80 Lactuca accessions. The accessions were also described morphologically, and all characterisation methods were evaluated against the genetic diversity assessed by a panel of three crop experts. The morphological data showed a low level of association with the molecular data, and did not display a consistently better relationship with the experts' assessments in comparison with the molecular data. In general, the diversity described by the targeted molecular markers did not differ markedly from that of the anonymous markers, resulting in only slight differences in performance when related to the expert-based assessments. It was argued that markers targeted to specific gene sequences may still behave as anonymous markers and that the type of marker system used is irrelevant when at low taxonomic levels a clear genetic structure is absent due to intensive breeding activities. PMID:19697006

van Treuren, R; van Hintum, Th J L

2009-08-21

348

Microevolution in the sicilian shrew crocidura sicula (Mammalia, Soricidae) tested by RAPD?PCR fingerprinting  

Microsoft Academic Search

Genetic variation in samples of the endemic Crocidura sicula living in Sicily and in two surrounding small islands, Marettimo and Ustica, was analysed by Random Amplified Polymorphic DNA fingerprinting (RAPD) and compared to morphometrics and external phenotypes. Molecular variation in the random sample of 99 DNA fragments of the Ustica shrews, showing.a melanic fur and a size?shape variation in skull

Maurizio Sarà; Cinzia Aiuto; Goffredo Cognetti

1997-01-01

349

[Use of molecular methods in food microbiology with the example of probiotic use of lactobacilli].  

PubMed

The aim of molecular methods in food microbiology is the identification or strain specific differentiation of microorganisms. Identification methods include besides taxonomic purposes also the detection of virulence genes or resistance markers. Strain specific differentiation is used for epidemiological investigations or the quality control of technologically used bacteria. Probiotic strains of the Lactobacillus acidophilus-group were investigated with different molecular methods: for identification proteinfingerprinting and RAPD-PCR (Random Amplified Polymorphic DNA-PCR) were applied, for strain specific differentiation pulsed field gel electrophoresis (PFGE) and again RAPD-PCR were used. The molecular methods applied should be chosen depending on the objective (identification, differentiation) and with respect to the organism to be tested. In case of probiotic lactic acid bacteria like the L. acidophilus-group proteinfingerprinting has proved to be successful for identification and with some limitation also RAPD-PCR. For differentiation PFGE is suitable as well as RAPD-PCR. Those methods differ substantially in their work load and in personal requirements, and show different power of discrimination and reproducibility within and between laboratories. This should be considered while choosing the appropriate method. PMID:14655631

Klein, Günter

350

Molecular markers of anti-malarial drug resistance in Lahj Governorate, Yemen: baseline data and implications  

PubMed Central

Background This is an investigation of anti-malarial molecular markers coupled with a therapeutic efficacy test of chloroquine (CQ) against falciparum malaria in an area of unstable malaria in Lahj Governorate, Yemen. The study was aimed at assessment of therapeutic response to CQ and elucidation of baseline information on molecular markers for Plasmodium falciparum resistance against CQ and sulphadoxine/pyrimethamine (SP). Methods Between 2002 and 2003 the field test was conducted according to the standard WHO protocol to evaluate the therapeutic efficacy of CQ in 124 patients with falciparum malaria in an endemic area in Lahj Governorate in Yemen. Blood samples collected during this study were analysed for P. falciparum chloroquine resistance transporter gene (pfcrt)-76 polymorphisms, mutation pfcrt-S163R and the antifolate resistance-associated mutations dihydrofolate reductase (dhfr)-C59R and dihydropteroate synthase (dhps)-K540E. Direct DNA sequencing of the pfcrt gene from three representative field samples was carried out after DNA amplification of the 13 exons of the pfcrt gene. Results Treatment failure was detected in 61% of the 122 cases that completed the 14-day follow-up. The prevalence of mutant pfcrt T76 was 98% in 112 amplified pre-treatment samples. The presence of pfcrt T76 was poorly predictive of in vivo CQ resistance (PPV = 61.8%, 95% CI = 52.7-70.9). The prevalence of dhfr Arg-59 mutation in 99 amplified samples was 5%, while the dhps Glu-540 was not detected in any of 119 amplified samples. Sequencing the pfcrt gene confirmed that Yemeni CQ resistant P. falciparum carry the old world (Asian and African) CQ resistant haplotype CVIETSESI at positions 72,73,74,75,76,220,271, 326 and 371. Conclusion This is the first study to report baseline information on the characteristics and implications of anti-malarial drug resistance markers in Yemen. It is also the first report of the haplotype associated with CQR P. falciparum parasites from Yemen. Mutant pfcrtT76 is highly prevalent but it is a poor predictor of treatment failure in the study population. The prevalence of mutation dhfrArg59 is suggestive of emerging resistance to SP, which is currently a component of the recommended combination treatment of falciparum malaria in Yemen. More studies on these markers are recommended for surveillance of resistance in the study area.

2011-01-01

351

Development of SCAR markers and a semi-selective medium for the quantification of strains Ach 1-1 and 1113-5, two Aureobasidium pullulans potential biocontrol agents  

Microsoft Academic Search

Aureobasidium pullulans strains Ach 1-1 and 1113-5 are two effective biocontrol agents against Botrytis cinerea and Penicillium expansum on stored apples. In the present work, a monitoring system allowing their identification and quantification was developed. The methodology used consisted of the development of both molecular markers and a semi-selective medium. The random amplified polymorphic DNA (RAPD) technique was applied to

Adil El Hamouchi; Mohammed Bajji; Damien Friel; Bouchra Najimi; El Hassan Achbani; Samir El Jaafari; Alain Durieux; M. Haïssam Jijakli

2008-01-01

352

Molecular markers for the detection of the wheat leaf rust resistance gene Lr10 in diverse genetic backgrounds  

Microsoft Academic Search

We recently showed that the Lr10 wheat leaf rust resistance gene cosegregated with the candidate resistance gene Lrk10 which encodes a putative receptor-like kinase. The aim of this study was to develop Lrk10-derived molecular markers for the detection of the Lr10 gene in breeding material. Different subfragments of Lrk10 were tested as RFLP markers for the Lr10 resistance gene. The

Gabriele Schachermayr; Catherine Feuillet; Beat Keller

1997-01-01

353

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea ( Cicer arietinum L.)  

Microsoft Academic Search

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single\\u000a nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based\\u000a markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume\\u000a crop of India. For SNP discovery

Neha Gujaria; Ashish Kumar; Preeti Dauthal; Anuja Dubey; Pavana Hiremath; A. Bhanu Prakash; Andrew Farmer; Mangla Bhide; Trushar Shah; Pooran M. Gaur; Hari D. Upadhyaya; Sabhyata Bhatia; Douglas R. Cook; Greg D. May; Rajeev K. Varshney

2011-01-01

354

Prostate cancer molecular markers GSTP1 and hTERT in expressed prostatic secretions as predictors of biopsy results  

Microsoft Academic Search

ObjectivesTo develop noninvasive diagnostic tools for the early detection of prostate cancer (PCa). Current screening for PCa lacks sensitivity and specificity. Two molecular markers, telomerase activity and aberrant methylation of the glutathione S-transferase P1 (GSTP1) promoter, are found in more than 90% of PCa specimens. Additionally, these markers can be detected in bodily fluids such as urine and postprostatic massage

Laura E. Crocitto; Darlynn Korns; Leo Kretzner; Taras Shevchuk; Sarah L. Blair; Timothy G. Wilson; Soroush A. Ramin; Mark H. Kawachi; Steven S. Smith

2004-01-01

355

Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava  

Microsoft Academic Search

The development of PCR-based, easily automated molecular genetic markers, such as SSR markers, are required for realistic\\u000a cost-effective marker-assisted selection schemes. This paper describes the development and characterization of 172 new SSR\\u000a markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also\\u000a reported. Two similar enrichment methods were

P. Stephenson; K. Edwards; S. Melzer; J. Nkumbira; U. Gullberg; K. Apel; M. Gale; J. Tohme; M. Fregene

2001-01-01

356

Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers.  

PubMed

Soybean mutant lines that differ in 11S glycinin and 7S ?-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A(4) null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A(1a)B(2), A(2)B(1a), A(1b) B(1b), and A(3)B(4) subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A(4) peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A(4) (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection. PMID:21959908

Jegadeesan, Souframanien; Yu, Kangfu; Woodrow, Lorna; Wang, Yi; Shi, Chun; Poysa, Vaino

2011-09-29

357

2007 EORTC-NCI-ASCO Annual Meeting: Molecular Markers in Cancer  

PubMed Central

The recent EORTC-NCI-ASCO Annual Meeting on ‘Molecular Markers in Cancer’ was held on 15–17 November 2007 in Brussels, Belgium. It was the largest meeting to date and marked the first year in which the American Association of Clinical Oncology (ASCO) joined in the efforts of the European Organisation for Research and Treatment of Cancer (EORTC) and the National Cancer Institute (NCI) in organizing this annual event. More than 300 clinicians, pathologists, laboratory scientists and representatives from regulatory agencies and the pharmaceutical industry came together for three days of intense discussion, debate and reflection on the latest biomarker therapeutic discoveries, strategies and clinical applications. The poster discussion sessions featured 79 research abstracts. The three most outstanding abstracts, all authored by young female researchers, were selected for presentation during the main meeting sessions. Highlights of each scientific session are presented.

Lukan, C

2008-01-01

358

Biological (molecular and cellular) markers of toxicity. Final report, September 15, 1988--September 14, 1991  

SciTech Connect

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.

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

1991-12-15

359

Molecular imprinted nanoelectrodes for ultra sensitive detection of ovarian cancer marker.  

PubMed

The relentless discovery of cancer biomarkers demands improved methods for their detection. In this work, we developed protein imprinted polymer on three-dimensional gold nanoelectrode ensemble (GNEE) to detect epithelial ovarian cancer antigen-125 (CA 125), a protein biomarker associated with ovarian cancer. CA 125 is the standard tumor marker used to follow women during or after treatment for epithelial ovarian cancer. The template protein CA 125 was initially incorporated into the thin-film coating and, upon extraction of protein from the accessible surfaces on the thin film, imprints for CA 125 were formed. The fabrication and analysis of the CA 125 imprinted GNEE was done by using cyclic voltammetry (CV), differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques. The surfaces of the very thin, protein imprinted sites on GNEE are utilized for immunospecific capture of CA 125 molecules, and the mass of bound on the electrode surface can be detected as a reduction in the faradic current from the redox marker. Under optimal conditions, the developed sensor showed good increments at the studied concentration range of 0.5-400 U mL(-1). The lowest detection limit was found to be 0.5 U mL(-1). Spiked human blood serum and unknown real serum samples were analyzed. The presence of non-specific proteins in the serum did not significantly affect the sensitivity of our assay. Molecular imprinting using synthetic polymers and nanomaterials provides an alternative approach to the trace detection of biomarker proteins. PMID:22265879

Viswanathan, Subramanian; Rani, Chinnakkaruppanan; Ribeiro, Susana; Delerue-Matos, Cristina

2012-01-05

360

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

SciTech Connect

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.

Rogge, W.F.; Cass, G.R. (California Inst. of Tech., Pasadena, CA (United States)); Hildemann, L.M. (Stanford Univ., CA (United States). Dept. of Civil Engineering); Mazurek, M.A. (Brookhaven National Lab., Upton, NY (United States)); Simoneit, B.R.T. (College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group)

1992-07-01

361

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

SciTech Connect

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.

Rogge, W.F.; Cass, G.R. [California Inst. of Tech., Pasadena, CA (United States); Hildemann, L.M. [Stanford Univ., CA (United States). Dept. of Civil Engineering; Mazurek, M.A. [Brookhaven National Lab., Upton, NY (United States); Simoneit, B.R.T. [College of Oceanography, Oregon State Univ., Corvallis, OR (United States) Environmental Geochemistry Group

1992-07-01

362

Photosynthetic and molecular markers of CO?-mediated photosynthetic downregulation in nodulated alfalfa.  

PubMed

Elevated CO? 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 CO? acclimation. In order to investigate the most sensitive photosynthetic and molecular markers of CO? acclimation, the effects of elevated CO?, 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 N?-fixation under higher temperatures. Photosynthesis measured at growth CO? 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

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

2013-06-24

363

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

PubMed

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

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

2004-09-01

364

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

NASA Astrophysics Data System (ADS)

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.

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

2005-12-01

365

Molecular markers in patients with chronic wounds to guide surgical debridement.  

PubMed

Chronic wounds, such as venous ulcers, are characterized by physiological impairments manifested by delays in healing, resulting in severe morbidity. Surgical debridement is routinely performed on chronic wounds because it stimulates healing. However, procedures are repeated many times on the same patient because, in contrast to tumor excision, there are no objective biological/molecular markers to guide the extent of debridement. To develop bioassays that can potentially guide surgical debridement, we assessed the pathogenesis of the patients' wound tissue before and after wound debridement. We obtained biopsies from three patients at two locations, the nonhealing edge (prior to debridement) and the adjacent, nonulcerated skin of the venous ulcers (post debridement), and evaluated their histology, biological response to wounding (migration) and gene expression profile. We found that biopsies from the nonhealing edges exhibit distinct pathogenic morphology (hyperproliferative/hyperkeratotic epidermis; dermal fibrosis; increased procollagen synthesis). Fibroblasts deriving from this location exhibit impaired migration in comparison to the cells from adjacent nonulcerated biopsies, which exhibit normalization of morphology and normal migration capacity. The nonhealing edges have a specific, identifiable, and reproducible gene expression profile. The adjacent nonulcerated biopsies have their own distinctive reproducible gene expression profile, signifying that particular wound areas can be identified by gene expression profiling. We conclude that chronic ulcers contain distinct subpopulations of cells with different capacity to heal and that gene expression profiling can be utilized to identify them. In the future, molecular markers will be developed to identify the nonimpaired tissue, thereby making surgical debridement more accurate and more efficacious. PMID:17515955

Brem, Harold; Stojadinovic, Olivera; Diegelmann, Robert F; Entero, Hyacinth; Lee, Brian; Pastar, Irena; Golinko, Michael; Rosenberg, Harvey; Tomic-Canic, Marjana

366

A Randomly Amplified Polymorphic DNA Marker Specific for the Bacillus cereus Group Is Diagnostic for Bacillus anthracis  

Microsoft Academic Search

Aiming to develop a DNA marker specific for Bacillus anthracis and able to discriminate this species from Bacillus cereus, Bacillus thuringiensis, and Bacillus mycoides, we applied the randomly amplified polymorphic DNA (RAPD) fingerprinting technique to a collection of 101 strains of the genus Bacillus, including 61 strains of the B. cereus group. An 838-bp RAPD marker (SG-850) specific for B.

DANIELE DAFFONCHIO; SARA BORIN; GIUSEPPE FROVA; ROMINA GALLO; ELENA MORI; RENATO FANI; CLAUDIA SORLINI

1999-01-01

367

A comparison of RAPD and isozyme analyses for determining the genetic relationships among Avena sterilis L. accessions  

Microsoft Academic Search

Isozyme analysis is a valuable tool for determining genetic relationships among breeding lines and populations. The recently developed DNA technologies which can assay a greater proportion of the plant genome are providing a plentiful array of additional genomic markers. The objective of this research was to compare random amplified polymorphic DNA (RAPD) versus isozyme-based estimation of relationships among 24 accessions

M. Heun; J. P. Murphy; T. D. Phillips

1994-01-01

368

RAPD-based genetic linkage map of blueberry derived from a cross between diploid species ( Vaccinium darrowi and V. elliottii )  

Microsoft Academic Search

An initial genetic linkage map for blueberry has been constructed from over 70 random amplified polymorphic DNA (RAPD) markers that segregated 1:1 in a testcross population of 38 plants. The mapping population was derived from a cross between two diploid blueberry plants: the F1 interspecific hybrid (Vaccinium darrowi Camp x V. elliottii Chapm.) and another V. darrowi plant. The map

L. J. Rowland; A. Levi

1994-01-01

369

Detection of genetic diversity using RAPD-PCR and sugar analysis in watermelon [ Citrullus lanantus (Thunb.) Mansf.] germplasm  

Microsoft Academic Search

RAPD (random amplified polymorphic DNA) markers generated by 15 arbitrary decamers were used to determine the frequency of DNA polymorphism in 39 watermelon [Citrullus lanantus (Thunb.) Mansf.] germplasms. Of the 15 primers tested, all except 1 (primer 275) directed the amplification of polymorphic products. A total of 162 amplification products were generated across all 39 genotypes. Among the 162 fragments,

S. J. Lee; J. S. Shin; K. W. Park; Y. P. Hong

1996-01-01

370

Development of SRAP, SNP and multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L.  

PubMed

Seed coat color inheritance in B. rapa was studied in F(1), F(2), F(3), and BC(1) progenies from a cross of a Canadian brown-seeded variety 'SPAN' and a Bangladeshi yellow sarson variety 'BARI-6'. A pollen effect was found when the yellow sarson line was used as the maternal parent. Seed coat color segregated into brown, yellow-brown and bright yellow classes. Segregation was under digenic control where the brown or yellow-brown color was dominant over bright yellow seed coat color. A sequence related amplified polymorphism (SRAP) marker linked closely to a major seed coat color gene (Br1/br1) was developed. This dominant SRAP molecular marker was successfully converted into single nucleotide polymorphism (SNP) markers and sequence characterized amplification region (SCAR) markers after the extended flanking sequence of the SRAP was obtained with chromosome walking. In total, 24 SNPs were identified with more than 2-kb sequence. A 12-bp deletion allowed the development of a SCAR marker linked closely to the Br1 gene. Using the five-fluorescence dye set supplied by ABI, four labeled M13 primers were integrated with different SCAR primers to increase the throughput of SCAR marker detection. Using multiplexed SCAR markers targeting insertions and deletions in a genome shows great potential for marker assisted selection in plant breeding. PMID:17846742

Rahman, Mukhlesur; McVetty, Peter B E; Li, Genyi

2007-09-05

371

Relationships among some cornelian cherry genotypes ( Cornus mas L.) based on RAPD analysis  

Microsoft Academic Search

Turkey is an important producer of cornelian cherries (Cornus mas L.), especially in northern Anatolia. Seed propagation and long-term human selection has given rise to a great diversity\\u000a of trees. Twenty-six cornelian cherry genotypes (CC1–CC26) from the Coruh Valley in northern Anatolia were evaluated for genetic\\u000a relationships by using Randomly Amplified Polymorphic DNA (RAPD) markers, based on 56 decamer random

Sezai Ercisli; Emine Orhan; Ahmet Esitken; Nalan Yildirim; Guleray Agar

2008-01-01

372

Determination of relatedness and geographical movements of Pistacia vera (Pistachio; Anacardiaceae) germplasm by RAPD analysis  

Microsoft Academic Search

The pistachio tree (Pistacia vera) has long been cultivated in south-central Asia and throughout the Mediterranean region of southern Europe, north Africa\\u000a and the Middle East. We examined genetic diversity and patterns of relatedness amongfifteen P. vera cultivars, representing\\u000a germplasm originating from throughout this range, by using Random Amplified Polymorphic DNA (RAPD) markers. The resulting\\u000a data were used to construct

J. I. Hormaza; L. Dollo; V. S. Polito

1994-01-01

373

Nicotine alters the expression of molecular markers of endocrine disruption in zebrafish.  

PubMed

Nicotine, a drug of abuse, has been reported to have many adverse effects on the developing nervous system. In rodents, chronic nicotine exposure inhibits estrogen-mediated neuroprotection against cerebral ischemia in females suggesting that nicotine could disrupt endocrine targets. Zebrafish have been used as a model system for examining mechanisms underlying nicotinic effects on neuronal development. Here, using zebrafish embryos, we demonstrate that nicotine alters the expression of the validated endocrine disruption (ED) biomarkers, vitellogenin (vtg 1 and vtg 2) and cytochrome p450 aromatase (cyp19a1a and cyp19a1b) at the transcriptional level. Increased expression of three of these molecular markers (vtg 1, vtg 2 and cyp19a1b) in response to 17?-estradiol (E2) was more pronounced in 48hpf (hours post-fertilization) embryos than in the 24hpf embryos. While 24hpf embryos were non-responsive in this regard to 25?M nicotine, a similar exposure of the 48hpf embryos for 24h significantly down-regulated the expression of all four ED biomarker genes indicating that nicotine's anti-estrogenic effects are detectable in the 48hpf zebrafish embryos. These results provide direct molecular evidence that nicotine is an endocrine disruptor in zebrafish. PMID:22922325

Kanungo, Jyotshna; Cuevas, Elvis; Guo, Xiaoqing; Lopez, Aida G; Ramirez-Lee, Manuel A; Trickler, William; Paule, Merle G; Ali, Syed F

2012-08-24

374

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

PubMed

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

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

375

Leishmania AFLP: paving the way towards improved molecular assays and markers of diversity.  

PubMed

Diversity, phylogenetic, and population genetic studies of the genus Leishmania, causative agent of leishmaniasis, nowadays generally involve multilocus microsatellite and multilocus sequence typing. Even though these are well established and useful applications, amplified fragment length polymorphisms (AFLP) can provide complementary information. In addition, as the technique essentially probes the entire genome at random, without prior sequence knowledge, it is ideally suited as a screening tool for molecular markers linked with biological and clinical traits. We developed an AFLP protocol adapted to the Leishmania genome, tested its repeatability, and validated it on a panel of samples from the Leishmania donovani complex previously analyzed by multiple molecular tests. The technique proved highly reproducible, and showed that genetic relationships between L. donovani strains generally reflect geographic distance. Four main groups were identified: Leishmania infantum, African L. donovani, Indian L. donovani, and a mixed group consisting of L. donovani from India and Africa. Results were highly congruent with previous analyses on essentially the same sample set, indicating that the developed assay produces trustworthy data. This opens possibilities for application in studies of speciation and population dynamics. Moreover, it allows random screening of the entire Leishmania genome for linkage with biological and clinical parasite properties, such as fitness, drug resistance, and disease profile. PMID:21439405

Odiwuor, Samwel; Vuylsteke, Marnik; De Doncker, Simonne; Maes, Ilse; Mbuchi, Margaret; Dujardin, Jean-Claude; Van der Auwera, Gert

2011-03-23

376

Molecular markers associated with outcome and metastasis in human pancreatic cancer  

PubMed Central

Background Pancreatic ductal adenocarcinoma (PDAC) is a heterogeneous cancer in which differences in survival rates might be related to a variety in gene expression profiles. Although the molecular biology of PDAC begins to be revealed, genes or pathways that specifically drive tumour progression or metastasis are not well understood. Methods We performed microarray analyses on whole-tumour samples of 2 human PDAC subpopulations with similar clinicopathological features, but extremely distinct survival rates after potentially curative surgery, i.e. good outcome (OS and DFS?>?50?months, n?=?7) versus bad outcome (OS?molecular markers in pancreatic cancer as their expression seems to be related with prognosis.

2012-01-01

377

Development of specific sequence-characterized amplified region markers for detecting Histoplasma capsulatum in clinical and environmental samples.  

PubMed

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, 1281-1283(220) and 1281-1283(230). 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 1281-1283(220) and 1281-1283(230) 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 1281-1283(220) SCAR marker was the most specific and detected the pathogen in all samples tested. In contrast, the 1281-1283(230) 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 1281-1283(220) marker can be used to detect and identify H. capsulatum in samples from different sources. PMID:22189121

Frías De León, María Guadalupe; Arenas López, Gabina; Taylor, Maria Lucia; Acosta Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2011-12-21

378

Development of Specific Sequence-Characterized Amplified Region Markers for Detecting Histoplasma capsulatum in Clinical and Environmental Samples  

PubMed Central

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.

Frias De Leon, Maria Guadalupe; Arenas Lopez, Gabina; Taylor, Maria Lucia; Acosta Altamirano, Gustavo

2012-01-01

379

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

PubMed Central

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.

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

2001-01-01

380

Prognostic molecular markers for planning adjuvant chemotherapy trials in Dukes' B colorectal cancer patients: how much evidence is enough?  

Microsoft Academic Search

The benefit of postoperative adjuvant chemotherapy in patients with Dukes' B colorectal cancer is still uncertain and its routine use is not recommended. Prognostic biomarkers may be useful for identifying high-risk patients with resected, node-negative disease, and this stratification may represent an innovative strategy for designing adjuvant chemotherapy trials. Featured prognostic molecular markers can be divided into the following categor-

F. Graziano; S. Cascinu

2003-01-01

381

Colorectal carcinomas with high microsatellite instability: Defining a distinct immunologic and molecular entity with respect to prognostic markers  

Microsoft Academic Search

Molecular analysis of hereditary nonpolyposis colorectal carcinomas (HNPCC) has identified DNA mismatch repair deficiencies with resulting microsatellite instability (MSI) as a pathway of carcinogenesis that appears to be relevant for prognosis, treatment, and possibly prevention. In this study, expression of cell cycle proteins and other known prognostic markers is correlated with the microsatellite status of colorectal cancers (CRC). One hundred

Tina Bocker Edmonston; Kimberly H. Cuesta; Susan Burkholder; Alan Barusevicius; Deborah Rose; Albert J. Kovatich; Bruce Boman; Robert Fry; Richard Fishel; Juan P. Palazzo

2000-01-01

382

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae  

Microsoft Academic Search

BACKGROUND: Oncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution. RESULTS: The complete chloroplast genome of the economically important Oncidium variety Onc. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain

Fu-Hui Wu; Ming-Tsair Chan; De-Chih Liao; Chen-Tran Hsu; Yi-Wei Lee; Henry Daniell; Melvin R Duvall; Choun-Sea Lin

2010-01-01

383

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...

384

In search of the Kumamoto oyster Crassostrea sikamea (Amemiya, 1928) based on molecular markers: is the natural resource at stake?  

Microsoft Academic Search

A cornerstone in conserving wildlife is to resolve taxonomic uncertainties over organisms so that conservationists can define\\u000a the entity that should be conserved. This is the case for two closely related Crassostrea oysters inhabiting the Ariake Sea (Kyushu, Japan) in sympatry, the kumamoto oyster C. sikamea and Pacific oyster C. gigas, where molecular markers have shed light on their taxonomic

Masashi Sekino

2009-01-01

385

MOLECULAR MAPPING OF HYBRID NECROSIS GENES NE1 AND NE2 IN HEXAPLOID WHEAT USING MICROSATELLITE MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Hybrid necrosis is the gradual pre-mature death of leaves or plants in certain F1 hybrids of wheat, and it is caused by the interaction of two dominant complementary genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. To date, molecular markers linked to these genes have not been...

386

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...

387

The estimation of genetic relationships using molecular markers and their efficiency in estimating heritability in natural populations  

PubMed Central

Molecular marker data collected from natural populations allows information on genetic relationships to be established without referencing an exact pedigree. Numerous methods have been developed to exploit the marker data. These fall into two main categories: method of moment estimators and likelihood estimators. Method of moment estimators are essentially unbiased, but utilise weighting schemes that are only optimal if the analysed pair is unrelated. Thus, they differ in their efficiency at estimating parameters for different relationship categories. Likelihood estimators show smaller mean squared errors but are much more biased. Both types of estimator have been used in variance component analysis to estimate heritability. All marker-based heritability estimators require that adequate levels of the true relationship be present in the population of interest and that adequate amounts of informative marker data are available. I review the different approaches to relationship estimation, with particular attention to optimizing the use of this relationship information in subsequent variance component estimation.

Thomas, Stuart C

2005-01-01

388

Laboratory studies of oxidation of primary emissions: Oxidation of organic molecular markers and secondary organic aerosol production  

NASA Astrophysics Data System (ADS)

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 str

Weitkamp, Emily A.

389

Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs.  

PubMed

Buffalograss [ Buchloe dactyloides (Nutt.) Englem.] is the only native grass that is being used extensively as a turfgrass in the Great Plains region. Its low-growth habit, drought resistance, and low-maintenance requirement make it attractive as a turfgrass species. Our objective was to obtain an overview on the genetic relatedness among and within seeded and vegetative biotype buffalograsses using inter-simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPDs), sequence-related amplified polymorphisms (SRAPs), and simple sequence repeats (SSRs) markers that were derived from related species (maize, pearl millet, sorghum, and sugarcane). Twenty individuals per cultivar were genotyped using 30 markers from each marker system. All buffalograss cultivars were uniquely fingerprinted by all four marker systems. Mean genetic similarities were estimated at 0.52, 0.51, 0.62, and 0.57 using SSRs, ISSRs, SRAPs, and RAPDs, respectively. Two main clusters separating the seeded-biotype from the vegetative-biotype cultivars were produced using UPGMA analysis. Further subgroupings were unequivocal. The Mantel test resulted in a very good fit (SRAP=0.92, ISSR=0.90) to good fit (RAPD=0.86, SSR=0.88) of cophenetic values. Comparing the four marker systems to each other, RAPD and SRAP similarity indices were highly correlated ( r=0.73), while Spearman's rank correlation coefficient between RAPDs and SSRs was r=0.24 and between ISSRs and SSRs was r=0.66. A genotype-assignment analytical approach might be useful for cultivar identification and property rights protection. Polymorphic SRAPs were abundant and demonstrated genetic diversity among closely related cultivars. PMID:15024466

Budak, H; Shearman, R C; Parmaksiz, I; Dweikat, I

2004-03-16

390

Genetic analysis of extended life span in Drosophila melanogaster I. RAPD screen for genetic divergence between selected and control lines  

Microsoft Academic Search

Using lines selected for long life by Luckinbill and his co-workers, we screened two selected and two control lines for allelic\\u000a frequency differences at 1200 randomly chosen RAPD marker loci. Twenty-three marker loci showed frequency differences in excess\\u000a of 80%, and five were greater than 90%. Age-specific effects of the five most differentiated loci were estimated by collecting\\u000a complete survival

James W. Curtsinger; Hank H. Fukui; Amy S. Resler; Kristi Kelly; Aziz A. Khazaeli

1998-01-01

391

Effects of ibuprofen on molecular markers of cartilage and synovium turnover in patients with knee osteoarthritis  

PubMed Central

Objective: The aim of this study was to evaluate the effect of ibuprofen on the urinary excretion of C-terminal crosslinking telopeptide of type II collagen (CTX-II) and urinary glucosyl galactosyl pyridinoline (Glc-Gal-PYD), two new molecular markers of cartilage and synovial tissue metabolism, respectively, in patients with knee osteoarthritis (OA). Methods: We studied 201 patients with knee pain and radiographic evidence of knee OA who were on treatment with non-steroidal anti-inflammatory drugs (NSAIDs) prior to study initiation. After an initial screening visit, patients were withdrawn from their pre-study NSAID and, following a flare of their OA symptoms, were randomised to ibuprofen (2400 mg/day) or placebo. Urinary CTX-II and Glc-Gal-PYD levels were measured at time of randomisation (baseline) and after 4–6 weeks of treatment. Results: After 4 to 6 weeks, urinary CTX-II (+17%, p = 0.023) and Glc-Gal-PYD (+10%, p = 0.020) increased significantly from baseline in the placebo group whereas marginal or no increase was observed in the ibuprofen group (CTX-II +2%, NS and Glc-Gal-PYD +4%, p = 0.045). For urinary CTX-II, the difference in the change from baseline between placebo and ibuprofen treated groups was significant (13%, p = 0.017). At baseline, urinary levels of CTX-II and Glc-Gal-PYD were higher in patients with knee swelling (n = 127) than in those without (n = 74) (p<0.02 for both markers). When patients were stratified according to presence or absence of knee swelling at baseline, the increases over 4–6 weeks of urinary CTX-II and Glc-Gal-PYD in the placebo group were restricted to patients with knee swelling (+22% from baseline, p = 0.001 and +12%, p = 0.011, for urinary CTX-II and Glc-Gal-PYD respectively). In patients with knee swelling who were treated with ibuprofen this increase was not observed and the difference from placebo was significant for urinary CTX-II (p = 0.014). Conclusion: In patients with a flare of knee OA, specifically in patients with evidence of joint inflammation documented by knee swelling, there was a significant increase in markers reflecting cartilage and synovium metabolism that could partly be prevented by high doses of ibuprofen. These data suggest that patients with a flare of knee OA are characterised by increased cartilage and synovial tissue degradation, which may be partly prevented by high doses of NSAIDs.

Gineyts, E; Mo, J; Ko, A; Henriksen, D; Curtis, S; Gertz, B; Garnero, P; Delmas, P

2004-01-01

392

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.).  

PubMed

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics. PMID:21384113

Gujaria, Neha; Kumar, Ashish; Dauthal, Preeti; Dubey, Anuja; Hiremath, Pavana; Bhanu Prakash, A; Farmer, Andrew; Bhide, Mangla; Shah, Trushar; Gaur, Pooran M; Upadhyaya, Hari D; Bhatia, Sabhyata; Cook, Douglas R; May, Greg D; Varshney, Rajeev K

2011-03-08

393

DNA Alterations in the Plasma and Serum of Cancer Patients: A Molecular Tumor Marker  

Microsoft Academic Search

SummaryConventional serum tumor markers are soluble glycoproteins that have proven clinically useful for the initial diagnosis as well as the follow-up in multiple tumor entities. However, a number of tumors lack known tumor markers or the tumor markers are characterized by either low sensitivity or specificity. The detection of disseminated tumor cells in the blood by reverse transcriptase polymerase chain

C. Goessl; R. Heicappell; K. Miller

2000-01-01

394

rpoB gene as a novel molecular marker to infer phylogeny in Planctomycetales.  

PubMed

The 16S rRNA gene has been used in the last decades as a gold standard for determining the phylogenetic position of bacteria and their taxonomy. It is a well conserved gene, with some variations, present in all bacteria and allows the reconstruction of genealogies of microorganisms. Nevertheless, this gene has its limitations when inferring phylogenetic relationships between closely related isolates. To overcome this problem, DNA-DNA hybridization appeared as a solution to clarify interspecies relationships when the sequence similarity of the 16S rRNA gene is above 97 %. However, this technique is time consuming, expensive and laborious and so, researchers developed other molecular markers such as sequencing of housekeeping or functional genes for accurate determination of bacterial phylogeny. One of these genes that have been used successfully, particularly in clinical microbiology, codes for the beta subunit of the RNA polymerase (rpoB). The rpoB gene is sufficiently conserved to be used as a molecular clock, it is present in all bacteria and it is a mono-copy gene. In this study, rpoB gene sequencing was applied to the phylum Planctomycetes. Based on the genomes of 19 planctomycetes it was possible to determine the correlation between the rpoB gene sequence and the phylogenetic position of the organisms at a 95-96 % sequence similarity threshold for a novel species. A 1200-bp fragment of the rpoB gene was amplified from several new planctomycetal isolates and their intra and inter-species relationships to other members of this group were determined based on a 96.3 % species border and 98.2 % for intraspecies resolution. PMID:23904187

Bondoso, Joana; Harder, Jens; Lage, Olga Maria

2013-08-01

395

Gene Expression Profiles in Cells of Peripheral Blood Identify New Molecular Markers of Acute Pancreatitis  

PubMed Central

Introduction Blood leukocytes play a major role in mediating local and systemic inflammation during acute pancreatitis. We hypothesize that peripheral blood mononuclear cells (PBMC) in circulation exhibit unique changes in gene expression, and could provide a “reporter” function that reflects the inflammatory response in pancreas of acute pancreatitis. Methods To determine specific changes in blood leukocytes during acute pancreatitis, we studied gene transcription profile of in peripheral blood mononuclear cells (PBMC) in a rat model of experimental pancreatitis (sodium taurocholate). Normal rats, saline controls and a model of septic shock were used as a controls. cRNA obtained from PBMC of each group (n = 3) were applied to Affymetrix rat genome DNA Gene Chip Arrays. Results From the 8,799 rat genes analyzed, 140 genes showed unique significant changes in their expression in PBMC during the acute phase of pancreatitis, but not in sepsis. Among the 140 genes, 57 were upregulated, while 69 were downregulated. Platelet-derived growth factor receptor, prostaglandin E2 receptor and phospholipase D1 are among the top upregulated genes. Others include genes involved in G protein-coupled receptor and TGF-?-mediated signaling pathways, while genes associated with apoptosis, glucocorticoid receptors and even the cholecystokinin receptor are downregulated. Conclusions Microarray analysis in transcriptional profiling of PBMC showed that genes that are uniquely related to molecular and pancreatic function display differential expression in acute pancreatitis. Profiling genes obtained from an easily accessible source during severe pancreatitis may identify surrogate markers for disease severity.

Bluth, Martin; Lin, Yin-yao; Zhang, Hong; Viterbo, Dominick; Zenilman, Michael

2009-01-01

396

Screening of Molecular Virulence Markers in Staphylococcus aureus and Pseudomonas aeruginosa Strains Isolated from Clinical Infections  

PubMed Central

Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections.

Cotar, Ani-Ioana; Chifiriuc, Mariana-Carmen; Dinu, Sorin; Bucur, Marcela; Iordache, Carmen; Banu, Otilia; Dracea, Olguta; Larion, Cristina; Lazar, Veronica

2010-01-01

397

Current Status of Molecular Markers for Early Detection of Sporadic Pancreatic Cancer  

PubMed Central

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.

Chakraborty, Subhankar; Baine, Michael J.; Sasson, Aaron R.; Batra, Surinder K.

2010-01-01

398

Diagnostic value of molecular markers in chloroquine-resistant falciparum malaria in Southern Mauritania.  

PubMed

Despite its diminishing efficacy because of increased resistance, chloroquine remains the primary antimalarial agent in many endemic areas. Evidence is mounting that point mutations on the Pfcrt and possibly the Pfmdr1 genes are conferring plasmodial resistance to chloroquine. In 1998, atypically strong rainfalls led to an increased activity of falciparum malaria in Mauritania that affected non-endemic regions bordering the Saharan desert. An in vivo study on chloroqine resistance was combined with studies for molecular markers of drug resistance. Detection of Pfmdr1-76-tyrosine showed an increased odds ratio (2.91) for resistance (P = 0.0195). However, by use of this codon alone, sensitivity for detection of resistance was 60.6%, and specificity was 65.3%. In comparison, detection of the K76T mutation at Pfcrt showed a very high sensitivity (100%) while specificity remained relatively low (65.4%). For the combination of mutations on both genes, the odds ratio for detection of resistance increased to 5.31 (P = 0.0005). Here, sensitivity was again decreased to 60.6% while specificity increased to 76.9%. The results of this study suggest that detection of Pfcrt T76 can be applied for predicting chloroquine resistance in epidemiologic settings with sufficiently high sensitivity to make it an attractive alternative to time- and labor-consuming in vivo trials. Additional testing for Pfmdr Y76 provides increased specificity to this approach. PMID:12479542

Jelinek, T; Aida, A O; Peyerl-Hoffmann, G; Jordan, S; Mayor, A; Heuschkel, C; el Valy, A O; von Sonnenburg, F; Christophel, E M

2002-11-01

399

Characterization of prenatally assessed de novo small supernumerary marker chromosomes by molecular cytogenetics.  

PubMed

Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be identified or characterized unambiguously by conventional banding cytogenetics alone, and they are generally equal in size or smaller than a chromosome 20 of the same metaphase spread. sSMC are reported in 0.043% of newborn infants and 0.075% of prenatal cases. Molecular cytogenetics is necessary to characterize the origin of an sSMC, and many highly sophisticated approaches are available throughout the literature for their comprehensive description. However, because in a prenatal diagnostic laboratory such techniques are not available, I suggest here a straightforward scheme to characterize at least the sSMC's chromosomal origin as quickly as possible. Based on this scheme, it is possible to compare the actual present case with similar cases from the literature, which are summarized on http://www.med.uni-jena.de/fish/sSMC/00START.htm./ For a more wide-ranging sSMC characterization, a specialized laboratory should be contacted, e.g., my laboratory. PMID:18425469

Liehr, Thomas

2008-01-01

400

Regulatory T cells and dendritic cells in transplantation tolerance: molecular markers and mechanisms.  

PubMed

Transplantation tolerance can be induced in adult rodents using monoclonal antibodies against coreceptor or costimulation molecules on the surface of T cells. There are currently two well-characterized populations of T cells, demonstrating regulatory capacity: the "natural" CD4+CD25+ T cells and the interleukin (IL)-10-producing Tr1 cells. Although both types of regulatory T cells can induce transplantation tolerance under appropriate conditions, it is not clear whether either one plays any role in drug-induced dominant tolerance, primarily due to a lack of clear-cut molecular or functional markers. Similarly, although dendritic cells (DCs) can be pharmacologically manipulated to promote tolerance, the phenotype of such populations remains poorly defined. We have used serial analysis of gene expression (SAGE) with 29 different T-cell and antigen-presenting cell libraries to identify gene-expression signatures associated with immune regulation. We found that independently derived, regulatory Tr1-like clones were highly concordant in their patterns of gene expression but were quite distinct from CD4+CD25+ regulatory T cells from the spleen. DCs that were treated with the tolerance-enhancing agents IL-10 or vitamin D3 expressed a gene signature reflecting a functional specification in common with the most immature DCs derived from embryonic stem cells. PMID:14617201

Cobbold, Stephen P; Nolan, Kathleen F; Graca, Luis; Castejon, Raquel; Le Moine, Alain; Frewin, Mark; Humm, Susan; Adams, Elizabeth; Thompson, Sara; Zelenika, Diana; Paterson, Alison; Yates, Stephen; Fairchild, Paul J; Waldmann, Herman

2003-12-01

401

Sensitivity of molecular marker-based CMB models to biomass burning source profiles  

NASA Astrophysics Data System (ADS)

To assess the contribution of sources to fine particulate organic carbon (OC) at four sites in North Carolina, USA, a molecular marker chemical mass balance model (MM-CMB) was used to quantify seasonal contributions for 2 years. The biomass burning contribution at these sites was found to be 30-50% of the annual OC concentration. In order to provide a better understanding of the uncertainty in MM-CMB model results, a biomass burning profile sensitivity test was performed on the 18 seasonal composites. The results using reconstructed emission profiles based on published profiles compared well, while model results using a single source test profile resulted in biomass burning contributions that were more variable. The biomass burning contribution calculated using an average regional profile of fireplace emissions from five southeastern tree species also compared well with an average profile of open burning of pine-dominated forest from Georgia. The standard deviation of the results using different source profiles was a little over 30% of the annual average biomass contributions. Because the biomass burning contribution accounted for 30-50% of the OC at these sites, the choice of profile also impacted the motor vehicle source attribution due to the common emission of elemental carbon and polycyclic aromatic hydrocarbons. The total mobile organic carbon contribution was less effected by the biomass burning profile than the relative contributions from gasoline and diesel engines.

Sheesley, Rebecca J.; Schauer, James J.; Zheng, Mei; Wang, Bo

402

Localization of the rice stripe disease resistance gene, Stv-bi, by graphical genotyping and linkage analyses with molecular markers  

Microsoft Academic Search

We used graphical genotyping and linkage analyses with molecular markers to determine the chromosomal location of the rice\\u000a stripe disease resistance gene, Stv-b\\u000a \\u000a \\u000a \\u000a i\\u000a \\u000a . The stripe resistance gene from the indica rice (Oryza sativa) cv ‘Modan’ was introgressed into several Japanese rice varieties. We found 4 RFLP markers in ‘Modan’, five susceptible parental\\u000a rice varieties (‘Norin No. 8’, ‘Sachihikari’,

Y. Hayano-Saito; T. Tsuji; K. Fujii; K. Saito; M. Iwasaki; A. Saito

1998-01-01

403

Genetic relationship among Hyacinth bean (Lablab purpureus) genotypes cultivars from different races based on quantitative traits and random amplified polymorphic DNA marker  

Microsoft Academic Search

Genetic improvement of the thirty Hyacinth bean cultivars from different races were evaluated using RAPD markers which is essential to enhance the crop for economically and agriculturally important traits. RAPD markers were efficient in separating cultivars according to different races. Twenty six decamer primers could generate a total number of 148 bands out which 70.27% (104) were polymorphic. The number

Ashish Kumar; M. Rai; Gandhi Nagar Naria; P. O. BHU

2010-01-01

404

Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis.  

PubMed

In traditional medicine, Lonicera japonica (Thunb.) has a notable place, and it has been used for thousands of years in China, Japan, Korea and other East-Asian countries for treating cancer, inflammation, hepatic complications, influenza and wounds. However, the molecular or genetic characteristic of this plant is not well defined. In this study, improved random amplified polymorphic DNA (RAPD) has been employed for the genetic characterization of five varieties of L. japonica collected from different geographic locations of Southern China. A total of 147 bands of DNA fragments were obtained in RAPD-PCR by using 18 primers, and the band sizes ranged from approximately 300-2,000 bp, with 3-11 amplified bands for each primer. Based on the RAPD amplification profiles, cluster dendrogram was obtained, which showed that the similarity coefficients among five varieties of L. japonica ranged from 0.59 to 0.77. To our knowledge, this is the first report of genetic characterization of L. japonica using improved RAPD analysis which has been validated by ISSR analysis, and this characterization may be useful for the preservation of genetic diversity and Lonicera population identification. Moreover, as an option, the improved method could be employed for a variety of applications in genetic diversity and fingerprinting analyses. PMID:24057241

Fu, Junjiang; Yang, Luquan; Khan, Md Asaduzzaman; Mei, Zhiqiang

2013-09-22

405

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

PubMed Central

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.

Zhang, Shouan; Gao, Muqiang; Zaitlin, David

2012-01-01

406

CD44 as a molecular marker to screen cancer stem cells in hypopharyngeal cancer.  

PubMed

Abstract Conclusions: The CD44(+) cells have a stronger proliferative capacity and higher tumorigenic potential than the CD44(-) cells, which suggests that the cancer stem cells of hypopharyngeal cancer may exist in the CD44(+) tumor cell population. Therefore, we propose that CD44 is an important biological marker to screen cancer stem cells of hypopharyngeal cancer. Objectives: To study the significance of CD44 as a molecular marker for screening cancer stem cells in hypopharyngeal cancer. Methods: The CD44 expression levels in the hypopharyngeal cancer cell line FaDu were analyzed using flow cytometry. To investigate the biological significance of the CD44(+) population, we sorted the CD44(+) and CD44(-) cell populations by using magnetic-associated cell sorting (MACS) technology. After the separation, the purity of the CD44(+) cells was determined using flow cytometry. The MTT method was used to detect the different proliferation capabilities of the CD44(+) and CD44(-) cells in vitro. The tumorigenicity of the CD44(+) and CD44(-) cells was determined by injecting CD44(+) or CD44(-) cells (1 × 10(6) and 1 × 10(5)) into the body of NOD/SCID mice. Results: Some (21.1 ± 1.56)% of the hypopharyngeal cancer cell line FaDu cells expressed CD44. The CD44(+) population was efficiently sorted by MACS, and after separation, the purity of the CD44(+) cells was (99.4 ± 0.29)%. The MTT assay indicated that the sorted CD44(+) cells had a stronger proliferative capacity than the CD44(-) cells. The tumorigenicity study showed that all the mice injected with 1 × 10(6) CD44(+) cells developed tumors (8/8), half the mice injected with 1 × 10(6) CD44(-) cells developed tumors (4/8), 1 of the 8 mice injected with 1 × 10(5) CD44(+) cells developed tumors (12.5%), but none of the mice injected with 1 × 10(5) CD44(-) cells developed any tumors (0/8). At the same concentration, the difference in tumorigenic rates between the CD44(+) and CD44(-) groups was statistically significant (Fisher's exact test, p < 0.05). Furthermore, the CD44(+) group had a shorter incubation period than the CD44(-) group. In addition, the average tumor volume of the CD44(+) group was (2017.81 ± 538.50) mm(3); however, the average tumor volume of the CD44(-) group was (1153.25 ± 503.18) mm(3). The difference was statistically significant (t = 2.67, p < 0.05). PMID:23837451

Shen, Chenling; Xiang, Mingliang; Nie, Chen; Hu, Haixia; Ma, Yan; Wu, Hao

2013-07-09

407

Interpopulation congruence in Chinese Primula ovalifolia revealed by chemical and molecular markers using essential oils and ISSRs.  

PubMed

The chemical composition of the essential oils of five natural populations of P. ovalifolia from central and southwest China and their interpopulation variability were first analyzed by using GC-MS. Twenty-two essential oil compounds were obtained, in which eighteen ones were identified and characterized representing 95%-96% of the oil composition. Three main chemotypes, i.e., the methyl-acetyl-hydroquinone-rich, hydroquinone-rich, and acetyl-hydroquinone-rich chemotypes, were then differentiated, corresponding to the three groups obtained from the cluster analysis based on the essential oil composition percentages. Genetic variations among the five populations were also investigated using the Inter-Simple Sequence Repeats (ISSR) markers. Finally, the Mantel test showed that there was a significant correlation between two distance matrices based on the chemical compounds of essential oils and ISSR markers, confirming the congruence of interpopulation relationships in the P. ovalifolia revealed by the chemical and molecular markers PMID:12622227

Nan, Peng; Peng, Shaolin; Shi, Suhua; Ren, Hai; Yang, Ji; Zhong, Yang

408

[A RAPD fingerprinting of sibling species of the Drosophila virilis group].  

PubMed

A comparative analysis of the sibling species of Drosophila virilis was performed by RAPD-PCR technique using a set of random primers. The degree of relatedness was studied by cluster analysis (UPGMA) and multi-dimensional scaling. The resulting pattern of species relationships contradicts the classical taxonomy. The main result of the cluster analysis is that D. virilis does not cluster with the remaining three species of its phylad, while according to multidimensional scaling, D. virilis is equidistant from all the species of its group, from both the species of its phylad and the species of the montana phylad. The montana phylad is extremely heterogeneous; moreover, the species D. littoralis, D. ezoana, and D. kanekoi appear to be closer to the virilis phylad than to the other species of the montana phylad, wherein these species are traditionally included. The phylogenetic relationships between the studied species discovered using RAPD fingerprinting comply with the results obtained using protein markers and quantitative traits. PMID:17333946

Mikha?lovski?, S S; Kulikov, A M; Potapov, S G; Lazebny?, O E; Mitrofanov, V G

2007-01-01

409

Molecular cytogenetic study of supernumerary marker chromosomes in an unselected group of children  

SciTech Connect

We report on an unselected group of 24 children with small supernumerary marker chromosomes, found in a large sample of 34,910 consecutive newborns karyotyped at birth. Sixteen of these were available for reexamination. With the use of in situ hybridization with {alpha}-satellite centromere probes and satellite III, ribosomal and {beta}-satellite DNA probes, we have characterized these markers. In 14 of the 16 cases we have been able to determine the chromosomal origin of the marker. Twelve of the markers are derived from the acrocentric chromosomes. Of these 12 markers, 4 are derived from chromosome 14, 4 from chromosome 22, 3 from chromosome 15 and one is from either chromosome 13 or 21. Ten of these markers were initially ascertained with the satellite III DNA probe, taking advantage of the fact that satellite III DNA is found in the centromeric region of the following chromosomes: 1, 5, 9, 13, 14, 15, 16, 20, 21, 22, and Y. Two markers were derived from chromosomes 4 and 8. The origin of the last 2 markers could not be determined with the techniques employed. Only one of these children is psychometrically retarded and has a peculiar appearance. Unfortunately we were not able to determine the origin of the marker in her case. All other children developed normally. 54 refs., 1 fig., 3 tabs.

Gravholt, C.H. [Aarhus Univ. Hospital, Risskov (Denmark); Friedrich, U. [Aarhus Univ. (Denmark)

1995-03-13

410

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

NASA Astrophysics Data System (ADS)

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.

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

2010-05-01

411

Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium  

PubMed Central

Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A–H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A–H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.

Pochon, Xavier; Putnam, Hollie M.; Burki, Fabien; Gates, Ruth D.

2012-01-01

412

Molecular markers in management of ex situ PGR-a case study.  

PubMed

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of longterm- stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50 years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement. PMID:23107922

Börner, Andreas; Khlestkina, Elena K; Chebotar, Sabina; Nagel, Manuela; Arif, Mian Abdur Rehman; Neumann, Kerstin; Kobiljski, Borislav; Lohwasser, Ulrike; Röder, Marion S

2012-11-01

413

Comparison between genetic and physical maps in Zea mays L. of molecular markers linked to resistance against Diatraea spp  

Microsoft Academic Search

In the pachytene stage, chromosomes are maximally extended and can easily be distinguished. Therefore, by applying fluorescence in situ hybridization (FISH) to pachytene chromosomes, it is possible to generate a high-resolution physical map of chromosome 9 in maize. Molecular markers (umc105a on the short arm of chromosome 9, csu145a on the long arm) were used that flank quantitative trait loci

M. Sadder; G. Weber

2002-01-01

414

Identification of a novel mitochondrial genome type and development of molecular markers for cytoplasm classification in radish ( Raphanus sativus L.)  

Microsoft Academic Search

Plant mitochondrial genomes have complex configurations resulting from the multipartite structures and highly rearranged substoichiometric\\u000a 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

Sunggil Kim; Heerae Lim; Kang-Hee Cho; Soon-Kee Sung; Dae-Geun Oh; Ki-Taek Kim

2007-01-01

415

Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome  

PubMed Central

Background Molecular markers facilitate both genotype identification, essential for modern animal and plant breeding, and the isolation of genes based on their map positions. Advancements in sequencing technology have made possible the identification of single nucleotide polymorphisms (SNPs) for any genomic regions. Here a sequence based polymorphic (SBP) marker technology for generating molecular markers for targeted genomic regions in Arabidopsis is described. Results A ~3X genome coverage sequence of the Arabidopsis thaliana ecotype, Niederzenz (Nd-0) was obtained by applying Illumina's sequencing by synthesis (Solexa) technology. Comparison of the Nd-0 genome sequence with the assembled Columbia-0 (Col-0) genome sequence identified putative single nucleotide polymorphisms (SNPs) throughout the entire genome. Multiple 75 base pair Nd-0 sequence reads containing SNPs and originating from individual genomic DNA molecules were the basis for developing co-dominant SBP markers. SNPs containing Col-0 sequences, supported by transcript sequences or sequences from multiple BAC clones, were compared to the respective Nd-0 sequences to identify possible restriction endonuclease enzyme site variations. Small amplicons, PCR amplified from both ecotypes, were digested with suitable restriction enzymes and resolved on a gel to reveal the sequence based polymorphisms. By applying this technology, 21 SBP markers for the marker poor regions of the Arabidopsis map representing polymorphisms between Col-0 and Nd-0 ecotypes were generated. Conclusions The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for cloning genes based on their genetic map positions and identifying tightly linked molecular markers for selecting desirable genotypes in animal and plant breeding experiments.

2012-01-01

416

MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY  

Technology Transfer Automated Retrieval System (TEKTRAN)

Unlike other major crops such as soybean and corn, cotton has no coordinated public marker database. Cotton Incorporated (CI) has identified the need for more markers and a database as critical action points. The Mid South Area Genomics Laboratory in cooperation with scientists from the Crop Genetic...

417

Supernumerary marker 15 chromosomes: a clinical, molecular and FISH approach to diagnosis and prognosis  

Microsoft Academic Search

Seventeen patients presenting with either de novo or familial supernumerary marker (mar) 15 chromosomes were shown by fluorescent in situ hybridization techniques (FISH) to have markers derived from and composed entirely of chromosome 15 material. Using a combination of conventional cytogenetics, FISH, Southern blotting and multiplex polymerase chain reaction (PCR) methods, it was possible to sub-classify the 17 mar(15)s into

John A. Crolla; John F. Harvey; Fiona L. Sitch; Nick R. Dennis

1995-01-01

418

Molecular-marker-facilitated investigations of quantitative trait loci in maize  

Microsoft Academic Search

Restriction fragment length polymorphisms have become powerful tools for genetic investigations in plant species. They allow a much greater degree of genome saturation with neutral markers than has been possible with isozymes or morphological loci. A previous investigation employed isozymes as genetic markers to infer the location of genetic factors influencing the expression of quantitative traits in the maize population:

M. D. Edwards; T. Helentjaris; S. Wright; C. W. Stuber

1992-01-01

419

MOLECULAR MARKERS RUN ON A TEST PANEL: A DATA SOURCE FOR THE COTTON COMMUNITY  

Technology Transfer Automated Retrieval System (TEKTRAN)

Unlike other major crops such as soybean and corn, cotton has no coordinated public marker database. Cotton Incorporated (CI) has identified the need for more markers and a database as critical action points. The Mid South Area Genomics Laboratory in cooperation with scientists from the Crop Genet...

420

Molecular detection of a bacterial contaminant Bacillus pumilus in symptomless potato plant tissue cultures  

Microsoft Academic Search

An aberrant random amplified polymorphic DNA (RAPD) marker in genomic DNA of tissue culture plantlets was frequently observed during a comparison of DNA fingerprints derived from potato germplasm grown in tissue culture and the field. The RAPD marker was cloned, sequenced and determined to be of bacterial origin. A bacterial contaminant was isolated from the tissue culture plants and identified

D. A. Isenegger; P. W. J. Taylor; K. Mullins; G. R. McGregor; M. Barlass; J. F. Hutchinson

2003-01-01

421

[RAPD analysis of plant pathogenic coryneform bacteria].  

PubMed

RAPD analysis was used for the taxonomy of plant pathogenic coryneform bacteria, especially for the classification of two new pathogens (Curtobacterium flaccumfaciens pv. basellae pv. nov. and Curtobacterium flaccumfaciens pv. beticola pv. nov.). 20 random primers were screened from 50 ones to detect polymorphism among the total strains used. 80.4% were polymorphic bands among the 225 ones produced. The results of pairwise similarity and UPGMA cluster analysis suggest that the two new pathovars of sugar beet (Beta vulgaris var. saccharifera) and malabar spinach (Basella rubra) are genetically close related with Curtobacterium flacumfaciens, and the minimal similarity coefficient is 0.6511. According to the RAPD analysis and previous research, some newly made taxonomic changes of the plant pathogenic coryneform bacteria are discussed. PMID:16496687

Yin, Yan-Ni; Chen, Yong-Fang; Li, Shi-Mo; Guo, Jian-Hua

2005-12-01

422

Randomly Amplified Polymorphic DNA (RAPD)  

Microsoft Academic Search

Genetic variability or molecular biodiversity, besides being important for evolution, can be used as instrument of inquiry in diverse areas, for example, to verify the affinities and the limits between species, to detect forms of reproduction and familiar structure, to evaluate levels of migration and dispersion in populations and for the identification of species threatened with extinction. The basic data

Lúcia Maria da Cunha Galvão; Eliane Lages-Silva

423

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus.  

PubMed

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D(2) statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F2 population of cross, BR11×Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model. PMID:23643394

Latif, Mohammad Abdul; Rahman, Mohammad Mahfuzur; Ali, Mohammad Eaqub; Ashkani, Sadegh; Rafii, Mohd Yusop

2013-03-21

424

DEVELOPMENT OF MOLECULAR DIAGNOSTIC MARKERS FOR GLASSY-WINGED AND SMOKETREE SHARPSHOOTERS FOR USE IN PREDATOR GUT CONTENT EXAMINATIONS Project Leaders  

Microsoft Academic Search

To aid in identifying key predators of Proconiini sharpshooter species present in California, we developed and tested molecular diagnostic markers for the glassy-winged sharpshooter Homalodisca coagulata (Say) and smoke-tree sharpshooter Homalodisca liturata (Ball) (Homoptera: Cicadellidae: Proconiini). Two different types of markers were compared, those targeting single-copy sequence characterized amplified regions (SCAR) and mitochondrial markers targeting the multi-copy cytochrome oxidase subunit

Jesse H. de León; James Hagler; Valerie Fournier; Kent Daane

425

Molecular Marker Approach on Characterizing and Quantifying Charcoal in Environmental Media  

NASA Astrophysics Data System (ADS)

Black carbon (BC) is widely distributed in natural environments including soils, sediments, freshwater, seawater and the atmosphere. It is produced mostly from the incomplete combustion of fossil fuels and vegetation. In recent years, increasing attention has been given to BC due to its potential influence in many biogeochemical processes. In the environment, BC exists as a continuum ranging from partly charred plant materials, charcoal residues to highly condensed soot and graphite particles. The heterogeneous nature of black carbon means that BC is always operationally-defined, highlighting the need for standard methods that support data comparisons. Unlike soot and graphite that can be quantified with well-established methods, it is difficult to directly quantify charcoal in geologic media due to its chemical and physical heterogeneity. Most of the available charcoal quantification methods detect unknown fractions of the BC continuum. To specifically identify and quantify charcoal in soils and sediments, we adopted and validated an innovative molecular marker approach that quantifies levoglucosan, a pyrogenic derivative of cellulose, as a proxy of charcoal. Levoglucosan is source-specific, stable and is able to be detected at low concentrations using gas chromatograph-mass spectrometer (GC-MS). In the present study, two different plant species, honey mesquite and cordgrass, were selected as the raw materials to synthesize charcoals. The lab-synthesize charcoals were made under control conditions to eliminate the high heterogeneity often found in natural charcoals. The effects of two major combustion factors, temperature and duration, on the yield of levoglucosan were characterized in the lab-synthesize charcoals. Our results showed that significant levoglucosan production in the two types of charcoal was restricted to relatively low combustion temperatures (150-350 degree C). The combustion duration did not cause significant differences in the yield of levoglucosan in the two charcoals. Interestingly, the low temperature charcoals are undetectable by the acid dichromate oxidation method, a popular soot/charcoal analytical approach. Our study demonstrates that levoglucosan can serve as a proxy of low temperature charcoals that are undetectable using other BC methods. Moreover, our study highlights the limitations of the common BC quantification methods to characterize the entire BC continuum.

Kuo, L.; Herbert, B. E.; Louchouarn, P.

2006-12-01

426

ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma  

PubMed Central

Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. Methods First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR) treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP). Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. Results The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR) demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM); tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC) was 76.2% compared