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

2014 ◽  
Vol 62 (4) ◽  
pp. 1649 ◽  
Author(s):  
Luquan Yang ◽  
Md. Asaduzzaman Khan ◽  
Zhiqiang Mei ◽  
Manman Yang ◽  
Tiandan Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Scar Marker ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Vital Role ◽  
Lonicera Japonica ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Young Leaves

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

scholarly journals PCR-based molecular markers for identification of taxa from the Calypogeia fissa complex (Jungermanniopsida, Calypogeiaceae)

2012 ◽  
Vol 28 (1) ◽  
pp. 9-18 ◽  
Author(s):  
Katarzyna Buczkowska ◽  
Patrycja Gonera ◽  
Bartosz Hornik
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Scar Marker ◽  
Issr Markers ◽  
Genetic Differences ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pcr Product ◽  
Isozyme Loci ◽  
Diagnostic Traits

Abstract Within Calypogeia fissa, two subspecies connected with geographic distribution are formally recognized: C. fissa subsp.fissa in Europe and C. fissa subsp.neogea in North America. Isoenzyme studies have shown that the European subspecies is genetically differentiated and composed of three genetically distinct groups PS, PB and G. The PS group has the most distinctive morphological features, but no morphological diagnostic traits have been found for groups PB and G. The sequence characterized amplified region (SCAR) markers developed on the basis of ISSR markers, applied in the study, allowed the delimitation of all groups distinguished in Europe within the C. fissa complex (PS, PB and G). The markers also revealed genetic differences between the European and American subspecies. Five primer pairs (Cal01, Cal03-Cal06) of the six pairs studied are useful as the diagnostic tool for the identification of particular groups from the C.fissa complex. The examined SCAR markers showed that the PS group of C.fissa subsp.fissa was the most distinct; it differed from both groups PB and G as well as from C.fissa subsp.neogea. All plants determined on the basis of diagnostic isozyme loci as the PS group amplified a longer product (380 bp) of the Cal04 primer pair than the rest of studied groups and yielded no amplification products in Cal03, Cal05 and Cal06 primers. The primer pair Cal03 distinguished the plants of the PB group from the remaining groups, since only the PB group generated a PCR product of about 290 bp. The genetic differences between all four studied groups of the C.fissa complex were supported by DNA sequences of the SCAR marker Cal04.

scholarly journals Identification of the B, Q, and native Brazilian biotypes of the Bemisia tabaci species complex using Scar markers

2016 ◽  
Vol 51 (5) ◽  
pp. 555-562 ◽  
Author(s):  
Paulo Roberto Queiroz ◽  
Erica Soares Martins ◽  
Nazaré Klautau ◽  
Luzia Lima ◽  
Lilian Praça ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Species Complex ◽  
Scar Marker ◽  
Random Amplified Polymorphic Dna ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Field Samples ◽  
Scar Primer ◽  
Q Biotype ◽  
B Biotype

Abstract: The objective of this work was to develop sequence-characterized amplified region (Scar) markers to identify the B, Q, and native Brazilian biotypes of the sweet potato whitefly [Bemisia tabaci (Hemiptera: Aleyrodidae)]. Random amplified polymorphic DNA (RAPD) amplification products, exclusive to the B and Brazilian biotypes, were selected after the analysis of 12,000 samples, in order to design a specific Scar primer set. The BT-B1 and BT-B3 Scar markers, used to detect the B biotype, produced PCR fragments of 850 and 582 bp, respectively. The BT-BR1 Scar marker, used to identify the Brazilian biotype, produced a PCR fragment of 700 bp. The Scar markers were tested against the Q biotype, and a flowchart was proposed to indicate the decision steps to use these primers, in order to correctly discriminate the biotypes. This procedure allowed to identify the biotypes that occur in field samples, such as the B biotype. The used set of primers allowed to discriminate the B, Q, and native Brazilian biotypes of B. tabaci. These primers can be successfully used to identify the B biotype of B. tabaci from field samples, showing only one specific biotype present in all cultures.

scholarly journals A DNA-Based Procedure for In Planta Detection of Fusarium oxysporum f. sp. phaseoli

2002 ◽  
Vol 92 (3) ◽  
pp. 237-244 ◽  
Author(s):  
Fernando M. Alves-Santos ◽  
Brisa Ramos ◽  
M. Asunción García-Sánchez ◽  
Arturo P. Eslava ◽  
José María Díaz-Mínguez
Keyword(s):  
Common Bean ◽  
Fusarium Oxysporum ◽  
Scar Marker ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
In Planta ◽  
Sequence Characterized Amplified Region ◽  
Polymerase Chain ◽  
Highly Virulent

We have characterized strains of Fusarium oxysporum from common bean fields in Spain that were nonpathogenic on common bean, as well as F. oxysporum strains (F. oxysporum f. sp. phaseoli) pathogenic to common bean by random amplified polymorphic DNA (RAPD) analysis. We identified a RAPD marker (RAPD 4.12) specific for the highly virulent pathogenic strains of the seven races of F. oxysporum f. sp. phaseoli. Sequence analysis of RAPD 4.12 allowed the design of oligonucleotides that amplify a 609-bp sequence characterized amplified region (SCAR) marker (SCAR-B310A280). Under controlled environmental and greenhouse conditions, detection of the pathogen by polymerase chain reaction was 100% successful in root samples of infected but still symptomless plants and in stem samples of plants with disease severity of ≥4 in the Centro Internacional de Agricultura Tropical (CIAT; Cali, Colombia) scale. The diagnostic procedure can be completed in 5 h and allows the detection of all known races of the pathogen in plant samples at early stages of the disease with no visible symptoms.

scholarly journals Development of Race-Specific SCAR Markers for Detection of Chinese Races CYR32 and CYR33 of Puccinia striiformis f. sp. tritici

Plant Disease ◽  
2010 ◽  
Vol 94 (2) ◽  
pp. 221-228 ◽  
Author(s):  
Baotong Wang ◽  
Xiaoping Hu ◽  
Qiang Li ◽  
Baojun Hao ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Stripe Rust ◽  
Genomic Dna ◽  
Puccinia Striiformis ◽  
Random Amplified Polymorphic Dna ◽  
Scar Markers ◽  
Wheat Stripe Rust ◽  
Wheat Genotypes ◽  
Sequence Characterized Amplified Region ◽  
Wheat Leaves

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a devastating disease in China. Races CYR32 and CYR33 have been predominant in the recent P. striiformis f. sp. tritici population. To develop molecular markers for these races, initially 86 isolates, most of which were collected in 2007 throughout China, were tested on the set of wheat genotypes for differentiating Chinese P. striiformis f. sp. tritici races, and their genomic DNA were amplified with 94 random amplified polymorphic DNA (RAPD) primers. Twelve isolates were identified as CYR33, 14 as CYR32, and 60 as 13 other races. A 320-bp band was identified to be associated with CYR32 with primer S1271 (5′-CTTCTCGGTC-3′), and a 550-bp band was identified to be specific to CYR33 with primer S1304 (5′-AGGAGCGACA-3′). The two bands were cloned and sequenced. Based on the sequences, sequence characterized amplified region (SCAR) markers CYR32sp1/sp2 and CYR33sp1/sp2 were developed to differentiate CYR32 and CYR33, respectively, from other races. The SCAR markers were validated with DNA samples from wheat leaves inoculated with selected isolates from the 86 isolates and urediniospore DNA samples from an additional 63 isolates collected from 2006 to 2009. The detection of CYR32 and CYR33 with the SCAR markers was completely consistent with the results of the race identification with the set of differential wheat genotypes. Thus, the markers are highly reliable for identification of the two races.

scholarly journals IDENTIFIKASI VARIETAS KENTANG “SUPERJOHN” BERDASARKAN PENANDA RAPD (Random Amplified Polymorphic DNA)

EUGENIA ◽  
2011 ◽  
Vol 17 (1) ◽  
Author(s):  
David S. Runtunuwu ◽  
J. E.X. Rogi ◽  
J. H. Palendeng
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Potato Variety ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Field Research ◽  
Morphological Characters ◽  
North Sulawesi ◽  
Field Identification ◽  
Young Leaves

ABSTRACT Identification using morphological characters has time consuming. Currently, identification using molecular markers has now been popular due to rapid, saving time and more precisely. Superjohn potato variety has been cultivated in North Sulawesi. However, the Superjohn potato variety has not been characterized using molecular markers. This research was aiming to identify “Superjohn” potato based on RAPD (Random Amplified Polymorphic DNA) markers. The research was conducted in field and laboratory. Field research was performed by taking some young leaves from “Superjohn”, Granola, and Atlantic variety from the field. Identification using molecular marker was conducted at laboratory.  Nine RAPD primers were used to identify the superjohn variety. The nine primers were OPA-1, OPA-2, OPA-3, OPA-4, OPA-5, OPA-7, OPA-9,  OPA-10, and  OPO-1.  The molecular identification revealed that “Superjohn” variety was different with Granola and Atlantic. OPA-9700 primer could be used for identification  “Superjohn” variety while OPA-101000 primer was suitable  for identification  Granola variety. Keywords:  Potatoes, variety, “Superjohn”, Granola, Atlantic, and RAPD ABSTRAK Penelitian ini dilakukan untuk mengidentikasi kentang “Superjohn” berdasarkan penanda RAPD (Random Amplified Polymorphic DNA).  Penelitian dilakukan di lapangan dan laboratorium. Penelitian lapangan dilakukan dengan mengambil beberapa daun muda dari varietas kentang “Superjohn”, Atlantik dan Granola. Kemudian  analisis DNA dilakukan di laboratorium menggunakan analisis RAPD. Berdasarkan penanda RAPD ternyata kentang “Superjohn” berbeda dari kentang Granola dan kentang Atlantik. Penanda RAPD OPA-9700 dapat digunakan untuk mengidentifikasi kentang“Superjohn” dan penanda RAPD  OPA-101000 dapat digunakan  untuk mengidentifikasi kentang Granola. Kata kunci:  Kentang,  varietas, Superjohn, Granola, Granola, RAPD

scholarly journals IDENTIFIKASI VARIETAS KENTANG SUPERJOHN BERDASARKAN PENANDA RAPD (Random Amplified Polymorphic DNA)

EUGENIA ◽  
2011 ◽  
Vol 17 (1) ◽  
pp. 52
Author(s):  
Runtunuwu D. S. ◽  
J. E. X. Rogi ◽  
J. H. Palendeng
Keyword(s):  
Molecular Markers ◽  
Molecular Marker ◽  
Potato Variety ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Field Research ◽  
Morphological Characters ◽  
North Sulawesi ◽  
Field Identification ◽  
Young Leaves

Identification using morphological characters has time consuming. Currently, identification usingmolecular markers has now been popular due to rapid, saving time and more precisely. Superjohnpotato variety has been cultivated in North Sulawesi. However, the Superjohn potato variety has notbeen characterized using molecular markers. This research was aiming to identify ―Superjohn‖ potatobased on RAPD (Random Amplified Polymorphic DNA) markers. The research was conducted in fieldand laboratory. Field research was performed by taking some young leaves from ―Superjohn‖, Granola,and Atlantic variety from the field. Identification using molecular marker was conducted at laboratory.Nine RAPD primers were used to identify the superjohn variety. The nine primers were OPA-1, OPA-2,OPA-3, OPA-4, OPA-5, OPA-7, OPA-9, OPA-10, and OPO-1. The molecular identification revealedthat ―Superjohn‖ variety was different with Granola and Atlantic. OPA-9700 primer could be used foridentification ―Superjohn‖ variety while OPA-101000 primer was suitable for identification Granolavariety.Keywords: Potatoes, variety, “Superjohn”, Granola, Atlantic, and RAPD ABSTRAKPenelitian ini dilakukan untuk mengidentikasi kentang ―Superjohn‖ berdasarkan penanda RAPD(Random Amplified Polymorphic DNA). Penelitian dilakukan di lapangan dan laboratorium. Penelitianlapangan dilakukan dengan mengambil beberapa daun muda dari varietas kentang ―Superjohn‖,Atlantik dan Granola. Kemudian analisis DNA dilakukan di laboratorium menggunakan analisis RAPD.Berdasarkan penanda RAPD ternyata kentang ―Superjohn‖ berbeda dari kentang Granola dan kentangAtlantik. Penanda RAPD OPA-9700 dapat digunakan untuk mengidentifikasi kentang―Superjohn‖ danpenanda RAPD OPA-101000 dapat digunakan untuk mengidentifikasi kentang Granola.

scholarly journals SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum

2019 ◽  
Vol 7 (1) ◽  
pp. 12 ◽  
Author(s):  
O-Chul Kwon ◽  
Chang-Soo Lee ◽  
Young-Jin Park
Keyword(s):  
Ganoderma Lucidum ◽  
Gene Sequence ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Pcr Analysis ◽  
Scar Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Specific Fragment

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

scholarly journals Efficiency of Randomly Amplified Polymorphic DNA to Sequence Characterized Amplified Region Marker Conversion and their Comparative Polymerase Chain Reaction Sensitivity in Cucumber

1999 ◽  
Vol 124 (2) ◽  
pp. 128-135 ◽  
Author(s):  
Thomas Horejsi ◽  
Jodie M. Box ◽  
Jack E. Staub
Keyword(s):  
Rapd Markers ◽  
Scar Marker ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pcr Product ◽  
Rapd Pcr ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Template Dna ◽  
Pcr Conditions

The conversion of randomly amplified polymorphic DNA (RAPD) markers to sequence characterized amplified region (SCAR) markers, and the effects of differing polymerase chain reaction (PCR) conditions were studied in cucumber (Cucumis sativus L.). Attempts were made to clone and sequence 75 RAPD PCR products to produce SCAR primers (16 to 22 nucleotides) designed to amplify original RAPD PCR products. The influence of template DNA source, purity, and concentration, MgCl2 concentration, Taq polymerase source, and type of thermocycler upon RAPD and SCAR marker performance was evaluated. Conversion of RAPD to SCAR markers was not universally successful, and SCAR primers reacted differently to varying PCR conditions. Only 48 (64%) of 75 RAPD markers were successfully converted to SCAR markers and 11 (15%) of these reproduced the polymorphism observed with the original RAPD PCR product. Moreover, some SCAR primer pairs produced multiple polymorphic PCR products. The band intensity of SCAR markers were brighter (P = 0.05) than their corresponding RAPD markers with only one exception. The SCAR markers examined were less influenced (P = 0.05) by MgCl2 concentration than their corresponding RAPD markers. However, some SCAR markers were more sensitive to reaction impurities than their RAPD counterparts and SCAR markers tended to be less readily visualized (decrease in frequency of visible PCR product) with low concentrations (1 and 2 mm) of template DNA than their corresponding RAPD markers. Neither the source of Taq nor the type of thermocycler used affected the performance of SCAR and RAPD markers. These data suggest that although SCAR markers may demonstrate enhanced performance over the RAPD markers from which they are derived, careful consideration must be given to both the costs and potential benefits of SCAR marker development in cucumber.

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