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.

SCAR molecular markers of the B biotype and two non-B populations of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

2006 ◽  
Vol 3 (3) ◽  
pp. 189-194 ◽  
Author(s):  
Zang Lian-Sheng ◽  
Jiang Tong ◽  
Xu Jing ◽  
Liu Shu-Sheng ◽  
Zhang You-Jun
Keyword(s):  
Bemisia Tabaci ◽  
Random Amplified Polymorphic Dna ◽  
Trialeurodes Vaporariorum ◽  
Chain Reaction ◽  
Specific Sequence ◽  
Sequence Characterized Amplified Region ◽  
Scar Primer ◽  
Polymerase Chain ◽  
Scar Primers ◽  
B Biotype

AbstractRandom amplified polymorphic DNA (RAPD) analyses were performed with random primer H16 for the B biotype and two non-B populations of Bemisia tabaci collected from Zhejiang (China). The specific sequence fragments containing 446, 390 and 1317 nucleotides were amplified for the B biotype, ZHJ-1, ZHJ-2 populations, respectively. The three specific fragments were cloned and sequenced, and three pairs of SCAR primers were designed according to the sequences determined. With improvement of the conditions of the polymerase chain reaction (PCR), the specific fragments of B biotype, ZHJ-1 and ZHJ-2 populations, namely 439, 366 and 1238 nucleotides, respectively, were amplified with the sequence characterized amplified region (SCAR) primer of the corresponding population, while specific fragments of the other populations of B. tabaci or Trialeurodes vaporariorum could not be amplified.

DNA markers for identifying biotypes B and Q of Bemisia tabaci (Hemiptera: Aleyrodidae) and studying population dynamics

2005 ◽  
Vol 95 (6) ◽  
pp. 605-613 ◽  
Author(s):  
V. Khasdan ◽  
I. Levin ◽  
A. Rosner ◽  
S. Morin ◽  
S. Kontsedalov ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Complete Agreement ◽  
Field Samples ◽  
Cleaved Amplified Polymorphic Sequences ◽  
Sequence Characterized Amplified Regions ◽  
Q Biotype ◽  
Mitochondrial Cytochrome Oxidase ◽  
B Biotype

AbstractThe two most widespread biotypes of Bemisia tabaci (Gennadius) in southern Europe and the Middle East are referred to as the B and Q-type, which are morphologically indistinguishable. In this study various DNA markers have been developed, applied and compared for studying genetic diversity and distribution of the two biotypes. For developing sequence characterized amplified regions (SCAR) and cleaved amplified polymorphic sequences (CAPS) techniques, single random amplified polymorphic DNA (RAPD) fragments of B and Q biotypes, respectively, were used. The CAPS were investigated on the basis of nuclear sodium channel and the mitochondrial cytochrome oxidase I genes (mtCOI) sequences. In general, complete agreement was found between the different markers used. Analysis of field samples collected in Israel for several years, using these markers, indicated that the percentage of the Q biotype tends to increase in field populations as time progresses. This may be attributed to the resistance of the Q biotype to neonicotinoids and pyriproxyfen and the susceptibility of the B biotype to these insecticides.

Development of silverleaf assay, protein and nucleic acid-based diagnostic techniques for the quick and reliable detection and monitoring of biotype B of the whitefly, Bemisia tabaci (Gennadius)

2007 ◽  
Vol 97 (5) ◽  
pp. 503-513 ◽  
Author(s):  
K.S. Shankarappa ◽  
K.T. Rangaswamy ◽  
D.S. Aswatha Narayana ◽  
A.R. Rekha ◽  
N. Raghavendra ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Scar Marker ◽  
Cost Effective ◽  
Diagnostic Techniques ◽  
Detection Methods ◽  
Agricultural Pests ◽  
Sequence Characterized Amplified Region ◽  
The North ◽  
Biotype B ◽  
B Biotype

AbstractThe aim of this study was to develop and optimize silverleaf bioassay, esterase analysis and PCR-based techniques to distinguish quickly and reliably biotype B of the whitefly, Bemisia tabaci (Gennadius), from Indian indigenous biotypes. Zucchini and squash readily develop silverleaf symptoms upon feeding by the B biotype, but they are not readily available in Indian markets. A local pumpkin variety ‘Big’ was, therefore, used in silverleaf assay, which developed symptoms similar to those on zucchini and squash and can be used reliably to detect B biotype. Analysis of non-specific esterases of B and the indigenous biotypes indicated both quantitative and qualitative differences in esterase patterns. Two high molecular weight bands were unique to B biotype and they occurred in abundance. These esterases were used to develop quick and field-based novel detection methods for differentiating B from the indigenous biotypes. Development of these simple and cost-effective protocols has wider application as they can be potentially used to identify other agricultural pests. Mitochondrial cytochrome oxidase I gene sequences and randomly amplified polymorphic DNA (RAPD) polymorphisms, generated using the primer OpB11, were also found useful for detecting B. tabaci biotypes. A B biotype-specific RAPD band of 800 bp was sequenced, which was used to a develop sequence characterized amplified region (SCAR) marker. The SCAR marker involved the development of B biotype-specific primers that amplified 550 bp PCR products only from B biotype genomic DNA. Silverleaf assay, esterases, RAPDs or a SCAR marker were used in combination to analyse whitefly samples collected from selected locations in India, and it was found that any of these techniques can be used singly or in combination to detect B biotype reliably. The B biotype was found in southern parts of India but not in the north in 2004–06.

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 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 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 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.

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.

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