scholarly journals Genetic authentication of Eclipta prostrate (Asteraceae) from Penthorum chinense (Penthoraceae) by Sequence Characterized Amplified Region (SCAR) markers

2020 ◽  
Vol 68 (1) ◽  
Author(s):  
Zhiqiang Mei ◽  
Md Asaduzzaman Khan ◽  
Junjiang Fu
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Enzymatic Digestion ◽  
Genetic Identification ◽  
Perennial Herb ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Penthorum Chinense Pursh ◽  
Living Organisms ◽  
Penthorum Chinense

Introduction: For the rapid and accurate genetic identification and authentication of living organisms, improved random amplified polymorphic DNA (RAPD) fragment based development of sequence-characterized amplified region (SCAR) markers is an important genetic technique. Objective: This study aimed to develop SCAR markers for perennial herb Eclipta prostrate (E. prostrate). Methods: Here the RAPD fragments by improved RAPD amplification with primers A11 and N-7 for E. prostrate were cloned into pGEX-T vector, and PCR amplification identified the positive clones. After the enzymatic digestion, they were sequenced with Sanger sequencing. Results: Two SCAR markers were developed, which were very specific to E. prostrate, not found in Penthorum chinense Pursh (P. chinense). The nucleotide sequence search by BLAST GenBank database showed that they are novel in E. prostrate, therefore they were deposited in Genbank with accession number KX671034, KX671035. The markers did not show any identity to other species. Conclusions: Thus, in this study two specific SCAR markers were developed for genetically distinguishing and identifying the plant species E. prostrate from herb P. chinense and others.

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 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 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 Molecular Identification of Two Vegetative Compatibility Groups of Fusarium oxysporum f. sp. cepae

2012 ◽  
Vol 102 (2) ◽  
pp. 204-213 ◽  
Author(s):  
Michael J. Southwood ◽  
Altus Viljoen ◽  
Glaudina Mostert ◽  
Adéle McLeod
Keyword(s):  
South Africa ◽  
Fusarium Oxysporum ◽  
Molecular Identification ◽  
Random Amplified Polymorphic Dna ◽  
Polymerase Chain Reaction Method ◽  
Vegetative Compatibility ◽  
Molecular Characteristics ◽  
Scar Markers ◽  
Vegetative Compatibility Groups ◽  
Sequence Characterized Amplified Region

Fusarium oxysporum f. sp. cepae, which causes basal rot of onion, consists of seven vegetative compatibility groups (VCGs 0420 to 0426) and several single-member VCGs (SMVs). F. oxysporum f. sp. cepae populations in South Africa and Colorado each consist of one main VCG (namely, VCG 0425 and 0421, respectively). The aim of this study was to develop sequence-characterized amplified region (SCAR) markers for the identification of VCGs 0425 and 0421, using 79 previously characterized F. oxysporum isolates. A second aim was to investigate the prevalence of VCG 0425 among 88 uncharacterized South African onion F. oxysporum isolates using (i) the developed SCAR markers and (ii) inter-retrotransposon (IR)- and random amplified polymorphic DNA (RAPD) fingerprinting. Only two RAPD primers provided informative fingerprints for VCG 0425 isolates but these could not be developed into SCAR markers, although they provided diagnostic fragments for differentiation of VCG 0425 from VCG 0421. IR fingerprinting data were used to develop a multiplex IR-SCAR polymerase chain reaction method for the identification of VCG 0421, VCG 0425, and SMV 4 isolates as a group. Molecular identification of the uncharacterized collection of 88 F. oxysporum isolates (65 F. oxysporum f. sp. cepae and 23 F. oxysporum isolates nonpathogenic to onion) confirmed that VCG 0425 is the main VCG in South Africa, with all but 3 of the 65 F. oxysporum f. sp. cepae isolates having the molecular characteristics of this VCG. Genotyping and VCG testing showed that two of the three aforementioned isolates were new SMVs (SMV 6 and SMV 7), whereas the third (previously known as SMV 3) now belongs to VGC 0247.

scholarly journals Identification of Raspberry Cultivars by Sequence Characterized Amplified Region DNA Analysis

HortScience ◽  
1998 ◽  
Vol 33 (1) ◽  
pp. 140-142 ◽  
Author(s):  
Jean-Guy Parent ◽  
Danièle Pagé
Keyword(s):  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Rubus Idaeus ◽  
Scar Markers ◽  
Certification Program ◽  
Red Raspberry ◽  
Sequence Characterized Amplified Region

Five polymorphic random amplified polymorphic DNA (RAPD) markers for 13 red raspberry (Rubus idaeus L.) and two purple raspberry (R. idaeus L. × R. occidentalis L.) cultivars were cloned and their termini sequenced. Sequence-specific 24-mer primer pairs were synthesized as extended RAPD primers and used in sequence characterized amplified region (SCAR) DNA analysis. All primer pairs generated polymorphic SCAR markers of the original RAPD marker sizes and length variants. Markers from four of the primer pairs could be easily scored and were adequate to identify the raspberry cultivars of the certification program of the province of Quebec.

scholarly journals Identification of Grape (Vitis) Rootstocks Using Sequence Characterized Amplified Region DNA Markers

HortScience ◽  
1996 ◽  
Vol 31 (2) ◽  
pp. 267-268 ◽  
Author(s):  
Hong Xu ◽  
Alan T. Bakalinsky
Keyword(s):  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Scar Markers ◽  
Polymorphic Markers ◽  
Sequence Characterized Amplified Region ◽  
Annealing Temperatures

Five sequence characterized amplified region (SCAR) DNA markers were reevaluated at substantially higher annealing temperatures than originally reported; four were polymorphic among nine rootstocks tested. Four new informative SCAR markers also are reported, based on redesigning primers from previously cloned random amplified polymorphic DNA (RAPD) markers. Based on the eight polymorphic markers, rootstocks MG 420A, MG101-14, Richter 99, Couderc 3309, and Kober 5BB were distinguishable. Riparia Gloire and Couderc 1616 could be distinguished from the others, but not from one another, and SO4 and 5C also could be distinguished from the others, but not from one another.

scholarly journals Development of SCAR Markers Based on Improved RAPD Amplification Fragments and Molecular Cloning for Authentication of Herbal Medicines Angelica sinensis, Angelica acutiloba and Levisticum officinale

2015 ◽  
Vol 10 (10) ◽  
pp. 1934578X1501001 ◽  
Author(s):  
Chun Zhang ◽  
Zhiqiang Mei ◽  
Jingliang Cheng ◽  
Yin He ◽  
Md. Asaduzzaman Khan ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Scar Marker ◽  
Herbal Medicines ◽  
Pcr Amplification ◽  
Angelica Sinensis ◽  
Scar Markers ◽  
Helpful Tool ◽  
Sequence Characterized Amplified Region ◽  
Ecological Conservation ◽  
Angelica Acutiloba

Molecular cloning from DNA fragments of improved RAPD amplification of Angelica sinensis, Angelica acutiloba and Levisticum officinale, provided novel sequence-characterized amplified region (SCAR) markers A13, A23, Al-34 and Al-0 whose sequences were deposited in the GenBank database with the accession numbers KP641315, KP641316, KP641317 and KP641318, respectively. By optional PCR amplification, the SCAR markers A13 and A23 are Levisticum officinale-specific, whereas the SCAR marker Al-34 is Angelica acutiloba-specific, and the SCAR marker Al-0 is Angelica sinensis-specific. These diagnostic SCAR markers may be useful for genetic authentications, for ecological conservation of all three medicinal plants and as a helpful tool for the genetic authentication of adulterant samples.

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 Evaluation of SCAR Markers to Identify Raspberry Cultivars

HortScience ◽  
1995 ◽  
Vol 30 (4) ◽  
pp. 856B-856 ◽  
Author(s):  
Jean-Guy Parent ◽  
Daniele Page
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Sequence Information ◽  
Scar Markers ◽  
Certification Program ◽  
Reaction Conditions ◽  
Sequence Characterized Amplified Region ◽  
Sequence Method ◽  
Scar Primers

Random amplified polymorphic DNA (RAPD) markers are used in Quebec's certification program to verify the identity of raspberry cultivars. However, sequence characterized amplified region (SCAR) markers, less sensitive to modifications in reaction conditions, could be derived from RAPD markers. Our objective was to evaluate the potential of SCAR markers to replace the RAPD ones. Five RAPD markers obtained with primer OPG06 (length of 520, 700, 825, 1450, and 2000 bp) were cloned in pTZ/PC or pCRII vectors. Extremities of the cloned markers were sequenced by the nonradioactive silver sequence method using pUC/M13 forward and reverse primers. Sequence information was used to make SCAR primers, similar in length to standard PCR primers. Some SCAR primers were elongated RAPD primers, whereas others were from internal regions. Ability of primer pairs and combination of primer pairs to discriminate cultivars of our certification program was compared with their RAPD counterparts as well as with the technical feasibility of both methods.

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