RAPD-PCR and real-time Pcr Hrm based genetic variation evaluations of &lt;i&gt;Urtica dioica&lt;/i&gt; parts, ecotypes and evaluations of morphotypes in Turkey

Uzonur, Irem; Akdeniz, Gamze; Katmer, Zeynep; Ersoy, Seyda Karaman

doi:10.4314/ajtcam.v10i2.7

Cited by 3 publications

(1 citation statement)

References 24 publications

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“…A 25-μL reaction system was chosen to optimize the RAPD reaction conditions based on previous work (Comes and Abbott et al, 2000;Esselman et al, 2000;Bautista et al, 2001;Lu et al, 2002;Collins et al, 2003;Uzonur et al, 2012;Xin et al, 2014).…”

Section: Establishing a Rapd Reaction Systemmentioning

confidence: 99%

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

Zhang

Wang

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The aims of this study were to establish a random amplified polymorphic DNA (RAPD) fingerprint database of chloroplast DNA (cpDNA) from different cultivars of Cornus officinalis and to convert RAPD markers to sequence characterized amplified regions (SCAR) markers. A method of extraction was established that was suitable for obtaining cpDNA from samples rapidly dried in silicone; an RAPD fingerprint database was built; and the genetic distance between samples was used as statistical clustering variables for calculating DICE genetic similarity coefficients and for building a kinship tree chart. RAPD markers were converted to SCAR markers to design specific primers, and samples from C. officinalis cultivars, plants of the same family, and its adulterants, were used for amplification and identification. Fifteen amplified primers with stable polymorphisms were screened for amplification of 130 copies of materials. In total, 57 sites were achieved, 40 of which were polymorphic, and the polymorphic rate was up to 70.18%. A genetic tree was built based on (2015) seven cultivars. SCAR markers of C. officinalis cpDNA were successfully converted into RAPD markers. cpDNA samples from hawthorn, C. officinalis, Cornus wood, and grape were used for SCAR amplification, and their bands were distinctly different. In conclusion, SCAR markers and cpDNA may be used for research on C. officinalis and its adulterants, and the results may provide a basis for identifying germplasm and screening fine varieties at a molecular level.

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Section: Establishing a Rapd Reaction Systemmentioning

confidence: 99%

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

Zhang

Wang

et al. 2015

Genet. Mol. Res.

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Potential Application of PCR Based Molecular Methods in Fish Pathogen Identification: A Review

Ador

Haque

Paul

et al. 2021

Aquaculture Studies

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Molecular biology developments have led to fast growth in new methods for fish disease diagnosis. Molecular diagnostic methods are rapid and more specific, more sensitive than the culture of pathogens, serology, histology, and biochemical methods which are traditionally utilized to identify causative agent fish disease. Molecular diagnostic methods are valuable for detecting specific pathogens that are difficult to culture in vitro or require a long cultivation period and it significantly more rapid in providing results compared to culture. It enables earlier informed decision-making and rapid diagnosis of bacteremia, particularly for low levels of bacteria in specimens. Molecular techniques which have the major significance are mainly PCR-based molecular diagnostic methods including Polymerase Chain Reaction (PCR), Real-Time Polymerase Chain Reaction (RT-PCR), Multiplex Polymerase Chain Reaction (multiplexPCR), and Random Amplified Polymorphic DNA (RAPD). These have been increasingly utilized to diagnose fish disease for the last recent years. Molecular diagnostic methods can detect pathogens from asymptomatic fish, so disease outbreaks could be prevented. As a consequence, antibiotic treatment can be reduced and the development of antibiotic-resistant bacteria can be eliminated. In this review paper, we attempt to summarize the potentiality of PCR-based molecular diagnostic methods and their application in fish pathogen identification.

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Ordu İli’nde Urtica türlerinin kloroplast DNA trnL-F gen bölgelerini kullanarak genetik çeşitliliğinin belirlenmesi

Kolören¹,

Eker²

2018

Anadolu Journal of Agricultural Sciences

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ÖZET Urtica spp, Karadeniz Bölgesi Ordu ilinde fındık alanlarında ve boş arazilerde en yaygın olan yabancı ot türlerinden biridir. Bu çalışmada, Urtica spp.'nin genetik farklılıklarının belirlenmesi amacıyla Ordu ilinden 20 adet Urtica spp. örnekleri toplanmış ve kloroplast trnL-F gen bölgelerine özgü primerler kullanılarak analiz edilmiştir. DNA izolasyonu, CTAB (hexadecyl-trimethyl-ammoniumbromide) protokolü modifiye edilerek gerçekleştirilmiştir. Kloroplast DNA trnL-F gen bölgeleri için, GenBank'tan temin edilen referans sekans dizileri ile çalışmada elde edilen sekans sonuçları karşılaştırılmıştır. Dizilerin genetik uzaklıkları MEGA6 paket programı kullanılarak hesaplanmış ve bu veri setleri yardımıyla filogenetik ağaç çizimi sağlanmıştır. Bölgede Urtica cinsine ait 4 örnek (Fatsa 1-U1, Ulubey-U2, Perşembe 1-U3 ve Altınordu 3-U4) seçilmiş ve genetik analizlerde kullanılmıştır. Çalışma sonucunda, bu örneklerin hepsinin Urtica dioica ile aynı soyda yer aldığı belirlenmiştir. Fatsa 1-U1 ve Ulubey-U2 örnekleri sırasıyla % 99.2 ve % 99.7 nükleotid dizisi benzerliği bakımından U. dioica'nın (KF138424) yakın akrabası olarak görülmüştür. Bu ilişkiler sırasıyla NJ, MP ve ML ağaçlarında yer alan % 100, % 100 ve % 99 algoritma değerleri ile desteklenmiştir. Perşembe 1-U3 ve Altınordu 3-U4 örnekleri ile U. dioica (AY208725) arasındaki nükleotid dizisi benzerlikleri sırasıyla % 99.5 ve % 100 bulunmuştur. Bu türün algoritma değerleri ise NJ, MP ve ML'de sırasıyla % 67, % 64 ve % 64 olarak belirlenmiştir. ABSTRACTThe main goal of this study is to determine genetic differences of Urtica spp. which are one of the most common weed species in the hazelnut and uncultivated areas of Ordu province in the Black Sea Region, by using primers specific to chloroplast trnL-F intergenic spacer. Twenty Urtica spp. samples were collected from hazelnut gardens and uncultivated areas in Ordu province. DNA extraction was made by modifying the CTAB (hexadecyl-trimethyl-ammonium bromide) protocol. The sequence data of these samples were compared with the reference sequences retrieved from GenBank for the chloroplast DNA trnL-F intergenic spacer region. Genetic distances among the sequences were calculated using MEGA6 packet program, and phylogeny trees were drawn using these data sets. Four Urtica samples (Fatsa 1-U1, Ulubey-U2, Persembe 1-U3 and Altinordu 3-U4) among our samples were selected and used in phylogenetic analysis. Our species were placed in the same lineage group with Urtica dioica. Fatsa 1-U1 and Ulubey-U2 appeared to have close to U. dioica (KF138424) with 99.2 % and 99.7 % nucleotide sequence similarity. This relations were supported with 100 %, 100 % and 99 % bootstrap values in the NJ, MP and ML trees, respectively. The nucleotide sequence similarities of Persembe 1-U3 and Altinordu 3-U4 with U. dioica (AY208725) were 99.5 % and 100 %, and bootstrap values of this species were 67 %, 64 % and 64 % in the NJ, MP and ML.

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RAPD-PCR and real-time Pcr Hrm based genetic variation evaluations of <i>Urtica dioica</i> parts, ecotypes and evaluations of morphotypes in Turkey

Cited by 3 publications

References 24 publications

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

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

Potential Application of PCR Based Molecular Methods in Fish Pathogen Identification: A Review

Ordu İli’nde Urtica türlerinin kloroplast DNA trnL-F gen bölgelerini kullanarak genetik çeşitliliğinin belirlenmesi

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