PCR-RFLP for authentication of different species of processed snappers using mitochondrial D-loop region by single enzyme

Sivaraman, Balasubramanian; Jeyasekaran, G.; Shakila, R. Jeya; Alamelu, Venkatesan; Wilwet, Lidiya; Aanand, S.; Sukumar, D.

doi:10.1016/j.foodcont.2018.02.028

Cited by 16 publications

(6 citation statements)

References 30 publications

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“…However, these methods also exhibit some limitations, such as complex procedures, poor stability, and poor reproducibility (Chapela et al, 2007;Larraín, Díaz, Lamas, Uribe, & Araneda, 2014;Rasmussen & Morrissey, 2009). The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique, which was developed based on fingerprinting technology, is most widely used for species identification because of its simple procedure, low cost, and good reproducibility (Sivaraman et al, 2018;Wilwet, Jeyasekaran, Shakila, Sivaraman, & Padmavathy, 2018). Moreover, it just needs PCR thermocycler and electrophoresis apparatus, which means most laboratories could bear the cost, that is also a realistic factor in most developing countries.…”

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confidence: 99%

Methodology and application of PCR‐RFLP for species identification in tuna sashimi

et al. 2020

Food Science & Nutrition

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The Thunnini, or tuna, comprise many species with very different commercial values. The principal raw tuna product on the market is sashimi, for which the species used is difficult to identify through conventional morphological analysis. The present study amplified the cytochrome b gene ( Cytb ) of 4 major tuna species used for preparing sashimi—yellowfin tuna ( Thunnus albacares ), southern bluefin tuna ( Thunnus maccoyii ), bigeye tuna ( Thunnus obesus ), and Atlantic bluefin tuna ( Thunnus thynnus )—and 4 species commonly mislabeled as components of tuna sashimi—albacore tuna ( Thunnus alalunga ), skipjack tuna ( Katsuwonus pelamis ), striped marlin ( Tetrapturus audax ), and swordfish ( Xiphias gladius ). Polymerase chain reaction (PCR) amplicons were digested with 5 restriction enzymes— Eco 147 I, Hinf I, Mbo I, Xag I, and Hind II—to obtain characteristic restriction maps of the above‐mentioned raw tuna species and the commonly mislabeled species. An identification method using PCR restriction fragment length polymorphism (PCR‐RFLP) was established and validated using 39 commercial tuna sashimi samples, which verified that this method provides results consistent with those obtained by classical sequencing. PCR‐RFLP has several advantages over classical sequencing, such as simplicity, speed and accuracy. This technique could support species identification for raw tuna and sashimi.

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confidence: 99%

Methodology and application of PCR‐RFLP for species identification in tuna sashimi

et al. 2020

Food Science & Nutrition

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“…Teknik PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) adalah metode yang paling cocok untuk autentikasi berbagai seafood yang dapat memfasilitasi lembaga inspeksi makanan untuk menegakkan peraturan pelabelan dan meminimalkan penipuan seafood (Sivaraman et al, 2018). Keunggulan utama PCR-RFLP adalah tekniknya sederhana, cepat, kuat, dan murah dibandingkan dengan barcode DNA menggunakan sekuensing mtDNA (Anjalia et al, 2019).…”

Section: Pendahuluanunclassified

“…Di lain sisi, spesies L. sanguineus dan L. erythopterus dibedakan dengan enzim restriksi endonuklease MaeII, karena profil RFLP dari dua spesies ini tidak bisa dibedakan dengan HaeIII, ScaI dan SnaBI (Zhang et al, 2006). Berdasarkan penelitian Sivaraman et al (2018), PCR-RFLP dengan menargetkan gen D-loop pada sembilan spesies kakap memberikan pola yang serupa pada spesies L. fulvus dan L. fulviflamma karena kesamaan identitas yang tinggi (94%), sedangkan tujuh spesies lainnya termasuk spesies kakap merah (L. argentimaculatus dan L. gibbus) dapat diferensiasi dengan jelas menggunakan enzim Tsp509I yang dipilih berdasarkan analisis in silico (WATCUT) dan laporan beberapa penelitian sebelumnya yang terbukti mampu membedakan spesies.…”

Section: Pendahuluanunclassified

PCR-RFLP Design for Authentication of Red Snapper Species Based on CYB Gene

Timbuleng¹,

Kolondam²,

Katili³

2021

JIP

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The PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique is a species identification method that can facilitate food inspection agencies to overcome mislabelling. In addition, this technique is simple, fast, powerful, and cheap compared to DNA barcodes. This study aimed to accommodate the problem in determining restriction endonuclease enzymes for the digestion of PCR end products through the design of snapper species authentication using the CYB gene in silico. Differentiation of CYB gene sequences with DNA barcoding showed that all species could be differentiated with the highest similarity level in Red Fish (Sebastes) species by 98.9% and snapper species between L. malabaricus and L. erythropterus by 99.8%. Enzyme tracing based on sequences variation of snapper species with substitution species found three potential enzymes from the CYB gene sequence, namely, Accl, Fnu4HI, and Tsp45I. Where all these enzymes can discriminate red snapper species among other.Key words: PCR-RFLP; CYB gene; Red snapperAbstrakTeknik PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) merupakan metode identifikasi spesies yang dapat memfasilitasi lembaga inspeksi makanan untuk mengatasi mislabelling. Selain itu, teknik ini sederhana, cepat, kuat, dan murah dibandingkan dengan barcode DNA. Penelitian ini bertujuan untuk mengakomodasi masalah dalam menentukan enzim restriksi endonuklease untuk digesti produk akhir PCR lewat perancangan autentikasi spesies ikan kakap menggunakan gen CYB secara in silico. Diferensiasi sekuens gen CYB dengan DNA barcoding menunjukkan semua spesies dapat dibedakan dengan tingkat kesamaan tertinggi pada spesies Red Fish (Sebastes) sebesar 98,9% dan spesies kakap antara L. malabaricus dan L. erythropterus sebesar 99,8%. Penelusuran enzim berdasarkan variasi sekuens spesies kakap dengan spesies substitusi ditemukan sebanyak tiga enzim yang berpotensi yaitu, Accl, Fnu4HI, dan Tsp45I. Semua enzim tersebut dapat memdiskriminasikan spesies kakap merah dari spesies lainnya.Kata kunci: PCR-RFLP; gen CYB; ikan kakap merah

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“…In RFLP, after PCR amplification, target DNA is digested using enzymes, and the resulting restriction profiles are monitored by gel electrophoresis, so the profiles of different samples can be compared . Recently, 5 tuna species, 9 different snapper species, and 16 commercial sea cucumber species have been discriminated by PCR-RFLP targeting mitochondrial regions. − An RFLP approach was also used for detecting cat-meat contents as low as 0.01% in mixtures and meatballs . In spite of being one of the techniques most frequently used, RFLP analyses and the use of other classical DNA markers suffer from being unsuitable for obtaining reliable quantitative information.…”

Section: Classical Dna Markersmentioning

confidence: 99%

Review of Recent DNA-Based Methods for Main Food-Authentication Topics

Böhme

Calo-Mata

Barros‐Velázquez

et al. 2019

J. Agric. Food Chem.

156

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Adulteration and mislabeling of food products and the commercial fraud derived, either intentionally or not, is a global source of economic fraud to consumers but also to all stakeholders involved in food production and distribution. Legislation has been enforced all over the world aimed at guaranteeing the authenticity of the food products all along the distribution chain, thereby avoiding food fraud and adulteration. Accordingly, there is a growing need for new analytical methods able to verify that all the ingredients included in a foodstuff match the qualities claimed by the manufacturer or distributor. In this sense, the improved performance of most recent DNA-based tools in term of sensitivity, multiplexing ability, high-throughput, and relatively low-cost give them a game-changing role in food-authenticity-related topics. Here, we provide a thorough and updated vision on the recently reported approaches that are applying these DNA-based tools to assess the authenticity of food components and products.

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PCR-RFLP for authentication of different species of processed snappers using mitochondrial D-loop region by single enzyme

Cited by 16 publications

References 30 publications

Methodology and application of PCR‐RFLP for species identification in tuna sashimi

Methodology and application of PCR‐RFLP for species identification in tuna sashimi

PCR-RFLP Design for Authentication of Red Snapper Species Based on CYB Gene

Review of Recent DNA-Based Methods for Main Food-Authentication Topics

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