Perbandingan Metode Isolasi DNA pada Produk Perikanan Segar dan Olahan Comparison of DNA Isolation Methods for Fresh and Processed Seafood
Article Sidebar
Accepted
31 October 2020
Published
22 December 2020
Keywords:
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CTAB, DNA isolation, DNA purification, identification
Abstract
Seafood product is an important commodity in the global trade market, however, seafood fraud has been increasingly reported. Therefore, a method to specifically identify species of seafood products is needed. DNA methods gain many interests for detection of seafood fraud due to its robustness. This study was aimed to determine the effectiveness of several methods for isolation of DNA from fresh and processed seafood. The DNA isolation methods used in this study were the CTAB DNAzol, TianGen, Qiagen, and Fasmac.. DNA concentration and purity were determinedusing nanodrop spectrofotometry and electrophoresis. DNA isolation showed that the DNA concentration of fresh seafood products was higher than the processed seafood products. DNA isolation using CTAB method have higher levels of DNA purity (1.60-2.00) than using commercial kits in all samples. The commercial kits offer a simple procedure and minimize the possibility of environmental contaminants.
References
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Bohme K, Calo-Mata P, Barros-Velazques J, Ortea I. 2019. Review of recent DNA-based methods for main food authentication topics. Journal of Agriculture and Food Chemistry. 67: 3854−3864.
Carvalho DC, Palhares RM, Drummond MG, Frigo TB. 2015. DNA barcoding identification of commercialized seafood in South Brazil: A governmental regulatory forensic program. Food Control. 50: 784–788.
Chen H, Rangasamy M, Tan SY, Wang H, Siegfried BD. 2010. Evaluation of five methods for total DNA extraction from western corn rootworm beetles. PLoS One. 5(8).
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Di Pinto A, Marchetti P, Mottola A, Bozzo G, Bonerba E, Ceci E, Bottaro M, Tantillo G. 2015. Species identification in fish fillet products using DNA barcoding. Journal of Fisheries Research. 170: 9- 13.
Dwiyitno, Hoffman S, Parmentier K, Van Keer C. 2018. Method comparison of DNA isolation and quantification for fish and seafood authenticity determination. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology 13(3):115-124.
Fitriya RS, Ibrahim M, Lisdiana L. 2015. Keefektifan metode isolasi DNA kit dan CTAB/NaCl yang dimodifikasi pada Staphylococcus aureus dan Shigella dysentriae. LenteraBio. 4(1): 87-92.
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Harahap MR. 2018. Elektroforesis: Analisis elektronika terhadap biokimia genetika. Jurnal Ilmiah Pendidikan Teknik Elektro. 2(1): 21-26.
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Lamendin R, Miller K, Ward RD. 2015. Labelling accuracy in Tasmanian seafood: An investigation using DNA barcoding. Food Control. 47(1): 436–443.
Lee JH, Park Y, Choi JR, Lee EK, Kim HS. 2010. Comparisons of three automated systems for genomic DNA extraction in a clinical diagnostic laboratory. Yonsei Medical Journal. 51(1): 104-110.
Lin Y, Yanhua J, Qingjiao L, Zhe S, Lianzhu W, Yuxiu Z. 2016. A comparison of eight methods for DNA etraction from processed seafood products. Food Science and Technology Research. 22 (6): 751-757.
Mackie IM, Pryde SE, Sotelo GC, Medina I, Martin IR, Quinteiro J, ReyMendez M, Rehbein H. 1999. Challenges in the identification of species of canned fish. Trend and Food Science and Technology. 10(1): 9-14.
Maulid YD, Nurilmala M. 2015. DNA Barcoding untuk Autentikasi Produk Ikan Tenggiri (Scomberomorus sp.) DNA. Jurnal Akuatika. 4: 154–160.
Maulid DY, Nurilmala M, Nurjanah, Maddupa H. 2016. Karakteristik molekuler cytochrome b untuk DNA barcoding ikan tenggiri. Jurnal Pengolahan Hasil Perikanan Indonesia. 19(1): 9-16.
Milana V, Fusari A, Rossi AR, Sola L. 2011. Molecular and morphological identification of an uncommon centrolophid fish. Central European Journal of Biology. 6(3): 440-445.
Muhammad H, Iqbal Z, Iqbal MU, Younas T, Bashir Q. 2016. An efficient method for DNA isolation from fish fin. Pakistan Journal of Agriculture Sciences. 53(4): 843–850.
Naaum AM, Warner K, Mariani S, Hanner RH, Carolin CD. 2016. Seafood mislabeling incidence and impacts. In A. Naaum, & R. Hanner (Eds.). Seafood mislabeling incidence and impacts seafood authenticity and traceability. San Diego (US): Academic Press.
Nichols PD, Glencross B, Petrie JR, Singh SP. 2014. Readily available sources of long-chain omega-3 oils: is farmed Australian seafood a better source of the good oil than wild-caught seafood?. Nutrients. 6(3): 1063–1079.
Sambrook J, Russel DW. 2001. Molecular Cloning: A Laboratory Manual. Edisi ke-3. New York (US): Cold Spring Harbor Laboratory Press.
Stevanofa P, Taseva M, Georgieva T, Gotcheva V, Angelov A. 2013. A modified CTAB method for DNA extraction from soybean and meat products. Biotechnology & Biotechnological Equipment. 27(3): 3803-3810.
Suparningtyas JF, Pramudyawardhani OD, Purwoko D, Tajuddin T. 2018. Analisis filogenetik beberapa klon karet dengan marka AFLP (Amplified Fragment Length Polymorphism). Jurnal Bioteknologi & Biosains Indonesia. 5(1): 8-19.
Wasko AP, Martins C, Oliveira C, Foresti F. 2003. Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales. Hereditas. 138:161–165.
Westermeier. 2004. Electrophoresis in Practice: A Guide to Theory and Practice. New Jersey (US): John Wiley & Sons Inc.
Wong EHK, Hanner RH. 2008. DNA barcoding detects market substitution in North American seafood. Food Research International. 41(8): 828–837.
Wongsawad C, Wongsawad P, Chai JY, Paratapsilpin T, Anuntalabhochai S. 2006. DNA quantities and qualities from various stages of some trematodes using optical and hat-RAPD methods. Southeast Asian Journal Tropical Medicines Public Health. 37(3): 62-68.
Zhang J, Hanner R. 2012. Molecular approach to the identification of fish in the South China Sea. PLoSONE. 7(2) : e30621
Abdullah A, Sativa HA, Nurhayati T, Nurilmala M. 2019a. Pemanfaatan DNA barcoding untuk ketertelusuran label berbagai produk olahan ikan berbasis surimi komersial. Jurnal Pengolahan Hasil Perikanan Indonesia. 22: 508–519.
Abdullah A, Nurilmala M, Sitaresmi KP. 2019b. DNA mini-barcodes sebagai penanda molekuler untuk ketertelusuran label pangan berbagai produk ikan layur. Jurnal Pengolahan Hasil Perikanan Indonesia. 22(1): 33-40.
Alaey M, Naderi R, Verzaei A, Khalighi A, Salami A. 2005. Comparing study between four different methods of genomic DNA extraction from Cyclamen persicum Mill. International Journal of Agriculture and Biology. 7(6): 882-884.
Armani A, Guardone L, La Castellana R, Gianfaldoni D, Guidi A, Castigliego L. 2015. DNA barcoding reveals commercial and health issues in ethnic seafood sold on the Italian market. Food Control. 55: 206–214.
Asche F, Bellemare MF, Roheim C, Smith MD, Tveteras S. 2015. Fair enough? Food security and the international trade of seafood. World Development. 67: 151–160.
Bellard MG, Outdet P, Chambon P. 1973. Isolation of high molecular weight DNA from mammalian cells. European Journal of Biochemistry. 36(1): 32-38.
Bohme K, Calo-Mata P, Barros-Velazques J, Ortea I. 2019. Review of recent DNA-based methods for main food authentication topics. Journal of Agriculture and Food Chemistry. 67: 3854−3864.
Carvalho DC, Palhares RM, Drummond MG, Frigo TB. 2015. DNA barcoding identification of commercialized seafood in South Brazil: A governmental regulatory forensic program. Food Control. 50: 784–788.
Chen H, Rangasamy M, Tan SY, Wang H, Siegfried BD. 2010. Evaluation of five methods for total DNA extraction from western corn rootworm beetles. PLoS One. 5(8).
Chowdhury MM, Rahman AS MS, Nahar L, Rahman M, Al Reza H, Ahmed MS. 2016. Efficiency of different DNA extraction methods for fish tissues: A comparative analysis. IOSR Journal of Pharmacy & Biologocal Science. 11(3): 11-15.
Dhaneesh KV, Noushad KM, Ajith KTT. 2012. Nutritional evaluation of commercially important fish species of Lakshadweep archipelago, India. PLoS One. 7(9): e45439.
Di Pinto A, Marchetti P, Mottola A, Bozzo G, Bonerba E, Ceci E, Bottaro M, Tantillo G. 2015. Species identification in fish fillet products using DNA barcoding. Journal of Fisheries Research. 170: 9- 13.
Dwiyitno, Hoffman S, Parmentier K, Van Keer C. 2018. Method comparison of DNA isolation and quantification for fish and seafood authenticity determination. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology 13(3):115-124.
Fitriya RS, Ibrahim M, Lisdiana L. 2015. Keefektifan metode isolasi DNA kit dan CTAB/NaCl yang dimodifikasi pada Staphylococcus aureus dan Shigella dysentriae. LenteraBio. 4(1): 87-92.
Gardenia L, Koesharyani I. 2011. Metode isolasi deoxyribo nucleic acid bakteri dari organ ikan nila (Oreochromis niloticus) untuk diagnosa Streptococcociasis dengan teknik Polymerase Chain Reaction. Jurnal Riset Akuakultur. 6(3): 469-477.
Harahap MR. 2018. Elektroforesis: Analisis elektronika terhadap biokimia genetika. Jurnal Ilmiah Pendidikan Teknik Elektro. 2(1): 21-26.
Hartati D, Anto K, Taryono, Endang S, Widyatmoko A. 2007. Pendugaan keragaman genetik di dalam dan antar provenan pulai (Alstonia scholaris (L.) R. Br.) menggunakan penanda RAPD. Jurnal Pemuliaan Tanaman Hutan. 1(2): 1-8.
Heptinstall J, Rapley R. 2000. The Nucleic Acid Protocold Handbook. Totowa NJ: Humana Press Inc.
Hu Q, Liu Y, Yi S, Huang D. 2015. A comparison of four methods for PCR inhibitor removal. Forensic Science International: Genetics. 16: 94–97.
Khaksar R, Carlson T, Schaffner DW, Ghorashi M, Best D, Jandhyala S. 2015. Unmasking seafood mislabeling in U.S. markets: DNA barcoding as a uniq technology for food authentication and quality control. Food Control. 56(1): 71–76.
Lai Y, Deepali S, Norman A, Fengzhu S. 2003. The mutation process of microsatellites during the polimerase chain reaction. Journal of Computational Biology. 10(2): 143-155
Lamendin R, Miller K, Ward RD. 2015. Labelling accuracy in Tasmanian seafood: An investigation using DNA barcoding. Food Control. 47(1): 436–443.
Lee JH, Park Y, Choi JR, Lee EK, Kim HS. 2010. Comparisons of three automated systems for genomic DNA extraction in a clinical diagnostic laboratory. Yonsei Medical Journal. 51(1): 104-110.
Lin Y, Yanhua J, Qingjiao L, Zhe S, Lianzhu W, Yuxiu Z. 2016. A comparison of eight methods for DNA etraction from processed seafood products. Food Science and Technology Research. 22 (6): 751-757.
Mackie IM, Pryde SE, Sotelo GC, Medina I, Martin IR, Quinteiro J, ReyMendez M, Rehbein H. 1999. Challenges in the identification of species of canned fish. Trend and Food Science and Technology. 10(1): 9-14.
Maulid YD, Nurilmala M. 2015. DNA Barcoding untuk Autentikasi Produk Ikan Tenggiri (Scomberomorus sp.) DNA. Jurnal Akuatika. 4: 154–160.
Maulid DY, Nurilmala M, Nurjanah, Maddupa H. 2016. Karakteristik molekuler cytochrome b untuk DNA barcoding ikan tenggiri. Jurnal Pengolahan Hasil Perikanan Indonesia. 19(1): 9-16.
Milana V, Fusari A, Rossi AR, Sola L. 2011. Molecular and morphological identification of an uncommon centrolophid fish. Central European Journal of Biology. 6(3): 440-445.
Muhammad H, Iqbal Z, Iqbal MU, Younas T, Bashir Q. 2016. An efficient method for DNA isolation from fish fin. Pakistan Journal of Agriculture Sciences. 53(4): 843–850.
Naaum AM, Warner K, Mariani S, Hanner RH, Carolin CD. 2016. Seafood mislabeling incidence and impacts. In A. Naaum, & R. Hanner (Eds.). Seafood mislabeling incidence and impacts seafood authenticity and traceability. San Diego (US): Academic Press.
Nichols PD, Glencross B, Petrie JR, Singh SP. 2014. Readily available sources of long-chain omega-3 oils: is farmed Australian seafood a better source of the good oil than wild-caught seafood?. Nutrients. 6(3): 1063–1079.
Sambrook J, Russel DW. 2001. Molecular Cloning: A Laboratory Manual. Edisi ke-3. New York (US): Cold Spring Harbor Laboratory Press.
Stevanofa P, Taseva M, Georgieva T, Gotcheva V, Angelov A. 2013. A modified CTAB method for DNA extraction from soybean and meat products. Biotechnology & Biotechnological Equipment. 27(3): 3803-3810.
Suparningtyas JF, Pramudyawardhani OD, Purwoko D, Tajuddin T. 2018. Analisis filogenetik beberapa klon karet dengan marka AFLP (Amplified Fragment Length Polymorphism). Jurnal Bioteknologi & Biosains Indonesia. 5(1): 8-19.
Wasko AP, Martins C, Oliveira C, Foresti F. 2003. Non-destructive genetic sampling in fish. An improved method for DNA extraction from fish fins and scales. Hereditas. 138:161–165.
Westermeier. 2004. Electrophoresis in Practice: A Guide to Theory and Practice. New Jersey (US): John Wiley & Sons Inc.
Wong EHK, Hanner RH. 2008. DNA barcoding detects market substitution in North American seafood. Food Research International. 41(8): 828–837.
Wongsawad C, Wongsawad P, Chai JY, Paratapsilpin T, Anuntalabhochai S. 2006. DNA quantities and qualities from various stages of some trematodes using optical and hat-RAPD methods. Southeast Asian Journal Tropical Medicines Public Health. 37(3): 62-68.
Zhang J, Hanner R. 2012. Molecular approach to the identification of fish in the South China Sea. PLoSONE. 7(2) : e30621
Authors
SetiaputriA. A., Rohmad BarokahG., Alsere Bardian SahabaM., Dini ArbajayantiR., FabellaN., Mustika PertiwiR., NurilmalaM., NugrahaR., & AbdullahA. (2020). Perbandingan Metode Isolasi DNA pada Produk Perikanan Segar dan Olahan: Comparison of DNA Isolation Methods for Fresh and Processed Seafood. Jurnal Pengolahan Hasil Perikanan Indonesia, 23(3), 447-458. https://doi.org/10.17844/jphpi.v23i3.32314
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