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Identification of different oyster species using RAPD-PCR

Yıl 2017, Cilt 34, Sayı 1, 25 - 30, 21.02.2017
https://doi.org/10.12714/egejfas.2017.34.1.04

Öz

Rapid determination of the genetic differences between some oyster samples observed in the Aegean Sea that were assumed as an invasive species and domestic oyster (Ostrea edulis, Linnaeus 1758) using RAPD (Random Amplified Polymorphic DNA)- PCR (Polymerase Chain Reaction) markers was aimed in this study. In this regard, domestic species samples and the other samples collected from Altınoluk coasts which were morphologically different than Ostrea species and were showing similarities to Crassostrea genus were genetically indetified by using 8 RAPD profiles. Total 343 bands were observed in the study. Polymorphism rate was found higher in the samples that might belong to Crassostrea genus. 6 of all loci considered in this study were found highly identical for these species. Total of 16 species-spesific diagnostic bands: 11 bands for the invasive species and 5 bands for the domestic species, were determined.

Kaynakça

  • Acarlı, S., Yıldız H., Gökçek Ö.E., Karahan, B., Lök, A., Vural, P., Gündüz, F. & Aydın, S. (2015a). Türkiye’de, Marmara, Ege ve Akdeniz Kıyılarındaki Yerli Akivades (Ruditapes decussatus) Populasyonları ile İstilacı Japon Akivadesi Populasyonlarının (Ruditapes philippinarium) Morfolojik ve Genetik Yapılarının İncelenmesi. 18. Ulusal Su Ürünleri Sempozyum Kitabı (1-4 Eylül 2015, İzmir), 482 (Poster Sunum)
  • Acarlı, S., Yıldız H., Gökçek Ö.E., Karahan, B., Lök, A., Vural, P., Gündüz, F. & Aydın, S. (2015b). Bandırma Körfezi İstiridye Populasyonunnu PCR Tabanlı Yöntemlerle İncelenmesi. 18. Ulusal Su Ürünleri Sempozyum Kitabı (1-4 Eylül 2015, İzmir), 483 (Poster Sunum)
  • Aljanabi, S. M,. & Martinez, I. (1997). Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques. Nucleic Acids Research, 25(22): 4692-4693. doi: 10.1093/nar/25.22.4692
  • Aranishi, F., & Okimoto, T. (2004). Genetic Relationship between Cultured Populations of Pacific Oyster Revealed by RAPD Analysis. Journal of Applied Genetics, 45: 435-443. doi: 10.1007/BF03194632
  • Atienzar, F., Evenden, A. J., Savva, D. & Depledge, M. (2000). Optimized RAPD analysis generates High Quality genomic DNA profilex at high annealing temprature. BioTechnniques, 28(1): 52- 53.
  • Atienzar, F.A,. & Jha, N.A. (2006). The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: A critical review. Mutation Research, 613, 76- 102. doi: 10.1016/j.mrrev.2006.06.001
  • Bilgen, G., Akhan, S., Arabacı, M., & Oğuz, İ. (2007). Genetic Diversity of Gilthead Seabream (Sparus aurata) Broodstocks as Determined by RAPD-PCR. The İsraeli Journal of Aquaculture- Bamidgeh, 59 (4): 217-233.
  • Crocetta, F., Mariottini, P., Salvi, D., & Oliverio, M. (2015). Does GenBank provide a reliable DNA barcode reference to identify small alien oysters invading the Mediterranean Sea? Journal of the Marine Biological Association of the United Kingdom, 95(1): 111–122. doi: 10.1017/S0025315414001027
  • Çınar, M.E., Bilecenoğlu, M., Öztürk, B., Katağan, T., Yokeş, M.B., Aysel, V., Açık, S., Dağlı, E., Özcan, T. & Erdoğan, H. (2011). An updated review of alien species on the coasts of Turkey. Mediterranean Marine Science. Mediterranean Marine Science, 12(2): 257-315.
  • David, D.C. & Savini, D. (2011). Molecular Approaches to Bivalve Population Studies: A Review. Analele Ştiinţifice ale Universităţii, Alexandru Ioan Cuza”, Secţiunea Genetică şi Biologie Moleculară, TOM XII, 1-14.
  • Doğan, A., Önen, M. & Öztürk, B. (2007). Ildır Körfezi (İzmir-Çeşme) Bivalvia (Mollusca) Faunası. Türk Sucul Yaşam Dergisi, 3-5 (5-8): 27-35.
  • Farhadi, A., Farahmand, H., Mirvaghefi, A., & Khalili, B. (2011). A Genotoxicological Study in Persian Gulf on Rock Oyster (Soccostrea cucullata) using Micronuclei and RAPID Assays. International Journal of Environmental Research, 5(2): 567- 572.
  • Gunter, G. (1950). The generic status of living oysters and scientific name of the common American species. American Midland Naturalist, 43 (2):438-449.
  • Hare, M.P. & Avise, J.C. (1998). Population structure in the American oyster as inferred by nuclear gene genealogies. Molecular Biology Evolotion, 15:119-128.
  • İlhak, O.İ. & Arslan, A. (2007). Rastgele Çoğaltılmış Polimorfik DNA Yöntemiyle Kanatlı Etlerinde Tür Tayini. Fırat Üniversitesi Sağlık Bilimleri Dergisi; 21 (4): 167-171.
  • Klinbunga, S., Amparyup, P., Khamnamtong, N., Tassanakajon, A., Jaraybhand, P. & Yoosukh W. (2000). Molecular Genetic Markers for Taxonomy of Oysters in Thailand. Fisheries Scicence, 68(2): 1087-1090.
  • Klinbunga, S., Ampayup, P., Tassanakajon, A., Jarayabhand, P. & Yoosukh, W. (2001). Genetic diversity and molecular markers of commercial oysters (Genera Crassostrea, Saccostrea and Striostrea) in Thailand determined by RAPD analysis. Marine Biotechnology, 3, 133–144. doi: 10.1007/s101260000057
  • Koh, M.C., Lim, C.H., Chua, S.B., Chew, S.T. & Phang, S.T.W. (1998). Random Amplified Polymorphic DNA (RAPD ) fingerprints for identification of red meat animal species. Meat Science, 48, 275-285. doi:10.1016/S0309-1740(97)00104-6
  • Lam, K. & Morton, B.(2003). Mitochondrial and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in Peral river Delta, Hong- Kong, China. Aquaculture 228: 1-13.
  • Lapègue S., Beaumont A., Boudry P., & Goulletquer P. (2008). European flat oyster – Ostrea edulis. Genimpact final scientific report, (s. 70-76).
  • Lee, C.J. & Chang, G.J. (1999). Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) fingerprints in forensic species identification. Forensic Science International, 67, 103-107.
  • Liua, Z.J. & Cordesb, J.F. (2004). DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238, 1– 37. doi: 10.1016/j.aquaculture.2004.05.027
  • Lök, A. (2000). İstiridye Biyolojisi ve Yetiştirme Teknikleri. T.C.Tarım Orman ve Köyişleri Bakanlığı, Tarımsal Üretim ve Geliştirme Genel Müdürlüğü, Ticari Balık Türlerinin Biyolojisi ve Yetiştirme Teknikleri Hizmet İçi Eğitim Seminer Eğitim Kitapçığı, Ankara: 102-121 (çağrılı bildiri)
  • Oliveria, A.L.D., Da Silva, D., Manzano, B.C., Abdel-Hamid, A.Z., Marcelino, M.Y., Zanotti-Magalhães, E.M., Magalhães, L.A. & Ribeiro-Paes, J.T. (2010). Genetic differences between strains of Biomphalaria glabrata (Planorbidae) that are susceptible and unsusceptible to schistosomiasis. Genetics and Molecular Research 9 (3): 1450-1459. doi: 10.4238/vol9-3gmr821
  • Öztürk, B., Doğan, A., Bitlis-Bakır, B. & Salman, A. (2014). Marine molluscs of the Turkish coasts: an updated checklist. Turkish Journal of Zoolgy, 38, 832-879. doi: 10.3906/zoo-1405-78
  • Rego, I., Martinez, A., Gonzalez-Tizon, A. G., Vieites, J., Leira, F. & Mendez, J. (2002). PCR Technique for Identification of Mussel Species. Journal of Agricultural and Food Chemistry, 50, 1780−1784.
  • Sleem, H.S. & Ali G.T. (2008). Application of RAPD-PCR in Taxonomy of Certain Freshwater Bivalves of Genus Caelatura. Global Journal of Molecular Sciences, 3 (1): 27- 31.
  • Toro, J.E. & Gonzalez, C.P. (2009). The genetic structure of the Chilean oyster (ostrea chilensis Philippi, 1845) in natural populations of southern Chile on RAPDs analysis. Revista de Biologia Marina Oceanografia, 44 (2): 467-476.
  • Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. & Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531-6535.
  • Yoosukh, W. & Duangdee, T. (1999). Living Oysters in Thailand. Phuket. Thailand: Phuket Marine Biological Center, 19: 363- 370.

Farklı istiridye türlerinin tespitinde RAPD-PZR kullanımı

Yıl 2017, Cilt 34, Sayı 1, 25 - 30, 21.02.2017
https://doi.org/10.12714/egejfas.2017.34.1.04

Öz

Bu çalışmada, Ege Denizi’nde gözlemlenen ve istilacı tür olduğu düşünülen bazı istiridye örnekleriyle, yerli istiridye türü olan Ostrea edulis (Linnaeus 1758) örnekleri arasındaki genetik farklılıkların tespitinin, RAPD (Rastgele Çoğaltılmış Polimorfik DNA)-PCR (Polimeraz Zincir Reaksiyonu) yardımıyla hızlı bir şekilde belirlenmesi amaçlanmıştır. Bu bağlamda, denizlerimizin yaygın türü olan Ostrea genusundan morfolojik olarak farklı olduğu gözlenen ve Crassostrea genusuna ait özellikler gösteren istiridye bireyleriyle, yerli tür 8 adet RAPD profili kullanılarak genetik olarak ayırt edilmiştir. Çalışmada toplam 343 bant elde edilmiştir. Polimorfizm oranı Crassostrea sp.’ye ait örneklerde daha yüksek bulunmuştur. Ele alınan lokuslardan 6 tanesinin ayrım gücü yüksek çıkmıştır. İstilacı türe ait 11, yerli türe ait 5 adet toplamda 16 adet türe-özgü diagnostik bant belirlenmiştir.

Kaynakça

  • Acarlı, S., Yıldız H., Gökçek Ö.E., Karahan, B., Lök, A., Vural, P., Gündüz, F. & Aydın, S. (2015a). Türkiye’de, Marmara, Ege ve Akdeniz Kıyılarındaki Yerli Akivades (Ruditapes decussatus) Populasyonları ile İstilacı Japon Akivadesi Populasyonlarının (Ruditapes philippinarium) Morfolojik ve Genetik Yapılarının İncelenmesi. 18. Ulusal Su Ürünleri Sempozyum Kitabı (1-4 Eylül 2015, İzmir), 482 (Poster Sunum)
  • Acarlı, S., Yıldız H., Gökçek Ö.E., Karahan, B., Lök, A., Vural, P., Gündüz, F. & Aydın, S. (2015b). Bandırma Körfezi İstiridye Populasyonunnu PCR Tabanlı Yöntemlerle İncelenmesi. 18. Ulusal Su Ürünleri Sempozyum Kitabı (1-4 Eylül 2015, İzmir), 483 (Poster Sunum)
  • Aljanabi, S. M,. & Martinez, I. (1997). Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques. Nucleic Acids Research, 25(22): 4692-4693. doi: 10.1093/nar/25.22.4692
  • Aranishi, F., & Okimoto, T. (2004). Genetic Relationship between Cultured Populations of Pacific Oyster Revealed by RAPD Analysis. Journal of Applied Genetics, 45: 435-443. doi: 10.1007/BF03194632
  • Atienzar, F., Evenden, A. J., Savva, D. & Depledge, M. (2000). Optimized RAPD analysis generates High Quality genomic DNA profilex at high annealing temprature. BioTechnniques, 28(1): 52- 53.
  • Atienzar, F.A,. & Jha, N.A. (2006). The random amplified polymorphic DNA (RAPD) assay and related techniques applied to genotoxicity and carcinogenesis studies: A critical review. Mutation Research, 613, 76- 102. doi: 10.1016/j.mrrev.2006.06.001
  • Bilgen, G., Akhan, S., Arabacı, M., & Oğuz, İ. (2007). Genetic Diversity of Gilthead Seabream (Sparus aurata) Broodstocks as Determined by RAPD-PCR. The İsraeli Journal of Aquaculture- Bamidgeh, 59 (4): 217-233.
  • Crocetta, F., Mariottini, P., Salvi, D., & Oliverio, M. (2015). Does GenBank provide a reliable DNA barcode reference to identify small alien oysters invading the Mediterranean Sea? Journal of the Marine Biological Association of the United Kingdom, 95(1): 111–122. doi: 10.1017/S0025315414001027
  • Çınar, M.E., Bilecenoğlu, M., Öztürk, B., Katağan, T., Yokeş, M.B., Aysel, V., Açık, S., Dağlı, E., Özcan, T. & Erdoğan, H. (2011). An updated review of alien species on the coasts of Turkey. Mediterranean Marine Science. Mediterranean Marine Science, 12(2): 257-315.
  • David, D.C. & Savini, D. (2011). Molecular Approaches to Bivalve Population Studies: A Review. Analele Ştiinţifice ale Universităţii, Alexandru Ioan Cuza”, Secţiunea Genetică şi Biologie Moleculară, TOM XII, 1-14.
  • Doğan, A., Önen, M. & Öztürk, B. (2007). Ildır Körfezi (İzmir-Çeşme) Bivalvia (Mollusca) Faunası. Türk Sucul Yaşam Dergisi, 3-5 (5-8): 27-35.
  • Farhadi, A., Farahmand, H., Mirvaghefi, A., & Khalili, B. (2011). A Genotoxicological Study in Persian Gulf on Rock Oyster (Soccostrea cucullata) using Micronuclei and RAPID Assays. International Journal of Environmental Research, 5(2): 567- 572.
  • Gunter, G. (1950). The generic status of living oysters and scientific name of the common American species. American Midland Naturalist, 43 (2):438-449.
  • Hare, M.P. & Avise, J.C. (1998). Population structure in the American oyster as inferred by nuclear gene genealogies. Molecular Biology Evolotion, 15:119-128.
  • İlhak, O.İ. & Arslan, A. (2007). Rastgele Çoğaltılmış Polimorfik DNA Yöntemiyle Kanatlı Etlerinde Tür Tayini. Fırat Üniversitesi Sağlık Bilimleri Dergisi; 21 (4): 167-171.
  • Klinbunga, S., Amparyup, P., Khamnamtong, N., Tassanakajon, A., Jaraybhand, P. & Yoosukh W. (2000). Molecular Genetic Markers for Taxonomy of Oysters in Thailand. Fisheries Scicence, 68(2): 1087-1090.
  • Klinbunga, S., Ampayup, P., Tassanakajon, A., Jarayabhand, P. & Yoosukh, W. (2001). Genetic diversity and molecular markers of commercial oysters (Genera Crassostrea, Saccostrea and Striostrea) in Thailand determined by RAPD analysis. Marine Biotechnology, 3, 133–144. doi: 10.1007/s101260000057
  • Koh, M.C., Lim, C.H., Chua, S.B., Chew, S.T. & Phang, S.T.W. (1998). Random Amplified Polymorphic DNA (RAPD ) fingerprints for identification of red meat animal species. Meat Science, 48, 275-285. doi:10.1016/S0309-1740(97)00104-6
  • Lam, K. & Morton, B.(2003). Mitochondrial and morphological identification of a new species of Crassostrea (Bivalvia: Ostreidae) cultured for centuries in Peral river Delta, Hong- Kong, China. Aquaculture 228: 1-13.
  • Lapègue S., Beaumont A., Boudry P., & Goulletquer P. (2008). European flat oyster – Ostrea edulis. Genimpact final scientific report, (s. 70-76).
  • Lee, C.J. & Chang, G.J. (1999). Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) fingerprints in forensic species identification. Forensic Science International, 67, 103-107.
  • Liua, Z.J. & Cordesb, J.F. (2004). DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238, 1– 37. doi: 10.1016/j.aquaculture.2004.05.027
  • Lök, A. (2000). İstiridye Biyolojisi ve Yetiştirme Teknikleri. T.C.Tarım Orman ve Köyişleri Bakanlığı, Tarımsal Üretim ve Geliştirme Genel Müdürlüğü, Ticari Balık Türlerinin Biyolojisi ve Yetiştirme Teknikleri Hizmet İçi Eğitim Seminer Eğitim Kitapçığı, Ankara: 102-121 (çağrılı bildiri)
  • Oliveria, A.L.D., Da Silva, D., Manzano, B.C., Abdel-Hamid, A.Z., Marcelino, M.Y., Zanotti-Magalhães, E.M., Magalhães, L.A. & Ribeiro-Paes, J.T. (2010). Genetic differences between strains of Biomphalaria glabrata (Planorbidae) that are susceptible and unsusceptible to schistosomiasis. Genetics and Molecular Research 9 (3): 1450-1459. doi: 10.4238/vol9-3gmr821
  • Öztürk, B., Doğan, A., Bitlis-Bakır, B. & Salman, A. (2014). Marine molluscs of the Turkish coasts: an updated checklist. Turkish Journal of Zoolgy, 38, 832-879. doi: 10.3906/zoo-1405-78
  • Rego, I., Martinez, A., Gonzalez-Tizon, A. G., Vieites, J., Leira, F. & Mendez, J. (2002). PCR Technique for Identification of Mussel Species. Journal of Agricultural and Food Chemistry, 50, 1780−1784.
  • Sleem, H.S. & Ali G.T. (2008). Application of RAPD-PCR in Taxonomy of Certain Freshwater Bivalves of Genus Caelatura. Global Journal of Molecular Sciences, 3 (1): 27- 31.
  • Toro, J.E. & Gonzalez, C.P. (2009). The genetic structure of the Chilean oyster (ostrea chilensis Philippi, 1845) in natural populations of southern Chile on RAPDs analysis. Revista de Biologia Marina Oceanografia, 44 (2): 467-476.
  • Williams, J.G.K., Kubelik, A.R., Livak, K.J., Rafalski, J.A. & Tingey, S.V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18, 6531-6535.
  • Yoosukh, W. & Duangdee, T. (1999). Living Oysters in Thailand. Phuket. Thailand: Phuket Marine Biological Center, 19: 363- 370.

Ayrıntılar

Konular Fen
Bölüm Makaleler
Yazarlar

Emel Özcan Gökçek
EGE UNIV
0000-0001-6566-7680
Türkiye


Aynur Lök


Bilge Karahan


Evrim Kurtay Bu kişi benim

Yayımlanma Tarihi 21 Şubat 2017
Başvuru Tarihi 4 Ekim 2016
Kabul Tarihi 22 Kasım 2016
Yayınlandığı Sayı Yıl 2017, Cilt 34, Sayı 1

Kaynak Göster

APA Gökçek, E. Ö. , Lök, A. , Karahan, B. & Kurtay, E. (2017). Identification of different oyster species using RAPD-PCR . Ege Journal of Fisheries and Aquatic Sciences , 34 (1) , 25-30 . DOI: 10.12714/egejfas.2017.34.1.04