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Genetic Diversity of Cultured Rainbow Trout (Oncorhynchus mykiss) Populations in Türkiye Based on Mitochondrial DNA Cytochrome b (cyt-b) Sequence Analysis

Yıl 2025, Cilt: 21 Sayı: 2, 100 - 114

Boran Karataş , İsmet Beyaz

https://doi.org/10.22392/actaquatr.1561214

Öz

This study aimed to investigate the genetic diversity and structure of rainbow trout (Oncorhynchus mykiss) cultured populations in different provinces of Türkiye, based on the cytochrome b (cyt-b) gene region of mitochondrial DNA (mtDNA). Tissue samples were collected from a total of 98 fish (seven fish per province) across 14 provinces, followed by DNA isolation. The mtDNA cyt-b gene region (754 bp) was amplified using PCR. Genetic diversity indices, genetic structure, and phylogenetic analyses were calculated from the cyt-b gene sequence data. The average nucleotide frequencies of the four nucleotides cytosine (C), thymine (T), adenine (A), and guanine (G) were found to be 26.2%, 24.9%, 26.2%, and 22.8%, respectively, with a higher A + T content (51%) compared to G + C content (49%). A total of 645 polymorphic nucleotides were identified across the 14 populations, and 50 distinct haplotypes were defined. Haplotypic diversity ranged from 0.91 to 0.48, while nucleotide diversity (π) varied between 0.26 and 0.00. The highest genetic diversity was observed in the Tokat and Van populations, whereas the lowest was recorded in the Elazığ and Kahramanmaraş populations. AMOVA analyses revealed that 71.1% of the genetic diversity was found between populations, while 28.9% was found within populations. Pairwise FST values ranged from 0.38 to 0.99, with an average FST of 0.71. Phylogenetic analyses indicated that the populations clustered into two main groups, with further sub-groupings within these clusters. Notably, the Kahramanmaraş and Elazığ populations were found to be significantly differentiated from other populations. In conclusion, despite rainbow trout not being a native species in Türkiye, the findings of this study indicate that the genetic diversity of the populations is at a good level. However, in order to preserve the genetic diversity of cultured rainbow trout populations and to increase effective population size, it is recommended that breeders engage in fry exchanges and import new rainbow trout specimens to enhance genetic diversity.

Anahtar Kelimeler

Cytochrome b Genetic structure Genetic diversity mtDNA Phylogenetic analysis

Etik Beyan

This study was conducted with the approval of Animal Experiments Local Ethics Committee of Van Yuzuncu Yıl University (protocol no: 2023/05–07).

Destekleyen Kurum

Scientific Research Projects Coordination Unit of Van Yüzüncü Yıl University

Proje Numarası

FYL-2023-10698.

Teşekkür

This study is derived from a master's thesis prepared under the supervision of the second author by the first author. The authors would like to thank Van Yuzuncu Yil University Scientific Research Projects Coordination Office for financial support.

Kaynakça

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Türkiye'deki Kültür Gökkuşağı Alabalığı (Oncorhynchus mykiss) Popülasyonlarının Mitokondriyal DNA Sitokrom b (cyt-b) Dizi Analizine Dayalı Genetik Çeşitliliği

Yıl 2025, Cilt: 21 Sayı: 2, 100 - 114

Boran Karataş , İsmet Beyaz

https://doi.org/10.22392/actaquatr.1561214

Öz

Bu çalışmada, Türkiye’deki farklı illerdeki gökkuşağı alabalığı (Oncorhynchus mykiss) kültür popülasyonlarının mitokondriyal DNA (mtDNA) sitokrom b (cyt-b) gen bölgesine dayalı genetik çeşitliliğinin ve yapısının incelenmesi amaçlanmıştır. Çalışma kapsamında 14 ildeki toplam 98 balıktan (il başına yedi balık) alınan doku örnekleri ile DNA izolasyonu yapılmış ve mtDNA cyt-b gen bölgesi (754 bp) PCR ile çoğaltılmıştır. Cyt-b gen bölgesi sekans verilerinden genetik çeşitlilik indeksleri, genetik yapı ve filogenetik analizlerle ilgili hesaplamalar yapılmıştır. Çalışmada dört nükleotidin (sitozin (C), timin (T), adenin (A) ve guanin (G)) ortalama frekansları sırasıyla %26.2, %24.9, %26.2 ve %22.8 olarak bulunmuş; A + T içeriğinin (%51) G + C içeriğinden (%49) daha yüksek olduğu belirlenmiştir. 14 popülasyondan toplam 645 polimorfik nükleotid tespit edilmiş ve 50 farklı haplotip tanımlanmıştır. Haplotip çeşitliliği 0.91 ile 0.48 arasında, nükleotid çeşitliliği ise 0.26 ile 0.00 arasında değişmiştir. En yüksek genetik çeşitlilik Tokat ve Van popülasyonlarında, en düşük ise Elazığ ve Kahramanmaraş popülasyonlarında gözlenmiştir. AMOVA analizleri, genetik çeşitliliğin %71.1'inin popülasyonlar arasında, %28.9'unun ise popülasyonlar içinde olduğunu göstermiştir. İkili FST değerleri 0.38 ile 0.99 arasında değişmiş ve ortalama FST değeri 0.71 olarak bulunmuştur. Filogenetik analizler, popülasyonların iki ana gruba ayrıldığını ve bu grupların kendi içinde farklı alt gruplar oluşturduğunu göstermiştir. Özellikle Kahramanmaraş ve Elazığ popülasyonlarının diğer popülasyonlardan belirgin şekilde farklılaştığı gözlenmiştir. Sonuç olarak gökkuşağı alabalıklarının gen kaynağı ülkemizde olmamasına rağmen çalışmada elde edilen bulgular popülasyonların genetik çeşitliliğinin iyi düzeyde olduğunu göstermektedir. Ancak gökkuşağı alabalığı kültür popülasyonlarının genetik çeşitliliğini korumak ve etkili popülasyon büyüklüğünü artırmak için yetiştiricilere yavru balıkları takas etmeleri ve genetik çeşitliliği artırmak için yeni gökkuşağı alabalıkları ithal etmeleri önerilebilir.

Anahtar Kelimeler

Filogenetik analiz Genetik yapı mtDNA Sitokrom b Genetik çeşitlilik

Etik Beyan

This study was conducted with the approval of Animal Experiments Local Ethics Committee of Van Yuzuncu Yıl University (protocol no: 2023/05–07).

Destekleyen Kurum

Scientific Research Projects Coordination Unit of Van Yüzüncü Yıl University

Proje Numarası

FYL-2023-10698.

Teşekkür

This study is derived from a master's thesis prepared under the supervision of the second author by the first author. The authors would like to thank Van Yuzuncu Yil University Scientific Research Projects Coordination Office for financial support.

Kaynakça

  • Abdullah, T., Nassiri, M., Safari, O., & Javadmanesh, A. (2019). Genetic diversity for three populations of Rainbow Trout (Oncorhynchus mykiss) based on sequencing of mtDNA genes. Marsh Bulletin, 14(1), 1-10.
  • Ağdamar, S. (2010). Türkiye’de üretilen gökkuşağı alabalığı (Oncorhynchus mykiss Walbaum, 1792) popülasyonlarının mikrosatellit DNA analizi, (Yüksek lisans tezi. Muğla Üniversitesi, Fen Bilimleri Enstitüsü, Muğla).
  • Akhan, S., & Canyurt, M. A. (2005). Üç farklı kuluçkahanedeki damızlık gökkuşağı alabalığı (Oncorhynchus mykiss Walbaum, 1792) stokları arasında genetik çeşitliliğin RAPD-PCR yöntemiyle belirlenmesi üzerine bir araştırma. Ege Üniversitesi Su Ürünleri Dergisi, 22 (1-2), 25–30.
  • Aksakal, E. (2009). Düşük ve yüksek canlı ağırlığa sahip gökkuşağı alabalıkları (Oncorhynchus mykiss Walbaum, 1792) arasındaki genetik varyasyonun mikrosatelit markırlar kullanılarak belirlenmesi, (Doktora tezi. Atatürk Üniversitesi, Fen Bilimleri Enstitüsü, Erzurum).
  • Baisvar, V. S., Singh, M., & Kumar, R. (2019). Population structuring of Channa striata from Indian waters using control region of mtDNA. Mitochondrial DNA Part A, 30(3), 414-423. https://doi.org/10.1080/24701394.2018.1532416
  • Carcamo, C. B., Diaz, N. F., & Winkler, F. M. (2015). Genetic diversity in Chilean populations of rainbow trout, Oncorhynchus mykiss. Latin American Journal of Aquatic Research, 43 (1), 59-70. http://doi.org/ 10.3856/vol43-issue1-fulltext-6
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  • de Araújo Júnior, N. T., Ianella, P., Yoshinaga, T. T., Butzge, A. J., & Caetano, A. R. (2023). Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers. Aquaculture Reports, 31, 101689. https://doi.org/10.1016/j.aqrep.2023.101689
  • DeSalle, R., Schierwater, B., & Hadrys, H. (2017). mtDNA: The small workhorse of evolutionary studies. Frontiers in Bioscience-Landmark, 22(5), 873-887.
  • Devaa, W., Panneerselvam, V., & Uthandakalaipandian, R. (2024). Estimation of genetic diversity of the exotic Indian trout populations by using microsatellite markers. Journal of Genetics, 103(1), 11. https://doi.org/10.1007/s12041-023-01462-6
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  • Faccenda, F., Lunelli, F., Gandolfi, A., & Bozzi, R. (2018). Microsatellite-based genetic diversity and admixture history of rainbow trout (Oncorhynchus mykiss–Walbaum, 1792) stocks in Trentino (Italy). Turkish Journal of Fisheries and Aquatic Sciences, 18(7), 881-889. https://doi.org/ 10.4194/1303-2712-v18_7_06
  • Fang, D. A., He, M., Ren, Y. F., Luo, H., Zhou, Y. F., Jiang, S. L., & You, Y. (2022). Assessment of genetic diversity of the Salangid, Neosalanx taihuensis, based on the mitochondrial COI gene in different Chinese River basins. Biology, 11(7), 968. https://doi.org/10.3390/biology11070968
  • FAO. (2020). The State of World Fisheries and Aquaculture: Sustainability in Action. In The State of World Fisheries and Aquaculture (SOFIA); FAO: Rome, Italy, ISBN 978-92-5-132692-3.
  • Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
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  • Grant Grant, W. S., Jasper, J., Bekkevold, D., & Adkison, M. (2017). Responsible genetic approach to stock restoration, sea ranching and stock enhancement of marine fishes and invertebrates. Reviews in Fish Biology and Fisheries, 27, 615-649. https://doi.org/10.1007/s11160-017-9489-7
  • Ha, T. T. T., Nga, T. T., Hang, T. N. A., & Alam, M. S. (2020). Genetic diversity in Pangasius spp. collected in Bangladesh based on mitochondrial cytochrome b gene sequence analysis. Aquac. Rep., 2020,100351. https://doi.org/10.1016/j.aqrep.2020.100351
  • Habib, M., Lakra, W. S., Mohindra, V., Khare, P., Barman, A. S., Singh, A., ... & Khan, A. A. (2011). Evaluation of cytochrome b mtDNA sequences in genetic diversity studies of Channa marulius (Channidae: Perciformes). Molecular Biology Reports, 38, 841-846. https://doi.org/10.1007/s11033-010-0175-2
  • Houston, R. D., Bean, T. P., Macqueen, D. J., Gundappa, M. K., Jin, Y. H., Jenkins, T. L., ... & Robledo, D. (2020). Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics, 21(7), 389-409. https://doi.org/10.1038/s41576-020-0227-y
  • Karataş, B. (2019). Van ili gökkuşağı alabalığı (Oncorhynchus mykiss, Walbaum, 1792) anaç popülasyonlarının büyüme hormonu (GH) gen ekspresyon seviyeleri, genetik polimorfizm ile bazı fenotipik parametrelere göre değerlendirilmesi ve yönetimine yönelik bir araştırma. (Doktora tezi, Van Yüzüncü Yıl Üniversitesi, Fen Bilimleri Enstitüsü, Van, Türkiye).
  • Kause, A., Nousiainen, A., & Koskinen, H. (2022). Improvement in feed efficiency and reduction in nutrient loading from rainbow trout farms: the role of selective breeding. Journal of Animal Science, 100(8), skac214. https://doi.org/10.1093/jas/skac214
  • Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120. https://doi.org/10.1007/BF01731581
  • Kumar, R., Pandey, B. K., Sarkar, U. K., Nagpure, N. S., Baisvar, V. S., Agnihotri, P., ... & Kumar, N. (2017). Population genetic structure and geographic differentiation in butter catfish, Ompok bimaculatus, from Indian waters inferred by cytochrome b mitochondrial gene. Mitochondrial DNA Part A, 28(3), 442-450. https://doi.org/10.3109/19401736.2015.1137898
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution, 35(6), 1547-1549. https://doi.org/ 10.1093/molbev/msy096
  • Kurta, K., Jeuthe, H., de Koning, D. J., & Palaiokostas, C. (2023). Insights from the early generations of the Swedish rainbow trout (Oncorhynchus mykiss) breeding program. Acta Agriculturae Scandinavica, Section A—Animal Science, 72(3-4), 88-99. https://doi.org/10.1080/09064702.2023.2245490
  • Leitwein, M., Garza, J. C., & Pearse, D. E. (2017). Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evolutionary Applications, 10(1), 56-67. https://doi.org/10.1111/eva.12416
  • Lhorente, J. P., Araneda, M., Neira, R., & Yáñez, J. M. (2019). Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects. Reviews in Aquaculture, 11(2), 340-353. https://doi.org/10.1111/raq.12335
  • Lind, C. E., Ponzoni, R. W., Nguyen, N. H., & Khaw, H. L. (2012). Selective breeding in fish and conservation of genetic resources for aquaculture. Reproduction in Domestic Animals, 47, 255-263. https://doi.org/10.1111/j.1439-0531.2012.02084.x
  • Liu, S., Palti, Y., Martin, K. E., Parsons, J. E., & Rexroad III, C. E. (2017). Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel. Aquaculture, 468, 120-125. https://doi.org/10.1016/j.aquaculture.2016.10.004
  • Longo, A., Kurta, K., Vanhala, T., Jeuthe, H., de Koning, D. J., & Palaiokostas, C. (2024). Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome‐wide SNP and haplotype data. Animal Genetics, 55(1), 87-98. https://doi.org/10.1111/age.13378
  • Martsikalis, P., Gkafas, G. A., Apostolidis, A. P., & Exadactylos, A. (2014). Genetic structure profile of rainbow trout (Oncorhynchus mykiss) farmed strains in Greece. Turkish Journal of Fisheries and Aquatic Sciences, 14(3), 749-757. https://doi.org/ 10.4194/1303-2712-v14_3_17
  • Naderi, M., Keyvanshokooh, S., Salati, A. P., & Ghaedi, A. (2017) Effects of chronic high stocking density on liver proteome of rainbow trout (Oncorhynchus mykiss). Fish. Physiol. Biochem., 43(5), 1373–1385. https://doi.org/10.1007/s10695-017-0378-8
  • Nei, M. (1987). Molecular Evolutionary Genetics, Columbia University Press, NY.
  • Oral, M., (2011). Türkiye’de Üretimi Yapılan Gökkuşağı Alabalığı (Oncorhynchus mykiss Walbaum, 1792) popülasyonlarının Genetik Karakterizasyonu. (Yüksek lisans tezi. Muğla Üniversitesi Fen Bilimleri Enstitüsü, Muğla).
  • Paul, K., D'Ambrosio, J., & Phocas, F. (2022). Temporal and region‐specific variations in genome‐wide inbreeding effects on female size and reproduction traits of rainbow trout. Evolutionary Applications, 15(4), 645-662. https://doi.org/10.1111/eva.13308
  • Peakall, R. O. D., & Smouse, P. E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1), 288-295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  • Peng, M., Zhu, W., Yang, C., Yao, J., Chen, H., Jiang, W., ... & Chen, X. (2021). Genetic diversity of mitochondrial D‐LOOP sequences in the spotted scat (Scatophagus argus) from different geographical populations along the northern coast of the South China Sea. Journal of Applied Ichthyology, 37(1), 73-82. https://doi.org/10.1111/jai.14121
  • Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Sahoo, L., Barat, A., Sahoo, S. K., Sahoo, B., Das, G., Das, P., ... & Swain, S. K. (2020). Genetic diversity and population structure of endangered Indian catfish, Clarias magur as revealed by mtDNA D-loop marker. Turkish Journal of Fisheries and Aquatic Sciences, 21(1), 09-18. http://doi.org/10.4194/1303-2712-v21_1_02
  • Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing Phylogenetic trees. Molecular Biology and Evolution, 4, 406-425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
  • Sarmaşık, A., Çolakoğlu, F.A, & Altun, T. (2008) Mitochondrial DNA sequence and body size variations in Turkish sardine (Sardina pilchardus) stocks. Turkish Journal of Zoology 32 (3), 229-237.
  • Saura, M., Caballero, A., Santiago, E., Fernández, A., Morales-González, E., Fernández, J., ... & Villanueva, B. (2021). Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes. Genetics Selection Evolution, 53, 1-8. https://doi.org/10.1186/s12711-021-00680-9
  • Stanković, D., Crivelli, A. J., & Snoj, A. (2015). Rainbow trout in Europe: introduction, naturalization, and impacts. Reviews in Fisheries Science and Aquaculture, 23(1), 39-71. https://doi.org/10.1080/23308249.2015.1024825
  • Sultana, S., Hasan, M. M., Hossain, M. S., Alim, M. A., Das, K. C., Moniruzzaman, M., ... & Alam, J. (2022). Assessment of genetic diversity and population structure of Tenualosa ilisha in Bangladesh based on partial sequence of mitochondrial DNA cytochrome b gene. Ecological Genetics and Genomics, 25, 100139. https://doi.org/10.1016/j.egg.2022.100139
  • Sun, C., Xuan, Z., Liu, H., Jiang, T., & Yang, J. (2019). Cyt b gene and D-loop sequence analyses of Coilia nasus from the Rokkaku River of Japan. Regional Studies in Marine Science, 32, 100840. https://doi.org/10.1016/j.rsma.2019.100840
  • Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105, 437-460. https://doi.org/10.1093/genetics/105.2.437
  • Tamura, K. (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution, 9, 678-687.
  • Tamura, K., Stecher, G., & Kumar, S. (2021). MEGA 11: Molecular Evolutionary Genetics Analysis Version 11. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msab120
  • Togan, İ., Ergüven, A., Emre, Y., Berkman, C. C., & Koban, E. (2002). Türkiye'de Güney Ege ve Akdeniz'de bulunan alabalık (Oncorhynchus mykiss) çiftlikleri stoklarının moleküler yöntemlerle korunması. TARP-1811, Ankara.
  • Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 1358-1370. https://doi.org/10.2307/2408641
  • Whitmore, D. H. (1990). Electrophoretic and isoelectric focusing techniques in fisheries management. CRC Press.
  • Wiens, G. D., Palti, Y., & Leeds, T. D. (2018). Three generations of selective breeding improved rainbow trout (Oncorhynchus mykiss) disease resistance against natural challenge with Flavobacterium psychrophilum during early life-stage rearing. Aquaculture, 497, 414-421. https://doi.org/10.1016/j.aquaculture.2018.07.064
  • Zhang, C., Li, Q., Wu, X., Liu, Q., & Cheng, Y. (2018). Genetic diversity and genetic structure of farmed and wild Chinese mitten crab (Eriocheir sinensis) populations from three major basins by mitochondrial DNA COI and Cyt b gene sequences. Mitochondrial DNA Part A, 29(7), 1081-1089. https://doi.org/10.1080/24701394.2017.1404048
  • Zhang, G., Chen, C., Lu, W., Li, J., Fang, T., Yang, K., ... & Liang, Y. (2023). Genetic diversity and phylogeography of Taenioides cirratus in five geographical populations based on mitochondrial COI and Cytb gene sequences. Journal of Applied Ichthyology, 2023(1), 4459823. https://doi.org/10.1155/2023/4459823
  • Zhu, Y., Cheng, Q., & Rogers, S. M. (2016). Genetic structure of Scomber japonicus (Perciformes: Scombridae) along the coast of China revealed by complete mitochondrial cytochrome b sequences. Mitochondrial DNA Part A, 27(6), 3828-3836. https://doi.org/10.3109/19401736.2014.958671
Toplam 59 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Balıkçılık Yönetimi, Sucul Kültür ve Balıkçılık (Diğer)
Bölüm Araştırma Makaleleri
Yazarlar

Boran Karataş 0000-0003-4353-1293

İsmet Beyaz 0009-0002-2511-9465

Proje Numarası FYL-2023-10698.
Erken Görünüm Tarihi 14 Mayıs 2025
Yayımlanma Tarihi
Gönderilme Tarihi 4 Ekim 2024
Kabul Tarihi 19 Aralık 2024
Yayımlandığı Sayı Yıl 2025 Cilt: 21 Sayı: 2

Kaynak Göster

APA Karataş, B., & Beyaz, İ. (2025). Genetic Diversity of Cultured Rainbow Trout (Oncorhynchus mykiss) Populations in Türkiye Based on Mitochondrial DNA Cytochrome b (cyt-b) Sequence Analysis. Acta Aquatica Turcica, 21(2), 100-114. https://doi.org/10.22392/actaquatr.1561214
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