Molecular Phylogenetic Analysis Of Morkaraman Sheeps In Bingol Region

Year 2021, Volume: 8 Issue: 1, 171 - 178, 23.01.2021

Oğuz Ağyar , Emin Özköse , Mehmet Sait Ekinci , İsmail Akyol

https://doi.org/10.30910/turkjans.642421

Abstract

In the present study, we report mitochondrial DNA (mtDNA) 16S rRNA gene sequence analysis of the Morkaraman ewe, (Ovis aries) was investigated. In domestic sheep, the 16S rRNA gene is ca 1574 bp in length. Partial fragment of 536 bp 16S rRNA gene of mtDNA was amplified by using designed primers from published data of Sheep sequences derived from National Center for Biotechnology Information (NCBI) web server (ncbi.nlm.nih.gov/NC_001941.1). Homology of the sequences obtained from the present work were performed by using BLAST program at NCBI. Obtained 16S rRNA gene sequences were submited to the GenBank database with accession numbers, KU686952.1, KU686953.1, KU686954.1, KU686955.1, KU686956.1, KU686957.1, KU686958.1, KU686959.1, KU686960.1, KU686961.1 and KU686962.1, respectively. According to nucleotide differences of mtDNA 16S rRNA gene region 10 polymorphic regions and 8 haplotypes were detected in Turkish domestic sheep Morkaraman (n=11). The nucleotide composition averages of all the sequences was 32.1% Adenine (A), 24.2% Thymine (T), 22.2% Cytosine (C) and 21.5% Guanine (G); G+C was 43.7%. DNA polymorphism based on 16S rRNA gene sequences, haplotype diversity (Hd) and nucleotide diversity (π) were found to be 0,9273±0,00442, and 0,00427±0,00125, respectively. Based on gene sequences information, in sheeps, mtDNA haplotypes, the phylogenetic relationship among mtDNA polymorphism, haplotypes and relationship between native sheep breeds and foreign sheep breeds were determined and discussed. Thus, sequence analysis of mitochondrial 16S rRNA gene can be used as a tool for phylogenetic analysis of Morkaraman sheep.

Keywords

Genetic Diversity,, Morkaraman (Ovis aries),, Phylogenetic,, mtDNA,, 16S rRNA

Molecular Phylogenetic Analysis Of Morkaraman Sheeps In Bingol Region

Abstract

Bu çalışmada, Morkaraman koyunlarının (Ovis aries) filogenetik ilişkileri mitokondriyal DNA (mtDNA) 16S rRNA gen dizisi analizi ile gerçekleştirilmiştir. Evcil koyunlarda, 16S rRNA geni 1574 baz çifti (bç) uzunluğundadır. Çalışmamızda mtDNA 16S rRNA gen bölgesi hedeflenerek, Ulusal Biyoteknoloji Bilgi Merkezi (NCBI) alınan örnek sekansla (NC_001941.1) tasarlanan primerler ile, 536 bç’lik sekans ürünleri elde edilmiştir. Elde edilen diziler için homoloji araştırması, NCBI'de BLAST kullanılarak yapılmıştır. Çalışma sonunda elde ettiğimiz 16S rRNA gen bölgesi dizi bilgileri GenBank veri tabanına sırası ile bu erişim numaralarıyla yer almaktadır; Sırasıyla KU686952.1, KU686953.1, KU686954.1, KU686955.1, KU686956.1, KU686957.1, KU686958.1, KU686959.1, KU686960.1, KU686961.1 ve KU686962.1. Morkaraman koyun örnekleri (n=11) üzerinde yapılan analizler sonunda, mtDNA 16S rRNA gen bölgesi sekanslarından nükleotit farklılıkları bakımından 10 polimorfik bölge ve 8 haplotip bölge tespit edilmiştir. Tüm dizilerin nükleotit kompozisyon ortalamaları % 32.1 Adenin (A), % 24.2 Timin (T), % 22.2 Sitosin (C) ve % 21.5 Guanin (G); G + C % 43.7 olarak bulundu. 16S rRNA gen dizileri, haplotip çeşitliliği (Hd) ve nükleotit çeşitliliğine (π) dayanan DNA polimorfizmi sırasıyla 0.9273 ± 0.00442 ve 0.00427 ± 0.00125 olarak bulunmuştur. Gen dizileri bilgisine dayanarak, koyunlarda, mtDNA haplotipleri, mtDNA polimorfizmi, haplotipleri arasındaki filogenetik ilişkiler ile belirlenen yerli ve yabancı koyun ırkları arasındaki filogenetik ilişkileri belirlenmiştir.

Keywords

Filogenetik, Genetik Çeşitlilik, Morkaraman (Ovis aries)

References

• Fan, H., Zhao, F., Zhu, C., Li, F., Liu, J., Zhang, L., Wei, C., Du, L. 2016. Complete Mitochondrial Genome Sequences of Chinese Indigenous Sheep with Different Tail Types and an Analysis of Phylogenetic Evolution in Domestic Sheep. Asian-Australasian Journal of Animal Sciences, 29(5), 631–639.
• Girish, P. S., Anjaneyulu, A. S. R., Viswas, K. N., Santhosh, F. H., Bhilegaonkar, K. N., Agarwal, R. K., Kondaiah, N., Nagappa, K. 2007. Polymerase chain reaction-restriction fragment length polymorphism of mitochondrial 12S rRNA gene: a simple method for identification of poultry meat species. Veterinary Research Communication, 31 : 447 - 455.
• Hiendleder, S., Lewalski, H., Wassmuth, R., Janke, A. 1998. The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major Ovine haplotypes. Journal of Molecular Evolution, 47 : 441-448.
• Kimura, M. (1983) “Rarevariant alleles in the light of the neutral theory”, Molecular Biology and Evolution 1, 84–93.
• Kirikci K., Noce A., Çam, M. A., Mercan, L., Amills, M. 2018. The analysis of mitochondrial data indicates the existence of population substructure in the Karayaka sheep, Small Ruminant Research, 162: 25 - 29
• Kul, B. C., Ertugrul, O. 2011. mtDNA diversity and phylogeography of some Turkish native goat breeds. Ankara Universitesi Veteriner Fakültesi Dergisi 58(2):129–134.
• Kurt, A. O. (2017). Anadolu’da İlk tapınak: Göbeklitepe. Cumhuriyet İlahiyat Dergisi, 1107-1138.
• Kuznetsova, M. V., Kholodova, M. V., Luschekina, A. A. 2002. Phylogenetic Analysis of Sequences of the 12S and 16S rRNA Mitochondrial Genes in the Family Bovidae: New Evidence. Russian Journal of Genetics, 38 (8) : 942–950.
• Lv, F. H., Peng, W. F., Yang, J., Zhao, Y. X., Li, W. R., Liu, M. J., Ma, Y. H., Zhao, Q. J., Yang, G. L., Wang, F., Li, J. Q., Liu, Y. G., Shen, Z. Q., Zhao, S. G., Hehua, E., Gorkhali, N. A., Vahidi, M. F., Muladno, M., Naqvi, A. N., Tabell, J., Iso-Touru, T., Bruford, M. V., Kantanen, J., Han, J. L., Li, M. H. 2015. Mitogenomic metaanalysis identifies two phases of migration in the history of eastern Eurasian sheep. Molecular Biology and Evolution, 32 (10) : 2515–33.
• Mane, B. G., Mendiratta, S. K., Tiwari, A. K., Narayan, R. 2013. Sequence analysis of mitochondrial 16S rRNA gene to identify meat species. Journal of Applied Animal Research, 41 (1) : 77-81.
• Meadows, J. R., Cemal, I., Karaca, O., Gootwıne, E., Kijas, J. W. 2007. Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics, 175 (3) : 1371-1379.
• Naderi, S., Rezaei, H-R, Taberlet, P., Zundel, S., Rafat, S-A, Naghash, H-R, El- Barody, M. A. A., Ertuğrul, O., Pompanon, F. 2007. Large-Scale Mitochondrial DNA Analysis of the Domestic Goat Reveals Six Haplogroups with High Diversity. PLoS ONE 2(10): e1012.
• Ramadan, H. A. I. 2011. Sequence of specific mitochondrial 16S rRNA gene fragment from Egyptian buffalo is used as a pattern for discrimination between river buffaloes, cattle, sheep and goats. Molecular Biology Reports, 38 (6) : 3929–3934.
• Resende, A., Gonçalves, J., Muigai, A. W. T., Pereira, F. 2016. Mitochondrial DNA variation of domestic sheep (Ovis aries) in Kenya. Animal Genetics, 47, 401-410.
• Sanna, D., Barbato, M., Hadjisterkotis, E., Cossu, P., Decandia, L., Trova, S., Pirastru, M., Leoni, G. G., Naitana, S., Francalacci, P., Masala, B., Manca, L., Mereu, P.. (2015) The First Mitogenome of the Cyprus Mouflon (Ovis gmelini ophion): New Insights into the Phylogeny of the Genus Ovis. PLoS ONE 10 (12): e0144257
• Sarri, C., Stamatis, C., Sarafidou, T., Galara, I., Godosopoulos, V., Kolovos, M., Liakou, C., Tastsoglou, S., Mamuris, Z. 2014. A new set of 16S rRNA universal primers for identification of animalspecies. Food Control 43, 35–41.
• Saikia, D. P., Kalita, D. J., Borah, P., Sharma, S., Barman, N. N., Dutta, R. 2015. Differentiation of sheep and goat speciesby PCR-RFLP of mitochondrial 16s rRNA gene. Journal Animal Research. 5: 213-217.
• Tapio M., Marzanov M., Ozerov M., Cinkulov M., Gonzarenko G., Kiselyova T., Murawski M., Viinalass H., Kantanen J. 2006. Sheep mitochondrial DNA variation in European, Caucasian and Central Asian areas. Molecular Biology and Evolution, 23:1776-1783.
• Togan, İ., Demirci, S., Özkan Ünal, E., Ayanoğlu, İ. C., Parmaksız, A., Dağtaş, N. D., Özer, F., Yüncü, E., Uzun, B., Chiriboga, F., Koban Baştanlar, E., Ergüven, A. 2013. Türkiye’deki Yerli Koyunlarda Genetik Çeşitlilik: Son Sonuçlar, Yeni Sorular. VIth International Balkan Animal Conference BALNIMALCON. 3-5 October 2013. Tekirdag / Turkey.
• Yalçın, B. C., 1986. Sheep and Goats in Turkey. FAO Animal Production and Health Paper, No: 60, Rome, Italy.