Phylogenetic Analysis of Abaza, Kaçkar, Georgian (Caucasian), Ovit Region (İspir) Native Goat Breeds Using mtDNA D-loop Sequences

Öz

The objective of this research was to determine genetic diversity of mtDNA D-Loop region in Abaza, Kaçkar, Georgian (Caucasian) and Ovit Region (İspir) breeds and their phylogenetic relationship with each other. The number of goat have decreased gradually due to many reasons in some regions of Turkey. Thus, non-scientific hypotheses about goats began to be produced. Therefore, the origin and gene flow of native goat breeds reared in Eastern of Turkey are needed to reveal by using DNA based methods. In this study, 200 individuals from four native breeds in eastern of Turkey were sampled for the mtDNA D-loop sequences. The haplotype and nucleotide diversities were estimated as 0.974 and 0.019, respectively. In total, 52 haplotypes were observed from 63 polymorphic sites in native goat populations. Only one haplogroup A were found in studied populations. With the participation of all sequences, an neighbor-joining tree of native breeds was constructed. The lowest genetic distances (0.011) was observed between Kaçkar and Ovit Region (İspir) which have relatively close genetic relationships.

Anahtar Kelimeler

• Abaza Goat
• Georgian (Caucasian) Goat
• Haplotype
• Kaçkar Goat
• Mitochondrial D-Loop
• Ovit Region (İspir) Goat

Abaza, Kaçkar, Gürcü (Kafkas), Ovit Bölgesi (İspir) Yerli Keçi Irklarının mtDNA D-Loop Dizileri Kullanılarak Filogenetik Analizi

Öz

Bu araştırmanın amacı, Abaza, Kaçkar, Gürcü (Kafkas) ve Ovit Bölgesi (İspir) keçi ırklarında mtDNA D-Loop bölgesinin genetik çeşitliliğini ve birbirleriyle olan filogenetik ilişkilerini belirlemektir. Türkiye'nin bazı bölgelerinde birçok nedenden dolayı keçi sayısı giderek azalmış, böylece keçiler hakkında bilimsel olmayan hipotezler üretilmeye başlanmıştır. Bu doğrultuda, Türkiye'nin Doğu ve Kuzeydoğu bölgelerinde yetiştirilen yerli keçi ırklarının kökeni ve gen akışının, DNA temelli yöntemler kullanılarak ortaya konması önemli bilgilerin elde dilmesine yardımcı olacaktır. Bu çalışmada, dört yerli ırktan 200 baş keçi mtDNA D-loop dizileri için örneklenmiştir. Haplotip ve nükleotid çeşitliliği sırasıyla 0.974 ve 0.019 olarak tahmin edilmiştir. Yerli keçi popülasyonlarında 63 polimorfik bölgeden toplam 52 haplotip gözlenmiştir. İncelenen popülasyonlarda sadece bir A haplogrubu bulunmuştur. Tüm sekansların katılımıyla, neighbor-joining tree (NJT) oluşturulmuştur. En düşük genetik uzaklıklar (0,011), Kaçkar ve Ovit Bölgesi (İspir) arasında gözlemlenmiştir.

Anahtar Kelimeler

• Abaza Keçisi
• Kaçkar Keçisi
• Ovit Bölgesi Keçisi (İspir)
• Haplotip
• Mitokondrial D-Loop

Kaynakça

1. Amills, M., Ramirez, O., Tomas, A., Badaoui, B., Marmi, J., Acosta, J., Sanchez, A., Capote, J. 2009. Mitochondrial DNA diversity and origins of South and Central American goats. Animal Genetics. 40: 315-322.
2. Azor, P.J., Monteagudo,L.V., Luque, M., Tejedor, M.J., Rodero, E., Sierra,I., Rodro, A., Arruga, M.V. 2005. Phylogenetic relationships among Spanish goats breeds. Animal Genetics. 36: 423–425.
3. Baker, A.J., Marshall, H.D. 1997. Mitochondrial control region sequences as tools for understanding evolution. In: Mindell DP (ed) Avian molecular evolution and systematic. Academic press, San Diego, pp 51–82
4. Batu, S. 1951. Turkey goat breeds and goat breeding information. Ankara Universty, Veterinary Faculty publications, 4.
5. Brown, J.R., Beckenbach, A.T., Smith, M.J. 1992. Mitochondrial DNA length variation and heteroplasmy in populations of white sturgeon (Acipenser transmontanus). Genetics. 132: 221-228. PMID: 1398055
6. Brown, W.M., Prager, E.M. Wang, A., Wilson, A.C. 1982. Mitochondrial DNA sequences of primates: tempo and mode of evolution. J. Mol. Evol., 18: 225-239.
7. Carmela, G., Reyes, A., Pesole, G., Saccone, C. 2000. Lineage-Specific Evolutionary Rate in Mammalian mtDNA. Mol. Biol. Evol., 17: 1022–1031.
8. Chen, S.Y., Su, Y.H., Wu, SF., Sha, T., Zhang, Y.P. 2005. Mitochondrial diversity and phylogeographic structure of Chinese domestic goats. Mol. Phylogenet. Evol., 37: 804-814.

9. Chen, S.Y., Duan, Z.Y., Sha, T., Xiangyu, J.T., Wu, S.F., Zhang, Y.P. 2006. Origin, genetic diversity, and population structure of Chinese domestic sheep. Genetics. 376: 216-223.
10. Excoffier, L., Lischer, H.E.L. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res., 10: 564–567. Fan, B., Chen, S.L., Kijas, J.H., Liu, B., Yu, M., Zhao, S.H., Zhu,M.J., Xiong, T.A., Li, K. 2007. Phylogenetic relationships among Chinese indigenous goat breeds inferred from mitochondrial control region sequence. Small Rumin. Res., 73: 262-266.
11. He, L., Dai, B., Zeng, B., Zhang, X., Chen, B., Yue, B., Li, J. 2009. The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Genetics. 435: 23 - 28.
12. Huson, D.H., Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23: 254-267.
13. Gyllensten, U., Wharton, D., Josephson, A., Wilson, A. 1991. Paternal inheritance of mitochondrial DNA in mice. Natur., 352: 255 - 257.
14. Joshi, M.B., Rout, P.K., Mandal, A.K., Tyler-Smith, C., Singh, L., Thangaraj, K. 2004. Phylogeography and origin of Indian domestic goats. Mol. Biol. Evol., 21: 454-462.
15. Kiraz, S. 2009. Studies on determination of phylogenetic structure of ovine animals in Şanlıurfa Region using molecular techniques. Doctora Thesis, Harran Univ., pp: 181, Şanlıurfa, Turkey.
16. Kul, B.Ç., 2010. Mitochondrial DNA Diversity of Turkey's indigenous goat breeds and its filocoğrafya. Doctora Thesis, Ankara Univ., Ankara, Turkey.
17. Kumar, S., Nei, M., Dudley, J., Tamura, K. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform., 9: 299-306.
18. Librado, P., Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
19. Lin, X., Luo, J., Zhang, L., Wang, W., Shi, H., Zhu, J. 2013. miR-27a suppresses triglyceride accumulation and affects gene mRNA expression associated with fat metabolism in dairy goat mammary gland epithelial cells. Genetics. 521: 15-23.
20. Liu, Y.P., Cao, S.X., Chen, S.Y., Yao, Y.G., Liu, T.Z. 2009. Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation. Journal of Animal Breeding and Genetics. 126: 80-89.
21. Liu, R.Y., Lei, C.Z., Liu, S.H., Yang, G.S. 2007. Genetic diversity and origin of Chinese domestic goats revealed by complete mtDNA D-loop sequence variation. Asianaustralasin J. Anim. Sci., 20: 178 - 183.
22. Luikart, G., Gielly, L., Excoffier, L., Vigne, J.D., Bouvet, J., Taberlet, P. 2001. Multiple maternal origins and weak phylogeographic structure in domestic goats. Proc. Natl. Acad. Sci., 98: 5927-5932.
23. Miller, K., Storts, D. 1996. An improved single buffer, two enzyme system for RT-PCR. J. NIH Res., 8: 48 - 50.
24. Miller, S.A., Dykes, D.O., Polesky, H.T. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res., 16: 1215 - 1218.
25. Naderi, S., Rezaei, H.R., Taberlet, P., Zundel, S., Rafat, S.A., Naghash, H.R., Elbarody, M.A.A., Ertugrul, O., Pompanon, F. 2007. Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE., 2: 1-12.
26. Odahara, S., Chung, H.J., Choi, S.H., Yu, S. L., Sasazaki, S., Mannen, H., Park, C. S., Lee, J.H. 2006. Mitochondrial DNA diversity of Korean native goats. Asian-Australasian Journal of Animal Sci., 19: 482-485.
27. Pereira, F., Pereira, L., Van Asch, B., Bradley, D.G., Amorim, A. 2005. The mtDNA catalogue of all Portuguese autochothonous goat (Capra hircus) breeds. Mol. Ecol., 14: 2313-2318.
28. Sardina, M.T., Ballester, M., Marmi, J., Finocchiaro, R., Van Kaam, J.B.C.H.M., Portolano, B., Folch, J.M. 2006. Phylogenetic analysis of Sicilian goats reveals a new mtDNA lineage. Animal Genetics. 37: 376-378.
29. Sezgin, E., Kopuzlu,, S., Yüksel, S. 2010a. Georgian Goat. National Goat Raising Congress, Çanakkale Eighteen Marsh Univ. Anim. Sci. Dep., pp: 237-240.
30. Sezgin, E., Kopuzlu, S., Yüksel, S. 2010b. Abaza Goat. National Goat Raising Congress, Çanakkale Eighteen Marsh Univ. Anim. Sci. Dep., pp: 241-244.
31. Smith, D.G., McDonough, J. 2005. Mitochondrial DNA variation in Chinese and Indian rhesus macaques (Macaca mulatta). American J. Primat., 65: 1-25.
32. Sultana, S., Hideyuki, M., Soichi. 2003. Mitochondrial DNA diversity of Pakistani goats. Animal Genetics. 34: 417- 421.
33. Wang, J., Chen, Y.L., Wang, X.L., Yang, Z.X. 2008. The genetic diversity of seven indigenous Chinese goat breeds. Small Rumin. Res., 74: 231-237.
34. Wayne, D., Willem, H., Ferguson, S., Paulette, B. 2002. Characterization and evolution of the mitochondrial DNA control region in hornbills (Bucerotiformes). J. Mol. Evol., 54: 794 - 806.
35. Wenink, PW., Baker, A.J., Tilanus, M.G.J. 1994. Mitochondrial control-region sequences in two shorebird species, the turnstone and the dunlin, and their utility in population genetics studies. Mol. Biol. Evol., 11: 22-31.
36. Wu, Y.P., Guan, W.J., Zhao, Q.J., He, X.H., Pu, Y.B., Hou, J.H., Xie, J.F., Han, J.L., Rao, S.Q., Ma, Y.H. 2009. A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds. Anim. Sci. J., 80: 372-380.
37. Zhao, Y., Zhao, E., Zhang, N., Duan, C. 2011. Mitochondrial DNA diversity, origin, and phylogenic relationships of three Chinese large-fat-tailed sheep breeds. Trop. Anim Health Prod., 43: 1405-1410.
38. Zhong, T., Zhao, Q.J., Niu, L.L., Wang, J., Jin, P.F., Zhao, W., Wang, L.J., Li, L., Zhang, H.P., Ma, Y.H. 2013. Genetic phylogeography and maternal lineages of 18 Chinese black goat breeds. Trop. Anim. Health Prod., 45: 1833 - 1836.