Use of RAPD-PCR for genetic analyses on the native cattle breeds in Turkey

Abstract

The purpose of this study was to identify the genetic relationship and variations within and between local cattle breeds of Turkey using RAPD-PCR method which needs fewer substructures when compared to other DNA fingerprinting methods. The RAPD-PCR method was performed on blood samples of 77 animals from four breeds namely Anatolian Black (AB), East Anatolian Red (EAR), South Anatolian Red (SAR) and Turkish Grey Steppe (TG). A set of ten arbitrary 10-mer primers were used to detect the DNA polymorphisms in the whole genome. Estimation of the genetic distances between the breeds was conducted through the FST Distant Estimation Method, and cluster trees were constructed by UPGMA Method. Based on the band sharing method, the average genetic variances of the breeds varied from 0.637 (in TG) to 0.809 (in SAR), AB and EAR had 0.792 and 0.787, respectively. It was concluded that AB breed is more closely related to EAR breed than to SAR breed while TG breed was determined as a distinct group from other breeds

Keywords

• Breed characterization
• native cattle breeds of Turkey
• DNA fingerprinting
• phylogeny
• RAPD-PCR

Türkiye’deki yerli sığır ırklarında genetik analiz için RAPD-PCR kullanımı

Abstract

Bu çalışmada, diğer DNA parmak izi yöntemleri ile karşılaştırıldığında daha az alt yapıya ihtiyaç duyan RAPD-PCR metodu kullanılarak Türkiye yerli sığır ırklarında ırk içi ve ırklar arası genetik ilişki ve genetik varyasyonların belirlenmesi amaçlanmıştır. RAPD-PCR metodu Yerli Kara (YK), Doğu Anadolu Kırmızısı (DAK), Güney Anadolu Kırmızısı (GAK) ve Boz Irk’tan (BI) toplam 77 hayvandan alınan kan örnekleri kullanılarak yapılmıştır. DNA’larda polimorfizmleri belirlemek için 10 bazdan oluşan 10 primer seti kullanılmıştır. Irklar arası mesafe FST Mesafe Tahmin Metoduyla, ırklara ait gruplama ağaçları UPGMA metoduyla yapılmıştır. Bantların varlığına göre ırkların ortalama genetik varyansları 0,637 (BI)’den 0,809 (GAK)’a kadar değiştiği görülmüştür. YK ırkının DAK ırkına GAK ırkından daha yakın olduğu, BI ise her üç ırktan farklı bir kümede bulunduğu belirlenmiştir

Keywords

• DNA parmak izi
• filogenetik
• ırk karakterizasyonu
• Türkiye yerli sığır ırkları
• RAPD-PCR

References

1. Abdel-Rahman SM, Hafez EE (2007): Genetic similarity among the three Egyptian water buffalo flocks using RAPD-PCR and PCR-RFLP techniques, Res J Agric & Biol Sci, 3, 351-355.
2. Ahlawat SPS, Sunder J, Kundu A, Chatterjee RN, Rai RB, Kumar B, Senani S, Saha SK, Yadav SP (2004): Use of RAPD-PCR for genetic analysis of Nicobari fowl of Andamans. Br Poult Sci, 45, 194–200.
3. Ali BA (2003): Genetics similarity among four breeds of sheep in Egypt detected by random amplified polymorphic DNA markers. Afr J Biotechnol, 2, 194-197.
4. Alpan O, Arpacik R (1996): Sığır Yetiştiriciliği. Ankara, Şahin Matbaası, pp.39-44.
5. Alves BCA, Unanian MM, Silva E, Oliveira M, Moreira-Filho CA (2005): Use of RAPD markers for identifying Nelore bulls with early reproductive maturation onset. Anim Reprod Sci, 85, 183–191.
6. Ambady S, Carpio CM, Ponce De León FA (1996): Optimization of RAPD-PCR conditions in cattle. Anim Biotechnol, 7, 99-122.
7. Anonym (2009): Türkiye İstatistik Kurumu. Erişim: http://www.tuik.gov.tr. Access Date: 15 May 2009.
8. Apostol BL, Black WC, Reiter P, Miller BR (1996): Population genetics with RAPD-PCR markers: the breeding structure of Aedes aegypti in Puerto Rico. Heredity, 76, 325-334.

9. Elmaci C, Oner Y, Ozis S, Tuncel E (2007): RAPD analysis of DNA polymorphism in Turkish sheep breeds. Biochem Genet, 45, 691–696.
10. Ertugrul O, Alpan O, Dogrul F (1991): Blood group polymorphism in Turkish cattle breeds. Doğa-Tr J of Vet Anim Sci, 15, 328-337.
11. Excoffier L, Smouse P, Quattro J (1992): Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479-491.
12. Li L, Zhang J, Zhu JJ, Gu S, Sun Q, Zhou GM, Fu CX, Li Q, Chen LY, Li DX, Liu SJ, Yang ZR (2006): Genetic diversity of nine populations of the Black Goat (Capra hircus) in Sichuan, PR China. Zoolog Sci, 23, 229- 234.
13. Loftus RT, Ertugrul O, Harba AH, El-Barody MAA, Machugh DE, Park SDE, Bradley DG (1999): A microsatellite survey of cattle from a centre of origin: the Near East. Mol Ecol, 8, 2015–2022.
14. Miller SA, Dykes DD, Polesky HF (1988): A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res, 16, 1215.
15. Ozbeyaz C (1991): Türkiye yerli sığır ırklarında hemoglobin polimorfizmi. Ankara Üniv Vet Fak Derg, 38, 53-59.
16. Parejo JC, Padilla JA, Rabasco A, Sansinforiano ME, Trancón MM (2002): Population structure in the endangered Blanca Cacereña bovine breed demonstrated by RAPD analyses. Genes Genet Syst, 77, 51-58.
17. Reynolds J, Weir BS, Cockerham CC, (1983): Estimation for the coancestry coefficient: a basis for short term genetic distance. Genetics, 105, 767-779.
18. Schneider S, Kueffer JM, Roessli D, Excoffıer L (1997): Arlequin: A software for population genetic data analysis, version 1.1. Genetics and Biometry Lab, Dept. of Anthropology, Univ Geneva.
19. Semyenova SK, Illarionova NA, Vasil’ev VA, Shubkina AV, Ryskov AP (2002): Genetic analysis and estimation of genetic diversity in East-European breeds of windhounds (Canis familiaris L.) based on the data of genomic studies using RAPD markers. Genetika, 38, 704– 713.
20. Singh RV, Sharma D (2002): Within-and between-strain genetic variability in White Leghorn population detected through RAPD markers. Br Poult Sci, 43, 33–37.
21. Sneath PH, Sokal RR (1973): Taxonomy structure. In numerical taxonomy. The Principle and Practice of Numerical Classification. Ed. Kennedy D and Park RB pp.134-230. San Francisco, CA: Freeman.
22. Talle SB, Chenyabuga WS, Fimland E, Syrstad O, Meuwissen T, Klungland H (2005): Use of DNA technologies for the conservation of animal genetic resources: A review. Acta Agr Scand A-An, 55, 1-8.
23. Yu Y, Lian LS, Wen JK, Shi XW, Zhu FX, Nie L, Zhang YP (2004): Genetic diversity and relationship of Yunnan native cattle breeds and introduced beef cattle breeds. Biochem Genet, 42, 1-9.
24. Zhang X, Leung FC, Chan DKO, Yang G, Wu C (2002b):
25. Genetic diversity of Chinese native chicken breeds based on protein polymorphism, randomly amplified polymorphic DNA, and microsatellite polymorphism. Poult Sci,81, 1463–1472.