Ercan KURAR, Zafer BULUT, Mehmet NİZAMNOĞLU

Sığır mikrosatellit test panelinin Türkiye'de ebeveyn tayini çalışmalarında kullanılabilirliği

Amaç: Türkiye'de yaygın olarak yetiştirilen sığır ırkları ve melezlerinin kimliklendirme çalışmalarında bir mikrosatellit test panelinin kullanılabilirliğinin araştırılmasıdır. Gereç ve Yöntem: Çalışmada 148 adet sığıra ait genomik DNA örneği kullanıldı. Toplam 11 adet mikrosatellit markörü ISAG ve FAO MoDAD listesinden seçildi. Genomik DNA örnekleri Polimeraz Zincir Reaksiyonu (PZR) metoduyla çoğaltılarak, kapiller elektroforez sonrası fragman analizi ile alleller tanımlandı. Genel populasyon parametrelerinden allel sayısı (Na), gözlenen (Ho) ve beklenen (He) heterozigotluk değerleri, Hardy-Weinberg dengesinden (HWE) sapma ile dışlama gücü (DG) değerleri hesaplandı. Bulgular: Lokus başına 6-17 arasında değişen 150 farklı allel tanımlandı. Ho ve He değerleri sırasıyla 0.435-0.884 ve 0.632- 0.887 arasında bulundu. DG-1 ve DG-2 değerleri lokus bazında 0.239-0.630 ve 0.419-0.774 arasında değişmekte olup, tüm lokuslar için toplam DG-2 değeri 0.999 olarak hesaplandı. Öneri: Test panelinin Türkiye'de sığır kimliklendirme çalışmalarında kullanılabileceği ancak lokus sayısının artırılması ve etkin multipleks sistemlerinin geliştirilmesinin uygun olacağı kanaatine varılmıştır.

Usefulness of a microsatellite test panel for cattle parentage testing in Turkey

Aim: The objective of this study was to test usefulness a microsatellite test panel for parentage analysis in widely reared cattle breeds in Turkey. Materials and Methods: In this study, genomic DNAs were used from 148 cattle. A total of eleven bovine microsatellite loci were selected from a list suggested by ISAG and FAO MoDAD. Genomic DNA samples were amplified by polymerase chain reaction (PCR). Alleles were determined by fragment analysis after capillary electrophoresis. General population parameters including allel numbers (Na), observed (Ho) and expected heterozygosities (He), deviation from Hardy-Weinberg Equilibrium (HWE) and power of exclusion (PE) at each microsatellite locus were calculated. Results: A total of 150 different alleles were determined ranging from 6 to 17 at each locus. The Ho and He were ranged from 0.435 to 0.884 and 0.632 to 0.887, respectively. Locus based PE-1 and PE-2 were varied as 0.239-0.630 and 0.419-0.774 and a total PE-2 value was calculated as 0.999. Conclusions: It was concluded that the test panel seems to be applied in cattle identification efforts; however, there is need for increasing the number of the locus in the panel and development of efficient multiplex systems.

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Altınalan A, 2005. Türkiyedeki yerli sığır ırklarının mikrosatellit DNA markırlarla genetik karakterizasyonu. Çukurova Üniversitesi Fen Bilimleri Enstitüsü, Doktora Tezi.
Baron EE, Martinez ML, Verneque RS, Coutinho LL, 2002. Parentage testing and effect of misidentification on the estimation of breeding value in Gir cattle. Genet Mol Biol, 25, 389-394.
Beechinor JG, Kelly EP, 1987. Errors of identification amongst cattle presented as progeny of some bulls used in the artificial insemination service in Ireland. Ir Vet J, 41, 348-353.
Canon J, Alexandrino P, Bessa I, Carleos C, Carretero Y, Dunner S, Ferran N, Garcia D, Jordana J, Laloë D, Pereira A, Sanchez A, Moazami-Goudarzi K, 2001. Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genet Sel Evol, 33, 311-332.
Cerit H, 2003. Bir Holştayn sığır populasyonunda bazı genomik lokusların allel frekanslarının belirlenmesi ve birey tanımlanmasındaki önemi. Tur J Vet Anim Sci, 27, 81-91.
Curi RA, Lopes CA, 2002. Evaluation of nine microsatellite loci and misidentification paternity frequency in a population of Gyr breed bovines. Braz J Vet Res Anim Sci, 39, 129-135.
Cymbron T, Freeman AR, Isabel Malheiro M, Vigne JD, Bradley DG, 2005.
Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Proceed Royal Soc London B, 272, 1837-1843.
Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS, 1991. Touchdown PCR to circumvent spurious priming during gene amplification. Nucl Acid Res, 19, 4008.
Geldermann H, Pieper U, Weber WE, 1986. Effect of misidentification on the estimation of breeding value and heritability in cattle. J Anim Sci, 63, 1759-1768.
Hoffmann I, Marsan PA, Barker JSF, Cothran EG, Hanotte O, Lenstra JA, Milan D, Weigend S, Simianer H, 2004. New MoDAD marker sets to be used in diversity studies for the major farm animal species: Recommendations of a joint ISAG/FAO working group. 29th ISAG (International Society of Animal Genetics) Congress, 11-16 September, Tokyo, 2004.
Israel C, Weller JI, 2000. Effect of misidentification on genetic gain and estimation of breeding value in dairy cattle populations. J Dairy Sci, 83, 181-187.
Kurar E, 2001. Comparative physical and linkage mapping of bovine chromosome 24 with human chromosome 18. Ph.D. Dissertation, University of Wisconsin-Madison, USA.
Li MH, Tapio I, Vilkki J, Ivanova Z, Kiselyova T, Marzanov N, Cinkulov M, Stojanović S, Ammosov I, Popov R, Kantanen J, 2007.
The genetic structure of cattle populations (Bos taurus) in Northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation. Mol Ecol, 16, 3839-3853.
Loftus RT, Ertugrul O, Harba AH, El-Barody MA, MacHugh DE, Park SD, Bradley DG, 1999. A microsatellite survey of cattle from a centre of origin: the Near East. Mol Ecol, 8, 2015-2022.
Marshall TC, Slate J, Kruuk LEB, Pemberton JM, 1998. Statistical confidence for likelihood- based paternity inference in natural populations. Mol Ecol, 7, 639-655.
Martin-Burriel I, Rodellar C, Lenstra JA, Sanz A, Cons C, Osta R, Reta M, De Argüello S, Sanz A, Zaragoza P, 2007. Genetic diversity and relationships of endangered Spanish cattle breeds. J Hered, 98, 687-691.
Maudet C, Luikart G, Taberlet P, 2002. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J Anim Sci, 80, 942-950.
Moioli B, Napolitano F, Catillo G, 2004. Genetic diversity between Piedmontese, Maremmana, and Podolica cattle breeds. J Hered, 95, 250-256.
Özkan E, 2005. Türkiyede yetiştirilen yerli ve kültür sığır ırklarının genetik yapılarının mikrosatelitler ile incelenmesi. Trakya Üniversitesi Fen Bilimleri Enstitüsü. Doktora Tezi.
Özkan E, Soysal MI, Özder M, Koban E, Şahin O, Togan I, 2009.
Evaluation of parentage testing in the Turkish Holstein population based on 12 microsatellite loci. Livest Sci, 124, 101-106.
Özşensoy Y, Kurar E, Doğan M, Bulut Z, Altunok V, Işık A, Çamlıdağ A, Nizamlıoğlu M, 2010a. Türkiyede bulunan bazı yerli sığır ırklarının STR markörler ile genetik karakterizasyonu. BIBAD, 3, 163-171.
Özşensoy Y, Kurar E, Doğan M, Bulut Z, Altunok V, Işık A, Çamlı- dağ A, Nizamlıoğlu M, 2010b. Mikrosatellit markörlerinin Türkiye yerli sığır ırklarının tanımlanması ve kimliklendirme çalışmalarında kullanılabilirliği. III. Ulusal Veteriner Zootekni Kongresi. 15-17 Temmuz 2010, Afyonkarahisar. Peakall R, Smouse PE, 2006. GENALEX 6: Genetic analysis in excel. Population genetic software for teaching and research. Mol Ecol Notes, 6, 288-295.
Peelman LJ, Mortiaux F, Van Zeveren A, Dansercoer A, Mommens G, Coopman F, Bouquet Y, Burny A, Renaville R, Portetelle D, 1998. Evaluation of the genetic variability of 23 bovine microsatellite markers in four Belgian cattle breeds. Anim Genet, 29, 161-167.
Rehout V, Hradecká E, Cítek J, 2006. Evaluation of parentage testing in the Czech population of Holstein cattle. Czech J Anim Sci, 51, 503-509.
Ron M, Blanc Y, Band M, Ezra E, Weller JI, 1996. Misidentification rate in the Israeli dairy cattle population and its implications for genetic improvement. J Dairy Sci, 79, 676-681.
Sambrook J, Fritsch EF, Maniatis T, 1989. Molecular Clonning: A Laboratory Manual. Second Edition, Cold-Spring Harbor, New York, USA, Volume 2, pp: 9.16-9.19.
Schmid M, Saitbekova N, Gaillard C, Dolf G, 1999. Genetic diversity in Swiss cattle breeds. J Anim Breed Genet, 116, 1-8.
Visscher PM, Woolliams JA, Smith D, Williams JL, 2002. Estimation of pedigree errors in the UK dairy population using microsatellite markers and the impact on selection. J Dairy Sci, 85, 2368-2375.
Weber JL, May PE, 1989. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. American J Hum Genet, 44, 388-396.
Zhang GX, Wang ZG, Chen WS, Wu CX, Han X, Chang H, Zan LS, Li RL, Wang JH, Song WT, Xu GF, Yang HJ, Luo YF, 2007. Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers. Anim Genet, 38, 550-559.