Abstract
Mitochondrial DNA is one of the most preferred markers being used in phylogenetic studies in domestic animals due to its unique features. In this study, the mitochondrial DNA control region was analyzed in Angora, Honamli, Kilis, Hair and Norduz goat breeds (n=252) to reveal diversity of mitochondrial DNA, differentiation of goat breeds, and relevance between genetic differentiations and geographic distributions. Based on the performed analysis methods, three different haplogroups; A, D and G were determined for breeds studied. Two duplication insertions (77bp) were observed in two animals from different breeds. In comparison with goat breeds throughout the world, the haplotype number, higher nucleotide and haplotype diversity values (π=0,02100, ±0,00073 and H=0,9982, ±0,0006 respectively) for goat breeds studied in the present study, indicate that Turkey has been situated in a central position during the domestication process of the goat specie. Based on our haplotype sharing detection results, Kilis and Norduz breeds, which are known as crossbreeds of Hair goats, do not share haplotypes with Hair goats, thus, the history of these breeds should be further investigated. The results of the study also gave hints that conservation flocks should be promoted immediately in local breeders for Norduz breed, which is under risk of extinction, along with a controlled mating program to prevent loss of genotypes. In this study, an inexpensive novel method based on PCR- RFLP was introduced to determine G haplotype, a unique haplotype to Fertile Crescent regions
References
- Akçapınar H (1994): Keçi Yetiştiriciliği Ders Notları. Ankara Üniversitesi Veteriner Fakültesi Zootekni Anabilim Dalı.
- Bandelt HJ, Forster P, Röhl A (1999): Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol, 16, 37-48.
- Batu S (1951): Türkiye Yerli Keçi Irkları ve Keçi Yetiştirme Bilgisi. Ankara Üniversitesi Veteriner Fakültesi Kitabı No:2.
- Excoffier L, Lischer HEL (2010): Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour, 10, 564-567.
- Fajardo V, Gonzalez I, Lopez-Calleja I, Martin I, Rojas M, Pavon MA, Garcia T, Hernandez PE, Martin R (2007): PCR identification of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon) targeting specific sequences from the mitochondrial D-loop region. Meat Sci, 76, 644- 652.
- Felsenstein J (2005): PHYLIP version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
- Fu YX (1997): Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.
- Guindon S, Gascuel O (2003): A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 52, 696-704.
- Hall TA (1999): BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp, 41, 95-98.
- Joshi MB, Rout PK, Mandal AK, Tyler-Smith C, Singh L, Thangaraj K (2004): Phylogeography and origin of Indian domestic goats. Mol Biol Evol, 21, 454-462.
- Kumar S, Dudley J, Nei M, Tamura K (2008): MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 9, 299-306.
- Librado P, Rozas J (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
- 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.
- Luikart G, Gielly L, Excoffier L, Vigne J-D, Bouvet J, Taberlet P (2001): From the Cover: Multiple maternal origins and weak phylogeographic structure in domestic goats. PNAS, 98, 5927-5932.
- MacHugh DE, Bradley DG (2001): Livestock genetic origins: Goats buck the trend. PNAS, 98, 5382-5384.
- Mannen H, Nagata Y, Tsuji S (2001): Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of Bezoar (Capra aegagrus). Biochem Genet, 39, 145-454.
- Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, Naghash HR, Elbarody MAA, Ertugrul O, Pompanon F (2007): Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE, 2,10, e1012.
- Naderi S, Rezaei HR, Pompanon F, Blum MG, Negrini R, Naghash HR, Balkiz O, Mashkour M, Gaggiotti OE, Ajmone-Marsan P, Kence A, Vigne JD Taberlet P (2008): The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. PNAS, 105, 17659-17664.
- Pereira F, Pereira L, Van Asch B, Bradley DG, Amorim A (2005): The mtDNA catalogue of all Portuguese autochthonous goat (C. hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol Ecol, 14, 2313–18.
- Porter V (1996): Goats of the World. Farming Press, Ipswich, UK.
- Sambrook J, Fritsch EF, Maniatis T (1989): Molecular Cloning: A Laboratory Manual, vol. I., 2ndedition. Cold Spring Harbor Laboratory Press.
- Sultana S, Mannen H, Tsuji S (2003): Mitochondrial DNA diversity of Pakistani goats. Anim Genet, 34, 417- 421.
- Tajima F (1989): Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
- Wu YP, Guan WJ, Zhao QJ, He XH, Pu YB, Huo JH, Xie JF, Han JL, Rao SQ, Ma YH (2009): A fine map for maternal lineage analysis by mitochondrial hyperviable region in 12 Chinese goat breeds. Anim Sci J, 80, 372– 380.
- Yalçın BC (1986): Sheep and Goats in Turkey. FAO Animal Production and Health Paper, 60.
- Zeder MA (2008): Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. PNAS, 19, 11597-11604. Geliş tarihi: 27.10.2010 / Kabul tarihi: 29.11.2010 Addres for correspondence: Bengi Çınar Kul, DVM, PhD Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara 06110, Turkey. Phone : 90 312 317 03 15 ext: 314 E-mail: bkul@veterinary.ankara.edu.tr
Abstract
Mitokondrial DNA, evcil hayvanların filogenetik çalışmalarında en fazla tercih edilen belirteçlerden birisidir. Bu çalışmada, Ankara, Honamlı, Kilis, Kıl ve Norduz keçi ırklarının (n=252) mitokondrial DNA çeşitlilikleri, ırklar arası farklılıkları ve bu farklılıkların coğrafik yerleşimleri ile olan ilişkisinin ortaya konulması amacıyla mitokondrial DNA kontrol bölgesi analiz edilmiştir. Analiz sonuçlarına göre iki farklı ırktan iki bireyde 77bp’lik tekrarlama mutasyonu belirlenmiştir. İncelenen ırklarda A, D ve G haplogrupları olmak üzere üç farklı haplogrup belirlenmiştir. Elde edilen yüksek haplotip sayısı, yüksek nükleotid (π=0,02100, +/-0,00073) ve haplotip çeşitliliği (H=0,9982, +/-0,0006) değerleri dünya keçi ırklarıyla karşılaştırıldığında, Türkiye’nin, keçilerin evciltilmesinde merkezi bir konumda olduğu düşünülmektedir. Haplotip paylaşımları göz önüne alındığında; Kıl keçisi melezi oldukları bilinen Kilis ve Norduz keçi ırklarının Kıl keçisiyle hiç haplotip paylaşmıyor olmaları ırkların tarihinin daha iyi araştırılmasının gerekliliğini ortaya koymuştur. Çalışmanın sonuçları aynı zamanda, yok olma açısından ağır tehdit altında olan Norduz keçi ırkı için acil olarak halk elinde koruma sürüleri oluşturulması ve mevcut genotiplerin kaybının önüne geçilebilmesi için kontrollü birleştirmelerin yapılması gerekliliğini ortaya koymaktadır. Bu çalışma sayesinde Verimli Hilal bölgesine özgü olan G haplogrubunun daha az maliyetle belirlenebilmesi için PZR-RFLP’ye dayanan yeni bir yöntem ortaya konulmuştur
References
- Akçapınar H (1994): Keçi Yetiştiriciliği Ders Notları. Ankara Üniversitesi Veteriner Fakültesi Zootekni Anabilim Dalı.
- Bandelt HJ, Forster P, Röhl A (1999): Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol, 16, 37-48.
- Batu S (1951): Türkiye Yerli Keçi Irkları ve Keçi Yetiştirme Bilgisi. Ankara Üniversitesi Veteriner Fakültesi Kitabı No:2.
- Excoffier L, Lischer HEL (2010): Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour, 10, 564-567.
- Fajardo V, Gonzalez I, Lopez-Calleja I, Martin I, Rojas M, Pavon MA, Garcia T, Hernandez PE, Martin R (2007): PCR identification of meats from chamois (Rupicapra rupicapra), pyrenean ibex (Capra pyrenaica), and mouflon (Ovis ammon) targeting specific sequences from the mitochondrial D-loop region. Meat Sci, 76, 644- 652.
- Felsenstein J (2005): PHYLIP version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
- Fu YX (1997): Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.
- Guindon S, Gascuel O (2003): A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol, 52, 696-704.
- Hall TA (1999): BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp, 41, 95-98.
- Joshi MB, Rout PK, Mandal AK, Tyler-Smith C, Singh L, Thangaraj K (2004): Phylogeography and origin of Indian domestic goats. Mol Biol Evol, 21, 454-462.
- Kumar S, Dudley J, Nei M, Tamura K (2008): MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 9, 299-306.
- Librado P, Rozas J (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
- 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.
- Luikart G, Gielly L, Excoffier L, Vigne J-D, Bouvet J, Taberlet P (2001): From the Cover: Multiple maternal origins and weak phylogeographic structure in domestic goats. PNAS, 98, 5927-5932.
- MacHugh DE, Bradley DG (2001): Livestock genetic origins: Goats buck the trend. PNAS, 98, 5382-5384.
- Mannen H, Nagata Y, Tsuji S (2001): Mitochondrial DNA reveal that domestic goat (Capra hircus) are genetically affected by two subspecies of Bezoar (Capra aegagrus). Biochem Genet, 39, 145-454.
- Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, Naghash HR, Elbarody MAA, Ertugrul O, Pompanon F (2007): Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE, 2,10, e1012.
- Naderi S, Rezaei HR, Pompanon F, Blum MG, Negrini R, Naghash HR, Balkiz O, Mashkour M, Gaggiotti OE, Ajmone-Marsan P, Kence A, Vigne JD Taberlet P (2008): The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. PNAS, 105, 17659-17664.
- Pereira F, Pereira L, Van Asch B, Bradley DG, Amorim A (2005): The mtDNA catalogue of all Portuguese autochthonous goat (C. hircus) breeds: high diversity of female lineages at the western fringe of European distribution. Mol Ecol, 14, 2313–18.
- Porter V (1996): Goats of the World. Farming Press, Ipswich, UK.
- Sambrook J, Fritsch EF, Maniatis T (1989): Molecular Cloning: A Laboratory Manual, vol. I., 2ndedition. Cold Spring Harbor Laboratory Press.
- Sultana S, Mannen H, Tsuji S (2003): Mitochondrial DNA diversity of Pakistani goats. Anim Genet, 34, 417- 421.
- Tajima F (1989): Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
- Wu YP, Guan WJ, Zhao QJ, He XH, Pu YB, Huo JH, Xie JF, Han JL, Rao SQ, Ma YH (2009): A fine map for maternal lineage analysis by mitochondrial hyperviable region in 12 Chinese goat breeds. Anim Sci J, 80, 372– 380.
- Yalçın BC (1986): Sheep and Goats in Turkey. FAO Animal Production and Health Paper, 60.
- Zeder MA (2008): Domestication and early agriculture in the Mediterranean Basin: Origins, diffusion, and impact. PNAS, 19, 11597-11604. Geliş tarihi: 27.10.2010 / Kabul tarihi: 29.11.2010 Addres for correspondence: Bengi Çınar Kul, DVM, PhD Department of Genetics, Faculty of Veterinary Medicine, Ankara University, Ankara 06110, Turkey. Phone : 90 312 317 03 15 ext: 314 E-mail: bkul@veterinary.ankara.edu.tr
Details
| Primary Language | English |
|---|---|
| Subjects | Veterinary Surgery |
| Other ID | JA66GS64RF |
| Journal Section | Research Article |
| Authors | |
| Publication Date | June 1, 2011 |
| Published in Issue | Year 2011 |