Genetic Diversity and Bottleneck Analysis of Endangered Güney Karaman Sheep

Year 2020, Volume: 3 Issue: 2, 143 - 154, 27.12.2020

Necdet Akay Tülay Canatan Onur Yılmaz Nezih Ata Orhan Karaca İbrahim Cemal

Abstract

The present study was performed to reveal genetic variability of autochthonous Güney Karaman sheep breed, which is conserved as a genetic resource, using sixteen microsatellites marker recommended by FAO. Animal material for the study was consisted of 119 Güney Karaman sheep raised in Bahri Dagdas International Agricultural Research Institute. A total of 277 alleles were detected from sixteen markers studied. Although total population size is very limited, the mean number of alleles (17.31), observed heterozygosity (0.81) and polymorphic information content (0.82) findings indicated that noticeable genetic variability in this population. Ten out of the sixteen microsatellite markers studied had a positive FIS value. The mean value of FIS was 0.042. The infinite allele model (IAM), two-phase mutation model (TPM) and stepwise mutation model (SMM) in the Bottleneck software were used to check genetic bottleneck. The L-shaped curve obtained from analyze indicates absence of bottleneck in Güney Karaman sheep population. These results will help to develop conservation strategies for the Güney Karaman sheep population.

Keywords

Genetic diversity, Genetic resource, Microsatellite, Population structure

Thanks

We acknowledge Republic of Turkey Ministry of Food, Agriculture and Livestock for supplying animal materials and The Agricultural Biotechnology and Food Safety Application and Research Centre (ADU-TARBIYOMER) of Adnan Menderes University for providing laboratory facilities to carry out molecular genetic analysis.

Yok Olma Tehlikesi Altındaki Güney Karaman Koyunlarda Genetik Çeşitlilik ve Genetik Darboğaz Analizleri

Abstract

Bu çalışma, FAO tarafından önerilen onaltı mikrosatellit belirteç kullanılarak genetik kaynak olarak korunan Güney Karaman koyun popülasyonuna yönelik genetik çeşitlilik ve darboğaz analizlerinin gerçekleştirilmesi amacıyla gerçekleştirilmiştir. Çalışmanın hayvan materyalini Bahri Dağdaş Uluslararası Tarımsal Araştırma Enstitüsü'nde yetiştirilen 119 Güney Karaman ırkı koyun oluşturmuştur. Çalışılan on altı mikrosatellit belirteçten toplam 277 allel tespit edilmiştir. Populasyon büyüklüğü çok sınırlı olmasına rağmen, ortalama alel sayısı (17.31), gözlemlenen heterozigotluk (0.81) ve polimorfik bilgi içeriği (0.82) bulguları, bu popülasyonda gözle görülür bir genetik çeşitlilik olduğuna işaret etmektedir. İncelenen on altı mikrosatellit belirteçin onunda pozitif FIS değeri elde edilmiştir. Ortalama FIS değeri 0.042 olmuştur. Genetik darboğazın tespiti için Bottleneck yazılımındaki sonsuz alel modeli (IAM), iki fazlı mutasyon modeli (TPM) ve aşamalı mutasyon modeli (SMM) gibi üç farklı model kullanılmıştır. Gerçekleştirilen darboğaz analizinden elde edilen L şeklindeki eğri, Güney Karaman koyun populasyonunda yakın zamanda herhangi bir genetik darboğaz olmadığını ortaya çıkarmıştır. Bu sonuçlar, Güney Karaman koyun populasyonu için koruma stratejilerinin geliştirilmesine yardımcı olacaktır.

Keywords

Genetik Çeşitlilik, Genetik Kaynak, Mikrosatellit, Populasyon yapısı

References

• Abdelkader A.A., N. Ata, M.T. Benyoucef, Djaout A., N. Azzi, O. Yilmaz, I. Cemal and S.B.S. Gaouar, 2018. New genetic identification and characterisation of 12 Algerian sheep breeds by microsatellite markers. Italian Journal of Animal Science, 17(1): 38-48.
• Arora R. and S. Bhatia, 2006. Genetic diversity of Magra sheep from India using microsatellite analysis. Asian Australasian Journal of Animal Science, 19(7): 938-942.
• Ben Sassi-Zaidy Y., F. Maretto, F. Charfi-Cheikhrouha, A. Mohamed-Brahmi and M. Cassandro, 2016. Contribution of microsatellites markers in the clarification of the origin, genetic risk factors, and implications for conservation of Tunisian native sheep breeds. Genetics and Molecular Research, 15(1).
• Bruford M.W., C. Ginja, I. Hoffmann, S. Joost, P. Orozco-Terwengell, F.J. Alberto, A.J. Amaral, M. Barbato, F. Biscarini, L. Colli, M. et al.,, 2015. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Frontier Genetics, 6.
• Canatan T., N. Akay, M. Kan and M. Kirbaş, 2014a. Native animal genetic resource in Turkey Southern Karaman sheep breed. Proc. International Participated Small Ruminant Congress, Konya, Turkey, 16-18 Oct. 2014, p.370.
• Canatan T., N. Akay, M. Kan and M. Kirbaş, 2014b. Some yield characteristics of Southern Karaman sheep breed as genetic resource. Proc. International Participated Small Ruminant Congress, Konya, Turkey, 16-18 Oct. 2014, p.368.
• Cemal I., O. Yilmaz, O. Karaca, P. Binbaş and N. Ata, 2013. Analysis of genetic diversity in indigenous Çine Çaparı sheep under conservation by microsatellite markers. Kafkas Universitesi Veteriner Fakültesi Dergisi, 19: 383-390.
• Cornuet J.M. and G. Luikart, 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4): 2001-2014.
• Dakin E.E. and J.C. Avise, 2004. Microsatellite null alleles in parentage analysis. Heredity, 93: 504-509.
• Dirienzo A., A.C. Peterson, J.C. Garza, A.M. Valdes, M. Slatkin and N.B. Freimer, 1994. Mutational processes of simple-sequence repeat loci in human-populations. Proceedings of National Academy of Sciences, 91(8):3166-3170.
• Ertuğrul M., G. Dellal, İ. Soysal, C. Elmaci, O. Akin, S. Arat, İ. Baritçi, E. Pehlivan and O. Yilmaz, 2009. Türkiye yerli koyun ırklarının korunması. Journal of Agriculture Faculty Bursa Uludag University, 23(2): 97-119 (in Turkish, English abstract).
• FAO, 2011. Molecular genetic characterization of animal genetic resources. Rome: FAO.
• FAO, 2015. The State of the World’s Animal Genetic Resources for Food and Agriculture. Rome: FAO Commission on Genetic Resources for Food and Agriculture Assessments.
• Guang-Xin E., T. Zhong, Y.H. Ma, H.J. Gao, J.N. He, N. Liu, Y.J. Zhao, J.H. Zhang and Y.F. Huang, 2016. Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers. Ecology and Evolution, 6(3):810-817.
• Hecker K.H. and K.H. Roux, 1996. High and low annealing temperatures increase both specifity and yield in touchdown and stepdown PCR. Biotechniques, 20:478-485.
• Hoda A., P.A. Marsan, 2012. Genetic characterization of Albanian sheep breeds by microsatellite markers. In: Analysis of genetic variation in animals, Caliskan, M. (eds). InTech Open Press, United Kingdom, pp. 3-26.
• Hoffmann I., D. Boerma and B. Scherf, 2011. The Global plan of action for animal genetic resources - The road to common understanding and agreement. Livestock Science, 136(1): 7-14.
• Kalinowski S.T., M.L. Taper and T.C. Marshall, 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16:1099-1106.
• Kdidi S., J.H. Calvo, L. Gonzalez-Calvo, M. Ben Sassi, T. Khorchani and M.H. Yahyaoui, 2015. Genetic relationship and admixture in four Tunisian sheep breeds revealed by microsatellite markers. Small Ruminant Reserach, 131:64-69.
• Kiraz S., N. Akay, M.E. Vural, A. Karataş and S. Koncagül, 2014. Phylogenetic relationships based on mitochondrial DNA haplogrups between Güney Karaman and some local sheep breeds. Proc. International Participated Small Ruminant Congress, Konya, Turkey, 16-18 Oct. 2014, p.372.
• Loukovitis D., A. Siasiou, I. Mitsopoulos, A.G. Lymberopoulos, V. Laga and D. Chatziplis, 2016. Genetic diversity of Greek sheep breeds and transhumant populations utilizing microsatellite markers. Small Ruminant Reserach, 136: 238-242.
• Luikart G., F.W Allendorf., J.M. Cornuet and W.B. Sherwin, 1998. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity, 89(3): 238-247.
• Luikart G. and J.M. Cornuet, 1998. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv. Biol. 12(1): 228-237.
• Marshall T.C., J. Slate, L.E.B. Kruuk and J.M. Pemberton, 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology, 7: 639-655.
• Miller S.A., D.D. Dykes and H.F. Polesky, 1988. A simple salting out procedure for extracting DNA from Human nucleated cells. Nucleic Acids Resesarch, 16(3):1215.
• Montgomery G.W. and J.A. Sise, 1990. Extraction of DNA from Sheep white blood-cells. New Zealand Journal of Agricultural Research, 33(3): 437-441.
• Ocampo R., H. Cardona and R. Martinez, 2016. Genetic diversity of Colombian sheep by microsatellite markers. Chilean Journal of Agricultural Research, 76(1): 40-47.
• Oner Y., H. Ustuner, A. Orman, O. Yilmaz and A. Yilmaz, 2014. Genetic diversity of Kivircik sheep breed reared in different regions and its relationship with other sheep breeds in Turkey. Italian Journal of Animal Science, 13(3):588-593.
• Peakall R. and P.E. Smouse, 2006. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6: 288-295.
• Peakall R. and P.E. Smouse, 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics, 28: 2537-2539.
• Piry S., G. Luikart and J.M.Cornuet, 1999. BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. Journal of Heredity, 90(4):502-503.
• Rege J.E.O. and J.P. Gibson, 2003. Animal genetic resources and economic development: issues in relation to economic valuation. Ecological Economics, 45(3): 319-330.
• Salamon D., B. Gutierrez-Gil, M. Simcic, D. Kompan and A. Dzidic, 2015. Microsatellite based genetic structure of regional transboundary Istrian sheep breed populations in Croatia and Slovenia. Mljekarstvo/Dairy, 65(1): 39-47.
• UNE, 1992. Nairobi final act of the conference for the adoption of the agreed text of the convention on biological diversity: United Nations Environment Programme (UNEP).
• Vahidi S.M.F., M.O. Faruque, M.F. Anbaran, F. Afraz, S.M. Mousavi, P. Boettcher, S. Joost, J.L. Han, L. Colli, K. Periasamy, R. Negrini and P. Ajmone-Marsan, 2016. Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep. Animal Genetics, 47(4): 463-470.
• Weir B.S. and C.C. Cockerham, 1984. Estimating F-statistics for the analysis of population-structure. Evolution, 38: 1358-1370.
• Wollny C.B.A., 2003. The need to conserve farm animal genetic resources in Africa: should policy makers be concerned? Ecological Economics, 45(3): 341-351.
• Wright S., 1990. Evolution in Mendelian populations (Reprinted from Genetics. 1990; Vol 16, Pg 97-159, 1931). Bulletin of Mathematical Biology, 52: 241-295.
• Yeh F.C., R. Yang and T. Boyle, 1997. POPGENE Version 1.32. Agriculture for Molecular Biology and Biotechnology Centre, University of Alberta and Center for International Forestry Research, Canada.
• Yilmaz, O., İ. Cemal, O. Karaca, 2014. Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis. Animal Genetics, 45(4): 604-608.
• Yilmaz, O., T. Sezenler, S. Sevim, İ. Cemal, O. Karaca, Y. Yaman and O. Karadağ, 2015. Genetic relationships among four Turkish sheep breeds using microsatellites. Kafkas Universitesi Veteriner Fakültesi Dergisi, 1411(46): 576-582.