Zühal GÜNDÜZ, Onur YILMAZ, İbrahim CEMAL, Osman BİÇER

Eski ve Modern Tip DNA Marker Teknolojilerinin Karşılaştırılması ve Bunların Hayvan Islahı Programlarına Etkisi

Son yıllarda, moleküler genetik teknolojiler hayvan ıslahı anlamında çiftlik hayvanlarının genetik yapısınıntanımlanması için oldukça önemli avantajlar sağlamıştır. Özellikle gelişmiş ülkelerde bu yöntemler hayvanıslahı çalışmalarında yaygın bir şekilde kullanılmaktadır. Çok fazla sayıda moleküler genetic işaretleyicidenbahsetmek mümkündür. Bu işaretleyiciler polimorfzm türü ve tarama tekniği gibi bir çok faktör dikkate alınaraksınıﬂandırılabilir. Eski tip moleküler genetik işaretleyiciler günümüzde yaygın olarak kullanılmasına rağmenbunlardan elde edilen moleküler bilgiler modern olanlara göre oldukça kısıtlıdır. Moleküler genetik alanda enönemli gelişmelerden olan ve modern genetik işaretleyici olarak bilinen SNP çip teknolojisi çiftlik hayvanlarındagenomik damızlık değer tahminlerinin yapılmasına ve genomik seleksiyona olanak sağlamaktadır. Bu derlemedeeski ve yeni tip moleküler işaretleyiciler karşılaştırılmış ve hayvan ıslahında kullanımları tartışılmıştır.

Anahtar Kelimeler:

Hayvan ıslahı, moleküler işaretleyiciler, SNPs

A Comparison of Old and Modern Type DNA Marker Technologies and Their Impact on Animal Breeding Programs

In recent years, molecular genetic technologies allowed to identify genetic structure in farm animalshave great advantages for animal breeding. Especially, in developed countries these methods began to be widely usedto assist animal breeding studies. It can be said that there are various molecular genetic markers. These markers canbe classifed by taking into consideration a number of factors such as the principle of the detection technique, typeof polymorphism. Although old type molecular genetic markers such as RFLP, AFLP, microsatellites are widelyused today, the information obtained from them is more limited than modern molecular genetic markers. SNP chiptechnologies, which known as modern molecular markers and are one of the most important developments in themolecular genetics feld, have provided genomic breeding value estimation and genomic selection in farm animals.In this review, old and new types of molecular markers were compared and their usage in animal breeding werediscussed.

Keywords:

Animal breeding, molecular markers, SNPs,

PDF

___

Acar H, 2010. Bioinformatic analyses in microsatellite-based genetic diversity of Turkish sheep breeds. Orta Doğu Teknik Üniversitesi, Fen Bilimleri Enstitüsü, Yüksek Lisans tezi, 147s.
Agaviezor BO, Peters SO, Adefenwa MA, Yakubu A, Adebambo OA, Ozoje MO, Ikeobi CO, Wheto M, Ajayi OO, Amusan SA, Ekundayo OJ, Sanni TM, Okpeku M, Onasanya GO, De Donato M, Ilori BM, Kizilkaya K, Imumorin IG, 2012.
Morphological and microsatellite DNA diversity of Nigerian indigenous sheep. Journal of Animal Science and Biotechnology, 3(1): 38.
Ahmed MMM, 2005. Species identifcation in meat origin farm animals through DNA technology. Biotechnology in Animal Husbandry, 21(1-2):13-24.
Akey JM, Sosnoski D, Parra E, Dios S, Hiester K, Su B, Bonilla C, Jin L, Shriver MD, 2001. Melting Curve Analysis of SNPs (McSNP): A Gel-Free and Inexpensive Approach for SNP Genotyping. BioTechniques 30:358-367
Ali BA, 2003. Genetics similarity among four breeds of sheep in Egypt detected by random amplifed polymorphic DNA markers. African Journal of Biotechnology, 2(7): 194-197.
Alvarez I, Capote J, Traore A, Fonseca N, Pérez K, Cuervo M, Fernandez I, Goyache F, 2012. Genetic relationships of the Cuban hair sheep inferred from microsatellite polymorphism. Small Ruminant Research, 104(1-3): 89– 93.
Arora RJ, Bhatia S, Mishra BP, Jain A, Prakash B, 2011. Diversity analysis of sheep breeds from Southern peninsular and Eastern regions of India. Tropical Animal Health and Production, 43(2):401–408.
Ashley MV, Dow BD, 1994. The use of microsatellite analysis in population biology: Background, methods and potential applications. Editors: Schierwater B, Streit B, Wagner GP, desalle R Boston. Birkhauser Verlag. Pp. 185-202.
Babalola OO, 2003. Molecular techniques: an overview of methods for the detection of bacteria. African Journal of Biotechnology, 2(12): 710-713.
Barendse W, Armitage SM, Kossarek LM, Shalom A, Kirkpatrick BW, Ryan AM, Clayton D, Li L, Neibergs HL, Zhang N, Grosse WM, Weiss J, Creighton P, McCarthy F, Ron M, Teale AJ, Fries R, McGraw RA, Moore SS, Georges M, Soller M, Womack JE, Hetzel DJS, 1994. A genetic linkage map of the bovine genome. Nature Genetics, 136:619–639.
Bastas E, Cravador A, Azevedo J, Guedes-Pinto H, 2001. Single strand conformation polymorphism (SSCP) detection in six genes in Porteguse indigenous sheep breed Cherra da Terra Quente. Biotechnology, Agronomy, Society and Environment, 5(1):7-15.
Beuzen ND, Stear MJ, Chang KC, 2000. Molecular markers and their use in animal breeding. The Veterinary Journal, 160: 42- 52.
Bhattacharya TK, Kumar P, Joshi JD, Kumar S, 2003. Estimation of inbreeding in cattle using RAPD markers. Journal of Dairy Research, 70:127–129.
Binbaş P, 2006. Çine çaparı koyunlarda genetik çeşitliliğin RAPD yöntemi ile belirlenmesi. Adnan Menderes Üniversitesi, Fen Bilimleri Enstitüsü, Yüksek Lisans tezi, 62s.
Bolormaa S, Pryce JE, Hayes BJ, Goddard ME, 2010. Multivariate analysis of a genomewide association study in dairy cattle. Journal of Dairy Science, 93:3818–3833.
Bolormaa S, Porto Neto LR, Zhang YD, Bunch RJ, Harrison BE, Goddard ME, Barendse W, 2011. A genome -wide association study of meat and carcass traits in australian cattle. Journal of Animal Science, 89:2297-309.
Bruford MW, Chessman DJ, Coote T, Gren HAA, Haines SA, O’Ryan C, Williams TR, 1996. Microsatelites and their application to conservation genetics. Molecular Genetic Approaches in Conservation. Oxford University Press. U.K. 278-297p.
Cemal I, Karaca O, Davis GM, Galloway SM, Yilmaz O, 2009. Molecular genetic testing of Karya sheep for Booroola and Inverdale mutations. International Scientifc Conference (BALNIMALCON- 2009): Challenges of the Balkan Animal Industry and the Role of Science and Cooperation. May 14-16, 2009,
Trakia University Stara Zagora – Bulgaria, 108-111 p.
Cemal I, Yilmaz O, Karaca O, Binbaş P, Ata N, 2013. Analysis of genetic diversity in indigenous Çine Çaparı sheep under conservation by microsatellite markers. Journal of the Faculty of Veterinary Medicine, Kafkas University, 19:383-90.
Daetwyler HD, Swan AA, Van Der Werf JHJ, Hayes BJ, 2012. Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genetics Selection Evolution, 33-44.
Eggen A, 2012. The development and application of genomic selection as a new breeding paradigm. Animal Frontiers, 2(1): 10-15.
Elmaci C, Öner Y, Ozis S, Tuncel E, 2007. RAPD analysis of DNA polymorphism in Turkish sheep breeds. Biochemical Genetics, 45(9-10):691-696.
Ellegren H, Moore S, Robinson N, Byrne K, Word W, Sheldons BC, 1997. Microsatellite evolution a reciprocal study of repeated lengths at homologous loci in cattle and sheep. Molecular Biology of Evolution, 14(8): 854-60.
Fan E, Levin DB, Glickman BW, Logan DM, 1993. Limitations in the use of SSCP analysis. Mutation Research, 288:85-92.
Foulley JL, Van Schriek MGM, Alderson L, Amigues Y, Bagga M, Boscher MY, Brugmans B, Cardellino R, Davoli R, Delgado JV, Fimland E, Gandini GC, Glodek P, Groenen MAM, Hammond K, Harlizius B, Heuven H, Joosten R, Martinez AM, Matassino D, Meyer JN, Peleman J, Ramos AM, Rattink AP, Russo V, Siggens KW, Vega-Pla, JL, Ollivier L, 2006. Genetic diversity analysis using lowly polymorphic dominant markers: The example of AFLP in pigs. Journal of Heredity, 97(3):244–252.
Forbes SH, Hogg JT, Buchanan FC, Crawford AM, Allendorf FW, 1995. Microsatellite evolution in congeneric mammals, domestic and Bighorn sheep. Molecular Biology and Evolution, 12(6):1106-1113.
Goddard ME, Hayes BJ, 2007. Genomic selection. Journal of Anim Breeding and Genetics, 124(6):323-330.
Hancock JM, 2001. Microsatellites and other simple sequences: genomic context and mutational mechanisms. Microsatellites evolution and application. Editors: Goldstein, D.B., Schlötterer, C. U.K.: Oxford University Press.
Hayashi K, 1991. PCR-SSCP: A simple and sensitive method for detection of mutations in genomic DNA. PCR Methods and Application, 1: 34-38.
Hayes B.J. 2007. QTL Mapping, MAS and Genomic Selection.A Shorth-Course Organized by Animal Breeding of Animal Science Iowa State University, USA.
Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME, 2009. Invited Review: Genomic Selection in Dairy Cattle: Progress and Challenges. Journal of Dairy Science, 92:433-443.
Jyotsana B, Jakhesara S, Prakash V, Rank DN, Vataliya PH, 2010. Genetic features of Patanwadi, Marwari and Dumba sheep breeds (India) inferred by microsatellite markers. Small Ruminant Research, 93(1):57-60.
Lander ES, 1996. The new genomics: global views of biology. Science, 274:536–539.
Kinghorn BP, Kennedy BW, Smith C, 1993. A method for screening for genes of major effect. Genetics, 134:351-360.
Kinghorn BP, 1997. An index of information content for genotype probabilities derived from segregation analysis. Genetics, 145:479-483.
Koopaee HK, Koshkoiyeh, AE, 2014. SNPs genotyping technologies and their applications in farm animals breeding programs: review. Brazilian Archives of Biology and Technology, 57(1): 87-95.
Kumar S, Kolte AP, Yadav BR, Kumar S, Arora AL, Singh VK, 2008. Genetic variability among sheep breeds by random amplifed polymorphic DNA-PCR. Indian Journal of Biotechnology, 7:482-486.
Kusza S, Ivankovic A, Ramljak J, Nagy I, Javor A, Kukovics S, 2011. Genetic structure of Tsigai, Ruda, Pramenka and other local sheep in Southern and Eastern Europe. Small Ruminant Research, 99(2-3): 130-134.
Landegren U, Nilsson M, Kwok PY, 1998. Reading bits of genetic information: Methods for single-nucleotide polymorphism analysis. Genome Research, 8:769–776.
Lasagna E, Bianchi M, Ceccobelli S, Landi V, Martínez AM, Pla JLV, Panella F, Bermejo JVD, Sarti FM, 2011. Genetic relationships and population structure in three Italian Merino-derived sheep breeds. Small Ruminant Reserach,96:111-119.
Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ, 1999. High density synthetic oligonucleotide arrays. Nature Genetics, 21(supp. 1): 20–24.
Liu W, Smith DI, Rechtzigel KJ, Thibodeau SN, James CD, 1998. Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations, Nucleic Acids Reserach, 26:1396-1400.
Montaldo HH, Meza-Herrera CA, 1998. Use of molecular markers and major genes in the genetic imrovement of livestock. Electronic Journal of Biotechnology, 1(2): 83-89.
Moreno Y, Ferrus AM, Vanoostende A, Hernandez J, Montes MR, Hernandez J, 2002. Comparison of 23S polymerase chain reaction-restriction fragment length polymorphism techniquesas typing systems for thermophilic campylobacters. FEMS Microbiology Letters, 211:97-103.
Naqvi AN, 2007. Applications of molecular genetic technologies in livestock production: Potentials for developing countries. Advances in Biological Research, 1(3-4) :72-84.
Negrini R, Milanesi E, Bozzi R, Pellecchia M, Ajmone-Marsan P, 2006. Tuscany autochthonous cattle breeds: an original genetic resource investigated by AFLP markers. Journal of Animal Breeding and Genetics, 123:10–16.
Negrini R, Nijman IJ, Milanesi E, Moazami-Goudarzi K, Williams JL, Erhardt G, Dunner S, Rodellar C, Valentini A, Bradley DG, Olsaker I, Kantanen J, Ajmone-Marsan P, Lenstra JA, the European Cattle Genetic Diversity Consortium, 2007. Differentiation of European cattle by AFLP fngerprinting Animal Genetics, 38: 60-66.
Nicholas FW, 1996. Introduction to veterinary genetics. Oxford University Press, New York 64–65.
Nijiman IJ, Bladley DG, Hannotte O, Otsen M, Lenstra JA, 1999. Satellite DNA polymorphisms and AFLP correlate with Bos indicus–taurus hybridization. Animal Genetics, 30:265-273.
Oner Y, Üstüner H, Orman A, Yılmaz O, Yılmaz A, 2014. Genetic diversity of Kıvırcık sheep breed reared in different regions and their relationship to other sheep breeds in Turkey. Italian Journal of Animal Science, 13:588-593.
Orita M, Iwahana H, Knazawa H, Hayashi K, Sekiya T, 1989. Detection of the polymorphisms of human DNA by gelelectrophoresis as single-strand conformation polymorphisms. Proceedings of the National Academy of Sciences, 86:2766-2770.
Otsen M, Denbieman M, Kuiper MTR, Pravenec M, Kren V, Kurtz TW, Jacob HJ, Lankhorst AE, Vanzutphen BFM, 1996. Use of AFLP markers for gene mapping and QTL detection in the rat. Genomics, 37:289-294.
Rao AKBC, Bhat KV, Totey SM, 1996. Detection of species-specific genetic markers in farm animals through random amplifed polymorphic DNA (RAPD). Genetic Analysis: Biomolecular Engineering, 13(5):135–138.
Rohrer GA, Alexander LJ, Keele JW, Smith TP, Beattie CW, 1994. A microsatellite linkage map of the porcine genome. Genetics, 136(1):231-245.
Sancristobal M, Chevalet C, Foulley JL, Ollivier L, 2003. Some methods for analysing genetic marker data in biodiversity setting example of the Pigbiodiv data. Archivos de Zootecnia, 52:173-183.
Schlötterer C, 1998. Genome evolution: Are microsatellites really simple sequences? Current Biology, 8:132-134.
Schlötterer C, 2004. The evolution of molecular markers just a matter of fashion. Nature Reviews Genetics, 5:63-69. Schmid M, Saitbekova N, Gaillard C, Dolf G, 1999. Genetic diversity in Swiss cattle breeds. Journal of Animal Breeding and Genetics, 116(1):1-8.
Sevim S, Yilmaz O, Karaca O, Cemal I, 2012. Mastitis resistance genes in dairy cattle. International Animal Science Congress of Turkish and Relatives Communities, September 11-13, 2012, Isparta.
Sheffeld VC, Beck JS, Kwitek AE, Sandstrom DW, Stone EM, 1993. The sensitivity of single-strand conformation polymorphism analysis for the detection of single base substitutions. Genomics, 16: 325-332.
Simm G, 1998. Genetic improvement of Cattle and Sheep. Farming Pres United Kingdom.
Slack-Smith A, Kingorhn BP, Hickey JM, Van Der Werf JHJ, 2010. The Accuracy of Genomic Selection in Predicting Carcass Traits in Meat Sheep. 9th World Congress on Genetics Applied to Livestock Production in Leipzig, Germany. Stoneking M, 2001. Single nucleotide polymorphisms: From the evolutionary past. Nature, 409: 821-822.
Solak M, Bağcı H, Şengil AZ, Öztaş S, 2000. Moleküler genetik ve rekombinant DNA teknolojisi (Temel İlkeler). Afyon Kocatepe Üniversitesi Eğitim, Sağlık ve Bilimsel Araştırmalar Vakfı Yay No: 5, Ankara.
Togan İ, Soysal İ, Berkman CC, Koban E, 2005. Irkların korunmasında moleküler işaretler. NKU Ziraat Fakültesi Dergisi, 2(1):44-49.
Toth G, Gaspari Z, Jurka J, 2000. Microsatellites in different eukaryotic genomes: Survey and Analysis. Genome Research, 10(7): 967-81.
Turner PC, Mclennan AG, Bates AD, White MRH, 2004. Moleküler Biyoloji (önemli notlar) (Çev. Ed. Muhsin Konuk). Nobel yay. No:613, Ankara.
Vignal A, Milan D, Sancristobal M, Eggen A, 2002. A review on Snp and other types of molecular markers and their use in animal genetics. Genetic Seleciton and Evolution, 34:275-305. Yang W, Kang X, Yang Q, Lin Y, Fang M, 2013. Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol, 4(1): 2.
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV, 1990. DNA polimorphism amplifed by arbitrary primers are useful as genetic markers. Nucleic Acids Research, 18:6531- 6535.
Welsh J, Mcclelland M, 1990. Fingerprinting Genomes Using PCR With Arbitrary Primers. Nucleic Acids Research, 18:7213- 7218.
Walsh B, 2000. Minireview: Quantitative genetics in the age of genomics. Theoretical Population Biology, 59:175-184.
Yilmaz O, Karaca O, 2012. “Paternity Analysis with Microsatellite Markers in Karya Sheep”, Journal of the the Faculty of Veterinary Medicine, Kafkas University, 18(5):807-813.
Yilmaz O, Cemal I, Karaca O, Ata N, Sevim S, Ozturk M, 2013.
Genetic diversity of Karya and Çine Çapari sheep. Scientifc Papers. Series D. Animal Science, LVI: 31-35.
Yilmaz O, Cemal İ, Karaca O, 2014. Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis. Animal Genetics, 45 (4): 604–608.
Yılmaz O, Öner Y, Karaman E, Cemal İ, 2015. Çiftlik hayvanlarında genom boyu ilişki analizleri ve genomik seleksiyon. 9. Ulusal Zootekni Bilim Kongresi. 3-5 Eylül 2015, Konya.