Onur YILMAZ, İbrahim CEMAL, Behiç COŞKUN, Yusuf Ziya OĞRAK, Nezih ATA, Orhan KARACA

Comparison of different paternity test panels in sheep

The aims of this study were to evaluate different paternity test panels with 17 microsatellite markers for their effectiveness in paternity analysis and to identify pedigree error rates in the Kangal Akkaraman breed of sheep. The animal material for the study consisted of 175 Kangal Akkaraman sheep, 35 rams, and their 140 offspring, raised on farms and bred using controlled mating. The panels were created according to probability of exclusion (PE) of 17 studied microsatellites. A total of 240 alleles were detected across 17 microsatellite loci. The overall mean value of the polymorphic information content (PIC) (0.78) indicated that the microsatellite panels were highly polymorphic. Probability of identity (PI) values ranged between 0.02 and 0.13. It can be said that pedigree error (2.94%) occurred at a low rate in this study. The highest combined PE values were obtained from Panel-16 (0.9999771) as expected. Panel-8 and Panel-9 met the PE value accepted in the literature (0.999). The results show that these panels are cheaper and more practical than other panels formed for Kangal Akkaraman.

Keywords:

Paternity test, microsatellite, probability of exclusion, sheep,

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Weller JI, Feldmesser E, Golik M, Tager-Cohen I, Domochovsky R, Alus O, Ezra E, Ron M. Factors affecting incorrect paternity assignment in the Israeli Holstein population. J Dairy Sci 2004; 87: 2627-2640.
Harder B, Bennewitz J, Reinsch N, Mayer M, Kalm E. Effect of missing sire information on genetic evaluation. Arch Tierzucht 2005; 48: 219-232.
Vandeputte M, Mauger S, Dupont-Nivet M. An evaluation of allowing for mismatches as a way to manage genotyping errors in parentage assignment by exclusion. Mol Ecol Notes 2006; 6: 265-267.
Sanders K, Bennewitz J, Kalm E. Wrong and missing sire information affects genetic gain in the Angeln dairy cattle population. J Dairy Sci 2006; 89: 315-321.
Geldermann H, Pieper U, Weber WE. Effect of misidentification on the estimation of breeding value and heritability in cattle. J Anim Sci 1986; 63: 1759-1768.
Arruga MV, Monteagudo LV, Tejedor MT, Barrao R, Ponz R. Analysis of microsatellites and paternity testing in Rasa Aragonesa sheep. Res Vet Sci 2011; 70: 271-273.
Banos G, Wiggans GR, Powell RL. Impact of paternity errors in cow identification on genetic evaluations and international comparisons. J Dairy Sci 2001; 84: 2523-2529.
Baron EE, Martinez ML, Verneque RS, Coutinho LL. Parentage testing and effect of misidentification on the estimation of breeding value in Gir cattle. Genet Mol Biol 2002; 25: 389-394.
Jimenez-Gamero I, Dorado G, Munoz-Serrano A, Analla M, Alonso-Moraga A. DNA microsatellites to ascertain pedigree- recorded information in a selecting nucleus of Murciano– Granadina dairy goats. Small Ruminant Res 2006; 65: 266-273.
Ma H, Zhu H, Guan F, Cherng S. Paternity Testing. J Amer Sci 2006; 2: 76-92.
Maichomo KM, Gitau WGK, Gathuma JM, Ndung’u JM, Kosura O, Olivier HO. Extent and implications of incorrect offspring-sire relationships in pastoral production system in Kajiado District, Kenya. Livest Res Rural Dev 2008; 20: e80.
Rosa AJM, Sardina MT, Mastrangelo S, Tolone M, Portolano B. Parentage verification of Valle del Belice dairy sheep using multiplex microsatellite panel. Small Ruminant Res 2013; 113: 62-65.
Heaton MP, Leymaster KA, Kalbfleisch TS, Kijas JW, Clarke SM, McEwan J, Maddox JF, Basnayake V, Petrik DT, Simpson B et al. The International Sheep Genomics Consortium. SNPs for parentage testing and traceability in globally diverse breeds of sheep. Plos One 2014; 9: e94851.
Simm G. Molecular genetic technologies. In: Simm G, editor. Genetic Improvement of Cattle and Sheep. Ipswich, UK: Farming Press; 1998. pp. 347-390.
Cunningham EP, Meghen CM. Biological identification systems: genetic markers. Rev Sci Tech 2001; 20: 491-499.
Anunciaçao CE, Filho SA. Paternity test in “Mangalarga- Marchador” equines by DNA-fingerprinting. Pesqui Agropecu Bras 2000; 35: 2007-2015.
Crawford AM, Dodds KG, Ede AJ, Pierson CA, Montgomery GW, Garmonsway HG, Beattie AE, Davies K, Maddox JF, Kappes SW. An autosomal genetic linkage map of the sheep genome. Genetics 1995; 140: 703-724.
Usha AP, Simpson SP, Williams JL. Probability of random sire exclusion using microsatellite markers for parentage verification. Anim Genet 1995; 26: 155-161.
Heyen DW, Beever JE, Da Y, Evert RE, Green C, Bates SR, Ziegle JS, Lewin HA. Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing. Anim Genet 1997; 28: 21-27.
Beuzen ND, Stear MJ, Chang KC. Review molecular markers and their use in animal breeding. Vet J 2000; 160: 42-52.
Vignal A, Milan D, Sancristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 2002; 34: 275-305.
Ağaoğlu Ö, Ertuğrul O. Importance and usage of microsatellites. Veteriner Hekimler Dergisi 2010; 81: 39-43 (article in Turkish with an English abstract).
Araujo AMD, Guimaraes SEF, Pereira CS, Lopes PS, Rodrigues MT, Machado TMM. Paternity in Brazilian goats through the use of DNA microsatellites. Rev Soc Bras Zootecn 2010; 39: 1011-1014.
Zhang Y, Wang Y, Sun D, Yu Y, Zhang Y. Validation of 17 microsatellite markers for parentage verification and identity test in Chinese Holstein cattle. Asian Austral J Anim 2010; 23: 425-429.
Souza CA, Paiva SR, McManus CM, Azevedo HC, Mariante AS, Grattapaglia D. Genetic diversity and assessment of 23 microsatellite markers for parentage testing of Santa Inês hair sheep in Brazil. Genet Mol Res 2012; 11: 1217-1229.
Yılmaz O, Karaca O. Paternity analysis with microsatellite markers in Karya sheep. Kafkas Univ Vet Fak Derg 2012; 18: 807-813 (article in Turkish with an English abstract).
Yılmaz O. Power of different microsatellite panels for paternity analysis in sheep. Anim Sci P 2016; 34: 155-164.
FAO. Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines. 2011; No: 9. FAO: Rome.
Peakall R, Smouse PE. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006; 6: 288-295.
Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research: an update. Bioinformatics 2012; 28: 2537-2539.
Marshall TC, Slate J, Kruuk LEB, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 1998; 7: 639-655.
Kalinowski ST, Taper ML, Marshall TC. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 2007; 16:1099-1106.
Baumung R, Cubric-Curik V, Schwend K, Achmann R, Solkner, J. Genetic characterization and breed assignment in Austrian sheep breeds using microsatellite marker information. J Anim Breed Genet 2006; 123: 265-271.
Arora RJ, Bhatia S, Mishra BP, Jain A, Prakash B. Diversity analysis of sheep breeds from Southern peninsular and Eastern regions of India. Trop Anim Health Pro 2011; 43: 401-408.
Mukesh M, Sodhi M, Bhatia S. Microsatellite-based diversity analysis and genetic relationships of three Indian sheep breeds. J Anim Breed Genet 2006; 123: 258-264.
Ligda C, Altarayrah J, Georgoudis A, the ECONOGENE Consortium. Genetic analysis of Greek sheep breeds using microsatellite markers for setting conservation priorities. Small Ruminant Res 2009; 83: 42-48.
Yilmaz O, Cemal I, Karaca O. Genetic diversity in nine native Turkish sheep breeds based on microsatellite analysis. Anim Genet 2014; 45: 604-608.
Yılmaz O, Sezenler T, Sevim S, Cemal İ, Karaca O, Yaman Y, Karadağ O. Genetic relationships among four Turkish sheep breeds using microsatellites. Kafkas Univ Vet Fak Derg 2015; 1411: 576-582.
Santos-Silva F, Ivo RS, Sousa MCO, Carolino MI, Ginja C, Gama LT. Assessing genetic diversity and differentiation in Portuguese coarse-wool sheep breeds with microsatellite markers. Small Ruminant Res 2008; 78: 32-40.
Cemal İ, Yilmaz O, Karaca O, Binbaş P, Ata N. Analysis of genetic diversity in indigenous Çine Çaparı sheep under conservation by microsatellite markers. Kafkas Univ Vet Fak Derg 2013; 19: 383-390.
Al-Atiyat RM. The power of 28 microsatellite markers for parentage testing in sheep. Electron J Biotechn 2015; 18: 116- 121.
Quanbari S, Nasab MP, Osfoori R, Nazari AH. Power of microsatellite markers for analysis of genetic variation and parentage verification in sheep. Pak J Biol Sci 2007; 10: 1632- 1638.
Dakin EE, Avise JC. Microsatellite null alleles in parentage analysis. Heredity 2004; 93: 504-509.
Van Eenennaam AL, Weaber RL, Drake DJ, Penedo MCT, Quaas RL, Garrick DJ, Pollak EJ. DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting. J Anim Sci 2007; 85: 3159-3169.
Zhao ZS, Wang GL, Guo JG, Li DQ. Polymorphism distributions of 9 microsatellite loci in Chinese Merino sheep. Yi Chuan 2006; 28: 939-944.
Luikart G, Biju-Duval MP, Ertuğrul O, Zagdsuren Y, Maudet C, Taberlet P. Power of 22 microsatellite markers in fluorescent multiplexes for parentage testing in goats ( Capra hircus ). Anim Genet 1999; 30: 431-438.
Sherman GB, Kachman SD, Hungerford LL, Rupp GP, Fox CP, Brown B, Feuz BM, Holm TR. Impact of candidate sire number and sire relatedness on DNA polymorphism-based measures of exclusion probability and probability of unambiguous parentage. Anim Genet 2004; 35: 220-226.
Waits LP, Luikart G, Taberlet P. Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 2001; 10: 249-256.