Study of Genetic diversity of indigenous (Afshari, Moghani and Ghezel) and exotic (Romney, Merinos and Dorper) sheep breeds using high-density SNP markers

Document Type : Research Paper


1 Former M. Sc. Student, Department of Animal Science, Faculty of Agriculture, University of Zanjan, Iran

2 Assistant Professor, Department of Animal Science, Faculty of Agriculture, University of Zanjan, Iran

3 Associate Professor, Department of Animal Science, Faculty of Agriculture, University of Zanjan, Iran


The use of molecular markers in recent years has been widely used to determine the genetic diversity between populations and animal species. Molecular genetics studies allow a comparison of genetic diversity within and across breeds and make a new insight to reconstruct the breed history and history of ancestral populations. The aim of this study was to investigate the genetic structure and genetic variation of indigenous and exotic sheep breeds using 50,000 SNP markers. Genotype data of indigenous breeds (Afshari, Ghezel and Moghani) and exotic breeds (Dorper, Merinos and Romney) were obtained from the Ovin HapMap project. Multiple population stratification analysis such as, population structure using multivariate statistics and model-based approach were applied. The result of all methods obviously showed the correct population differentiation. In DAPC K=4 inferred best cluster results by BIC. Despite the use of different methods, all of these methods showed a distinct structure for indigenous and exotic populations and it can be concluded that Iranian sheep breeds has more genetic similarity rather than exotic breeds and Iranian sheep breeds grouped as one category and Romney, Merinos and Dorper breeds were separated as distant groups. However, when the indigenous breeds were studied alone, the breeds were genetically separated and population differentiation statistic (Fst) for Afshari, Moghani and Qezel was 0.038, 0.107, and 0.298, respectively.


  1. Askari, N., Abadi, M. M. & Baghizadeh, A. (2011). ISSR markers for assessing DNA polymorphism and genetic characterization of cattle, goat and sheep populations. Iranian Journal of Biotechnology, 9(3), 222-9.
  2. Azizi, Z., Moradi Shahrbabak, H. & Shahrbaba, M. (2017). Comparison of PCA and DAPC methods for analysis of Iranian Buffalo population structure using SNPchip90k data. Iranian Journal of Animal Science, 48(2), (153-161). (in Farsi)
  3. Barendse, W., Harrison, B. E., Bunch, R. J., Thomas, M. B. & Turner, L. B. (2009). Genome wide signatures of positive selection. The comparison of independent samples and the identification of regions associated to traits. BMC Genomics, 10, 178.
  4. Beynon, S. E., Slavov, G. T., Farré, M., Sunduimijid, B., Waddams, K., Davies, B., Haresign, W., Kijas, J., Macleod, L. M., Jamie Newblod, C., Davies, L. & Larkin, D.M. (2015). Population structure and history of the Welsh sheep breeds determined by whole genome genotyping. BMC Genetics, 16(1), 65.
  5. Cloete, J. J. E., Cloete, S. W. P., Olivier, J. J. & Hoffman, L. C. (2007). Terminal crossbreeding of Dorper ewes to Ile de France, Merino Landsheep and SA Mutton Merino sires: Ewe production and lamb performance. Small Ruminant Research,69(1-3), 28-35
  6. Cloete, S. W. P. & Olivier, J. J. (2010). South African sheep and wool industries. International Sheep and Wool Handbook, 95-104.
  7. Dekkers, J. C. (2004). Commercial application of marker-and gene-assisted selection in livestock: strategies and lessons. Journal of animal science, 82(13-suppl), E313-E328.
  8. Elsik, C. G., Tellam, R. L. & Worley, K. C. (2009). The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science, 324(5926), 522-528.
  9. Evanno, G., Regnaut, S. & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular ecology, 14(8), 2611-2620.
  10. Frankham, R. (1994). Conservation genetics. Annual Review of Genetics, 29(1), 305-327.
  11. Fernández, M. E., Goszczynski, D. E., Lirón, J. P., Villegas-Castagnasso, E. E., Carino, M. H., Ripoli, M. V., Rogberg-Muñoz, A., Posik, D. M., Peral-García, P. & Giovambattista, G. (2013). Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd. Genetics and Molecular Biology, 36(2), 185-191.
  12. Kalinowski, S. T. (2004). Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conservation Genetics, 5(4), 539-543.
  13. McKay, S. D., Schnabel, R. D., Murdoch, B. M., Matukumalli, L. K., Aerts, J., Coppieters, W. & Mannen, H. (2007). Whole genome linkage disequilibrium maps in cattle. BMC Genetics, 8(1), 74.
  14. Glaubitz, J. C. (2004). Convert: a user‐friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes, 4(2), 309-310.
  15. Goddard, M. E. & Hayes, B. J. (2007). Genomic selection. Journal of Animal breeding and Genetics, 124(6), 323-330.
  16. Groenen, M. A., Archibald, A. L., Uenishi, H., Tuggle, C. K., Takeuchi, Y., Rothschild, M. F. & Li, S. (2012). Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491(7424), 393-398
  17. Holsinger, K. E. & Wallace, L. E. (2004). Bayesian approaches for the analysis of population genetic structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology, 13(4), 887-894.
  18. Jombart, T. (2008). Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405.
  19. Jombart, T., Devillard, S. & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics, 11(1), 94.
  20. Jombart, T. & Collins, C. (2015). A tutorial for discriminant analysis of principal components (DAPC) using adegenet 2.0. 0. London: Imperial College London, MRC Centre for Outbreak Analysis and Modelling.
  21. Karimi, K., Koshkoiyeh, A. E. & Fuzi, M. A. (2015). Analysis of genetic structure of Iranian indigenous cattle populations using dense single nucleotide polymorphism markers. Animal Production Research,4(3).
  22. Kijas, J. W., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. F., McGrath, A. & Tang, D. (2009). A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PloSOne, 4(3), e4668.
  23. Kijas, J. W., Lenstra, J. A., Hayes, B., Boitard, S., Neto, L. R. P., San Cristobal, M. & Paiva, S. (2012). Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology, 10(2), e1001258.
  24. Lao, O., Lu, T. T., Nothnagel, M., Junge, O., Freitag-Wolf, S., Caliebe, A. & Holmlund, G. (2008). Correlation between genetic and geographic structure in Europe. Current Biology, 18(16), 1241-1248.
  25. Lee, C., Abdool, A. & Huang, C.-H. (2009). PCA-based population structure inference with generic clustering algorithms. BMC bioinformatics, 10(Suppl 1), S73.
  26. Liu, N. & Zhao, H. (2006). A non-parametric approach to population structure inference using multilocus genotypes. Human Genomics, 2(6), 1.
  27. Mehri, H. (2006). Study of genetic structure and evolutionary relationships of six sheep breeds of Iran using microsatellite markers. Master's thesis on livestock breeding, Faculty of Agriculture, Zanjan University. 100 p. (in Farsi)
  28. Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds, K. G. & McEwan, J. C. (2012). Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, 13(1), 10.
  29. Pan, D., Zhang, S., Jiang, J., Jiang, L., Zhang, Q & Liu, J. F. (2013). Genome-Wide detection of Selective Signature in Chinese Holstein. Public Library of Science, 8, 2-9.
  30. Patterson, N., Price, A. L. & Reich, D. (2006). Population structure and eigenanalysis. PLoS Genet, 2(12), e190.
  31. Pertoldi, C., Tokarska, M., Wójcik, J. M., Kawałko, A., Randi, E., Kristensen, T. N. & Bendixen, C. (2010). Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip. Acta Theriologica, 55(2), 97-108.
  32. Petersen, J. L., Mickelson, J. R., Cothran, E. G., Andersson, L. S., Axelsson, J., Bailey, E. & da Câmara Machado, A. (2013). Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One, 8(1), e54997.
  33. Pirkhezraeeian, Z., Tahmorespour, M., Mohammadhashemi, A., Pirani, N. & Azghandi, M. (2015). Genetic and phylogenetic analyses of HVR-I region of mtDNA in Afshari sheep breed. Biological Biotechnology in Agriculture (Scientific-Research), 6 (1), 65-71. (in Farsi)
  34. Pometti, C. L., Bessega, C. F., Saidman, B. O. & Vilardi, J. C. (2014). Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods. Genetics and Molecular Biology, 37(1),
  35. Porras-Hurtado, L., Ruiz, Y., Santos, C., Phillips, C., Carracedo, A. & Lareu, M. (2013). An overview of STRUCTURE: applications, parameter settings, and supporting software. Frontiers in Genetics, 4, 98.
  36. Pritchard, J. K., Stephens, M. & Donnelly, P. (2000(. Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
  37. Pritchard, J. K., Wen, X. & Falush, D. (2010). Documentation for STRUCTURE software, version 2.3. University of Chicago, Chicago, IL.
  38. Purcell, S. (2010). PLINK, version 1.07.URL: purcell/pink.
  39. Sethuraman A. (2013). On inferring and interpreting genetic population structure-applications to conservation, and the estimation of pairwise genetic relatedness. Ph.D. dissertation, Iowa State University, Iowa State.
  40. Shojaei, M., Abadi, M. M., Fozi, M. A., Dayani, O., Khezri, A. & Akhondi, M. (2010). Association of growth trait and Leptin gene polymorphism in Kermani sheep. In Journal of Cell and Molecular Research, 2 (1), 67-73
  41. Teo, Y. Y., Fry, A. E., Clark, T. G., Tai, E. S. & Seielstad, M. (2007). On the usage of HWE for identifying genotyping errors. Annals of Human Genetics, 71(5), 701-703.
  42. Vahidi, S. M. F., Tarang, A. R., Anbaran, M. F., Boettcher, P., Joost, S., Colli, L., Garcia, J. F. & Ajmone-Marsan, P. (2014). Investigation of the genetic diversity of domestic Capra hircus breeds reared within an early goat domestication area in Iran. Genetics Selection Evolution, 46(1), 27.
  43. Vahidi, S. M. F., Faruque, M. O., Falahati Anbaran, M., Afraz, F., Mousavi, S. M., Boettcher, P. & Negrini, R. (2016). Multilocus genotypic data reveal high genetic diversity and low population genetic structure of Iranian indigenous sheep. Animal Genetics, 47(4), 463-470.
  44. Vonholdt B. M., Pollinger J. P., Lohmueller K. E., Han E., Parker H. G., Quignon P., Degenhardt J. D., Boyko A. R., Earl D. A., Auton A., Reynolds A., Bryc K., Brisbin A., Knowles J. C., Mosher D. S., Spady T. C., Elkahloun A., Geffen E., Pilot M., Jedrzejewski W., Greco C., Randi E., Bannasch D., Wilton A., Shearman J., Musiani M., Cargill M., Jones P. G., Qian Z., Huang W., Ding Z. L., Zhang Y. P., Bustamante C. D., Ostrander E. A., Novembre J. & Wayne R. K. (2010). Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature, 464, 898-902.
  45. Wei, C., Wang, H., Liu, G., Wu, M., Cao, J., Liu, Z. and Liu, C. (2015). Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds. BMC Genomics, 16(1), 194.
  46. Zamani, P., Akhondi, M., Mohammadabadi, M. R., Saki, A. A., Ershadi, A., Banabazi, M. H. & Abdolmohammadi, A. R. (2011). Genetic variation of Mehraban sheep using two intersimple sequence repeat (ISSR) markers. African Journal of Biotechnology, 10(10), 1812-1817.