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Volume 11, Pages 1641-1659
http://dx.doi.org/10.1100/2011/186342
Research Article

Genetic Diversity of Sheep Breeds from Albania, Greece, and Italy Assessed by Mitochondrial DNA and Nuclear Polymorphisms (SNPs)

1Department for Innovation in Biological, Agro-Food and Forest Systems, Tuscia University, 01100 Viterbo, Italy
2Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
3Istituto di Zootecnica, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
4School of Biosciences, University of Wales, Cardiff CF10 3NS, UK

Received 12 April 2011; Revised 30 July 2011; Accepted 8 August 2011

Academic Editor: Dirk-Jan de Koning

Copyright © 2011 Lorraine Pariset et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. D. Vigne, I. Carrère, and J. Guilaine, “Unstable status of early domestic ungulates in the Near East: the example of Shillourokambos (Cyprus, IX-VIIIth millennia Cal. B.C.),” Bulletin de Correspondance Hellenique, vol. 43, supplement, pp. 239–251, 2003. View at Google Scholar
  2. C. F. Nadler, K. V. Korobitsina, R. S. Hoffmann, and N. N. Vorontsov, “Cytogenetic differentiation, geographic distribution, and domestication in Palaearctic sheep (Ovis),” Zeitschrift für Säugetierkunde, vol. 38, pp. 109–125, 1973. View at Google Scholar
  3. T. D. Bunch, W. C. Foote, and J. J. Spillett, “Translocations of acrocentric chromosomes and their implications in the evolution of sheep (Ovis),” Cytogenetics and Cell Genetics, vol. 17, no. 3, pp. 122–136, 1976. View at Google Scholar · View at Scopus
  4. K. Dobney and G. Larson, “Genetics and animal domestication: new windows on an elusive process,” Journal of Zoology, vol. 269, no. 2, pp. 261–271, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. M. A. Zeder, “Domestication and early agriculture in the Mediterranean Basin: origins, diffusion, and impact,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 33, pp. 11597–11604, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. J. Zilhão, “Radiocarbon evidence for maritime pioneer colonization at the origins of farming in west Mediterranean Europe,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 24, pp. 14180–14185, 2001. View at Publisher · View at Google Scholar · View at Scopus
  7. M. Tapio, N. Marzanov, M. Ozerov et al., “Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas,” Molecular Biology and Evolution, vol. 23, no. 9, pp. 1776–1783, 2006. View at Publisher · View at Google Scholar · View at Scopus
  8. F. Pereira, S. J. M. Davis, L. Pereira, B. McEvoy, D. G. Bradley, and A. Amorim, “Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry,” Molecular Biology and Evolution, vol. 23, no. 7, pp. 1420–1426, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. F. Pereira, L. Pereira, B. Van Asch, D. G. Bradley, and A. Amorim, “The mtDNA catalogue of all Portuguese autochthonous goat (Capra hircus) breeds: high diversity of female lineages at the western fringe of European distribution,” Molecular Ecology, vol. 14, no. 8, pp. 2313–2318, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. L. Pariset, A. Cuteri, C. Ligda, P. Ajmone-Marsan, and A. Valentini, “Geographical patterning of sixteen goat breeds from Italy, Albania and Greece assessed by Single Nucleotide Polymorphisms,” BMC Ecology, vol. 9, article 20, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. T. Cymbron, A. R. Freeman, M. I. Malheiro, J. D. Vigne, and D. G. Bradley, “Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations,” Proceedings of the Royal Society B, vol. 272, no. 1574, pp. 1837–1843, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Pellecchia, R. Negrini, L. Colli et al., “The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA,” Proceedings of the Royal Society B, vol. 274, no. 1614, pp. 1175–1179, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. J. R. S. Meadows, O. Hanotte, C. Drögemüller et al., “Globally dispersed Y chromosomal haplotypes in wild and domestic sheep,” Animal Genetics, vol. 37, no. 5, pp. 444–453, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. J. R. S. Meadows and J. W. Kijas, “Re-sequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes,” Animal Genetics, vol. 40, no. 1, pp. 119–123, 2009. View at Publisher · View at Google Scholar · View at Scopus
  15. L. J. Lawson Handley, K. Byrne, F. Santucci et al., “Genetic structure of European sheep breeds,” Heredity, vol. 99, no. 6, pp. 620–631, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. C. Peter, M. Bruford, T. Perez, S. Dalamitra, G. Hewitt, and G. Erhardt, “Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds,” Animal Genetics, vol. 38, no. 1, pp. 37–44, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. J. W. Kijas, D. Townley, B. P. Dalrymple et al., “A genome wide survey of SNP variation reveals the genetic structure of sheep breeds,” PLoS ONE, vol. 4, no. 3, Article ID e4668, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. B. Chessa, F. Pereira, F. Arnaud et al., “Revealing the history of sheep domestication using retrovirus integrations,” Science, vol. 324, no. 5926, pp. 532–536, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Y. Chen, Z. Y. Duan, T. Sha, J. Xiangyu, S. F. Wu, and Y. P. Zhang, “Origin, genetic diversity, and population structure of Chinese domestic sheep,” Gene, vol. 376, no. 2, pp. 216–223, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Pedrosa, M. Uzun, J. J. Arranz, B. Gutiérrez-Gil, F. San Primitivo, and Y. Bayón, “Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events,” Proceedings of the Royal Society B, vol. 272, no. 1577, pp. 2211–2217, 2005. View at Publisher · View at Google Scholar · View at Scopus
  21. J. R. S. Meadows, K. Li, J. Kantanen et al., “Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe,” Journal of Heredity, vol. 96, no. 5, pp. 494–501, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. J. R. S. Meadows, I. Cemal, O. Karaca, E. Gootwine, and J. W. Kijas, “Five ovine mitochondrial lineages identified from sheep breeds of the near east,” Genetics, vol. 175, no. 3, pp. 1371–1379, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. N. J. Wood and S. H. Phua, “Variation in the control region sequence of the sheep mitochondrial genome,” Animal Genetics, vol. 27, no. 1, pp. 25–33, 1996. View at Google Scholar · View at Scopus
  24. S. Hiendleder, H. Lewalski, R. Wassmuth, and A. Janke, “The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype,” Journal of Molecular Evolution, vol. 47, no. 4, pp. 441–448, 1998. View at Publisher · View at Google Scholar · View at Scopus
  25. S. Hiendleder, B. Kaupe, R. Wassmuth, and A. Janke, “Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies,” Proceedings of the Royal Society B, vol. 269, no. 1494, pp. 893–904, 2002. View at Publisher · View at Google Scholar · View at Scopus
  26. J. Guo, L. X. Du, Y. H. Ma et al., “A novel maternal lineage revealed in sheep (Ovis aries),” Animal Genetics, vol. 36, no. 4, pp. 331–336, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. J. Flanders, G. Jones, P. Benda et al., “Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data,” Molecular Ecology, vol. 18, no. 2, pp. 306–318, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. G. Heckel, R. Burri, S. Fink, J. F. Desmet, and L. Excoffier, “Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis,” Evolution, vol. 59, no. 10, pp. 2231–2242, 2005. View at Publisher · View at Google Scholar · View at Scopus
  29. J. Bryja, C. Smith, A. Konečný, and M. Reichard, “Range-wide population genetic structure of the European bitterling (Rhodeus amarus) based on microsatellite and mitochondrial DNA analysis,” Molecular Ecology, vol. 19, no. 21, pp. 4708–4722, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. M. M. Tollefsrud, J. H. Sønstebø, C. Brochmann, O. Johnsen, T. Skrøppa, and G. G. Vendramin, “Combined analysis of nuclear and mitochondrial markers provide new insight into the genetic structure of North European Picea abies,” Heredity, vol. 102, no. 6, pp. 549–562, 2009. View at Publisher · View at Google Scholar · View at Scopus
  31. J. W. O. Ballard and M. C. Whitlock, “The incomplete natural history of mitochondria,” Molecular Ecology, vol. 13, no. 4, pp. 729–744, 2004. View at Publisher · View at Google Scholar · View at Scopus
  32. G. L. Gonçalves, G. R. P. Moreira, T. R. O. Freitas, D. Hepp, D. T. Passos, and T. A. Weimer, “Mitochondrial and nuclear DNA analyses reveal population differentiation in Brazilian Creole sheep,” Animal Genetics, vol. 41, no. 3, pp. 308–310, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Hiendleder, K. Mainz, Y. Plante, and H. Lewalski, “Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from urial and argali sheep,” Journal of Heredity, vol. 89, no. 2, pp. 113–120, 1998. View at Publisher · View at Google Scholar · View at Scopus
  34. T. A. Hall, “BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT,” Nucleic Acids Symposium Series, vol. 41, pp. 95–98, 1999. View at Google Scholar
  35. P. Librado and J. Rozas, “DnaSP v5: a software for comprehensive analysis of DNA polymorphism data,” Bioinformatics, vol. 25, no. 11, pp. 1451–1452, 2009. View at Publisher · View at Google Scholar · View at Scopus
  36. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution. In press. View at Publisher · View at Google Scholar
  37. L. Excoffier, G. Laval, and S. Schneider, “Arlequin ver. 3.0: an integrated software package for population genetics data analysis,” Evolutionary Bioinformatics Online, vol. 1, pp. 47–50, 2005. View at Google Scholar
  38. S. Joost, L. Colli, P. V. Baret et al., “Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources,” Animal Genetics, vol. 41, no. 1, pp. 47–63, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. L. Pariset, I. Cappuccio, P. Ajmone-Marsan et al., “Characterization of 37 breed-specific single-nucleotide polymorphisms in sheep,” Journal of Heredity, vol. 97, no. 5, pp. 531–534, 2006. View at Publisher · View at Google Scholar
  40. J. Goudet, “FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3),” 2001, http://www2.unil.ch/popgen/softwares/fstat.htm.
  41. B. S. Weir and C. C. Cockerham, “Estimating F-statistics for the analysis of population structure,” Evolution, vol. 38, no. 6, pp. 1358–1370, 1984. View at Google Scholar · View at Scopus
  42. R. Peakall and P. E. Smouse, “GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research,” Molecular Ecology Notes, vol. 6, no. 1, pp. 288–295, 2006. View at Publisher · View at Google Scholar · View at Scopus
  43. K. Belkhir, P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme, (1996–2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier, France.
  44. M. Nei, “Genetic distance between populations,” American Naturalist, vol. 106, no. 949, p. 283, 1972. View at Google Scholar
  45. J. Reynolds, B. S. Weir, and C. C. Cockerham, “Estimation of the coancestry coefficient: basis for a short-term genetic distance,” Genetics, vol. 105, no. 3, pp. 767–779, 1983. View at Google Scholar · View at Scopus
  46. K. Liu and S. V. Muse, “PowerMaker: an integrated analysis environment for genetic maker analysis,” Bioinformatics, vol. 21, no. 9, pp. 2128–2129, 2005. View at Publisher · View at Google Scholar · View at Scopus
  47. M. Nei, “Analysis of gene diversity in subdivided populations,” Proceedings of the National Academy of Sciences of the United States of America, vol. 70, no. 12, pp. 3321–3323, 1973. View at Google Scholar · View at Scopus
  48. M. Nei, Molecular Evolutionary Genetics, Columbia University Press, New York, NY, USA, 1987.
  49. M. Slatkin and R. R. Hudson, “Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations,” Genetics, vol. 129, no. 2, pp. 555–562, 1991. View at Google Scholar · View at Scopus
  50. J. Diamond, “Evolution, consequences and future of plant and animal domestication,” Nature, vol. 418, no. 6898, pp. 700–707, 2002. View at Publisher · View at Google Scholar · View at Scopus
  51. C. Berthouly, B. Bed’Hom, M. Tixier-Boichard et al., “Using molecular and multivariate methods to study the genetic diversity on local European and Asian chickens breeds,” Animal Genetics, vol. 39, pp. 121–129, 2008. View at Google Scholar
  52. S. Naderi, H. R. Rezaei, P. Taberlet et al., “Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity,” PLoS ONE, vol. 2, no. 10, Article ID e1012, 2007. View at Publisher · View at Google Scholar · View at Scopus
  53. M. W. Bruford, D. G. Bradley, and G. Luikart, “DNA markers reveal the complexity of livestock domestication,” Nature Reviews Genetics, vol. 4, no. 11, pp. 900–910, 2003. View at Publisher · View at Google Scholar · View at Scopus
  54. G. M. Hewitt, “Genetic consequences of climatic oscillations in the Quaternary,” Philosophical Transactions of the Royal Society B, vol. 359, no. 1442, pp. 183–195, 2004. View at Publisher · View at Google Scholar · View at Scopus
  55. V. C. Pardeshi, N. Y. Kadoo, M. N. Sainani, J. R. S. Meadows, J. W. Kijas, and V. S. Gupta, “Mitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds,” Animal Genetics, vol. 38, no. 5, pp. 460–466, 2007. View at Publisher · View at Google Scholar · View at Scopus
  56. M. Ćinkulov, Z. Popovski, K. Porcu et al., “Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis,” Journal of Animal Breeding and Genetics, vol. 125, no. 6, pp. 417–426, 2008. View at Publisher · View at Google Scholar · View at Scopus
  57. I. Cappuccio, L. Pariset, P. Ajmone-Marsan et al., “Allele frequencies and diversity parameters of 27 single nucleotide polymorphisms within and across goat breeds,” Molecular Ecology Notes, vol. 6, no. 4, pp. 992–997, 2006. View at Publisher · View at Google Scholar · View at Scopus
  58. L. Pariset, I. Cappuccio, S. Joost et al., “Characterization of single nucleotide polymorphisms (SNPs) in sheep and their variation as an evidence of selection,” Animal Genetics, vol. 37, pp. 290–292, 2006. View at Google Scholar
  59. J. Cañón, D. García, M. A. García-Atance et al., “Geographical partitioning of goat diversity in Europe and the Middle East,” Animal Genetics, vol. 37, no. 4, pp. 327–334, 2006. View at Publisher · View at Google Scholar · View at Scopus
  60. G. Luikart, L. Gielly, L. Excoffier, J. D. Vigne, J. Bouvet, and P. Taberlet, “Multiple maternal origins and weak phylogeographic structure in domestic goats,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 10, pp. 5927–5932, 2001. View at Publisher · View at Google Scholar · View at Scopus
  61. H. Fernández, S. Hughes, J. D. Vigne et al., “Divergent mtDNA lineages of goats in an Early Neolithic site, far from the initial domestication areas,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 42, pp. 15375–15379, 2006. View at Publisher · View at Google Scholar · View at Scopus