DOI QR코드

DOI QR Code

Genetic Diversity of mtDNA D-loop and Maternal Origin of Three Chinese Native Horse Breeds

  • Zhang, Tao (School of Bioscience and Engineering, Shaanxi University of Technology) ;
  • Lu, Hongzhao (School of Bioscience and Engineering, Shaanxi University of Technology) ;
  • Chen, Chen (School of Bioscience and Engineering, Shaanxi University of Technology) ;
  • Jiang, Hai (School of Bioscience and Engineering, Shaanxi University of Technology) ;
  • Wu, Sanqiao (School of Bioscience and Engineering, Shaanxi University of Technology)
  • Received : 2011.12.13
  • Accepted : 2012.05.04
  • Published : 2012.07.01

Abstract

In order to protect the genetic resource of native horse breeds, the genetic diversity of mitochondrial DNA (mtDNA) D-loop of three native horse breeds in western China were investigated. Forty-three 600 bp mtDNA D-loop sequences were analyzed by PCR and sequencing techniques, 33 unique haplotypes with 70 polymorphic sites were detected in these horses, which account for 11.67% of 600 bp sequence analyzed, showing the abundant genetic diversity of the three native horse breeds in western China. The Neighbour-Joining (NJ) phylogenetic tree based on 247 bp of 43 D-loop sequences demonstrated the presence of seven major lineages (A to G), indicating that the three native horse breeds in western China originated from multiple maternal origins. Consistent with the front, the NJ phylogenetic tree based on 600 bp of mtDNA D-loop sequences of 43 Chinese western native horses and 81 sequences of six horse breeds from GenBank indicated that the three horse breeds had distributed into the seven major lineages (A to G). The structure of the phylogenic tree is often blurred because the variation in a short segment of the mitochondrial genome is often accompanied by high levels of recurrent mutations. Consequently, longer D-loop sequences are helpful in achieving a higher level of molecular resolution in horses.

Keywords

Chinese Western Native Horses;Mitochondrial DNA D-loop;Genetic Diversity;Maternal Origin

Acknowledgement

Supported by : Education Department of Shaanxi Province

References

  1. Achilli, A., S. Bonfiglio, A. Olivieri, A. Malusa, M. Pala, B. Hooshiar Kashani, U. A. Perego, P. Ajmone-Marsan, L. Liotta, O. Semino, H. J. Bandelt, L. Ferretti and A. Torroni. 2009. The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS. One. 4:e5753. https://doi.org/10.1371/journal.pone.0005753
  2. Achilli, A., A. Olivieri, P. Soares, H. Lancioni, B. Hooshiar Kashani, U. A. Perego, S. G. Nergadze, V. Carossa, M. Santagostino, S. Capomaccio, M. Felicetti, W. Al-Achkar, M. C. Penedo, A. Verini-Supplizi, M. Houshmand, S. R. Woodward, O. Semino, M. Silvestrelli, E. Giulotto, L. Pereira, H. J. Bandelt and A. Torroni. 2012. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc. Natl. Acad. Sci. USA. 109:2449-2454. https://doi.org/10.1073/pnas.1111637109
  3. Asakawa, S., Y. Kumazawa, T. Araki, H. Himeno, K. Miura and K. Watanabe. 1991. Strand-specific nucleotide composition bias in echinoderm and vertebrate mitochondrial genomes. J. Mol. Evol. 32:511-20. https://doi.org/10.1007/BF02102653
  4. Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780. https://doi.org/10.1093/nar/27.8.1767
  5. Bowling, A. T., A. Del Valle and M. Bowling. 2000. A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses. Anim. Genet. 31:1-7. https://doi.org/10.1046/j.1365-2052.2000.00558.x
  6. Chang, H. 2009. Animal genetic resources. Science Press.
  7. Du, D., L. Deng, C. J. Zhao, G. C. Han and C. X. Wu. 2009. Study on the genetic diversity of Ningqiang pony and Mongolian horse using microsatellite markers. Chinese J. Anim. Sci. 45:10-13.
  8. Hou, W. T., G. M. Li and D. R. Wolstenholme. 1992. Genetic novelties in mitochondrial genomes of multicellular animals. Curr. Opin. Genet. Dev. 2:918-925. https://doi.org/10.1016/S0959-437X(05)80116-9
  9. Ishida, N., T. Oyunsuren, S. Mashima, H. Mukoyama and N. Saitou. 1995. Mitochondrial DNA sequences of various species of the Genus Equus with special reference to the phylogenetic relationship between Przewalskii's wild horse and domestic horse. J. Mol. Evol. 41:180-188.
  10. Jansen, T., P. Forster, M. A. Levine, H. Oelke, M. Hurles, C. Renfrew, J. Weber and K. Olek. 2002. Mitochondrial DNA and the origins of the domestic horse. Proc. Natl. Acad. Sci. USA. 99:10905-10910. https://doi.org/10.1073/pnas.152330099
  11. Ji, X., X. Wu, P. Yan and G. Amato. 2008. Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis). Mol. Biol. Rep. 35:133-138. https://doi.org/10.1007/s11033-007-9062-x
  12. Jiang, Q., Y. Wei, Y. Huang, H. Jiang, Y. Guo, G. Lan and J. Liao. 2011. The complete mitochondrial genome and phylogenetic analysis of the Debao pony (Equus caballus). Mol. Biol. Rep. 38:593-599. https://doi.org/10.1007/s11033-010-0145-8
  13. Kakoi, H., T. Tozaki and H. Gawahara. 2007. Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochem. Genet. 45:375-395. https://doi.org/10.1007/s10528-007-9083-0
  14. Ki, J. S., D. S. Hwang, T. J. Park, S. H. Han and J. S. Lee. 2010. A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae). Mol. Biol. Rep. 37:1943-1955. https://doi.org/10.1007/s11033-009-9641-0
  15. Kim, K. I., Y. H. Yang, S. S. Lee, C. Park, R. Ma, J. L. Bouzat and H. A. Lewin. 1999. Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Anim. Genet. 30:102-108. https://doi.org/10.1046/j.1365-2052.1999.00419.x
  16. Lei, C. Z., H. Chen, G. S. Yang, W. B. Sun, X. Q. Lei, Q. L. Ge, Z. F. Wang, N. Lu, X. Gao and W. T. Hou. 2005. Study on mitochondrial DNA D-loop polymorphism in Chinese donkeys. Yi Chuan Xue Bao. 32:481-486.
  17. Lei, C. Z., R. Su, M. A. Bower, C. J. Edwards, X. B. Wang, S. Weining, L. Liu, W. M. Xie, F. Li, R. Y. Liu, Y. S. Zhang, C. M. Zhang and H. Chen. 2009. Multiple maternal origins of native modern and ancient horse populations in China. Anim. Genet. 40:933-944. https://doi.org/10.1111/j.1365-2052.2009.01950.x
  18. Li, J. L., Y. Shi, C. Fan and D. J. Manglai. 2008. mtDNA diversity and original of Chinese Mongolian horse. Asian-Aust. J. Anim. Sci. 21:1696-1702. https://doi.org/10.5713/ajas.2008.80193
  19. Lister, A. M., M. Kadwell, L. M. Kaagan, W. C. Jordan, M. B. Richards and H. F. Stanley. 1998 Ancient and modern DNA in study of horse domestication. Anc. Biomol. 2:267-280.
  20. McGahern, A., M. A. Bower, C. J. Edwards, P. O. Brophy, G. Sulimova, I. Zakharov, M. Vizuete-Forster, M. Levine, S. Li, D. E. MacHugh and E. W. Hill. 2006. Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations. Anim. Genet. 37:494-497. https://doi.org/10.1111/j.1365-2052.2006.01495.x
  21. Outram, A. K., N. A. Stear, R. Bendrey, S. Olsen, A. Kasparov, V. Zaibert, N. Thorpe and R. P. Evershed. 2009. The earliest horse harnessing and milking. Science 323:1332-1335. https://doi.org/10.1126/science.1168594
  22. Peng, R., B. Zeng, X. Meng, B. Yue, Z. Zhang and F. Zou. 2007. The complete mitochondrial genome and phylogenetic analysis of the giant panda (Ailuropoda melanoleuca). Genes 397:76-83.
  23. Rozas, J., J. C. Sanchez-DelBarrio, X. Messeguer and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. https://doi.org/10.1093/bioinformatics/btg359
  24. Statistic Report in China Editing Commission. 2004. Statistic Report in China. Statistic Report in China Editing Commission. Beijing, China.
  25. Tamura, K., J. Dudley, M. Nei and S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599. https://doi.org/10.1093/molbev/msm092
  26. Vila, C., J. A. Leonard, A. Gotherstom, S. Marklund, K. Sandberg, K. Linden, R. K. Wayne and H. Ellegren. 2001. Wide spread origin of domestic horse lineages. Science 291:474-477. https://doi.org/10.1126/science.291.5503.474
  27. Wallner, B., G. Brem, M. Muller and R. Achmann. 2003. Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus. Anim. Genet. 34:453-456. https://doi.org/10.1046/j.0268-9146.2003.01044.x
  28. Wang, W., A. H. Liu, S. Y. Lin, H. Lan, B. Su, D. W. Xie and L. M. Shi. 1994. Multiple genotypes of mitochondrial DNA within a horse population from a small region in Yunnan Province of China. Biochem. Genet. 32:371-378. https://doi.org/10.1007/BF02426899
  29. Wolstenholme, D. R. 1992. Genetic novelties in mitochondrial genomes of multicellular animals. Curr. Opin. Genet. Dev. 2:918-925. https://doi.org/10.1016/S0959-437X(05)80116-9
  30. Xie, C. X. 1987. Horse and ass breeds in China. Shanghai Scientific and Technical Publishing House, Shanghai, China.
  31. Xu, S., J. Luosang, S. Hua, J. He, A. Ciren, W. Wang, X. Tong, Y. Liang, J. Wang and X. Zheng. 2007. High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome. J. Genet. Genomics 34:720-729. https://doi.org/10.1016/S1673-8527(07)60081-2
  32. Yang, Y. H., K. I. Kim, E. G. Cothran and A. R. Flannery. 2002. Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism. Biochem. Genet. 40:175-186. https://doi.org/10.1023/A:1015884125507

Cited by

  1. Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines vol.12, pp.8, 2017, https://doi.org/10.1371/journal.pone.0184309
  2. D-loop haplotype diversity in Brazilian horse breeds vol.40, pp.3, 2017, https://doi.org/10.1590/1678-4685-gmb-2016-0166
  3. Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing vol.6, pp.2167-8359, 2018, https://doi.org/10.7717/peerj.4198
  4. Genetic Diversity of Mitochondrial DNA of Chinese Black-bone Chicken vol.20, pp.3, 2018, https://doi.org/10.1590/1806-9061-2018-0739
  5. Genetic variability of Akhal-Teke horses bred in Italy vol.6, pp.2167-8359, 2018, https://doi.org/10.7717/peerj.4889
  6. The complete mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken pp.1466-1799, 2018, https://doi.org/10.1080/00071668.2018.1514581