A Genetic Analysis of Taoyuan Pig and Its Phylogenetic Relationship to Eurasian Pig Breeds

  • Li, Kuan-Yi (Department of Animal Science and Technology, National Taiwan University) ;
  • Li, Kuang-Ti (Institute of History and Philology, Academia Sinica) ;
  • Cheng, Chun-Chun (Graduate Institute of Hakka Cultural Industry, National Pingtung University of Science and Technology) ;
  • Chen, Chia-Hsuan (Division of Breeding and Genetics, Livestock Research Institute, Council of Agriculture, Executive Yuan) ;
  • Hung, Chien-Yi (Department of Animal Science and Technology, National Taiwan University) ;
  • Ju, Yu-Ten (Department of Animal Science and Technology, National Taiwan University)
  • Received : 2014.08.04
  • Accepted : 2014.10.31
  • Published : 2015.04.01


Taoyuan pig is a native Taiwan breed. According to the historical record, the breed was first introduced to Taiwan from Guangdong province, Southern China, around 1877. The breed played an important role in Taiwan's early swine industry. It was classified as an indigenous breed in 1986. After 1987, a conserved population of Taoyuan pig was collected and reared in isolation. In this study, mitochondrial DNA sequences and 18 microsatellite markers were used to investigate maternal lineage and genetic diversity within the Taoyuan pig population. Population differentiation among Taoyuan, Asian type, and European type pig breeds was also evaluated using differentiation indices. Only one D-loop haplotype of the Taoyuan pig was found. It clustered with Lower Changjiang River Basin and Central China Type pig breeds. Based on the polymorphism of microsatellite markers, a positive fixation index value ($F_{IS}$) indicates that the conserved Taoyuan population suffers from inbreeding. In addition, high $F_{ST}$ values (>0.2105) were obtained, revealing high differentiation among these breeds. Non-metric multi-dimensional scaling showed a clear geometric structure among 7 breeds. Together these results indicate that maternally Taoyuan pig originated in the Lower Changjiang River Basin and Central China; however, since being introduced to Taiwan differentiation has occurred. In addition, Taoyuan pig has lost genetic diversity in both its mitochondrial and nuclear genomes.


Supported by : National Science Council of Taiwan


  1. Bond, J. M., E. M. Veenendaal, D. D. Hornby, and A. J. Gray. 2002. Looking for progenitors: A molecular approach to finding the origins of an invasive weed. Biol. Invasions 4:349-357.
  2. Carr, M. R. 1996. PRIMER User Manual. Ver 4.0. Plymouth Routines in Multivariate Ecological Research. Plymouth Marine Laboratory, Plymouth, UK.
  3. Chang, W. H., H. P. Chu, Y. N. Jiang, S. H. Li, Y. Wang, C. H. Chen, K. J. Chen, C. Y. Lin, and Y. T. Ju. 2009. Genetic variation and phylogenetics of Lanyu and exotic pig breeds in Taiwan analyzed by nineteen microsatellite markers. J. Anim. Sci. 87:1-8.
  4. Cheng, P. L. 1986. Description of Chinese pig breeds. In: Pig Breeds in China (Ed. Z. Zhang). Shanghai Scientific and Technical Publishers, Shanghai. pp. 25-178.
  5. Chyr, S. C., K. J. Lin, H. L. Chang, T. S. Yang, and H. T. Yen. 2001. Breeds and genetic improvement. In: Guidelines in Animal Science-Swine Production (Ed. S. C. Chyr). Chinese Society for Animal Science Press, Taipei. pp. 29-95.
  6. Cummins, J. 2001. Mitochondrial DNA and the Y chromosome: Parallels and paradoxes. Reprod. Fertil. Dev. 13:533-542.
  7. Dieringer, D. and C. Schlötterer. 2003. MICROSATELLITEANALYSER (MSA): A platform independent analysis tool forlarge microsatellite data sets. Mol. Ecol. Notes 3:167-169.
  8. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166.
  9. Food and Agriculture Organization of the United Nations (FAO). 2004. Secondary Guidelines for Development of National Farm Animal Genetic Resources Management Plans. Measurement of Domestic Animal Diversity (MoDAD): Recommended Microsatellite Markers. FAO, Rome.
  10. Gongora, J., P. Fleming, P. B. S. Spencer, R. Mason, O. Garkavenko, J. N. Meyer, C. Droegemueller, J. H. Lee, and C. Moran. 2004. Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype. Mol. Phylogenet. Evol. 33:339-348.
  11. Hein, J. and J. Stovlbaek. 1996. Combined DNA and protein alignment. Methods Enzymol. 266:402-418.
  12. Jiang, Y. N., C. Y. Wu, C. Y. Huang, H. P. Chu, M. W. Ke, M. S. Kung, K. Y. Li, C. H. Wang, S. H. Li, Y. Wang, and Y. T. Ju. 2008. Interpopulation and intrapopulation maternal lineage genetics of the Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences. J. Anim. Sci. 86:2461-2470.
  13. Kimura, M. and J. F. Crow. 1964. The number of alleles that can be maintained in a finite population. Genetics 49:725-738.
  14. Krzanowski, W. J. 1988. Principles of Multivariate Analysis: A User's Perspective. Oxford University Press, Oxford.
  15. Larson, G., K. Dobney, U. Albarella, M. Fang, E. Matisoo-Smith, J. Robins, S. Lowden, H. Finlayson, T. Brand, E. Willerslev, P. Rowley-Conwy, L. Andersson, and A. Cooper. 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307:1618-1621.
  16. Li, S. J., S. H. Yang, S. H. Zhao, B. Fan, M. Yu, H. S. Wang, M. H. Li, B. Liu, T. A. Xiong, and K. Li. 2004. Genetic diversity analyses of 10 indigenous Chinese pig populations based on 20 microsatellites. J. Anim. Sci. 82:368-374.
  17. Marshall, T. C., J. Slate, L. E. B. Kruuk, and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7:639-655.
  18. Matsui, A. 1997. Animal remains in Gushibaru shellmidden. In: Report on Cultural Assets of Okinawa Prefecture Vol. 130 (Ed. Okinawa Prefectural Board of Education). Okinawa Prefectural Board of Education, Naha, Japan. pp. 159-187.
  19. Nishimoto, T. 1993. The physical character of the pig in the Yayoi Period. B. Natl. Mus. Jpn. Hist. 50:49-70.
  20. Posada, D. and K. A. Crandall. 1998. MODELTEST: Testing the model of DNA substitution. Bioinformatics 14:817-818.
  21. Raymond, M. and F. Rousset. 1995. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 86:248-249.
  22. 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.
  23. Wang, X., J. Ou, L. Huang, M. Nishihara, J. Li, N. Manabe, and Y. Zhang. 2006. Genetic characteristics of inbred Wuzhishan miniature pigs, a native Chinese breed. J. Reprod. Develop. 52:639-643.
  24. Watanobe, T., N. Ishiguro, M. Nakano, H. Takamiya, A. Matsui, and H. Hongo. 2002. Prehistoric introduction of domestic pigs onto the Okinawa Islands: ancient mitochondrial DNA evidence. J. Mol. Evol. 55:222-231.
  25. Wrobel, B. 2008. Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods. J. Appl. Genet. 49:49-67.
  26. Wu, C. Y., Y. N. Jiang, H. P. Chu, S. H. Li, Y. Wang, Y. H. Li, Y. Chang, and Y. T. Ju. 2007. The type I Lanyu pig has a maternal genetic lineage distinct from Asian and European pigs. Anim. Genet. 38:499-505.
  27. Yang, S. L., Z. G. Wang, B. Liu, G. X. Zhang, S. H. Zhao, M. Yu, B. Fan, M. H. Li, T. A. Xiong, and K. Li. 2003. Genetic variation and relationships of eighteen Chinese indigenous pig breeds. Genet. Sel. Evol. 35:657-671.
  28. Yang, S. L., H. Zhang, H. M. Mao, D. W. Yan, S. X. Lu, L. S. Lian, G. Y. Zhao, Y. L. Yan, W. D. Deng, X. W. Shi, S. X. Han, S. Li, X. J. Wang and X. Gou. 2011. The local origin of the Tibetan pig and additional insights into the origin of Asian pigs. PLoS ONE 6(12):e28215.
  29. Zheng, C. C. and Y. T. Zhu. 2013. On pig breeding culture in Taiwan rural areas during the period of Japanese occupation. Taiwan Res. J. 125:55-64.