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Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region

  • Touma, Shihei (Okinawa Prefectural Livestock and Grassland Research Center) ;
  • Shimabukuro, Hirotoshi (Okinawa Prefectural Livestock Breeding Center) ;
  • Arakawa, Aisaku (Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO)) ;
  • Oikawa, Takuro (Faculty of Agriculture, University of the Ryukyus)
  • Received : 2018.05.18
  • Accepted : 2018.09.14
  • Published : 2019.04.01

Abstract

Objective: The Agu is the only native pig breed in Japan, which is reared in Okinawa prefecture, the southernmost region in Japan. Its origins are considered to be of Asian lineage; however, the genetic background of the Agu is still unclear. The objective of this study was to elucidate the maternal lineage of the Okinawa indigenous Agu pig with the use of the mitochondrial DNA (mtDNA) control region. Methods: The mtDNA control regions of Agu pigs were sequenced and the phylogenetic relationship among Agu, East Asian and European pigs was investigated with the use of 78 Agu individuals. Results: Twenty-seven polymorphic sites and five different haplotypes (type 1 to type 5) were identified within the Agu population. Phylogenetic analysis indicated that types 1 and 2 were included in East Asian lineages; however, the remaining types 3, 4, and 5 were of European lineages, which showed a gene flow from European pigs in the 20th century. Sixty-seven out of 78 Agu individuals (85.9%) possessed mtDNA haplotypes 1 and 2 of the East Asian lineage, which were identical to two haplotypes of ancient mtDNA (7,200 to 1,700 years before the present) excavated at archaeological sites in Okinawa. Conclusion: This study confirmed that the East Asian lineage is dominant in the maternal genetic background of the Agu population, supporting the hypothesis that the ancestors of the Agu pig were introduced from the Asian continent.

Keywords

Okinawa Indigenous Pig;Agu;Mitochondrial DNA;Maternal Lineage;Haplotype

References

  1. Touma S, Oikawa T. Breed characteristics of indigenous Okinawa Agu pigs analyzed by body measurements and reproductive traits. Jpn J Anim Sci 2017;88:103-13.
  2. Touma S, Onaga M, Toubaru N, Oikawa T. Breed characteristics of indigenous pigs in Okinawa: growth performance, carcass traits and meat quality. Jpn J Swine Sci 2017;54:121-9. https://doi.org/10.5938/youton.54.3_121
  3. Shimabukuro M. The pigs and goats in Okinawa (Okinawa no buta to yagi). Naha, Japan: Hirugi sha; 1989.
  4. Keruma T. Okinawan customs, biographies and legends (Ryukyu tigusa no maki). Naha, Japan: Ryukyu siryou kenkyuukai; 1962.
  5. Iha M. The animal history in Okinawa (Ryukyu doubutu shi). Naha, Japan: Hirugi sha; 1979.
  6. Watanobe T, Ishiguro N, Nakano M, et al. Prehistoric introduction of domestic pigs onto the Okinawa Islands: ancient mitochondrial DNA evidence. J Mol Evol 2002;55:222-31. https://doi.org/10.1007/s00239-002-2320-6
  7. Takahashi R, Ishiguro N, Matsui A, Anezaki T, Hongo H. Morphological and molecular phylogenetic characteristics of dwarf Sus specimens from the Noguni shell middens in the Ryukyu Islands. Anthropol Sci 2012;120:39-50. https://doi.org/10.1537/ase.100929
  8. Ozawa N. Origin of the Ryukyuan native pigs inferred from mitochondrial DNA sequences. Rep Soc Res Native Livest 2000;18:209-16.
  9. Watanobe T, Okumura N, Ishiguro N, et al. Genetic relationship and distribution of the Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus) analyzed by mitochondrial DNA. Mol Ecol 1999;8:1509-12. https://doi.org/10.1046/j.1365-294x.1999.00729.x
  10. Okumura N, Kurosawa Y, Kobayashi E, et al. Genetic relationship amongst the major non-coding regions of mitochondrial DNAs in wild boars and several breeds of domesticated pigs. Anim Genet 2001;32:139-47. https://doi.org/10.1046/j.1365-2052.2001.00757.x
  11. Takada M, Oka T, Takahashi R, et al. Phylogenetic study of Okinawa and Amami native pig based on mitochondrial DNA sequence. Jpn J Swine Sci 2008;45:187-92. https://doi.org/10.5938/youton.45.187
  12. Wu CY, Jiang YN, Chu HP, et al. The type I Lanyu pig has a maternal genetic lineage distinct from Asian and European pigs. Anim Genet 2007;38:499-505. https://doi.org/10.1111/j.1365-2052.2007.01646.x
  13. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-80. https://doi.org/10.1093/nar/22.22.4673
  14. Hasegawa M, Kishino H, Yano T. Dating the human-ape split by a molecular clock of mitochondrial DNA. J Mol Evol 1985;22:160-74. https://doi.org/10.1007/BF02101694
  15. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870-4. https://doi.org/10.1093/molbev/msw054
  16. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783-91. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
  17. Bandelt HJ, Forster P, Rohl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999;16:37-48. https://doi.org/10.1093/oxfordjournals.molbev.a026036
  18. Giuffra E, Kijas JM, Amarger V, et al. The origin of the domesticpig: independent domestication and subsequent introgression. Genetics 2000;154:1785-91.
  19. Kim KI, Lee JH, Li K, et al. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA control region sequence polymorphism. Anim Genet 2002;33:19-25. https://doi.org/10.1046/j.1365-2052.2002.00784.x
  20. Gongora J, Fleming P, Spencer PB, et al. Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype. Mol Phylogenet Evol 2004;33:339-48. https://doi.org/10.1016/j.ympev.2004.06.004
  21. Editorial committee of the history of Okinawa agriculture and forestry fisheries administration. History of Okinawa agriculture and forestry fisheries administration Vol 12 (Agricultural material part). Tokyo Nourintoukei kyoukai; 1982.
  22. Editorial committee of the history of Okinawa agriculture and forestry fisheries administration. History of Okinawa agriculture and forestry fisheries administration Vol 5 (Animal industry and sericulture). Tokyo Nourintoukei kyoukai; 1986.
  23. Oshiro I, Nohara T. Distribution of Pleistocene terrestrial vertebrates and their migration to the Ryukyus. Tropics 2000;10:41-50. https://doi.org/10.3759/tropics.10.41