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Evaluation of the genetic structure of indigenous Okinawa Agu pigs using microsatellite markers

  • Touma, Shihei (Okinawa Prefectural Livestock and Grassland Research 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 : 2019.01.12
  • Accepted : 2019.05.07
  • Published : 2020.02.01

Abstract

Objective: Agu pigs are indigenous to the Okinawa prefecture, which is the southernmost region of Japan. Agu pigs were exposed to a genetic bottleneck during the 20th century, due to the introduction of European pig breeds. The objective of this study was to elucidate the genetic structure of Agu pigs and to determine their relationships with those of five European breeds, two Chinese breeds and Ryukyu wild boar using microsatellite markers. Methods: A total of 203 DNA samples from 8 pig breeds were used in this study. Genotyping was performed using 21 microsatellite markers distributed across 17 chromosomes. Results: Numbers of effective alleles in Agu pigs were fewer than in European breeds and Ryukyu wild boar. Among domestic pigs, Agu pigs had the lowest heterozygosity (0.423) and highest inbreeding coefficient (FIS = 0.202), indicating a severe loss of heterozygosity in Agu pigs possibly due to inbreeding. Neighbor-joining tree analysis was performed based on Reynolds' genetic distances, which clustered Agu pigs with Duroc pigs. However, principal component analysis revealed a unique genetic position of the Agu pig, and the second principal component separated Agu pigs from all other breeds. Structure analysis with the optimal assumption of seven groups (K = 7) indicated that Agu pigs form an independent cluster from the other breeds. In addition, high and significant FST values (0.235 to 0.413) were identified between Agu pigs and the other breeds. Conclusion: This study revealed a substantial loss of genetic diversity among Agu pigs due to inbreeding. Our data also suggest that Agu pigs have a distinctive genetic structure, although gene flows from European breeds were observed.

References

  1. Editorial Committee of the History of Nago City. The history of Nago city book of materials. 1. Statistical material of early modern times. Okinawa, Japan: Nago City Public Office; 1980. p. 294-5.
  2. Miyagi Y. Okinawa zairaibuta Agu no fukugen to Okinawa no shokubunnka (The restoration of Okinawa indigenous pig Agu and food culture of Okinawa). The Livestock Industry Magazine 1998;407:46-50.
  3. 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 https://doi.org/10.1046/j.1365-2052.2001.00757.x
  4. Li KY, Li KT, Cheng CC, Chen CH, Hung CY, Ju YT. A genetic analysis of Taoyuan pig and its phylogenetic relationship to Eurasian pig breeds. Asian-Australas J Anim Sci 2015;28:457-66. https://doi.org/10.5713/ajas.14.0595 https://doi.org/10.5713/ajas.14.0595
  5. Touma S, Shimabukuro H, Arakawa A, Oikawa T. Maternal lineage of Okinawa indigenous Agu pig inferred from mitochondrial DNA control region. Asian-Australas J Anim Sci 2019;32:501-7. https://doi.org/10.5713/ajas.18.0378
  6. 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 https://doi.org/10.5938/youton.54.3_121
  7. Peakall R, Smouse PE. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 2006;6:288-95. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  8. FSTAT. A program to estimate and test gene diversities and fixation indices (version 2.9.3) [Internet]. Goudet J.; c2005 [cited 2018 Sep 11]. Available from http://www2.unil.ch/popgen/softwares/fstat.htm
  9. Raymond M, Rousset F. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. J Hered 1995;86:248-9. https://doi.org/10.1093/oxfordjournals.jhered.a111573 https://doi.org/10.1093/oxfordjournals.jhered.a111573
  10. Marshall TC, Slate J, Kruuk LE, Pemberton JM. Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 1998;7:639-55. https://doi.org/10.1046/j.1365-294x.1998.00374.x https://doi.org/10.1046/j.1365-294x.1998.00374.x
  11. Reynolds J, Weir BS, Cockerham CC. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 1983;105:767-79.
  12. Langella O. Populations 1.2.32: a population genetic software; c1999 [cited 2019 Feb 10]. Available from http://bioinformatics.org/-tryphon/populations/
  13. Dieringer D. Schlotterer D. Microsatellite analyzer (MSA): A platform independent analysis tool for large microsatellite data sets. Mol Ecol Notes 2003;3:167-9. https://doi.org/10.1046/j.1471-8286.2003.00351.x https://doi.org/10.1046/j.1471-8286.2003.00351.x
  14. 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 https://doi.org/10.1093/molbev/msw054
  15. PCAGEN. A program to perform a principal component analysis (PCA) on genetic data [Internet]. Goudet J.; c2005 [cited 2018 Sep 11]. Available from: http://www2.uni.ch/popgen/pcagen.htm
  16. Pritchard JK, Stephans M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000;155: 945-59.
  17. Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 2005;14:2611-20. https://doi.org/10.1111/ j.1365-294X.2005.02553.x https://doi.org/10.1111/j.1365-294X.2005.02553.x
  18. Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. CLUMPAK: a program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 2015;15:1179-91. https://doi.org/10.1111/1755-0998.12387 https://doi.org/10.1111/1755-0998.12387
  19. Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980;32:314-31.
  20. Hartl DL, Clark AG. Principles of population genetics. 3rd ed. Sunderland, Sinauer Associates Inc; 1997. p. 118-9.
  21. Kim TH, Kim KS, Choi BH, et al. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J Anim Sci 2005;83:2255-63. https://doi.org/10.2527/2005.83102255x https://doi.org/10.2527/2005.83102255x
  22. Vicente AA, Carolino MI, Sousa MC, et al. Genetic diversity in native and commercial breeds of pigs in Portugal assessed by microsatellites. J Anim Sci 2008;86:2496-507. https://doi.org/10.2527/jas.2007-0691 https://doi.org/10.2527/jas.2007-0691
  23. Luetkemeier ES, Sodhi M, Schook LB, Malhi RS. Multiple Asian pig origins revealed through genomic analyses. Mol Phylogenet Evol 2010;54:680-6. https://doi.org/10.1016/j.ympev.2009.11.004 https://doi.org/10.1016/j.ympev.2009.11.004
  24. Murakami K, Yoshikawa S, Konishi S, Ueno Y, Watanabe S, Mizoguchi Y. Evaluation of genetic introgression from domesticated pigs into the Ryukyu wild boar population on Iriomote Island in Japan. Anim Genet 2014;45:517-23. https://doi.org/10.1111/age.12157 https://doi.org/10.1111/age.12157
  25. Li SJ, Yang SL, Zhao SH, et al. Genetic diversity analyses of 10 indigenous Chinese pig populations based on 20 microsatellites. J Anim Sci 2004;82:368-74. https://doi.org/10.2527/2004.822368x https://doi.org/10.2527/2004.822368x
  26. Wang X, Cao HH, Geng SM, Li HB. Genetic diversity of 10 Indigenous Pig breeds in China by Using microsatellite markers. Asian-Australas J Anim Sci 2004;17:1219-22. https://doi.org/10.5713/ajas.2004.1219 https://doi.org/10.5713/ajas.2004.1219
  27. Touma S, Oikawa T. Breed characteristics of indigenous Okinawa Agu pigs analyzed by body measurements and reproductive traits. Nihon Chikusan Gakkaiho 2017;88:103-13. https://doi.org/10.2508/chikusan.88.103 https://doi.org/10.2508/chikusan.88.103
  28. Yamauchi S, Nakamura S, Yoshimoto T, Nakada T, Ashizawa K, Tatemoto H. Prediction of the estrous cycle and optimal insemination time by monitoring vaginal electrical resistance (VER) in order to improve the reproductive efficiency of the Okinawan native Agu pig. Anim Reprod Sci 2009;113:311-6. https://doi.org/10.1016/j.anireprosci.2008.08.005 https://doi.org/10.1016/j.anireprosci.2008.08.005
  29. 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 https://doi.org/10.3759/tropics.10.41
  30. Wahlund S. Composition of population and correlation phenomenon from the point of view of inheritance theory. Hereditas 1928;11:65-106.