Asian-Australasian Journal of Animal Sciences

  • 제32권10호
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  • Pages.1491-1500
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  • 2019
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  • 1011-2367(pISSN)
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  • 1976-5517(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
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Genetic diversity analysis of Thai indigenous pig population using microsatellite markers

  • Charoensook, Rangsun (Division of Animal Science and Feed Technology, Department of Agricultural Sciences, Faculty of Agriculture Natural Resources and Environment, Naresuan University) ;
  • Gatphayak, Kesinee (Department of Animal and Aquatic Science, Faculty of Agriculture, Chiang Mai University) ;
  • Brenig, Bertram (Division of Molecular Biology of Livestock and Molecular Diagnostics, Faculty of Agricultural Sciences, Georg-August University of Gottingen) ;
  • Knorr, Christoph (Division of Livestock Biotechnology and Reproduction, Faculty of Agricultural Sciences, Georg-August University of Gottingen)
  • 투고 : 2018.11.02
  • 심사 : 2019.02.16
  • 발행 : 2019.10.01
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초록

Objective: European pigs have been imported to improve the economically important traits of Thai pigs by crossbreeding and was finally completely replaced. Currently Thai indigenous pigs are particularly kept in a small population. Therefore, indigenous pigs risk losing their genetic diversity and identity. Thus, this study was conducted to perform large-scale genetic diversity and phylogenetic analyses on the many pig breeds available in Thailand. Methods: Genetic diversity and phylogenetics analyses of 222 pigs belonging to Thai native pigs (TNP), Thai wild boars (TWB), European commercial pigs, commercial crossbred pigs, and Chinese indigenous pigs were investigated by genotyping using 26 microsatellite markers. Results: The results showed that Thai pig populations had a high genetic diversity with mean total and effective ($N_e$) number of alleles of 14.59 and 3.71, respectively, and expected heterozygosity ($H_e$) across loci (0.710). The polymorphic information content per locus ranged between 0.651 and 0.914 leading to an average value above all loci of 0.789, and private alleles were found in six populations. The higher $H_e$ compared to observed heterozygosity ($H_o$) in TNP, TWB, and the commercial pigs indicated some inbreeding within a population. The Nei's genetic distance, mean $F_{ST}$ estimates, neighbour-joining tree of populations and individual, as well as multidimensional analysis indicated close genetic relationship between Thai indigenous pigs and some Chinese pigs, and they are distinctly different from European pigs. Conclusion: Our study reveals a close genetic relationship between TNP and Chinese pigs. The genetic introgression from European breeds is found in some TNP populations, and signs of genetic erosion are shown. Private alleles found in this study should be taken into consideration for the breeding program. The genetic information from this study will be a benefit for both conservation and utilization of Thai pig genetic resources.

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참고문헌

  1. Visitpanich T, Falvey L. A survey of highland pig industry. Thai J Agric Sci 1980;13:259-67.
  2. Rattanaronchart S. Present situation of Thai native pigs. Chiang Mai, Thailand: Scientific Report of the Department of Animal Science, Faculty of Agriculture, Chiang Mai University; 1994.
  3. Charoensook R, Knorr C, Brenig B, et al. Thai pig and cattle production, genetic diversity of livestock and strategies for preserving animal genetic resources. Maejo Int Sci Technol 2013;7:113-32.
  4. Rege JEO, Okeyo AM. Improving our knowledge of tropical indigenous animal genetic resources. Animal Genetics Training Resource, CD Version 2. Nairobi, Kenya: International Livestock Research Institute (ILRI); 2006.
  5. Kim TH, Kim K, 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
  6. Vicente AA, Carolino MI, Sousa MCO, 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
  7. Fang M, Hu X, Jin W, et al. Genetic uniqueness of Chinese village pig populations inferred from microsatellite markers. J Anim Sci 2009;87:3445-50. https://doi.org/10.2527/jas.2008-1632
  8. Chaiwatanasin W, Chantsawang S, Tabchareon S. Genetic diversity of four pig breeds in Thailand based on microsatellite analysis. Kasetsart J (Nat Sci) 2002;36:248-52.
  9. Charoensook R, Brenig B, Gatphayak K, Knorr C. Genetic identity of native pig breeds in northern Thailand evidenced by microsatellite markers. Proceeding of Tropentag 2009, International Conference on Research for Development in Agriculture and Forestry, Food and Natural Resource Management. Hamburg, Germany: University of Hamburg; 2009.
  10. Charoensook R, Brenig B, Gatphayak K, Knorr C. Further resolution of porcine phylogeny in Southeast Asia by Thai mtDNA haplotypes. Anim Genet 2011;42:445-50. https://doi.org/10.1111/j.1365-2052.2011.02175.x
  11. FASS. Guide for the care and use of agricultural animals in agricultural research and teaching. 1st ed. Savoy, IL, USA:Federation of Animal Science Societies; 1999.
  12. Chen K, Knorr C, Bornemann-Kolatzki K, et al. Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones. BMC Genet 2005;6:54. https://doi.org/10.1186/1471-2156-6-54
  13. Sambrook J, Frisch EF, Maniatis T. Molecular Cloning: a laboratory manual. 2nd ed. New York, USA: Cold Spring Harbor Laboratory Press; 1989.
  14. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16:1215. https://doi.org/10.1093/nar/16.3.1215
  15. Belkhir K, Borsa P, Goudet J, et al. Genetix, WindowsTM software for population genetics. CNRS UPR 9060. Montpellier, France: Genome and Populations Laboratory, University of Montpellier.
  16. Yeh FC, Yang R, Bozle T. POPGENE Version 1.31, MS Windows-based freeware for population genetic analysis. Edmonton, AB, Canada: University of Alberta and Center for International Forestry Research; 1999.
  17. Botstein D, White RL, Skolmick H, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 1980;32:314-31.
  18. Marshall TC, Slate J, Kruuk LEB, 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
  19. Goudet J. FSTAT, a program to estimate and test gene diversities and fixation indices 2001; (version 2.9.3). [2017 Oct 27]. Available from: https://www2.unil.ch/popgen/softwares/fstat.htm
  20. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406-25. https://doi.org/10.1093/oxfordjournals.molbev.a040454
  21. Felsenstein J. Phylogeny Inference Package (PHYLIP). Seattle, WA, USA: Genomes Sciences, Department of Genetics, University of Washington; 1993-2002. Available from: http://evolution.gs.washington.edu/phylip.html
  22. Page RDM. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 1996;12:357-8.
  23. Peakall R, Smouse PE. GENEALEX 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
  24. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24:1596-9. https://doi.org/10.1093/molbev/msm092
  25. ISAG/FAO Standing Committee. Secondary guidelines for development of national farm animal genetic resources management plans. Measurement of Domestic Animal Diversity 2004; (MoDAD) Recommended Microsatellite Markers [cited 2017 Oct 27]. Available from: http://www.fao.org/3/a-aq569e.pdf
  26. Thuy NTD, Melchinger-Wild E, Kuss AW, Cuong NV, Bartenschlager H, Geldermann H. Comparison of Vietnamese and European pig breeds using microsatellites. J Anim Sci 2006;84:2601-8. https://doi.org/10.2527/jas.2005-641
  27. Lemus-Flores C, Ulloa-Arvizu R, Ramos-Kuri M, Estrada FJ, Alonso RA. Genetic analysis of Mexican hairless pig populations. J Anim Sci 2001;79:3021-6. https://doi.org/10.2527/2001.79123021x
  28. Fabuel E, Barragan C, Silio L, Rodriguez MC, Toro MA. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 2004;93:104-13. https://doi.org/10.1038/sj.hdy.6800488
  29. Li SJ, Yang SH, 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
  30. Yang SL, Wang ZG, Liu B, et al. Genetic variation and relationships of eighteen Chinese indigenous pig breeds. Genet Sel Evol 2003;35:657-71. https://doi.org/10.1186/1297-9686-35-7-657
  31. Maudet C, Luikart G, Taberlet P. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J Anim Sci 2002;80:942-50. https://doi.org/10.2527/2002.804942x
  32. Nei M. Genetic distance between populations. Am Nat 1972;106:283-92. https://doi.org/10.1086/282771
  33. Laval G, Iannuccelli N, Legault C, et al. Genetic diversity of eleven European pig breeds. Genet Sel Evol 2000;32:187. https://doi.org/10.1186/1297-9686-32-2-187
  34. Martinez AM, Delgado JV, Rodero A, Vega-Pla JL. Genetic structure of the Iberian pig breed using microsatellites. Anim Genet 2000;31:295-301. https://doi.org/10.1046/j.1365-2052. 2000.00645.x
  35. Fan B, Wang ZG, Li YJ, et al. Genetic variation analysis within and among Chinese indigenous swine populations using microsatellite markers. Anim Genet 2002;33:422-7. https://doi.org/10.1046/j.1365-2052.2002.00898.x
  36. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 1978;89:583-90. https://doi.org/10.1093/genetics/89.3.583
  37. Kimloon T. The specific nature and native pig raising at Huai Ngu sing village, Thung Hua Chang district, Lamphun province [MS. Thesis]. Chiangmai Thailand: Department of Animal Science, Faculty of Agriculture Chiangmai University;1998. 62 p. (in Thai).

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