Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

  • Seo, Dongwon (Division of Animal and Dairy Science, Chungnam National University) ;
  • Bhuiyan, Md. Shamsul Alam (Department of Animal Breeding and Genetics, Bangladesh Agricultural University) ;
  • Sultana, Hasina (Division of Animal and Dairy Science, Chungnam National University) ;
  • Heo, Jung Min (Division of Animal and Dairy Science, Chungnam National University) ;
  • Lee, Jun Heon (Division of Animal and Dairy Science, Chungnam National University)
  • Received : 2015.11.11
  • Accepted : 2016.01.14
  • Published : 2016.04.01


Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS) markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC) value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.


Grant : BK21플러스

Supported by : 충남대학교


  1. Alyethodi, R. and S. Kumar, 2010. Genetic characterization of moti indian native duck using microsatellite markers. J. Appl. Anim. Res. 38:223-227.
  2. Ayres, K. L. and A. D. J. Overall, 2004. Api-calc 1.0: A computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives. Mol. Ecol. Notes 4:315-318.
  3. Berthouly, C., B. Bed'Hom, M. Tixier-Boichard, C. F. Chen, Y. P. Lee, D. Laloe, H. Legros, E. Verrier, and X. Rognon. 2008. Using molecular markers and multivariate methods to study the genetic diversity of local european and Asian chicken breeds. Anim. Genet. 39:121-129.
  4. Botstein, D., R. L. White, M. Skolnik, and R. W. Davis, 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314-331.
  5. Dalvit, C., M. De Marchi, and M. Cassandro. 2007. Genetic traceability of livestock products: A review. Meat Sci. 77:437-449.
  6. Fulton, J. E. and M. E. Delany. 2003. Poultry genetic resources-operation rescue needed. Science 300:1667-1668.
  7. Groenen, M. A. M., R. P. M. A. Crooijmans, A. Veenendaal, H. H. Cheng, M. Siwek, and J. J. van der Poel, 1998. A comprehensive microsatellite linkage map of the chicken genome. Genomics 49:265-274.
  8. Groepper, S. R., T. J. DeLiberto, M. P. Vrtiska, K. Pedersen, S. R. Swafford, and S. E. Hygnstrom, 2014. Avian influenza virus prevalence in migratory waterfowl in the united states, 2007-2009. Avian Dis. 58:531-540.
  9. Hebert, P. D., A. Cywinska, and S. L. Ball. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. London B: Biol. Sci. 270:313-321.
  10. Huang, Y., Y. Zhao, C. S. Haley, S. Hu, J. Hao, C. Wu, and N. Li. 2006. A genetic and cytogenetic map for the duck (Anas platyrhynchos). Genetics 173:287-296.
  11. Jin, S., M. R. Hoque, D. Seo, W. Paek, T. Kang, H. Kim, and J. Lee. 2014. Phylogenetic analysis between domestic and wild duck species in korea using mtdna d-loop sequences. Mol. Biol. Rep. 41:1645-1652.
  12. Jin, S. D., M. R. Hoque, D. W. Seo, I. K. Kim, C. Jo, W. K. Paek, and J. H. Lee. 2012. Phylogenetic relationships among dabbling duck species in Korea using COI gene variations in mtdna. Japan Poult. Sci. 49:163-170.
  13. Kim, H. K., B. S. Kang, J. Hwangbo, C. D. Kim, K. N. Heo, H. J. Choo, D. S. Park, O. S. Seo, and E. H. Hong. 2012. The study on growth performance and carcass yield of meat-type Korean native ducks. Korean J. Poult. Sci. 39:45-52.
  14. Kranis, A., A. A. Gheyas, C. Boschiero, F. Turner, L. Yu, S. Smith, R. Talbot, A. Pirani, F. Brew, P. Kaiser, P. M. Hocking, M. Fife, N. Salmon, J. Fulton, T. M. Strom, G. Haberer, S. Weigend, R. Preisinger, M. Gholami, S. Qanbari, H. Simianer, K. A. Watson, J. A. Woolliams, and D. W. Burt. 2013. Development of a high density 600k snp genotyping array for chicken. BMC Genomics 14:59.
  15. Kraus, R. H., H. H. Kerstens, P. Van Hooft, R. P. Crooijmans, J. J. Van Der Poel, J. Elmberg, A. Vignal, Y. Huang, N. Li, H. H. Prins, and M. A. Groenen. 2011. Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics. 12: 150.
  16. Liu, K. J. and S. V. Muse. 2005. Powermarker: An integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
  17. Liu, W., Z. C. Hou, L. J. Qu, Y. H. Huang, J. F. Yao, N. Li, and N. Yang. 2008. Population structure and biodiversity of chinese indigenous duck breeds revealed by 15 microsatellite markers. Asian Australas. J. Anim. Sci. 21:314-319.
  18. Maak, S., K. Wimmers, S. Weigend, and K. Neumann. 2003. Isolation and characterization of 18 microsatellites in the peking duck (Anas platyrhynchos) and their application in other waterfowl species. Mol. Ecol. Notes 3:224-227.
  19. 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.
  20. MIFFAF (Ministry for Food, Agriculture, Forestry). 2013. Primary Statistics of Food, Agriculture, Forestry and Fisheries, Sejong, Korea.
  21. Omland, K. E. 1997. Examining two standard assumptions of ancestral reconstructions: Repeated loss of dichromatism in dabbling ducks (Anatini). Evolution 51:1636-1646.
  22. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  23. Ramey, A. M., R. L. Poulson, A. S. Gonzalez-Reiche, D. R. Perez, D. E. Stallknecht, and J. D. Brown. 2014. Genomic characterization of H14 subtype influenza a viruses in new world waterfowl and experimental infectivity in mallards (Anas platyrhynchos). Plos One 9:e95620.
  24. Ramos, A. M., R. P. M. A. Crooijmans, N. A. Affara, A. J. Amaral, A. L. Archibald, J. E. Beever, C. Bendixen, C. Churcher, R. Clark, P. Dehais, M. S. Hansen, J. Hedegaard, Z. L. Hu, H. H. Kerstens, A. S. Law, H. J. Megens, D. Milan, D. J. Nonneman, G. A. Rohrer, M. F. Rothschild, T. P. L. Smith, R. D. Schnabel, C. P. Van Tassell, J. F. Taylor, R. T. Wiedmann, L. B. Schook, and M. A. M. Groenen. 2009. Design of a high density snp genotyping assay in the pig using snps identified and characterized by next generation sequencing technology. Plos One. 4:e6524.
  25. Seo, D. W., S. Hasina, N. R. Choi, Y. S. Kim, S. Jin, K. N. Heo, S. D. Jin, and J. H. Lee. 2015. Investigation of microsatellite markers for traceability and individual discrimination of Korean native ducks. Korean J. Poult. Sci. 42:1-8.
  26. Stothard, P., J. W. Choi, U. Basu, J. M. Sumner-Thomson, Y. Meng, X. P. Liao, and S. S. Moore. 2011. Whole genome resequencing of black angus and holstein cattle for SNP and CNV discovery. BMC Genomics 12:559.
  27. Tadano, R., M. Nishibori, N. Nagasaka, and M. Tsudzuki. 2007. Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poult. Sci. 86:2301-2308.
  28. Yinhua, H., T. Jianfeng, C. Xuebo, T. Bo, H. Xiaoxiang, L. Zhaoliang, F. Jidong, L. Yankun, L. Li, and X. Ke. 2005. Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos) genome and cross-amplification in other birds. Genet. Sel. Evol. 37:455-472.

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