Assessment of Population Structure and Genetic Diversity of 15 Chinese Indigenous Chicken Breeds Using Microsatellite Markers

  • Chen, Guohong (Animal Science and Technology College, Yangzhou University) ;
  • Bao, Wenbin (Animal Science and Technology College, Yangzhou University) ;
  • Shu, Jingting (Animal Science and Technology College, Yangzhou University) ;
  • Ji, Congliang (Guangdong Wen's Group) ;
  • Wang, Minqiang (Chemical Biology and Physics College, Yantai University) ;
  • Eding, Herwin (Institute for Animal Breeding, Federal Agricultural Research Centre) ;
  • Muchadeyi, Farai (Institute for Animal Breeding, Federal Agricultural Research Centre) ;
  • Weigend, Steffen (Institute for Animal Breeding, Federal Agricultural Research Centre)
  • Received : 2007.02.21
  • Accepted : 2007.10.12
  • Published : 2008.03.01


The genetic structure and diversity of 15 Chinese indigenous chicken breeds was investigated using 29 microsatellite markers. The total number of birds examined was 542, on average 36 birds per breed. A total of 277 alleles (mean number 9.55 alleles per locus, ranging from 2 to 25) was observed. All populations showed high levels of heterozygosity with the lowest estimate of 0.440 for the Gushi chickens, and the highest one of 0.644 observed for Wannan Three-yellow chickens. The global heterozygote deficit across all populations (FIT) amounted to 0.180 (p<0.001). About 16% of the total genetic variability originated from differences between breeds, with all loci contributing significantly to this differentiation. An unrooted consensus tree was constructed using the Neighbour-Joining method and pair-wise distances based on marker estimated kinships. Two main groups were found. The heavy-body type populations grouped together in one cluster while the light-body type populations formed the second cluster. The STRUCTURE software was used to assess genetic clustering of these chicken breeds. Similar to the phylogenetic analysis, the heavy-body type and light-body type populations separated first. Clustering analysis provided an accurate representation of the current genetic relations among the breeds. Remarkably similar breed rankings were obtained with all methods.


Chicken;Microsatellites;Genetic Differentiation;Genetic Structure


Supported by : Institute of Poultry Science, Academy of Agriculture of China


  1. Rosenberg, N. A., J. K. Pritchard, J. L. Weber, H. M. Cann, K. K. Kidd, L. A. Zhivotovsky and M. W. Feldman. 2002. Genetic structure of human populations. Sci. 298:2981-2985.
  2. Saitbekova, N., C. Gaillard, G. Obexer-Ruff and G. Dolf. 1999. Genetic diversity in Swiss goat breeds based on microsatellite analysis. Anim. Genet. 30:36-41.
  3. Saitou, N. and M. Nei. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
  4. Raymond, M. and F. Rousset. 1995. GENEPOP (version 1.2): Population genetics software for exact test and ecumenicism. J. Hered. 86:248-249.
  5. Romanov, M. N. and S. Weigend. 2001. Analysis of genetic relationships between various populations of domestic and jungle fowl using microsatellite markers. Poult. Sci. 80:1057- 1063.
  6. Rosenberg, N. A. 2004. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4: 17-138.
  7. Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual. 3rd Ed. Cold Spring Harbor Laboratory, New York, USA.
  8. Slatkin, M. and N. H. Barton. 1989. A comparison of three indirect methods of estimating average levels of gene flow. Evol. 43:1349-1368.
  9. Weigend, S., E. Vef, G. Wesch, E. Meckenstock, R. Seibold and F. Ellendorff. 1995. Conception for conserving genetic resources in poultry in Germany. Archiv fur Gefugelkunde. 59:327-334.
  10. Weir, B. S. and C. C. Cockerham. 1984. Estimation F-statistics for the analysis of population structure. Evol. 38:1358-1370.
  11. Wimmers, K., S. Ponsuksill, T. Hardge, A. Valle-Zarate, P. K. Mathur and P. Horst. 2000. Genetic distinctness of Afican, Asian and South American local chickens. Anim. Genet. 31: 159-165.
  12. Hochberg, Y. 1988. A sharper Bonferroni procedure for multiple test of significance. Biometrika. 75:800-802.
  13. Ibeagha-Awemu, E. M. and G. Erhardt. 2005. Genetic structure and differentiation of 12 African Bos indicus and Bos Taurus cattle breeds, inferred from protein and microsatellite polymorphisms. J. Anim. Breed. Genet. 122:12-20.
  14. Li, S. Z. 1983. Compendium of material medica. People's Medical Publishing House, Beijing, China.
  15. Hillel, J., A. M. M. Groenen, M. Tixier-Boichard, A. B. Korol, L. David, V. M. Kirzhner, T. Burke, A. Barre-Dirie, R. P. M. A. Crooijmans, K. Elo, M. W. Feldman, P. J. Freidlin, A. Maki- Tanila, M. Oortwijn, P. Thomson, A. Vignal, K. Wimmers and S. Weigend. 2003. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol. 35:533-557.
  16. Du, Z. Q., L. J. Qu, X. Y. Li, X. X. Hu, Y. H. Huang, N. Li and N. Yang. 2004. Genetic diversity in Tibetan Chicken. HEDITAS (Beijing). 26:167-171.
  17. Eding, H. and T. H. E. Meuwissen. 2001. Marker-based estimate of between and within population kinships for the conservation of genetic diversity. J. Anim. Breed. Genet. 118:141-159.
  18. Eding, H. and T. H. E. Meuwissen. 2003. Linear methods to estimate kinships from genetic marker data for the construction of core sets in genetic conservation schemes. J. Anim. Breed. Genet. 120:289-302.
  19. FAO. 2004. Guidelines for development of national management of farm animal genetic resources plans. refer/library/guidelin/marker.pdf
  20. Felsentein, J. 1995. PHYLIP (Phylogeny inference package) version 3.57c. Department of Genetics, University of Washington, Seattle, USA.
  21. Gao, Y. S., N. Yang, H. F. Li, K. H. Wang and H. B. Tong. 2004. Analysis of genetic diversity of preserved population of native chicken breeds by microsatellites and file foundation of markers. HEDITAS (Beijing). 26:859-864.
  22. Goudet, J. 2002. FSTAT version Department of ecology and evolution, University of Lausanne, LAUSANNE, Switzerland.
  23. Chen, G. H., X. S. Wu, D. Q. Wang, J. Qin, S. L. Wu, Q. L. Zhou, F. Xie, R. Cheng, Q. Xu, B. Liu, X. Y. Zhang and O. Olowofeso. 2004b. Cluster analysis of 12 Chinese native chicken populations using microsatellite markers. Asian-Aust. J. Anim. Sci. 17:1047-1052.
  24. Crooijmans, R. P. M. A., A. F. Groen, A. J. A. van Kampen, J. J. van der Poel and M. A. M. Groenen. 1996. Microsatellite polymorphism in commercial broiler and layer lines estimated using pooled blood samples. Poult. Sci. 75:904-909.
  25. Barker, J. S. F. 1999. Conservation of livestock breeds diversity. Anim. Genet. Res. Inf. 25:33-43.
  26. Chen, G. H., K. H. Wang, J. Y. Wang, C. Ding and N. Yang. 2004a. Poultry Genetic Resources in China. 1st edn. Shanghai Scientific and Technological Press, Shanghai, China.
  27. Liu, R. S., Q. Yu, G. C. Cheng and K. F. Liu. 1996. Studies on the origin of fowl breeds. Acta Zoologica Sinica. 42 (Suppl.):165-167.
  28. Mateus, J. C., H. Eding, M. C. T. Penedo and M. T. Rangel- Figueiredo. 2004. Contributions of Portuguese cattle breeds to genetic diversity using marker-estimated kinships. Anim. Genet. 35:305-313.
  29. Ministry of Agriculture of China. 2004. The state of animal genetics resource in China. China Agricultural Publishing House, Beijing, China
  30. Park, S. D. E. 2001. The Excel Microsatellite Toolkit (version 3.1). Animal Genomics Laboratory, UCD, Ireland. http://animal
  31. Pritchard, J. K., M. Stephens and P. Donnely. 2000. Inference of population structure using multilocus genotype data. Genetics. 155: 945-959.
  32. Qu, L. J., G. Q. Wu, X. Y. Li and N. Yang. 2004. Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers. ACTA GENETICA SINICA. 31:591-595.
  33. Qu, L. J., X. Y. Li, G. F. Xu, K. W. Chen, H. J. Yang, L. C. Zhang. G. Q. Wu, Z. C. Hou, G. Y. Xu and N. Yang. 2006. Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Sci. China C Life Sci. 49(4):332-41.
  34. Surridge, A. K., D. J. Bell, K. M. Iberhim and G. T. Hewitt. 1999. Population structure and genetic variation of European wild rabbits (Oryctolagus cuniculus) in East Angle. Heredity. 82: 479-487.
  35. Wright, S. 1978. Evolution and the genetics of populationsvariability within and among natrual populations. 4th Ed. University of Chicago press, Chicago, IL, USA.
  36. Zhou, H. and S. J. Lamond. 1999. Genetic characterisation of biodiversity in highly inbred chicken lines by microsatellite markers. Anim. Genet. 30:256-264.

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