Advanced SearchSearch Tips
Assessment of Population Structure and Genetic Diversity of 15 Chinese Indigenous Chicken Breeds Using Microsatellite Markers
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
 Title & Authors
Assessment of Population Structure and Genetic Diversity of 15 Chinese Indigenous Chicken Breeds Using Microsatellite Markers
Chen, Guohong; Bao, Wenbin; Shu, Jingting; Ji, Congliang; Wang, Minqiang; Eding, Herwin; Muchadeyi, Farai; Weigend, Steffen;
  PDF(new window)
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;
 Cited by
MS 마커를 이용한 토종닭 브랜드의 유전적 특성 및 개체 식별력 분석,서상원;조창연;김재환;최성복;김영신;김현;성환후;임현태;조재현;고응규;

Journal of Animal Science and Technology, 2013. vol.55. 3, pp.185-194 crossref(new window)
Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers,;;;;;;;;;;;

아세아태평양축산학회지, 2014. vol.27. 10, pp.1399-1405 crossref(new window)
Genetic structure of a wide-spectrum chicken gene pool, Animal Genetics, 2009, 40, 5, 686  crossref(new windwow)
Analysis of genetic structure and relationship among nine indigenous Chinese chicken populations by the Structure program, Journal of Genetics, 2009, 88, 2, 197  crossref(new windwow)
Genetic diversity in farm animals - a review, Animal Genetics, 2010, 41, 13652052, 6  crossref(new windwow)
Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker, Journal of Animal Science and Technology, 2013, 55, 3, 185  crossref(new windwow)
Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers, Asian-Australasian Journal of Animal Sciences, 2014, 27, 10, 1399  crossref(new windwow)
Global diversity and genetic contributions of chicken populations from African, Asian and European regions, Animal Genetics, 2014, 45, 6, 836  crossref(new windwow)
Assessment of genetic diversity and conservation priority of Omani local chickens using microsatellite markers, Tropical Animal Health and Production, 2014, 46, 5, 747  crossref(new windwow)
A genome-wide association study identifies novel single nucleotide polymorphisms associated with dermal shank pigmentation in chickens, Poultry Science, 2014, 93, 12, 2983  crossref(new windwow)
Genetic Diversity of Five Local Swedish Chicken Breeds Detected by Microsatellite Markers, PLOS ONE, 2015, 10, 4, e0120580  crossref(new windwow)
The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region, PLOS ONE, 2017, 12, 3, e0173192  crossref(new windwow)
Assessment of the population structure and genetic diversity of Denizli chicken subpopulations using SSR markers, Italian Journal of Animal Science, 2017, 1828-051X, 1  crossref(new windwow)
Barker, J. S. F. 1999. Conservation of livestock breeds diversity. Anim. Genet. Res. Inf. 25:33-43. crossref(new window)

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.

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. crossref(new window)

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. crossref(new window)

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.

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. crossref(new window)

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. crossref(new window)

FAO. 2004. Guidelines for development of national management of farm animal genetic resources plans. refer/library/guidelin/marker.pdf

Felsentein, J. 1995. PHYLIP (Phylogeny inference package) version 3.57c. Department of Genetics, University of Washington, Seattle, USA.

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.

Goudet, J. 2002. FSTAT version Department of ecology and evolution, University of Lausanne, LAUSANNE, Switzerland.

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. crossref(new window)

Hochberg, Y. 1988. A sharper Bonferroni procedure for multiple test of significance. Biometrika. 75:800-802. crossref(new window)

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. crossref(new window)

Li, S. Z. 1983. Compendium of material medica. People's Medical Publishing House, Beijing, China.

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.

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. crossref(new window)

Ministry of Agriculture of China. 2004. The state of animal genetics resource in China. China Agricultural Publishing House, Beijing, China

Park, S. D. E. 2001. The Excel Microsatellite Toolkit (version 3.1). Animal Genomics Laboratory, UCD, Ireland. http://animal

Pritchard, J. K., M. Stephens and P. Donnely. 2000. Inference of population structure using multilocus genotype data. Genetics. 155: 945-959.

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.

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. crossref(new window)

Raymond, M. and F. Rousset. 1995. GENEPOP (version 1.2): Population genetics software for exact test and ecumenicism. J. Hered. 86:248-249. crossref(new window)

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. crossref(new window)

Rosenberg, N. A. 2004. Distruct: a program for the graphical display of population structure. Molecular Ecology Notes 4: 17-138. crossref(new window)

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.

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. crossref(new window)

Saitou, N. and M. Nei. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.

Sambrook, J. and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual. 3rd Ed. Cold Spring Harbor Laboratory, New York, USA.

Slatkin, M. and N. H. Barton. 1989. A comparison of three indirect methods of estimating average levels of gene flow. Evol. 43:1349-1368. crossref(new window)

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. crossref(new window)

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.

Weir, B. S. and C. C. Cockerham. 1984. Estimation F-statistics for the analysis of population structure. Evol. 38:1358-1370. crossref(new window)

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. crossref(new window)

Wright, S. 1978. Evolution and the genetics of populationsvariability within and among natrual populations. 4th Ed. University of Chicago press, Chicago, IL, USA.

Zhou, H. and S. J. Lamond. 1999. Genetic characterisation of biodiversity in highly inbred chicken lines by microsatellite markers. Anim. Genet. 30:256-264. crossref(new window)