Abstract
The genetic structure and diversity of 10 Chinese indigenous egg-type duck breeds were investigated using 29 microsatellite markers. The total number of animals examined were 569, on average 57 animals per breed were selected. The microsatellite marker set analysed provided 177 alleles (mean 6.1 alleles per locus, ranging from 3 to 10). All populations showed high levels of heterozygosity with the lowest estimate of 0.539 for the Jinding ducks, and the highest 0.609 observed for Jingjiang partridge ducks. The global heterozygote deficit across all populations (F IT) amounted to −0.363. About 10% of the total genetic variability originated from differences among breeds, with all loci contributing significantly. An unrooted consensus tree was constructed using the NeighborNet tree based on the Reynold’s genetic distance. The structure software was used to assess genetic clustering of these egg-type duck breeds. Clustering analysis provided an accurate representation of the current genetic relations among the breeds. An integrated analysis was undertaken to obtain information on the population dynamics in Chinese indigenous egg-type duck breeds, and to better determine the conservation priorities.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Barker J. S. F. 1994 A global protocol for determining genetic distance among domestic livestock breeds. In Proceedings of 5th world congress on genetic application of livestock production. Guelph, Canada. 21, 501–508.
Barker J. S. F. 1999 Conservation of livestock breeds diversity. Anim. Genet. Res. Inf. 25, 33–43.
Botstein D., White R. L., Skolnick M. and Davis R. W. 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32, 314–331.
Cheng Y. S., Rouvier R., Hu Y. H., Tai J. J. L. and Tai C. 2003 Breeding and genetics of waterfowl. World’s Poult. Sci. J. 59, 511–521.
Chine Agriculture Press 2004 Country report for the preparation of SoW-AnGR Report on domestic animal genetic resources in China. China Agriculture Press, Beijing, P. R. China.
Denk G. A., Gautschi B., Carter K. and Kempenaers B. 2004 Seven polymorphic microsatellite loci for paternity assessment in the mallard (Anas platyrhynchos). Mol. Ecol. 4, 506–508.
Eding H. 2001 Conservation of genetic diversity: assessing genetic variation using marker estimated kinships. Ph.D. thesis, Animal Breeding and Genetics Group, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands.
Falconer D. S. and Mackay T. F. C. 1996 Introduction to quantitative genetics. Longman House, Harlow, UK.
FAO 2004 Guidelines for development of national management of farm animal genetic resources plans. http://dad.fao.org/en/refer/library/guidelin/marker.pdf.
Goudet J. 2002 FSTAT version 2.9.3.2. Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
Hillel J., Groenen A.M. M., Tixier-Boichard A. B., Korol L., David V. M. and Kirzhner T. 2003 Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol. 35, 533–557.
Hochberg Y. 1988 A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75, 800–802.
Hudson D. H. and Bryant D. 2006 Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254–267.
Ibeagha-Awemu E. M. and Erhardt G. 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.
Jakobsson M. and Rosenberg N. A. 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806.
Li H. F., Li B. C., Chen K.W., Yang N., Ma Y. H., Tang Q. P. and Tu Y. J. 2006 Study on molecular genetic diversity of native duck breeds in China. Acta Vet. Zootech. Sin. 37, 1107–1113.
Liu K., Goodman M., Muse S., Smith J. S., Buckler E. and Doebley J. 2003 Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165, 2117–2128.
Maak S., Neumann K. and von Lengerken G. 2000 First seven microsatellites developed for the Peking duck (Anas platyrhynchos). Anim. Genet. 31, 233.
Mckay J. K., Bisshop J. G., Lin J., Richards J. H. and Sala A. 2001 Local adaptation across a climatic gradient despite small effective population size in the rare sapphire rockcress. Proc. R. Soc. Lond. B 268, 1715–1721.
Park S. D. E. 2001 The Excel microsatellite toolkit, version 3.1. Animal Genomics Laboratory, University College Dublin, Ireland. (http://animalgenomics.ucd.ie/sdepark/ms-toolkit).
Paulus B. K. and Tiedemann R. 2003 Ten polymorphic autosomal microsatellite loci for the Eider duck Somateria mollissima and their cross-species applicability among waterfowl species (Anatidae). Mol. Ecol. 3, 250–252.
Pritchard J. K., Stephens M. and Donnely P. 2000 Inference of population structure using multilocus genotype data. Genetics 155, 945–959.
Qu L. J., Li X. Y., Xu G. F., Chen K. W., Yang H. J., Zhang L. C. et al. 2006 Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Sci. Chin. C Life Sci. 49, 332–341.
Raymond M. and Rousset F. 1995 GENEPOP (version 1.2): population genetics software for exact test and ecumenicism. J. Hered. 86, 248–249.
Reynolds J., Weir B. S. and Cockerham C. C. 1983 Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105, 767–779.
Rosenberg N. A. 2007 Distruct: a program for the graphical display of population structure. (http://rosenberglab.bioinformatics.med.umich.edu/distruct.html).
Rosenberg N. A., Burke T., Elo K., Feldman M. W., Freidlin P. J., Groenen M. A. M. et al. 2001 Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159, 699–713.
Rosenberg N. A., Pritchard J. K., Weber J. L., Cann H. M., Kidd K. K., Zhivotovsky L. A. and Feldman M. W. 2002 Genetic structure of human populations. Science 298, 2981–2985.
Ruane J. 1999 A critical review of the value of genetic distances studies in conservation of animal genetic resources. J. Anim. Breed. Genet. 116, 317–323.
Sambrook J. and Russell D. W. 2001 Molecular cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory, New York, USA.
Slatkin M. and Barton N. H. 1989 A comparison of three indirect methods of estimating average levels of gene flow. Evolution 43, 1349–1368.
Su Y., Long R. J., Chen G. H., Wu X. S., Xie K. Z. and Wan J. H. 2007 Genetic analysis of six endangered local duck populations in China based on microsatellite markers. J. Genet. Genomics 34, 1010–1018.
Tang Q. P., Li H. F., Tu Y. J. and Chen K. W. 2007 Analysis of genetic diversity of the domestic concern duck breeds in China. Journal of Northwest A & F University (Nat Sci Ed). 35, 47–52.
Weigend S., Vef E., Wesch G., Meckenstock E., Seibold R. and Ellendorff F. 1995 Conception for conserving genetic resources in poultry in Germany. Arch. Geflügelkunde 59, 327–334.
Weir B. S. and Cockerham C. C. 1984 Estimation of F-statistics for the analysis of population structure. Evolution 38, 1358–1370.
Williams L. C., Homan H. J., Johnston J. J. and Linz G. M. 2004 Microsatellite variation in red-winged blackbirds (Agelaius phoenixceus). Biochem. Genet. 42, 35–41.
Wright S. 1978 Evolution and the genetics of populations, vol. 4. Variability within and among natural populations. University of Chicago Press, Chicago, USA.
Xiao T. F., Ke L. Y., Zhang L. and Jiang X. B. 2009 Genetic diversity of duck breeds: a study with microsatellite markers. Chin. J. Appl. Ecol. 20, 190–196.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Li, HF., Song, WT., Shu, JT. et al. Genetic diversity and population structure of 10 Chinese indigenous egg-type duck breeds assessed by microsatellite polymorphism. J Genet 89, 65–72 (2010). https://doi.org/10.1007/s12041-010-0012-3
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12041-010-0012-3