DOI QR코드

DOI QR Code

Discrimination of Korean Native Chicken Lines Using Fifteen Selected Microsatellite Markers

  • Seo, D.W. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Hoque, M.R. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Choi, N.R. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Sultana, H. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Park, H.B. (Department of Animal Science, Gyeongsang National University) ;
  • Heo, K.N. (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Kang, B.S. (Poultry Science Division, National Institute of Animal Science, RDA) ;
  • Lim, H.T. (Department of Animal Science, Gyeongsang National University) ;
  • Lee, S.H. (Hanwoo Experiment Station, National Institute of Animal Science, RDA) ;
  • Jo, C. (Department of Animal Science and Biotechnology, Chungnam National University) ;
  • Lee, J.H. (Department of Animal Science and Biotechnology, Chungnam National University)
  • Received : 2012.09.03
  • Accepted : 2012.10.31
  • Published : 2013.03.01

Abstract

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$) were estimated at $7.98{\times}10^{-29}$, $2.88{\times}10^{-20}$ and $1.25{\times}10^{-08}$, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.

Keywords

Discrimination;Diversity;Microsatellite;Korean Native Chicken;Traceability

Acknowledgement

Supported by : Rural Development Administration

References

  1. Almasy, L. and J. Blangero. 2009. Human QTL linkage mapping. Genetica. 136:333-340. https://doi.org/10.1007/s10709-008-9305-3
  2. 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. https://doi.org/10.1111/j.1365-2052.2008.01703.x
  3. Blott, S. C., J. L. Williams and C. S. Haley. 1999. Discriminating among cattle breeds using genetic markers. Heredity. 82:613-619. https://doi.org/10.1046/j.1365-2540.1999.00521.x
  4. Bodzsar, N., H. Eding, T. Revay, A. Hidas and S. Weigend. 2009. Genetic diversity of hungarian indigenous chicken breeds based on microsatellite markers. Anim. Genet. 40:516-523. https://doi.org/10.1111/j.1365-2052.2009.01876.x
  5. 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.
  6. Cheng, H. H. and L. B. Crittenden. 1994. Microsatellite markers for genetic-mapping in the chicken. Poult. Sci. 73:539-546. https://doi.org/10.3382/ps.0730539
  7. Dalvit, C., M. DeMarchi and M. Cassandro. 2007. Genetic traceability of livestock products: A review. Meat Sci. 77:437-449. https://doi.org/10.1016/j.meatsci.2007.05.027
  8. Ding, F. X., G. X. Zhang, J. Y. Wang, Y. Li, L. J. Zhang, Y. Wei, H. H. Wang, L. Zhang and Q. R. Hou. 2010. Genetic diversity of a Chinese native chicken breed, Bian chicken, based on twenty-nine microsatellite markers. Asian-Aust. J. Anim. Sci. 23:154-161.
  9. FAO. 2007. Status of animal genetic resources. In: The state of the world's animal genetic resources for food and agriculture (Ed. B. Rischkowsky and D. Pilling). Commission on Genetic Resources for Food and Agriculture, Rome, Italy. pp. 23-49.
  10. Hillel, J., M. A. Groenen, M. Tixier-Boichard, A. B. Korol, L. David, V. M. Kirzhner, T. Burke, A. B. Dirie, R. P. 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. https://doi.org/10.1186/1297-9686-35-6-533
  11. Hoque, M. R., K. C. Jung, B. K. Park, K. D. Choi and J. H. Lee. 2009. Genetic variability of mtDNA D-loop region in Korean native chickens. Korean J. Poult. Sci. 36:323-328. https://doi.org/10.5536/KJPS.2009.36.4.323
  12. Hoque, M. R., S. H. Lee, K. C. Jung, B. S. Kang, M. N. Park, H. K. Lim, K. D. Choi and J. H. Lee. 2011. Discrimination of Korean native chicken populations using SNPs from mtDNA and MHC polymorphisms. Asian-Aust. J. Anim. Sci. 24:1637-1643. https://doi.org/10.5713/ajas.2011.11144
  13. Jacobsson, L., H. B. Park, P. Wahlberg, S. Jiang, P. B. Siegel and L. Andersson. 2004. Assignment of fourteen microsatellite markers to the chicken linkage map. Poult. Sci. 83:1825-1831. https://doi.org/10.1093/ps/83.11.1825
  14. Kaya, M. and M. A. Yildiz. 2008. Genetic diversity among turkish native chickens, denizli and gerze, estimated by microsatellite markers. Biochem. Genet. 46:480-491. https://doi.org/10.1007/s10528-008-9164-8
  15. Kong, H. S., J. D. Oh, J. H. Lee, K. J. Jo, B. D. Sang, C. H. Choi, S. D. Kim, S. J. Lee, S. H. Yeon, G. J. Jeon and H. K. Lee. 2006. Genetic variation and relationships of Korean native chickens and foreign breeds using 15 microsatellite markers. Asian-Aust. J. Anim. Sci. 19:1546-1550. https://doi.org/10.5713/ajas.2006.1546
  16. Liu, K. and S. V. Muse. 2005. Powermarker: An integrated analysis environment for genetic marker analysis. Bioinformatics. 21:2128-2129. https://doi.org/10.1093/bioinformatics/bti282
  17. Marshall, T. C., J. Slate, L. E. Kruuk and J. M. Pemberton. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Mol. Ecol. 7:639-655. https://doi.org/10.1046/j.1365-294x.1998.00374.x
  18. Miller, S. A., D. D. Dykes and H. F. Polesky. 1988. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16:1215. https://doi.org/10.1093/nar/16.3.1215
  19. Muchadeyi, F. C., H. Eding, C. B. Wollny, E. Groeneveld, S. M. Makuza, R. Shamseldin, H. Simianer and S. Weigend. 2007. Absence of population substructuring in zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim. Genet. 38:332-339. https://doi.org/10.1111/j.1365-2052.2007.01606.x
  20. MIFAFF. 2009. Primary statistics of Food, Agriculture, Forestry and Fisheries, Korea.
  21. Mwacharo, J. M., K. Nomura, H. Hanada, H. Jianlin, O. Hanotte and T. Amano. 2007. Genetic relationships among kenyan and other east african indigenous chickens. Anim. Genet. 38:485-490. https://doi.org/10.1111/j.1365-2052.2007.01641.x
  22. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
  23. Nei, M., F. Tajima and Y. Tateno. 1983. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 19:153-170. https://doi.org/10.1007/BF02300753
  24. Pritchard, J. K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
  25. Tadano, R., M. Nishibori, Y. Imamura, M. Matsuzaki, K. Kinoshita, M. Mizutani, T. Namikawa and M. Tsudzuki. 2008. High genetic divergence in miniature breeds of japanese native chickens compared to red junglefowl, as revealed by microsatellite analysis. Anim. Genet. 39:71-78. https://doi.org/10.1111/j.1365-2052.2007.01690.x
  26. Tadano, R., M. Nishibori, N. Nagasaka and M. Tsudzuki. 2007a. Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poult. Sci. 86:2301-2308. https://doi.org/10.3382/ps.2007-00233
  27. Tadano, R., M. Sekino, M. Nishibori and M. Tsudzuki. 2007b. Microsatellite marker analysis for the genetic relationships among japanese long-tailed chicken breeds. Poult. Sci. 86:460-469. https://doi.org/10.1093/ps/86.3.460
  28. Wright, S. 1965. The interpretation of population structure by f-statistics with special regard to systems of mating. Evol. 19:395-420. https://doi.org/10.2307/2406450

Cited by

  1. Association of SNPs in ODC and PRDM16 with Body Weight Traits in Korean Native Chicken vol.40, pp.2, 2013, https://doi.org/10.5536/KJPS.2013.40.2.157
  2. FABP3 and FABP4 Genes Are the Potential Candidates for Body Weights in Korean Native Chicken vol.40, pp.2, 2013, https://doi.org/10.5536/KJPS.2013.40.2.091
  3. Analysis of Genetic Characteristics and Probability of Individual Discrimination in Korean Indigenous Chicken Brands by Microsatellite Marker vol.55, pp.3, 2013, https://doi.org/10.5187/JAST.2013.55.3.185
  4. Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers vol.27, pp.10, 2014, https://doi.org/10.5713/ajas.2014.14016
  5. Variance Component Quantitative Trait Locus Analysis for Body Weight Traits in Purebred Korean Native Chicken vol.29, pp.1, 2015, https://doi.org/10.5713/ajas.15.0193
  6. Investigation of Microsatellite Markers for Traceability and Individual Discrimination of Korean Native Ducks vol.42, pp.1, 2015, https://doi.org/10.5536/KJPS.2014.42.1.1
  7. Studies on Genetic Diversity and Phylogenetic Relationships of Korean Native Chicken using the Microsatellite Marker vol.42, pp.1, 2015, https://doi.org/10.5536/KJPS.2014.42.1.15
  8. Comparison of Production Performance and Egg Quality Characteristics of Five Strains of Korean Native Chickens vol.42, pp.4, 2015, https://doi.org/10.5536/KJPS.2015.42.4.299
  9. Discrimination of the commercial Korean native chicken population using microsatellite markers vol.57, pp.1, 2015, https://doi.org/10.1186/s40781-015-0044-6
  10. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand vol.29, pp.3, 2016, https://doi.org/10.5713/ajas.15.0270
  11. DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review vol.43, pp.2, 2016, https://doi.org/10.5536/KJPS.2016.43.2.63
  12. Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers vol.30, pp.10, 2017, https://doi.org/10.5713/ajas.16.0514
  13. The breeding history and commercial development of the Korean native chicken vol.73, pp.01, 2017, https://doi.org/10.1017/S004393391600088X
  14. Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines vol.13, pp.2, 2018, https://doi.org/10.1371/journal.pone.0192063
  15. Genetic characterization and population structure of six brown layer pure lines using microsatellite markers vol.32, pp.1, 2019, https://doi.org/10.5713/ajas.17.0870