Asian-Australasian Journal of Animal Sciences

Asian Australasian Association of Animal Production Societies (아세아태평양축산학회)
권호 표지
DOI QR코드

DOI QR Code

Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers

  • Suh, Sangwon (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Kim, Young-Sin (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Cho, Chang-Yeon (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Byun, Mi-Jeong (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Choi, Seong-Bok (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Ko, Yeoung-Gyu (Animal Genetic Resources Station, National Institute of Animal Science, RDA) ;
  • Lee, Chang Woo (Gangwon Provincial Livestock Research Center) ;
  • Jung, Kyoung-Sub (Chungbuk Institute of Livestock and Veterinary Research) ;
  • Bae, Kyoung Hun (Jeju Special Self-Governing Province Livestock Promotion) ;
  • Kim, Jae-Hwan (Animal Genetic Resources Station, National Institute of Animal Science, RDA)
  • Received : 2014.06.12
  • Accepted : 2014.09.23
  • Published : 2014.11.01
Download PDF
⟨ Previous Next ⟩

Abstract

Four Korean native cattle (KNC) breeds-Hanwoo, Chikso, Heugu, and Jeju black-are entered in the Domestic Animal Diversity Information System of the United Nations Food and Agriculture Organization (FAO). The objective of this study was to assess the genetic diversity, phylogenetic relationships and population structure of these KNC breeds (n = 120) and exotic breeds (Holstein and Charolais, n = 56). Thirty microsatellite loci recommended by the International Society for Animal Genetics/FAO were genotyped. These genotypes were used to determine the allele frequencies, allelic richness, heterozygosity and polymorphism information content per locus and breed. Genetic diversity was lower in Heugu and Jeju black breeds. Phylogenetic analysis, Factorial Correspondence Analysis and genetic clustering grouped each breed in its own cluster, which supported the genetic uniqueness of the KNC breeds. These results will be useful for conservation and management of KNC breeds as animal genetic resources.

Keywords

References

  1. Acosta, A. C., O. Uffo, A. Sanz, R. Ronda, R. Osta, C. Rodellar, I. Martin-Burriel, and P. Zaragoza. 2013. Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci. J. Anim. Breed. Genet. 130:79-86. https://doi.org/10.1111/j.1439-0388.2012.00988.x
  2. Belkhir, K., P. Borsa, L. Chikhi, N. Raufaste, and F. Bonhomme. 2004. GENETIX ver. 4.05, Logiciel sous WindowsTM pour la Genetique des Populations. Laboratoire Genome et Population, Universite Montpellier II, Montpellier, France. http://kimura.univ-montp2.fr/genetix/ Accessed May 30, 2014.
  3. Botstein, D., R. L. White, M. Skolnick, 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.
  4. Choi, T. J., S. S. Lee, D. H. Yoon, H. S. Kang, C. D. Kim, I. H. Hwang, C. Y. Kim, X. Jin, C. G. Yang, and K. S. Seo. 2012. Determination of genetic diversity among Korean Hanwoo cattle based on physical characteristics. Asian Australas. J. Anim. Sci. 25:1205-1215. https://doi.org/10.5713/ajas.2012.12124
  5. Dadi, H., M. Tibbo, Y. Takahashi, K. Nomura, H. Hanada, and T. Amano. 2008. Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations. Anim. Genet. 39:425-431. https://doi.org/10.1111/j.1365-2052.2008.01748.x
  6. Dieringer, D. and C. Schlotterer. 2003. Microsatellite analyzer (MSA): A platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes 3:167-169. https://doi.org/10.1046/j.1471-8286.2003.00351.x
  7. Earl, D. A. and B. M. vonHoldt. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359-361. https://doi.org/10.1007/s12686-011-9548-7
  8. Egito, A. A., S. R. Paiva, Maria do Socorro M. Albuquerque, A. S. Mariante, L. D. Almeida, S. R. Castro, and D. Grattapaglia. 2007. Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil. BMC Genet. 8:83.
  9. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  10. Goudet, J. 2002. FSTAT version 2.9.3.2. department of ecology and evolution, University of Lausanne, Swizeland.
  11. Groeneveld, L. F., J. A. Lenstra, H. Eding, M. A. Toro, B. Scherf, D. Pilling, R. Negrini, E. K. Finlay, H. Jianlin, E. Groeneveld, and S. Weigend. 2010. Genetic diversity in farm animals-A review. Anim. Genet. 41: 6-31. https://doi.org/10.1111/j.1365-2052.2010.02038.x
  12. Hoffmann, I., P. A. Marsan, J. S. F. Barker, E. G. Cothran, O. Hanotte, J. A. Lenstra, D. Milan, S. Weigend, and H. Simianer. 2004. New MoDAD marker sets to be used in diversity studies for the major farm animal species: recommendations of a joint ISAG/FAO working group. Proceedings of the 29th International Conference on Animal Genetics. Toyko, Japan. pp. 11-16.
  13. IUCN (International Union for Conservation of Nature). 2000. The IUCN Red List Categories and Criteria Version 3.1. Gland, Switzerland.
  14. Jakobsson, M. and N. A. Rosenberg. 2007. CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801-1806. https://doi.org/10.1093/bioinformatics/btm233
  15. Kalinowski, S. T., M. L. Taper, and T. C. Marshall. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16:1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x
  16. Kim, J. B. and C. Lee. 2000. Historical look at the genetic improvement in Korean cattle - Review -. Asian Australas. J. Anim. Sci. 13:1467-1481. https://doi.org/10.5713/ajas.2000.1467
  17. Kim, J. H., M. J. Byun, M. J. Kim, S. W. Suh, Y. G. Ko, C. W. Lee, K. S. Jung, E. S. Kim, D. J. Yu, W. Y. Kim, and S. B. Choi. 2013. mtDNA diversity and phylogenetic state of Korean cattle breed, Chikso. Asian Australas. J. Anim. Sci. 26:163-170. https://doi.org/10.5713/ajas.2012.12499
  18. Kim, K. S., J. S. Yeo, and C. B. Choi. 2002. Genetic diversity of north-east Asian cattle based on microsatellite data. Anim. Genet. 33:201-204. https://doi.org/10.1046/j.1365-2052.2002.00848.x
  19. Leroy, G., E. Verrier, J. C. Meriaux, and X. Rognon. 2009. Genetic diversity of dog breeds: between-breed diversity, breed assignation and conservation approaches. Anim. Genet. 40:333-343. https://doi.org/10.1111/j.1365-2052.2008.01843.x
  20. MAF (Ministry of Agriculture and Forestry, Republic of Korea). 2004. National Report on the State of Animal Genetic Resources. Seoul, Rep of Korea. p. 20-21. ftp://ftp.fao.org/docrep/fao/010/a1250e/annexes/CountryRepor ts/KoreanRepublic.pdf/ Accessed May 30, 2014.
  21. Martin-Burriel, I., C. Rodellar, J. A. Lenstra, A. Sanz, C. Cons, R. Osta, M. Reta, S. D. Arguello, S. Sanz, and P. Zaragoza. 2007. Genetic diversity and relationships of endangered Spanish cattle breeds. J. Hered. 98:687-691. https://doi.org/10.1093/jhered/esm096
  22. Maudet, C., G. Luikart, and P. Taberlet. 2002. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J. Anim. Sci. 80:942-950.
  23. Na, G. J. 2008. Characteristics of Korean native cattle (in Korean). Korea Animal Improvement Association Bulletin 1:42-52.
  24. 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
  25. Padilla, J. A ., E. Sansinforiano, J. C. Parejo, A. Rabasco, and M. Martinez-Trancon. 2009. Inference of admixture in the endangered Blanca Cacerena bovine breed by microsatellite analyses. Livest. Sci. 122:314-322. https://doi.org/10.1016/j.livsci.2008.09.016
  26. Pham, L. D., D. N. Do, N. T. Binh, L. Q. Nam, N. V. Ba, T. T. T. Thuy, T. X. Hoan, V. C. Cuong, and H. N. Kadarmideen. 2013. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites. Livest. Sci. 155:17-22. https://doi.org/10.1016/j.livsci.2013.04.006
  27. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  28. Rosenberg, N. A. 2004. DISTRUCT: A program for the graphical display of population structure. Mol. Ecol. Notes 4:137-138.
  29. Wiener, P., D. Burton, and J. L. Williams. 2004. Breed relationships and definition in British cattle: A genetic analysis. Heredity 93:597-602. https://doi.org/10.1038/sj.hdy.6800566
  30. Yoon, D. H., E. W. Park, S. H. Lee, H. K. Lee, S. J. Oh, I. C. Cheong, and K. C. Hong. 2005. Assessment of genetic diversity and relationships between Korean cattle and other cattle breeds by microsatellite loci. J. Anim. Sci. Technol. (Kor.) 47:341-354. https://doi.org/10.5187/JAST.2005.47.3.341
  31. Zhang, G. X., Z. G. Wang, W. S. Chen, C. X. Wu, X. Han, H. Chang, L. S. Zan, R. L. Li, J. H. Wang, W. T. Song, G. F. Xu, H. J. Yang, and Y. F. Luo. 2007. Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers. Anim. Genet. 38:550-559. https://doi.org/10.1111/j.1365-2052.2007.01644.x

Cited by

  1. Towards breed formation by island model divergence in Korean cattle vol.15, pp.1, 2015, https://doi.org/10.1186/s12862-015-0563-2
  2. Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers vol.29, pp.2, 2015, https://doi.org/10.5713/ajas.15.0155
  3. Haplogroup Classification of Korean Cattle Breeds Based on Sequence Variations of mtDNA Control Region vol.29, pp.5, 2016, https://doi.org/10.5713/ajas.15.0692
  4. Genome-wide linkage disequilibrium and past effective population size in three Korean cattle breeds vol.48, pp.1, 2016, https://doi.org/10.1111/age.12488
  5. Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry vol.3, pp.None, 2014, https://doi.org/10.7717/peerj.1318
  6. Signatures of positive selection underlying beef production traits in Korean cattle breeds vol.62, pp.3, 2014, https://doi.org/10.5187/jast.2020.62.3.293
  7. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle vol.10, pp.9, 2014, https://doi.org/10.3390/ani10091493
  8. Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes vol.10, pp.9, 2014, https://doi.org/10.3390/ani10091584