Genetic structure of and evidence for admixture between Western and Korean native pig breeds revealed by single Nucleotide Polymorphisms

Asian-Australasian Journal of Animal Sciences

Volumn 27, Issue 9, 2014, Pages 1263-1269

  Edea, Zewdu ^a   Kim, Sang Wook ^a   Lee, Kyung Tai ^a,b   Kim, Tae Hun ^a,b   Kim, Kwan Suk ^a  

^a Chungbuk National University   (South Korea)

^b National Institute of Animal Science   (South Korea)

Author keywords

Admixture; Genetic Diversity; Korean Native Pig; Single Nucleotide Polymorphism

Indexed keywords

EID: 84907377256     PISSN: 10112367     EISSN: 19765517     Source Type: Journal    
DOI: 10.5713/ajas.2014.14096     Document Type: Article

References (27)

1. Abecasis, G. R., E. Noguchi, A. Heinzmann, J. A. Traherne, S. Bhattacharyya, N. I. Leaves, G. G. Anderson, Y. Zhang, N. J. Lench, A. Carey, L. R. Cardon, M. F. Moffatt, and W. O. C. Cookson. 2001. Extent and distribution of linkage disequilibrium in three genomic regions. Am. J. Hum. Genet. 68: 191-197.
2. Ai, H., L. Huang, and J. Ren. 2013. Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers. PLoS ONE, 8: e56001.
3. Chen, Y., C. H. Lin, and C. Sabatti. 2006. Volume measures for linkage disequilibrium. BMC Genet. 7: 54.
4. Duran, C., N. Appleby, D. Edwards, and J. Batley. 2009. Molecular genetic markers: Discovery, applications, data storage and visualization. Curr. Bioinform. 4: 16-27.
5. Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinform. Online 1: 47-50.
6. Ficetola, G. F., T. W. Garner, and F. De Bernardi. 2007. Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latastei. Mol. Ecol. 16: 1787-1797.
7. Food and Agriculture Organization of the United Nations. 2007. The state of the world's animal genetic resources for food and agriculture - in brief (Eds. D. Pilling and B. Rischkowsky). Rome.
8. Giuffra, E., J. M. Kijas, V. Amarger, O. Carlborg, J. T. Jeon, and L. Andersson. 2000. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 154: 1785-1791.
9. Hill, W. G. 1981. Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 38: 209-216.
10. Larson, G., K. Dobney, U. Albarella, M. Fang, E. Matisoo-Smith, J. Robins, S. Lowden, H. Finlayson, T. Brand, E. Willerslew, P. Rowley-Conwy, L. Andersson, and A. Cooper. 2005. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307: 1618-1621.
11. Liu, K. and S. V. Muse. 2005. PowerMarker: Integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129.
12. Kijas, J. M. and L. Andersson. 2001. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J. Mol. EVol. 52: 302-308.
13. Kim, K. S. and C. B. Choi. 2002. Genetic structure of Korean native pig using microsatellite markers. Kor. J. Genet. 24: 1-7.
14. Kim, K. I., J. H. Lee, K. Li, Y. P. Zhang, S. S. Lee, J. Gongora, and C. Moran. 2002a. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet. 33: 19-25.
15. Kim, T. H., K. S. Kim, B. H Choi, D. H. Yoon, G. W. Jang, K. T. Lee, H. Y. Chung, H. Y Lee, H. S. Park, and J. W Lee. 2005. Genetic structure of pig breeds from Korea and China using microsatellite loci analysis. J. Anim. Sci. 83: 2255-2263.
16. Kim, S. W., X. P. Li, Y. M. Lee, Y. I. Choi, B. W. Cho, B. H. Choi, T. H. Kim, J. J. Kim, and K. S. Kim. 2011. QTL scan for meat quality traits using high-density SNP chip analysis in cross between Korean native pig and Yorkshire. Asian Australas. J. Anim. Sci. 24: 1184-1191.
17. Nidup, K. and C. Moran. 2001. Genetic diversity of domestic pigs as revealed by microsatellites: A mini review. Genomics Quant. Genet. 2: 5-18.
18. Nsengimana, J., P. Baret, C. S. Haley, and P. M. Visscher. 2004. Linkage disequilibrium in the domesticated pig. Genetics 166: 1395-1404.
19. Park, B. Y., N. K. Kim, C. S. Lee, and I. H. Hwang. 2007. Effect of fiber type on postmortem proteolysis in longisimus muscle of Landrace and Korean native black pigs. Meat Sci. 77: 482-491.
20. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
21. Ramos, A. M., R. P. M. A. Crooijmans, N. A. Affara, A. J. Amaral, A. L. Archibald, J. E. Beever, C. Bendixen, C. Churcher, R. Clark, P. Dehais, M. S. Hansen, J. Hedegaard, Z. L Hu, H. H. Kerstens, A. S. Law, H.-J. Megens, D. Milan, D. J. Nonneman, G. A. Rohrer, M. F. Rothschild, T. P. L. Smith, R. D. Schnabel, C. P. Van Tassell, J. F. Taylor, R. T. Wiedmann, L. B. Schook, and M. A. M. Groene. 2009. Design of a high-density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One 4: e6524.
22. Reynolds, J., B. S. Weir, and C. C. Cockerham. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105: 767-779.
23. SNP and Variation Suite Version 7. Golden Helix Inc. www.goldenhelix.com. Accessed March April 2014.
24. Suh, Y. and J. Vijg. 2005. SNP discovery in associating genetic variation with human disease phenotypes. Mutat. Res. Fundam. Mol. Mech. Mutagen. 573: 41-53.
25. Weir, B. S. and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
26. Yang, S. L., Z. G. Wang, B. Liu, G. X. Zhang, S. H. Zhao, M. Yu, B. Fan, M. H Li, T. A. Xiong, and K. Li. 2003. Genetic variation and relationships of eighteen Chinese indigenous pig breeds. Genet. Sel. EVol. 35: 657-671.
27. Yeo, J. S., J. W. Kim, T. K. Chang, Y. A. Park, and D. H. Nam. 2000. Utilization of DNA marker-assisted selection in Korean native animals. Biotechnol. Bioprocess Eng. 5: 71-78.