Accurate estimation of effective population size in the Korean dairy cattle based on linkage disequilibrium corrected by genomic relationship matrix

Asian-Australasian Journal of Animal Sciences

Volumn 26, Issue 12, 2013, Pages 1672-1679

  Shin, Dong Hyun ^a   Cho, Kwang Hyun ^b   Park, Kyoung Do ^c   Lee, Hyun Jeong ^b   Kim, Heebal ^a  

^a Seoul National University   (South Korea)

^b National Institute of Animal Science   (South Korea)

^c Hankyong National University   (South Korea)

Author keywords

Dairy cattle; Effective population size; Linkage disequilibrium; SNP

Indexed keywords

EID: 84887891441     PISSN: 10112367     EISSN: 19765517     Source Type: Journal    
DOI: 10.5713/ajas.2013.13320     Document Type: Article

References (34)

1. Ardlie, K. G., L. Kruglyak, and M. Seielstad. 2002. Patterns of linkage disequilibrium in the human genome. Nat. Rev. Genet. 3:299-309.
2. Arias, J. A., M. Keehan, P. Fisher, W. Coppieters, and R. Spelman 2009. A high density linkage map of the bovine genome. BMC Genet. 10:18.
3. Calus, M., A. de Roos, and R. Veerkamp. 2008. Accuracy of genomic selection using different methods to define haplotypes. Genetics 178:553-561.
4. Corbin, L., S. Bishop, J. Swinburne, M. Vaudin, S. Blott, and J. Woolliams. 2010. The impact of method on the estimated effective population size of a Thoroughbred population using genotype data. Proceedings of the 9th World Congress on Genetics Applied to Livestock Production.
5. Corbin, L., S. Blott, J. Swinburne, M. Vaudin, S. Bishop, and J. Woolliams. 2010. Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Anim. Genet. 41:8-15.
6. Daetwyler, H. D., R. Pong-Wong, B. Villanueva, and J. A. Woolliams. 2010. The impact of genetic architecture on genome-wide evaluation methods. Genetics 185:1021-1031.
7. De Roos, A., B. J. Hayes, R. Spelman, and M. E. Goddard. 2008. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 179:1503-1512.
8. DerSimonian, R. and N. Laird. 1986. Meta-analysis in clinical trials. Control. Clin. Trials 7:177-188.
9. Du, F.-X., A. C. Clutter, and M. M. Lohuis. 2007. Characterizing linkage disequilibrium in pig populations. Int. J. Biol. Sci. 3: 166-178.
10. Falconer, D. S., T. F. Mackay, and R. Frankham. 1996. Introduction to Quantitative Genetics (4th edn). Trends in Genetics 12:280.
11. Flury, C., M. Tapio, T. Sonstegard, C. Drögemüller, T. Leeb, H. Simianer, O. Hanotte, and S. Rieder. 2010. Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. J. Anim. Breed. Genet. 127:339-347.
12. Goddard, K. A., P. J. Hopkins, J. M. Hall, and J. S. Witte. 2000. Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations. Am. J. Hum. Genet. 66:216-234.
13. Hayes, B., P. Bowman, A. Chamberlain, and M. Goddard. 2009. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92:433-443.
14. Hayes, B. and M. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
15. Hayes, B. J., P. M. Visscher, H. C. McPartlan, and M. E. Goddard. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 13:635-643.
16. Hill, W. and A. Robertson. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38:226-231.
17. Huang, W., B. Kirkpatrick, G. Rosa, and H. Khatib. 2010. A genome-wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle. Anim. Genet. 41:570-578.
18. Jiang, L., J. Liu, D. Sun, P. Ma, X. Ding, Y. Yu, and Q. Zhang. 2010. Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One 5(10):e13661.
19. Khatkar, M. S., F. W. Nicholas, A. R. Collins, K. R. Zenger, J. A. Cavanagh, W. Barris, R. D. Schnabel, J. F. Taylor, and H. W. Raadsma. 2008. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9:187.
20. Mangin, B., A. Siberchicot, S. Nicolas, A. Doligez, P. This, and C. Cierco-Ayrolles. 2012. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity 108:285-291.
21. Muir, W., G. Wong, Y. Zhang, J. Wang, M. Groenen, R. Crooijmans, H.-J. Megens, H. Zhang, J. McKay, and S. McLeod. 2008. Review of the initial validation and characterization of a 3K chicken SNP array. World's Poult. Sci. J. 64:219-226.
22. Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira, D. Bender, J. Maller, P. Sklar, P. I. De Bakker, and M. J. Daly. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81: 559-575.
23. Qanbari, S., E. Pimentel, J. Tetens, G. Thaller, P. Lichtner, A. Sharifi, and H. Simianer. 2010. The pattern of linkage disequilibrium in German Holstein cattle. Anim. Genet. 41: 346-356.
24. Sahana, G., B. Guldbrandtsen, C. Bendixen, and M. Lund. 2010. Genome-wide association mapping for female fertility traits in Danish and Swedish Holstein cattle. Anim. Genet. 41:579-588.
25. Schaeffer, L. 2006. Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 123:218-223.
26. Shifman, S., J. Kuypers, M. Kokoris, B. Yakir, and A. Darvasi. 2003. Linkage disequilibrium patterns of the human genome across populations. Hum. Mol. Genet. 12:771-776.
27. Sved, J. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2:125-141.
28. Tenesa, A., P. Navarro, B. J. Hayes, D. L. Duffy, G. M. Clarke, M. E. Goddard, and P. M. Visscher. 2007. Recent human effective population size estimated from linkage disequilibrium. Genome Res. 17:520-526.
29. Thevenon, S., G.-K. Dayo, S. Sylla, I. Sidibe, D. Berthier, H. Legros, D. Boichard, A. Eggen, and M. Gautier. 2007. The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Anim. Ggenet. 38:277-286.
30. Toosi, A., R. Fernando, and J. Dekkers. 2010. Genomic selection in admixed and crossbred populations. J. Anim. Sci. 88:32-46.
31. Villa-Angulo, R., L. K. Matukumalli, C. A. Gill, J. Choi, C. P. Van Tassell, and J. J. Grefenstette. 2009. High-resolution haplotype block structure in the cattle genome. BMC Genet. 10:19.
32. Wang, J. 2005. Estimation of effective population sizes from data on genetic markers. Phil. Trans. R. Soc. B: Biol. Sci. 360:1395-1409.
33. Yu, J., G. Pressoir, W. H. Briggs, I. V. Bi, M. Yamasaki, J. F. Doebley, M. D. McMullen, B. S. Gaut, D. M. Nielsen, and J. B. Holland. 2005. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38:203-208.
34. Zhao, H., D. Nettleton, M. Soller, and J. Dekkers. 2005. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genet. Res. 86:77-87.