Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle

  • Lee, S.H. (Hanwoo Experiment Station, National Institute of Animal Science, RDA) ;
  • Cho, Y.M. (Research Policy Bureau, Rural Development Administration) ;
  • Lim, D. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Kim, H.C. (Hanwoo Experiment Station, National Institute of Animal Science, RDA) ;
  • Choi, B.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Park, H.S. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Kim, O.H. (Department of Animal Science, Kon-Kuk University) ;
  • Kim, S. (Research Policy Bureau, Rural Development Administration) ;
  • Kim, T.H. (Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA) ;
  • Yoon, D. (Department of Animal Science, Kyung-Pook National University) ;
  • Hong, S.K. (Hanwoo Experiment Station, National Institute of Animal Science, RDA)
  • Received : 2011.06.01
  • Accepted : 2011.09.22
  • Published : 2011.12.01


This study presents a linkage disequilibrium (LD) analysis and effective population size ($N_e$) for the entire Hanwoo Korean cattle genome, which is the first LD map and effective population size estimate ever calculated for this breed. A panel of 4,525 markers was used in the final LD analysis. The pairwise $r^2$ statistic of SNPs up to 50 Mb apart across the genome was estimated. A mean value of $r^2$ = 0.23 was observed in pairwise distances of <25 kb and dropped to 0.1 at 40 to 60 kb, which is similar to the average intermarker distance used in this study. The proportion of SNPs in useful LD ($r^2{\geq}0.25$) was 20% for the distance of 10 and 20 kb between SNPs. Analyses of past effective population size estimates based on direct estimates of recombination rates from SNP data demonstrated that a decline in effective population size to $N_e$ = 98.1 occurred up to three generations ago.


Linkage Disequilibrium (LD);Effective Population Size ($N_e$);Hanwoo


  1. Abecasis, G. R., S. S. Cherny, W. O. Cookson and L. R. Cardon. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet. 30:97-101.
  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. 10:1471-2156.
  3. Bohmanova, J., M. Sargolzaei and F. S. Schenkel. 2010. Characteristics of linkage disequilibrium in North American Holsteins. BMC Genomics 11: doi:10.1186/1471-2164-11-421
  4. Decker, J. E., J. C. Pires, G. C. Conant, S. D. Mckay, M. P. Heaton, K. Chen, A. Cooper, J. Vilkki, C. M. Seabury, A. R. Caetano, G. S. Johnson, R. A. Brennenman, O. Hanotte, L. S. Eggert, P. Wiener, J. J. Kim, K. S. Kim, T. S. Sonstegard, C. P. van Tassell, H. L. Neibergs, J. C. McEwan, R. Brauning, L. L. Coutinho, M. E. Babar G. A. Wilson, M. C. McClue, M. M. Rolf, J. W. Kim, R. D. Schnabel and J. E. Taylor. 2009. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. PNAS 106:18644-18649
  5. Du, F. X., A. C. Clutter and M. M. Lohuis. 2007. Characterizing linkage disequilibrium in pig population. Int. J. Biol. Sci. 3:166-178.
  6. Han, S. W. 1996. The breed of cattles. Sun-Jin publishing pp. 148-160.
  7. Hayes, B. J. 2008. QTL mapping, MAS and Genomic selection. Text book for Armidale summer animal breeding course pp. 6-10.
  8. Hedrick, P. 1987. Gametic disequilibrium measures: proceed with caution. Genetics 117:331-341.
  9. Khatkar, M. S., K. R. Zenger, M. Hobbs, R. J. Hawken, J. A. L. Cavanagh, W. Barris, A. E. McClintock, S. McClintock, P. C. Thomson, B. Tier, F. W. Nicholas and H. W. Raadsma. 2007. A primary assembly of a bovine haplotype block map based on a 15 k SNP panel genotyped in Holstein-Friesian cattle. Genetics 176:763-772.
  10. Kim, E. S. and B. W. Kirkpatrick. 2009. Linkage disequilibrium in the North American Holstein population. Anim. Genet. 40:279-288.
  11. Lee, C. and E. J. Pollak. 2002. Genetic antagonism between body weight and milk production in beef cattle. J. Anim. Sci 80:316-321.
  12. Lee, S. H. 2010. Genome analysis to identify QTL and genes affecting carcass traits in Hanwoo (Korean cattle). The University of New England, PhD thesis, pp. 10-20.
  13. Lewontin, R. C. 1964. The interaction of selection and linkage. I. General considerations; heterotic model. Genetics 49:49-67.
  14. Lindblad-Toh, K et al. 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438:803-819.
  15. Hill, W. G, and A. Roberson. 1968. Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38:226-231.
  16. McKay, S. D., R. D. Schnabel, B. M. Murdoch, L. K. Matukumalli, J. Aerts, W. Coppieters, D. Crews E. D. Neto, C. A. Gill, Chuan Gao, H. Mannen, P. Stothard, Z. Wang C. P. van Tassell, J. L. Williams J. F. Taylor, and S. S. Moore. 2007. Whole genome linkage disequilibrium maps in cattle. BMC Genet. 8:74. doi: 10.1186/1471-2156-8-74.
  17. Meuwissen, T. H. E., B. J. Hayes and M. E. Goddard. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819-1829.
  18. R Development Core Team: R: a language and environment for statistical computing. 2008 R Foundation for statistical computing, Vienna, Austria.
  19. Sved, J. V. 1971 Linkage disequilibrium and homozygosity of chromosome segments in finite population. Theor. Popul. Biol. 2:125-141.
  20. 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.
  21. The international HapMap Consortium 2005. A haplotype map of the human genome. Nature 437:1299-1320.
  22. 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(3):341-354.

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