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Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle

  • Lee, S.H. ;
  • Cho, Y.M. ;
  • Lim, D. ;
  • Kim, H.C. ;
  • Choi, B.H. ;
  • Park, H.S. ;
  • Kim, O.H. ;
  • Kim, S. ;
  • Kim, T.H. ;
  • Yoon, D. ;
  • Hong, S.K.
  • Received : 2011.06.01
  • Accepted : 2011.09.22
  • Published : 2011.12.01

Abstract

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.

Keywords

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

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