Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle

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 inter-marker distance used in this study. The proportion of SNPs in useful LD (r(2)>= 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.