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Animal Breeding and Genetics
Asian-Australasian Journal of Animal Sciences 2011;24(12): 1660-1665.
DOI: https://doi.org/10.5713/ajas.2011.11165    Published online October 24, 2011.
Linkage Disequilibrium and Effective Population Size in Hanwoo Korean Cattle
S. H. Lee, Y. M. Cho, D. Lim, H. C. Kim, B. H. Choi, H. S. Park, O. H. Kim, S. Kim, T. H. Kim, D. Yoon, S. K. Hong
This study presents a linkage disequilibrium (LD) analysis and effective population size (Ne) 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 r2 statistic of SNPs up to 50 Mb apart across the genome was estimated. A mean value of r2 = 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 (r2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 Ne = 98.1 occurred up to three generations ago.
Keywords: Linkage Disequilibrium (LD); Effective Population Size (Ne); Hanwoo

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