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http://dx.doi.org/10.5713/ajas.2011.11165

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)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.24, no.12, 2011 , pp. 1660-1665 More about this Journal
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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