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http://dx.doi.org/10.7465/jkdi.2017.28.3.597

Estimation of the effective population size using single-nucleotide polymorphism (SNP) information in Korean Holstein dairy cattle  

Cho, Kwang-Hyun (National Institute of Animal Science, RDA)
Do, Kyoung-Tag (Department of Animal Biotechnology, Jeju National University)
Park, Kyung-Do (Department of Animal Biotechnology, Chonbuk National University)
Publication Information
Journal of the Korean Data and Information Science Society / v.28, no.3, 2017 , pp. 597-604 More about this Journal
Abstract
In this study, we investigated the genetic characteristics and the effective population size of domestic dairy cattle using 42,201 SNPs for 923 heads of Holstein cattle. The estimate for the average linkage disequilibrium ($r^2$) among the adjacent SNPs by chromosome was 0.22, and it was highest (0.26) in chromosome 14 and lowest (0.17) in chromosome 27. When the physical distance among SNPs was less than 25Kb, the estimate for the average $r^2$ was $0.31{\pm}0.33$ and it was markedly decreased as the physical distance increased. When the physical distance among SNPs was larger than 25Mb, the estimate for the average $r^2$ was 0.04, and it decreased by 0.27 (87.1%) compared with case of physical distance of less than 25Kb. There was a trend that the effective population size in Holstein dairy cattle decreased over generations and the estimate for the effective population size in the first 5 generations (1~5th generation) was 110 heads.
Keywords
Effective population size; Holstein; linkage disequilibrium; physical distance; single nucleotide polymorphism (SNP);
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