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Estimation of the effective population size using single-nucleotide polymorphism (SNP) information in Korean Holstein dairy cattle
Journal of the Korean Data & Information Science Society 2017;28:597-604
Published online May 31, 2017
© 2017 Korean Data & Information Science Society.

Kwang-Hyun Cho1 · Kyoung-Tag Do2 · Kyung-Do Park3

1National Institute of Animal Science, RDA
2Department of Animal Biotechnology, Jeju National University
3Department of Animal Biotechnology, Chonbuk National University
Correspondence to: Kyung-Do Park
Research professor, Department of Animal Biotechnology, Chonbuk National University, Jeonju 54896, Korea. E-mail: doobalo@jbnu.ac.kr
Received March 2, 2017; Revised May 12, 2017; Accepted May 18, 2017.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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 (r2) 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 r2 was 0.31±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 r2 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).