Asian-Australasian Journal of Animal Sciences

  • 제26권12호
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  • Pages.1672-1679
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  • 2013
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  • 1011-2367(pISSN)
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  • 1976-5517(eISSN)
아세아태평양축산학회 (Asian Australasian Association of Animal Production Societies)
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Accurate Estimation of Effective Population Size in the Korean Dairy Cattle Based on Linkage Disequilibrium Corrected by Genomic Relationship Matrix

  • Shin, Dong-Hyun (Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University) ;
  • Cho, Kwang-Hyun (Division of Animal Breeding and Genetics, National Institute of Animal Science, Rural Development Administration) ;
  • Park, Kyoung-Do (Genomic Informatics Center, Hankyong National University) ;
  • Lee, Hyun-Jeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal science, Rural Development Administration) ;
  • Kim, Heebal (Department of Agricultural Biotechnology, Animal Biotechnology Major, Research Institute for Agriculture and Life Sciences, Seoul National University)
  • 투고 : 2013.06.04
  • 심사 : 2013.10.02
  • 발행 : 2013.12.01
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초록

Linkage disequilibrium between markers or genetic variants underlying interesting traits affects many genomic methodologies. In many genomic methodologies, the effective population size ($N_e$) is important to assess the genetic diversity of animal populations. In this study, dairy cattle were genotyped using the Illumina BoviveHD Genotyping BeadChips for over 777,000 SNPs located across all autosomes, mitochondria and sex chromosomes, and 70,000 autosomal SNPs were selected randomly for the final analysis. We characterized more accurate linkage disequilibrium in a sample of 96 dairy cattle producing milk in Korea. Estimated linkage disequilibrium was relatively high between closely linked markers (>0.6 at 10 kb) and decreased with increasing distance. Using formulae that related the expected linkage disequilibrium to $N_e$, and assuming a constant actual population size, $N_e$ was estimated to be approximately 122 in this population. Historical $N_e$, calculated assuming linear population growth, was suggestive of a rapid increase $N_e$ over the past 10 generations, and increased slowly thereafter. Additionally, we corrected the genomic relationship structure per chromosome in calculating $r^2$ and estimated $N_e$. The observed $N_e$ based on $r^2$ corrected by genomics relationship structure can be rationalized using current knowledge of the history of the dairy cattle breeds producing milk in Korea.

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