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Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing Open Access


Author or creator
Choi, Jung-Woo
Liao, Xiaoping
Stothard, Paul
Chung, Won-Hyong
Jeon, Heoyn-Jeong
Miller, Stephen P.
Choi, So-Young
Lee, Jeong-Koo
Yang, Bokyoung
Lee, Kyung-Tai
Han, Kwang-Jin
Kim, Hyeong-Cheol
Jeong, Dongkee
Oh, Jae-Don
Kim, Namshin
Kim, Tae-Hun
Lee, Hak-Kyo
Lee, Sung-Jin
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Genomic Databases
Variant Genotypes
Genome Sequencing
Sequence Assembly Tools
Animal Sexual Behavior
Gene Ontologies
Genomic Libraries
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A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.
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Choi, J. W., Liao, X., Stothard, P., Chung, W. H., Jeon, H. J., Miller, S. P., Choi, S. Y., Lee, J. K., Yang, B., Lee, K. T., Han, K. J., Kim, H. C., Jeong, D., Oh, J. D., Kim, N., Kim, T. H., Lee, H. K., & Lee, S. J. (2014). Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing. PLoS ONE, 9(7), e101127 [13 pages].


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