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PLoS One. 2014 Jul 3;9(7):e101127. doi: 10.1371/journal.pone.0101127. eCollection 2014.

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

Author information

1
Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph, Guelph, Ontario, Canada; Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
2
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada.
3
Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
4
Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration, Suwon, Republic of Korea.
5
Centre for Genetic Improvement of Livestock, Animal & Poultry Science, University of Guelph, Guelph, Ontario, Canada.
6
College of Animal Life Sciences, Kangwon National University, Chuncheon, Republic of Korea.
7
Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea.
8
Dairy Cattle Improvement Center, National Agricultural Cooperative Federation, Goyang-Si, Republic of Korea.
9
Hanwoo Experiment Station, National Institute of Animal Science, Rural Development Administration, Gangwon-do, Republic of Korea.
10
Department of Biotechnology, Jeju National University, Jeju, Republic of Korea.
11
Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.

Abstract

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.

PMID:
24992012
PMCID:
PMC4081042
DOI:
10.1371/journal.pone.0101127
[Indexed for MEDLINE]
Free PMC Article

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