Whole genome resequencing of Heugu (Korean black cattle) for the genome-wide SNP discovery

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dc.contributor.authorJ W Choi-
dc.contributor.authorWon Hyong Jung-
dc.contributor.authorK T Lee-
dc.contributor.authorJ W Choi-
dc.contributor.authorK S Jung-
dc.contributor.authorY Cho-
dc.contributor.authorNamshin Kim-
dc.contributor.authorT H Kim-
dc.date.accessioned2017-04-19T09:49:34Z-
dc.date.available2017-04-19T09:49:34Z-
dc.date.issued2013-
dc.identifier.issn12258563-
dc.identifier.uri10.5851/kosfa.2013.33.6.715ko
dc.identifier.urihttps://oak.kribb.re.kr/handle/201005/11761-
dc.description.abstractHeugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.-
dc.publisherSouth Korea-
dc.titleWhole genome resequencing of Heugu (Korean black cattle) for the genome-wide SNP discovery-
dc.title.alternativeWhole genome resequencing of Heugu (Korean black cattle) for the genome-wide SNP discovery-
dc.typeArticle-
dc.citation.titleKorean Journal for Food Science of Animal Resources-
dc.citation.number6-
dc.citation.endPage722-
dc.citation.startPage715-
dc.citation.volume33-
dc.contributor.affiliatedAuthorNamshin Kim-
dc.contributor.alternativeName최정우-
dc.contributor.alternativeName정원형-
dc.contributor.alternativeName이경태-
dc.contributor.alternativeName최재원-
dc.contributor.alternativeName정경섭-
dc.contributor.alternativeName조용민-
dc.contributor.alternativeName김남신-
dc.contributor.alternativeName김태훈-
dc.identifier.bibliographicCitationKorean Journal for Food Science of Animal Resources, vol. 33, no. 6, pp. 715-722-
dc.identifier.doi10.5851/kosfa.2013.33.6.715-
dc.subject.keywordHeugu-
dc.subject.keywordKorean Black Cattle-
dc.subject.keywordSingle nucleotide polymorphisms-
dc.subject.keywordWhole genome resequencing-
dc.subject.localHeugu-
dc.subject.localKorean Black Cattle-
dc.subject.localSingle nucleotide polymorphisms-
dc.subject.localSingle nucleotide polymorphism (SNP)-
dc.subject.localWhole genome resequencing-
dc.description.journalClassN-
Appears in Collections:
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
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