Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity

Lee, Kyung-Tai, Chung, Won-Hyong, Lee, Sung-Yeoun, Choi, Jung-Woo, Kim, Jiwoong, Lim, Dajeong, Lee, Seunghwan, Jang, Gul-Won, Kim, Bumsoo, Choy, Yun Ho, Liao, Xiaoping, Stothard, Paul, Moore, Stephen S., Lee, Sang-Heon, Ahn, Sungmin, Kim, Namshin and Kim, Tae-Hun (2013) Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity. BMC Genomics, 14 1: 519.1-519.14. doi:10.1186/1471-2164-14-519


Author Lee, Kyung-Tai
Chung, Won-Hyong
Lee, Sung-Yeoun
Choi, Jung-Woo
Kim, Jiwoong
Lim, Dajeong
Lee, Seunghwan
Jang, Gul-Won
Kim, Bumsoo
Choy, Yun Ho
Liao, Xiaoping
Stothard, Paul
Moore, Stephen S.
Lee, Sang-Heon
Ahn, Sungmin
Kim, Namshin
Kim, Tae-Hun
Title Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2013-07
Sub-type Article (original research)
DOI 10.1186/1471-2164-14-519
Open Access Status DOI
Volume 14
Issue 1
Start page 519.1
End page 519.14
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2014
Language eng
Formatted abstract
Background: Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo.

Results: The Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. 'Regulation of actin filament length' was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus.

Conclusions: We identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.
Keyword Hanwoo
Resequencing
NS/SS/I
ROH
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2014 Collection
 
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