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Open Access Research article

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

Kyung-Tai Lee1, Won-Hyong Chung2, Sung-Yeoun Lee3, Jung-Woo Choi4, Jiwoong Kim2, Dajeong Lim1, Seunghwan Lee5, Gul-Won Jang1, Bumsoo Kim1, Yun Ho Choy6, Xiaoping Liao4, Paul Stothard4, Stephen S Moore47, Sang-Heon Lee28, Sungmin Ahn3*, Namshin Kim28* and Tae-Hun Kim1*

Author Affiliations

1 Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Republic of Korea

2 Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea

3 Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science, Incheon, Korea

4 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada

5 Hanwoo Experiment Station, National Institute of Animal Science, Rural Development Administration, Gangwon-do 323-950, Korea

6 Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 331-801, Korea

7 Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Queensland, Australia

8 Department of Bioinformatics, University of Science and Technology, Daejeon 305-806, Korea

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BMC Genomics 2013, 14:519  doi:10.1186/1471-2164-14-519

Published: 30 July 2013

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.

Keywords:
Hanwoo; Resequencing; NS/SS/I; ROH