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

Lee KT, Chung WH, Lee SY, Choi JW, Kim J, Lim D, Lee S, Jang GW, Kim B, Choy YH, Liao X, Stothard P, Moore SS, Lee SH, Ahn S, Kim N, Kim TH - BMC Genomics (2013)

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

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Integrated ROH and QTL maps of Bos taurus chromosomes. NGS ROHs (ROH defined by the SNP derived from NGS) are positioned onto a chromosome image. The left side of a chromosome shows Chip ROH (ROH defined by the SNP derived from the SNP chip) information. The line chart at the left of a chromosome indicates the Hanwoo homozygosity ratio defined by the SNP chip; ratios from 0.5 to 0.8 are shaded in yellow and ratios >0.8 are shaded in green. The bars at the left of the line chart indicate the Chip ROH. The right side of a chromosome shows QTL and trait-associated genes. The bars at the right of a chromosome indicate the genomic positions of meat and milk-related QTLs. At the right of the QTL bars, five types of trait-associated genes point to their genomic locations.
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Figure 2: Integrated ROH and QTL maps of Bos taurus chromosomes. NGS ROHs (ROH defined by the SNP derived from NGS) are positioned onto a chromosome image. The left side of a chromosome shows Chip ROH (ROH defined by the SNP derived from the SNP chip) information. The line chart at the left of a chromosome indicates the Hanwoo homozygosity ratio defined by the SNP chip; ratios from 0.5 to 0.8 are shaded in yellow and ratios >0.8 are shaded in green. The bars at the left of the line chart indicate the Chip ROH. The right side of a chromosome shows QTL and trait-associated genes. The bars at the right of a chromosome indicate the genomic positions of meat and milk-related QTLs. At the right of the QTL bars, five types of trait-associated genes point to their genomic locations.

Mentions: Our criteria were as follows: the ROH detection window was 400 kb and 20% of heterozygous SNPs were allowed for Hanwoo, Black Angus, and Holstein (Figure 2). We defined 16, 78, and 51 ROHs in Hanwoo, Black Angus, and Holstein, respectively (Table 2 and Additional file 8). Angus and Holstein were bred for meat and milk production, respectively. In contrast, Hanwoo was raised as a draft animal until the 1970s. Since 1979, Hanwoo has been bred as beef cattle according to the Hanwoo genetic improvement national program organized by the government. Here, we suggest that the total lengths of ROHs in Holstein and Black Angus are longer than those of Hanwoo because Holstein and Black Angus have been artificially selected for a longer period of time. Overall, the dispersing pattern of ROHs in chromosomes was variable and also differed in the overlapping pattern of ROHs between breeds; we found two overlapping regions between Hanwoo and Black Angus, three overlapping regions between Hanwoo and Holstein, and 14 overlapping regions between Black Angus and Holstein (Additional file 8). These patterns would result from different origins and breeding strategies among the three breeds because Black Angus and Holstein originated in Aberdeen, Scotland and the Netherlands, respectively, and have been bred as beef and dairy cattle, respectively, while Hanwoo was bred independently as beef cattle in the Korean peninsula since 1979.


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

Lee KT, Chung WH, Lee SY, Choi JW, Kim J, Lim D, Lee S, Jang GW, Kim B, Choy YH, Liao X, Stothard P, Moore SS, Lee SH, Ahn S, Kim N, Kim TH - BMC Genomics (2013)

Integrated ROH and QTL maps of Bos taurus chromosomes. NGS ROHs (ROH defined by the SNP derived from NGS) are positioned onto a chromosome image. The left side of a chromosome shows Chip ROH (ROH defined by the SNP derived from the SNP chip) information. The line chart at the left of a chromosome indicates the Hanwoo homozygosity ratio defined by the SNP chip; ratios from 0.5 to 0.8 are shaded in yellow and ratios >0.8 are shaded in green. The bars at the left of the line chart indicate the Chip ROH. The right side of a chromosome shows QTL and trait-associated genes. The bars at the right of a chromosome indicate the genomic positions of meat and milk-related QTLs. At the right of the QTL bars, five types of trait-associated genes point to their genomic locations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750754&req=5

Figure 2: Integrated ROH and QTL maps of Bos taurus chromosomes. NGS ROHs (ROH defined by the SNP derived from NGS) are positioned onto a chromosome image. The left side of a chromosome shows Chip ROH (ROH defined by the SNP derived from the SNP chip) information. The line chart at the left of a chromosome indicates the Hanwoo homozygosity ratio defined by the SNP chip; ratios from 0.5 to 0.8 are shaded in yellow and ratios >0.8 are shaded in green. The bars at the left of the line chart indicate the Chip ROH. The right side of a chromosome shows QTL and trait-associated genes. The bars at the right of a chromosome indicate the genomic positions of meat and milk-related QTLs. At the right of the QTL bars, five types of trait-associated genes point to their genomic locations.
Mentions: Our criteria were as follows: the ROH detection window was 400 kb and 20% of heterozygous SNPs were allowed for Hanwoo, Black Angus, and Holstein (Figure 2). We defined 16, 78, and 51 ROHs in Hanwoo, Black Angus, and Holstein, respectively (Table 2 and Additional file 8). Angus and Holstein were bred for meat and milk production, respectively. In contrast, Hanwoo was raised as a draft animal until the 1970s. Since 1979, Hanwoo has been bred as beef cattle according to the Hanwoo genetic improvement national program organized by the government. Here, we suggest that the total lengths of ROHs in Holstein and Black Angus are longer than those of Hanwoo because Holstein and Black Angus have been artificially selected for a longer period of time. Overall, the dispersing pattern of ROHs in chromosomes was variable and also differed in the overlapping pattern of ROHs between breeds; we found two overlapping regions between Hanwoo and Black Angus, three overlapping regions between Hanwoo and Holstein, and 14 overlapping regions between Black Angus and Holstein (Additional file 8). These patterns would result from different origins and breeding strategies among the three breeds because Black Angus and Holstein originated in Aberdeen, Scotland and the Netherlands, respectively, and have been bred as beef and dairy cattle, respectively, while Hanwoo was bred independently as beef cattle in the Korean peninsula since 1979.

Bottom Line: 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.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.

View Article: PubMed Central - HTML - PubMed

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

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.

Show MeSH
Related in: MedlinePlus