Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generatio...
Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.
Hanwoo, a Korean native cattle (Bos taurus coreana), has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs) in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3%) and 982,674 (40.9%) novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1) and 28,613 SNPs (Btau 4.6.1) that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns) SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.
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제안 방법
1 , using the ‘find_variations’ program in CLC Assembly Cell along with stringent parameters as follows: minimum depth = 5; minimum mismatch count (show information when more than a given number of reads is different from the consensus) = 3; limit fraction (Show information when more than a given fraction of reads is different from the consensus) ≥20%. In order to compare our findings with dbSNP database, we carried out the liftover from dbSNP set to Btau 4.6.1 and UMD 3.1, respectively, since the dbSNP set is not yet mapped to the Btau 4.6.1 and UMD 3.1 assemblies. We thus compared our SNPs with dbSNPs (Btau 4.
In this study, we carried out whole-genome sequencing of Hanwoo bulls using Illumina Genome Analyzer IIx platform to discover SNP variation that may be related to economic traits and to characterize the genetics and molecular biology of Hanwoo, which would enable efficient Hanwoo breeding.
, 2010). In this study, we identified a set of 232 genes and found 22 nsSNP in hemicentin 1 (HMCN1, 437 sSNPs, 3 nsSNPs) and EGF (124 sSNPs, 2 nsSNPs). Also, significant SNPs were found in the promoter region of RUNX1, ME1, and ASAP1.
0 based on literature-search algorithm. The results were imported into Pathway Studio 9 (Elsevier Research Solutions, Amsterdam, Netherlands), in which pathway-based analysis was performed using mammalian ResNet database and customized bovine ResNet database. Conversion of genes having human Gene ID into bovine Gene ID was performed using HomoloGene, which is a database to automatically detect homologs including orthologs among the annotated genes of 20 completely sequenced eukaryotic genomes.
es/). This analysis carried out based on GO, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, interpro motifs, and Panther pathways.
The information of entities and relations was extracted from the selected papers, but entities having no relations were used for this analysis. To obtain the accurate results, we checked whether the genes were involved in physiological processes associated with the five traits (Supplementary Tables 1 and Table 2).
대상 데이터
1 were identified, respectively, (Table 3). Among the SNPs, 46,301 Hanwoospecific SNPs that were based on UMD 3.1 were chosen for further analysis.
Sequencing generated 27 Gbp of high quality sequences on paired-end libraries (76-bp reads and 84-bp reads) with insert size of 500 bp. The genome sequence traces were submitted to the NCBI Short Read Archive (SRA) as accession SRP060306. Preprocessed clean reads were mapped on two reference genome assemblies, giving an average depth of 9.
Heterozygous and homozygous SNPs were determined with 50% cut-off of aligned reads identifying the SNP, but homozygous alleles which be constituted exclusively same bases were applied in order to unravel Hanwoo-specific SNPs. The study for promoter and downstream SNPs was conducted in upstream 2 kb and downstream 1 kb of each gene, respectively.
이론/모형
The ten samples were chosen, so as not to be genetically related, and to reflect genetic diversity of the Hanwoo population. The genomic DNA was extracted using standard phenol/chloroform extraction method.
성능/효과
In this study, we investigated the genetic variations related with economically important traits by using whole-genome resequencing of Korean native cattle, Hanwoo. A total of 2.47 million SNPs were identified, of which more than 1.1 million SNPs (44%) were found to be novel. Among the SNPs, many of the nsSNPs were in the genes that were reported as candidates for QTL affecting economically important traits such as meat quality, milk production, and exterior traits in other cattle breeds.
1) SNPs were identified. Among the SNPs, 2,234,514 (90.3%) were heterozygous and 239,370 (9.7%) were homozygous for UMD 3.1 (cut-off: 50% alleles), whereas 2,162,910 (90.0%) were heterozygous and 240,087 (10.0%) were homozygous for Btau 4.1.6 (Table 2). This result suggests that substantial variations exist between the ten individuals.
In particular, a set of 136 Hanwoo-specific genes including 446 SNPs were found in the genes related to the above traits. Among the genes, CAPN1, CAST, LEP, ANK1, ADIPOQ, IGF1, NR3C1, PPARG, and FN1 were included, which were known to be related with marbling, tenderness and juiciness. We identified Hanwoo specific genes, for yellow hair, meat quality, and milk production.
In order to reduce the false-discovery rate, stringent criteria for SNP calling were applied (materials and methods). As a result, 2,473,884 (UMD 3.1) and 2,402,997 (Btau 4.6.1) SNPs were identified. Among the SNPs, 2,234,514 (90.
We isolated 100% homozygous SNPs for discovering SNPs associated with Hanwoo-specific phenotypes. As a result, 46,301 SNPs (1.9%) for UMD 3.1 and 28,613 SNPs (1.2%) for Btau 4.6.1 were identified, respectively, (Table 3). Among the SNPs, 46,301 Hanwoospecific SNPs that were based on UMD 3.
Firstly, although mapping with default parameter (identity 80% and HSP coverage 50%) increased mapping coverage of 98.73% (UMD 3.1) and 93.79% (Btau 4.6.1), we produced reliable sequencing data with the optimized parameter, which caused the diminished coverage.
1) mapped by SNP location of dbSNP. Heterozygous and homozygous SNPs were determined with 50% cut-off of aligned reads identifying the SNP, but homozygous alleles which be constituted exclusively same bases were applied in order to unravel Hanwoo-specific SNPs. The study for promoter and downstream SNPs was conducted in upstream 2 kb and downstream 1 kb of each gene, respectively.
, 2010). In our study, a total of 3,935 and 5,144 SNPs, including 58 and 82 Hanwoo-specific SNPs, were found in UMD and Btau, respectively (Supplementary Table 2). Particularly, the Hanwoo-specific SNPs will be a valuable genetic resource to characterize beef quality of Hanwoo.
, 2008). In this study, LEP, calpain 1, (mu/I) large subunit (CAPN1), CAST, adiponectin,C1Q and collagen domain containing (ADIPOQ), peroxisome proliferator-activated receptor gamma (PPARG), insulin-like growth factor 1 (somatomedin C) (IGF1), fibronectin ED-B+ region (FN1), sorbin and SH3 domain containing 1 (SORBS1), myosin, light chain 12A, regulatory, non-sarcomeric (MYL12B), SH3-domain kinase binding protein 1 (SH3KBP1), acyl-CoA synthetase long-chain family member 1 (ACSL1), myosin light chain kinase (MYLK), ATP-binding cassette, sub-family A, member 1 (ABCA1), insulin receptor (INSR), protein kinase C, alpha (PRKCA) and similar to Retinoblastoma-associated protein (RB1) were newly identified as marbling-related (Supplementary Table 2). As an inhibitor to the growth of muscle tissue, myostatin is involved in muscle marbling during fattening period by inhibiting myogenesis and promoting adipogenesis (Shibata et al.
Synonymous SNPs (sSNPs) and nonsynonymous SNPs (nsSNPs) in exon region was 11,196 (1.38%) and 3,137 (0.39%) for UMD 3.1, while 11,356 (1.50%) and 3,311 (0.44%) for Btau 4.6.1 were defined in the exon regions for the sSNPs and nsSNPs, respectively (Figure 2).
Many Hanwoo calves were born between the late 1980s and 2000 from the ten sires. The ten samples were chosen, so as not to be genetically related, and to reflect genetic diversity of the Hanwoo population. The genomic DNA was extracted using standard phenol/chloroform extraction method.
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