Publications (17)40.91 Total impact
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Article: QTL and gene expression analyses identify genes affecting carcass weight and marbling on BTA14 in Hanwoo (Korean Cattle).
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ABSTRACT: Causal mutations affecting quantitative trait variation can be good targets for marker-assisted selection for carcass traits in beef cattle. In this study, linkage and linkage disequilibrium analysis (LDLA) for four carcass traits was undertaken using 19 markers on bovine chromosome 14. The LDLA analysis detected quantitative trait loci (QTL) for carcass weight (CWT) and eye muscle area (EMA) at the same position at around 50 cM and surrounded by the markers FABP4SNP2774C>G and FABP4_μsat3237. The QTL for marbling (MAR) was identified at the midpoint of markers BMS4513 and RM137 in a 3.5-cM marker interval. The most likely position for a second QTL for CWT was found at the midpoint of tenth marker bracket (FABP4SNP2774C>G and FABP4_μsat3237). For this marker bracket, the total number of haplotypes was 34 with a most common frequency of 0.118. Effects of haplotypes on CWT varied from a -5-kg deviation for haplotype 6 to +8 kg for haplotype 23. To determine which genes contribute to the QTL effect, gene expression analysis was performed in muscle for a wide range of phenotypes. The results demonstrate that two genes, LOC781182 (p = 0.002) and TRPS1 (p = 0.006) were upregulated with increasing CWT and EMA, whereas only LOC614744 (p = 0.04) has a significant effect on intramuscular fat (IMF) content. Two genetic markers detected in FABP4 were the most likely QTL position in this QTL study, but FABP4 did not show a significant effect on both traits (CWT and EMA) in gene expression analysis. We conclude that three genes could be potential causal genes affecting carcass traits CWT, EMA, and IMF in Hanwoo.Mammalian Genome 07/2011; 22(9-10):589-601. · 2.89 Impact Factor -
Article: Heat shock protein B1 and its regulator genes are negatively correlated with intramuscular fat content in the longissimus thoracis muscle of Hanwoo (Korean cattle) steers.
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ABSTRACT: In previous proteomic studies, heat shock protein β 1 (HSPB1) was detected as a candidate protein related to meat quality in cattle. This study sought to determine if its gene expression was associated with intramuscular fat content in the longissimus thoracis muscle of Korean cattle (Hanwoo). Tissue from two groups of 10 steers each, low-marbling (mean intramuscular fat content, 7.4 ± 1.5%) and high-marbling (23.5 ± 2.8%), were used for immunoblotting, real-time PCR, and statistical analyses. HSPB1 expression in both mRNA and protein was shown to be negatively related to intramuscular fat content (P < 0.05). Pathway analysis found two genes, TNF receptor superfamily member 6 (FAS) and angiotensinogen (AGT), that were regulators of the HSPB1 gene. The expression of the two genes showed a negative correlation with intramuscular fat content (P < 0.05). These results suggest that HSPB1, FAS, and AGT may be good candidate genes associated with intramuscular fat content in the longissimus muscle of Korean cattle.Journal of Agricultural and Food Chemistry 05/2011; 59(10):5657-64. · 2.82 Impact Factor -
Article: Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study.
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ABSTRACT: Obesity represents a major global public health problem that increases the risk for cardiovascular or metabolic disease. The pigs represent an exceptional biomedical model related to energy metabolism and obesity in humans. To pinpoint causal genetic factors for a common form of obesity, we conducted local genomic de novo sequencing, 18.2 Mb, of a porcine QTL region affecting fatness traits, and carried out SNP association studies for backfat thickness and intramuscular fat content in pigs. In order to relate the association studies in pigs to human obesity, we performed a targeted genome wide association study for subcutaneous fat thickness in a cohort population of 8,842 Korean individuals. These combined association studies in human and pig revealed a significant SNP located in a gene family with sequence similarity 73, member A (FAM73A) associated with subscapular skin-fold thickness in humans (rs4121165, GC-corrected p-value = 0.0000175) and with backfat thickness in pigs (ASGA0029495, p-value = 0.000031). Our combined association studies also suggest that eight neuronal genes are responsible for subcutaneous fat thickness: NEGR1, SLC44A5, PDE4B, LPHN2, ELTD1, ST6GALNAC3, ST6GALNAC5, and TTLL7. These results provide strong support for a major involvement of the CNS in the genetic predisposition to a common form of obesity.PLoS ONE 01/2011; 6(2):e16356. · 4.09 Impact Factor -
Article: Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle).
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ABSTRACT: Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular fat deposition on highly divergent marbling phenotypes in adult Hanwoo cattle. Bovine genome array analysis was conducted to detect differentially expressed genes (DEGs) in m. longissimus with divergent marbling phenotype (marbling score 2 to 7). Three data-processing methods (MAS5.0, GCRMA and RMA) were used to test for differential expression (DE). Statistical analysis identified 21 significant transcripts from at least two data-processing methods (P < 0.01). All 21 differentially expressed genes were validated by real-time PCR. Results showed a high concordance in the gene expression fold change between the microarrays and the real time PCR data. Gene Ontology (GO) and pathway analysis demonstrated that some genes (ADAMTS4, CYP51A and SQLE) over expressed in high marbled animals are involved in a protein catabolic process and a cholesterol biosynthesis process. In addition, pathway analysis also revealed that ADAMTS4 is activated by three regulators (IL-17A, TNFα and TGFβ1). QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFβ1 are associated with increasing marbling fat. An ADAMTS4/TGFβ1 pathway seems to be associated with the phenotypic differences between high and low marbled groups. Marbling differences are possibly a function of complex signaling pathway interactions between muscle and fat. These results suggest that ADAMTS4, which is involved in connective tissue degradation, could play a role in an important biological pathway for building up marbling in cattle. Moreover, ADAMTS4 and TGFβ1could potentially be used as an early biological marker for marbling fat content in the early stages of growth.BMC Genomics 11/2010; 11:623. · 4.07 Impact Factor -
Article: Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo ( Korean Cattle )
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ABSTRACT: Abstract Background Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular fat deposition on highly divergent marbling phenotypes in adult Hanwoo cattle. Results Bovine genome array analysis was conducted to detect differentially expressed genes (DEGs) in m. longissimus with divergent marbling phenotype (marbling score 2 to 7). Three data-processing methods (MAS5.0, GCRMA and RMA) were used to test for differential expression (DE). Statistical analysis identified 21 significant transcripts from at least two data-processing methods (P < 0.01). All 21 differentially expressed genes were validated by real-time PCR. Results showed a high concordance in the gene expression fold change between the microarrays and the real time PCR data. Gene Ontology (GO) and pathway analysis demonstrated that some genes (ADAMTS4, CYP51A and SQLE) over expressed in high marbled animals are involved in a protein catabolic process and a cholesterol biosynthesis process. In addition, pathway analysis also revealed that ADAMTS4 is activated by three regulators (IL-17A, TNFα and TGFβ1). QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFβ1 are associated with increasing marbling fat. An ADAMTS4/TGFβ1 pathway seems to be associated with the phenotypic differences between high and low marbled groups. Conclusions Marbling differences are possibly a function of complex signaling pathway interactions between muscle and fat. These results suggest that ADAMTS4, which is involved in connective tissue degradation, could play a role in an important biological pathway for building up marbling in cattle. Moreover, ADAMTS4 and TGFβ1could potentially be used as an early biological marker for marbling fat content in the early stages of growth.BMC Genomics. 01/2010; -
Article: Gene expression profiling of metabolism-related genes between top round and loin muscle of Korean cattle (Hanwoo).
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ABSTRACT: Using differential display reverse transcriptase polymerase chain reaction, we detected 11 differentially expressed genes between top round and loin muscle in Korean cattle (Hanwoo). In the loin muscle, the lightness (L*) value (P<0.01) and marbling fat content (P<0.01), which are important factors in determining meat quality, were higher than in top round muscle. Three of the 11 genes were validated as significant genes between two types of muscle by real-time polymerase chain reaction (P<0.05). To determine whether the three genes were associated with meat quality traits, a regression analysis was preformed. The result demonstrated that two genes (NADH dehydrogenase 2 and cytochrome oxidase III), which are involved in oxidative phosphorylation in mitochondria, were significantly correlated with marbling fat content in the loin muscle (P<0.01), while two genes were not significant with marbling fat content in top round muscle. No significant effects for two genes on other meat quality traits such as meat color (redness and yellowness value), Warner-Bratzler shear force, and water-holding capacity were detected in this study.Journal of Agricultural and Food Chemistry 10/2009; 57(22):10898-903. · 2.82 Impact Factor -
Article: Proteome analysis of the m. longissimus dorsi between fattening stages in Hanwoo steer.
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ABSTRACT: The objective of this study was to identify proteins in the m. longissimus dorsi between early (12 months of age) and late (27 months of age) fattening stages of Hanwoo (Korean cattle) steers. Using two-dimensional electrophoresis and mass spectrometry, 8 proteins of 11 differentially expressed spots between the 12 and 27 month age groups were identified in the loin muscle. Among those that were differentially expressed, zinc finger 323 and myosin light chain were highly expressed in late-fattening stage, and two catabolic enzymes, triosephosphate isomerase (TPI) and succinate dehydrogenase (SDH) were expressed more in the early versus the late-fattening stage. In particular, the quantification of TPI and SDH by immunoblotting correlated well with fat content. Our data suggested that TPI and SDH are potential candidates as markers and their identification provides new insight into the molecular mechanisms and pathways associated with intramuscular fat contents of bovine skeletal muscle.BMB reports 08/2009; 42(7):433-8. · 1.72 Impact Factor -
Article: The Pig Genome Database (PiGenome): an integrated database for pig genome research.
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ABSTRACT: We established the Pig Genome Database (PiGenome) for pig genome research. The PiGenome integrates and analyzes all publicly available genome-wide data on pigs, including UniGenes, sequence tagged sites (STS) markers, quantitative trait loci (QTLs) data, and bacterial artificial chromosome (BAC) contigs. In addition, we produced 69,545 expressed sequence tags (ESTs) from the full-length enriched cDNA libraries of six tissues and 182 BAC contig sequences, which are also included in the database. QTLs, genetic markers, and BAC end-sequencing information were collected from public databases. The full-length enriched EST data were clustered and assembled into unique sequences, contigs, and singletons. The PiGenome provides functional annotation, identification of transcripts, mapping of coding sequences, and SNP information. It also provides an advanced search interface, a disease browser, alternative-splicing events, and a comparative gene map of the pig. A graphical map view and genome browser can map ESTs, contigs, BAC contigs (from the National Institute of Animal Science), Sino-Danish Pig Genome Project transcripts, and UniGene onto pig genome sequences which include our 182 BAC contigs and publically available BAC sequences of the Wellcome Trust Sanger Institute. The PiGenome is accessible at http://pigenome.nabc.go.kr/ .Mammalian Genome 01/2009; 20(1):60-6. · 2.89 Impact Factor -
Article: Proteins in longissimus muscle of Korean native cattle and their relationship to meat quality.
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ABSTRACT: Proteomic profiling by two-dimensional gel electrophoresis and mass spectrometry of longissimus dorsi muscle tissue from Korean native cattle identified seven proteins that are differentially expressed in animals producing low and high quality grade beef. The expression level of alpha actin is increased in high quality grade beef and the expression levels of T-complex protein 1 (TCP-1), heat shock protein beta-1 (HSP27), and inositol 1,4,5-triphosphate receptor type1 (IP3R1), a new protein to be associated with meat quality, are increased in low quality grade beef. In particular, the quantitation of HSP27 and IP3R1 by both silver staining and immunoblotting correlated well with intramuscular fat content, meat tenderness, and free calcium levels. The data suggest that HSP27 and IP3R1 are potential meat quality biomarkers and their identification provides new insight into the molecular mechanisms and pathways associated with overall beef quality.Meat Science 12/2008; 80(4):1068-73. · 2.28 Impact Factor -
Article: Identification of marbling-related candidate genes in M. longissimus dorsi of high- and low marbled Hanwoo (Korean Native Cattle) steers.
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ABSTRACT: This study was conducted to identify marbling-related candidate genes in M. longissimus dorsi of high- and low-marbled Hanwoo. The longissimus dorsi muscles were selected for gene expression from eight Hanwoo steer carcasses based on crude fat content. In the analysis of variance, gene expression of five candidate genes, FABP4, SCD, PPARgamma, Titin and Nebulin was determined to be significantly different between high- and low-marbled Hanwoo steers (P < 0.0001). The Pik-4 and CaMK II genes were also shown to have a significant effect on crude fat content (P < 0.01). In the analysis of the differential expression between high- and low marbled groups, FABP4 gene expression was approximately 2 times higher in the high marbled group relative to the low marbled group. However, the PPARgamma and SCD gene were highly expressed in the low marbled group. In addition, Titin and Nebulin were highly expressed in the low marbled group when placed under relatively high shear force. Finally, the Pik-4 and CaM K II gene also displayed a high expression pattern in the low marbled group.BMB reports 12/2008; 41(12):846-51. · 1.72 Impact Factor -
Article: Minimizing a QTL region for intramuscular fat content by characterizing the porcine Phosphodiesterase 4B (PDE4B) gene.
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ABSTRACT: Three isoforms of pig PDE4B were cloned and classified as two forms: PDE4B1 and PDE4B3, which contain UCR1 and UCR2; and PDE4B2, which contains only UCR2. The amino acid sequences of each isoform showed good conservation in human and rat. PDE4B2 is expressed in a wide range of tissues, but PDE4B1 and PDE4B3 are not. Using an informative SNP for the Iberian x Landrace intercross detected from intron 12, a linkage map was constructed. The location of PDE4B was estimated at 123.6 cM outside of the QTL-CI (124-128 cM) for IMF. However, the QTL-CI for IMF was reconfirmed with high significance, and its position was narrowed down to an interval of 4 cM (the region defined by markers PDE4B and SW1881). Using radiation hybrid mapping, LEPR, LEPROT, DNAJC6, AK3L1 and AK3L2 were selected as positional and/or functional candidates related to the QTL.BMB reports 07/2008; 41(6):466-71. · 1.72 Impact Factor -
Article: Characterization of beef transcripts correlated with tenderness and moisture.
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ABSTRACT: To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r|>0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.Molecules and Cells 06/2008; 25(3):428-37. · 2.18 Impact Factor -
Article: Identification of differentially expressed genes related to intramuscular fat development in the early and late fattening stages of hanwoo steers.
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ABSTRACT: Marbling of cattle meat is dependent on the coordinated expression of multiple genes. Cattle dramatically increase their intramuscular fat content in the longissimus dorsi muscle between 12 and 27 months of age. We used the annealing control primer (ACP)-differential display RT-PCR method to identify differentially expressed genes (DEGs) that may participate in the development of intramuscular fat between early (12 months old) and late fattening stages (27 months old). Using 20 arbitrary ACP primers, we identified and sequenced 14 DEGs. BLAST searches revealed that expression of the MDH, PI4-K, ferritin, ICER, NID-2, WDNMI, telethonin, filamin, and desmin (DES) genes increased while that of GAPD, COP VII, ACTA1, CamK II, and nebulin decreased during the late fattening stage. The results of functional categorization using the Gene Ontology database for 14 known genes indicated that MDH, GAPD, and COP VII are involved in metabolic pathways such as glycolysis and the TCA cycle, whereas telethonin, filamin, nebulin, desmin, and ACTA1 contribute to the muscle contractile apparatus, and PI4-K, CamK II, and ICER have roles in signal transduction pathways regulated by growth factor or hormones. The final three genes, NID-2, WDNMI, and ferritin, are involved in iron transport and extracellular protein inhibition. The expression patterns were confirmed for seven genes (MDH, PI4-K, ferritin, ICER, nebulin, WDNMI, and telethonin) using real-time PCR. We found that the novel transcription repressor ICER gene was highly expressed in the late fattening stage and during bovine preadipocyte differentiation. This information may be helpful in selecting candidate genes that participate in intramuscular fat development in cattle.Journal of biochemistry and molecular biology 10/2007; 40(5):757-64. · 2.02 Impact Factor -
Article: An accurate method for quantifying and analyzing copy number variation in porcine KIT by an oligonucleotide ligation assay.
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ABSTRACT: Aside from single nucleotide polymorphisms, copy number variations (CNVs) are the most important factors in susceptibility to genetic disorders because they affect expression levels of genes. In previous studies, pyrosequencing, mini-sequencing, real-time PCR, invader assays and other techniques have been used to detect CNVs. However, the higher the copy number in a genome, the more difficult it is to resolve the copies, so a more accurate method for measuring CNVs and assigning genotype is needed. PCR followed by a quantitative oligonucleotide ligation assay (qOLA) was developed for quantifying CNVs. The accuracy and precision of the assay were evaluated for porcine KIT, which was selected as a model locus. Overall, the root mean squares of bias and standard deviation of qOLA were 2.09 and 0.45, respectively. These values are less than half of those in the published pyrosequencing assay for analyzing CNV in porcine KIT. Using a combined method of qOLA and another pyrosequencing for quantitative analysis of KIT copies with spliced forms, we confirmed the segregation of KIT alleles in 145 F1 animals with pedigree information and verified the correct assignment of genotypes. In a diagnostic test on 100 randomly sampled commercial pigs, there was perfect agreement between the genotypes obtained by grouping observations on a scatter plot and by clustering using the nearest centroid sorting method implemented in PROC FASTCLUS of the SAS package. In a test on 159 Large White pigs, there were only two discrepancies between genotypes assigned by the two clustering methods (98.7% agreement), confirming that the quantitative ligation assay established here makes genotyping possible through the accurate measurement of high KIT copy numbers (>4 per diploid genome). Moreover, the assay is sensitive enough for use on DNA from hair follicles, indicating that DNA from various sources could be used. We have established a high resolution quantification method using an oligonucleotide ligation assay to measure CNVs, and verified the reliability of genotype assignment for random animal samples using the nearest centroid sorting method. This new method will make it more practical to determine KIT CNV and to genotype the complicated Dominant White/KIT locus in pigs. This procedure could have wide applications for studying gene or segment CNVs in other species.BMC Genetics 01/2007; 8:81. · 2.47 Impact Factor -
Article: Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries.
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ABSTRACT: Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.Journal of biochemistry and molecular biology 04/2006; 39(2):183-8. · 2.02 Impact Factor -
Article: Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6.
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ABSTRACT: On pig chromosome 6, the SW71 microsatellite is located in the region corresponding to several quantitative trait loci (QTL), such as those for intramuscular fat content and for body weight at 4 weeks of age. The genomic sequence of approximately 909 kb was obtained from seven BAC clones encompassing the SW71 region corresponding to human 18q11.21-q11.22. By searching the NCBI GenBank using BLASTX and BLASTN, this 909-kb segment was found to contain eight genes, RAB31, TXNDC2, VAPA, APCDD1, NAPG, FAM38B, C18orf30, and C18orf58, and one putative gene (DN119777). The average G + C content in the sequence of this contig was 45.75% and 33 CpG islands were detected. CpG islands were scattered throughout the region in which most of the putative genes were located. Dense CpG islands of approximately 840 bp were observed, including within the 5' UTR and exon 1 of the orthologs of the RAB31, VAPA, APCDD1, and NAPG genes. Comparative analysis of conserved segments of six species showed that K(a)/K(s) ratios of the TXNDC2 gene in collinear and rearranged segments were significantly different at 4.1 and 1.3, respectively. In conclusion, we demonstrated the genomic organization of pig chromosome 6, including the gene order surrounding SW71, which provides important information for comparative mapping. Moreover, the genes revealed in this study may be positional candidate genes associated with QTL on chromosome 6 that affect fat deposition in pigs.Genomics 03/2006; 87(2):218-24. · 3.02 Impact Factor -
Article: A large-insert porcine library with sevenfold genome coverage: a tool for positional cloning of candidate genes for major quantitative traits.
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ABSTRACT: A porcine genomic bacterial artificial chromosome (BAC) library was constructed by cloning partial EcoRI-digested high-molecular-weight DNA from a Korean native boar into the EcoRI site of the pBACe3.6 vector. The library consists of about 165,000 clones with an average insert size of 125 kb, representing about seven genome equivalents of coverage. About 130,000 clones (corresponding to fivefold genome coverage) were arrayed in 14 superpools which were organized as four dimensional pools. The library was further characterized by PCR screening of 38 microsatellite probes. An average of 4.84 positive clones were selected per marker. This indicates that the library is unbiased and will be useful for initiating fine scale physical mapping of major QTL in pigs. The library is being used to isolate specific clones by screening with type I and type II marker clones located in the QTL region affecting intramuscular fat content on SSC6.Molecules and Cells 09/2003; 16(1):113-6. · 2.18 Impact Factor
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2008–2011
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National Institute of Animal Science
Seoul, Seoul, South Korea
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