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In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

A portable CE system was developed for the identification of cattle breeds. The system had a width of 44 cm, depth of 27 cm, height of 13 cm, and a weight of only approximately 8 kg and included an LIF detector, with everything integrated into a small box. The specific sizes of genes were quickly separated and detected with a high sensitivity based on the difference in the DNA mobility using a diode-pumped solid-state LIF detector. Using this system, the 100-bp DNA ladder was analyzed under a 1.0% PVP (M(r)=300 000) sieving gel matrix in a fused silica capillary with LODs of 4.4-13.0 pg/microL (S/N=3) for 100-3000 bp DNAs, which indicates ten times improved value than other commercialized portable CE system. The migration times and the peak areas showed good reproducibilities with relative standard deviations that were less than 0.49 and 1.3% (n=5), respectively. Based on the difference in the DNA mobility of the microsatellite and SNP markers, Korean cattle and Holstein were exactly identified as the model cattle breeds within 32 and 3.5 min, respectively.

Helper 17 T (Th17) effector cells are a recently identified Th subset and possess a unique property that distinguishes them from Th1 and Th2 subsets. The functional role of Th17 effector cells involves inflammatory responses, including autoimmunity and infection of specific pathogens. Therefore, IL-17A and its receptors may play a key role in determining the progression of certain inflammatory reactions. However, the relationship between IL-17A and adipogenesis has not yet been examined. Therefore, in this study, the effect of IL-17A on the adipogenic transdifferentiation of mouse myoblast (C2C12) cells was examined. CAAT/enhancer binding-protein β (C/EPBβ) signaling through the IL-17A receptor promoted adipogenic transdifferentiation of myoblast cells by activating peroxisome proliferator-activated receptor γ (PPARγ). These results will advance our understanding of the physiological function of IL-17A in myoblasts during inflammation, as well as the relationship between adipogenesis and inflammation.

A large data set of Hanwoo (Korean cattle) ESTs was analyzed to obtain differential gene expression results for the following three libraries: intramuscular fat, longissimus dorsi muscle and liver. To better understand the gene expression profiles, we identified differentially expressed genes (DEGs) via digital gene expression analysis. Hierarchical clustering of genes was performed according to their relative abundance within the six separate groups (Hanwoo fat versus non-Hanwoo fat, Hanwoo muscle versus non-Hanwoo muscle and Hanwoo liver versus non-Hanwoo liver), producing detailed patterns of gene expression. We determined the quantitative traits associated with the highly expressed genes. We also provide the first list of putative regulatory elements associated with differential tissue expression in Hanwoo cattle. In addition, we conducted evolutionary analysis that suggests a subset of genes accelerated in the bovine lineage are strongly correlated with their expression in Hanwoo muscle.

Two genetically different pig breeds, the Korean native pig (KNP) and the Western meat-producing Landrace, show breed-specific traits in stress responsiveness (stress hormone levels), growth performance (live weight), and meat quality (intramuscular fat content). We analyzed expression levels within the proteome and transcriptome of the longissimus muscles of both breeds using two-dimensional electrophoresis (2-DE) and microarray analysis. We constructed a porcine proteome database focused mainly on mitochondrial proteins. In total, 101 proteins were identified, of which approximately 60% were metabolic enzymes and mitochondrial proteins. We screened several proteins and genes related to stress and metabolism in skeletal muscles using comparative analysis. In particular, three stress-related genes (heat shock protein beta-1, stress-70 protein, and heat shock 70 kDa protein) were more highly expressed in the Landrace than in the KNP breed. Six metabolism-related genes (peroxisome proliferative activated receptor alpha, short-chain acyl-CoA dehydrogenase, succinate dehydrogenase, NADH-ubiquinone oxidoreductase, glycerol-3-phosphate dehydrogenase, and sterol regulatory element binding protein-1c), all of which are involved in energy and lipid metabolism, were more highly expressed at the protein or mRNA level in the KNP breed. These data may reflect the breed dependence of traits such as stress responsiveness, growth performance, and meat quality.

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 (P0.01) and marbling fat content (P0.01), 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 (P0.05). 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 (P0.01), 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.

Marbling score (MS) is the major trait that affects carcass quality in beef cattle. In this study, we investigated the association between genetic polymorphisms of the adipose differentiation-related protein gene (ADFP) and carcass traits in Korean cattle (also known as Hanwoo). Using direct DNA sequencing in 24 unrelated Korean cattle, 25 novel polymorphisms were identified within all exons and their flanking regions of ADFP, including the promoter region (1.5 kb). Among them, 21 polymorphic sites were selected for genotyping in the beef cattle (n = 425). Statistical analyses revealed that one promoter polymorphism (c.-56-18A ＞ G) was associated with MS (P = 0.009). The “A” allele of c.-56-18A ＞ G exerted a lowering effect on MS, e.g., the lowest MS was found in “A/A” (MS = 2.09 ± 1.23), intermediate in “A/G” (MS = 2.11 ± 1.31), and the highest in “G/G” (MS = 2.47 ± 1.47). Our findings suggest that these polymorphisms in ADFP might be important genetic factors involved in carcass quality in beef cattle. [BMB reports 2009; 42(8): 529-534]

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.

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, PPAR gamma, 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 PPAR gamma 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. Refereed/Peer-reviewed

Background Marbling score (MS) is the major quantitative trait that affects carcass quality in beef cattle. In this study, we examined the association between genetic polymorphisms of the micromolar calcium-activated neutral protease gene (micro-calpain, CAPN1) and carcass traits in Korean cattle (also known as Hanwoo). Results By direct DNA sequencing in 24 unrelated Korean cattle, we identified 39 sequence variants within exons and their flanking regions in CAPN1. Among them, 12 common polymorphic sites were selected for genotyping in the beef cattle (n = 421). Statistical analysis revealed that a polymorphism in the 3'UTR (c.2151*479C>T) showed significant association with MS (P cor.= 0.02). Conclusion Our findings suggest that polymorphisms in CAPN1 might be one of the important genetic factors involved in carcass quality in beef cattle, although it could be false positive association.

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.