• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1065-1070
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• 2006

The avian uncoupling protein (avUCP) is a member of the mitochondrial transporter superfamily that uncouples proton entry in the mitochondrial matrix from ATP synthesis. The sequencing analysis method was used to identify nucleotide polymorphisms within the avUCP gene in Korean native chicken (KNC). This study identified ten single nucleotide polymorphisms (SNPs) in the avUCP gene. We analyzed the SNPs of the avUCP gene to investigate whether polymorphism in the gene might be responsible for quantitative variations in economic traits in KNC. Three significant polymorphic sites for economic traits were avUCP C+282T (mean body weight, p<0.05), avUCP C+433T (daily percent lay, p<0.05), and avUCP T+1316C (daily percent lay, p<0.05). The frequency of each SNP was 0.125 (C+282T in avUCP gene exon 1 region), 0.150 (C+433T in avUCP gene intron 1 region), and 0.15 (T+1316C in avUCP gene exon 3 region), respectively. Among the identified SNPs, one pair of SNPs (genotype CC, C+282T and TT, avUCP C+433T) showed the highest daily percent lay (p<0.05) and mean body weight (p<0.05) and the frequency was 0.067. This study of the avUCP gene could be useful for genetic studies of this gene and selection on economic traits for KNC.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.10
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• pp.1359-1364
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• 2013

The purpose of this study was to find any association of the bovine growth hormone (bGH) gene with growth and carcass quality traits in Korean native cattle, Hanwoo. Genomic DNA was extracted from 21 Hanwoo individuals, and the 47 to 2,528 bp region of the bGH 2,856 bp (GenBank accession number M57764) including the promoter and the five exons was sequenced. A total of ten bGH SNPs were confirmed, including four (253 C>T, 303 C>T, 502 C>T, and 559 G>A) in the promoter, one (679 C>T) in exon 1, one (1,692 T>C) in intron 3, and four (2141 C>G, 2258 C>T, 2277 C>T, and 2291 A>C) in exon 5. The ten bGH SNPs were genotyped for a sample of 242 Hanwoo steers and association tests were performed to find any significant SNP that was correlated with growth and carcass quality. Of the SNPs, the 303 C>T SNP in the promoter region was significantly associated with 6-month-old weight, the 559 G>A SNP with longissimus dorsi muscle area, the 2141 C>G SNP in exon 5 with daily weight gain, and the 2258 C>T SNP with daily weight gain and carcass weight (p<0.05). The significant SNPs need to be verified in other Hanwoo populations before considering implementation of marker-assisted selection for genetic improvement of growth and carcass quality in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.12
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• pp.1689-1695
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• 2017

Objective: The cytokine inducible SH2-containing protein (CISH), which might play a role in porcine intestine immune responses, was one of the promising candidate genes for piglet anti-disease traits. An experiment was conducted to characterize the porcine CISH (pCISH) gene and to evaluate its genetic effects on pig anti-disease breeding. Methods: Both reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to obtain the sequence of pCISH gene. A pEGFP-C1-CISH vector was constructed and transfected into PK-15 cells to analysis the distribution of pCISH. The sequences of individuals were compared with each other to find the polymorphisms in pCISH gene. The association analysis was performed in Min pigs and Landrace pigs to evaluate the genetic effects on piglet diarrhea traits. Results: In the present research, the coding sequence and genomic sequence of pCISH gene was obtained. Porcine CISH was mainly localized in cytoplasm. TaqI and HaeIII PCR restriction fragment length polymorphism (RFLP) assays were established to detect single nucleotide polymorphisms (SNPs); A-1575G in promoter region and A2497C in Intron1, respectively. Association studies indicated that SNP A-1575G was significantly associated with diarrhea index of Min piglets (p<0.05) and SNP A2497C was significantly associated with the diarrhea trait of both Min pig and Landrace piglets (p<0.05). Conclusion: This study suggested that the pCISH gene might be a novel candidate gene for pig anti-disease traits, and further studies are needed to confirm the results of this preliminary research.

• Journal of Microbiology and Biotechnology
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• v.23 no.6
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• pp.759-765
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• 2013

The gene encoding squalene synthase (SQS) of the lipid-producing heterotrophic microalga Aurantiochytrium sp. KRS101 was cloned and characterized. The krsSQS gene is 1,551 bp in length and has two exons and one intron. The open reading frame of the gene is 1,164 bp in length, yielding a polypeptide of 387 predicted amino acid residues with a molecular mass of 42.7 kDa. The deduced krsSQS sequence shares at least four conserved regions known to be required for SQS enzymatic activity in other species. The protein, tagged with $His_6$, was expressed into soluble form in Escherichia coli. The purified protein catalyzed the conversion of farnesyl diphosphate to squalene in the presence of NADPH and $Mg^{2+}$. This is the first report on the characterization of an SQS from a Thraustochytrid microalga.

• Journal of Animal Science and Technology
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• v.53 no.6
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• Korean Journal of Agricultural Science
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• v.40 no.3
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• pp.215-220
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• 2013

Fatty acids (FAs) were considered in activating nuclear hormone receptors that play significant roles in the cellular lipid metabolism by the regulation of several genes. Previously, fatty acid synthase (FASN) and stearoyl-CoA desaturase (SCD) genes have been known to regulating the FA metabolism. In this study, associations of FASN and SCD genes with fatty acid (FA) composition in broilers were investigated. Tissue samples from 95 Cobb 500 broilers were used for DNA extraction. The g.1222 A>G SNP located in intron 42 of FASN gene and 2 SNPs in SCD gene, one in exon 2 (g.3728A>G) and the other in exon 4 (g.12903G>A), were subjected for genotyping using PCR-RFLP method. One of the SNPs in SCD gene, SNP g.3728A>G had significant association with myristoleic acid (C14:1; P<0.05), palmitic acid (C16:0; P<0.05), palmitoleic acid (C16:1; P<0.05) and saturated FA (SFA; P<0.05). However, the SNP g.1222A>G in FASN gene had only suggestive association with arachidic acid (C20:0; P=0.08). The findings in this study suggest that the SNP in exon 2 of SCD gene can be used as a molecular marker for selecting birds having desirable FA composition in broilers.

• Genomics & Informatics
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• v.7 no.1
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• pp.13-19
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• 2009

Osteoporosis is characterized by impaired osteogenesis. BMD is a major determinant of bone strength. The role of the VDR gene in predisposition to primary osteoporosis has been recognized. However, population-based case-control studies have been reported controversial results for known candidate genes in an ethnically distinct group. To determine the genetic effects of VDR variants on osteoporosis and BMD, we directly sequenced the VDR gene in 24 unrelated Korean individuals and identified eighteen sequence variants. We investigated the potential involvement of eight SNPs in osteoporosis in postmenopausal women (n = 729). Two SNPs (LD) in intron 2, -5294G>C (rs2238135) and -4817G>A (rs17882443) showed the evidence of association with enhanced BMD of the femoral neck ($p_{additive}$=0.031 for rs2238135; $p_{additive}$=0.017 and $p_{dominant}$= 0.019 for 17882443). Moreover, VDR -4817G>A was significantly associated with protective effect on all fracture risk ($p_{recessive}$=0.035, OR=0.2, 95% CI=$0.05{\sim}0.89$), and tended to be higher BMD values at various proximal femur sites. Therefore, we suggest that the -4817G>A may be useful genetic marker for vitamin D-related metabolism and may have an important role in the increased BMD of the proximal femur in postmenopausal Korean women.

• Journal of Genetic Medicine
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• v.9 no.1
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• pp.42-46
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• 2012

Short-chain acyl-CoA dehydrogenase deficiency (SCADD; OMIM # 201470) is an autosomal recessive inborn error of mitochondrial fatty acid ${\beta}$-oxidation, presenting with a variety of clinical signs and symptoms. Developmental delay, hypertonia or hypotonia, ketotic hypoglycemia, and epilepsy are most frequently reported. In general, patients diagnosed through newborn screening have shown normal growth and development in contrast to those diagnosed as a result of clinically initiated evaluations. Here, the case of an asymptomatic Korean newborn with SCADD identified by tandem mass spectrometry is reported. The patient showed an elevated concentration of butyrylcarnitine detected on newborn screening. Urinary excretion of ethylmalonic acid was elevated by urine organic acid analysis. To confirm the diagnosis of SCADD, a direct sequencing analysis of 10 coding exons and the exon-intron boundaries of the ACADS gene were performed. Genetic analysis of ACADS showed the following novel compound heterozygous missense mutations: c.277C>A (p.Leu93Ile) on exon3 and c.682G>A (p.Glu288Lys) on exon6. These results will provide further evidence of mutational heterogeneity for SCADD.

• Korean Journal of Breeding Science
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• v.42 no.4
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• pp.365-373
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• 2010

TILLING (Targeting Induced Local Lesions IN Genomes) is broadly regarded as an excellent methodology for reverse genetics applications. Approximately 15,000 $M_3$ TILLING lines have been developed via the application of gamma-ray irradiation to rice seeds (cv. Donganbyeo), followed by subsequent selections. In an effort to evaluate the genetic diversity of the TILLING population, we have employed the AFLP multiple dominant marker technique. A total of 96 (0.64%) TILLING lines as well as Donganbyeo were selected randomly and their genetic diversity was assessed based on AFLP marker polymorphisms using 5 primer combinations. An average of 100.4 loci in a range of 97 to 106 was detected using these primer combinations, yielding a total of 158 (31.4%) polymorphic loci between Donganbyeo and each of the 96 lines. A broad range of similarity from 80% to 96% with an average of 89.4% between Donganbyeo and each of the 96 lines was also observed, reflecting the genetic diversity of the TILLING population. Approximately 28 polymorphic loci have been cloned and their sequences were BLAST-searched against rice whole genome sequences, resulting in 20 matches to each of the gene bodies including exon, intron, 1 kb upstream and 1 kb downstream regions. Six polymorphic loci evidenced changes in the coding regions of genes as compared to the rice pseudomolecules, 4 loci of which exhibited missense mutations and 2 loci of which exhibited silent mutations. Therefore, the results of our study show that the TILLING rice population should prove to be a useful genetic material pool for functional genomics as well as mutation breeding applications.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.1-10
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• 2010

Five mutants were investigated at the molecular level to determine the factors responsible for mutated endosperm types. They were classified as high (HA) or low amylose (LA) phenotypes based on the amylose content in endosperm. The five were previously produced from Ilpum and Shindongjin cultivar treated with N-methyl-N-nitrosourea and gamma-ray irradiation, respectively. Analysis of the genomic structure and expression of Granule-bounded Starch Synthase I (GBSSI) genes revealed that mutants generally showed a higher incidence of nucleotide transition than transversion, and the $A:T{\rightarrow}G:C$ transition was particularly prevalent. The rates of nucleotide substitution in HA mutants were generally higher than those in the LA mutants, leading to higher substitutions of amino acid in the HA mutants. Neither nucleotide substitutions interfering with intron splicing or causing early termination of protein translation were found, nor any large-sized deletions or additions were found in all the mutants. In principle, amylose content can be regulated by three factors: internal alterations of GBSSI protein, the strength of gene expression, and other unknown external factors. Our results indicate that the endosperm mutants from Shindongjin arose from internal alterations of GBSSI proteins, which may be the result of amino acid substitutions. On the other hand, the Ilpum mutants might be principally caused by the alteration of gene expression level. Analysis of another three glutinous cultivars revealed that the major factor leading to glutinous phenotypes is the 23-bp duplicative motif (5'-ACGGGTTCCAGGGCCTCAAGCCC-3') commonly found in exon 2, which results in the premature termination of protein translation leading to the production of a non-functional GBSSI enzyme.