• Food Science of Animal Resources
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• v.31 no.4
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• pp.537-542
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• 2011

Biological or physiological genes that regulate metabolism and energy partitioning have the potential to influence economically important traits such as carcass and meat quality traits in beef cattle. The neuropeptide Y (NPY) functions as a central appetite stimulator and plays a major role in feed intake and energy-balance control. Therefore, the NPY gene is an excellent biological and physiological candidate gene for body weight, feeding, fatness or growth related traits in beef cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the NPY gene and to evaluate the association of NPY SNP markers with carcass and meat quality traits in Korean cattle. The genomic region (711 bp) including intron 2 of NPY gene was amplified and sequenced, and five SNPs, g.4389 Del(C), g.4371Del(C), g.4271T>C, g.1899A>G and g.1517A>C, were identified. The PCR-RFLP method was then developed to genotype the individuals examined. The g.4271T>C SNP was significantly associated with M. Longissimus dori area (LDA) value (p<0.027). Animals with the TT ($78.144{\pm}0.950\;cm^2$) genotype had higher LDA than those with the CC ($72.266{\pm}2.039\;cm^2$), and animals with TC genotype showed intermediate value. This SNP genotype also showed a highly significant additive genetic effect for the LDA (p<0.01). No significant associations, however, was detected between any of the SNP genotype and other carcass traits measured in this study. In conclusion, SNP genotype of the NPY gene may be used as DNA markers to select animals that have a higher meat yield.

• Food Science of Animal Resources
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• v.31 no.4
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• pp.530-536
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• 2011

It is well established that uncoupling protein 3 (UCP3) is expressed largely in skeletal muscle, white adipose tissue and brown adipose tissue and has been suggested to play important roles in regulating energy expenditure, body weight, thermoregulation as well as fatty acid metabolism and obesity. Therefore, the UCP3 gene was selected as a candidate gene for carcass and meat quality traits in Korean cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the UCP3 gene and to evaluate the association of UCP3 SNP markers with carcass and meat quality traits in Korean cattle. The five exons in the UCP3 gene were sequenced, and ten SNPs were identified. The PCR-SSCP method was then developed to genotype the individuals examined. The g.3076A>G genotype was significantly associated with marbling score (MS) of Korean cattle. Animals with the AA genotype had a higher MS than those with the AG and GG genotypes. No significant associations of the SNP g.3076A>G were observed for any traits. In conclusion, although SNP g.3076A>G, which showed an association with MS, does not cause amino acid changes, this SNP may be used as a DNA marker to select animals that have higher intramuscular fat content.

• Journal of Nutrition and Health
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• v.43 no.4
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• pp.357-366
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• 2010

There has been no genome-wide association study (GWAS) for macronutrient intake as a quantitative trait. To explore genetic loci associated with total calorie and macronutrient intake, genome-wide association data of autosomal single nucleotide polymorphisms (SNPs) from Korean adults were analyzed. We conducted a GWAS in 3,690 men and women aged 40 to 60 years from an urban population-based cohort. At the baseline examination (June 18, 2001 through January 29, 2003), DNA samples of the study subjects were collected and analyzed for genotyping. The information of average daily consumption of total calorie, carbohydrate, protein, and fat was obtained from a semi-quantitative food frequency questionnaire and transformed by natural logarithm for analyses after adjustment of calorie intake. Using multivariate linear regression analysis adjusted for age, sex, and height, we tested for 352,021 SNPs and found weak associations, which do not reach genome-wide association significance, with calorie and macronutrient intake. However, a number of SNPs were found to have potential associations with macronutrient intake; in particular, signals in SORBS1 and those in PRKCB1 were likely associated with carbohydrate and fat intake, respectively. We observed an inverse association between the minor allele of the SNPs in these genes and the amount of consumption of carbohydrate or fat. Our GWAS identified loci and minor alleles weakly associated with macronutrient intake. Because SORBS1 and PRKCB1 are reportedly associated with the metabolism of glucose and lipid as well as with obesity-related diseases, further investigations on biological and functional roles of polymorphism of these genes in the relation to macronutrient intake are warranted.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1150-1159
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• 2018

Objective: Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods: nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results: Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion: Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

• Biomedical Science Letters
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• v.25 no.2
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• pp.190-195
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• 2019

Hemoglobin (Hb) concentrations and hematocrit (Hct) values can be changed by factors such as erythrocyte production, destruction, and bleeding. In addition, variants in the protein expression involved in the amount of red blood cells that determine Hb metabolism or Hct value can increase susceptibility to complex blood diseases. Previous studies have reported significant single nucleotide polymorphisms (SNPs) by applying a genome-wide association study (GWAS) on Hb levels and Hct values in European population. In this study, we confirmed whether the significant SNPs are replicated in Koreans. In previous studies, 26 and 18 SNPs with a significant correlation Hb and Hct were identified in Korean genotype data, and 21 and 12 SNPs were selected, respectively. The SNPs of PRKCE (rs10495928), TMPRSS6 (rs2235321, rs5756505, rs855791) were significantly associated with Hb (P<0.05). In the association analysis of Hct, the SNPs of HBS1L (rs6920211, rs9389268, rs9483788), PRKCE (rs4953318), SCGN (rs9348689) and TMPRSS6 (rs2413450) genes showed a significant correlation (P<0.05). Replicated SNPs and not replicated SNPs showed the difference of genetic distance calculated by Fst. The replicated SNPs with a significant correlation showed similar allele frequencies, whereas the not replicated SNPs showed a large difference in allele frequency. All replicated SNPs with significant correlations had Fst values less than 0.05, indicating that the genetic distance between the groups was close. On the other hand, the not replicated SNPs showed that the Fst value was 0.05 or more and the genetic distance was relatively large.

• Molecules and Cells
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• v.42 no.1
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• pp.56-66
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• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.5
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• pp.607-613
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• 2019

Objective: Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods: We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results: A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion: These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.

• The Journal of the Korea Contents Association
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• v.21 no.4
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• pp.825-832
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• 2021

In this study, by selecting specific aptamers that selectively detection on P. gingivalis, the main cause of periodontal disease, and purifying and identifying protein molecules that bind to the selected aptamers, the mechanism of action of P. gingivalis was investigated. A DNA library having 39 random sequences was prepared, and aptamers with specificity for P. gingivalis were selected using the SELEX method, and the nucleotide sequence was analyzed by cloning using PCR2.1 cloning vector. 8 of aptamers with different nucleotide sequences were selected, and modified weston blot was performed using APG-3 among the selected aptamers to identify 11 proteins that act directly, and proteins were analyzed. As a result, a protein that selectively binds to P. gingivalis was isolated and identified. Therefore, aptamer selectively binds and attaches to proteins related to inhibition of sugar metabolism and cell activity of P. gingivalis, suggesting the possibility of a sensor for diagnosis of periodontal disease.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.214-214
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• 2022

Soluble starch synthases (SSs) elongate α-glucans from ADP-Glc to the glucan nonreducing ends and play a critical role in synthesizing resistant starch in the rice. A total of 10 SSs isoforms were reported in rice, including granules-bound starch synthase I (GBSSI), GBSSII, starch synthase I (SSI), SSIIa (SSII-3), SSIIb (SSII-2), SSIIc (SSII-1), SSIIIa (SSIII-2), SSIIIb (SSIII-1), SSIVa (SSIV-1), and SSIVb (SSIV-2). SSIII proteins are involved in forming the B chain and elongating cluster filling chains in amylopectin metabolism. The functions of SSIIIb (SSIII-1) are less clear as compared to SSs. Here, we sought to shed light on the genetic diversity profiling of the SSIII-1 gene in 374 rice accessions composed of 54 wild-type accessions and 320 bred cultivars (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture). In total, 17 haplotypes were identified in the SSIII-1 coding region of 320 bred cultivars, while 44 haplotypes were detected from 54 wild-type accessions. The genetic diversity indices revealed the most negative Tajima's D value in the temperate-japonica, followed by the wild type, while Tajima's D values in other ecotypes were positive, indicating balancing selection. Nucleotide diversity in the SSIII-1 region was highest in the wild group (0.0047) while lowest in temperate-japonica. Lower nucleotide diversity in the temperate-japonica is evidenced by the negative Tajima's D and suggested purifying selection. The fixation index (F_ST) revealed a very high level of gene flow (low F_ST) between the tropical-japonica and admixture groups (F_ST=-0.21) followed by admixture and wild groups (-0.04), indica and admixture groups (0.02), while low gene flow with higher F_ST estimates between the temperate-japonica and aus groups (0.72), tropical-japonica and aromatic groups (0.71), and temperate-japonica and admixture groups (0.52). Taken together, our study offers insights into haplotype diversity and evolutionary fingerprints of SSIII-1. It provides genomic information to increase the resistant starch content of cooked rice.

• Animal Bioscience
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• v.37 no.12
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• pp.2044-2053
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• 2024

Objective: The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed. Methods: In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle. Results: Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy-Weinberg equilibrium. Conclusion: These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.