• Asian-Australasian Journal of Animal Sciences
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• 제27권3호
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• pp.303-309
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• 2014

The increasing importance of meat quality has implications for animal breeding programs. Research has revealed much about the genetic background of pigs, and many studies have revealed the importance of various genetic factors. Since meat quality is a complex trait which is affected by many factors, consideration of the overall phenotype is very useful to study meat quality. For integrating the phenotypes, we used principle component analysis (PCA). The significant SNPs refer to results of the GRAMMAR method against PC1, PC2 and PC3 of 14 meat quality traits of 181 Duroc pigs. The Genome-wide association study (GWAS) found 26 potential SNPs affecting various meat quality traits. The loci identified are located in or near 23 genes. The SNPs associated with meat quality are in or near five genes (ANK1, BMP6, SHH, PIP4K2A, and FOXN2) and have been reported previously. Twenty-five of the significant SNPs also located in meat quality-related QTL regions, these result supported the QTL effect indirectly. Each single gene typically affects multiple traits. Therefore, it is a useful approach to use integrated traits for the various traits at the same time. This innovative approach using integrated traits could be applied on other GWAS of complex-traits including meat-quality, and the results will contribute to improving meat-quality of pork.

• Asian Pacific Journal of Cancer Prevention
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• 제17권4호
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• pp.1925-1931
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• 2016

Background: The XRCC1 protein facilitates various DNA repair pathways; single-nucleotide polymorphisms (SNPs) in this gene are associated with a risk of gastrointestinal cancer (GIC) with inconsistent results, but no data have been previously reported for the Sabah, North Borneo, population. We accordingly investigated the XRCC1 Arg194Trp and Arg399Gln SNPs in terms of GIC risk in Sabah. Materials and Methods: We performed genotyping for both SNPs for 250 GIC patients and 572 healthy volunteers using a polymerase chain reaction-restriction fragment length polymorphism approach. We validated heterozygosity and homozygosity for both SNPs using direct sequencing. Results: The presence of a variant 194Trp allele in the Arg194Trp SNP was significantly associated with a higher risk of GIC, especially with gastric and colorectal cancers. We additionally found that the variant 399Gln allele in Arg399Gln SNP was associated with a greater risk of developing gastric cancer. Our combined analysis revealed that inheritance of variant alleles in both SNPs increased the GIC risk in Sabah population. Based on our etiological analysis, we found that subjects ${\geq}50years$ and males who carrying the variant 194Trp allele, and Bajau subjects carrying the 399Gln allele had a significantly increased risk of GIC. Conclusions: Our findings suggest that inheritance of variant alleles in XRCC1 Arg194Trp and Arg399Gln SNPs may act as biomarkers for the early detection of GIC, especially for gastric and colorectal cancers in the Sabah population.

• 한국균학회지
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• 제25권3호통권82호
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• pp.167-175
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• 1997

Penicillium diversum KCTC 6786으로부터 두개의 chitin synthase 유전자 절편(PdCHSl과 PdCHS2)을 PCR로 증폭하고 cloning하였다. PdCHSl과 PdCHS2는 primer 서열을 제외하면 각각 570 bp 길이의 연속된 open reading frame (ORF)을 포함하고 있었다. BLASTP를 이용하여 유추된 아미노산 서열의 유사도를 분석한 결과, P. diversum은 자낭균류와 상당한 진화적 유연관계가 있음을 알 수 있었다. 이들 아미노산 서열을 CLASTAL W를 이용하여 분석한 결과, 본 실험에서 분리된 두 유전자 절편은 Bowen 등 (1992)이 제시한 몇 부류 중 서로 다른 부류, 즉, PdCHSl은 Class I에, PdCHS2는 Class II에 각각 속하는 것으로 확인되었다. 또한, Southern blot 분석을 통하여, 각 유전자는 P. diversum KCTC 6786의 genome에 1개씩만 존재함을 알 수 있었다.

• Plant Resources
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• 제6권2호
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• pp.120-128
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• 2003

The objectives of this study, an analysis of the variation for leaf and fruit characteristics among the selected ten populations of Sorbus commixta Hedl. could be used for the conservation of gene resources and could provide information to superior trees selection. The results obtained from this study can be summarized as follows; Approximately, the Mt. Sungin population at Ulleung island showed larger values in overall characteristics and populations. On the other hand, Mt. Halla population at Jeju island showed the smaller values of the overall characteristics and populations. ANOV A tests showed that there were statistically significant differences in all leaf characteristics among the populations as well as individual trees within populations. But, for fruit characteristics, differences were statistically significant only among the populations. Cluster analysis using single linkage method based on leaf and fruit characteristics showed that ten selected populations of S. commixta in Korea could be clustered into three groups. Group I is Mt. Sungin at Ulleung island, Group II is Mt. Halla at Jeju island, and Group III comprises Osan, Mt. Kaji, Mt. Duckyoo, Mt. Balwang, Mt. Sobaek, Mt. O-dae, Mt. Jiri, and Mt. Taebaek. The selection level based on major agronomic traits, which are the Number of Fruit per Fruiting Lateral(NFL) over 50, and Fruit Length(FL) and Width(FW) over 10 mm, and Weight of 100 Fruit(WFI00) over 66 g, was applied on 100 sample trees, and five trees were selected. The selection effects from selected trees in NFL, FL, FW, and WF100 were evaluated as 132%, 151 %, 142%, and 264% compared to the mean of those 100 sample trees, respectively. Especially, Ulleung 2 showed excellent values that NFL and WFI00 were 95, and 69 g, respectively, suggesting a promising new cultivar for larger fruit and high productivity.

• Journal of Radiation Protection and Research
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• 제40권1호
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• pp.25-35
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• 2015

We analyzed the differential effects of histopathology, apoptosis and expression of radiation response genes after chronic low dose rate (LDR) and acute high dose rate (HDR) radiation exposure in spleen, lung and liver of rats. Female 6-week-old Sprague-Dawley rats were used. For chronic low-dose whole body irradiation, rats were maintained for 14 days in a $^{60}Co$ gamma ray irradiated room and received a cumulative dose of 2 Gy or 5 Gy. Rats in the acute whole body exposure group were exposed to an equal dose of radiation delivered as a single pulse ($^{137}Cs$-gamma). At 24 hours after exposure, spleen, lung and liver tissues were extracted for histopathologic examination, western blotting and RT-PCR analysis. 1. The spleen showed the most dramatic differential response to acute and chronic exposure, with the induction of substantial tissue damage by HDR but not by LDR radiation. Effects of LDR radiation on the lung were only apparent at the higher dose (5 Gy), but not at lower dose (2 Gy). In the liver, HDR and LDR exposure induced a similar damage response at both doses. RT-PCR analysis identified cyclin G1 as a LDR-responsive gene in the spleen of rats exposed to 2 Gy and 5 Gy gamma radiation and in the lung of animals irradiated with 5 Gy. 2. The effects of LDR radiation differed among lung, liver, and spleen tissues. The spleen showed the greatest differential effect between HDR and LDR. The response to LDR radiation may involve expression of cyclin G1.

• 한국항해항만학회:학술대회논문집
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• 한국항해항만학회 2006년도 추계학술대회 논문집(제1권)
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• pp.205-210
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• 2006

해양구조물 설계시 급격한 파랑에 의한 충격력은 구조물 안전을 위한 중요한 설계인자이다. 이러한 충격력은 과도한 하중이 극히 짧은 시간 사이에 발생하는 현상으로 실험적 또는 수치해석적으로 해석하기 매우 어려운 문제이다. 본 연구에서는 급격한 파랑에 의한 충격력을 해석하기 위하여 수치파수조를 이용하여 N.S. 방정식에 기반한 수치해석을 수행하였다. 임의파를 선형중첩에 기반하여 조파기를 작동시켜 재현하였고 다블록격자하에서 수직실린더에 작용하는 충격력을 수치해석하였다. 한편 자유표면은 V.O.F. 및 local height function을 이용하여 추적하였다. 수치해석 검증을 위하여 수치해석 및 실험 결과와 비교를 수행하였는데 비교적 만족할 수 있는 결과를 확인하였으나 해양구조물 설계시 유용한 결과를 얻기 위해서는 쇄파와 같은 극한파 재현과 극한파에 의한 충격력에 대한 많은 연구가 지속되어야 함을 알 수 있었다.

• Genomics & Informatics
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• 제7권4호
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• pp.187-194
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• 2009

Cytochrome P450 2E1 (CYP2E1) is a member of the cytochrome P450 superfamily, and it is a key enzyme responsible for the metabolic activation of many smallmolecular-weight compounds such as alcohol, which is classified as a human carcinogen. In this study, we identified 19 single nucleotide polymorphisms (SNPs) in CYP2E1 in Korean population. In these SNPs, we examined possible genetic association of CYP2E1 polymorphisms with HBV clearance and the risk of hepatocellular carcinoma (HCC). Five common polymorphic sites were selected, CYP2E1 polymorphisms at rs381-3867, rs3813870, rs2070673, rs2515641 and rs2480257, considering their allele frequencies, haplotype-tagging status and LDs for genotyping in larger-scale subjects (n=1,092). Statistical analysis demonstrated that CYP2E1 polymorphisms and haplotypes show no significant association with HBV clearance, HCC occurrence and onset age of HCC (p>0.05). Previous studies, however, have shown contradictory findings on associations of CYP2E1 polymorphisms with CYP2E1 activities and HCC risk. Comparing the contrasting results of previous researches suggest that CYP2E1 polymorphism is associated with CYP2E1 activity induced by ethanol, but is not directly associated with HCC risk. CYP2E1 variation/haploype information identified in this study will provide valuable information for future studies on CYP2E1.

• International Journal of Industrial Entomology and Biomaterials
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• 제14권2호
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• pp.107-112
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• 2007

The mole crickets, Gryllotalpa, are insect pest distributed in the world. In Korea, G. orientalis was reported to occur, but previous ecological studies suggested the presence of two ecological types. To test this hypothesis, we sequenced a portion of mitochondrial (mt) genome from 48 G. orientali individuals collected over five Korean localities: Busan, Suwon, Okchon, Wonju, and Gangneung. From the sequence analysis, only two haplotypes were obtained, but the sequence divergence between the two haplotypes was 11 %, suggesting the presence of two distinct genetic groups in Korea. Although the population of Busan, Okchon, Wonju, and Gangneung was identified as a single haplotype, but that of Suwon was occupied by both hapotypes. Considering sequence divergence of other insect species occurring in Korea, the divergence estimate found between the two haplotypes seems to be too large to be considered as identical species. This result may suggest that the two differentiated haplotypes found in this study may reflect the previously reported two ecological types found in Suwon, Korea. To further understand the genetic divergence of the two phylogenetic groups, analysis of more variable regions of G. orientalis genome is required.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.413-425
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• 2018

A previous work developed and identified a new omega-5 gliadin deficient wheat line named O-free by crossing Keumkang and Olgeuru, which is nutritionally quite meaningful in that omega-5 gliadin is one of the known wheat allergens. To verify the characteristics of the O-free, we performed RNA sequencing (RNAseq) analysis of the O-free and the two parent lines (Keumkang and Olgeuru). The results of the similarity analysis with the ESTs for gliadins and glutenins showed that the O-free ESTs had no similarity with the omega-5 gliadin sequences but had similarity to other gliadins and glutenins. Furthermore, mapping results between the raw RNAseq data from the O-free and the omega-5 gliadin sequence showed a clear deletion of the N-terminal sequences which are an important signature of omega-5 gliadin. We also designed specific PCR primers that could identify omega-5 gliadin in the genomic DNA. The results showed that no omega-5 gliadin fragments were detected in the O-free. According to these results, we confirmed that the deficiency of omega-5 gliadin in the O-free is not caused by post-transcriptional or post-translational regulations such as epigenetic phenomena but by a simple deletion in the chromosome. Furthermore, we showed that the low-molecular weight glutenin subunit (LMW-GS) gene in the O-free had a single nucleotide polymorphism (SNP) causing a premature stop codon, resulting in a truncated polypeptide. We expect that the O-free line may serve as an excellent source of wheat that could prevail in the hypo-allergen wheat market, which has recently gained interest world-wide.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.354-362
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• 2018

Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.