• Journal of Life Science
• /
• v.28 no.11
• /
• pp.1255-1261
• /
• 2018

Whole genome analysis have been made possible with the development of DNA sequencing technologies and discovery of many single nucleotide polymorphisms (SNPs). Large number of SNP can be analyzed with SNP chips, since SNPs of human as well as livestock genomes are available. Among the various missing nucleotide imputation programs, Minimac3 software is suggested to be highly accurate, with a simplified workflow and relatively fast. In the present study, we used Minimac3 program to perform genomic missing value substitution 1,226 animals 770K SNP chip and imputing missing SNPs with next generation sequencing data from 311 animals. The accuracy on each chromosome was about 94~96%, and individual sample accuracy was about 92~98%. After imputation of the genotypes, SNPs with R Square ($R^2$) values for three conditions were 0.4, 0.6, and 0.8 and the percentage of SNPs were 91%, 84%, and 70% respectively. The differences in the Minor Allele Frequency gave $R^2$ values corresponding to seven intervals (0, 0.025), (0.025, 0.05), (0.05, 0.1), (0.1, 0.2), (0.2, 0.3). (0.3, 0.4) and (0.4, 0.5) of 64~88%. The total analysis time was about 12 hr. In future SNP chip studies, as the size and complexity of the genomic datasets increase, we expect that genomic imputation using Minimac3 can improve the reliability of chip data for Hanwoo discrimination.

• Korean Journal of Ichthyology
• /
• v.33 no.4
• /
• pp.226-239
• /
• 2021

Sebastes minor, Sebastes trivittatus, Sebastes owstoni, and Sebastes steindachneri are indigenous fish species inhabiting the central part of the East Sea, Korea. In order to understand the molecular evolution of these four rockfishes, we sequenced the complete mitochondrial genomes (mitogenomes) of S. minor and S. trivittatus. To further analyze the phylogeny of Sebastes species, the mitogenomes of 16 rockfishes were comparatively investigated. The complete mitochondrial DNA (mtDNA) nucleotide sequences of S. minor and S. trivittatus were 16,408 bp and 16,409 bp in length, respectively. A total of 37 genes were found in mtDNA of S. minor and S. trivittatus, including 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which exhibited similar characters with other Sebastes species in the East Sea, Korea. In addition, we detected a conserved motif "ATGTA" in the control region of the four Sebastes species, but no tandem repeat units. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that control regions were more variable than the concatenated protein-coding genes. As a result of analysing phylogenetic relationships of four Sebastes species by using concatenated nucleotide sequences of 13 protein-coding genes, S. minor, S. trivittatus, S. owstoni and S. steindachneri were clustered into three clades. The phylogenetic tree exhibited that S. minor and S. steindachneri shared a closer relationship, whereas S. trivittatus and S. vulpes formed another distinct clade. Our results contribute to a better understanding of evolutionary patterns of Sebastes species inhabiting the middle East Sea, Korea.

• Korean Journal of Plant Resources
• /
• v.36 no.4
• /
• pp.369-380
• /
• 2023

Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.

• Journal of Life Science
• /
• v.33 no.10
• /
• pp.808-819
• /
• 2023

This study was conducted to develop a selection marker for the identification of the Bacillus licheniformis K12 strain in microbial communities. The strain not only demonstrates good growth at moderate temperatures but also contains enzymes that catalyze the decomposition of various polymer materials, such as proteases, amylases, cellulases, lipases, and xylanases. To identify molecular markers appropriate for use in a microbial community, a search was conducted to identify variable gene regions that show considerable genetic mutations, such as recombinase, integration, and transposase sites, as well as phase-related genes. As a result, five areas were identified that have potential as selection markers. The candidate markers were two recombinase sites (BLK1 and BLK2), two integration sites (BLK3 and BLK4), and one phase-related site (BLK5). A PCR analysis performed with different Bacillus species (e.g., B. licheniformis, Bacillus velezensis, Bacillus subtilis, and Bacillus cereus) confirmed that PCR products appeared at specific locations in B. licheniformis: BLK1 in recombinase, BLK2 in recombinase family protein, and BLK3 and BLK4 as site-specific integrations. In addition, BLK1 and BLK3 were identified as good candidate markers via a PCR analysis performed on subspecies of standard B. licheniformis strains. Therefore, the findings suggest that BLK1 can be used as a selection marker for B. licheniformis species and subspecies in the microbiome.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.68 no.3
• /
• pp.134-146
• /
• 2023

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ² = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.

• Journal of Life Science
• /
• v.28 no.9
• /
• pp.1030-1041
• /
• 2018

Abiotic stresses limit the growth and productivity of plants. Cellular adaptation to abiotic stresses requires coordinated regulation in gene expression directed by complex mechanisms. This study used the activation tagging system to identify novel salt stress-responsive genes. The study selected 9 activation tagging lines that showed salt stress-tolerant phenotypes during their germination stages. Thermal asymmetric interlaced-PCR (TAIL-PCR) was used to identify the T-DNA tagging sites on the Arabidopsis genome in selected activation tagging lines, including AT7508, AT7512, AT7527, AT7544, AT7548, and AT7556. RT-PCR analysis showed that ClpC2/HSP93-III (At3g48870), plant thionin family (At2g20605), anti-muellerian hormone type-2 receptor (At3g50685), vacuolar iron transporter family protein (At4g27870), and microtubule-associated protein (At5g16730) were activated in AT7508, AT7512, AT7527, AT7544, and AT7556, respectively. Interestingly, in AT7548, both the genes adjacent to the T-DNA insertion site were activated: Arabinogalactan protein 13 (AGP13) (At4g26320) and F-box/RNI-like/FBD-like domains-containing protein (At4g26340). All of the seven genes were newly identified as salt stress-responsive genes from this study. Among them, the expression of ClpC2/HSP93-III, AGP13, F-box/RNI-like/FBD-like domains-containing protein gene, and microtubule-associated protein gene were increased under salt-stress condition. In addition, AT7508, AT7527, and AT7544 were more tolerant to salt stress than wild type at seedling development stage, functionally validating the screening results of the activation tagging lines. Taken together, our results demonstrate that the activation tagging system is useful for identifying novel stress-responsive genes.

• Journal of Applied Biological Chemistry
• /
• v.52 no.1
• /
• pp.1-7
• /
• 2009

For the development of qualitative PCR detection method of genetically modified (CM) rice, rice species-specific gene, OsCc-1 (rice cytochrome c gene), was selected as suitable far use as an endogenous gene in rice. The primer pair OsCytC-5'/3'with 111 bp amplicon was used for PCR amplification of the rice endogenous gene, OsCc-1 and no amplified product was observed from 8 different crops as templates. Qualitative PCR method was carried out with stack traits of L528$\times$CryIAc1 GM rice developed in Korea. For the qualitative PCRs, some primer pairs were designed with a construct-specific and event-specific type based on T-DNA and junction sequences of T-DNA in GM rice. Actck-5'/3' amplifying between actin promoter and OsCK1 gene introduced in LS28 gave rise to an amplicon 306 bp; also, CrLB-5'/3' from CryIAcl and CKRB-5'/3'amplifying the junction region of T-DNA and genome sequence from LS28 as event-specific primers gave rise to an amplicon 142 bp and 91 bp, respectively. These primer pairs for the detection of event-specific targets not produced PCR amplicons on non-CM rice and various crops in contrast to event lines. Therefore, in this study we verified that event-specific primers were effective to specifically detect stack trait lines and demonstrated that this method presented could be provided with the detection-method data for risk assessment analysis of GM rice to be commercialized.

• Tuberculosis and Respiratory Diseases
• /
• v.45 no.3
• /
• pp.587-595
• /
• 1998

Background: Recombinant adenovirus hold promise as vectors to carry therapeutic genes for several reasons: 1) they can infect both dividing and non-dividing cells; 2) they have the ability to directly transduce tissues in vivo; 3) they can easily be produced in high titer; and 4) they have an established record of safety as vaccination material. However, one of the major limitation in the use of adenoviruses is that transgene expression is quite short because adenovirusees insert their DNA genome episomally rather than by chromosomal integration, and an immune response against the virus destroys cells expressing the therapeutic gene. Since sodium butyrate has been reported to induce adenovirus-mediated gene expression, we hypothesized that treatment of tumor cells, transduced with herpes simples virus thymidine kinase(HSVtk) gene using adenoviral vector, with butyrate could augment the effect of gene therapy. Methods: We transduced HSVtk gene, driven by the cytomegalovirus promoter, into REN cell line(human mesothelioma cell line). Before proceeding with the comparison of HSVtk/ganciclovir mediated bystander killing, we evaluated the effect of butyrate on the growth of tumor cells in order to rule out a potential antitumor effect of butyrate alone, and also on expression of HSVtk gene by Western blot analysis. Then we determined the effects of butyrate on bystander-mediated cell killing in vitro. Results: There was no inhibition of growth of cells exposed to butyrate for 24 hours at a concentration of 1.5mM/L. Toxic effects were seen when the concentration of butyrate was greater than 2.0mM/L. Gene expression was more stable and bystander effect was augmented by butyrate treatment of a concentration of 1.5mM/L. Conclusion: These results provide evidence that butyrate can augment the efficiency of cell killing with HSVtk/GCV system by inducing transgene expression and may thus by a promising new approach to improve responses in gene therapy using adenoviral vectors.

• Journal of Plant Biotechnology
• /
• v.37 no.3
• /
• pp.313-318
• /
• 2010

To develop edible vaccines for swine, the embryogenic calli (type II) derived from HiII genotype were inoculated with A. tumefaciens strain C58C1 containing the binary vector pMYV611, 613, 616, and V621, 622 and 623 respectively. Six of those vectors carry nptII gene which confers resistance to paromomycin and apxIIA gene producing ApxII toxin which is generated in various serum types of A. pleuropneumoniae as a target gene. The 4,120 callus clones for pMYV611, 5,959 callus clones for pMYV613, 7,581 callus clones for pMYV616, 52,329 callus clones for V621, 48,948 callus clones for V622, and 56,188 callus clones for V623 were inoculated. The frequency of positive response clone was confirmed into range of 2.3% - 4.4% for each vectors by NPTII ELISA kit assay, and the selected callus clones of them were finally 3 callus clones from pMYV611 (0.07%), 4 callus clones from pMYV613 (0.07%), 2 callus clones from pMYV616 (0.03%), 51 callus clones from V621 (0.1%), 72 callus clones from V622 (0.15%), and 102 callus clones from V623 (0.18%) respectively. From the selected callus clones of each binary vector, the integration of the apxIIA gene into maize genome was detected from 2 plants of pMYV613 and 2 plants of V623 by Southern blot analysis.

• Journal of The Korean Society of Inherited Metabolic disease
• /
• v.17 no.3
• /
• pp.96-102
• /
• 2017

Glycogen storage disease type IX (GSD IX) is caused by deficiency of phosphorylase kinase which plays a role in breakdown of glycogen. Mutations in PHKA2 are the most common cause of GSD IX (GSD IXa). Clinical manifestations of GSD IXa include hepatomegaly, elevation of liver enzyme, growth retardation, fasting hypoglycemia, and fasting ketosis. However, the symptoms overlap with those of other types of GSDs. Here, we report Korean familial cases with GSD IXa whose diagnosis was confirmed by targeted exome sequencing. A 4-year old male patient was presented with hepatomegaly and persistently elevated liver enzyme. Liver biopsy revealed swollen hepatocyte filled with glycogen storage, suggesting GSDs. Targeted exome sequencing was performed for the differential molecular diagnosis of various types of GSDs. A hemizygous mutation in PHKA2 were detected by targeted exome sequencing and confirmed by Sanger sequencing: c.3632C>T (p.Thr121Met), which was previously reported. The familial genetic analysis revealed that his mother was heterozygous carrier of c.3632C>T mutation and his 28-month old brother had hemizygous mutation. His brother also had hepatomegaly and elevated liver enzyme. The hypoglycemia was prevented by frequent meals with complex carbohydrate, as well as cornstarch supplements. Their growth and development is in normal range. We suggest that targeted exome sequencing could be a useful diagnostic tool for the genetically heterogeneous and clinically indistinguishable GSDs. A precise molecular diagnosis of GSD can provide appropriate therapy and genetic counseling for the family.