• Genomics & Informatics
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• v.6 no.2
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• pp.64-67
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• 2008

The Korean Rice Ds-tagging lines Database (KRDD) is designed to provide information about Ac/Ds insertion lines and activation tagging lines using japonica rice. This database has provided information on 18,158 Ds lines, which includes the ID, description, photo image, sequence information, and gene characteristics. The KRDD is visualized using a web-based graphical view, and anonymous users can query and browse the data using the search function. It has four major menus of web pages: (i) a Blast Search menu of a mutant line; Blast from rice Ds-tagging mutant lines; (ii) a primer design tool to identify genotypes of Ds insertion lines; (iii) a Phenotype menu for Ds lines, searching by identification name and phenotype characteristics; and (iv) a Management menu for Ds lines.

• Korean Journal of Microbiology
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• v.29 no.2
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• pp.75-79
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• 1991

The yeast L-A virus (4.6 kb dsRNA genome) encodes the major coat protein and a "gag-pol" fusion minor coat protein that separately encapsidate itself and $M_{1}$, a 1.8 kb dsRNA satellite virus encoding a secreted protein toxin (the killer toxin). The teast chromosomal SKI genes prevent viral cytopathology by lowering the virus copy number. Thus, $ski^{-}$ mutants are ts and cs for growth. We transformed a ski2-2 virus-infested mutant with a yeast bank in a high copy cloning vector and selected the rare healthy transformants for analysis. One type of transformant segregated M-O L-A-O cells with high frequency. Elimination of the DNA clone from the ski2-2 strain eliminated this phinotype and introduction of the DNA clone recovered from such transformants into the parent ski2-2 strain, or into ski3 or ski6 mutants gave the same phenotype. This killer-curing phenotype was due to the curing of the helper L-A dsRNA virus. The 6.5 kb insert only had this activity when carried on a high copy vector and in $ski^{-}$ cells (not in $SKI^{+}$ cells). This 6.5 kb insert acts as a mutagen on L-A dsRNA producing a high rate of deletion mutations.mutations.

• Korean Journal of Microbiology
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• v.30 no.3
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• pp.177-180
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• 1992

Among 120 U. maydis strains isolated in Korea 14 different strains containing specific viral dsRNA segments were analyzed for the distribution of dsRNA and the production of toxin protein. Several distinctive dsRNA patterns were identified, 9 cases of P type with typical H, M and L ds RNA and one case of non-P-type, the frequency of a specific isolate was decreased with increasing number of dsRNA segments. The presence of dsRNA had no effect on the cultural or morphological phenotype of the host. Two isolates containing P type dsRNA segments appeared to produce toxin protein (killer strains) which inhibited the growth of 4 isolates (sensitive strain) with different susceptibility. Two killer strains contain unique M dsRNA segment which may code for toxin protein. However, the presence of toxin-sensitive strains among dsRNA-free isolates was similar to that of ds RNA containing strains.

• Journal of Genetic Medicine
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• v.10 no.2
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• pp.120-123
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• 2013

This report describes three cases of 22q11.2 deletion syndrome (22q11.2DS) diagnosed by array comparative genomic hybridization with final adult height and bone phenotype. The cases involved a 57-year-old woman with hypocalcemic seizure, an 18-year-old man with short stature, and a 24-year-old woman incidentally diagnosed as 22q11.2DS. The first two patients revealed short stature and low bone mineral density, and their deletion sites included the $TBX_1$. The third patient had normal stature and normal bone mineral density, and the deletion site did not include the $TBX_1$. The deletion of specific genes including the $TBX_1$ could be an important factor of skeletal development including height and bone mineral density of 22q11.2DS.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.90-90
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• 2017

Regulation of seed dormancy is important in many grains to prevent pre-harvest sprouting. To identify and understand the gene related to seed dormancy regulation, we have screened for viviparous phenotypes of rice mutant lines generated by insertion of Ds transposon in a Korean Japonica cultivar (Dongjin) background. One of the mutants, which represented viviparous phenotype, was selected for further seed dormancy regulation studies and designated dor1. The dor1 mutant has single Ds insertion in the second exon of OsDor1 gene encoding glycine-rich protein. The seeds of dor1 mutant showed a higher germination potential and reduced abscisic acid (ABA) sensitivity compared to wild type Dongjin. Over-expression of Dor1 complements the viviparous phenotype of dor1 mutant, indicating that Dor1 function in seed dormancy regulation. Subcellular localization assay of Dor1-GFP fusion protein revealed that the OsDor1 protein mainly localized to membrane and the localization of OsDOR1 was influenced by presence of a giberelin (GA) receptor OsGID1. Further bimolecular fluorescence complementation (BiFC) analysis indicated that OsDOR1 interact with OsGID1. The combined results suggested that OsDOR1 regulates seed dormancy by interacting with OsGID1 in GA response. Additionally, expression of OsDOR1 partially complemented the cold sensitivity of Escherichia coli BX04 mutant lacking four cold shock proteins, indicating that OsDOR1 possessed RNA chaperone activity.

• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.271-276
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• 2009

Functional gene studies in the cultivated white button mushroom Agaricus bisporus have been constrained by the absence of effective gene-silencing tools. Using two endogenous genes from A. bisporus, we have tested the utility of dsRNA hairpin constructs to mediate downregulation of specific genes. Hairpin constructs for genes encoding orotidine 5'-monophosphate decarboxylase (URA3) and carboxin resistance (CBX) were introduced into A. bisporus using Agrobacteriummediated transfection. Although predicted changes in phenotype were not observed in vitro, quantitative-PCR analyses indicated unambiguously that transcripts in several transformants were substantially reduced compared with the non-transformed controls. Interestingly, some hairpin transformants exhibited increased transcription of target genes. Our observations show that hairpin transgenic sequences can mediate downregulation of A. bisporus endogenous genes and that the technology has the potential to expedite functional genomics of the mushroom.

• Journal of Plant Biotechnology
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• v.37 no.4
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• pp.483-493
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• 2010

Knock-out of a gene by insertional mutagenesis is a direct way to address its function through the mutant phenotype. Among ca. 15,000 gene-trapped Ds insertion lines of rice, we identified one line from selected sensitive lines in highly salt stress. We conducted gene tagging by TAIL-PCR, and DNA gel blot analysis from salt sensitive mutant. A gene encoding an oligopeptide transporter (OPT family) homologue was disrupted by the insertion of a Ds transposon into the OsOPT10 gene that was located shot arm of chromosome 8. The OsOPT10 gene (NP_001062118.) has 6 exons and encodes a protein (752 aa) containing the OPT family domain. RT-PCR analysis showed that the expression of OsOPT10 gene was rapidly and strongly induced by stresses such as high-salinity (250 mM), osmotic, drought, $100\;{\mu}M$ ABA. The subcellular localization assay indicated that OsOPT10 was localized specifically in the plasma membrane. Overexpression of OsOPT10 in Arabidopsis thaliana and rice conferred tolerance of transgenic plants to salt stress. Further we found expression levels of some stress related genes were inhibited in OsOPT10 transgenic plants. These results suggested that OsOPT10 might play crucial but differential roles in plant responses to various abiotic stresses.

• Journal of Plant Biotechnology
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• v.37 no.2
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• pp.125-132
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• 2010

Rice is the staple food of more than 50% of the worlds population. Cultivated rice has the AA genome (diploid, 2n=24) and small genome size of only 430 megabase (haploid genome). As the sequencing of rice genome was completed by the International Rice Genome Sequencing Project (IRGSP), many researchers in the world have been working to explore the gene function on rice genome. Insertional mutagenesis has been a powerful strategy for assessing gene function. In maize, well characterized transposable elements have traditionally been used to clone genes for which only phenotypic information is available. In rice endogenous mobile elements such as MITE and Tos (Hirochika. 1997) have been used to generate gene-tagged populations. To date T-DNA and maize transposable element systems has been utilized as main insertional mutagens in rice. A main drawback of a T-DNA scheme is that Agrobacteria-mediated transformation in rice requires extensive facilities, time, and labor. In contrast, the Ac/Ds system offers the advantage of generating new mutants by secondary transposition from a single tagged gene. Revertants can be utilized to correlate phenotype with genotype. To enhance the efficiency of gene detection, advanced gene-tagging systems (i.e. activation, gene or enhancer trap) have been employed for functional genomic studies in rice. Internationally, there have been many projects to develop large scales of insertionally mutagenized populations and databases of insertion sites has been established. Ultimate goals of these projects are to supply genetic materials and informations essential for functional analysis of rice genes and for breeding using agronomically important genes. In this report, we summarize the current status of Ac/Ds-mediated gene tagging systems that has been launched by collaborative works from 2001 in Korea.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.307-316
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• 2008

Transposon-mediated insertional mutagenesis is one of powerful strategy for assessing functions of genes in higher plants. In this report, we have selected highly susceptible and tolerance plant by screening about high salt (3% NaCl) and cold stresses ($4^{\circ}C$) from F2 seeds of 30,000 Ac/Ds insertional mutagenesis lines in rice (Oryza sativa L. cv. Dongjin). In order to identify the gene tagging, insertion of Ds element was analyzed by Southern blot and these results revealed that 19 lines were matched genotype of selected lines with phenotype from the first selected 212 lines, and 13 lines have one copy of Ds elements. The Franking Sequence Tags (FSTs) of selected mutant lines showed high similarities with the following known function genes: signal transduction and regulation of gene expression (transpoter, protease family protein and apical meristem family protein), osmotic stress response (heat shock protein, O-methyltransferase, glyceraldehyde-3-phosphate dehydrogenase and drought stress induce protein), vesicle trafficking (SYP 5 family protein) and senescence associated protein. The expression pattern of 19 genes were analyzed using RT-PCR under the abiotic stresses of 9 class; 250mM NaCl, osmotic, drought, 3% $H_2O_2$, $100{\mu}M$ ABA, $100{\mu}M$ IAA, 0.1 ppm 2,4-D, $4^{\circ}C$ cold and $38^{\circ}C$ high temperature. Isolated knock-out genes showed the positive response about 250 mM NaCl, drought, $H_2O_2$, PEG, IAA, 2,4-D, ABA treatment and low ($4^{\circ}C$) and high temperature ($38^{\circ}C$). The results from this study indicate that function of selected knock-out genes could be useful in improving of tolerance to abiotic stresses as an important transcriptional activators in rice.